5 CFR 850.303 - Return of personal documents.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., OPM may provide the individual with a copy of the document that is derived from electronic records. ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Return of personal documents. 850.303 Section 850.303 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE...

5 CFR 850.303 - Return of personal documents.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., OPM may provide the individual with a copy of the document that is derived from electronic records. ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Return of personal documents. 850.303 Section 850.303 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE...

5 CFR 850.303 - Return of personal documents.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., OPM may provide the individual with a copy of the document that is derived from electronic records. ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Return of personal documents. 850.303 Section 850.303 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE...

5 CFR 850.303 - Return of personal documents.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., OPM may provide the individual with a copy of the document that is derived from electronic records. ... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false Return of personal documents. 850.303 Section 850.303 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE...

78 FR 9796 - Airworthiness Directives; Cessna Aircraft Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-12

... against the right steering tube assembly during rudder pedal actuation. This AD requires you to install... between the fuel return line assembly and the steering tube assembly and clearance between the fuel return...://www.cessnasupport.com . You may review copies of the referenced service information at the FAA, Small...

75 FR 21148 - Proposed Collection; Comment Request for Form 4506-T

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

... 4506-T AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice and request for comments... Form 4506-T Request for Transcript of Tax Return. DATES: Written comments should be received on or... 4506-T. Abstract: Internal Revenue Code section 7513 allows taxpayers to request a copy of a tax return...

26 CFR 1.6012-3 - Returns by fiduciaries.

Code of Federal Regulations, 2010 CFR

2010-04-01

...), accompanied by a written declaration of the fiduciary under the penalties of perjury that it is a true and... of the fiduciary under the penalties of perjury that it is a true and complete copy, shall be... such decedent. For the decedent's taxable year which ends with the date of his death, the return shall...

26 CFR 25.6019-3 - Contents of return.

Code of Federal Regulations, 2010 CFR

2010-04-01

...'s worth if divorce occurs within 2 years. In any case where a husband and wife enter into a written agreement of the type contemplated by section 2516 and the final decree of divorce is not granted on or... the return. In addition, a certified copy of the final divorce decree shall be furnished the internal...

26 CFR 25.6019-3 - Contents of return.

Code of Federal Regulations, 2012 CFR

2012-04-01

...'s worth if divorce occurs within 2 years. In any case where a husband and wife enter into a written agreement of the type contemplated by section 2516 and the final decree of divorce is not granted on or... the return. In addition, a certified copy of the final divorce decree shall be furnished the internal...

26 CFR 25.6019-3 - Contents of return.

Code of Federal Regulations, 2011 CFR

2011-04-01

...'s worth if divorce occurs within 2 years. In any case where a husband and wife enter into a written agreement of the type contemplated by section 2516 and the final decree of divorce is not granted on or... the return. In addition, a certified copy of the final divorce decree shall be furnished the internal...

26 CFR 25.6019-3 - Contents of return.

Code of Federal Regulations, 2014 CFR

2014-04-01

...'s worth if divorce occurs within 2 years. In any case where a husband and wife enter into a written agreement of the type contemplated by section 2516 and the final decree of divorce is not granted on or... the return. In addition, a certified copy of the final divorce decree shall be furnished the internal...

26 CFR 25.6019-3 - Contents of return.

Code of Federal Regulations, 2013 CFR

2013-04-01

...'s worth if divorce occurs within 2 years. In any case where a husband and wife enter into a written agreement of the type contemplated by section 2516 and the final decree of divorce is not granted on or... the return. In addition, a certified copy of the final divorce decree shall be furnished the internal...

26 CFR 1.6695-1 - Other assessable penalties with respect to the preparation of tax returns for other persons.

Code of Federal Regulations, 2010 CFR

2010-04-01

... information from partners of a partnership and to make decisions with respect to the proper application of the... information is deleted from the copy in order to preserve or maintain this arrangement. (b) Failure to sign... taxpayer. The signing tax return preparer, however, must furnish all of the information that will be...

19 CFR 10.66 - Articles exported for temporary exhibition and returned; horses exported for horse racing and...

Code of Federal Regulations, 2011 CFR

2011-04-01

... livestock or other animals, exported for temporary exhibition and returned and claimed to be exempt from... animals of foreign origin taken abroad for exhibition in connection with a circus or menagerie, a copy of an inventory of these animals filed prior to their leaving the country with the director of the port...

19 CFR 10.66 - Articles exported for temporary exhibition and returned; horses exported for horse racing and...

Code of Federal Regulations, 2014 CFR

2014-04-01

... livestock or other animals, exported for temporary exhibition and returned and claimed to be exempt from... animals of foreign origin taken abroad for exhibition in connection with a circus or menagerie, a copy of an inventory of these animals filed prior to their leaving the country with the director of the port...

19 CFR 10.66 - Articles exported for temporary exhibition and returned; horses exported for horse racing and...

Code of Federal Regulations, 2012 CFR

2012-04-01

... livestock or other animals, exported for temporary exhibition and returned and claimed to be exempt from... animals of foreign origin taken abroad for exhibition in connection with a circus or menagerie, a copy of an inventory of these animals filed prior to their leaving the country with the director of the port...

19 CFR 10.66 - Articles exported for temporary exhibition and returned; horses exported for horse racing and...

Code of Federal Regulations, 2013 CFR

2013-04-01

... livestock or other animals, exported for temporary exhibition and returned and claimed to be exempt from... animals of foreign origin taken abroad for exhibition in connection with a circus or menagerie, a copy of an inventory of these animals filed prior to their leaving the country with the director of the port...

The transcription factor titration effect dictates level of gene expression.

PubMed

Brewster, Robert C; Weinert, Franz M; Garcia, Hernan G; Song, Dan; Rydenfelt, Mattias; Phillips, Rob

2014-03-13

Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle. Copyright © 2014 Elsevier Inc. All rights reserved.

Selective sweep on human amylase genes postdates the split with Neanderthals

PubMed Central

Inchley, Charlotte E.; Larbey, Cynthia D. A.; Shwan, Nzar A. A.; Pagani, Luca; Saag, Lauri; Antão, Tiago; Jacobs, Guy; Hudjashov, Georgi; Metspalu, Ene; Mitt, Mario; Eichstaedt, Christina A.; Malyarchuk, Boris; Derenko, Miroslava; Wee, Joseph; Abdullah, Syafiq; Ricaut, François-Xavier; Mormina, Maru; Mägi, Reedik; Villems, Richard; Metspalu, Mait; Jones, Martin K.; Armour, John A. L.; Kivisild, Toomas

2016-01-01

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content. PMID:27853181

Selective sweep on human amylase genes postdates the split with Neanderthals.

PubMed

Inchley, Charlotte E; Larbey, Cynthia D A; Shwan, Nzar A A; Pagani, Luca; Saag, Lauri; Antão, Tiago; Jacobs, Guy; Hudjashov, Georgi; Metspalu, Ene; Mitt, Mario; Eichstaedt, Christina A; Malyarchuk, Boris; Derenko, Miroslava; Wee, Joseph; Abdullah, Syafiq; Ricaut, François-Xavier; Mormina, Maru; Mägi, Reedik; Villems, Richard; Metspalu, Mait; Jones, Martin K; Armour, John A L; Kivisild, Toomas

2016-11-17

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

76 FR 78072 - Bureau of Educational and Cultural Affairs (ECA) Request for Grant Proposals (RFGP...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-15

... exceed participants by more than a factor of two-to-one. 10. Return Travel Allowance. A return travel... include one extra copy of the completed SF-424 form and place it in an envelope addressed to ``ECA/EX/PM..., Program Management Division, ECA-IIP/EX/PM, Ref.: ECA/PE/C/SU-12-15, SA-5, Floor 4, Department of State...

47 CFR 14.52 - Copies; service; separate filings against multiple defendants.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false Copies; service; separate filings against multiple defendants. 14.52 Section 14.52 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Recordkeeping, Consumer...

47 CFR 14.52 - Copies; service; separate filings against multiple defendants.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 1 2012-10-01 2012-10-01 false Copies; service; separate filings against multiple defendants. 14.52 Section 14.52 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Recordkeeping, Consumer...

47 CFR 14.52 - Copies; service; separate filings against multiple defendants.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 1 2013-10-01 2013-10-01 false Copies; service; separate filings against multiple defendants. 14.52 Section 14.52 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Recordkeeping, Consumer...

Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families.

PubMed

Mark Welch, David B; Cummings, Michael P; Hillis, David M; Meselson, Matthew

2004-02-10

Rotifers of the asexual class Bdelloidea are unusual in possessing two or more divergent copies of every gene that has been examined. Phylogenetic analysis of the heat-shock gene hsp82 and the TATA-box-binding protein gene tbp in multiple bdelloid species suggested that for each gene, each copy belonged to one of two lineages that began to diverge before the bdelloid radiation. Such gene trees are consistent with the two lineages having descended from former alleles that began to diverge after meiotic segregation ceased or from subgenomes of an alloploid ancestor of the bdelloids. However, the original analyses of bdelloid gene-copy divergence used only a single outgroup species and were based on parsimony and neighbor joining. We have now used maximum likelihood and Bayesian inference methods and, for hsp82, multiple outgroups in an attempt to produce more robust gene trees. Here we report that the available data do not unambiguously discriminate between gene trees that root the origin of hsp82 and tbp copy divergence before the bdelloid radiation and those which indicate that the gene copies began to diverge within bdelloid families. The remarkable presence of multiple diverged gene copies in individual genomes is nevertheless consistent with the loss of sex in an ancient ancestor of bdelloids.

27 CFR 46.241 - Required records.

Code of Federal Regulations, 2010 CFR

2010-04-01

... CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette... all controlled group members, if applicable; (d) A copy of the tax return, if the dealer filed one; (e...

27 CFR 46.241 - Required records.

Code of Federal Regulations, 2014 CFR

2014-04-01

... CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette... all controlled group members, if applicable; (d) A copy of the tax return, if the dealer filed one; (e...

27 CFR 46.241 - Required records.

Code of Federal Regulations, 2011 CFR

2011-04-01

... CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette... all controlled group members, if applicable; (d) A copy of the tax return, if the dealer filed one; (e...

27 CFR 46.241 - Required records.

Code of Federal Regulations, 2013 CFR

2013-04-01

... CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette... all controlled group members, if applicable; (d) A copy of the tax return, if the dealer filed one; (e...

27 CFR 46.241 - Required records.

Code of Federal Regulations, 2012 CFR

2012-04-01

... CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette... all controlled group members, if applicable; (d) A copy of the tax return, if the dealer filed one; (e...

Multiple Genetic Backgrounds of the Amplified Plasmodium falciparum Multidrug Resistance (pfmdr1) Gene and Selective Sweep of 184F Mutation in Cambodia

PubMed Central

Vinayak, Sumiti; Alam, Md Tauqeer; Sem, Rithy; Shah, Naman K.; Susanti, Augustina I.; Lim, Pharath; Muth, Sinuon; Maguire, Jason D.; Rogers, William O.; Fandeur, Thierry; Barnwell, John W.; Escalante, Ananias A.; Wongsrichanalai, Chansuda; Ariey, Frederick; Meshnick, Steven R.; Udhayakumar, Venkatachalam

2011-01-01

Background The emergence of artesunate-mefloquine (AS+MQ)–resistant Plasmodium falciparum in the Thailand-Cambodia region is a major concern for malaria control. Studies indicate that copy number increase and key alleles in the pfmdr1 gene are associated with AS+MQ resistance. In the present study, we investigated evidence for a selective sweep around pfmdr1 because of the spread of adaptive mutation and/or multiple copies of this gene in the P. falciparum population in Cambodia. Methods We characterized 13 microsatellite loci flanking (± 99 kb) pfmdr1 in 93 single-clone P. falciparum infections, of which 31 had multiple copies and 62 had a single copy of the pfmdr1 gene. Results Genetic analysis revealed no difference in the mean (± standard deviation) expected heterozygosity (He) at loci around single (0.75 ± 0.03) and multiple (0.76 ± 0.04) copies of pfmdr1. Evidence of genetic hitchhiking with the selective sweep of certain haplotypes was seen around mutant (184F) pfmdr1 allele, irrespective of the copy number. There was an overall reduction of 28% in mean He (± SD) around mutant allele (0.56 ± 0.05), compared with wild-type allele (0.84 ± 0.02). Significant linkage disequilibrium was also observed between the loci flanking mutant pfmdr1 allele. Conclusion The 184F mutant allele is under selection, whereas amplification of pfmdr1 gene in this population occurs on multiple genetic backgrounds. PMID:20367478

Seismic Response to Sonic Boom-Coupled Rayleigh Waves

DTIC Science & Technology

1990-06-28

90 \\" VA ’ NOTICE When Government drawings, specifications, or other data are used for any purpose other than in connection with a definitely...your organization no longer employs the addressee, please nofify HSD/XART, Brooks AFB TX 78235-5000 to help us maintain a current mailing list. Copies...of this report should not be returned unless return is required by security considerations, contractual obligations, or notice on a specific document

26 CFR 25.2512-3 - Valuation of interest in businesses.

Code of Federal Regulations, 2010 CFR

2010-04-01

... AND GIFT TAXES GIFT TAX; GIFTS MADE AFTER DECEMBER 31, 1954 Transfers § 25.2512-3 Valuation of... with the return, including copies of reports of examinations of the business made by accountants...

Hormone Replacement Therapy: Can It Cause Vaginal Bleeding?

MedlinePlus

... hormone therapy for menopause symptoms, and my monthly menstrual periods have returned. Is this normal? Answers from ... Advertising and sponsorship opportunities Reprint Permissions A single copy of these materials may be reprinted for noncommercial ...

Evidence for the packaging of multiple copies of Tf1 mRNA into particles and the trans priming of reverse transcription.

PubMed

Haag, A L; Lin, J H; Levin, H L

2000-08-01

Long terminal repeat (LTR)-containing retrotransposons and retroviruses are close relatives that possess similar mechanisms of reverse transcription. The particles of retroviruses package two copies of viral mRNA that both function as templates for the reverse transcription of the element. We studied the LTR-retrotransposon Tf1 of Schizosaccharomyces pombe to test whether multiple copies of transposon mRNA participate in the production of cDNA. Using the unique self-priming property of Tf1, we obtained evidence that multiple copies of Tf1 mRNA were packaged into virus-like particles. By coexpressing two distinct versions of Tf1, we found that the bulk of reverse transcription that was initiated on one mRNA template was subsequently transferred to others. In addition, the first 11 nucleotides of one mRNA were able to prime, in trans, the reverse transcription of another mRNA.

Robustness of Feedback Systems with Several Modelling Errors

DTIC Science & Technology

1990-06-01

Patterson AFB, OH 45433-6553 to help us maintain a current mailing list. Copies of this report should not be returned unless return is required by security...Wright Research (If applicable) and Development Center WRDC/FIGC F33615-88-C-3601 8c. ADDRESS (City, State, and ZIP Code) 10. SOURCE OF FUNDING NUMBERS...feedback systems with several sources of modelling uncertainty. We assume that each source of uncertainty is modelled as a stable unstructured

Simultaneous Use of Multiple Answer Copying Indexes to Improve Detection Rates

ERIC Educational Resources Information Center

Wollack, James A.

2006-01-01

Many of the currently available statistical indexes to detect answer copying lack sufficient power at small [alpha] levels or when the amount of copying is relatively small. Furthermore, there is no one index that is uniformly best. Depending on the type or amount of copying, certain indexes are better than others. The purpose of this article was…

14 CFR Appendix B to Part 382 - Cross-Reference Table

Code of Federal Regulations, 2012 CFR

2012-01-01

... assistive devices, POCs and other respiratory assistive devices. 43(a) 129(b) Timely return of assistive...) 45 Availability of copy of rule. 47(a) 43 TTY's and reservations systems. 47(b) 69 Accessibility of...

14 CFR Appendix B to Part 382 - Cross-Reference Table

Code of Federal Regulations, 2013 CFR

2013-01-01

... assistive devices, POCs and other respiratory assistive devices. 43(a) 129(b) Timely return of assistive...) 45 Availability of copy of rule. 47(a) 43 TTY's and reservations systems. 47(b) 69 Accessibility of...

14 CFR Appendix B to Part 382 - Cross-Reference Table

Code of Federal Regulations, 2014 CFR

2014-01-01

... assistive devices, POCs and other respiratory assistive devices. 43(a) 129(b) Timely return of assistive...) 45 Availability of copy of rule. 47(a) 43 TTY's and reservations systems. 47(b) 69 Accessibility of...

26 CFR 301.6104(d)-2 - Making applications and returns widely available.

Code of Federal Regulations, 2010 CFR

2010-04-01

... document is posted in a format that, when accessed, downloaded, viewed and printed in hard copy, exactly... computer hardware or software required for that format (other than software that is readily available to...

The positioning logic and copy number control of genes in bacteria under stress

NASA Astrophysics Data System (ADS)

Zhang, Qiucen; Austin, Robert; Vyawahare, Saurabh; Lau, Alexandra

2013-03-01

Escherichia coli (E. coli) cells when challenged with sublethal concentrations of the genotoxic antibiotic ciprofloxacin cease to divide and form long filaments which contain multiple bacterial chromosomes. These filaments are individual mesoscopic environmental niches which provide protection for a community of chromosomes (as opposed to cells) under mutagenic stress and can provide an evolutionary fitness advantage within the niche. We use comparative genomic hybridization to show that the mesoscopic niche evolves within 20 minutes of ciprofloxacin exposure via replication of multiple copies of genes expressing ATP dependent transporters. We show that this rapid genomic amplification is done in a time efficient manner via placement of the genes encoding the pumps near the origin of replication on the bacterial chromosome. The de-amplification of multiple copies back to the wild type number is a function of the duration is a function of the ciprofloxacin exposure duration: the longer the exposure, the slower the removal of the multiple copies. The project described was supported by the National Science Foundation and the National Cancer Institute

Isolation and characterization of novel mutations in the pSC101 origin that increase copy number

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

Thompson, Mitchell G.; Sedaghatian, Nima; Barajas, Jesus F.

pSC101 is a narrow host range, low-copy plasmid commonly used for genetically manipulating Escherichia coli. As a byproduct of a genetic screen for a more sensitive lactam biosensor, we identified multiple novel mutations that increase the copy number of plasmids with the pSC101 origin. All mutations identified in this study occurred on plasmids which also contained at least one mutation localized to the RepA protein encoded within the origin. Homology modelling predicts that many of these mutations occur within the dimerization interface of RepA. Mutant RepA resulted in plasmid copy numbers between ~31 and ~113 copies/cell, relative to ~5 copies/cellmore » in wild-type pSC101 plasmids. Combining the mutations that were predicted to disrupt multiple contacts on the dimerization interface resulted in copy numbers of ~500 copies/cell, while also attenuating growth in host strains. Fluorescent protein production expressed from an arabinose-inducible promoter on mutant origin derived plasmids did correlate with copy number. Plasmids harboring RepA with one of two mutations, E83K and N99D, resulted in fluorescent protein production similar to that from p15a- (~20 copies/cell) and ColE1- (~31 copies/cell) based plasmids, respectively. The mutant copy number variants retained compatibility with p15a, pBBR, and ColE1 origins of replication. Thus, these pSC101 variants may be useful in future metabolic engineering efforts that require medium or high-copy vectors compatible with p15a- and ColE1-based plasmids.« less

Isolation and characterization of novel mutations in the pSC101 origin that increase copy number

DOE PAGES

Thompson, Mitchell G.; Sedaghatian, Nima; Barajas, Jesus F.; ...

2018-01-25

pSC101 is a narrow host range, low-copy plasmid commonly used for genetically manipulating Escherichia coli. As a byproduct of a genetic screen for a more sensitive lactam biosensor, we identified multiple novel mutations that increase the copy number of plasmids with the pSC101 origin. All mutations identified in this study occurred on plasmids which also contained at least one mutation localized to the RepA protein encoded within the origin. Homology modelling predicts that many of these mutations occur within the dimerization interface of RepA. Mutant RepA resulted in plasmid copy numbers between ~31 and ~113 copies/cell, relative to ~5 copies/cellmore » in wild-type pSC101 plasmids. Combining the mutations that were predicted to disrupt multiple contacts on the dimerization interface resulted in copy numbers of ~500 copies/cell, while also attenuating growth in host strains. Fluorescent protein production expressed from an arabinose-inducible promoter on mutant origin derived plasmids did correlate with copy number. Plasmids harboring RepA with one of two mutations, E83K and N99D, resulted in fluorescent protein production similar to that from p15a- (~20 copies/cell) and ColE1- (~31 copies/cell) based plasmids, respectively. The mutant copy number variants retained compatibility with p15a, pBBR, and ColE1 origins of replication. Thus, these pSC101 variants may be useful in future metabolic engineering efforts that require medium or high-copy vectors compatible with p15a- and ColE1-based plasmids.« less

Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging.

PubMed

Ridge, Perry G; Maxwell, Taylor J; Foutz, Spencer J; Bailey, Matthew H; Corcoran, Christopher D; Tschanz, JoAnn T; Norton, Maria C; Munger, Ronald G; O'Brien, Elizabeth; Kerber, Richard A; Cawthon, Richard M; Kauwe, John S K

2014-01-01

The mitochondria are essential organelles and are the location of cellular respiration, which is responsible for the majority of ATP production. Each cell contains multiple mitochondria, and each mitochondrion contains multiple copies of its own circular genome. The ratio of mitochondrial genomes to nuclear genomes is referred to as mitochondrial copy number. Decreases in mitochondrial copy number are known to occur in many tissues as people age, and in certain diseases. The regulation of mitochondrial copy number by nuclear genes has been studied extensively. While mitochondrial variation has been associated with longevity and some of the diseases known to have reduced mitochondrial copy number, the role that the mitochondrial genome itself has in regulating mitochondrial copy number remains poorly understood. We analyzed the complete mitochondrial genomes from 1007 individuals randomly selected from the Cache County Study on Memory Health and Aging utilizing the inferred evolutionary history of the mitochondrial haplotypes present in our dataset to identify sequence variation and mitochondrial haplotypes associated with changes in mitochondrial copy number. Three variants belonging to mitochondrial haplogroups U5A1 and T2 were significantly associated with higher mitochondrial copy number in our dataset. We identified three variants associated with higher mitochondrial copy number and suggest several hypotheses for how these variants influence mitochondrial copy number by interacting with known regulators of mitochondrial copy number. Our results are the first to report sequence variation in the mitochondrial genome that causes changes in mitochondrial copy number. The identification of these variants that increase mtDNA copy number has important implications in understanding the pathological processes that underlie these phenotypes.

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism.

PubMed

Liu, Zhenhua; Tavares, Raquel; Forsythe, Evan S; André, François; Lugan, Raphaël; Jonasson, Gabriella; Boutet-Mercey, Stéphanie; Tohge, Takayuki; Beilstein, Mark A; Werck-Reichhart, Danièle; Renault, Hugues

2016-10-07

Expansion of the cytochrome P450 gene family is often proposed to have a critical role in the evolution of metabolic complexity, in particular in microorganisms, insects and plants. However, the molecular mechanisms underlying the evolution of this complexity are poorly understood. Here we describe the evolutionary history of a plant P450 retrogene, which emerged and underwent fixation in the common ancestor of Brassicales, before undergoing tandem duplication in the ancestor of Brassicaceae. Duplication leads first to gain of dual functions in one of the copies. Both sister genes are retained through subsequent speciation but eventually return to a single copy in two of three diverging lineages. In the lineage in which both copies are maintained, the ancestral functions are split between paralogs and a novel function arises in the copy under relaxed selection. Our work illustrates how retrotransposition and gene duplication can favour the emergence of novel metabolic functions.

Mitochondrial DNA copy numbers in pyramidal neurons are decreased and mitochondrial biogenesis transcriptome signaling is disrupted in Alzheimer's disease hippocampi.

PubMed

Rice, Ann C; Keeney, Paula M; Algarzae, Norah K; Ladd, Amy C; Thomas, Ravindar R; Bennett, James P

2014-01-01

Alzheimer's disease (AD) is the major cause of adult-onset dementia and is characterized in its pre-diagnostic stage by reduced cerebral cortical glucose metabolism and in later stages by reduced cortical oxygen uptake, implying reduced mitochondrial respiration. Using quantitative PCR we determined the mitochondrial DNA (mtDNA) gene copy numbers from multiple groups of 15 or 20 pyramidal neurons, GFAP(+) astrocytes and dentate granule neurons isolated using laser capture microdissection, and the relative expression of mitochondrial biogenesis (mitobiogenesis) genes in hippocampi from 10 AD and 9 control (CTL) cases. AD pyramidal but not dentate granule neurons had significantly reduced mtDNA copy numbers compared to CTL neurons. Pyramidal neuron mtDNA copy numbers in CTL, but not AD, positively correlated with cDNA levels of multiple mitobiogenesis genes. In CTL, but not in AD, hippocampal cDNA levels of PGC1α were positively correlated with multiple downstream mitobiogenesis factors. Mitochondrial DNA copy numbers in pyramidal neurons did not correlate with hippocampal Aβ1-42 levels. After 48 h exposure of H9 human neural stem cells to the neurotoxic fragment Aβ25-35, mtDNA copy numbers were not significantly altered. In summary, AD postmortem hippocampal pyramidal neurons have reduced mtDNA copy numbers. Mitochondrial biogenesis pathway signaling relationships are disrupted in AD, but are mostly preserved in CTL. Our findings implicate complex alterations of mitochondria-host cell relationships in AD.

Evidence for the Packaging of Multiple Copies of Tf1 mRNA into Particles and the trans Priming of Reverse Transcription

PubMed Central

Haag, Amanda Leigh; Lin, Jia-Hwei; Levin, Henry L.

2000-01-01

Long terminal repeat (LTR)-containing retrotransposons and retroviruses are close relatives that possess similar mechanisms of reverse transcription. The particles of retroviruses package two copies of viral mRNA that both function as templates for the reverse transcription of the element. We studied the LTR-retrotransposon Tf1 of Schizosaccharomyces pombe to test whether multiple copies of transposon mRNA participate in the production of cDNA. Using the unique self-priming property of Tf1, we obtained evidence that multiple copies of Tf1 mRNA were packaged into virus-like particles. By coexpressing two distinct versions of Tf1, we found that the bulk of reverse transcription that was initiated on one mRNA template was subsequently transferred to others. In addition, the first 11 nucleotides of one mRNA were able to prime, in trans, the reverse transcription of another mRNA. PMID:10888658

A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans.

PubMed

Jeon, Jae Pil; Shim, Sung Mi; Jung, Jong Sun; Nam, Hye Young; Lee, Hye Jin; Oh, Berm Seok; Kim, Kuchan; Kim, Hyung Lae; Han, Bok Ghee

2009-09-30

To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.

Intelligent Multi-Media Integrated Interface Project

DTIC Science & Technology

1990-06-01

RADC (COES) Griffiss AFB NY 13441-5700. This will assist us in main- taining a current mailing list. Do not return copies of this report unless...contractual obligations or notices on a specific document require that it be returned. INTELLIGENT MULTI-MEDIA INTEGRATED INTERFACE PROJECT J. G. Neal J. M...lure ag. A = W qMN 1. AGENCY USE ONLY AM BW 2. REPORT DATE R,,PE AND DATES COYERED June 1990 Final Oct 87 to Oct 89 4. TTLE AND SUIlllLE S. FUNDING

Estimating the Probability of Traditional Copying, Conditional on Answer-Copying Statistics.

PubMed

Allen, Jeff; Ghattas, Andrew

2016-06-01

Statistics for detecting copying on multiple-choice tests produce p values measuring the probability of a value at least as large as that observed, under the null hypothesis of no copying. The posterior probability of copying is arguably more relevant than the p value, but cannot be derived from Bayes' theorem unless the population probability of copying and probability distribution of the answer-copying statistic under copying are known. In this article, the authors develop an estimator for the posterior probability of copying that is based on estimable quantities and can be used with any answer-copying statistic. The performance of the estimator is evaluated via simulation, and the authors demonstrate how to apply the formula using actual data. Potential uses, generalizability to other types of cheating, and limitations of the approach are discussed.

Kidney School

MedlinePlus

... copies? Read our licensing agreement Living Successfully with Kidney Disease People with kidney disease can live long ... Listen Printing multiple copies? Read our licensing agreement Kidneys: How They Work, How They Fail, What You ...

Integrity Verification for Multiple Data Copies in Cloud Storage Based on Spatiotemporal Chaos

NASA Astrophysics Data System (ADS)

Long, Min; Li, You; Peng, Fei

Aiming to strike for a balance between the security, efficiency and availability of the data verification in cloud storage, a novel integrity verification scheme based on spatiotemporal chaos is proposed for multiple data copies. Spatiotemporal chaos is implemented for node calculation of the binary tree, and the location of the data in the cloud is verified. Meanwhile, dynamic operation can be made to the data. Furthermore, blind information is used to prevent a third-party auditor (TPA) leakage of the users’ data privacy in a public auditing process. Performance analysis and discussion indicate that it is secure and efficient, and it supports dynamic operation and the integrity verification of multiple copies of data. It has a great potential to be implemented in cloud storage services.

High-Performance, Multi-Node File Copies and Checksums for Clustered File Systems

NASA Technical Reports Server (NTRS)

Kolano, Paul Z.; Ciotti, Robert B.

2012-01-01

Modern parallel file systems achieve high performance using a variety of techniques, such as striping files across multiple disks to increase aggregate I/O bandwidth and spreading disks across multiple servers to increase aggregate interconnect bandwidth. To achieve peak performance from such systems, it is typically necessary to utilize multiple concurrent readers/writers from multiple systems to overcome various singlesystem limitations, such as number of processors and network bandwidth. The standard cp and md5sum tools of GNU coreutils found on every modern Unix/Linux system, however, utilize a single execution thread on a single CPU core of a single system, and hence cannot take full advantage of the increased performance of clustered file systems. Mcp and msum are drop-in replacements for the standard cp and md5sum programs that utilize multiple types of parallelism and other optimizations to achieve maximum copy and checksum performance on clustered file systems. Multi-threading is used to ensure that nodes are kept as busy as possible. Read/write parallelism allows individual operations of a single copy to be overlapped using asynchronous I/O. Multinode cooperation allows different nodes to take part in the same copy/checksum. Split-file processing allows multiple threads to operate concurrently on the same file. Finally, hash trees allow inherently serial checksums to be performed in parallel. Mcp and msum provide significant performance improvements over standard cp and md5sum using multiple types of parallelism and other optimizations. The total speed-ups from all improvements are significant. Mcp improves cp performance over 27x, msum improves md5sum performance almost 19x, and the combination of mcp and msum improves verified copies via cp and md5sum by almost 22x. These improvements come in the form of drop-in replacements for cp and md5sum, so are easily used and are available for download as open source software at http://mutil.sourceforge.net.

COPI selectively drives maturation of the early Golgi

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

Papanikou, Effrosyni; Day, Kasey J.; Austin, II, Jotham

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generatemore » partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Lastly, our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins.« less

COPI selectively drives maturation of the early Golgi

DOE PAGES

Papanikou, Effrosyni; Day, Kasey J.; Austin, II, Jotham; ...

2015-12-28

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generatemore » partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Lastly, our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins.« less

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

PubMed

Zaccaria, Simone; El-Kebir, Mohammed; Klau, Gunnar W; Raphael, Benjamin J

2018-04-16

Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy-number data from multiple samples of a tumor. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that either perform deconvolution/factorization of mixed tumor samples or build phylogenetic trees assuming homogeneous tumor samples. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher resolution view of copy-number evolution of this cancer than published analyses.

Multiple copies of genes coding for electron transport proteins in the bacterium Nitrosomonas europaea.

PubMed

McTavish, H; LaQuier, F; Arciero, D; Logan, M; Mundfrom, G; Fuchs, J A; Hooper, A B

1993-04-01

The genome of Nitrosomonas europaea contains at least three copies each of the genes coding for hydroxylamine oxidoreductase (HAO) and cytochrome c554. A copy of an HAO gene is always located within 2.7 kb of a copy of a cytochrome c554 gene. Cytochrome P-460, a protein that shares very unusual spectral features with HAO, was found to be encoded by a gene separate from the HAO genes.

Equivalent D = 3 supergravity amplitudes from double copies of three-algebra and two-algebra gauge theories.

PubMed

Huang, Yu-tin; Johansson, Henrik

2013-04-26

We show that three-dimensional supergravity amplitudes can be obtained as double copies of either three-algebra super-Chern-Simons matter theory or two-algebra super-Yang-Mills theory when either theory is organized to display the color-kinematics duality. We prove that only helicity-conserving four-dimensional gravity amplitudes have nonvanishing descendants when reduced to three dimensions, implying the vanishing of odd-multiplicity S-matrix elements, in agreement with Chern-Simons matter theory. We explicitly verify the double-copy correspondence at four and six points for N = 12,10,8 supergravity theories and discuss its validity for all multiplicity.

Multiple copies of orbital angular momentum states through second-harmonic generation in a two-dimensional periodically poled LiTaO{sub 3} crystal

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

Fang, Xinyuan; Wei, Dunzhao; Liu, Dongmei

We experimentally demonstrate multiple copies of optical orbital angular momentum (OAM) states through quasi-phase-matched (QPM) second-harmonic (SH) generation in a 2D periodically poled LiTaO{sub 3} (PPLT) crystal. Since the QPM condition is satisfied by involving different reciprocal vectors in the 2D PPLT crystal, collinear and noncollinear SH beams carrying OAMs of l{sub 2} are simultaneously generated by the input fundamental beam with an OAM of l{sub 1}. The OAM conservation law (i.e., l{sub 2} = 2l{sub 1}) holds well in the experiment, which can tolerate certain phase-mismatch between the interacting waves. Our results provide an efficient way to obtain multiple copies ofmore » the wavelength-converted OAM states, which can be used to enhance the capacity in optical communications.« less

COPI selectively drives maturation of the early Golgi

PubMed Central

Papanikou, Effrosyni; Day, Kasey J; Austin, Jotham; Glick, Benjamin S

2015-01-01

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generate partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins. DOI: http://dx.doi.org/10.7554/eLife.13232.001 PMID:26709839

47 CFR 1.1112 - Form of payment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Commission. Failure to comply with the Commission's procedures will result in the return of the application... not receive final payment and such failure is not excused by bank error. (2) The Commission will... attached to the receipt copy a stamped self-addressed envelope of sufficient size to contain the date...

40 CFR 46.190 - Fellowship agreement amendments.

Code of Federal Regulations, 2010 CFR

2010-07-01

... return one copy of each amendment to the award official. If you make the change before you receive the... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Fellowship agreement amendments. 46.190 Section 46.190 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY GRANTS AND OTHER FEDERAL...

6 CFR 13.21 - Discovery.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the return date, such date will be suspended pending the ALJ's final action on the motion. (4) The... the creation of a Document. (c) Motions for discovery. (1) A party seeking discovery may file a motion. Such a motion will be accompanied by a copy of the request for production of Documents, request for...

12 CFR 622.9 - Subpoenas.

Code of Federal Regulations, 2010 CFR

2010-01-01

... subpoena was issued pay in advance the reasonable cost of copying and transporting the documentary evidence... therein by personal service or certified mail with a return receipt to the last known address of the... required by this paragraph shall be paid by the party upon whose application the subpoena is issued. (e...

Diversity in copy number and structure of a silkworm morphogenetic gene as a result of domestication.

PubMed

Sakudoh, Takashi; Nakashima, Takeharu; Kuroki, Yoko; Fujiyama, Asao; Kohara, Yuji; Honda, Naoko; Fujimoto, Hirofumi; Shimada, Toru; Nakagaki, Masao; Banno, Yutaka; Tsuchida, Kozo

2011-03-01

The carotenoid-binding protein (CBP) of the domesticated silkworm, Bombyx mori, a major determinant of cocoon color, is likely to have been substantially influenced by domestication of this species. We analyzed the structure of the CBP gene in multiple strains of B. mori, in multiple individuals of the wild silkworm, B. mandarina (the putative wild ancestor of B. mori), and in a number of other lepidopterans. We found the CBP gene copy number in genomic DNA to vary widely among B. mori strains, ranging from 1 to 20. The copies of CBP are of several types, based on the presence of a retrotransposon or partial deletion of the coding sequence. In contrast to B. mori, B. mandarina was found to possess a single copy of CBP without the retrotransposon insertion, regardless of habitat. Several other lepidopterans were found to contain sequences homologous to CBP, revealing that this gene is evolutionarily conserved in the lepidopteran lineage. Thus, domestication can generate significant diversity of gene copy number and structure over a relatively short evolutionary time. © 2011 by the Genetics Society of America

Diversity in Copy Number and Structure of a Silkworm Morphogenetic Gene as a Result of Domestication

PubMed Central

Sakudoh, Takashi; Nakashima, Takeharu; Kuroki, Yoko; Fujiyama, Asao; Kohara, Yuji; Honda, Naoko; Fujimoto, Hirofumi; Shimada, Toru; Nakagaki, Masao; Banno, Yutaka; Tsuchida, Kozo

2011-01-01

The carotenoid-binding protein (CBP) of the domesticated silkworm, Bombyx mori, a major determinant of cocoon color, is likely to have been substantially influenced by domestication of this species. We analyzed the structure of the CBP gene in multiple strains of B. mori, in multiple individuals of the wild silkworm, B. mandarina (the putative wild ancestor of B. mori), and in a number of other lepidopterans. We found the CBP gene copy number in genomic DNA to vary widely among B. mori strains, ranging from 1 to 20. The copies of CBP are of several types, based on the presence of a retrotransposon or partial deletion of the coding sequence. In contrast to B. mori, B. mandarina was found to possess a single copy of CBP without the retrotransposon insertion, regardless of habitat. Several other lepidopterans were found to contain sequences homologous to CBP, revealing that this gene is evolutionarily conserved in the lepidopteran lineage. Thus, domestication can generate significant diversity of gene copy number and structure over a relatively short evolutionary time. PMID:21242537

An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.

PubMed Central

Głowacka, Katarzyna; Kromdijk, Johannes; Leonelli, Lauriebeth; Niyogi, Krishna K.; Clemente, Tom E.

2016-01-01

Abstract Stable transformation of plants is a powerful tool for hypothesis testing. A rapid and reliable evaluation method of the transgenic allele for copy number and homozygosity is vital in analysing these transformations. Here the suitability of Southern blot analysis, thermal asymmetric interlaced (TAIL‐)PCR, quantitative (q)PCR and digital droplet (dd)PCR to estimate T‐DNA copy number, locus complexity and homozygosity were compared in transgenic tobacco. Southern blot analysis and ddPCR on three generations of transgenic offspring with contrasting zygosity and copy number were entirely consistent, whereas TAIL‐PCR often underestimated copy number. qPCR deviated considerably from the Southern blot results and had lower precision and higher variability than ddPCR. Comparison of segregation analyses and ddPCR of T1 progeny from 26 T0 plants showed that at least 19% of the lines carried multiple T‐DNA insertions per locus, which can lead to unstable transgene expression. Segregation analyses failed to detect these multiple copies, presumably because of their close linkage. This shows the importance of routine T‐DNA copy number estimation. Based on our results, ddPCR is the most suitable method, because it is as reliable as Southern blot analysis yet much faster. A protocol for this application of ddPCR to large plant genomes is provided. PMID:26670088

Determination of Type I Error Rates and Power of Answer Copying Indices under Various Conditions

ERIC Educational Resources Information Center

Yormaz, Seha; Sünbül, Önder

2017-01-01

This study aims to determine the Type I error rates and power of S[subscript 1] , S[subscript 2] indices and kappa statistic at detecting copying on multiple-choice tests under various conditions. It also aims to determine how copying groups are created in order to calculate how kappa statistics affect Type I error rates and power. In this study,…

Factors Influencing Response Rates in Online Student Evaluation Systems: A Systematic Review Approach

ERIC Educational Resources Information Center

Asare, Samuel; Daniel, Ben Kei

2018-01-01

Students' feedback on teaching activities significantly contributes to the enhancement of the quality of teaching and learning. Conventionally students evaluate teaching activities through paper based systems, where they fill out and return paper copies of teaching or course evaluation. In the last decades, institutions are moving student…

DNA Copy Number Signature to Predict Recurrence in Early-Stage Ovarian Cancer

DTIC Science & Technology

2015-08-01

RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE August 2015 2. REPORT TYPE Annual 3. DATES COVERED 1 August 2014 – 31 July 2015 4. TITLE AND...Partners Translational Core in Cambridge MA, 2) RPCI Genomics Shared Resources at Roswell Park Cancer Institute. Results for the two core

19 CFR 206.17 - Limited disclosure of certain confidential business information under administrative protective...

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 3 2012-04-01 2012-04-01 false Limited disclosure of certain confidential... attesting to his personal, good faith belief that all copies of such material have been returned or..., 2003; 70 FR 8511, Feb. 22, 2005; 76 FR 61942, Oct. 6, 2011] ...

19 CFR 206.17 - Limited disclosure of certain confidential business information under administrative protective...

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 3 2014-04-01 2014-04-01 false Limited disclosure of certain confidential... attesting to his personal, good faith belief that all copies of such material have been returned or..., 2003; 70 FR 8511, Feb. 22, 2005; 76 FR 61942, Oct. 6, 2011] ...

19 CFR 206.17 - Limited disclosure of certain confidential business information under administrative protective...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 3 2013-04-01 2013-04-01 false Limited disclosure of certain confidential... attesting to his personal, good faith belief that all copies of such material have been returned or..., 2003; 70 FR 8511, Feb. 22, 2005; 76 FR 61942, Oct. 6, 2011] ...

7 CFR 1735.80 - Submission of data.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 11 2010-01-01 2010-01-01 false Submission of data. 1735.80 Section 1735.80... Mergers Not Involving Additional Loan Funds § 1735.80 Submission of data. When a borrower is not... RUS, two copies of it shall be returned to the borrower. (l) Any other data deemed necessary by the...

Collaborative ring trial of the papaya endogenous reference gene and its polymerase chain reaction assays for genetically modified organism analysis.

PubMed

Wei, Jiaojun; Li, Feiwu; Guo, Jinchao; Li, Xiang; Xu, Junfeng; Wu, Gang; Zhang, Dabing; Yang, Litao

2013-11-27

The papaya (Carica papaya L.) Chymopapain (CHY) gene has been reported as a suitable endogenous reference gene for genetically modified (GM) papaya detection in previous studies. Herein, we further validated the use of the CHY gene and its qualitative and quantitative polymerase chain reaction (PCR) assays through an interlaboratory collaborative ring trial. A total of 12 laboratories working on detection of genetically modified organisms participated in the ring trial and returned test results. Statistical analysis of the returned results confirmed the species specificity, low heterogeneity, and single-copy number of the CHY gene among different papaya varieties. The limit of detection of the CHY qualitative PCR assay was 0.1%, while the limit of quantification of the quantitative PCR assay was ∼25 copies of haploid papaya genome with acceptable PCR efficiency and linearity. The differences between the tested and true values of papaya content in 10 blind samples ranged from 0.84 to 6.58%. These results indicated that the CHY gene was suitable as an endogenous reference gene for the identification and quantification of GM papaya.

Unambiguous discrimination between linearly dependent equidistant states with multiple copies

NASA Astrophysics Data System (ADS)

Zhang, Wen-Hai; Ren, Gang

2018-07-01

Linearly independent quantum states can be unambiguously discriminated, but linearly dependent ones cannot. For linearly dependent quantum states, however, if C copies of the single states are available, then they may form linearly independent states, and can be unambiguously discriminated. We consider unambiguous discrimination among N = D + 1 linearly dependent states given that C copies are available and that the single copies span a D-dimensional space with equal inner products. The maximum unambiguous discrimination probability is derived for all C with equal a priori probabilities. For this classification of the linearly dependent equidistant states, our result shows that if C is even then adding a further copy fails to increase the maximum discrimination probability.

Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes.

PubMed

Ziemons, Sandra; Koutsantas, Katerina; Becker, Kordula; Dahlmann, Tim; Kück, Ulrich

2017-02-16

Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster. We performed pulsed-field gel electrophoresis (PFGE), quantitative qRT-PCR, and penicillin bioassays to investigate production, deletion and overexpression strains generated in the P. chrysogenum P2niaD18 background, in order to determine the copy number of the penicillin biosynthesis gene cluster, and study the expression of one penicillin biosynthesis gene, and the penicillin titer. Analysis of production and recombinant strain showed that the enhanced penicillin titer did not depend on the copy number of the penicillin gene cluster. Our assumption was strengthened by results with a penicillin null strain lacking pcbC encoding isopenicillin N synthase. Reintroduction of one or two copies of the cluster into the pcbC deletion strain restored transcriptional high expression of the pcbC gene, but recombinant strains showed no significantly different penicillin titer compared to parental strains. Here we present a molecular genetic analysis of production and recombinant strains in the P2niaD18 background carrying different copy numbers of the penicillin biosynthesis gene cluster. Our analysis shows that the enhanced penicillin titer does not strictly depend on the copy number of the cluster. Based on these overall findings, we hypothesize that instead, complex regulatory mechanisms are prominently implicated in increased penicillin biosynthesis in production strains.

78 FR 34016 - Wireline Competition Bureau Seeks Comment on Options To Promote Rural Broadband in Rate-Of-Return...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-06

... document is available for inspection and copying during normal business hours in the FCC Reference... carriers supports such networks, and indeed, under the USF/ICC Transformation Order, 76 FR 73830, November... originally sought comment on this proposal in the USF/ICC Transformation Order FNPRM, 76 FR 73830, November...

26 CFR 31.6051-1 - Statements for employees.

Code of Federal Regulations, 2010 CFR

2010-04-01

... the remuneration paid by such employer to such employee during the calendar year, the tax return copy... paragraph (b)(8) of § 31.3401(a)-1. (v) In the case of remuneration paid for service described in section... 3121(i)(2) and section 3122. (vi) In the case of remuneration in the form of tips received by an...

20 CFR 655.900 - Purpose, procedure and applicability of subparts J and K of this part.

Code of Federal Regulations, 2010 CFR

2010-04-01

... attestation initially: (i) With the appropriate Regional Office of ETA only; or (ii) Simultaneously with the DSO and the appropriate Regional Office of ETA. In either instance, under paragraph (b)(3) of this section, ETA will return to the employer a copy of the attestation with ETA's acceptance indicated thereon...

7 CFR 1980.453 - Review of requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... requirements. (a) Immediately after reviewing the conditions and requirements in Form FmHA or its successor... of Conditions,” and return a copy to the FmHA or its successor agency under Public Law 103-354 State... FmHA or its successor agency under Public Law 103-354. (b) If the lender indicates in the “Acceptance...

46 CFR 201.124 - Service and quashing of subpoenas.

Code of Federal Regulations, 2010 CFR

2010-10-01

... or at any time prior to the return date thereof, whichever is earlier, file a motion to quash or modify the subpoena with the officer who issued the subpoena for action by him, and serve a copy of such motion to quash upon the party requesting the subpoena. If the person to whom the motion to modify or...

46 CFR 201.124 - Service and quashing of subpoenas.

Code of Federal Regulations, 2011 CFR

2011-10-01

... or at any time prior to the return date thereof, whichever is earlier, file a motion to quash or modify the subpoena with the officer who issued the subpoena for action by him, and serve a copy of such motion to quash upon the party requesting the subpoena. If the person to whom the motion to modify or...

18 CFR 1309.14 - How will complaints against recipients be processed?

Code of Federal Regulations, 2010 CFR

2010-04-01

... need not meet with the mediator at the same time. (2) If the complainant and recipient reach a mutually... writing. The mediator shall send a copy of the settlement to TVA. No further action shall be taken based... the agreement. (3) Not more than 60 days after the complaint is filed, the mediator shall return a...

Statistical tools for transgene copy number estimation based on real-time PCR.

PubMed

Yuan, Joshua S; Burris, Jason; Stewart, Nathan R; Mentewab, Ayalew; Stewart, C Neal

2007-11-01

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination. Three experimental designs and four data quality control integrated statistical models are presented. For the first method, external calibration curves are established for the transgene based on serially-diluted templates. The Ct number from a control transgenic event and putative transgenic event are compared to derive the transgene copy number or zygosity estimation. Simple linear regression and two group T-test procedures were combined to model the data from this design. For the second experimental design, standard curves were generated for both an internal reference gene and the transgene, and the copy number of transgene was compared with that of internal reference gene. Multiple regression models and ANOVA models can be employed to analyze the data and perform quality control for this approach. In the third experimental design, transgene copy number is compared with reference gene without a standard curve, but rather, is based directly on fluorescence data. Two different multiple regression models were proposed to analyze the data based on two different approaches of amplification efficiency integration. Our results highlight the importance of proper statistical treatment and quality control integration in real-time PCR-based transgene copy number determination. These statistical methods allow the real-time PCR-based transgene copy number estimation to be more reliable and precise with a proper statistical estimation. Proper confidence intervals are necessary for unambiguous prediction of trangene copy number. The four different statistical methods are compared for their advantages and disadvantages. Moreover, the statistical methods can also be applied for other real-time PCR-based quantification assays including transfection efficiency analysis and pathogen quantification.

Method and apparatus for collaborative use of application program

DOEpatents

Dean, Craig D.

1994-01-01

Method and apparatus permitting the collaborative use of a computer application program simultaneously by multiple users at different stations. The method is useful with communication protocols having client/server control structures. The method of the invention requires only a sole executing copy of the application program and a sole executing copy of software comprising the invention. Users may collaboratively use a set of application programs by invoking for each desired application program one copy of software comprising the invention.

Preparation of 13C/15N-labeled oligomers using the polymerase chain reaction

DOEpatents

Chen, Xian; Gupta, Goutam; Bradbury, E. Morton

2001-01-01

Preparation of .sup.13 C/.sup.15 N-labeled DNA oligomers using the polymerase chain reaction (PCR). A PCR based method for uniform (.sup.13 C/.sup.15 N)-labeling of DNA duplexes is described. Multiple copies of a blunt-ended duplex are cloned into a plasmid, each copy containing the sequence of interest and restriction Hinc II sequences at both the 5' and 3' ends. PCR using bi-directional primers and uniformly .sup.13 C/.sup.15 N-labeled dNTP precursors generates labeled DNA duplexes containing multiple copies of the sequence of interest. Twenty-four cycles of PCR, followed by restriction and purification, gave the uniformly .sup.13 C/.sup.15 N-labeled duplex sequence with a 30% yield. Such labeled duplexes find significant applications in multinuclear magnetic resonance spectroscopy.

Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum

PubMed Central

Wang, Jianjun; Du, Yuzhou; Wang, Suzhi; Brown, Sue; Park, Yoonseong

2011-01-01

The piggyBac transposable element, originally discovered in the cabbage looper, Trichoplusia ni, has been widely used in insect transgenesis including the red flour beetle Tribolium castaneum. We surveyed piggyBac-like (PLE) sequences in the genome of Tribolium castaneum by homology searches using as queries the diverse PLE sequences that have been described previously. The search yielded a total of 32 piggyBac-like elements (TcPLEs) which were classified into 14 distinct groups. Most of the TcPLEs contain defective functional motifs in that they are lacking inverted terminal repeats or have disrupted open reading frames. Only one single copy of TcPLE1 appears to be intact with imperfect 16 bp inverted terminal repeats flanking an open reading frame encoding a transposase of 571 amino acid residues. Many copies of TcPLEs were found to be inserted into or close to other transposon-like sequences. This large diversity of TcPLEs with generally low copy numbers suggests multiple invasions of the TcPLEs over a long evolutionary time without extensive multiplications or occurrence of rapid loss of TcPLEs copies. PMID:18342253

Discovery and analysis of an active long terminal repeat-retrotransposable element in Aspergillus oryzae.

PubMed

Jie Jin, Feng; Hara, Seiichi; Sato, Atsushi; Koyama, Yasuji

2014-01-01

Wild-type Aspergillus oryzae RIB40 contains two copies of the AO090005001597 gene. We previously constructed A. oryzae RIB40 strain, RKuAF8B, with multiple chromosomal deletions, in which the AO090005001597 copy number was found to be increased significantly. Sequence analysis indicated that AO090005001597 is part of a putative 6,000-bp retrotransposable element, flanked by two long terminal repeats (LTRs) of 669 bp, with characteristics of retroviruses and retrotransposons, and thus designated AoLTR (A. oryzae LTR-retrotransposable element). AoLTR comprised putative reverse transcriptase, RNase H, and integrase domains. The deduced amino acid sequence alignment of AoLTR showed 94% overall identity with AFLAV, an A. flavus Tf1/sushi retrotransposon. Quantitative real-time RT-PCR showed that AoLTR gene expression was significantly increased in the RKuAF8B, in accordance with the increased copy number. Inverse PCR indicated that the full-length retrotransposable element was randomly integrated into multiple genomic locations. However, no obvious phenotypic changes were associated with the increased AoLTR gene copy number.

Integrated Defense: Lessons Learned from Joint Base Balad

DTIC Science & Technology

2013-01-01

Fall 2004): 65–74. http://www.airpower.au.af.mil/airchronicles /apj/apj04/fal04/Fal04.pdf. Butterfield, SSgt Phillip . “Iraqi Army Returns to Joint...PhD Air University Press Team Chief Editor Jerry L. Gantt Copy Editor Sherry Terrell Cover Art and Book Design Daniel Armstrong Composition and Prepress Production Nedra Looney Print Preparation and Distribution Diane Clark

Work-Family Conflict, Job Satisfaction and Labour Turnover Intentions among State University Lecturers

ERIC Educational Resources Information Center

Oredein, Afolakemi Olasumbo; Alao, Foluso Toyin

2010-01-01

Examining the extent at which work-family conflict and job satisfaction could predict the labour turnover intentions among lecturers, Olabisi Onabanjo University, Nigeria, as a case study, is the purpose of this study. 229 (95%) respondents out of 240 returned their copies of the questionnaire for data analysis. The results reveal that there was a…

78 FR 58605 - Proposed Collection; Comment Request for Form 8453-EMP, Form 8453-F, Form 8453-FE, Form 8879-F...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-24

... Declaration and Signature for Electronic and Magnetic Made Filing; Form 8453-FE, U.S. Estate or Trust... information or copies of the form and instructions should be directed to Gerald J. Shields, Internal Revenue....Shields@irs.gov . SUPPLEMENTARY INFORMATION: Title: Employment Tax Declaration for an IRS e-file Return...

XNDM: An Experimental Network Data Manager.

DTIC Science & Technology

1981-06-01

return this copy. Retain or destroy. t t , UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE fWln Dtet Entred) READ INSTRUCTIONSREPORT DOCUMENTATION...MONITORING AGENCY NAME & AODRESS(IE’ different Irom Controlling Office) 15 SECURITY CLASS, (I this report) UNCLASSIFIED Same Is DECLASSIFICATION...DD JAN% 1473 EDITION OF I NOV 65 IS OBSOLETE UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE ("hen Date Entered) -: o . <. UNCLASSIFIED SECURITY

20 CFR 418.1265 - What kind of significant modified adjusted gross income reduction evidence will you need to...

Code of Federal Regulations, 2011 CFR

2011-04-01

... Adjustment Amount Determinations Using A More Recent Tax Year's Modified Adjusted Gross Income § 418.1265... more recent tax year you request we use. (c) When a copy of your filed Federal income tax return is not available for the more recent tax year in which your modified adjusted gross income was significantly...

20 CFR 418.1265 - What kind of significant modified adjusted gross income reduction evidence will you need to...

Code of Federal Regulations, 2013 CFR

2013-04-01

... Adjustment Amount Determinations Using A More Recent Tax Year's Modified Adjusted Gross Income § 418.1265... more recent tax year you request we use. (c) When a copy of your filed Federal income tax return is not available for the more recent tax year in which your modified adjusted gross income was significantly...

20 CFR 418.1265 - What kind of significant modified adjusted gross income reduction evidence will you need to...

Code of Federal Regulations, 2012 CFR

2012-04-01

... Adjustment Amount Determinations Using A More Recent Tax Year's Modified Adjusted Gross Income § 418.1265... more recent tax year you request we use. (c) When a copy of your filed Federal income tax return is not available for the more recent tax year in which your modified adjusted gross income was significantly...

20 CFR 418.1265 - What kind of significant modified adjusted gross income reduction evidence will you need to...

Code of Federal Regulations, 2014 CFR

2014-04-01

... Adjustment Amount Determinations Using A More Recent Tax Year's Modified Adjusted Gross Income § 418.1265... more recent tax year you request we use. (c) When a copy of your filed Federal income tax return is not available for the more recent tax year in which your modified adjusted gross income was significantly...

20 CFR 418.1265 - What kind of significant modified adjusted gross income reduction evidence will you need to...

Code of Federal Regulations, 2010 CFR

2010-04-01

... Adjustment Amount Determinations Using A More Recent Tax Year's Modified Adjusted Gross Income § 418.1265... more recent tax year you request we use. (c) When a copy of your filed Federal income tax return is not available for the more recent tax year in which your modified adjusted gross income was significantly...

Social Media and Academic Performance of Business Education Students in South-East Nigeria

ERIC Educational Resources Information Center

Nwazor, Joseph Chukwudi; Godwin-Maduike, Chinwe Constance

2015-01-01

The aim of the study was to analyze effects of social media on academic performance of business education students in south-east Nigeria. To achieve this, an instrument was designed and sent out to four universities in south-east Nigeria. Out of the 600 copies of the questionnaire distributed, 520 were completely filled and returned giving a…

Resolving multiple propagation paths in time of flight range cameras using direct and global separation methods

NASA Astrophysics Data System (ADS)

Whyte, Refael; Streeter, Lee; Cree, Michael J.; Dorrington, Adrian A.

2015-11-01

Time of flight (ToF) range cameras illuminate the scene with an amplitude-modulated continuous wave light source and measure the returning modulation envelopes: phase and amplitude. The phase change of the modulation envelope encodes the distance travelled. This technology suffers from measurement errors caused by multiple propagation paths from the light source to the receiving pixel. The multiple paths can be represented as the summation of a direct return, which is the return from the shortest path length, and a global return, which includes all other returns. We develop the use of a sinusoidal pattern from which a closed form solution for the direct and global returns can be computed in nine frames with the constraint that the global return is a spatially lower frequency than the illuminated pattern. In a demonstration on a scene constructed to have strong multipath interference, we find the direct return is not significantly different from the ground truth in 33/136 pixels tested; where for the full-field measurement, it is significantly different for every pixel tested. The variance in the estimated direct phase and amplitude increases by a factor of eight compared with the standard time of flight range camera technique.

Multiple Smaller Missions as a Direct Pathway to Mars Sample Return

NASA Technical Reports Server (NTRS)

Niles, P. B.; Draper, D. S.; Evans, C. A.; Gibson, E. K.; Graham, L. D.; Jones, J. H.; Lederer, S. M.; Ming, D.; Seaman, C. H.; Archer, P. D.;

Strategies for Sharing Seismic Data Among Multiple Computer Platforms

NASA Astrophysics Data System (ADS)

Baker, L. M.; Fletcher, J. B.

2001-12-01

Seismic waveform data is readily available from a variety of sources, but it often comes in a distinct, instrument-specific data format. For example, data may be from portable seismographs, such as those made by Refraction Technology or Kinemetrics, from permanent seismograph arrays, such as the USGS Parkfield Dense Array, from public data centers, such as the IRIS Data Center, or from personal communication with other researchers through e-mail or ftp. A computer must be selected to import the data - usually whichever is the most suitable for reading the originating format. However, the computer best suited for a specific analysis may not be the same. When copies of the data are then made for analysis, a proliferation of copies of the same data results, in possibly incompatible, computer-specific formats. In addition, if an error is detected and corrected in one copy, or some other change is made, all the other copies must be updated to preserve their validity. Keeping track of what data is available, where it is located, and which copy is authoritative requires an effort that is easy to neglect. We solve this problem by importing waveform data to a shared network file server that is accessible to all our computers on our campus LAN. We use a Network Appliance file server running Sun's Network File System (NFS) software. Using an NFS client software package on each analysis computer, waveform data can then be read by our MatLab or Fortran applications without first copying the data. Since there is a single copy of the waveform data in a single location, the NFS file system hierarchy provides an implicit complete waveform data catalog and the single copy is inherently authoritative. Another part of our solution is to convert the original data into a blocked-binary format (known historically as USGS DR100 or VFBB format) that is interpreted by MatLab or Fortran library routines available on each computer so that the idiosyncrasies of each machine are not visible to the user. Commercial software packages, such as MatLab, also have the ability to share data in their own formats across multiple computer platforms. Our Fortran applications can create plot files in Adobe PostScript, Illustrator, and Portable Document Format (PDF) formats. Vendor support for reading these files is readily available on multiple computer platforms. We will illustrate by example our strategies for sharing seismic data among our multiple computer platforms, and we will discuss our positive and negative experiences. We will include our solutions for handling the different byte ordering, floating-point formats, and text file ``end-of-line'' conventions on the various computer platforms we use (6 different operating systems on 5 processor architectures).

The role of redundant information in cultural transmission and cultural stabilization.

PubMed

Acerbi, Alberto; Tennie, Claudio

2016-02-01

Redundant copying has been proposed as a manner to achieve the high-fidelity necessary to pass on and preserve complex traits in human cultural transmission. There are at least 2 ways to define redundant copying. One refers to the possibility of copying repeatedly the same trait over time, and another to the ability to exploit multiple layers of information pointing to the same trait during a single copying event. Using an individual-based model, we explore how redundant copying (defined as in the latter way) helps to achieve successful transmission. The authors show that increasing redundant copying increases the likelihood of accurately transmitting a behavior more than either augmenting the number of copying occasions across time or boosting the general accuracy of social learning. They also investigate how different cost functions, deriving, for example, from the need to invest more energy in cognitive processing, impact the evolution of redundant copying. The authors show that populations converge either to high-fitness/high-costs states (with high redundant copying and complex culturally transmitted behaviors; resembling human culture) or to low-fitness/low-costs states (with low redundant copying and simple transmitted behaviors; resembling social learning forms typical of nonhuman animals). This outcome may help to explain why cumulative culture is rare in the animal kingdom. (c) 2016 APA, all rights reserved).

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

PubMed Central

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

Entanglement-assisted transformation is asymptotically equivalent to multiple-copy transformation

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

Duan Runyao; Feng Yuan; Ying Mingsheng

2005-08-15

We show that two ways of manipulating quantum entanglement - namely, entanglement-assisted local transformation [D. Jonathan and M. B. Plenio, Phys. Rev. Lett. 83, 3566 (1999)] and multiple-copy transformation [S. Bandyopadhyay, V. Roychowdhury, and U. Sen, Phys. Rev. A 65, 052315 (2002)]--are equivalent in the sense that they can asymptotically simulate each other's ability to implement a desired transformation from a given source state to another given target state with the same optimal success probability. As a consequence, this yields a feasible method to evaluate the optimal conversion probability of an entanglement-assisted transformation.

Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena.

PubMed

McGill, Susan E; Barker, Daniel

2017-07-20

" Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, "Candidatus R. magnifica" and "Candidatus V. okutanii", may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities. In particular, we used the OrthoMCL algorithm to sort proteins into groups of putative orthologs on the basis of sequence similarity. The OrthoMCL inflation parameter was tuned using biological criteria. Using the tuned value, OrthoMCL delimited 1070 protein groups. 63.5% of these groups contained one protein from each species. Two groups contained duplicate protein copies from all three species. 123 groups were unique to T. crunogena and ten groups included multiple copies of T. crunogena proteins but only single copies from the other species. "Candidatus R. magnifica" had one unique group, and had multiple copies in one group where the other species had a single copy. There were no groups unique to "Candidatus V. okutanii", and no groups in which there were multiple "Candidatus V. okutanii" proteins but only single proteins from the other species. Results align with previous suggestions that all three species share a common ancestor. However this is not definitive evidence to make taxonomic conclusions and the possibility of horizontal gene transfer was not investigated. Methodologically, the tuning of the OrthoMCL inflation parameter using biological criteria provides further methods to refine the OrthoMCL procedure.

Reduction of IgE binding and nonpromotion of Aspergillus flavus fungal growth by simultaneously silencing Ara h 2 and Ara h 6 in peanut.

USDA-ARS?s Scientific Manuscript database

The most potent peanut allergens, Ara h 2 and 6, were silenced in transgenic plants by RNA interference. Three independent transgenic lines were recovered after microprojectile bombardment, of which two contained single, integrated copies of the transgene. The third line contained multiple copies ...

On the Optimality of Answer-Copying Indices: Theory and Practice

ERIC Educational Resources Information Center

Romero, Mauricio; Riascos, Álvaro; Jara, Diego

2015-01-01

Multiple-choice exams are frequently used as an efficient and objective method to assess learning, but they are more vulnerable to answer copying than tests based on open questions. Several statistical tests (known as indices in the literature) have been proposed to detect cheating; however, to the best of our knowledge, they all lack mathematical…

Effects of the Copy-Cover-Compare Strategy on Acquisition, Maintenance, and Generalization of Spelling Sight Words for Elementary Students with Attention Deficit/Hyperactivity Disorder

ERIC Educational Resources Information Center

Moser, Lauren A.; Fishley, Katelyn M.; Konrad, Moira; Hessler, Terri

2012-01-01

Students with attention deficit/hyperactivity disorder (ADHD) often struggle with spelling. Research shows this population benefits from self-management interventions, structured practice opportunities, and immediate feedback--all components of the copy-cover-compare strategy. This empirical investigation used a multiple-baseline experimental…

An Algorithm to Improve Test Answer Copying Detection Using the Omega Statistic

ERIC Educational Resources Information Center

Maeda, Hotaka; Zhang, Bo

2017-01-01

The omega (?) statistic is reputed to be one of the best indices for detecting answer copying on multiple choice tests, but its performance relies on the accurate estimation of copier ability, which is challenging because responses from the copiers may have been contaminated. We propose an algorithm that aims to identify and delete the suspected…

Phylogeny of the cycads based on multiple single copy nuclear genes: congruence of concatenation and species tree inference methods

USDA-ARS?s Scientific Manuscript database

Despite a recent new classification, a stable tree of life for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study we apply five single copy nuclear genes (SCNGs) to the phylogeny of the order Cycadales. We specifically aim to evaluate seve...

Using Cover, Copy, and Compare Spelling with and without Timing for Elementary Students with Behavior Disorders

ERIC Educational Resources Information Center

Darrow, Danette; McLaughlin, T. F.; Derby, K. Mark; Johnson, Kathy

2012-01-01

The purpose of this study was to determine the effectiveness of cover, copy, and compare (CCC) procedures on spelling performance with two students. The participants were two elementary students enrolled in a self-contained behavior intervention classroom. A multiple baseline design across participants was employed to evaluate the effects of CCC…

Multiple sclerosis-associated retrovirus, Epstein-Barr virus, and vitamin D status in patients with relapsing remitting multiple sclerosis.

PubMed

Mostafa, Aliehossadat; Jalilvand, Somayeh; Shoja, Zabihollah; Nejati, Ahmad; Shahmahmoodi, Shohreh; Sahraian, Mohammad Ali; Marashi, Sayed Mahdi

2017-07-01

The relationship between infections and autoimmune diseases is complex and there are several reports highlighting the role of human endogenous retroviruses (HERVs) in these patients. The levels of multiple sclerosis-associated retrovirus (MSRV)-type DNA of Env gene was measured in peripheral blood mononuclear cells from 52 patients with relapsing-remitting multiple sclerosis (RRMS) and 40 healthy controls using specific quantitative PCR (qPCR) analysis. Furthermore, we analyzed the status of HERV-W/MSRV in these patients with regards to both EBV (DNA load and anti-EBNA1 IgG antibody) and vitamin D concentration. MSRV DNA copy number were significantly higher in RRMS patients than healthy controls (P < 0.0001). Interestingly, an inverse correlation was found between MSRV DNA copy number and serum vitamin D concentration (P < 0.01), but not for EBV load or anti-EBNA-1 IgG antibody. © 2017 Wiley Periodicals, Inc.

8 CFR 245.22 - Evidence to demonstrate an alien's physical presence in the United States on a specific date.

Code of Federal Regulations, 2010 CFR

2010-01-01

... has been issued in the 8 CFR, such regulation is controlling to the extent that it conflicts with this... record; (4) A public college or public school transcript; (5) Income tax records; (6) A certified copy of... submitted an income tax return, property tax payment, or similar submission or payment to the Federal, State...

75 FR 34369 - Safety Zones; City of Chicago's July 4th Celebration Fireworks, Lake Michigan, Chicago, IL

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-17

... is also available for inspection or copying at the Docket Management Facility (M-30), U.S. Department....; then north to 41[deg]53'24'' N., 087[deg]36'09'' W.; then west returning to the point of origin. The... Management and Budget has not reviewed it under that Order. This determination is based on the minimal time...

Very Long Wave Length IR Detectors

DTIC Science & Technology

2015-02-01

STINFO COPY AIR FORCE RESEARCH LABORATORY MATERIALS AND MANUFACTURING DIRECTORATE WRIGHT-PATTERSON AIR FORCE BASE, OH 45433-7750 AIR FORCE...to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE...NAME(S) AND ADDRESS(ES) Air Force Research Laboratory Materials and Manufacturing Directorate Wright-Patterson Air Force Base, OH 45433-7750 Air

32 CFR Appendix A to Part 292 - Uniform Agency Fees for Search and Duplication Under the Freedom of Information Act (as Amended)

Code of Federal Regulations, 2010 CFR

2010-07-01

... PROGRAM DEFENSE INTELLIGENCE AGENCY (DIA) FREEDOM OF INFORMATION ACT Pt. 292, App. A Appendix A to Part... search site, conducting the search and return may be charged as FOIA search costs. General Pre-Printed material, per printed page .02 Office copy, per page .15 Microfiche, per page .25 Aerial Photography...

Analysis of Major Genome Loci Underlying Artemisinin Resistance and pfmdr1 Copy Number in pre- and post-ACTs in Western Kenya

PubMed Central

Ngalah, Bidii S.; Ingasia, Luiser A.; Cheruiyot, Agnes C.; Chebon, Lorna J.; Juma, Dennis W.; Muiruri, Peninah; Onyango, Irene; Ogony, Jack; Yeda, Redemptah A.; Cheruiyot, Jelagat; Mbuba, Emmanuel; Mwangoka, Grace; Achieng, Angela O.; Ng'ang'a, Zipporah; Andagalu, Ben; Akala, Hoseah M.; Kamau, Edwin

2015-01-01

Genetic analysis of molecular markers is critical in tracking the emergence and/or spread of artemisinin resistant parasites. Clinical isolates collected in western Kenya pre- and post- introduction of artemisinin combination therapies (ACTs) were genotyped at SNP positions in regions of strong selection signatures on chromosome 13 and 14, as described in Southeast Asia (SEA). Twenty five SNPs were genotyped using Sequenom MassArray and pfmdr1 gene copy number by real-time PCR. Parasite clearance half-life and in vitro drug sensitivity testing were performed using standard methods. One hundred twenty nine isolates were successfully analyzed. Fifteen SNPs were present in pre-ACTs isolates and six in post-ACTs. None of the SNPs showed association with parasite clearance half-life. Post-ACTs parasites had significantly higher pfmdr1 copy number compared to pre-ACTs. Seven of eight parasites with multiple pfmdr1 were post-ACTs. When in vitro IC50s were compared for parasites with single vs. multiple gene copies, only amodiaquine and piperaquine reached statistical significance. Data showed SNPs on chromosome 13 and 14 had different frequency and trend in western Kenya parasites compared SEA. Increase in pfmdr1 gene copy is consistent with recent studies in African parasites. Data suggests genetic signature of artemisinin resistance in Africa might be different from SEA. PMID:25655315

Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.

PubMed

Urrutia, Eugene; Chen, Hao; Zhou, Zilu; Zhang, Nancy R; Jiang, Yuchao

2018-06-15

Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies. In cancer genomics, detection of somatic copy number changes and profiling of allele-specific copy number (ASCN) are complicated by experimental biases and artifacts as well as normal cell contamination and cancer subclone admixture. Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. Here we describe a flexible computational pipeline, MARATHON, which integrates multiple related statistical software for copy number profiling and downstream analyses in disease genetic studies. MARATHON is publicly available at https://github.com/yuchaojiang/MARATHON. Supplementary data are available at Bioinformatics online.

Cryptology Management in a Quantum Computing Era

DTIC Science & Technology

2012-06-01

HOW IT WORKS (BLACK BOX) ...........................7 1. Schrodinger’s Cat Theory ......................7 2. Multiverse Theory...the macroscopic scale of an animal through the mechanism of a hammer activated by the decay of the radioactive substance. 2. Multiverse Theory...quantum mechanics is the multiverse theory. This theory states that at every decision, the universe splits into multiple copies; the number of copies is

Crime in the Classroom: Analysis over 26 Years

ERIC Educational Resources Information Center

Harrp, David N.

2018-01-01

Copying adjacent answer sheets on the oft-used multiple-choice exams can be prevented if exam material is scrambled. The latter mode has been a requirement for all exams of this type at McGill University for 26 years. Cheating by copying has been reduced to nearly zero in this time. The experiment carried out used permissive seating and a single…

Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci.

Treesearch

John Syring; Ann Willyard; Richard Cronn; Aaron Liston

2005-01-01

Sequence data from nrITS and cpDNA have failed to fully resolve phylogenetic relationships among Pinus species. Four low-copy nuclear genes, developed from the screening of 73 mapped conifer anchor loci, were sequenced from 12 species representing all subsections. Individual loci do not uniformly support either the nrITS or cpDNA hypotheses and in...

The cost of copy number in a selfish genetic element: the 2-μm plasmid of Saccharomyces cerevisiae.

PubMed

Harrison, Ellie; Koufopanou, V; Burt, A; MacLean, R C

2012-11-01

Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2 μm is a multicopy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2 μm is that plasmid copy number evolves as a trade-off between selection for increased vertical transmission, favouring high copy number, and selection for decreased virulence, favouring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2 μm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (± 0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast per 2 μm associations and pave the way for future studies examining how selection can shape the cost of multicopy elements. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.

PubMed

Szatkiewicz, Jin P; Wang, WeiBo; Sullivan, Patrick F; Wang, Wei; Sun, Wei

2013-02-01

Structural variation is an important class of genetic variation in mammals. High-throughput sequencing (HTS) technologies promise to revolutionize copy-number variation (CNV) detection but present substantial analytic challenges. Converging evidence suggests that multiple types of CNV-informative data (e.g. read-depth, read-pair, split-read) need be considered, and that sophisticated methods are needed for more accurate CNV detection. We observed that various sources of experimental biases in HTS confound read-depth estimation, and note that bias correction has not been adequately addressed by existing methods. We present a novel read-depth-based method, GENSENG, which uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the effects of multiple confounders. Based on extensive calibration using multiple HTS data sets, we conclude that our method outperforms existing read-depth-based CNV detection algorithms. The concept of simultaneous bias correction and CNV detection can serve as a basis for combining read-depth with other types of information such as read-pair or split-read in a single analysis. A user-friendly and computationally efficient implementation of our method is freely available.

K13 mutations and pfmdr1 copy number variation in Plasmodium falciparum malaria in Myanmar.

PubMed

Win, Aye A; Imwong, Mallika; Kyaw, Myat P; Woodrow, Charles J; Chotivanich, Kesinee; Hanboonkunupakarn, Borimas; Pukrittayakamee, Sasithon

2016-02-24

Artemisinin-based combination therapy has been first-line treatment for falciparum malaria in Myanmar since 2005. The wide extent of artemisinin resistance in the Greater Mekong sub-region and the presence of mefloquine resistance at the Myanmar-Thailand border raise concerns over resistance patterns in Myanmar. The availability of molecular markers for resistance to both drugs enables assessment even in remote malaria-endemic areas. A total of 250 dried blood spot samples collected from patients with Plasmodium falciparum malarial infection in five malaria-endemic areas across Myanmar were analysed for kelch 13 sequence (k13) and pfmdr1 copy number variation. K13 mutations in the region corresponding to amino acids 210-726 (including the propeller region of the protein) were detected by nested PCR amplification and sequencing, and pfmdr1 copy number variation by real-time PCR. In two sites, a sub-set of patients were prospectively followed up for assessment of day-3 parasite clearance rates after a standard course of artemether-lumefantrine. K13 mutations and pfmdr1 amplification were successfully analysed in 206 and 218 samples, respectively. Sixty-nine isolates (33.5 %) had mutations within the k13 propeller region with 53 of these (76.8 %) having mutations already known to be associated with artemisinin resistance. F446I (32 isolates) and P574L (15 isolates) were the most common examples. K13 mutation was less common in sites in western border regions (29 of 155 isolates) compared to samples from the east and north (40 of 51 isolates; p < 0.0001). The overall proportion of parasites with multiple pfmdr1 copies (greater than 1.5) was 5.5 %. Seven samples showed both k13 mutation and multiple copies of pfmdr1. Only one of 36 patients followed up after artemether-lumefantrine treatment still had parasites at day 3; molecular analysis indicated wild-type k13 and single copy pfmdr1. The proportion of P. falciparum isolates with mutations in the propeller region of k13 indicates that artemisinin resistance extends across much of Myanmar. There is a low prevalence of parasites with multiple pfmdr1 copies across the country. The efficacy of artemisinin-based combination therapy containing mefloquine and lumefantrine is, therefore, expected to be high, although regular monitoring of efficacy will be important.

A Study on Software-based Sensing Technology for Multiple Object Control in AR Video

PubMed Central

Jung, Sungmo; Song, Jae-gu; Hwang, Dae-Joon; Ahn, Jae Young; Kim, Seoksoo

2010-01-01

Researches on Augmented Reality (AR) have recently received attention. With these, the Machine-to-Machine (M2M) market has started to be active and there are numerous efforts to apply this to real life in all sectors of society. To date, the M2M market has applied the existing marker-based AR technology in entertainment, business and other industries. With the existing marker-based AR technology, a designated object can only be loaded on the screen from one marker and a marker has to be added to load on the screen the same object again. This situation creates a problem where the relevant marker’should be extracted and printed in screen so that loading of the multiple objects is enabled. However, since the distance between markers will not be measured in the process of detecting and copying markers, the markers can be overlapped and thus the objects would not be augmented. To solve this problem, a circle having the longest radius needs to be created from a focal point of a marker to be copied, so that no object is copied within the confines of the circle. In this paper, software-based sensing technology for multiple object detection and loading using PPHT has been developed and overlapping marker control according to multiple object control has been studied using the Bresenham and Mean Shift algorithms. PMID:22163444

A study on software-based sensing technology for multiple object control in AR video.

PubMed

Jung, Sungmo; Song, Jae-Gu; Hwang, Dae-Joon; Ahn, Jae Young; Kim, Seoksoo

2010-01-01

Researches on Augmented Reality (AR) have recently received attention. With these, the Machine-to-Machine (M2M) market has started to be active and there are numerous efforts to apply this to real life in all sectors of society. To date, the M2M market has applied the existing marker-based AR technology in entertainment, business and other industries. With the existing marker-based AR technology, a designated object can only be loaded on the screen from one marker and a marker has to be added to load on the screen the same object again. This situation creates a problem where the relevant marker'should be extracted and printed in screen so that loading of the multiple objects is enabled. However, since the distance between markers will not be measured in the process of detecting and copying markers, the markers can be overlapped and thus the objects would not be augmented. To solve this problem, a circle having the longest radius needs to be created from a focal point of a marker to be copied, so that no object is copied within the confines of the circle. In this paper, software-based sensing technology for multiple object detection and loading using PPHT has been developed and overlapping marker control according to multiple object control has been studied using the Bresenham and Mean Shift algorithms.

Multidimensional Filtering Investigations.

DTIC Science & Technology

1987-02-01

organization , please notify RADC (DCCD) Griffis. An NY 13441-5700. This will assist us in main- taming a current mailing list. Do not return copies of...OF REPORT N/A Approved for public release; distribution Zb. DECLASSIFICATION/IDOWNGRADING SCHEDUL.E unlimited. MIA 4. PERFORMING ORGANIZATION REPORT...NUMBER(S) S. MONITORING ORGANIZATION REPORT NUMBER(S) N/A ADC-TR-86-231 Ge. NAME OF PERFORMING ORGANIZATION 6Gb. OFFICE SYMBOL 7a. NAME OF MONITORING

Time to viral load suppression in antiretroviral-naive and -experienced HIV-infected pregnant women on highly active antiretroviral therapy: implications for pregnant women presenting late in gestation.

PubMed

Aziz, N; Sokoloff, A; Kornak, J; Leva, N V; Mendiola, M L; Levison, J; Feakins, C; Shannon, M; Cohan, D

2013-11-01

To compare time to achieve viral load <400 copies/ml and <1000 copies/ml in HIV-infected antiretroviral (ARV) -naive versus ARV-experienced pregnant women on highly active antiretroviral therapy (HAART). Retrospective cohort study. Three university medical centers, USA. HIV-infected pregnant women initiated or restarted on HAART during pregnancy. We calculated time to viral load <400 copies/ml and <1000 copies/ml in HIV-infected pregnant women on HAART who reported at least 50% adherence, stratifying based on previous ARV exposure history. Time to HIV viral load <400 copies/ml and <1000 copies/ml. We evaluated 138 HIV-infected pregnant women, comprising 76 ARV-naive and 62 ARV-experienced. Ninety-three percent of ARV-naive women achieved a viral load < 400 copies/ml during pregnancy compared with 92% of ARV-experienced women (P = 0.82). The median number of days to achieve a viral load < 400 copies/ml in the ARV-naive cohort was 25.0 (range 3.5-133; interquartile range 16-34) days compared with 27.0 (range 8-162.5; interquartile range 18.5-54.3) days in the ARV-experienced cohort (P = 0.02). In a multiple predictor analysis, women with higher adherence (adjusted relative hazard [aRH] per 10% increase in adherence 1.29, 95% confidence interval [CI] 1.08-1.54, P = 0.01) and receiving a non-nucleotide reverse transcriptase inhibitor (NNRTI) -based regimen (aRH 2.48, 95% CI 1.33-4.63, P = 0.01) were more likely to achieve viral load <400 copies/ml earlier. Increased baseline HIV log10 viral load was associated with a later time of achieving viral load <400 copies/ml (aRH 0.60, 95% CI 0.39-0.92, P = 0.02). In a corresponding model of time to achieve viral load <1000 copies/ml, adherence (aRH per 10% increase in adherence 1.79, 95% CI 1.34-2.39, P < 0.001), receipt of NNRTI (aRH 2.95, 95% CI 1.23-7.06, P = 0.02), and CD4 cell count (aRH per 50 count increase in CD4 1.12, 95% CI 1.03-1.22, P = 0.01) were associated with an earlier time to achieve viral load below this threshold. Increasing baseline HIV log10 viral load was associated with a longer time of achieving viral load <1000 copies/ml (aRH 0.54, 95% CI 0.34-0.86, P = 0.01). In multiple predictor models, previous ARV exposure was not significantly associated with time to achieve viral load below thresholds of <400 copies/ml and <1000 copies/ml. Pregnant women with ≥50% adherence, whether ARV-naive or ARV-experienced, on average achieve a viral load <400 copies/ml within a median of 26 days and a viral load of <1000 copies/ml within a median of 14 days of HAART initiation. Increased adherence, receipt of NNRTI-based regimen and lower baseline HIV log10 viral load were all statistically significant predictors of earlier time to achieve viral load <400 copies/ml and <1000 copies/ml. Increased CD4 count was statistically significant as a predictor of earlier time to achieve viral load <1000 copies/ml. © 2013 The Authors BJOG An International Journal of Obstetrics and Gynaecology © 2013 RCOG.

Adaptive and bounded investment returns promote cooperation in spatial public goods games.

PubMed

Chen, Xiaojie; Liu, Yongkui; Zhou, Yonghui; Wang, Long; Perc, Matjaž

2012-01-01

The public goods game is one of the most famous models for studying the evolution of cooperation in sizable groups. The multiplication factor in this game can characterize the investment return from the public good, which may be variable depending on the interactive environment in realistic situations. Instead of using the same universal value, here we consider that the multiplication factor in each group is updated based on the differences between the local and global interactive environments in the spatial public goods game, but meanwhile limited to within a certain range. We find that the adaptive and bounded investment returns can significantly promote cooperation. In particular, full cooperation can be achieved for high feedback strength when appropriate limitation is set for the investment return. Also, we show that the fraction of cooperators in the whole population can become larger if the lower and upper limits of the multiplication factor are increased. Furthermore, in comparison to the traditionally spatial public goods game where the multiplication factor in each group is identical and fixed, we find that cooperation can be better promoted if the multiplication factor is constrained to adjust between one and the group size in our model. Our results highlight the importance of the locally adaptive and bounded investment returns for the emergence and dominance of cooperative behavior in structured populations.

Adaptive and Bounded Investment Returns Promote Cooperation in Spatial Public Goods Games

PubMed Central

Chen, Xiaojie; Liu, Yongkui; Zhou, Yonghui; Wang, Long; Perc, Matjaž

2012-01-01

The public goods game is one of the most famous models for studying the evolution of cooperation in sizable groups. The multiplication factor in this game can characterize the investment return from the public good, which may be variable depending on the interactive environment in realistic situations. Instead of using the same universal value, here we consider that the multiplication factor in each group is updated based on the differences between the local and global interactive environments in the spatial public goods game, but meanwhile limited to within a certain range. We find that the adaptive and bounded investment returns can significantly promote cooperation. In particular, full cooperation can be achieved for high feedback strength when appropriate limitation is set for the investment return. Also, we show that the fraction of cooperators in the whole population can become larger if the lower and upper limits of the multiplication factor are increased. Furthermore, in comparison to the traditionally spatial public goods game where the multiplication factor in each group is identical and fixed, we find that cooperation can be better promoted if the multiplication factor is constrained to adjust between one and the group size in our model. Our results highlight the importance of the locally adaptive and bounded investment returns for the emergence and dominance of cooperative behavior in structured populations. PMID:22615836

Cloud Effects in Hyperspectral Imagery from First-Principles Scene Simulations

DTIC Science & Technology

2009-01-01

SPIE. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, or distribution to multiple locations...scattering and absorption, scattering events, surface scattering with material-dependent bidirectional reflectances, multiple surface adjacency...aerosols or clouds, they may be absorbed, or they may reflect off the ground or an object. A given photon may undergo multiple scattering events

A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

PubMed

Brown, Angus M

2010-04-01

The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110.

PubMed

Fomukong, N G; Tang, T H; al-Maamary, S; Ibrahim, W A; Ramayah, S; Yates, M; Zainuddin, Z F; Dale, J W

1994-12-01

DNA fingerprinting with the insertion sequence IS6110 (also known as IS986) has become established as a major tool for investigating the spread of tuberculosis. Most strains of Mycobacterium tuberculosis have multiple copies of IS6110, but a small minority carry a single copy only. We have examined selected strains from Malaysia, Tanzania and Oman, in comparison with M. bovis isolates and BCG strains carrying one or two copies of IS6110. The insertion sequence appears to be present in the same position in all these strains, which suggests that in these organisms the element is defective in transposition and that the loss of transposability may have occurred at an early stage in the evolution of the M. tuberculosis complex.

Development of Protoporphyrinogen Oxidase as an Efficient Selection Marker for Agrobacterium tumefaciens-Mediated Transformation of Maize

PubMed Central

Li, Xianggan; Volrath, Sandy L.; Nicholl, David B.G.; Chilcott, Charles E.; Johnson, Marie A.; Ward, Eric R.; Law, Marcus D.

2003-01-01

In this article, we report the isolation of plant protoporphyrinogen oxidase (PPO) genes and the isolation of herbicide-tolerant mutants. Subsequently, an Arabidopsis double mutant (Y426M + S305L) was used to develop a selectable marker system for Agrobacterium tumefaciens-mediated transformation of maize (Zea mays) and to obtain multiple events tolerant to the PPO family of herbicides. Maize transformants were produced via butafenacil selection using a flexible light regime to increase selection pressure. Butafenacil selection per se did not change transgene copy number distribution relative to other selectable marker systems, but the most tolerant events identified in the greenhouse were more likely to contain multiple copies of the introduced mutant PPO gene. To date, more than 2,500 independent transgenic maize events have been produced using butafenacil selection. The high frequency of A. tumefaciens-mediated transformation via PPO selection enabled us to obtain single-copy transgenic maize lines tolerant to field levels of butafenacil. PMID:12972658

Different small, acid-soluble proteins of the alpha/beta type have interchangeable roles in the heat and UV radiation resistance of Bacillus subtilis spores.

PubMed Central

Mason, J M; Setlow, P

1987-01-01

Spores of Bacillus subtilis strains which carry deletion mutations in one gene (sspA) or two genes (sspA and sspB) which code for major alpha/beta-type small, acid-soluble spore proteins (SASP) are known to be much more sensitive to heat and UV radiation than wild-type spores. This heat- and UV-sensitive phenotype was cured completely or in part by introduction into these mutant strains of one or more copies of the sspA or sspB genes themselves; multiple copies of the B. subtilis sspD gene, which codes for a minor alpha/beta-type SASP; or multiple copies of the SASP-C gene, which codes for a major alpha/beta-type SASP of Bacillus megaterium. These findings suggest that alpha/beta-type SASP play interchangeable roles in the heat and UV radiation resistance of bacterial spores. Images PMID:3112127

Association of Higher Defensin β-4 Genomic Copy Numbers with Behçet's Disease in Iraqi Patients.

PubMed

Hameed, Ammar F; Jaradat, Sameh; Al-Musawi, Bassam M; Sharquie, Khalifa; Ibrahim, Mazin J; Hayani, Raafa K; Norgauer, Johannes

2015-11-01

Behçet's disease (BD) is an immune-mediated small vessel systemic vasculitis. Human β-defensins are antimicrobial peptides associated with many inflammatory diseases and are encoded by the β-defensin family of multiple-copy genes. However, their role in BD necessitates further investigation. The aim of the present study was to investigate the possible association of BD in its various clinical forms with defensin β-4 (DEFB4) genomic copy numbers. This case-control study was conducted from January to September 2011 and included 50 control subjects and 27 unrelated Iraqi BD patients registered at Baghdad Teaching Hospital, Bagdad, Iraq. Copy numbers of the DEFB4 gene were determined using the comparative cycle threshold method by duplex real-time polymerase chain reaction technology at the Department of Dermatology of Jena University Hospital, Jena, Germany. DEFB4 genomic copy numbers were significantly higher in the BD group compared to the control group (P = 0.010). However, no statistically significant association was found between copy numbers and clinical variables within the BD group. The DEFB4 copy number polymorphism may be associated with BD; however, it is not associated with different clinical manifestations of the disease.

Inhibition-of-return at multiple locations in visual space.

PubMed

Wright, R D; Richard, C M

1996-09-01

Inhibition-of-return is thought to be a visual search phenomenon characterized by delayed responses to targets presented at recently cued or recently fixated locations. We studied this inhibition effect following the simultaneous presentation of multiple location cues. The results indicated that response inhibition can be associated with as many as four locations at the same time. This suggests that a purely oculomotor account of inhibition-of-return is oversimplified. In short, although oculomotor processes appear to play a role in inhibition-of-return they may not tell the whole story about how it occurs because we can only program and execute eye movements to one location at a time.

Return to the Primary Acute Care Service Among Patients With Multiple Myeloma on an Acute Inpatient Rehabilitation Unit.

PubMed

Fu, Jack B; Lee, Jay; Shin, Ben C; Silver, Julie K; Smith, Dennis W; Shah, Jatin J; Bruera, Eduardo

2017-06-01

Pancytopenia, immunosuppression, and other factors may place patients with multiple myeloma at risk for medical complications. These patients often require inpatient rehabilitation. No previous studies have looked at risk factors for return to the primary acute care service of this patient population. To determine the percentage of and factors associated with return to the primary acute care service of multiple myeloma rehabilitation inpatients. Retrospective review. Acute inpatient rehabilitation unit within a National Cancer Institute Comprehensive Cancer Center. All patients with multiple myeloma admitted to the inpatient rehabilitation unit between March 1, 2004, and February 28, 2015. Return to the primary acute care service was analyzed with demographic information, multiple myeloma characteristics, medications, laboratory values, and hospital admission characteristics. One hundred forty-three inpatient rehabilitation admissions were found during the study period. After we removed multiple admissions of the same patients and planned transfers to the primary acute care service, 122 admissions were analyzed. Thirty-two (26%) patients transferred back to the primary acute care service for unplanned reasons. Multivariate analysis revealed male gender and thrombocytopenia as significantly associated with return to the primary acute care service. The median survival of patients who transferred back to the inpatient primary acute care service was 180 days versus 550 days for those who did not (P < .001). Because of their medical fragility, clinicians caring for rehabilitation inpatients with multiple myeloma should maintain close contact with the primary oncology service. Factors associated with an increased risk of transfer back to the primary acute care service include male gender and thrombocytopenia. IV. Copyright © 2017 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

The Effects of Cover, Copy, and Compare to Teach Spelling to Middle School Students with Learning Disabilities and OHI

ERIC Educational Resources Information Center

Kinney, Michelle; Hochstetler, Elizabeth; McLaughlin, T. F.; Derby, K. Mark

2013-01-01

The purpose of this study was to assess the effects of cover, copy, and compare (CCC) on the spelling performance of three male middle school students. Two of the participants had learning disabilities and the third was health impaired. The study was conducted in a public school resource room in the Pacific Northwest. A multiple-baseline across…

An exploratory study of parental knowledge of early childhood oral health care in Southland, New Zealand.

PubMed

Chia, Leonard; Densie, Ian; Morgan, Christian

2015-03-01

The primary objective was to clearly assess the oral health care knowledge of Southland parents. The secondary objective was to identify whether inequalities exist between parents with different ethnicity, education or income. An exploratory study based on a simple online/ paper questionnaire. Participants were recruited through Southland early childcare centres. Researchers contacted 115 centres, 66 agreed to participate and 58 returned questionnaires. Questionnaires were distributed to each centre to be completed by the parents. The questionnaire was able to be completed online or as a paper copy. Centres were supplied with dental brochures, which were distributed after the questionnaires were returned. Questionnaires were collated and the responses analysed. Six hundred and seventy questionnaires were returned, 213 online and 457 paper copies. The typical participant was a mother (93.9%), age 34 years (median), a non-smoker (86.3%), non-Maori (87.1%), with a university degree (33.9%) and an annual household income between $60,001 and $100,000 (36.5%). Twenty of the 47 questions were selected to reflect parental knowledge. Overall, 65.1% of the respondents answered all 20 questions correctly. Differences in knowledge were identified between mothers and other participants (65.4% vs. 59.4%), smokers and non-smokers (61.3% vs. 65.7%), Maori and non-Maori (61.6% vs. 65.6%) and education level (Primary 58.0% vs. Degree 68.7%) (P < 0.05). This study revealed differences in knowledge in early childhood oral health care. Participants who identified as non-mothers (fathers, step-fathers, legal care givers or other), smokers, Maori or low education displayed significantly less knowledge. Further education and oral health care promotion may be needed to improve this disparity.

Tester Independent Support Software System (TISSS)

DTIC Science & Technology

1991-08-01

AD-A240 668 RL-TR-91-163 Final Technical Report August 1991 TESTER INDEPENDENT SUPPORT SOFTWARE SYSTEM (TISSS) Harris Corporation Dr. Robert Rolfe...Laboratory Air Force Systems Command Griffiss Air Force Base, NY 13441-5700 9_1 9 17 o15 This report has been reviewed by the Rome Laboratory Public...will assist us in maintaining a current mailing list. Do not return copies of this report unless contractual obligations or notices on a specific

Who Benefits Most from a University Degree?: A Cross-National Comparison of Selection and Wage Returns in the US, UK, and Germany

ERIC Educational Resources Information Center

Luthra, Renee Reichl; Flashman, Jennifer

2017-01-01

Recent research on economic returns to higher education in the United States suggests that those with the highest wage returns to a college degree are least likely to obtain one. We extend the study of heterogeneous returns to tertiary education across multiple institutional contexts, investigating how the relationship between wage returns and the…

Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae)

PubMed Central

Zuo, Hongwei; Wu, Panpan; Wu, Dexiang; Sun, Genlou

2015-01-01

To study origin and evolutionary dynamics of tetraploid Elymus trachycaulus that has been cytologically defined as containing StH genomes, thirteen accessions of E. trachycaulus were analyzed using two low-copy nuclear gene Pepc (phosphoenolpyruvate carboxylase) and Rpb2 (the second largest subunit of RNA polymerase II), and one chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Our chloroplast data indicated that Pseudoroegneria (St genome) was the maternal donor of E. trachycaulus. Rpb2 data indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum (H genome)-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus was contributed by multiple sources, whether due to multiple origins or introgression resulting from subsequent hybridization. Failure to recovering St copy of Pepc sequence in most accessions of E. trachycaulus might be caused by genome convergent evolution in allopolyploids. Multiple copies of H-like Pepc sequence from each accession with relative large deletions and insertions might be caused by either instability of Pepc sequence in H- genome or incomplete concerted evolution. Our results highlighted complex evolutionary history of E. trachycaulus. PMID:25946188

CLIPS, AppleEvents, and AppleScript: Integrating CLIPS with commercial software

NASA Technical Reports Server (NTRS)

Compton, Michael M.; Wolfe, Shawn R.

1994-01-01

Many of today's intelligent systems are comprised of several modules, perhaps written in different tools and languages, that together help solve the user's problem. These systems often employ a knowledge-based component that is not accessed directly by the user, but instead operates 'in the background' offering assistance to the user as necessary. In these types of modular systems, an efficient, flexible, and eady-to-use mechanism for sharing data between programs is crucial. To help permit transparent integration of CLIPS with other Macintosh applications, the AI Research Branch at NASA Ames Research Center has extended CLIPS to allow it to communicate transparently with other applications through two popular data-sharing mechanisms provided by the Macintosh operating system: Apple Events (a 'high-level' event mechanism for program-to-program communication), and AppleScript, a recently-released scripting language for the Macintosh. This capability permits other applications (running on either the same or a remote machine) to send a command to CLIPS, which then responds as if the command were typed into the CLIPS dialog window. Any result returned by the command is then automatically returned to the program that sent it. Likewise, CLIPS can send several types of Apple Events directly to other local or remote applications. This CLIPS system has been successfully integrated with a variety of commercial applications, including data collection programs, electronics forms packages, DBMS's, and email programs. These mechanisms can permit transparent user access to the knowledge base from within a commercial application, and allow a single copy of the knowledge base to service multiple users in a networked environment.

More nonlocality with less purity.

PubMed

Bandyopadhyay, Somshubhro

2011-05-27

Quantum information is nonlocal in the sense that local measurements on a composite quantum system, prepared in one of many mutually orthogonal states, may not reveal in which state the system was prepared. It is shown that in the many copy limit this kind of nonlocality is fundamentally different for pure and mixed quantum states. In particular, orthogonal mixed states may not be distinguishable by local operations and classical communication, no matter how many copies are supplied, whereas any set of N orthogonal pure states can be perfectly discriminated with m copies, where m

Array-CGH analysis in Rwandan patients presenting development delay/intellectual disability with multiple congenital anomalies.

PubMed

Uwineza, Annette; Caberg, Jean-Hubert; Hitayezu, Janvier; Hellin, Anne Cecile; Jamar, Mauricette; Dideberg, Vinciane; Rusingiza, Emmanuel K; Bours, Vincent; Mutesa, Leon

2014-07-12

Array-CGH is considered as the first-tier investigation used to identify copy number variations. Right now, there is no available data about the genetic etiology of patients with development delay/intellectual disability and congenital malformation in East Africa. Array comparative genomic hybridization was performed in 50 Rwandan patients with development delay/intellectual disability and multiple congenital abnormalities, using the Agilent's 180 K microarray platform. Fourteen patients (28%) had a global development delay whereas 36 (72%) patients presented intellectual disability. All patients presented multiple congenital abnormalities. Clinically significant copy number variations were found in 13 patients (26%). Size of CNVs ranged from 0,9 Mb to 34 Mb. Six patients had CNVs associated with known syndromes, whereas 7 patients presented rare genomic imbalances. This study showed that CNVs are present in African population and show the importance to implement genetic testing in East-African countries.

Method and apparatus for obtaining stack traceback data for multiple computing nodes of a massively parallel computer system

DOEpatents

Gooding, Thomas Michael; McCarthy, Patrick Joseph

2010-03-02

A data collector for a massively parallel computer system obtains call-return stack traceback data for multiple nodes by retrieving partial call-return stack traceback data from each node, grouping the nodes in subsets according to the partial traceback data, and obtaining further call-return stack traceback data from a representative node or nodes of each subset. Preferably, the partial data is a respective instruction address from each node, nodes having identical instruction address being grouped together in the same subset. Preferably, a single node of each subset is chosen and full stack traceback data is retrieved from the call-return stack within the chosen node.

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat.

PubMed

Würschum, Tobias; Boeven, Philipp H G; Langer, Simon M; Longin, C Friedrich H; Leiser, Willmar L

2015-07-29

Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown. Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties' region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time. In conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.

Interface Message Processors for the ARPA Computer Network

DTIC Science & Technology

1976-07-01

and then clear the location) as its primitive locking facility (i.e., as the necessary multiprocessor lock equivalent to Dijkstra semaphores )[37]. To...of the extra storage required for the redundant copies. There is the problem of maintaining synchronization of multiple copy data bases in the presence...through any of the data base sites. I Update synchronization . Races between conflicting, "concurrent" update requests are resolved in a manner that j

An Adaptive Grid Algorithm for Nonequilibrium Hypersonic Flows

DTIC Science & Technology

1990-04-01

FORCE SYSTEMS COMMAND WRIGHT-PATTERSON AIR FORCE BASE, OHIO 45433-6553 NOTICE When Government drawings, specifications, or other data are used for any...any rights or permission to manufacture, use , or sell any patented invention that may in any way be related thereto. This technical report has been...WRDC/FIMN, WPAFB OH 45433-6553 to help us maintain a current mailing list. Copies of this report should not be returned unless it is required by security

A Guide to the Estimation of the Hazard Presented by Chemicals in Human Milk.

DTIC Science & Technology

1985-11-01

Occupational and Environmental Health Laboratory Aerospace Medical Division (AFSC) Brooks Air Force Base , Texas 78235-5501 i "-_,-..,,," ,_. .,..,;.: 1...AD-RISS 651 A GUIDE TO THE ESTIMATION OF THE HZRR PRESENTED BY CHEMICALS IN HUMAN M.. (U) AIR FORCE OCCUPATIONAL ANo ENYIRONMENTAL HEALTH LAD BROOKS...illustration purposes and does not constitute endorsement or recommendation for use by the United States Air Force . Do not return this copy. Retain or

Translations on Eastern Europe, Political, Sociological, and Military Affairs, Number 1555

DTIC Science & Technology

1978-06-29

Available Copy - a - [III - EE - 6.3J J INTERNATIONAL AFFAIRS HUNGARIAN WRITER FROM ROMANIA PUBLICIZES NEW LITERARY WORKS Budapest ELET ES...8217 In Budapest "] [Text] Sandor Huszar, chief editor of our sister paper, A HET in Bucharest, visited us last in March 1977. And because he returned...what business are you this time? [Answer] I flew to Budapest as a human advertisement. I came to our friends with the problems of A HET. [Questions

Improvement of ECM Techniques through Implementation of a Genetic Algorithm

DTIC Science & Technology

2008-03-01

Range Gate Pull-Off (RGPO), where pulse returns are time - delayed to induce an increase in target distance, and Velocity Gate Pull-Off (VGPO), which...estima- tion, the assumption given is that the signal is a stationary, bandlimited process, 13 where the time delay will be fixed for each interval [11...This configuration, known as a transponder system with constant gain, uses time delayed copies of the original to rebroadcast back into the environment

Co-arrays in the Next Fortran Standard

DOE PAGES

Reid, John; Numrich, Robert W.

2007-01-01

The WG5 committee, at its meeting in Delft, May 2005, decided to include co-arrays in the next Fortran Standard. A Fortran program containing co-arrays is interpreted as if it were replicated a fixed number of times and all copies were executed asynchronously. Each copy has its own set of data objects and is called an image. The array syntax of Fortran is extended with additional trailing subscripts in square brackets to give a clear and straightforward representation of access to data on other images. References without square brackets are to local data, so code that can run independently is uncluttered.more » Any occurrence of square brackets is a warning about communication between images. The additional syntax requires support in the compiler, but it has been designed to be easy to implement and to give the compiler scope both to apply its optimizations within each image and to optimize the communication between images. The extension includes execution control statements for synchronizing images and intrinsic procedures to return the number of images, to return the index of the current image, and to perform collective operations. The paper does not attempt to describe the full details of the feature as it now appears in the draft of the new standard. Instead, we describe a subset and demonstrate the use of this subset with examples.« less

Non-fluent speech following stroke is caused by impaired efference copy.

PubMed

Feenaughty, Lynda; Basilakos, Alexandra; Bonilha, Leonardo; den Ouden, Dirk-Bart; Rorden, Chris; Stark, Brielle; Fridriksson, Julius

2017-09-01

Efference copy is a cognitive mechanism argued to be critical for initiating and monitoring speech: however, the extent to which breakdown of efference copy mechanisms impact speech production is unclear. This study examined the best mechanistic predictors of non-fluent speech among 88 stroke survivors. Objective speech fluency measures were subjected to a principal component analysis (PCA). The primary PCA factor was then entered into a multiple stepwise linear regression analysis as the dependent variable, with a set of independent mechanistic variables. Participants' ability to mimic audio-visual speech ("speech entrainment response") was the best independent predictor of non-fluent speech. We suggest that this "speech entrainment" factor reflects integrity of internal monitoring (i.e., efference copy) of speech production, which affects speech initiation and maintenance. Results support models of normal speech production and suggest that therapy focused on speech initiation and maintenance may improve speech fluency for individuals with chronic non-fluent aphasia post stroke.

Obstacle penetrating dynamic radar imaging system

DOEpatents

Romero, Carlos E [Livermore, CA; Zumstein, James E [Livermore, CA; Chang, John T [Danville, CA; Leach, Jr Richard R. [Castro Valley, CA

2006-12-12

An obstacle penetrating dynamic radar imaging system for the detection, tracking, and imaging of an individual, animal, or object comprising a multiplicity of low power ultra wideband radar units that produce a set of return radar signals from the individual, animal, or object, and a processing system for said set of return radar signals for detection, tracking, and imaging of the individual, animal, or object. The system provides a radar video system for detecting and tracking an individual, animal, or object by producing a set of return radar signals from the individual, animal, or object with a multiplicity of low power ultra wideband radar units, and processing said set of return radar signals for detecting and tracking of the individual, animal, or object.

Electronic Submissions of Pesticide Applications

EPA Pesticide Factsheets

Applications for pesticide registration can be submitted electronically, including forms, studies, and draft product labeling. Applicants need not submit multiple electronic copies of any pieces of their applications.

Specification/Verification of Temporal Properties for Distributed Systems: Issues and Approaches. Volume 1

DTIC Science & Technology

1990-02-01

copies Pl ,...,P. of a multiple module fp resolve nondeterminism (local or global) in an identical manner. 5. The copies PI,...,P, axe physically...recovery block. A recovery block consists of a conventional block (like in ALGOL or PL /I) which is provided with a means of error detection, called an...improved failures model for communicating processes. In Proceeding. NSF- SERC Seminar on Concurrency, volume 197 of Lecture Notes in Computer Science

DUF1220 protein domains drive proliferation in human neural stem cells and are associated with increased cortical volume in anthropoid primates.

PubMed

Keeney, J G; Davis, J M; Siegenthaler, J; Post, M D; Nielsen, B S; Hopkins, W D; Sikela, J M

2015-09-01

Genome sequences encoding DUF1220 protein domains show a burst in copy number among anthropoid species and especially humans, where they have undergone the greatest human lineage-specific copy number expansion of any protein coding sequence in the genome. While DUF1220 copy number shows a dosage-related association with brain size in both normal populations and in 1q21.1-associated microcephaly and macrocephaly, a function for these domains has not yet been described. Here we provide multiple lines of evidence supporting the view that DUF1220 domains function as drivers of neural stem cell proliferation among anthropoid species including humans. First, we show that brain MRI data from 131 individuals across 7 anthropoid species shows a strong correlation between DUF1220 copy number and multiple brain size-related measures. Using in situ hybridization analyses of human fetal brain, we also show that DUF1220 domains are expressed in the ventricular zone and primarily during human cortical neurogenesis, and are therefore expressed at the right time and place to be affecting cortical brain development. Finally, we demonstrate that in vitro expression of DUF1220 sequences in neural stem cells strongly promotes proliferation. Taken together, these data provide the strongest evidence so far reported implicating DUF1220 dosage in anthropoid and human brain expansion through mechanisms involving increasing neural stem cell proliferation.

Multiple-copy state discrimination: Thinking globally, acting locally

NASA Astrophysics Data System (ADS)

Higgins, B. L.; Doherty, A. C.; Bartlett, S. D.; Pryde, G. J.; Wiseman, H. M.

2011-05-01

We theoretically investigate schemes to discriminate between two nonorthogonal quantum states given multiple copies. We consider a number of state discrimination schemes as applied to nonorthogonal, mixed states of a qubit. In particular, we examine the difference that local and global optimization of local measurements makes to the probability of obtaining an erroneous result, in the regime of finite numbers of copies N, and in the asymptotic limit as N→∞. Five schemes are considered: optimal collective measurements over all copies, locally optimal local measurements in a fixed single-qubit measurement basis, globally optimal fixed local measurements, locally optimal adaptive local measurements, and globally optimal adaptive local measurements. Here an adaptive measurement is one in which the measurement basis can depend on prior measurement results. For each of these measurement schemes we determine the probability of error (for finite N) and the scaling of this error in the asymptotic limit. In the asymptotic limit, it is known analytically (and we verify numerically) that adaptive schemes have no advantage over the optimal fixed local scheme. Here we show moreover that, in this limit, the most naive scheme (locally optimal fixed local measurements) is as good as any noncollective scheme except for states with less than 2% mixture. For finite N, however, the most sophisticated local scheme (globally optimal adaptive local measurements) is better than any other noncollective scheme for any degree of mixture.

Multiple-copy state discrimination: Thinking globally, acting locally

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

Higgins, B. L.; Pryde, G. J.; Wiseman, H. M.

2011-05-15

We theoretically investigate schemes to discriminate between two nonorthogonal quantum states given multiple copies. We consider a number of state discrimination schemes as applied to nonorthogonal, mixed states of a qubit. In particular, we examine the difference that local and global optimization of local measurements makes to the probability of obtaining an erroneous result, in the regime of finite numbers of copies N, and in the asymptotic limit as N{yields}{infinity}. Five schemes are considered: optimal collective measurements over all copies, locally optimal local measurements in a fixed single-qubit measurement basis, globally optimal fixed local measurements, locally optimal adaptive local measurements,more » and globally optimal adaptive local measurements. Here an adaptive measurement is one in which the measurement basis can depend on prior measurement results. For each of these measurement schemes we determine the probability of error (for finite N) and the scaling of this error in the asymptotic limit. In the asymptotic limit, it is known analytically (and we verify numerically) that adaptive schemes have no advantage over the optimal fixed local scheme. Here we show moreover that, in this limit, the most naive scheme (locally optimal fixed local measurements) is as good as any noncollective scheme except for states with less than 2% mixture. For finite N, however, the most sophisticated local scheme (globally optimal adaptive local measurements) is better than any other noncollective scheme for any degree of mixture.« less

Requirements for rapid plasmid ColE1 copy number adjustments: a mathematical model of inhibition modes and RNA turnover rates.

PubMed

Paulsson, J; Nordström, K; Ehrenberg, M

1998-01-01

The random distribution of ColE1 plasmids between the daughter cells at cell division introduces large copy number variations. Statistic variation associated with limited copy number in single cells also causes fluctuations to emerge spontaneously during the cell cycle. Efficient replication control out of steady state is therefore important to tame such stochastic effects of small numbers. In the present model, the dynamic features of copy number control are divided into two parts: first, how sharply the replication frequency per plasmid responds to changes in the concentration of the plasmid-coded inhibitor, RNA I, and second, how tightly RNA I and plasmid concentrations are coupled. Single (hyperbolic)- and multiple (exponential)-step inhibition mechanisms are compared out of steady state and it is shown how the response in replication frequency depends on the mode of inhibition. For both mechanisms, sensitivity of inhibition is "bought" at the expense of a rapid turnover of a replication preprimer, RNA II. Conventional, single-step, inhibition kinetics gives a sloppy replication control even at high RNA II turnover rates, whereas multiple-step inhibition has the potential of working with unlimited precision. When plasmid concentration changes rapidly, RNA I must be degraded rapidly to be "up to date" with the change. Adjustment to steady state is drastically impaired when the turnover rate constants of RNA I decrease below certain thresholds, but is basically unaffected for a corresponding increase. Several features of copy number control that are shown to be crucial for the understanding of ColE1-type plasmids still remain to be experimentally characterized. It is shown how steady-state properties reflect dynamics at the heart of regulation and therefore can be used to discriminate between fundamentally different copy number control mechanisms. The experimental tests of the predictions made require carefully planned assays, and some suggestions for suitable experiments arise naturally from the present work. It is also discussed how the presence of the Rom protein may affect dynamic qualities of copy number control. Copyright 1998 Academic Press.

Application of next generation sequencing toward sensitive detection of enteric viruses isolated from celery samples as an example of produce.

PubMed

Yang, Zhihui; Mammel, Mark; Papafragkou, Efstathia; Hida, Kaoru; Elkins, Christopher A; Kulka, Michael

2017-11-16

Next generation sequencing (NGS) holds promise as a single application for both detection and sequence identification of foodborne viruses; however, technical challenges remain due to anticipated low quantities of virus in contaminated food. In this study, with a focus on data analysis using several bioinformatics tools, we applied NGS toward amplification-independent detection and identification of norovirus at low copy (<10 3 copies) or within multiple strains from produce. Celery samples were inoculated with human norovirus (stool suspension) either as a single norovirus strain, a mixture of strains (GII.4 and GII.6), or a mixture of different species (hepatitis A virus and norovirus). Viral RNA isolation and recovery was confirmed by RT-qPCR, and optimized for library generation and sequencing without amplification using the Illumina MiSeq platform. Extracts containing either a single virus or a two-virus mixture were analyzed using two different analytic approaches to achieve virus detection and identification. First an overall assessment of viral genome coverage for samples varying in copy numbers (1.1×10 3 to 1.7×10 7 ) and genomic content (single or multiple strains in various ratios) was completed by reference-guided mapping. Not unexpectedly, this targeted approach to identification was successful in correctly mapping reads, thus identifying each virus contained in the inoculums even at low copy (estimated at 12 copies). For the second (metagenomic) approach, samples were treated as "unknowns" for data analyses using (i) a sequence-based alignment with a local database, (ii) an "in-house" k-mer tool, (iii) a commercially available metagenomics bioinformatic analysis platform cosmosID, and (iv) an open-source program Kraken. Of the four metagenomics tools applied in this study, only the local database alignment and in-house k-mer tool were successful in detecting norovirus (as well as HAV) at low copy (down to <10 3 copies) and within a mixture of virus strains or species. The results of this investigation provide support for continued investigation into the development and integration of these analytical tools for identification and detection of foodborne viruses. Published by Elsevier B.V.

Potential Benefits of Rib Fracture Fixation in Patients with Flail Chest and Multiple Non-flail Rib Fractures.

PubMed

Qiu, Meiguang; Shi, Zhanjun; Xiao, Jun; Zhang, Xuming; Ling, Shishui; Ling, Hao

2016-12-01

The purpose of this study is to evaluate the potential benefits of rib fracture fixation in patients with flail chest and multiple non-flail rib fractures versus conventional treatment modalities. A retrospective reviewed study compared 86 cases which received surgical treatment between June 2009 and May 2013 to 76 cases which received conservative treatment between January 2006 and May 2009. The patients were divided into the flail chest ( n  = 38) and multiple non-flail rib fracture groups ( n  = 124). In the flail chest group, the mechanical ventilation time, ICU monitoring time, tracheostomies, thoracic deformity, and impaired pulmonary function and return to full-time employment were compared. In the multiple non-flail rib fracture group, fracture healing, visual analog scale (VAS) pain score, inpatient length of stay, atelectatic, pulmonary complications, and normal activity-returning time were compared. Patients in the flail chest operative fixation group had significantly shorter ICU stay, decreased ventilator requirements, fewer tracheostomies, less thoracic deformity and impaired pulmonary function, and more returned to full-time employment. Patients in the multiple non-flail rib fracture operative fixation had shorter hospital stay, less pain, earlier return to normal activity, more fracture healing, less atelectasis, and fewer pulmonary infections. This study demonstrates the potential benefits of surgical stabilization of flail chest and multiple non-flail rib fractures with plate fixation. When compared with conventional conservative management, operatively managed patients demonstrated improved clinical outcomes.

Assessing the potential impact of non-proprietary drug copies on quality of medicine and treatment in patients with relapsing multiple sclerosis: the experience with fingolimod.

PubMed

Correale, Jorge; Chiquete, Erwin; Milojevic, Snezana; Frider, Nadina; Bajusz, Imre

2014-01-01

Fingolimod is a once-daily oral treatment for relapsing multiple sclerosis, the proprietary production processes of which are tightly controlled, owing to its susceptibility to contamination by impurities, including genotoxic impurities. Many markets produce nonproprietary medicines; assessing their efficacy and safety is difficult as regulators may approve nonproprietary drugs without bioequivalence data, genotoxic evaluation, or risk management plans (RMPs). This assessment is especially important for fingolimod given its solubility/bioavailability profile, genotoxicity risk, and low-dose final product (0.5 mg). This paper presents an evaluation of the quality of proprietary and nonproprietary fingolimod variants. Proprietary fingolimod was used as a reference substance against which eleven nonproprietary fingolimod copies were assessed. The microparticle size distribution of each compound was assessed by laser light diffraction, and inorganic impurity content by sulfated ash testing. Heavy metals content was quantified using inductively coupled plasma optical emission spectrometry, and levels of unspecified impurities by high-performance liquid chromatography. Solubility was assessed in a range of solvents at different pH values. Key information from the fingolimod RMP is also presented. Nonproprietary fingolimod variants exhibited properties out of proprietary or internationally accepted specifications, including differences in particle size distribution and levels of impurities such as heavy metals. For microparticle size and heavy metals, all tested fingolimod copies were out-of-specification by several-fold magnitudes. Proprietary fingolimod has a well-defined RMP, highlighting known and potential mid- to long-term safety risks, and risk-minimization and pharmacovigilance procedures. Nonproprietary fingolimod copies produced by processes less well controlled than or altered from proprietary production processes may reduce product reproducibility and quality, potentially presenting risks to patients. Safety data and risk-minimization strategies for proprietary fingolimod may not apply to the nonproprietary fingolimod copies evaluated here. Market authorization of nonproprietary fingolimod copies should require an appropriate RMP to minimize risks to patients.

THE USE OF MULTIPLE DISPLACEMENT AMPLIFICATION TO INCREASE THE DETECTION AND GENOTYPING OF TRYPANOSOMA SPECIES SAMPLES IMMOBILISED ON FTA FILTERS

PubMed Central

MORRISON, LIAM J.; McCORMACK, GILLIAN; SWEENEY, LINDSAY; LIKEUFACK, ANNE C. L.; TRUC, PHILIPPE; TURNER, C. MICHAEL; TAIT, ANDY; MacLEOD, ANNETTE

2007-01-01

Whole genome amplification methods are a recently developed tool for amplifying DNA from limited template. We report its application in trypanosome infections, characterised by low parasitaemias. Multiple Displacement Amplification (MDA) amplifies DNA with a simple in vitro step, and was evaluated on mouse blood samples on FTA filter cards with known numbers of Trypanosoma brucei parasites. The data showed a twenty-fold increase in the number of PCRs possible per sample, using primers diagnostic for the multi-copy ribosomal ITS region or 177 bp repeats, and a twenty-fold increase in sensitivity over nested PCR against a single copy microsatellite. Using MDA for microsatellite genotyping caused allele dropout at low DNA concentrations, which was overcome by pooling multiple MDA reactions. The validity of using MDA was established with samples from Human African Trypanosomiasis patients. The use of MDA allows maximal use of finite DNA samples and may prove a valuable tool in studies where multiple reactions are necessary, such as population genetic analyses. PMID:17556624

Ectopic Integration of Transforming DNA Is Rare among Neurospora Transformants Selected for Gene Replacement

PubMed Central

Miao, VPW.; Rountree, M. R.; Selker, E. U.

1995-01-01

In a variety of organisms, DNA-mediated transformation experiments commonly produce transformants with multiple copies of the transforming DNA, including both selected and unselected molecules. Such ``cotransformants'' are much more common than expected from the individual transformation frequencies, suggesting that subpopulations of cells, or nuclei, are particularly competent for transformation. We found that Neurospora crassa transformants selected for gene replacement at the am gene had not efficiently incorporated additional DNA, suggesting that nuclei that undergo transformation by homologous recombination are not highly competent at integration of DNA by illegitimate recombination. Spheroplasts were treated with DNA fragments homologous to am and with an Escherichia coli hph plasmid. Transformants were initially selected for hph (hygromycin(R)), allowed to conidiate to generate homokaryons and then selected for either Am(-) (gene replacements) or hph. Surprisingly, most am replacement strains were hygromycin(S) (124/140) and carried no extraneous DNA (116/140). Most transformants selected for hph also had ectopic copies of am DNA and/or multiple copies of hph sequences (32/35), generally at multiple sites, confirming that efficient cotransformation could occur. To test the implication that cotransformation involving gene replacement and ectopic integration is rare, we compared the yields of am replacement strains with or without prior selection for hph. The initial selection did not appreciably help (or hinder) recovery of strains with replacements. PMID:7789758

Identification of multiple serine to asparagine sequence variation sites in an intended copy product of LUCENTIS® by mass spectrometry.

PubMed

Griaud, François; Winter, Andrej; Denefeld, Blandine; Lang, Manuel; Hensinger, Héloïse; Straube, Frank; Sackewitz, Mirko; Berg, Matthias

Patent expiration of first-generation biologics and the high cost of innovative biologics are 2 drivers for the development of biosimilar products. There are, however, technical challenges to the production of exact copies of such large molecules. In this study, we performed a head-to-head comparison between the originator anti-VEGF-A Fab product LUCENTIS® (ranibizumab) and an intended copy product using an integrated analytical approach. While no differences could be observed using size-exclusion chromatography, capillary electrophoresis-sodium dodecyl sulfate and potency assays, different acidic peaks were identified with cation ion exchange chromatography and capillary zone electrophoresis. Further investigation of the intact Fab, subunits and primary sequence with mass spectrometry demonstrated the presence of a modified light chain variant in the intended copy product batches. This variant was characterized with a mass increase of 27.01 Da compared to the originator sequence and its abundance was estimated in the range of 6-9% of the intended copy product light chain. MS/MS spectra interrogation confirmed that this modification relates to a serine to asparagine sequence variant found in the intended copy product light chain. We demonstrated that the integration of high-resolution and sensitive orthogonal technologies was beneficial to assess the similarity of an originator and an intended copy product.

Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data.

PubMed

Zhao, Liang; Jiang, Xi-Wang; Zuo, Yun-Juan; Liu, Xiao-Lin; Chin, Siew-Wai; Haberle, Rosemarie; Potter, Daniel; Chang, Zhao-Yang; Wen, Jun

2016-01-01

Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification.

Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data

PubMed Central

Zuo, Yun-juan; Liu, Xiao-Lin; Chin, Siew-Wai; Haberle, Rosemarie; Potter, Daniel; Chang, Zhao-Yang; Wen, Jun

2016-01-01

Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification. PMID:27294529

Plasmodium vivax multidrug resistance-1 gene polymorphism in French Guiana.

PubMed

Faway, Emilie; Musset, Lise; Pelleau, Stéphane; Volney, Béatrice; Casteras, Jessica; Caro, Valérie; Menard, Didier; Briolant, Sébastien; Legrand, Eric

2016-11-08

Plasmodium vivax malaria is a major public health problem in French Guiana. Some cases of resistance to chloroquine, the first-line treatment used against P. vivax malaria, have been described in the Brazilian Amazon region. The aim of this study is to investigate a possible dispersion of chloroquine-resistant P. vivax isolates in French Guiana. The genotype, polymorphism and copy number variation, of the P. vivax multidrug resistance gene-1 (pvmdr1) have been previously associated with modification of the susceptibility to chloroquine. The pvmdr1 gene polymorphism was evaluated by sequencing and copy number variation was assessed by real-time PCR, in P. vivax isolates obtained from 591 symptomatic patients from 1997 to 2013. The results reveal that 1.0% [95% CI 0.4-2.2] of French Guiana isolates carry the mutations Y976F and F1076L, and that the proportion of isolates with multiple copies of pvmdr1 has significantly decreased over time, from 71.3% (OR = 6.2 [95% CI 62.9-78.7], p < 0.0001) in 1997-2004 to 12.8% (OR = 0.03 [95% CI 9.4-16.9], p < 0.0001) in 2009-2013. A statistically significant relationship was found between Guf-A (harboring the single mutation T958M) and Sal-1 (wild type) alleles and pvmdr1 copy number. Few P. vivax isolates harboring chloroquine-resistant mutations in the pvmdr1 gene are circulating in French Guiana. However, the decrease in the prevalence of isolates carrying multiple copies of pvmdr1 might indicate that the P. vivax population in French Guiana is evolving towards a decreased susceptibility to chloroquine.

Target Glow Analysis Program for Air Force Maui Optical Station

DTIC Science & Technology

1993-06-15

organization, please norif.PrSI, Hanscom AFB, MA 01731-3010. This will assist us in maintaining a current mailing list. Do not return copies of this report...34 Ottice o! mAafaernert a" ,uCe:. Paperwork Reduction Project (0704-018). Washington. DC 2003. 1. AGENCY USE ONLY L~eave blank) 2. REPORT DATE 3. REPORT TYPE...Interactions Technology research to observe and analyze the glow surrounding space- craft using the AMOS ground-based telescope facility. This unique

Ballistic Analysis of Firing Table Data for 155MM, M825 Smoke Projectile

DTIC Science & Technology

1990-09-01

PROVING GROUND , MARYLAND I I 4 .i. NOTICES Destroy this report when it is no longer needed. DO NOT return it to the originator. Additional copies of this...ADDRESS(ES) 10. SPONSORING MONITORING U.S. Army Ballistic Research Laboratory AGENCY REPORT NUMBER ATTN: SLCBR-DD-T BRL-R-3865 Aberdeen Proving Ground ...thru September 1988 at Dugway Proving Ground . Such an analysis will consider whether the M825 MOD PIP Base projectile is ballistically matched or

Computer Implementation of a Muzzle Blast Prediction Technique

DTIC Science & Technology

1985-05-01

AVERDEEN PROVING GROUND , MARYLAND • 1y 4 4q* Destroy this report when it is no longer needed. Do not return it to the originator. Additional copies of this...Laboratory AREA & WORK UNIT NUMBERS ATTN: APXBR-LFD Aberdeevi Proving Ground , MD 21005-5066 RDT&E 1LI61102AH43 Ii. CONTROLLING OFFICE NAME AND ADDRESS 12...REPORT DATE !I.S. Army Ballistic Research Laboratory May 1985 ATTN: AMXBR-OD-ST 13. NUMBER OF PAGES Aberdeen Proving Ground , MD. 21005-5066 . 89 14

Synoptic Aspects of the Climate of Japan: A Preliminary Report

DTIC Science & Technology

1945-08-01

COPY TO* €AJD0» L1 tQISffiiBUTIoN LWTEB TO; COPJ?S OSTA1NA3LE FRO«; SPECIAL JHSTßUCTIONS: ’ UK CADO CONTROL HO: US CLASSIFICATION: ATI NO...confidential Approved for public release; distribution is unlimited. Distribution authorized to DoD only; Administrative/Operational Use ; AUG 1945. Other...FILED UNDER: ORIGINAL LOAN RETURNED TO OWNER (DATE): CAPO CONTROL NO: ATI NO: ABSTRACT 7092k INSPECTED BY: CAÖO-D1 CADO-Pi CAD0-P2, US CAD0

Column Network Study for a Planar Array Used with an Unattended Radar

DTIC Science & Technology

1980-06-01

This will assist us In maintaining a current mailing list. Do not return this copy. Retain or destroy. UNCLASSIFIED SECURITY CLASSIFICATION OF THIS...0.nt from Controlling Office) IS. SECURITY CLASS. (o1 this report) SaetVŕ ’UDNCLASSIFIED IS.. DECL ASSI FIC ATI ON,’OWN GRADING t, / -/ ./N N...installation costs are being studied. "(Coni’d) DD I1JANp73 1473k EDITION OF I NOV 65 IS OBSOLETE UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE (When

Basic EMC Technology Advancement for C(3) Systems - SHIELD. Volume IV B. A Digital Computer Program for Computing Crosstalk between Shielded Cables

DTIC Science & Technology

1982-11-01

your organization , please notify RADC OBCT) Griffiss AFB NY 13441. This will assist us in maintaining a current mailing list. Do not return copies of...RMING ORGANIZATION NAME r AND ADDRESS 10. PROGRAM ELEMENT. PROJECT. TASK Southeastern Center for Electrical AREA6WORKUNITNUMBERS Engineering Education...The program requires that the input data groups be organized as shown in Table 1 where the number of unshielded wires is U and the number of shielded

Self-sequencing of amino acids and origins of polyfunctional protocells

NASA Technical Reports Server (NTRS)

Fox, S. W.

1984-01-01

The role of proteins in the origin of living things is discussed. It has been experimentally established that amino acids can sequence themselves under simulated geological conditions with highly nonrandom products which accordingly contain diverse information. Multiple copies of each type of macromolecule are formed, resulting in greater power for any protoenzymic molecule than would accrue from a single copy of each type. Thermal proteins are readily incorporated into laboratory protocells. The experimental evidence for original polyfunctional protocells is discussed.

[Impact of the labour market on vocational retraining centre participants' return to work: a study on employment agencies level].

PubMed

Hetzel, C; Flach, T; Schmidt, C

2012-08-01

This paper is aimed at identifying labour market factors impacting vocational retraining centre participants' return to work on Employment Agencies level and at comparing results to unemployed people's return to work (Social Code Book III). Databases are regional return to work rates of 2006 graduates, selected labour market indicators 2007, and the 2007 labour market classification of the Institute for Employment Research (IAB). The n = 75 Employment Agency districts where 74.5 % of the participants followed-up lived were analyzed using analyses of variance and multiple loglinear regression. Compared to the unemployment context (Social Code Book III), the impact of the labour market is much lower and less complex. In the multiple model, the regional unemployment rate and the regional tertiarization rate (size of the service sector) are found to be significant and superior to the IAB-classification. Hence, participants' return to work is less dependent on labour market conditions than unemployed people's return to work (Social Code Book III). © Georg Thieme Verlag KG Stuttgart · New York.

The Display of Multiple Choice Question Bank on Microfilm

ERIC Educational Resources Information Center

Stevens, J. M.; Harris, F. T. C.

1977-01-01

An automated question bank maintained by the Department of Research and Services in Education at the Middlesex Hospital Medical School provides a printed copy of each of 25,000 multiple choice questions (95 percent relating to the whole spectrum of the medical curriculum). Problems with this procedure led to experimental work storing the data on…

Static Multiple-Pole Homopolar Generator With a Superconducting Screen,

DTIC Science & Technology

1983-11-03

STANAR193-A OlCFILE GORY 00 FOREIGN TECHNOLOGY DIVISION STATIC MULTIPLE-POLE HOMOPOLAR GENERATOR WITH A SUPERC9ONDUCTING SCREEN by V.P. Kartsev, avld...November 1983 MICROFICHE MJR: FTD-83-C-001336 STATIC %fULTIPLE-POLE HOMOPOLAR GENERATOR WITH A SUPRCONDUCTING SCREEN By: V.P. Kartsev, and I.M. Yegorov...this translation were extracted from the best quality copy available. STATIC MULTIPLE-POLE HOMOPOLAR GENERATOR WITH A SUPERCONDUCTING SCREEN V.P

Evaluation of a real-time PCR assay for malaria diagnosis in patients from Vietnam and in returned travellers.

PubMed

Vo, Thi Kim Duy; Bigot, Patricia; Gazin, Pierre; Sinou, Veronique; De Pina, Jean Jacques; Huynh, Dinh Chien; Fumoux, Francis; Parzy, Daniel

2007-05-01

Real-time PCR diagnosis of malaria has advantages over traditional microscopic methods, especially when parasitaemia is low and when dealing with mixed infections. We have developed a new real-time PCR with specific genes in each Plasmodium species present only in one copy to identify the four pathogenic Plasmodium spp. for humans. The sensitivity was less than 25 parasites/microl. No cross-hybridisation was observed with human DNA or among the four Plasmodium spp. Using LightCycler PCR and conventional microscopy, we compared the diagnosis of malaria in patients from Vietnam and in returned European travellers with suspicion of malaria. In patients from Vietnam with suspicion of malaria, one mixed infection was observed by PCR only; the remaining data (54 of 55 patients) correlated with microscopy. In 79 patients without symptoms, low parasitaemia was detected in 7 samples by microscopy and in 16 samples by PCR. In returned travellers, PCR results were correlated with microscopy for all four species in 48 of 56 samples. The eight discrepant results were resolved in favour of real-time PCR diagnosis. This new real-time PCR is a rapid, accurate and efficient method for malaria diagnosis in returned travellers as well as for epidemiological studies or antimalarial efficiency trials in the field.

Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate.

PubMed

Ebhardt, H Alexander; Sabidó, Eduard; Hüttenhain, Ruth; Collins, Ben; Aebersold, Ruedi

2012-04-01

Selected or multiple reaction monitoring is a targeted mass spectrometry method (S/MRM-MS), in which many peptides are simultaneously and consistently analyzed during a single liquid chromatography-mass spectrometry (LC-S/MRM-MS) measurement. These capabilities make S/MRM-MS an attractive method to monitor a consistent set of proteins over various experimental conditions. To increase throughput for S/MRM-MS it is advantageous to use scheduled methods and unfractionated protein extracts. Here, we established the practically measurable dynamic range of proteins reliably detectable and quantifiable in an unfractionated protein extract from a human cell line using LC-S/MRM-MS. Initially, we analyzed S/MRM transition peak groups in terms of interfering signals and compared S/MRM transition peak groups to MS1-triggered MS2 spectra using dot-product analysis. Finally, using unfractionated protein extract from human cell lysate, we quantified the upper boundary of copies per cell to be 35 million copies per cell, while 7500 copies per cell represents a lower boundary using a single 35 min linear gradient LC-S/MRM-MS measurement on a current, standard commercial instrument. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments.

PubMed

Li, Chunmei; Yu, Zhilong; Fu, Yusi; Pang, Yuhong; Huang, Yanyi

2017-04-26

We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multifraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infer CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of a reaction mix before amplification. By examining the sequencing result of each fraction for a specific fragment and applying a segment-merge maximum likelihood algorithm to the calculation of copy number, we digitize the sequencing-depth-based CNV identification and thus provide a method that is less sensitive to the amplification bias. In this paper, we demonstrate a mfA platform through multiple displacement amplification (MDA) chemistry. When performing the mfA platform, the noise of MDA is reduced; therefore, the resolution of single-cell CNV identification can be improved to 100 kb. We can also determine the genomic region free of allelic drop-out with mfA platform, which is impossible for conventional single-cell amplification methods.

Behavior Knowledge Space-Based Fusion for Copy-Move Forgery Detection.

PubMed

Ferreira, Anselmo; Felipussi, Siovani C; Alfaro, Carlos; Fonseca, Pablo; Vargas-Munoz, John E; Dos Santos, Jefersson A; Rocha, Anderson

2016-07-20

The detection of copy-move image tampering is of paramount importance nowadays, mainly due to its potential use for misleading the opinion forming process of the general public. In this paper, we go beyond traditional forgery detectors and aim at combining different properties of copy-move detection approaches by modeling the problem on a multiscale behavior knowledge space, which encodes the output combinations of different techniques as a priori probabilities considering multiple scales of the training data. Afterwards, the conditional probabilities missing entries are properly estimated through generative models applied on the existing training data. Finally, we propose different techniques that exploit the multi-directionality of the data to generate the final outcome detection map in a machine learning decision-making fashion. Experimental results on complex datasets, comparing the proposed techniques with a gamut of copy-move detection approaches and other fusion methodologies in the literature show the effectiveness of the proposed method and its suitability for real-world applications.

Dynamics in copy numbers of five plasmids of a dairy Lactococcus lactis in dairy-related conditions including near-zero growth rates.

PubMed

van Mastrigt, Oscar; Lommers, Marcel M A N; de Vries, Yorick C; Abee, Tjakko; Smid, Eddy J

2018-03-23

Lactic acid bacteria can carry multiple plasmids affecting their performance in dairy fermentations. The expression of plasmid-encoded genes and the activity of the corresponding proteins is severely affected by changes in the number of plasmid copies. We studied the impact of growth rate on dynamics of plasmid copy numbers at high growth rates in chemostat cultures and down to near-zero growth rates in retentostat cultures. Five plasmids of the dairy strain Lactococcus lactis FM03-V1 were selected which varied in size (3 to 39 kb), in replication mechanism (theta or rolling-circle) and in putative (dairy-associated) functions. Copy numbers ranged from 1.5 to 40.5 and the copy number of theta-type replicating plasmids were negatively correlated to the plasmid size. Despite the extremely wide range of growth rates (0.0003 h -1 to 0.6 h -1 ), copy numbers of the five plasmids were stable and only slightly increased at near-zero growth rates showing that the plasmid replication rate was strictly controlled. One low-copy number plasmid, carrying a large exopolysaccharide gene cluster, was segregationally unstable during retentostat cultivations reflected in complete loss of the plasmid in one of the retentostat cultures. The copy number of the five plasmids was also hardly affected by varying the pH value, nutrient limitation or presence of citrate (maximum 2.2-fold) signifying the stability in copy number of the plasmids. Importance Lactococcus lactis is extensively used in starter cultures for dairy fermentations. Important traits for growth and survival of L. lactis in dairy fermentations are encoded by genes located on plasmids, such as genes involved in lactose and citrate metabolism, protein degradation and oligopeptide uptake and bacteriophage resistance. Because the number of plasmid copies could affect the expression of plasmid-encoded genes, it is important to know the factors that influence the plasmid copy numbers. We monitored plasmid copy numbers of L. lactis at near-zero growth rates, characteristic for cheese ripening. Moreover, we analysed the effect of pH, nutrient limitation and presence of citrate. This showed that plasmid copy numbers were stable giving insight into plasmid copy number dynamics in dairy fermentations. Copyright © 2018 American Society for Microbiology.

Three copies of a single protein II-encoding sequence in the genome of Neisseria gonorrhoeae JS3: evidence for gene conversion and gene duplication.

PubMed

van der Ley, P

1988-11-01

Gonococci express a family of related outer membrane proteins designated protein II (P.II). These surface proteins are subject to both phase variation and antigenic variation. The P.II gene repertoire of Neisseria gonorrhoeae strain JS3 was found to consist of at least ten genes, eight of which were cloned. Sequence analysis and DNA hybridization studies revealed that one particular P.II-encoding sequence is present in three distinct, but almost identical, copies in the JS3 genome. These genes encode the P.II protein that was previously identified as P.IIc. Comparison of their sequences shows that the multiple copies of this P.IIc-encoding gene might have been generated by both gene conversion and gene duplication.

Novel applications of array comparative genomic hybridization in molecular diagnostics.

PubMed

Cheung, Sau W; Bi, Weimin

2018-05-31

In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

Effects of a petunia scaffold/matrix attachment region on copy number dependency and stability of transgene expression in Nicotiana tabacum.

PubMed

Dietz-Pfeilstetter, Antje; Arndt, Nicola; Manske, Ulrike

2016-04-01

Transgenes in genetically modified plants are often not reliably expressed during development or in subsequent generations. Transcriptional gene silencing (TGS) as well as post-transcriptional gene silencing (PTGS) have been shown to occur in transgenic plants depending on integration pattern, copy number and integration site. In an effort to reduce position effects, to prevent read-through transcription and to provide a more accessible chromatin structure, a P35S-ß-glucuronidase (P35S-gus) transgene flanked by a scaffold/matrix attachment region from petunia (Petun-SAR), was introduced in Nicotiana tabacum plants by Agrobacterium tumefaciens mediated transformation. It was found that Petun-SAR mediates enhanced expression and copy number dependency up to 2 gene copies, but did not prevent gene silencing in transformants with multiple and rearranged gene copies. However, in contrast to the non-SAR transformants where silencing was irreversible and proceeded during long-term vegetative propagation and in progeny plants, gus expression in Petun-SAR plants was re-established in the course of development. Gene silencing was not necessarily accompanied by DNA methylation, while the gus transgene could still be expressed despite considerable CG methylation within the coding region.

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile.

PubMed

Huang, Yen-Tsung; Hsu, Thomas; Christiani, David C

2014-01-01

The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X (2) distributions that can be obtained using permutation with scaled X (2) approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (<2.8 × 10(-5)), including the PTEN pathway (7.8 × 10(-7)), the gene set up-regulated under heat shock (3.6 × 10(-6)), the gene sets involved in the immune profile for rejection of kidney transplantation (9.2 × 10(-6)) and for transcriptional control of leukocytes (2.2 × 10(-5)), and the ganglioside biosynthesis pathway (2.7 × 10(-5)). In conclusion, we present a new method for pathway analyses of copy number data, and causal mechanisms of the five pathways require further study.

Novel genomic findings in multiple myeloma identified through routine diagnostic sequencing.

PubMed

Ryland, Georgina L; Jones, Kate; Chin, Melody; Markham, John; Aydogan, Elle; Kankanige, Yamuna; Caruso, Marisa; Guinto, Jerick; Dickinson, Michael; Prince, H Miles; Yong, Kwee; Blombery, Piers

2018-05-14

Multiple myeloma is a genomically complex haematological malignancy with many genomic alterations recognised as important in diagnosis, prognosis and therapeutic decision making. Here, we provide a summary of genomic findings identified through routine diagnostic next-generation sequencing at our centre. A cohort of 86 patients with multiple myeloma underwent diagnostic sequencing using a custom hybridisation-based panel targeting 104 genes. Sequence variants, genome-wide copy number changes and structural rearrangements were detected using an inhouse-developed bioinformatics pipeline. At least one mutation was found in 69 (80%) patients. Frequently mutated genes included TP53 (36%), KRAS (22.1%), NRAS (15.1%), FAM46C/DIS3 (8.1%) and TET2/FGFR3 (5.8%), including multiple mutations not previously described in myeloma. Importantly we observed TP53 mutations in the absence of a 17 p deletion in 8% of the cohort, highlighting the need for sequencing-based assessment in addition to cytogenetics to identify these high-risk patients. Multiple novel copy number changes and immunoglobulin heavy chain translocations are also discussed. Our results demonstrate that many clinically relevant genomic findings remain in multiple myeloma which have not yet been identified through large-scale sequencing efforts, and provide important mechanistic insights into plasma cell pathobiology. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Single-site labeling of lysine in proteins through a metal-free multicomponent approach.

PubMed

Chilamari, Maheshwerreddy; Kalra, Neetu; Shukla, Sanjeev; Rai, Vishal

2018-06-15

We report a chemoselective and site-selective approach that distinguishes one Lys from its multiple copies, N-terminus, and other competitors. The phospha-Mannich protocol works with multiple proteins and installs probes without structural and functional perturbations. It delivers an antibody-drug conjugate with selective anti-proliferative activity towards HER2 expressing SKBR3 breast cancer cells.

Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach

PubMed Central

Shi, Xingjie; Zhao, Qing; Huang, Jian; Xie, Yang; Ma, Shuangge

2015-01-01

Motivation: Both gene expression levels (GEs) and copy number alterations (CNAs) have important biological implications. GEs are partly regulated by CNAs, and much effort has been devoted to understanding their relations. The regulation analysis is challenging with one gene expression possibly regulated by multiple CNAs and one CNA potentially regulating the expressions of multiple genes. The correlations among GEs and among CNAs make the analysis even more complicated. The existing methods have limitations and cannot comprehensively describe the regulation. Results: A sparse double Laplacian shrinkage method is developed. It jointly models the effects of multiple CNAs on multiple GEs. Penalization is adopted to achieve sparsity and identify the regulation relationships. Network adjacency is computed to describe the interconnections among GEs and among CNAs. Two Laplacian shrinkage penalties are imposed to accommodate the network adjacency measures. Simulation shows that the proposed method outperforms the competing alternatives with more accurate marker identification. The Cancer Genome Atlas data are analysed to further demonstrate advantages of the proposed method. Availability and implementation: R code is available at http://works.bepress.com/shuangge/49/ Contact: shuangge.ma@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26342102

The Origin of Mutants Under Selection: How Natural Selection Mimics Mutagenesis (Adaptive Mutation)

PubMed Central

Maisnier-Patin, Sophie; Roth, John R.

2015-01-01

Selection detects mutants but does not cause mutations. Contrary to this dictum, Cairns and Foster plated a leaky lac mutant of Escherichia coli on lactose medium and saw revertant (Lac+) colonies accumulate with time above a nongrowing lawn. This result suggested that bacteria might mutagenize their own genome when growth is blocked. However, this conclusion is suspect in the light of recent evidence that revertant colonies are initiated by preexisting cells with multiple copies the conjugative F′lac plasmid, which carries the lac mutation. Some plated cells have multiple copies of the simple F′lac plasmid. This provides sufficient LacZ activity to support plasmid replication but not cell division. In nongrowing cells, repeated plasmid replication increases the likelihood of a reversion event. Reversion to lac+ triggers exponential cell growth leading to a stable Lac+ revertant colony. In 10% of these plated cells, the high-copy plasmid includes an internal tandem lac duplication, which provides even more LacZ activity—sufficient to support slow growth and formation of an unstable Lac+ colony. Cells with multiple copies of the F′lac plasmid have an increased mutation rate, because the plasmid encodes the error-prone (mutagenic) DNA polymerase, DinB. Without DinB, unstable and stable Lac+ revertant types form in equal numbers and both types arise with no mutagenesis. Amplification and selection are central to behavior of the Cairns–Foster system, whereas mutagenesis is a system-specific side effect or artifact caused by coamplification of dinB with lac. Study of this system has revealed several broadly applicable principles. In all populations, gene duplications are frequent stable genetic polymorphisms, common near-neutral mutant alleles can gain a positive phenotype when amplified under selection, and natural selection can operate without cell division when variability is generated by overreplication of local genome subregions. PMID:26134316

The Influence of Multiple Host Contacts on the Acquisition and Transmission of Dengue-2 Virus

DTIC Science & Technology

1993-01-01

5500 Stanoard Form 298 (Rev 2-89) PIs~~ bv AtI %t .34-| II Best Available Copy ABSTRACT Title of Dissertation: THE INFLUENCE OF MULTIPLE HOST CONTACTS...ABSTRACT Title of the Dissertaton: THE INFLUENCE OF MULTIPLE HOST CONTACTS ON THE ACQUISITION AND TRANSMISSION OF DENGUE-2 VIRUS BY A=DISAEX2 . John L...virus does not alter the feeding behavior of An. n•ngy~i. THE INFLUENCE OF MULTIPLE HOST CONTACTS ON THE ACQUISITION AND TRANSMISSION OF DENGUE-2 VIRUS BY

Preventing Return of Fear in an Animal Model of Anxiety: Additive Effects of Massive Extinction and Extinction in Multiple Contexts

PubMed Central

Laborda, Mario A.; Miller, Ralph R.

2013-01-01

Fear conditioning and experimental extinction have been presented as models of anxiety disorders and exposure therapy, respectively. Moreover, the return of fear serves as a model of relapse after exposure therapy. Here we present two experiments, with rats as subjects in a lick suppression preparation, in which we assessed the additive effects of two different treatments to attenuate the return of fear. First, we evaluated whether two phenomena known to generate return of fear (i.e., spontaneous recovery and renewal) summate to produce a stronger reappearance of extinguished fear. At test, rats evaluated outside the extinction context following a long delay after extinction (i.e., a delayed context shift) exhibited greater return of extinguished fear than rats evaluated outside the extinction context alone, but return of extinguished fear following a delayed context shift did not significantly differ from the return of fear elicited in rats tested following a long delay after extinction alone. Additionally, extinction in multiple contexts and a massive extinction treatment each attenuated the strong return of fear produced by a delayed context shift. Moreover, the conjoint action of these treatments was significantly more successful in preventing the reappearance of extinguished fear, suggesting that extensive cue exposure administered in several different therapeutic settings has the potential to reduce relapse after therapy for anxiety disorders, more than either manipulation alone. PMID:23611075

Decreasing pfmdr1 Copy Number Suggests that Plasmodium falciparum in Western Cambodia Is Regaining In Vitro Susceptibility to Mefloquine

PubMed Central

Lim, Pharath; Dek, Dalin; Try, Vorleak; Sreng, Sokunthea; Suon, Seila

2015-01-01

Dihydroartemisinin-piperaquine is the current frontline artemisinin combination therapy (ACT) for Plasmodium falciparum malaria in Cambodia but is now failing in several western provinces. To investigate artesunate plus mefloquine (AS+MQ) as a replacement ACT, we measured the prevalence of multiple pfmdr1 copies—a molecular marker for MQ resistance—in 844 P. falciparum clinical isolates collected in 2008 to 2013. The pfmdr1 copy number is decreasing in Western Cambodia, suggesting that P. falciparum is regaining in vitro susceptibility to MQ. PMID:25712365

Error recovery to enable error-free message transfer between nodes of a computer network

DOEpatents

Blumrich, Matthias A.; Coteus, Paul W.; Chen, Dong; Gara, Alan; Giampapa, Mark E.; Heidelberger, Philip; Hoenicke, Dirk; Takken, Todd; Steinmacher-Burow, Burkhard; Vranas, Pavlos M.

2016-01-26

An error-recovery method to enable error-free message transfer between nodes of a computer network. A first node of the network sends a packet to a second node of the network over a link between the nodes, and the first node keeps a copy of the packet on a sending end of the link until the first node receives acknowledgment from the second node that the packet was received without error. The second node tests the packet to determine if the packet is error free. If the packet is not error free, the second node sets a flag to mark the packet as corrupt. The second node returns acknowledgement to the first node specifying whether the packet was received with or without error. When the packet is received with error, the link is returned to a known state and the packet is sent again to the second node.

76 FR 30322 - Notice of Submission for OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-25

... information is necessary for the proper performance of the functions of the agency, including whether the... under which a borrower may receive loans for a single academic year or multiple academic years. Copies...

Effect of pencil grasp on the speed and legibility of handwriting after a 10-minute copy task in Grade 4 children.

PubMed

Schwellnus, Heidi; Carnahan, Heather; Kushki, Azadeh; Polatajko, Helene; Missiuna, Cheryl; Chau, Tom

2012-06-01

To investigate the impact of common pencil grasp patterns on the speed and legibility of handwriting after a 10-minute copy task, intended to induce muscle fatigue, in typically developing children and in those non-proficient in handwriting. A total of 120 Grade 4 students completed a standardised handwriting assessment before and after a 10-minute copy task. The students indicated the perceived difficulty of the handwriting task at baseline and after 10 minutes. The students also completed a self-report questionnaire regarding their handwriting proficiency upon completion. The majority of the students rated higher effort after the 10-minute copy task than at baseline (rank sum: P = 0.00001). The effort ratings were similar for the different grasp patterns (multiple linear regression: F = 0.37, P = 0.895). For both typically developing children and those with handwriting issues, the legibility of the writing samples decreased after the 10-minute copy task but the speed of writing increased. CONCLUSIONS AND SIGNIFICANCE OF THE STUDY: The quality of the handwriting decreased after the 10-minute copy task; however, there was no difference in the quality or speed scores among the different pencil grasps before and after the copy task. The dynamic tripod pencil grasp did not offer any advantage over the lateral tripod or the dynamic or lateral quadrupod pencil grasps in terms of quality of handwriting after a 10-minute copy task. These four pencil grasp patterns performed equivalently. Our findings question the practice of having students adopt the dynamic tripod pencil grasp. © 2012 The Authors Australian Occupational Therapy Journal © 2012 Occupational Therapy Australia.

High Spectral Resolution Lidar Measurements of Multiple Scattering

NASA Technical Reports Server (NTRS)

Eloranta, E. W.; Piironen, P.

1996-01-01

The University of Wisconsin High Spectral Resolution Lidar (HSRL) provides unambiguous measurements of backscatter cross section, backscatter phase function, depolarization, and optical depth. This is accomplished by dividing the lidar return into separate particulate and molecular contributions. The molecular return is then used as a calibration target. We have modified the HSRL to use an I2 molecular absorption filter to separate aerosol and molecular signals. This allows measurement in dense clouds. Useful profiles extend above the cloud base until the two way optical depth reaches values between 5 and 6; beyond this, photon counting errors become large. In order to observe multiple scattering, the HSRL includes a channel which records the combined aerosol and molecular lidar return simultaneously with the spectrometer channel measurements of optical properties. This paper describes HSRL multiple scattering measurements from both water and ice clouds. These include signal strengths and depolarizations as a function of receiver field of view. All observations include profiles of extinction and backscatter cross sections. Measurements are also compared to predictions of a multiple scattering model based on small angle approximations.

Distributed Database Control and Allocation. Volume 3. Distributed Database System Designer’s Handbook.

DTIC Science & Technology

1983-10-01

Multiversion Data 2-18 2.7.1 Multiversion Timestamping 2-20 2.T.2 Multiversion Looking 2-20 2.8 Combining the Techniques 2-22 3. Database Recovery Algorithms...See rTHEM79, GIFF79] for details. 2.7 Multiversion Data Let us return to a database system model where each logical data item is stored at one DM...In a multiversion database each Write wifxl, produces a new copy (or version) of x, denoted xi. Thus, the value of z is a set of ver- sions. For each

E and F Layer H.F. Volume Backscatter Reflectivities.

DTIC Science & Technology

1980-02-01

organization , please notify RADC (EEP), Hanscom AFB MA 01731. This will assist us in maintaining a current mailing list. Do not return this copy. Retain...6rd F19628-8C06 9. PERFORMING ORGANIZATION NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJECT. TASKARE A & WORK UNIT NUMBERS Deputy for Electronic Technology...p&U?4 and executeA weeath, devetopment, tet and ee.ted atcqu1,6tion p’wgAam6 in a6uppo’cL 06 Command, ContAot Coffexmlico.tionI and InteLigence (C31

Clinical and molecular evaluation of SHOX/PAR1 duplications in Leri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS).

PubMed

Benito-Sanz, S; Barroso, E; Heine-Suñer, D; Hisado-Oliva, A; Romanelli, V; Rosell, J; Aragones, A; Caimari, M; Argente, J; Ross, J L; Zinn, A R; Gracia, R; Lapunzina, P; Campos-Barros, A; Heath, K E

2011-02-01

Léri-Weill dyschondrosteosis (LWD) is a skeletal dysplasia characterized by disproportionate short stature and the Madelung deformity of the forearm. SHOX mutations and pseudoautosomal region 1 deletions encompassing SHOX or its enhancers have been identified in approximately 60% of LWD and approximately 15% of idiopathic short stature (ISS) individuals. Recently SHOX duplications have been described in LWD/ISS but also in individuals with other clinical manifestations, thus questioning their pathogenicity. The objective of the study was to investigate the pathogenicity of SHOX duplications in LWD and ISS. Multiplex ligation-dependent probe amplification is routinely used in our unit to analyze for SHOX/pseudoautosomal region 1 copy number changes in LWD/ISS referrals. Quantitative PCR, microsatellite marker, and fluorescence in situ hybridization analysis were undertaken to confirm all identified duplications. During the routine analysis of 122 LWD and 613 ISS referrals, a total of four complete and 10 partial SHOX duplications or multiple copy number (n > 3) as well as one duplication of the SHOX 5' flanking region were identified in nine LWD and six ISS cases. Partial SHOX duplications appeared to have a more deleterious effect on skeletal dysplasia and height gain than complete SHOX duplications. Importantly, no increase in SHOX copy number was identified in 340 individuals with normal stature or 104 overgrowth referrals. MLPA analysis of SHOX/PAR1 led to the identification of partial and complete SHOX duplications or multiple copies associated with LWD or ISS, suggesting that they may represent an additional class of mutations implicated in the molecular etiology of these clinical entities.

Amplification of a Gene Related to Mammalian mdr Genes in Drug-Resistant Plasmodium falciparum

NASA Astrophysics Data System (ADS)

Wilson, Craig M.; Serrano, Adelfa E.; Wasley, Annemarie; Bogenschutz, Michael P.; Shankar, Anuraj H.; Wirth, Dyann F.

1989-06-01

The malaria parasite Plasmodium falciparum contains at least two genes related to the mammalian multiple drug resistance genes, and at least one of the P. falciparum genes is expressed at a higher level and is present in higher copy number in a strain that is resistant to multiple drugs than in a strain that is sensitive to the drugs.

Behavioral techniques for attenuating the expression of fear associations in an animal model of anxiety.

PubMed

Laborda, Mario A; Polack, Cody W; Miguez, Gonzalo; Miller, Ralph R

2014-09-01

Recent data indicate that extinguished fear often returns when the testing conditions differ from those of treatment. Several manipulations including extensive extinction training, extinction in multiple contexts, and spacing the extinction trials and sessions reduce the return of fear. Moreover, extensive extinction and extinction in multiple contexts summate in reducing return of fear, and the spacing of the extinction trials and the spacing of extinction sessions summate in reducing return of fear. Here we evaluated whether these techniques also attenuate the context specificity of latent inhibition, and whether they summate to further decrease fear responding at test. In two experiments, with rats as subjects in a lick suppression preparation, we assessed the effects of massive CS preexposure, CS preexposure in multiple contexts, and of spacing the CS-preexposure trials and sessions, in reducing the context specificity of latent inhibition. Fear responding was attenuated by all four manipulations. Moreover, extensive CS preexposure in multiple contexts, and conjoint spacing of the CS-preexposure trials and sessions, were more effective in reducing the context specificity of latent inhibition than each manipulation alone. Our experimental designs evaluated degrees of context specificity of latent inhibition but omitted groups in which latent inhibition was assessed without a context shift away from the context of latent inhibition treatment. This precluded us from drawing conclusions concerning absolute (as opposed to relative) levels of recovery from latent inhibition. Techniques effective in decreasing the return of conditioned fear following extinction are also effective in decreasing the context specificity of latent inhibition in an animal model of anxiety. Fear and anxiety disorders might be prevented in anxious human participants with the same techniques used here, but that is still an empirical question. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements

PubMed Central

Liu, Pengfei; Erez, Ayelet; Sreenath Nagamani, Sandesh C.; Dhar, Shweta U.; Kołodziejska, Katarzyna E.; Dharmadhikari, Avinash V.; Cooper, M. Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A.; Bacino, Carlos A.; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R.; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A.; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R.; McLean, Scott D.; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L.; Patel, Ankita; Cheung, Sau Wai; Hastings, P. J.; Stankiewicz, Paweł; Lupski, James R.; Bi, Weimin

2011-01-01

SUMMARY Complex genomic rearrangements (CGR) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated we observed localization and multiple copy number changes including deletions, duplications and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism’s life cycle. PMID:21925314

Design of monodisperse and well-defined polypeptide-based polyvalent inhibitors of anthrax toxin.

PubMed

Patke, Sanket; Boggara, Mohan; Maheshwari, Ronak; Srivastava, Sunit K; Arha, Manish; Douaisi, Marc; Martin, Jacob T; Harvey, Ian B; Brier, Matthew; Rosen, Tania; Mogridge, Jeremy; Kane, Ravi S

2014-07-28

The design of polyvalent molecules, presenting multiple copies of a specific ligand, represents a promising strategy to inhibit pathogens and toxins. The ability to control independently the valency and the spacing between ligands would be valuable for elucidating structure-activity relationships and for designing potent polyvalent molecules. To that end, we designed monodisperse polypeptide-based polyvalent inhibitors of anthrax toxin in which multiple copies of an inhibitory toxin-binding peptide were separated by flexible peptide linkers. By tuning the valency and linker length, we designed polyvalent inhibitors that were over four orders of magnitude more potent than the corresponding monovalent ligands. This strategy for the rational design of monodisperse polyvalent molecules may not only be broadly applicable for the inhibition of toxins and pathogens, but also for controlling the nanoscale organization of cellular receptors to regulate signaling and the fate of stem cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Micro-Plasticity of Genomes As Illustrated by the Evolution of Glutathione Transferases in 12 Drosophila Species

PubMed Central

Saisawang, Chonticha; Ketterman, Albert J.

2014-01-01

Glutathione transferases (GST) are an ancient superfamily comprising a large number of paralogous proteins in a single organism. This multiplicity of GSTs has allowed the copies to diverge for neofunctionalization with proposed roles ranging from detoxication and oxidative stress response to involvement in signal transduction cascades. We performed a comparative genomic analysis using FlyBase annotations and Drosophila melanogaster GST sequences as templates to further annotate the GST orthologs in the 12 Drosophila sequenced genomes. We found that GST genes in the Drosophila subgenera have undergone repeated local duplications followed by transposition, inversion, and micro-rearrangements of these copies. The colinearity and orientations of the orthologous GST genes appear to be unique in many of the species which suggests that genomic rearrangement events have occurred multiple times during speciation. The high micro-plasticity of the genomes appears to have a functional contribution utilized for evolution of this gene family. PMID:25310450

Multiplicity of genome equivalents in the radiation-resistant bacterium Micrococcus radiodurans.

PubMed Central

Hansen, M T

1978-01-01

The complexity of the genome of Micrococcus radiodurans was determined to be (2.0 +/- 0.3) X 10(9) daltons by DNA renaturation kinetics. The number of genome equivalents of DNA per cell was calculated from the complexity and the content of DNA. A lower limit of four genome equivalents per cell was approached with decreasing growth rate. Thus, no haploid stage appeared to be realized in this organism. The replication time was estimated from the kinetics and amount of residual DNA synthesis after inhibiting initiation of new rounds of replication. From this, the redundancy of terminal genetic markers was calculated to vary with growth rate from four to approximately eight copies per cell. All genetic material, including the least abundant, is thus multiply represented in each cell. The potential significance of the maintenance in each cell of multiple gene copies is discussed in relation to the extreme radiation resistance of M. radiodurans. PMID:649572

Replication and meiotic transmission of yeast ribosomal RNA genes.

PubMed

Brewer, B J; Zakian, V A; Fangman, W L

1980-11-01

The yeast Saccharomyces cerevisiae has approximately 120 genes for the ribosomal RNAs (rDNA) which are organized in tandem within chromosomal DNA. These multiple-copy genes are homogeneous in sequence but can undergo changes in copy number and topology. To determine if these changes reflect unusual features of rDNA metabolism, we have examined both the replication of rDNA in the mitotic cell cycle and the inheritance of rDNA during meiosis. The results indicate that rDNA behaves identically to chromosomal DNA: each rDNA unit is replicated once during the S phase of each cell cycle and each unit is conserved through meiosis. Therefore, the flexibility in copy number and topology of rDNA does not arise from the selective replication of units in each S phase nor by the selective inheritance of units in meiosis.

Gene duplication, silencing and expression alteration govern the molecular evolution of PRC2 genes in plants.

PubMed

Furihata, Hazuka Y; Suenaga, Kazuya; Kawanabe, Takahiro; Yoshida, Takanori; Kawabe, Akira

2016-10-13

PRC2 genes were analyzed for their number of gene duplications, d N /d S ratios and expression patterns among Brassicaceae and Gramineae species. Although both amino acid sequences and copy number of the PRC2 genes were generally well conserved in both Brassicaceae and Gramineae species, we observed that some rapidly evolving genes experienced duplications and expression pattern changes. After multiple duplication events, all but one or two of the duplicated copies tend to be silenced. Silenced copies were reactivated in the endosperm and showed ectopic expression in developing seeds. The results indicated that rapid evolution of some PRC2 genes is initially caused by a relaxation of selective constraint following the gene duplication events. Several loci could become maternally expressed imprinted genes and acquired functional roles in the endosperm.

Dead Element Replicating: Degenerate R2 Element Replication and rDNA Genomic Turnover in the Bacillus rossius Stick Insect (Insecta: Phasmida)

PubMed Central

Martoni, Francesco; Eickbush, Danna G.; Scavariello, Claudia; Luchetti, Andrea; Mantovani, Barbara

2015-01-01

R2 is an extensively investigated non-LTR retrotransposon that specifically inserts into the 28S rRNA gene sequences of a wide range of metazoans, disrupting its functionality. During R2 integration, first strand synthesis can be incomplete so that 5’ end deleted copies are occasionally inserted. While active R2 copies repopulate the locus by retrotransposing, the non-functional truncated elements should frequently be eliminated by molecular drive processes leading to the concerted evolution of the rDNA array(s). Although, multiple R2 lineages have been discovered in the genome of many animals, the rDNA of the stick insect Bacillus rossius exhibits a peculiar situation: it harbors both a canonical, functional R2 element (R2Brfun) as well as a full-length but degenerate element (R2Brdeg). An intensive sequencing survey in the present study reveals that all truncated variants in stick insects are present in multiple copies suggesting they were duplicated by unequal recombination. Sequencing results also demonstrate that all R2Brdeg copies are full-length, i. e. they have no associated 5' end deletions, and functional assays indicate they have lost the active ribozyme necessary for R2 RNA maturation. Although it cannot be completely ruled out, it seems unlikely that the degenerate elements replicate via reverse transcription, exploiting the R2Brfun element enzymatic machinery, but rather via genomic amplification of inserted 28S by unequal recombination. That inactive copies (both R2Brdeg or 5'-truncated elements) are not eliminated in a short term in stick insects contrasts with findings for the Drosophila R2, suggesting a widely different management of rDNA loci and a lower efficiency of the molecular drive while achieving the concerted evolution. PMID:25799008

An Energy-Aware Hybrid ARQ Scheme with Multi-ACKs for Data Sensing Wireless Sensor Networks.

PubMed

Zhang, Jinhuan; Long, Jun

2017-06-12

Wireless sensor networks (WSNs) are one of the important supporting technologies of edge computing. In WSNs, reliable communications are essential for most applications due to the unreliability of wireless links. In addition, network lifetime is also an important performance metric and needs to be considered in many WSN studies. In the paper, an energy-aware hybrid Automatic Repeat-reQuest protocol (ARQ) scheme is proposed to ensure energy efficiency under the guarantee of network transmission reliability. In the scheme, the source node sends data packets continuously with the correct window size and it does not need to wait for the acknowledgement (ACK) confirmation for each data packet. When the destination receives K data packets, it will return multiple copies of one ACK for confirmation to avoid ACK packet loss. The energy consumption of each node in flat circle network applying the proposed scheme is statistical analyzed and the cases under which it is more energy efficiency than the original scheme is discussed. Moreover, how to select parameters of the scheme is addressed to extend the network lifetime under the constraint of the network reliability. In addition, the energy efficiency of the proposed schemes is evaluated. Simulation results are presented to demonstrate that a node energy consumption reduction could be gained and the network lifetime is prolonged.

Results of an assessment of information needs among speech-language pathologists and audiologists in Idaho.

PubMed

Guo, Ruiling; Bain, Barbara A; Willer, Janene

2008-04-01

The research assesses the information needs of speech-language pathologists (SLPs) and audiologists in Idaho and identifies specific needs for training in evidence-based practice (EBP) principles and searching EBP resources. A survey was developed to assess knowledge and skills in accessing information. Questionnaires were distributed to 217 members of the Idaho Speech-Language-Hearing Association, who were given multiple options to return the assessment survey (web, email, mail). Data were analyzed descriptively and statistically. The total response rate was 38.7% (84/217). Of the respondents, 87.0% (73/84) indicated insufficient knowledge and skills to search PubMed. Further, 47.6% (40/84) indicated limited knowledge of EBP. Of professionals responding, 52.4% (44/84) reported interest in learning more about EBP and 47.6% (40/84) reported interest in learning to search PubMed. SLPs and audiologists who graduated within the last 10 years were more likely to respond online, while those graduating prior to that time preferred to respond via hard copy. DISCUSSIONS/CONCLUSION: More effort should be made to ensure that SLPs and audiologists develop skills in locating information to support their practice. Results from this information needs assessment were used to design a training and outreach program on EBP and EBP database searching for SLPs and audiologists in Idaho.

An International Survey of Gross Anatomy Courses in Chiropractic Colleges

PubMed Central

Ball, Jennette J.; Petrocco-Napuli, Kristina L.; Zumpano, Michael P.

2012-01-01

Purpose: The purpose of this study is to provide the first comprehensive description of gross anatomy course design in chiropractic colleges internationally and to provide baseline data for future investigation, future comparison with other health care professions, and identification of trends. Methods: A 72-question cross-sectional electronic survey was sent to the anatomy department chair at 36 chiropractic colleges internationally using Zoomerang, a web-based survey instrument. To augment the survey response data, public sources of data also were collected. Results: Forty-four percent of the electronic surveys were returned and information was gathered for 31 institutions from public sources. These results indicate (1) the most common degrees held by anatomy faculty were MS and PhD in anatomy, and DC degrees; (2) 75% of institutions utilized human cadavers and 75% presented laboratory anatomical demonstrations; (3) 62% used PowerPoint and 100% provided students with copies of lecture presentations; (4) 88% required attendance in laboratory and 50% in lecture; (5) 69% issued one grade for lecture and laboratory; (6) 100% of laboratory examinations were anatomical identification; and (7) 80% of written examinations were multiple-choice format. Conclusions: While individual variations existed, chiropractic institutions internationally have similar gross anatomy faculty, course design, delivery methods, and assessment methods. PMID:23362365

Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages.

PubMed

Mahelka, Václav; Krak, Karol; Kopecký, David; Fehrer, Judith; Šafář, Jan; Bartoš, Jan; Hobza, Roman; Blavet, Nicolas; Blattner, Frank R

2017-02-14

The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley ( Hordeum ) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.

iGC-an integrated analysis package of gene expression and copy number alteration.

PubMed

Lai, Yi-Pin; Wang, Liang-Bo; Wang, Wei-An; Lai, Liang-Chuan; Tsai, Mong-Hsun; Lu, Tzu-Pin; Chuang, Eric Y

2017-01-14

With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels.

PubMed

Hernández-Prieto, Miguel A; Lin, Yuankui; Chen, Min

2017-02-09

Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina , multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA , we detected a similar transcriptional pattern for psbJ and psbU , which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels. Copyright © 2017 Hernandez-Prieto et al.

Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.

PubMed

Chau, John H; Rahfeldt, Wolfgang A; Olmstead, Richard G

2018-03-01

Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants. We identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific data set produced the best-supported tree, but all data sets showed improved resolution over previous non-sequence capture data sets. General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

PubMed Central

Hernández-Prieto, Miguel A.; Lin, Yuankui; Chen, Min

2016-01-01

Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels. PMID:27974439

Simultaneous Authentication and Certification of Arms-Control Measurement Systems

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

MacArthur, Duncan W.; Hauck, Danielle K.; Thron, Jonathan L.

2012-07-09

Most arms-control-treaty-monitoring scenarios involve a host party that makes a declaration regarding its nuclear material or items and a monitoring party that verifies that declaration. A verification system developed for such a use needs to be trusted by both parties. The first concern, primarily from the host party's point of view, is that any sensitive information that is collected must be protected without interfering in the efficient operation of the facility being monitored. This concern is addressed in what can be termed a 'certification' process. The second concern, of particular interest to the monitoring party, is that it must bemore » possible to confirm the veracity of both the measurement system and the data produced by this measurement system. The monitoring party addresses these issues during an 'authentication' process. Addressing either one of these concerns independently is relatively straightforward. However, it is more difficult to simultaneously satisfy host party certification concerns and monitoring party authentication concerns. Typically, both parties will want the final access to the measurement system. We will describe an alternative approach that allows both parties to gain confidence simultaneously. This approach starts with (1) joint development of the measurement system followed by (2) host certification of several copies of the system and (3) random selection by the inspecting party of one copy to be use during the monitoring visit and one (or more) copy(s) to be returned to the inspecting party's facilities for (4) further hardware authentication; any remaining copies are stored under joint seal for use as spares. Following this process, the parties will jointly (5) perform functional testing on the selected measurement system and then (6) use this system during the monitoring visit. Steps (1) and (2) assure the host party as to the certification of whichever system is eventually used in the monitoring visit. Steps (1), (3), (4), and (5) increase the monitoring party's confidence in the authentication of the measurement system.« less

WORM - WINDOWED OBSERVATION OF RELATIVE MOTION

NASA Technical Reports Server (NTRS)

Bauer, F.

1994-01-01

The Windowed Observation of Relative Motion, WORM, program is primarily intended for the generation of simple X-Y plots from data created by other programs. It allows the user to label, zoom, and change the scale of various plots. Three dimensional contour and line plots are provided, although with more limited capabilities. The input data can be in binary or ASCII format, although all data must be in the same format. A great deal of control over the details of the plot is provided, such as gridding, size of tick marks, colors, log/semilog capability, time tagging, and multiple and phase plane plots. Many color and monochrome graphics terminals and hard copy printer/plotters are supported. The WORM executive commands, menu selections and macro files can be used to develop plots and tabular data, query the WORM Help library, retrieve data from input files, and invoke VAX DCL commands. WORM generated plots are displayed on local graphics terminals and can be copied using standard hard copy capabilities. Some of the graphics features of WORM include: zooming and dezooming various portions of the plot; plot documentation including curve labeling and function listing; multiple curves on the same plot; windowing of multiple plots and insets of the same plot; displaying a specific on a curve; and spinning the curve left, right, up, and down. WORM is written in PASCAL for interactive execution and has been implemented on a DEC VAX computer operating under VMS 4.7 with a virtual memory requirement of approximately 392K of 8 bit bytes. It uses the QPLOT device independent graphics library included with WORM. It was developed in 1988.

Single-cell analysis of transcription kinetics across the cell cycle

PubMed Central

Skinner, Samuel O; Xu, Heng; Nagarkar-Jaiswal, Sonal; Freire, Pablo R; Zwaka, Thomas P; Golding, Ido

2016-01-01

Transcription is a highly stochastic process. To infer transcription kinetics for a gene-of-interest, researchers commonly compare the distribution of mRNA copy-number to the prediction of a theoretical model. However, the reliability of this procedure is limited because the measured mRNA numbers represent integration over the mRNA lifetime, contribution from multiple gene copies, and mixing of cells from different cell-cycle phases. We address these limitations by simultaneously quantifying nascent and mature mRNA in individual cells, and incorporating cell-cycle effects in the analysis of mRNA statistics. We demonstrate our approach on Oct4 and Nanog in mouse embryonic stem cells. Both genes follow similar two-state kinetics. However, Nanog exhibits slower ON/OFF switching, resulting in increased cell-to-cell variability in mRNA levels. Early in the cell cycle, the two copies of each gene exhibit independent activity. After gene replication, the probability of each gene copy to be active diminishes, resulting in dosage compensation. DOI: http://dx.doi.org/10.7554/eLife.12175.001 PMID:26824388

The human clinical phenotypes of altered CHRNA7 copy number.

PubMed

Gillentine, Madelyn A; Schaaf, Christian P

2015-10-15

Copy number variants (CNVs) have been implicated in multiple neuropsychiatric conditions, including autism spectrum disorder (ASD), schizophrenia, and intellectual disability (ID). Chromosome 15q13 is a hotspot for such CNVs due to the presence of low copy repeat (LCR) elements, which facilitate non-allelic homologous recombination (NAHR). Several of these CNVs have been overrepresented in individuals with neuropsychiatric disorders; yet variable expressivity and incomplete penetrance are commonly seen. Dosage sensitivity of the CHRNA7 gene, which encodes for the α7 nicotinic acetylcholine receptor in the human brain, has been proposed to have a major contribution to the observed cognitive and behavioral phenotypes, as it represents the smallest region of overlap to all the 15q13.3 deletions and duplications. Individuals with zero to four copies of CHRNA7 have been reported in the literature, and represent a range of clinical severity, with deletions causing generally more severe and more highly penetrant phenotypes. Potential mechanisms to account for the variable expressivity within each group of 15q13.3 CNVs will be discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae.

PubMed

Turmel, Monique; Otis, Christian; Lemieux, Claude

2017-04-20

The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.

A diffusion model for the fate of tandem gene duplicates in diploids.

PubMed

O'Hely, Martin

2007-06-01

Suppose one chromosome in one member of a population somehow acquires a duplicate copy of the gene, fully linked to the original gene's locus. Preservation is the event that eventually every chromosome in the population is a descendant of the one which initially carried the duplicate. For a haploid population in which the absence of all copies of the gene is lethal, the probability of preservation has recently been estimated via a diffusion approximation. That approximation is shown to carry over to the case of diploids and arbitrary strong selection against the absence of the gene. The techniques used lead to some new results. In the large population limit, it is shown that the relative probability that descendants of a small number of individuals carrying multiple copies of the gene fix in the population is proportional to the number of copies carried. The probability of preservation is approximated when chromosomes carrying two copies of the gene are subject to additional, fully non-functionalizing mutations, thereby modelling either an additional cost of replicating a longer genome, or a partial duplication of the gene. In the latter case the preservation probability depends only on the mutation rate to null for the duplicated portion of the gene.

Evaluation of low immunization coverage among the Amish population in rural Ohio.

PubMed

Kettunen, Christine; Nemecek, John; Wenger, Olivia

2017-06-01

The Centers for Disease Control and Prevention's Morbidity and Mortality Weekly Review included childhood immunizations among the 10 great public health achievements in the United States in the 20th century. Despite this acknowledged success, childhood immunization rates continue to be much lower in select populations. Amish communities have persistently lower immunization rates. Recent outbreaks in Amish communities include a 2014 measles outbreak in Ohio, resulting in 368 cases reported. A recent outbreak of pertussis in an Amish community in Ohio resulted in the death of a 6-week-old Amish baby. A study was designed to determine the knowledge, beliefs, attitudes, and opinions of Amish parents relative to the immunization of Amish children. Data were collected through a questionnaire. Each potential participant was mailed a copy of a letter describing the proposed study. The questionnaire, a copy of the current immunization schedule, and a return stamped envelope were also included in the mailed packet. The study sample consisted of 84 Amish individuals who voluntarily filled out and returned questionnaires. The findings from the data analysis demonstrated that fear, especially concern over too many recommended immunizations and immunizations overwhelming the child's system, was the most frequent reported reasons for not having children immunized according to recommendations. Religious factors and access to care were not among reasons most reported. Designing an educational campaign for educating Amish parents on the risks and benefits of immunizations with focus on specific concerns may improve immunization rates. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Reachability bounds for chemical reaction networks and strand displacement systems.

PubMed

Condon, Anne; Kirkpatrick, Bonnie; Maňuch, Ján

2014-01-01

Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs and DSDs fail to work correctly if the length of the shortest sequence of reactions needed to produce any given molecule exceeds a threshold that grows polynomially with attributes of the system.

Simulation studies of the fidelity of biomolecular structure ensemble recreation

NASA Astrophysics Data System (ADS)

Lätzer, Joachim; Eastwood, Michael P.; Wolynes, Peter G.

2006-12-01

We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Gō-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" ϕ values, were first constructed from this reference ensemble. The resulting ϕ values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the ϕ values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average ϕ values, but allow fluctuations in ϕ for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in ϕ comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in ϕ (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.

MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.

PubMed

Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi

2018-03-05

Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes. Each component in this mixture density applies a Binomial distribution for modeling the number of mate pairs with aberration in the insertion size and also a Poisson distribution for emitting the read counts, in each genomic position. MSeq-CNV is applied on simulated data and also on real data of six HapMap individuals with high-coverage sequencing, in 1000 Genomes Project. These individuals include a CEU trio of European ancestry and a YRI trio of Nigerian ethnicity. Ancestry of these individuals is studied by clustering the identified CNVs. MSeq-CNV is also applied for detecting CNVs in two samples with low-coverage sequencing in 1000 Genomes Project and six samples form the Simons Genome Diversity Project.

Flight crew sleep during multiple layover polar flights

NASA Technical Reports Server (NTRS)

Sasaki, Mitsuo; Kurosaki, Yuko S.; Spinweber, Cheryl L.; Graeber, R. C.; Takahashi, Toshiharu

1993-01-01

This study investigated changes in sleep after multiple transmeridian flights. The subjects were 12 B747 airline pilots operating on the following polar flight: Tokyo (TYO)-Anchorage (ANC)-London (LON)-Anchorage-Tokyo. Sleep polysmonograms were recorded on two baseline nights (B1, B2), during layovers, and, after returning to Tokyo, two recovery nights were recorded (R1, R2). In ANC (outbound), total sleep time was reduced and, sleep efficiency was low (72.0 percent). In London, time in bed increased slightly, but sleep efficiency was still reduced. On return to ANC (inbound), there was considerable slow wave sleep rebound and multiple awakenings reduced sleep efficiency to 76.8 percent. Sleep efficiency on R2 was significantly lower than on B1 but not different from R1. To sum up, sleep of aircrews flying multiple transmeridian flights is disrupted during layovers and this effect persists during the two recovery nights. As a result, there is a marked cumulative sleep loss during multilegs polar route trip in comparison to single leg flights. These findings suggest that following such extensive transmeridian trips, crews should have at least three nights of recovery sleep in their home time zone before returning to duty.

International collaborative study of the endogenous reference gene, sucrose phosphate synthase (SPS), used for qualitative and quantitative analysis of genetically modified rice.

PubMed

Jiang, Lingxi; Yang, Litao; Zhang, Haibo; Guo, Jinchao; Mazzara, Marco; Van den Eede, Guy; Zhang, Dabing

2009-05-13

One rice ( Oryza sativa ) gene, sucrose phosphate synthase (SPS), has been proven to be a suitable endogenous reference gene for genetically modified (GM) rice detection in a previous study. Herein are the reported results of an international collaborative ring trial for validation of the SPS gene as an endogenous reference gene and its optimized qualitative and quantitative polymerase chain reaction (PCR) systems. A total of 12 genetically modified organism (GMO) detection laboratories from seven countries participated in the ring trial and returned their results. The validated results confirmed the species specificity of the method through testing 10 plant genomic DNAs, low heterogeneity, and a stable single-copy number of the rice SPS gene among 7 indica varieties and 5 japonica varieties. The SPS qualitative PCR assay was validated with a limit of detection (LOD) of 0.1%, which corresponded to about 230 copies of haploid rice genomic DNA, while the limit of quantification (LOQ) for the quantitative PCR system was about 23 copies of haploid rice genomic DNA, with acceptable PCR efficiency and linearity. Furthermore, the bias between the test and true values of eight blind samples ranged from 5.22 to 26.53%. Thus, we believe that the SPS gene is suitable for use as an endogenous reference gene for the identification and quantification of GM rice and its derivates.

Nucleic Acid Research Group (NARG) 2009-2010 Study : Optimal Priming Strategies for cDNA Synthesis in Real-Time RT-qPCR

PubMed Central

Hunter, T.C.; Knudtson, K.L.; Nadella, V.; Sol-Church, K.; Taylor, W.L.; Tighe, S.; Yueng, A.T.; Chittur, S.

2010-01-01

r1-1 Real-time reverse transcriptase quantitative PCR (RT-qPCR) is a widely used technique for measuring transcript levels. Priming strategy and reverse transcriptase enzyme are key elements that affect sensitivity and variability of RT-qPCR and microarray results. Previously, the Nucleic Acid Research Group (NARG) had conducted preliminary studies within the group to examine the effects of priming strategy on generating cDNA for use with qPCR. This year's study was an open study in which the qPCR community was invited to participate. Participants received the RT primers and RNA template and were asked to perform the RT reaction using their preferred reaction conditions. Each participating laboratory was provided at least two RNA templates of varying quality. The RT products were returned to the NARG and all RT reactions were used in a qPCR reaction. The qPCR assays looked at three genes of varying abundance, b-actin (high copy), b-glucuronidase (medium copy) and TATA binding protein (low copy) as well as varying distance from the 3? end for each transcript. Results from participating laboratories will be evaluated to determine the impact of priming strategy, assay chemistry and experimental setup on the RT step. Additionally, we will address the impact of RNA integrity on cDNA synthesis.

Real Time Location of Targets in Cluttered Environments

DTIC Science & Technology

2014-03-13

7 Return Signal computation from a single wind turbine ...7 Return Signal From Multiple Wind Turbines With and Without Aircraft...signals to the far field. 2. Validated using analytical signals. 3. Inner field scattering from a wind turbine and aircraft is computed 4. An

A sparse representation-based approach for copy-move image forgery detection in smooth regions

NASA Astrophysics Data System (ADS)

Abdessamad, Jalila; ElAdel, Asma; Zaied, Mourad

2017-03-01

Copy-move image forgery is the act of cloning a restricted region in the image and pasting it once or multiple times within that same image. This procedure intends to cover a certain feature, probably a person or an object, in the processed image or emphasize it through duplication. Consequences of this malicious operation can be unexpectedly harmful. Hence, the present paper proposes a new approach that automatically detects Copy-move Forgery (CMF). In particular, this work broaches a widely common open issue in CMF research literature that is detecting CMF within smooth areas. Indeed, the proposed approach represents the image blocks as a sparse linear combination of pre-learned bases (a mixture of texture and color-wise small patches) which allows a robust description of smooth patches. The reported experimental results demonstrate the effectiveness of the proposed approach in identifying the forged regions in CM attacks.

Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits

PubMed Central

Rodrigo, Guillermo; Poyatos, Juan F.

2016-01-01

Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic noise enhances information transfer in the presence of multiple circuit copies. The result is due to the contribution of noise to the generation of autonomous responses by each copy, which are altogether associated with a common decision. Moreover, factors that correlate the responses of the redundant units (extrinsic noise or regulatory cross-talk) contribute to reduce fidelity, while those that further uncouple them (heterogeneity within the copies) can lead to stronger information gain. Overall, our study emphasizes how the interplay of signal thresholding, redundancy, and noise influences the accuracy of cellular decision making. Understanding this interplay provides a basis to explain collective cell signaling mechanisms, and to engineer robust decisions with noisy genetic circuits. PMID:27741249

Nest site preference depends on the relative density of conspecifics and heterospecifics in wild birds.

PubMed

Samplonius, Jelmer M; Kromhout Van Der Meer, Iris M; Both, Christiaan

2017-01-01

Social learning allows animals to eavesdrop on ecologically relevant knowledge of competitors in their environment. This is especially important when selecting a habitat if individuals have relatively little personal information on habitat quality. It is known that birds can use both conspecific and heterospecific information for social learning, but little is known about the relative importance of each information type. If provided with the choice between them, we expected that animals should copy the behaviour of conspecifics, as these confer the best information for that species. We tested this hypothesis in the field for Pied Flycatchers Ficedula hypoleuca arriving at their breeding grounds to select a nest box for breeding. We assigned arbitrary symbols to nest boxes of breeding pied flycatchers (conspecifics) and blue and great tits, Cyanistes caeruleus and Parus major (heterospecifics), in 2014 and 2016 in two areas with different densities of tits and flycatchers. After ca 50% of flycatchers had returned and a flycatcher symbol was assigned to their nest box, we gave the later arriving flycatchers the choice between empty nest boxes with either a conspecific (flycatcher) or a heterospecific (tit) symbol. As expected, Pied Flycatchers copied the perceived nest box choice of conspecifics, but only in areas that were dominated by flycatchers. Against our initial expectation, flycatchers copied the perceived choice of heterospecifics in the area heavily dominated by tits, even though conspecific minority information was present. Our results confirm that the relative density of conspecifics and heterospecifics modulates the propensity to copy or reject novel behavioural traits. By contrasting conspecific and heterospecific ecology in the same study design we were able to draw more general conclusions about the role of fluctuating densities on social information use.

78 FR 4812 - Endangered and Threatened Wildlife and Plants; Removal of the Valley Elderberry Longhorn Beetle...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-23

... a separate document, our preferred file format is Microsoft Word. If you attach multiple comments (such as form letters), our preferred format is a Microsoft Excel spreadsheet. (2) By Hard Copy: Submit...

A Complex 6p25 Rearrangement in a Child With Multiple Epiphyseal Dysplasia

PubMed Central

Bedoyan, Jirair K.; Lesperance, Marci M.; Ackley, Todd; Iyer, Ramaswamy K.; Innis, Jeffrey W.; Misra, Vinod K.

2015-01-01

Genomic rearrangements are increasingly recognized as important contributors to human disease. Here we report on an 11½-year-old child with myopia, Duane retraction syndrome, bilateral mixed hearing loss, skeletal anomalies including multiple epiphyseal dysplasia, and global developmental delay, and a complex 6p25 genomic rearrangement. We have employed oligonucleotide-based comparative genomic hybridization arrays (aCGH) of different resolutions (44 and 244K) as well as a 1 M single nucleotide polymorphism (SNP) array to analyze this complex rearrangement. Our analyses reveal a complex rearrangement involving a ~2.21 Mb interstitial deletion, a ~240 kb terminal deletion, and a 70–80 kb region in between these two deletions that shows maintenance of genomic copy number. The interstitial deletion contains eight known genes, including three Forkhead box containing (FOX) transcription factors (FOXQ1, FOXF2, and FOXC1). The region maintaining genomic copy number partly overlaps the dual specificity protein phosphatase 22 (DUSP22) gene. Array analyses suggest a homozygous loss of genomic material at the 5′ end of DUSP22, which was corroborated using TaqMan® copy number analysis. It is possible that this homozygous genomic loss may render both copies of DUSP22 or its products non-functional. Our analysis suggests a rearrangement mechanism distinct from a previously reported replication-based error-prone mechanism without template switching for a specific 6p25 rearrangement with a 1.22 Mb interstitial deletion. Our study demonstrates the utility and limitations of using oligonucleotide-based aCGH and SNP array technologies of increasing resolutions in order to identify complex DNA rearrangements and gene disruptions. PMID:21204225

Return on Investment in Disease Management: A Review

PubMed Central

Goetzel, Ron Z.; Ozminkowski, Ronald J.; Villagra, Victor G.; Duffy, Jennifer

2005-01-01

The results of 44 studies investigating financial impact and return on investment (ROI) from disease management (DM) programs for asthma, congestive heart failure (CHF), diabetes, depression, and multiple illnesses were examined. A positive ROI was found for programs directed at CHF and multiple disease conditions. Some evidence suggests that diabetes programs may save more than they cost, but additional studies are needed. Results are mixed for asthma management programs. Depression management programs cost more than they save in medical expenses, but may save money when considering productivity outcomes. PMID:17288065

Return on investment in disease management: a review.

PubMed

Goetzel, Ron Z; Ozminkowski, Ronald J; Villagra, Victor G; Duffy, Jennifer

2005-01-01

The results of 44 studies investigating financial impact and return on investment (ROI) from disease management (DM) programs for asthma, congestive heart failure (CHF), diabetes, depression, and multiple illnesses were examined. A positive ROI was found for programs directed at CHF and multiple disease conditions. Some evidence suggests that diabetes programs may save more than they cost, but additional studies are needed. Results are mixed for asthma management programs. Depression management programs cost more than they save in medical expenses, but may save money when considering productivity outcomes.

Repeat testing of low-level HIV-1 RNA: assay performance and implementation in clinical trials.

PubMed

White, Kirsten; Garner, Will; Wei, Lilian; Eron, Joseph J; Zhong, Lijie; Miller, Michael D; Martin, Hal; Plummer, Andrew; Tran-Muchowski, Cecilia; Lindstrom, Kim; Porter, James; Piontkowsky, David; Light, Angela; Reiske, Heinz; Quirk, Erin

2018-05-15

Assess the performance of HIV-1 RNA repeat testing of stored samples in cases of low-level viremia during clinical trials. Prospective and retrospective analysis of randomized clinical trial samples and reference standards. To evaluate assay variability of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test, v2.0, three separate sources of samples were utilized: the World Health Organization (WHO) HIV reference standard (assayed using 50 independent measurements at six viral loads <200 copies/ml), retrospective analysis of four to six aliquots of plasma samples from four clinical trial participants, and prospective repeat testing of 120 samples from participants in randomized trials with low-level viremia. The TaqMan assay on the WHO HIV-1 RNA standards at viral loads <200 copies/ml performed within the expected variability according to assay specifications. However, standards with low viral loads of 36 and 18 copies/ml reported values of ≥ 50 copies/ml in 66 and 18% of tests, respectively. In participants treated with antiretrovirals who had unexpected viremia of 50-200 copies/ml after achieving <50 copies/ml, retesting of multiple aliquots of stored plasma found <50 copies/ml in nearly all cases upon retesting (14/15; 93%). Repeat testing was prospectively implemented in four clinical trials for all samples with virologic rebound of 50-200 copies/ml (n = 120 samples from 92 participants) from which 42% (50/120) had a retest result of less than 50 copies/ml and 58% (70/120) retested ≥ 50 copies/ml. The TaqMan HIV-1 RNA assay shows variability around 50 copies/ml that affects clinical trial results and may impact clinical practice. In participants with a history of viral load suppression, unexpected low-level viremia may be because of assay variability rather than low drug adherence or true virologic failure. Retesting a stored aliquot of the same sample may differentiate between assay variability and virologic failure as the source of viremia. This retesting strategy could save time, money, and anxiety for patients and their providers, as well as decrease follow-up clinic visits without increasing the risk of virologic failure and resistance development.

Tripartite-to-Bipartite Entanglement Transformation by Stochastic Local Operations and Classical Communication and the Structure of Matrix Spaces

NASA Astrophysics Data System (ADS)

Li, Yinan; Qiao, Youming; Wang, Xin; Duan, Runyao

2018-03-01

We study the problem of transforming a tripartite pure state to a bipartite one using stochastic local operations and classical communication (SLOCC). It is known that the tripartite-to-bipartite SLOCC convertibility is characterized by the maximal Schmidt rank of the given tripartite state, i.e. the largest Schmidt rank over those bipartite states lying in the support of the reduced density operator. In this paper, we further study this problem and exhibit novel results in both multi-copy and asymptotic settings, utilizing powerful results from the structure of matrix spaces. In the multi-copy regime, we observe that the maximal Schmidt rank is strictly super-multiplicative, i.e. the maximal Schmidt rank of the tensor product of two tripartite pure states can be strictly larger than the product of their maximal Schmidt ranks. We then provide a full characterization of those tripartite states whose maximal Schmidt rank is strictly super-multiplicative when taking tensor product with itself. Notice that such tripartite states admit strict advantages in tripartite-to-bipartite SLOCC transformation when multiple copies are provided. In the asymptotic setting, we focus on determining the tripartite-to-bipartite SLOCC entanglement transformation rate. Computing this rate turns out to be equivalent to computing the asymptotic maximal Schmidt rank of the tripartite state, defined as the regularization of its maximal Schmidt rank. Despite the difficulty caused by the super-multiplicative property, we provide explicit formulas for evaluating the asymptotic maximal Schmidt ranks of two important families of tripartite pure states by resorting to certain results of the structure of matrix spaces, including the study of matrix semi-invariants. These formulas turn out to be powerful enough to give a sufficient and necessary condition to determine whether a given tripartite pure state can be transformed to the bipartite maximally entangled state under SLOCC, in the asymptotic setting. Applying the recent progress on the non-commutative rank problem, we can verify this condition in deterministic polynomial time.

[Multiple organ failure after spontaneous return of circulation in cardiac arrest in children].

PubMed

Carbayo, Tania; de la Mata, Alba; Sánchez, Marina; López-Herce, Jesús; Del Castillo, Jimena; Carrillo, Angel

2017-07-01

To assess the frequency of the multiple organ failure and the prognostic value of multiple organ failure scores in children who have recovered from an in-hospital cardiac arrest. A single centre, observational, and retrospective study was conducted on children between 1 month and 16 years old who suffered an in-hospital cardiac arrest and achieved return of spontaneous circulation (ROSC). In the first 24-48hours and between the fifth and the seventh day after ROSC, a record was made of the scores on paediatric severity (PRISM and PIM II) and multiple organ failure scales (PELOD and P-MODS), along with the clinical and analytical data, and including monitoring and treatment, mortality and cause of death. Of the total of 41 children studied, 70.7% male were male, and the median age was 38 months. The overall mortality during admission was 41.5%, with 14.6% dying in the first 48hours, and 7.6% in the following 3 to 5 days. In the first 48hours, clinical severity and multiple organ failure scores were higher in the patients that died than in survivors (PRISM 29 vs. 21) P=.125, PIM II (26.8% vs. 9.2%) P=.02, PELOD (21 vs. 12) P=.005, and P-MODS (9 vs. 6) P=.001. Between the fifth and seventh day, the scores on the four scales were also higher in patients who died, but only those of the PELOD (20.5 vs. 11) p=.002 and P-MODS (6.5 vs. 3) P=.003 reached statistical significance. Mortality in children after return of spontaneous circulation after cardiac arrest is high. The multiple organ failure after return of spontaneous circulation after cardiac arrest in children is associated with increased mortality. Copyright © 2016 Asociación Española de Pediatría. Publicado por Elsevier España, S.L.U. All rights reserved.

Linear viral load increase of a single HPV-type in women with multiple HPV infections predicts progression to cervical cancer.

PubMed

Depuydt, Christophe E; Thys, Sofie; Beert, Johan; Jonckheere, Jef; Salembier, Geert; Bogers, Johannes J

2016-11-01

Persistent high-risk human papillomavirus (HPV) infection is strongly associated with development of high-grade cervical intraepithelial neoplasia or cancer (CIN3+). In single type infections, serial type-specific viral-load measurements predict the natural history of the infection. In infections with multiple HPV-types, the individual type-specific viral-load profile could distinguish progressing HPV-infections from regressing infections. A case-cohort natural history study was established using samples from untreated women with multiple HPV-infections who developed CIN3+ (n = 57) or cleared infections (n = 88). Enriched cell pellet from liquid based cytology samples were subjected to a clinically validated real-time qPCR-assay (18 HPV-types). Using serial type-specific viral-load measurements (≥3) we calculated HPV-specific slopes and coefficient of determination (R(2) ) by linear regression. For each woman slopes and R(2) were used to calculate which HPV-induced processes were ongoing (progression, regression, serial transient, transient). In transient infections with multiple HPV-types, each single HPV-type generated similar increasing (0.27copies/cell/day) and decreasing (-0.27copies/cell/day) viral-load slopes. In CIN3+, at least one of the HPV-types had a clonal progressive course (R(2)  ≥ 0.85; 0.0025copies/cell/day). In selected CIN3+ cases (n = 6), immunostaining detecting type-specific HPV 16, 31, 33, 58 and 67 RNA showed an even staining in clonal populations (CIN3+), whereas in transient virion-producing infections the RNA-staining was less in the basal layer compared to the upper layer where cells were ready to desquamate and release newly-formed virions. RNA-hybridization patterns matched the calculated ongoing processes measured by R(2) and slope in serial type-specific viral-load measurements preceding the biopsy. In women with multiple HPV-types, serial type-specific viral-load measurements predict the natural history of the different HPV-types and elucidates HPV-genotype attribution. © 2016 UICC.

DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses.

PubMed

Zepeda-Mendoza, Marie Lisandra; Bohmann, Kristine; Carmona Baez, Aldo; Gilbert, M Thomas P

2016-05-03

DNA metabarcoding is an approach for identifying multiple taxa in an environmental sample using specific genetic loci and taxa-specific primers. When combined with high-throughput sequencing it enables the taxonomic characterization of large numbers of samples in a relatively time- and cost-efficient manner. One recent laboratory development is the addition of 5'-nucleotide tags to both primers producing double-tagged amplicons and the use of multiple PCR replicates to filter erroneous sequences. However, there is currently no available toolkit for the straightforward analysis of datasets produced in this way. We present DAMe, a toolkit for the processing of datasets generated by double-tagged amplicons from multiple PCR replicates derived from an unlimited number of samples. Specifically, DAMe can be used to (i) sort amplicons by tag combination, (ii) evaluate PCR replicates dissimilarity, and (iii) filter sequences derived from sequencing/PCR errors, chimeras, and contamination. This is attained by calculating the following parameters: (i) sequence content similarity between the PCR replicates from each sample, (ii) reproducibility of each unique sequence across the PCR replicates, and (iii) copy number of the unique sequences in each PCR replicate. We showcase the insights that can be obtained using DAMe prior to taxonomic assignment, by applying it to two real datasets that vary in their complexity regarding number of samples, sequencing libraries, PCR replicates, and used tag combinations. Finally, we use a third mock dataset to demonstrate the impact and importance of filtering the sequences with DAMe. DAMe allows the user-friendly manipulation of amplicons derived from multiple samples with PCR replicates built in a single or multiple sequencing libraries. It allows the user to: (i) collapse amplicons into unique sequences and sort them by tag combination while retaining the sample identifier and copy number information, (ii) identify sequences carrying unused tag combinations, (iii) evaluate the comparability of PCR replicates of the same sample, and (iv) filter tagged amplicons from a number of PCR replicates using parameters of minimum length, copy number, and reproducibility across the PCR replicates. This enables an efficient analysis of complex datasets, and ultimately increases the ease of handling datasets from large-scale studies.

Predictability of Bristol Bay, Alaska, sockeye salmon returns one to four years in the future

USGS Publications Warehouse

Adkison, Milo D.; Peterson, R.M.

2000-01-01

Historically, forecast error for returns of sockeye salmon Oncorhynchus nerka to Bristol Bay, Alaska, has been large. Using cross-validation forecast error as our criterion, we selected forecast models for each of the nine principal Bristol Bay drainages. Competing forecast models included stock-recruitment relationships, environmental variables, prior returns of siblings, or combinations of these predictors. For most stocks, we found prior returns of siblings to be the best single predictor of returns; however, forecast accuracy was low even when multiple predictors were considered. For a typical drainage, an 80% confidence interval ranged from one half to double the point forecast. These confidence intervals appeared to be appropriately wide.

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Quantitative gene expression analysis in intact single cells can be achieved using single molecule- based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple FISH sub-probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific binding of sub-probes and tissue autofluorescence, limiting its accuracy. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on blinking frequencies of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses blinking frequency patterns, emitted frommore » a transcript bound to multiple sub-probes, which are distinct from blinking patterns emitted from partial or nonspecifically bound sub-probes and autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2, and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct blinking frequency patterns, laying the foundation for reliable single-cell transcriptomics.« less

High-level expression of two thermophilic β-mannanases in Yarrowialipolytica.

PubMed

YaPing, Wang; Ben, Rao; Ling, Zhang; Lixin, Ma

2017-05-01

Two thermophilic β-mannanases (ManA and ManB)were successfully expressed in Yarrowialipolytica using vector pINA1296I. The sequences of manA from Aspergillus niger CBS 513.88 and manB from Bacillus subtilis BCC41051 were optimized based on codon-usage bias in Y.lipolytica and synthesized by overlapping polymerase chain reaction (PCR). We utilized the pINA1296I vector, which allows inserting and expression of multiple copies of an expression cassette, to engineer recombinant strains containing multiple copies of manA or manB. Following verification of target-gene expression by quantitative PCR, fermentation experiments indicated that recombinant protein levels and enzyme activity increased along with increasing manA/manB copy number.After production in a 10 l fermenter, we obtained maximum enzyme activity from strains YLA6 and YLB6 of3024 U/mL and 1024 U/mL, respectively. Additionally, purification and characterization results revealed that the optimum pH and temperature for manA activity were pH∼5 and ∼70 °C, and for manB activity were pH∼7 and 60 °C, respectively. These results indicated that the thermo stabilities of these two enzymes were higher than most other mannanases, making them potentially useful for industrial applications. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular Characterization of Transgene Integration by Next-Generation Sequencing in Transgenic Cattle

PubMed Central

Zhang, Ran; Yin, Yinliang; Zhang, Yujun; Li, Kexin; Zhu, Hongxia; Gong, Qin; Wang, Jianwu; Hu, Xiaoxiang; Li, Ning

2012-01-01

As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species. PMID:23185606

THE SCREENING AND RANKING ALGORITHM FOR CHANGE-POINTS DETECTION IN MULTIPLE SAMPLES

PubMed Central

Song, Chi; Min, Xiaoyi; Zhang, Heping

2016-01-01

The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based. Only a few multiple sample methods have been proposed using scan statistics that are computationally intensive and designed toward either common or rare change-points detection. In this paper, we propose a novel multiple sample method by adaptively combining the scan statistic of the screening and ranking algorithm (SaRa), which is computationally efficient and is able to detect both common and rare change-points. We prove that asymptotically this method can find the true change-points with almost certainty and show in theory that multiple sample methods are superior to single sample methods when shared change-points are of interest. Additionally, we report extensive simulation studies to examine the performance of our proposed method. Finally, using our proposed method as well as two competing approaches, we attempt to detect CNVs in the data from the Primary Open-Angle Glaucoma Genes and Environment study, and conclude that our method is faster and requires less information while our ability to detect the CNVs is comparable or better. PMID:28090239

Beyond "Multicultural Moments" (Middle Ground).

ERIC Educational Resources Information Center

Miller, Howard M.

1997-01-01

Discusses how to teach students the values of "understanding, tolerance, caring, and respect," and to help them understand and appreciate cultures other than their own. Focuses on five levels: building a classroom library of multicultural literature; using "lit sets" (multiple copies of the same book) to promote multicultural…

DIALOGLINK: Shortcuts and Quick Tips.

ERIC Educational Resources Information Center

Koga, James S.

1989-01-01

Describes the use of DIALOGLINK, a searching software for online systems that can be used with microcomputers. Topics discussed include buffer size; multiple copies; screen speedup; print spooler; startup shortcuts; accounting files; type-ahead buffers; and logon macros for use with other online services. (12 references) (LRW)

Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations

PubMed Central

Brown, David; Smeets, Dominiek; Székely, Borbála; Larsimont, Denis; Szász, A. Marcell; Adnet, Pierre-Yves; Rothé, Françoise; Rouas, Ghizlane; Nagy, Zsófia I.; Faragó, Zsófia; Tőkés, Anna-Mária; Dank, Magdolna; Szentmártoni, Gyöngyvér; Udvarhelyi, Nóra; Zoppoli, Gabriele; Pusztai, Lajos; Piccart, Martine; Kulka, Janina; Lambrechts, Diether; Sotiriou, Christos; Desmedt, Christine

2017-01-01

Several studies using genome-wide molecular techniques have reported various degrees of genetic heterogeneity between primary tumours and their distant metastases. However, it has been difficult to discern patterns of dissemination owing to the limited number of patients and available metastases. Here, we use phylogenetic techniques on data generated using whole-exome sequencing and copy number profiling of primary and multiple-matched metastatic tumours from ten autopsied patients to infer the evolutionary history of breast cancer progression. We observed two modes of disease progression. In some patients, all distant metastases cluster on a branch separate from their primary lesion. Clonal frequency analyses of somatic mutations show that the metastases have a monoclonal origin and descend from a common ‘metastatic precursor’. Alternatively, multiple metastatic lesions are seeded from different clones present within the primary tumour. We further show that a metastasis can be horizontally cross-seeded. These findings provide insights into breast cancer dissemination. PMID:28429735

Design of a platform technology for systemic delivery of siRNA to tumours using rolling circle transcription

NASA Astrophysics Data System (ADS)

Jang, Mihue; Kim, Jong Hwan; Nam, Hae Yun; Kwon, Ick Chan; Ahn, Hyung Jun

2015-08-01

For therapeutic applications of siRNA, there are technical challenges with respect to targeted and systemic delivery. We here report a new siRNA carrier, RNAtr NPs, in a way that multiple tandem copies of RNA hairpins as a result of rolling circle transcription (RCT) can be readily adapted in tumour-targeted and systemic siRNA delivery. RNAtr NPs provide a means of condensing large amounts of multimeric RNA transcripts into the compact nanoparticles, especially without the aid of polycationic agents, and thus reduce the risk of immunogenicity and cytotoxicity by avoiding the use of synthetic polycationic reagents. This strategy allows the design of a platform technology for systemic delivery of siRNA to tumour sites, because RCT reaction, which enzymatically generates RNA polymers in multiple copy numbers at low cost, can lead to directly accessible routes to targeted and systemic delivery. Therefore, RNAtr NPs suggest great potentials as the siRNA therapeutics for cancer treatment.

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds

PubMed Central

Verma, Vikash; Mallik, Leena; Hariadi, Rizal F.; Sivaramakrishnan, Sivaraj; Skiniotis, Georgios; Joglekar, Ajit P.

2015-01-01

DNA origami provides a versatile platform for conducting ‘architecture-function’ analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis. PMID:26348722

Flight crew sleep during multiple layover polar flights.

PubMed

Sasaki, M; Kurosaki, Y S; Spinweber, C L; Graeber, R C; Takahashi, T

1993-07-01

This study investigated changes in sleep after multiple transmeridian flights. The subjects were 12 B747 airline pilots operating on the following polar flight: Tokyo (TYO)-Anchorage (ANC)-London (LON)-Anchorage-Tokyo. Sleep polysomnograms were recorded on two baseline nights (B1, B2), during layovers, and, after returning to Tokyo, two recovery nights were recorded (R1, R2). In ANC (outbound), total sleep time (TST) was reduced and, sleep efficiency was low (72.0%). In London, time in bed (TIB) increased slightly, but sleep efficiency was still reduced. On return to ANC (inbound), there was considerable slow wave sleep (SWS) rebound and multiple awakenings reduced sleep efficiency to 76.8%. Sleep efficiency on R2 was significantly lower than on B1 (t-test, p < 0.05) but not different from R1. To sum up, sleep of aircrews flying multiple transmeridian flights is disrupted during layovers and this effect persists during the two recovery nights. As a result, there is a marked cumulative sleep loss during multi-legs polar route trip in comparison to single leg flights. These findings suggest that following such extensive transmeridian trips, crews should have at least three nights of recovery sleep in their home time zone before returning to duty.

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases ▿ †

PubMed Central

Zielonka, Jörg; Bravo, Ignacio G.; Marino, Daniela; Conrad, Elea; Perković, Mario; Battenberg, Marion; Cichutek, Klaus; Münk, Carsten

2009-01-01

The mammalian APOBEC3 (A3) proteins comprise a multigene family of cytidine deaminases that act as potent inhibitors of retroviruses and retrotransposons. The A3 locus on the chromosome 28 of the horse genome contains multiple A3 genes: two copies of A3Z1, five copies of A3Z2, and a single copy of A3Z3, indicating a complex evolution of multiple gene duplications. We have cloned and analyzed for expression the different equine A3 genes and examined as well the subcellular distribution of the corresponding proteins. Additionally, we have tested the functional antiretroviral activity of the equine and of several of the human and nonprimate A3 proteins against the Equine infectious anemia virus (EIAV), the Simian immunodeficiency virus (SIV), and the Adeno-associated virus type 2 (AAV-2). Hematopoietic cells of horses express at least five different A3s: A3Z1b, A3Z2a-Z2b, A3Z2c-Z2d, A3Z2e, and A3Z3, whereas circulating macrophages, the natural target of EIAV, express only part of the A3 repertoire. The five A3Z2 tandem copies arose after three consecutive, recent duplication events in the horse lineage, after the split between Equidae and Carnivora. The duplicated genes show different antiviral activities against different viruses: equine A3Z3 and A3Z2c-Z2d are potent inhibitors of EIAV while equine A3Z1b, A3Z2a-Z2b, A3Z2e showed only weak anti-EIAV activity. Equine A3Z1b and A3Z3 restricted AAV and all equine A3s, except A3Z1b, inhibited SIV. We hypothesize that the horse A3 genes are undergoing a process of subfunctionalization in their respective viral specificities, which might provide the evolutionary advantage for keeping five copies of the original gene. PMID:19458006

"The role of redundant information in cultural transmission and cultural stabilization": Correction to Acerbi and Tennie (2016).

PubMed

2016-05-01

Reports an error in "The role of redundant information in cultural transmission and cultural stabilization" by Alberto Acerbi and Claudio Tennie (Journal of Comparative Psychology, 2016[Feb], Vol 130[1], 62-70). In the article the copyright should have been "© 2016 The Author(s)". The author note also should have included the following license statement "This article has been published under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright for this article is retained by the author(s). Author(s) grant(s) the American Psychological Association the exclusive right to publish the article and identify itself as the original publisher." The online version of this article has been corrected. (The following abstract of the original article appeared in record 2016-07004-005.) Redundant copying has been proposed as a manner to achieve the high-fidelity necessary to pass on and preserve complex traits in human cultural transmission. There are at least 2 ways to define redundant copying. One refers to the possibility of copying repeatedly the same trait over time, and another to the ability to exploit multiple layers of information pointing to the same trait during a single copying event. Using an individual-based model, we explore how redundant copying (defined as in the latter way) helps to achieve successful transmission. The authors show that increasing redundant copying increases the likelihood of accurately transmitting a behavior more than either augmenting the number of copying occasions across time or boosting the general accuracy of social learning. They also investigate how different cost functions, deriving, for example, from the need to invest more energy in cognitive processing, impact the evolution of redundant copying. The authors show that populations converge either to high-fitness/high-costs states (with high redundant copying and complex culturally transmitted behaviors; resembling human culture) or to low-fitness/low-costs states (with low redundant copying and simple transmitted behaviors; resembling social learning forms typical of nonhuman animals). This outcome may help to explain why cumulative culture is rare in the animal kingdom. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

My46: a web-based tool for self-guided management of genomic test results in research and clinical settings

PubMed Central

Tabor, Holly K.; Jamal, Seema M.; Yu, Joon-Ho; Crouch, Julia M.; Shankar, Aditi G.; Dent, Karin M.; Anderson, Nick; Miller, Damon A.; Futral, Brett T.; Bamshad, Michael J.

2016-01-01

A major challenge to implementing precision medicine is the need for an efficient and cost-effective strategy for returning individual genomic test results that is easily scalable and can be incorporated into multiple models of clinical practice. My46 is a web-based tool for managing the return of genetic results that was designed and developed to support a wide range of approaches to results disclosure, ranging from traditional face-to-face disclosure to self-guided models. My46 has five key functions: set and modify results return preferences, return results, educate, manage return of results, and assess return of results. These key functions are supported by six distinct modules and a suite of features that enhance the user experience, ease site navigation, facilitate knowledge sharing, and enable results return tracking. My46 is a potentially effective solution for returning results and supports current trends toward shared decision-making between patient and provider and patient-driven health management. PMID:27632689

A Novel Center Star Multiple Sequence Alignment Algorithm Based on Affine Gap Penalty and K-Band

NASA Astrophysics Data System (ADS)

Zou, Quan; Shan, Xiao; Jiang, Yi

Multiple sequence alignment is one of the most important topics in computational biology, but it cannot deal with the large data so far. As the development of copy-number variant(CNV) and Single Nucleotide Polymorphisms(SNP) research, many researchers want to align numbers of similar sequences for detecting CNV and SNP. In this paper, we propose a novel multiple sequence alignment algorithm based on affine gap penalty and k-band. It can align more quickly and accurately, that will be helpful for mining CNV and SNP. Experiments prove the performance of our algorithm.

Evidence for speckle effects on pulsed CO2 lidar signal returns from remote targets

NASA Technical Reports Server (NTRS)

Menzies, R. T.; Kavaya, M. J.; Flamant, P. H.

1984-01-01

A pulsed CO2 lidar was used to study statistical properties of signal returns from various rough surfaces at distances near 2 km. These included natural in situ topographic materials as well as man-made hard targets. Three lidar configurations were used: heterodyne detection with single temporal mode transmitter pulses, and direct detection with single and multiple temporal mode pulses. The significant differences in signal return statistics, due largely to speckle effects, are discussed.

Techniques for computing the discrete Fourier transform using the quadratic residue Fermat number systems

NASA Technical Reports Server (NTRS)

Truong, T. K.; Chang, J. J.; Hsu, I. S.; Pei, D. Y.; Reed, I. S.

1986-01-01

The complex integer multiplier and adder over the direct sum of two copies of finite field developed by Cozzens and Finkelstein (1985) is specialized to the direct sum of the rings of integers modulo Fermat numbers. Such multiplication over the rings of integers modulo Fermat numbers can be performed by means of two integer multiplications, whereas the complex integer multiplication requires three integer multiplications. Such multiplications and additions can be used in the implementation of a discrete Fourier transform (DFT) of a sequence of complex numbers. The advantage of the present approach is that the number of multiplications needed to compute a systolic array of the DFT can be reduced substantially. The architectural designs using this approach are regular, simple, expandable and, therefore, naturally suitable for VLSI implementation.

Safely coupling livestock and crop production systems: how rapidly do antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure?

PubMed

Marti, Romain; Tien, Yuan-Ching; Murray, Roger; Scott, Andrew; Sabourin, Lyne; Topp, Edward

2014-05-01

Animal manures recycled onto crop production land carry antibiotic-resistant bacteria. The present study evaluated the fate in soil of selected genes associated with antibiotic resistance or genetic mobility in field plots cropped to vegetables and managed according to normal farming practice. Referenced to unmanured soil, fertilization with swine or dairy manure increased the relative abundance of the gene targets sul1, erm(B), str(B), int1, and IncW repA. Following manure application in the spring of 2012, gene copy number decayed exponentially, reaching background levels by the fall of 2012. In contrast, gene copy number following manure application in the fall of 2012 or spring of 2013 increased significantly in the weeks following application and then declined. In both cases, the relative abundance of gene copy numbers had not returned to background levels by the fall of 2013. Overall, these results suggest that under conditions characteristic of agriculture in a humid continental climate, a 1-year period following a commercial application of raw manure is sufficient to ensure that an additional soil burden of antibiotic resistance genes approaches background. The relative abundance of several gene targets exceeded background during the growing season following a spring application or an application done the previous fall. Results from the present study reinforce the advisability of treating manure prior to use in crop production systems.

Does the use of a glossary aid patient understanding of the letters sent to their general practitioner?

PubMed

Brown, Clare E; Roberts, Nicola J; Partridge, Martyn R

2007-10-01

The NHS Plan suggests that all patients should be offered copies of letters regarding their treatment which are currently sent from a specialist clinic to their general practitioner (GP). Previous work has suggested that this enhances patient satisfaction, but medical letters can be difficult to understand. This report concerns the production and evaluation of a lung disease glossary to enhance patient understanding of terms used within the letter sent to their GP. Non-clinical staff reviewed 219 letters sent to GPs and words not likely to be understood by patients were listed and used to produce a glossary of 133 terms. One hundred and thirty-one participants from nine respiratory outpatient clinics in a London teaching hospital were sent the glossary and a questionnaire with their copy of the letter also sent to their GP Of the 131 participants, 93 patients (71%) returned the questionnaire. Eighty-three (89%) found the glossary useful and the number of words checked ranged from 0 to 14 with a median of three words. Those who did not find the glossary useful explained that their understanding was already optimal or that the words they did not understand were not contained within the glossary. This was usually because the words related to non-respiratory comorbidities. This study confirms that the inclusion of a specialty specific glossary with the patients' copy of the letter being sent to their GP is appreciated by patients and appears to aid their understanding.

Results of an assessment of information needs among speech-language pathologists and audiologists in Idaho*

PubMed Central

Guo, Ruiling; Bain, Barbara A.; Willer, Janene

2008-01-01

Objectives: The research assesses the information needs of speech-language pathologists (SLPs) and audiologists in Idaho and identifies specific needs for training in evidence-based practice (EBP) principles and searching EBP resources. Methods: A survey was developed to assess knowledge and skills in accessing information. Questionnaires were distributed to 217 members of the Idaho Speech-Language-Hearing Association, who were given multiple options to return the assessment survey (web, email, mail). Data were analyzed descriptively and statistically. Results: The total response rate was 38.7% (84/217). Of the respondents, 87.0% (73/84) indicated insufficient knowledge and skills to search PubMed. Further, 47.6% (40/84) indicated limited knowledge of EBP. Of professionals responding, 52.4% (44/84) reported interest in learning more about EBP and 47.6% (40/84) reported interest in learning to search PubMed. SLPs and audiologists who graduated within the last 10 years were more likely to respond online, while those graduating prior to that time preferred to respond via hard copy. Discussions/Conclusion: More effort should be made to ensure that SLPs and audiologists develop skills in locating information to support their practice. Results from this information needs assessment were used to design a training and outreach program on EBP and EBP database searching for SLPs and audiologists in Idaho. PMID:18379669

Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death

PubMed Central

Cele, Sandile; Ferreira, Isabella Markham; Young, Andrew C; Karim, Farina; Madansein, Rajhmun; Dullabh, Kaylesh J; Chen, Chih-Yuan; Buckels, Noel J; Ganga, Yashica; Khan, Khadija; Boulle, Mikael; Lustig, Gila; Neher, Richard A

2018-01-01

HIV has been reported to be cytotoxic in vitro and in lymph node infection models. Using a computational approach, we found that partial inhibition of transmissions of multiple virions per cell could lead to increased numbers of live infected cells. If the number of viral DNA copies remains above one after inhibition, then eliminating the surplus viral copies reduces cell death. Using a cell line, we observed increased numbers of live infected cells when infection was partially inhibited with the antiretroviral efavirenz or neutralizing antibody. We then used efavirenz at concentrations reported in lymph nodes to inhibit lymph node infection by partially resistant HIV mutants. We observed more live infected lymph node cells, but with fewer HIV DNA copies per cell, relative to no drug. Hence, counterintuitively, limited attenuation of HIV transmission per cell may increase live infected cell numbers in environments where the force of infection is high. PMID:29555018

Almahata Sitta and Brecciated Ureilites: Insights into the Heterogeneity of Asteroids and Implications for Sample Return

NASA Technical Reports Server (NTRS)

Ross, A. J.; Herrin, J. S.; Alexander, L.; Downes, H.; Smith, C. L.; Jenniskens, P.

2011-01-01

Analysis of samples returned to terrestrial laboratories enables more precise measurements and a wider range of techniques to be utilized than can be achieved with either remote sensing or rover instruments. Furthermore, returning samples to Earth allows them to be stored and re-examined with future technology. Following the success of the Hayabusa mission, returning samples from asteroids should be a high priority for understanding of early solar system evolution, planetary formation and differentiation. Meteorite falls provide us with materials and insight into asteroidal compositions. Almahata Sitta (AS) was the first meteorite fall from a tracked asteroid (2008 TC3) [1] providing a rare opportunity to compare direct geochemical observations with remote sensing data. Although AS is predominantly ureilitic, multiple chondritic fragments have been associated with this fall [2,3]. This is not unique, with chondritic fragments being found in many howardite samples (as described in a companion abstract [4]) and in brecciated ureilites, some of which are known to represent ureilitic regolith [5-7]. The heterogeneity of ureilite samples, which are thought to all originate from a single asteroidal ureilite parent body (UPB) [5], gives us information about both internal and external asteroidal variations. This has implications both for the planning of potential sample return missions and the interpretation of material returned to Earth. This abstract focuses on multiple fragments of two meteorites: Almahata Sitta (AS); and Dar al Gani (DaG) 1047 (a highly brecciated ureilite, likely representative of ureilite asteroidal regolith).

Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples.

PubMed

Mandage, Rajendra; Telford, Marco; Rodríguez, Juan Antonio; Farré, Xavier; Layouni, Hafid; Marigorta, Urko M; Cundiff, Caitlin; Heredia-Genestar, Jose Maria; Navarro, Arcadi; Santpere, Gabriel

2017-01-01

Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced EBV-mapping reads from 1,753 LCL samples derived from 19 populations worldwide that were sequenced within the context of the 1000 Genomes Project. An in silico methodology was developed to estimate the number of EBV copy number in LCLs and validated these estimations by real-time PCR. After experimentally confirming that EBV relative copy number remains stable over cell passages, we performed a genome wide association analysis (GWAS) to try detecting genetic variants of the host that may be associated with EBV copy number. Our GWAS has yielded several genomic regions suggestively associated with the number of EBV genomes per cell in LCLs, unraveling promising candidate genes such as CAND1, a known inhibitor of EBV replication. While this GWAS does not unequivocally establish the degree to which genetic makeup of individuals determine viral levels within their derived LCLs, for which a larger sample size will be needed, it potentially highlighted human genes affecting EBV-related processes, which constitute interesting candidates to follow up in the context of EBV related pathologies.

Distributed process manager for an engineering network computer

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

Gait, J.

1987-08-01

MP is a manager for systems of cooperating processes in a local area network of engineering workstations. MP supports transparent continuation by maintaining multiple copies of each process on different workstations. Computational bandwidth is optimized by executing processes in parallel on different workstations. Responsiveness is high because workstations compete among themselves to respond to requests. The technique is to select a master from among a set of replicates of a process by a competitive election between the copies. Migration of the master when a fault occurs or when response slows down is effected by inducing the election of a newmore » master. Competitive response stabilizes system behavior under load, so MP exhibits realtime behaviors.« less

Combined coding and delay-throughput analysis for fading channels of mobile satellite communications

NASA Technical Reports Server (NTRS)

Wang, C. C.; Yan, Tsun-Yee

1986-01-01

This paper presents the analysis of using the punctured convolutional code with Viterbi decoding to improve communications reliability. The punctured code rate is optimized so that the average delay is minimized. The coding gain in terms of the message delay is also defined. Since using punctured convolutional code with interleaving is still inadequate to combat the severe fading for short packets, the use of multiple copies of assignment and acknowledgment packets is suggested. The performance on the average end-to-end delay of this protocol is analyzed. It is shown that a replication of three copies for both assignment packets and acknowledgment packets is optimum for the cases considered.

Application of Array Comparative Genomic Hybridization in Newborns with Multiple Congenital Anomalies.

PubMed

Szczałuba, Krzysztof; Nowakowska, Beata; Sobecka, Katarzyna; Smyk, Marta; Castaneda, Jennifer; Klapecki, Jakub; Kutkowska-Kaźmierczak, Anna; Śmigiel, Robert; Bocian, Ewa; Radkowski, Marek; Demkow, Urszula

2016-01-01

Major congenital anomalies are detectable in 2-3 % of the newborn population. Some of their genetic causes are attributable to copy number variations identified by array comparative genomic hybridization (aCGH). The value of aCGH screening as a first-tier test in children with multiple congenital anomalies has been studied and consensus adopted. However, array resolution has not been agreed upon, specifically in the newborn or infant population. Moreover, most array studies have been focused on mixed populations of intellectual disability/developmental delay with or without multiple congenital anomalies, making it difficult to assess the value of microarrays in newborns. The aim of the study was to determine the optimal quality and clinical sensitivity of high-resolution array comparative genomic hybridization in neonates with multiple congenital anomalies. We investigated a group of 54 newborns with multiple congenital anomalies defined as two or more birth defects from more than one organ system. Cytogenetic studies were performed using OGT CytoSure 8 × 60 K microarray. We found ten rearrangements in ten newborns. Of these, one recurrent syndromic microduplication was observed, whereas all other changes were unique. Six rearrangements were definitely pathogenic, including one submicroscopic and five that could be seen on routine karyotype analysis. Four other copy number variants were likely pathogenic. The candidate genes that may explain the phenotype were discussed. In conclusion, high-resolution array comparative hybridization can be applied successfully in newborns with multiple congenital anomalies as the method detects a significant number of pathogenic changes, resulting in early diagnoses. We hypothesize that small changes previously considered benign or even inherited rearrangements should be classified as potentially pathogenic at least until a subsequent clinical assessment would exclude a developmental delay or dysmorphism.

Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics

PubMed Central

Hanemaaijer, Nicolien M; Sikkema-Raddatz, Birgit; van der Vries, Gerben; Dijkhuizen, Trijnie; Hordijk, Roel; van Essen, Anthonie J; Veenstra-Knol, Hermine E; Kerstjens-Frederikse, Wilhelmina S; Herkert, Johanna C; Gerkes, Erica H; Leegte, Lamberta K; Kok, Klaas; Sinke, Richard J; van Ravenswaaij-Arts, Conny M A

2012-01-01

The correct interpretation of copy number gains in patients with developmental delay and multiple congenital anomalies is hampered by the large number of copy number variations (CNVs) encountered in healthy individuals. The variable phenotype associated with copy number gains makes interpretation even more difficult. Literature shows that inheritence, size and presence in healthy individuals are commonly used to decide whether a certain copy number gain is pathogenic, but no general consensus has been established. We aimed to develop guidelines for interpreting gains detected by array analysis using array CGH data of 300 patients analysed with the 105K Agilent oligo array in a diagnostic setting. We evaluated the guidelines in a second, independent, cohort of 300 patients. In the first 300 patients 797 gains of four or more adjacent oligonucleotides were observed. Of these, 45.4% were de novo and 54.6% were familial. In total, 94.8% of all de novo gains and 87.1% of all familial gains were concluded to be benign CNVs. Clinically relevant gains ranged from 288 to 7912 kb in size, and were significantly larger than benign gains and gains of unknown clinical relevance (P<0.001). Our study showed that a threshold of 200 kb is acceptable in a clinical setting, whereas heritability does not exclude a pathogenic nature of a gain. Evaluation of the guidelines in the second cohort of 300 patients revealed that the interpretation guidelines were clear, easy to follow and efficient. PMID:21934709

An Organization's Economic Return on Training Investment.

ERIC Educational Resources Information Center

Pucel, David J.; Lyau, Nyan-Myau

A study examined the relationship between investment in training and labor productivity in a sample of 237 large and medium-size Taiwanese firms producing auto parts. Of the 162 firms (68.4%) that returned usable questionnaires, 142 (59.9%) had training programs and 131 (55.3%) provided full cost data. The data were analyzed by multiple regression…

76 FR 76252 - Proposed Revision of Annual Information Return/Reports

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-06

...This document contains proposed revisions to the Form 5500 Annual Return/Report filed by administrators of employee benefit plans. The proposed revisions are intended to enhance the Department of Labor's ability to enforce the reporting requirements for multiple employer welfare arrangements (MEWAs) under Title I of the Employee Retirement Income Security Act of 1974, as amended (ERISA).

26 CFR 1.72-5 - Expected return.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the joint and survivor annuity element 110.40 Multiple from Table I (male, age 60) 18.2 Number of... anticipatable with respect to the joint and survivor annuity element 124.80 Multiple from Table V (age 60) 24.2... annuity payments to be received annually by the multiple shown in Table I or V (whichever is applicable...

26 CFR 1.72-5 - Expected return.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the joint and survivor annuity element 110.40 Multiple from Table I (male, age 60) 18.2 Number of... anticipatable with respect to the joint and survivor annuity element 124.80 Multiple from Table V (age 60) 24.2... annuity payments to be received annually by the multiple shown in Table I or V (whichever is applicable...

26 CFR 1.72-5 - Expected return.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the joint and survivor annuity element 110.40 Multiple from Table I (male, age 60) 18.2 Number of... anticipatable with respect to the joint and survivor annuity element 124.80 Multiple from Table V (age 60) 24.2... annuity payments to be received annually by the multiple shown in Table I or V (whichever is applicable...

26 CFR 1.72-5 - Expected return.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the joint and survivor annuity element 110.40 Multiple from Table I (male, age 60) 18.2 Number of... anticipatable with respect to the joint and survivor annuity element 124.80 Multiple from Table V (age 60) 24.2... annuity payments to be received annually by the multiple shown in Table I or V (whichever is applicable...

Evaluation of trade-offs in costs and environmental impacts for returnable packaging implementation

NASA Astrophysics Data System (ADS)

Jarupan, Lerpong; Kamarthi, Sagar V.; Gupta, Surendra M.

2004-02-01

The main thrust of returnable packaging these days is to provide logistical services through transportation and distribution of products and be environmentally friendly. Returnable packaging and reverse logistics concepts have converged to mitigate the adverse effect of packaging materials entering the solid waste stream. Returnable packaging must be designed by considering the trade-offs between costs and environmental impact to satisfy manufacturers and environmentalists alike. The cost of returnable packaging entails such items as materials, manufacturing, collection, storage and disposal. Environmental impacts are explicitly linked with solid waste, air pollution, and water pollution. This paper presents a multi-criteria evaluation technique to assist decision-makers for evaluating the trade-offs in costs and environmental impact during the returnable packaging design process. The proposed evaluation technique involves a combination of multiple objective integer linear programming and analytic hierarchy process. A numerical example is used to illustrate the methodology.

The Electrosome: A Surface-Displayed Enzymatic Cascade in a Biofuel Cell’s Anode and a High-Density Surface-Displayed Biocathodic Enzyme

PubMed Central

Szczupak, Alon; Aizik, Dror; Moraïs, Sarah; Vazana, Yael; Barak, Yoav; Bayer, Edward A.; Alfonta, Lital

2017-01-01

The limitation of surface-display systems in biofuel cells to a single redox enzyme is a major drawback of hybrid biofuel cells, resulting in a low copy-number of enzymes per yeast cell and a limitation in displaying enzymatic cascades. Here we present the electrosome, a novel surface-display system based on the specific interaction between the cellulosomal scaffoldin protein and a cascade of redox enzymes that allows multiple electron-release by fuel oxidation. The electrosome is composed of two compartments: (i) a hybrid anode, which consists of dockerin-containing enzymes attached specifically to cohesin sites in the scaffoldin to assemble an ethanol oxidation cascade, and (ii) a hybrid cathode, which consists of a dockerin-containing oxygen-reducing enzyme attached in multiple copies to the cohesin-bearing scaffoldin. Each of the two compartments was designed, displayed, and tested separately. The new hybrid cell compartments displayed enhanced performance over traditional biofuel cells; in the anode, the cascade of ethanol oxidation demonstrated higher performance than a cell with just a single enzyme. In the cathode, a higher copy number per yeast cell of the oxygen-reducing enzyme copper oxidase has reduced the effect of competitive inhibition resulting from yeast oxygen consumption. This work paves the way for the assembly of more complex cascades using different enzymes and larger scaffoldins to further improve the performance of hybrid cells. PMID:28644390

MVisAGe Identifies Concordant and Discordant Genomic Alterations of Driver Genes in Squamous Tumors.

PubMed

Walter, Vonn; Du, Ying; Danilova, Ludmila; Hayward, Michele C; Hayes, D Neil

2018-06-15

Integrated analyses of multiple genomic datatypes are now common in cancer profiling studies. Such data present opportunities for numerous computational experiments, yet analytic pipelines are limited. Tools such as the cBioPortal and Regulome Explorer, although useful, are not easy to access programmatically or to implement locally. Here, we introduce the MVisAGe R package, which allows users to quantify gene-level associations between two genomic datatypes to investigate the effect of genomic alterations (e.g., DNA copy number changes on gene expression). Visualizing Pearson/Spearman correlation coefficients according to the genomic positions of the underlying genes provides a powerful yet novel tool for conducting exploratory analyses. We demonstrate its utility by analyzing three publicly available cancer datasets. Our approach highlights canonical oncogenes in chr11q13 that displayed the strongest associations between expression and copy number, including CCND1 and CTTN , genes not identified by copy number analysis in the primary reports. We demonstrate highly concordant usage of shared oncogenes on chr3q, yet strikingly diverse oncogene usage on chr11q as a function of HPV infection status. Regions of chr19 that display remarkable associations between methylation and gene expression were identified, as were previously unreported miRNA-gene expression associations that may contribute to the epithelial-to-mesenchymal transition. Significance: This study presents an important bioinformatics tool that will enable integrated analyses of multiple genomic datatypes. Cancer Res; 78(12); 3375-85. ©2018 AACR . ©2018 American Association for Cancer Research.

Rapid evolution and copy number variation of primate RHOXF2, an X-linked homeobox gene involved in male reproduction and possibly brain function.

PubMed

Niu, Ao-lei; Wang, Yin-qiu; Zhang, Hui; Liao, Cheng-hong; Wang, Jin-kai; Zhang, Rui; Che, Jun; Su, Bing

2011-10-12

Homeobox genes are the key regulators during development, and they are in general highly conserved with only a few reported cases of rapid evolution. RHOXF2 is an X-linked homeobox gene in primates. It is highly expressed in the testicle and may play an important role in spermatogenesis. As male reproductive system is often the target of natural and/or sexual selection during evolution, in this study, we aim to dissect the pattern of molecular evolution of RHOXF2 in primates and its potential functional consequence. We studied sequences and copy number variation of RHOXF2 in humans and 16 nonhuman primate species as well as the expression patterns in human, chimpanzee, white-browed gibbon and rhesus macaque. The gene copy number analysis showed that there had been parallel gene duplications/losses in multiple primate lineages. Our evidence suggests that 11 nonhuman primate species have one RHOXF2 copy, and two copies are present in humans and four Old World monkey species, and at least 6 copies in chimpanzees. Further analysis indicated that the gene duplications in primates had likely been mediated by endogenous retrovirus (ERV) sequences flanking the gene regions. In striking contrast to non-human primates, humans appear to have homogenized their two RHOXF2 copies by the ERV-mediated non-allelic recombination mechanism. Coding sequence and phylogenetic analysis suggested multi-lineage strong positive selection on RHOXF2 during primate evolution, especially during the origins of humans and chimpanzees. All the 8 coding region polymorphic sites in human populations are non-synonymous, implying on-going selection. Gene expression analysis demonstrated that besides the preferential expression in the reproductive system, RHOXF2 is also expressed in the brain. The quantitative data suggests expression pattern divergence among primate species. RHOXF2 is a fast-evolving homeobox gene in primates. The rapid evolution and copy number changes of RHOXF2 had been driven by Darwinian positive selection acting on the male reproductive system and possibly also on the central nervous system, which sheds light on understanding the role of homeobox genes in adaptive evolution.

Multiple volume compressor for hot gas engine

DOEpatents

Stotts, Robert E.

1986-01-01

A multiple volume compressor for use in a hot gas (Stirling) engine having a plurality of different volume chambers arranged to pump down the engine when decreased power is called for and return the working gas to a storage tank or reservoir. A valve actuated bypass loop is placed over each chamber which can be opened to return gas discharged from the chamber back to the inlet thereto. By selectively actuating the bypass valves, a number of different compressor capacities can be attained without changing compressor speed whereby the capacity of the compressor can be matched to the power available from the engine which is used to drive the compressor.

Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series.

PubMed

Shwan, Nzar A A; Louzada, Sandra; Yang, Fengtang; Armour, John A L

2017-05-01

The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation (CNV) of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of CNV has only been defined in detail very recently. In this work, we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A, and AMY2B. We use fiber-FISH (fluorescence in situ hybridization) to define unexpected complexity in the accompanying rearrangements. These findings demonstrate recurrent involvement of the amylase gene region in genomic instability, involving at least five independent rearrangements of the pancreatic amylase genes (AMY2A and AMY2B). Structural features shared by fundamentally distinct lineages strongly suggest that the common ancestral state for the human amylase cluster contained more than one, and probably three, copies of AMY1. © 2017 WILEY PERIODICALS, INC.

Organizational strategies mediate nonverbal memory impairment in obsessive-compulsive disorder.

PubMed

Savage, C R; Baer, L; Keuthen, N J; Brown, H D; Rauch, S L; Jenike, M A

1999-04-01

Previous neuropsychological studies of obsessive-compulsive disorder (OCD) have indicated impaired executive functioning and nonverbal memory. The extent to which impaired executive functioning impacts nonverbal memory has not been established. The current study investigated the mediating effects of organizational strategies used when copying a figure on subsequent nonverbal memory for that figure. We examined neuropsychological performance in 20 unmedicated subjects with OCD and 20 matched normal control subjects. Subjects were administered the Rey-Osterrieth Complex Figure Test (RCFT) and neuropsychological tests assessing various aspects of executive function. OCD subjects differed significantly from healthy control subjects in the organizational strategies used to copy the RCFT figure, and they recalled significantly less information on both immediate and delayed testing. Multiple regression analyses indicated that group differences in immediate percent recall were significantly mediated by copy organizational strategies. Further exploratory analyses indicated that organizational problems in OCD may be related to difficulties shifting mental and/or spatial set. Immediate nonverbal memory problems in OCD subjects were mediated by impaired organizational strategies used during the initial copy of the RCFT figure. Thus, the primary deficit was one affecting executive function, which then had a secondary effect on immediate memory. These findings are consistent with current theories proposing frontal-striatal system dysfunction in OCD.

Circumlunar Free-Return Cycler Orbits for a Manned Earth-Moon Space Station

NASA Technical Reports Server (NTRS)

Genova, Anthony L.; Aldrin, Buzz

2015-01-01

Multiple free-return circumlunar cycler orbits were designed to allow regular travel between the Earth and Moon by a manned space station. The presented cycler orbits contain circumlunar free-return "figure-8" segments and yield lunar encounters every month. Smaller space "taxi" vehicles can rendezvous with (and depart from) the cycling Earth-Moon space station to enter lunar orbit (and/or land on the lunar surface), return to Earth, or reach destinations including Earth-Moon L1 and L2 halo orbits, near-Earth objects (NEOs), Venus, and Mars. To assess the practicality of the selected orbits, relevant cycler characteristics (including (Delta)V maintenance requirements) are presented and compared.

Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes.

PubMed

Turner, Peter C; Yomano, Lorraine P; Jarboe, Laura R; York, Sean W; Baggett, Christy L; Moritz, Brélan E; Zentz, Emily B; Shanmugam, K T; Ingram, Lonnie O

2012-04-01

Escherichia coli KO11 (ATCC 55124) was engineered in 1990 to produce ethanol by chromosomal insertion of the Zymomonas mobilis pdc and adhB genes into E. coli W (ATCC 9637). KO11FL, our current laboratory version of KO11, and its parent E. coli W were sequenced, and contigs assembled into genomic sequences using optical NcoI restriction maps as templates. E. coli W contained plasmids pRK1 (102.5 kb) and pRK2 (5.4 kb), but KO11FL only contained pRK2. KO11FL optical maps made with AflII and with BamHI showed a tandem repeat region, consisting of at least 20 copies of a 10-kb unit. The repeat region was located at the insertion site for the pdc, adhB, and chloramphenicol-resistance genes. Sequence coverage of these genes was about 25-fold higher than average, consistent with amplification of the foreign genes that were inserted as circularized DNA. Selection for higher levels of chloramphenicol resistance originally produced strains with higher pdc and adhB expression, and hence improved fermentation performance, by increasing the gene copy number. Sequence data for an earlier version of KO11, ATCC 55124, indicated that multiple copies of pdc adhB were present. Comparison of the W and KO11FL genomes showed large inversions and deletions in KO11FL, mostly enabled by IS10, which is absent from W but present at 30 sites in KO11FL. The early KO11 strain ATCC 55124 had no rearrangements, contained only one IS10, and lacked most accumulated single nucleotide polymorphisms (SNPs) present in KO11FL. Despite rearrangements and SNPs in KO11FL, fermentation performance was equal to that of ATCC 55124.

Copy Number Variation of the Beta Defensin Gene Cluster on Chromosome 8p Influences the Bacterial Microbiota within the Nasopharynx of Otitis-Prone Children

PubMed Central

Bevins, Charles L.; Hollox, Edward J.; Bakaletz, Lauren O.

2014-01-01

As there is increasing evidence that aberrant defensin expression is related to susceptibility for infectious disease and inflammatory disorders, we sought to determine if copy number of the beta-defensin gene cluster located on chromosome 8p23.1 (DEFB107, 106, 105, 104, 103, DEFB4 and SPAG11), that shows copy number variation as a block, was associated with susceptibility to otitis media (OM). The gene DEFB103 within this complex encodes human beta defensin-3 (hBD-3), an antimicrobial peptide (AP) expressed by epithelial cells that line the mammalian airway, important for defense of mucosal surfaces and previously shown to have bactericidal activity in vitro against multiple human pathogens, including the three that predominate in OM. To this end, we conducted a retrospective case-control study of 113 OM prone children and 267 controls aged five to sixty months. We identified the copy number of the above defined beta-defensin gene cluster (DEFB-CN) in each study subject by paralogue ratio assays. The mean DEFB-CN was indistinguishable between subjects classified as OM prone based on a recent history of multiple episodes of OM and control subjects who had no history of OM (4.4±0.96 versus 4.4±1.08, respectively: Odds Ratio [OR]: 1.16 (95% CI: 0.61, 2.20). Despite a lack of direct association, we observed a statistically significant correlation between DEFB-CN and nasopharyngeal bacterial colonization patterns. Collectively, our findings suggested that susceptibility to OM might be mediated by genetic variation among individuals, wherein a DEFB-CN less than 4 exerts a marked influence on the microbiota of the nasopharynx, specifically with regard to colonization by the three predominant bacterial pathogens of OM. PMID:24867293

Multi-hazard Assessment and Scenario Toolbox (MhAST): A Framework for Analyzing Compounding Effects of Multiple Hazards

NASA Astrophysics Data System (ADS)

Sadegh, M.; Moftakhari, H.; AghaKouchak, A.

2017-12-01

Many natural hazards are driven by multiple forcing variables, and concurrence/consecutive extreme events significantly increases risk of infrastructure/system failure. It is a common practice to use univariate analysis based upon a perceived ruling driver to estimate design quantiles and/or return periods of extreme events. A multivariate analysis, however, permits modeling simultaneous occurrence of multiple forcing variables. In this presentation, we introduce the Multi-hazard Assessment and Scenario Toolbox (MhAST) that comprehensively analyzes marginal and joint probability distributions of natural hazards. MhAST also offers a wide range of scenarios of return period and design levels and their likelihoods. Contribution of this study is four-fold: 1. comprehensive analysis of marginal and joint probability of multiple drivers through 17 continuous distributions and 26 copulas, 2. multiple scenario analysis of concurrent extremes based upon the most likely joint occurrence, one ruling variable, and weighted random sampling of joint occurrences with similar exceedance probabilities, 3. weighted average scenario analysis based on a expected event, and 4. uncertainty analysis of the most likely joint occurrence scenario using a Bayesian framework.

Teachers' Unions and Compensation: The Impact of Collective Bargaining on Salary Schedules and Performance Pay Schemes

ERIC Educational Resources Information Center

West, Kristine Lamm; Mykerezi, Elton

2011-01-01

This study examines the impact that collective bargaining has on multiple dimensions of teacher compensation, including average and starting salaries, early and late returns to experience, returns to graduate degrees, and the incidence of different pay for performance schemes. Using data from the School and Staffing Survey (SASS) and a more recent…

Statistical analysis of electric field parameters for negative lightning in Malaysia

NASA Astrophysics Data System (ADS)

Wooi, Chin-Leong; Abdul-Malek, Zulkurnain; Ahmad, Noor-Azlinda; El Gayar, Ali I.

2016-08-01

This paper presents a comparative study on the electric field and its derivative parameters of negative lightning in Malaysia and other regions. This study is the first in Malaysia where the parameters of negative electric field and its derivative are thoroughly analyzed. 104 negative lightning flashes containing 277 negative return strokes occurring within 10-100 km from the measuring station and recorded during monsoon period in the state of Johor, Malaysia had been analyzed. It was found that 73% of the recorded flashes are multiple strokes with an average multiplicity of 2.6 strokes per flash. For first return strokes, the arithmetic mean (AM) of initial peak electric field and the AM of initial peak electric field derivative are 21.8 V/m and 11.3 V/m/μs, respectively. The initial peaks of electric field and its derivative for first return strokes are larger than those for the subsequent return strokes. Comparison of overall results with those obtained earlier in Sri Lanka, Germany, Sweden, Japan, Florida indicates that several electric field and its derivative parameters are affected by propagation media and geographical region. Similarity of results with other countries having the same climatic condition is also observed.

The enablers and barriers to continue breast milk feeding in women returning to work.

PubMed

Sulaiman, Zaharah; Liamputtong, Pranee; Amir, Lisa H

2016-04-01

To describe the enablers and barriers working women experience in continuing breast milk feeding after they return to work postpartum in urban Malaysia. In Malaysia, urban working women have low rates of breastfeeding and struggle to achieve the recommended 6 months exclusive breastfeeding. A qualitative enquiry based on a phenomenological framework and multiple methods were used to explore women's experiences in depth. Multiple qualitative methods using face-to-face interview and participant diary were used. Data collection took place in urban suburbs around Penang and Klang Valley, Malaysia from March-September 2011. Participants were 40 employed women with infants less than 24 months. Only 11 of the participants worked from home. Based on the women's experiences, we categorized them into three groups: 'Passionate' women with a strong determination and exclusively breastfed for 6 months, 'Ambivalent' women who initiated breastfeeding, but were unable to sustain exclusive breastfeeding after returning to work and 'Equivalent' women who introduced infant formula prior to returning to work. Passion and to a lesser extent intention, influenced women's choice. Women's characteristics played a greater role in their infant feeding outcomes than their work environment. © 2016 John Wiley & Sons Ltd.

Inventory decision in a closed-loop supply chain with inspection, sorting, and waste disposal

NASA Astrophysics Data System (ADS)

Dwicahyani, A. R.; Jauhari, W. A.; Kurdhi, N. A.

2016-02-01

The study of returned item inventory management in a closed-loop supply chain system has become an important issue in recent years. So far, investigations about inventory decision making in a closed-loop supply chain system have been confined to traditional forward and reverse oriented material flow supply chain. In this study, we propose an integrated inventory model consisting a supplier, a manufacturer, and a retailer where the manufacturer inspects all of the returned items collected from the customers and classifies them as recoverable or waste. Returned items that recovered through the remanufacturing process and the newly manufactured products are then used to meet the demand of the retailer. However, some recovered items which are not comparable to the ones in quality, classified as refurbished items, are sold to a secondary market at a reduced price. This study also suggests that the flow of returned items is controlled by a decision variable, namely an acceptance quality level of recoverable item in the system. We apply multiple remanufacturing cycle and multiple production cycle policy to the proposed model and give the corresponding iterative procedure to determine the optimal solutions. Further, numerical examples are presented for illustrative purpose.

Primary simian immunodeficiency virus SIVmnd-2 infection in mandrills (Mandrillus sphinx).

PubMed

Onanga, Richard; Souquière, Sandrine; Makuwa, Maria; Mouinga-Ondeme, Augustin; Simon, François; Apetrei, Cristian; Roques, Pierre

2006-04-01

Mandrills are the only nonhuman primate (NHP) naturally infected by two types of simian immunodeficiency virus (SIV): SIVmnd-1 and SIVmnd-2. We have already reported that the high SIVmnd-1 replication during primary infection contrasts with only transient changes in CD4+ and CD8+ cell counts. Since early virus-host interactions predict viral control and disease progression in human immunodeficiency virus-infected patients, we investigated the dynamics of SIVmnd-2 primary infection in mandrills to examine the impact on immune effectors in blood and lymph nodes (LNs). To avoid in vitro strain selection, all mandrills in this study received plasma from SIVmnd-2-infected mandrills. SIVmnd-2 plasma viremia peaked at 10(7) to 10(8) RNA copies/ml between days 7 and 10. This peak was followed in all four monkeys by a decline in virus replication, with a set point level of 10(5) to 10(6) RNA copies/ml at day 42 postinfection (p.i.). Viral DNA load in PBMC and LNs also peaked between days 7 and 10 (10(5) to 10(6) DNA copies/10(6) cells) and stabilized at 10(3) to 10(4) DNA copies/10(6) cells during the chronic phase. Anti-SIVmnd-2 antibodies were detected starting from days 28 to 32. A transitory decline of CD3+ CD4+ cells in the LNs occurred in animals with high peak VLs. CD4+ and CD8+ T-cell activation in blood and LNs was noted between days 5 and 17 p.i., surrounding the peak of viral replication. This was most significant in the LNs. Activation markers then returned to preinfection values despite continuous and active viral replication during the chronic infection. The dynamics of SIVmnd-2 infection in mandrills showed a pattern similar to that of SIVmnd-1 infection. This might be a general feature of nonpathogenic SIV natural African NHP models.

A de novo atypical ring sSMC(22) characterized by array CGH in a boy with cat-eye syndrome.

PubMed

Haltrich, Irén; Pikó, Henriett; Kiss, Eszter; Tóth, Zsuzsa; Karcagi, Veronika; Fekete, György

2014-01-01

Microduplications 22q11 have been characterized as a genomic duplication syndrome mediated by nonallelic homologous recombination between region-specific low-copy repeats. Here we report on a 19 years old boy with intellectual disability having an unexpected structurally complex ring small supernumerary marker chromosome (sSMC) originated from a larger trisomy and a smaller tetrasomy of proximal 22q11 harboring additional copies of cat eye syndrome critical regions genes. PRINCIPAL CLINICAL FEATURES WERE: anorectal and urogenital malformations, total anomalous pulmonary venous return with secundum ASD, hearing defect, preauricular pits, seizure and eczema. The proband also presented some rare or so far not reported clinical findings such as hyperinsulinaemia, severe immunodeficiency and grave cognitive deficits. Chromosome analysis revealed a mosaic karyotype with the presence of a small ring-like marker in 60% of cells. Array CGH detected approximately an 1,2 Mb single and a 0,2 Mb double copy gain of the proximal long arm of chromosome 22. The 1,3 Mb intervening region of chromosome 22 from centromere to the breakpoints showed no copy alteration. The karyotype of the patient was defined as 47,XY,+mar[60]/46,XY[40].ish idic r(22)(q11.1.q11.21) × 4.arr 22q11(17,435, 645-18,656,678) × 3,(17,598,642-17,799,783) × 4 dn. The present report is the first one with a detailed description of clinical presentation in a patient carrying an atypical size ring sSMC (22) analyzed by array CGH. The specialty of the finding is emphasized by the fact that although the patient had a mosaic sSMC and the amplified region was smaller than in typical cat eye syndrome cases, the clinical presentation was severe.

40 CFR 63.7555 - What records must I keep?

Code of Federal Regulations, 2011 CFR

2011-07-01

... hydrogen chloride emission rates. You can use the results from one fuel analysis for multiple boilers and... fuel input, or hydrogen chloride emission rate, for each boiler and process heater. (5) A copy of all... submitted, according to the requirements in § 63.10(b)(2)(xiv). (2) Records of performance tests, fuel...

Newer Technologies for School Security. ERIC Digest Number 145.

ERIC Educational Resources Information Center

Schneider, Tod

This digest describes several technologies that can be used to control access to, and improve surveillance of, school grounds. Access can be controlled by using "smart" cards to control keyed entries. Many schools have problems with multiple copies of keys, and these card systems are integrated with computer software that allows for…

A Social Judgment Analysis of Information Source Preference Profiles: An Exploratory Study to Empirically Represent Media Selection Patterns.

ERIC Educational Resources Information Center

Stefl-Mabry, Joette

2003-01-01

Describes a study that empirically identified individual preferences profiles to understand information-seeking behavior among professional groups for six selected information sources. Highlights include Social Judgment Analysis; the development of the survey used, a copy of which is appended; hypotheses tested; results of multiple regression…

40 CFR 142.16 - Special primacy requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... thereto. (ii) Section 141.82(g)—Designating an alternative approach for aggregating multiple measurements... adopt a formula other than the one specified in § 141.82(g)(1) of this chapter. (2) Sections 141.83(b)(2... enforcement responsibility must maintain a copy of the reports for a period of one year and the certifications...

Host mitochondrial association evolved in the human parasite Toxoplasma gondii via neofunctionalization of a gene duplicate

USDA-ARS?s Scientific Manuscript database

In Toxoplasma gondii, an intracellular parasite of humans and other warm-blooded animals, the ability to associate with host mitochondria (HMA) is driven by a locally expanded gene family that encodes multiple mitochondrial association factor 1 (MAF1) proteins. The importance of copy number in the e...

Observing and Deterring Social Cheating on College Exams

ERIC Educational Resources Information Center

Fendler, Richard J.; Yates, Michael C.; Godbey, Johnathan M.

2018-01-01

This research introduces a unique multiple choice exam design to observe and measure the degree to which students copy answers from their peers. Using data collected from the exam, an empirical experiment is conducted to determine whether random seat assignment deters cheating relative to a control group of students allowed to choose their seats.…

Copying Helps Novice Learners Build Orthographic Knowledge: Methods for Teaching Devanagari Akshara

ERIC Educational Resources Information Center

Bhide, Adeetee

2018-01-01

Hindi graphs, called akshara, are difficult to learn because of their visual complexity and large set of graphs. Akshara containing multiple consonants (complex akshara) are particularly difficult. In Hindi, complex akshara are formed by fusing individual consonantal graphs. Some complex akshara look similar to their component parts (transparent),…

Exit Exam as Academic Performance Indicator

ERIC Educational Resources Information Center

Al Ahmad, Mahmoud; Al Marzouqi, Ali H.; Hussien, Mousa

2014-01-01

This paper focuses on the impact of exit exams on different elements of the educational process, namely: curriculum development, students and instructors. A 50-question multiple-choice Exit Exam was prepared by Electrical Engineering (EE) faculty members covering a poll of questions from EE core courses. A copy of the Exit Exam applied during each…

Interactive comparison and remediation of collections of macromolecular structures.

PubMed

Moriarty, Nigel W; Liebschner, Dorothee; Klei, Herbert E; Echols, Nathaniel; Afonine, Pavel V; Headd, Jeffrey J; Poon, Billy K; Adams, Paul D

2018-01-01

Often similar structures need to be compared to reveal local differences throughout the entire model or between related copies within the model. Therefore, a program to compare multiple structures and enable correction any differences not supported by the density map was written within the Phenix framework (Adams et al., Acta Cryst 2010; D66:213-221). This program, called Structure Comparison, can also be used for structures with multiple copies of the same protein chain in the asymmetric unit, that is, as a result of non-crystallographic symmetry (NCS). Structure Comparison was designed to interface with Coot(Emsley et al., Acta Cryst 2010; D66:486-501) and PyMOL(DeLano, PyMOL 0.99; 2002) to facilitate comparison of large numbers of related structures. Structure Comparison analyzes collections of protein structures using several metrics, such as the rotamer conformation of equivalent residues, displays the results in tabular form and allows superimposed protein chains and density maps to be quickly inspected and edited (via the tools in Coot) for consistency, completeness and correctness. © 2017 The Protein Society.

Copy number variations of six and seven α-globin genes in a family with intermedia and major thalassemia phenotypes.

PubMed

Farashi, Samaneh; Vakili, Shadi; Faramarzi Garous, Negin; Ashki, Mehri; Imanian, Hashem; Azarkeivan, Azita; Najmabadi, Hossein

2015-10-01

Copy number variations in α-globin genes are results of unequal crossover between homologous segments in the α-globin gene cluster that misalign during the meiosis phase of the gametogenesis process. Reduction or augmentation of α-globin genes leads to imbalance of α/β chains in hemoglobin tetramer and consequently attenuate or worsen the β-thal clinical symptoms, respectively. Multiplications in α-globin genes have been found in some populations, justifying unexpected severe phenotype of β-thal carriers. Unexpected severe phenotype in the family members may result from coexistence of extra α-globin genes, which is an important factor in the causation of thalassemia intermedia and major in heterozygous β-thalassemia. We described different multiplications in α-globin locus in an Iranian family with one, two or three extra α-globin genes (ααα/αα, αααα/αα and αααα/ααα). The excess α-globin gene/genes cause increment in β/α chain imbalance and leads to worsening pathophysiology and clinical severity of β-thalassemia carriers.

Deterring watermark collusion attacks using signal processing techniques

NASA Astrophysics Data System (ADS)

Lemma, Aweke N.; van der Veen, Michiel

2007-02-01

Collusion attack is a malicious watermark removal attack in which the hacker has access to multiple copies of the same content with different watermarks and tries to remove the watermark using averaging. In the literature, several solutions to collusion attacks have been reported. The main stream solutions aim at designing watermark codes that are inherently resistant to collusion attacks. The other approaches propose signal processing based solutions that aim at modifying the watermarked signals in such a way that averaging multiple copies of the content leads to a significant degradation of the content quality. In this paper, we present signal processing based technique that may be deployed for deterring collusion attacks. We formulate the problem in the context of electronic music distribution where the content is generally available in the compressed domain. Thus, we first extend the collusion resistance principles to bit stream signals and secondly present experimental based analysis to estimate a bound on the maximum number of modified versions of a content that satisfy good perceptibility requirement on one hand and destructive averaging property on the other hand.

Elders' Experiences During Return Visits to the Emergency Department: A Phenomenographic Study in Taiwan.

PubMed

Han, Chin-Yen; Lin, Chun-Chih; Goopy, Suzanne; Hsiao, Ya-Chu; Barnard, Alan

Elders often experience multiple chronic diseases associated with frequent early return visits to emergency departments (EDs). There is limited knowledge of the experiences and concerns of elders during ED return visits. The purpose of the research was to explore the experiences of elders during ED return visits, with a view toward identifying factors that contribute to return visits. The qualitative approach of phenomenography was used. Data were collected at one ED in a 3,000-bed medical center in Taiwan. Inclusion criteria were aged 65 or above and return visits to the ED within 72 hours of discharge from an index ED visit. The seven steps of qualitative data analysis for a phenomenographic study were employed to develop understanding of participants' experiences. Thirty return-visit elders were interviewed in 2014. Four categories of description were established from the participants' accounts. These were "being tricked by ED staff," "doctor shopping," "a sign of impending death," and "feeling fatalistic." The outcome space of elders with early return visits to ED was characterized as "seeking the answer." Index ED visits are linked to return visits for Taiwanese elders through physiological, psychological, and social factors.

Internal cycle modeling and environmental assessment of multiple cycle consumer products.

PubMed

Tsiliyannis, C A

2012-01-01

Dynamic annual flow models incorporating consumer discard and usage loss and featuring deterministic and stochastic end-of-cycle (EOC) return by the consumer are developed for reused or remanufactured products (multiple cycle products, MCPs), including fast and slow cycling, short and long-lived products. It is shown that internal flows (reuse and overall consumption) increase proportionally to the dimensionless internal cycle factor (ICF) which is related to environmental impact reduction factors. The combined reuse/recycle (or cycle) rate is shown capable for shortcut, albeit effective, monitoring of environmental performance in terms of waste production, virgin material extraction and manufacturing impacts of all MCPs, a task, which physical variables (lifetime, cycling frequency, mean or total number of return trips) and conventional rates, via which environmental policy has been officially implemented (e.g. recycling rate) cannot accomplish. The cycle rate is shown to be an increasing (hyperbolic) function of ICF. The impact of the stochastic EOC return characteristics on total reuse and consumption flows, as well as on eco-performance, is assessed: symmetric EOC return has a small, positive effect on performance compared to deterministic, while early shifted EOC return is more beneficial. In order to be efficient, environmental policy should set higher minimum reuse targets for higher trippage MCPs. The results may serve for monitoring, flow accounting and comparative eco-assessment of MCPs. They may be useful in identifying reachable and efficient reuse/recycle targets for consumer products and in planning return via appropriate labelling and digital coding for enhancing environmental performance, while satisfying consumer demand. Copyright © 2011 Elsevier Ltd. All rights reserved.

Communicating with employers: experiences of occupational therapists treating people with musculoskeletal conditions.

PubMed

Coole, Carol; Birks, Emily; Watson, Paul J; Drummond, Avril

2014-09-01

Many employed people with musculoskeletal conditions rely on healthcare practitioners, including occupational therapists, for work-related advice and support. Good communication between healthcare practitioners and employers is considered vital in facilitating work retention and return to work. The purpose of this study was to explore the experiences of occupational therapists in communicating with patients' employers. Qualitative data were collected from the responses of occupational therapists to ten statements/open questions in a questionnaire survey of UK occupational therapists. Data were copied verbatim into word documents and analysed thematically. A total of 649 comments were made by 143 respondents. Five themes were identified that were associated with communicating with employers: patient-dependent; employer-dependent; therapist-dependent; extrinsic factors; methods of communication. This study has identified that communication between occupational therapists and employers is influenced by a number of factors, including those which are outside the therapists' control. These need to be acknowledged and addressed by therapists, their professional organisation, employers, commissioners, therapy service managers, educators and employees in order to support return-to-work and work retention of people with musculoskeletal conditions.

Basic principles of dental office logistics: organizing dental supplies and equipment for optimal accessibility.

PubMed

Mamoun, John

2012-01-01

To maximize office production, dentists should continuously perform treatment-related tasks throughout the workday. To this end, the office should logically organize and store dental instruments, disposables, materials, handpieces, and small equipment to optimize accessibility of these items at the moment when the dentist needs them. The office needs multiple copies of these items to prevent their inaccessibility during the workday due to breakdown, inventory depletion, or lack of a sterilized copy of the item when needed. Staff should know where all items are located in the office at all times to minimize the time needed to search for them. This article describes how to organize dental items in an office for optimal accessibility to the dentist during procedures.

Simultaneous and Sequential Integration by Cre/loxP Site-Specific Recombination in Saccharomyces cerevisiae.

PubMed

Choi, Ho-Jung; Kim, Yeon-Hee

2018-05-28

A Cre/ loxP -δ-integration system was developed to allow sequential and simultaneous integration of a multiple gene expression cassette in Saccharomyces cerevisiae . To allow repeated integrations, the reusable Candida glabrata MARKER ( CgMARKER ) carrying loxP sequences was used, and the integrated CgMARKER was efficiently removed by inducing Cre recombinase. The XYLP and XYLB genes encoding endoxylanase and β-xylosidase, respectively, were used as model genes for xylan metabolism in this system, and the copy number of these genes was increased to 15.8 and 16.9 copies/cell, respectively, by repeated integration. This integration system is a promising approach for the easy construction of yeast strains with enhanced metabolic pathways through multicopy gene expression.

Motivating medical information system performance by system quality, service quality, and job satisfaction for evidence-based practice.

PubMed

Chang, Ching-Sheng; Chen, Su-Yueh; Lan, Yi-Ting

2012-11-21

No previous studies have addressed the integrated relationships among system quality, service quality, job satisfaction, and system performance; this study attempts to bridge such a gap with evidence-based practice study. The convenience sampling method was applied to the information system users of three hospitals in southern Taiwan. A total of 500 copies of questionnaires were distributed, and 283 returned copies were valid, suggesting a valid response rate of 56.6%. SPSS 17.0 and AMOS 17.0 (structural equation modeling) statistical software packages were used for data analysis and processing. The findings are as follows: System quality has a positive influence on service quality (γ11= 0.55), job satisfaction (γ21= 0.32), and system performance (γ31= 0.47). Service quality (β31= 0.38) and job satisfaction (β32= 0.46) will positively influence system performance. It is thus recommended that the information office of hospitals and developers take enhancement of service quality and user satisfaction into consideration in addition to placing b on system quality and information quality when designing, developing, or purchasing an information system, in order to improve benefits and gain more achievements generated by hospital information systems.

Long interspersed nuclear elements (LINEs) show tissue-specific, mosaic genome and methylation-unrestricted, widespread expression of noncoding RNAs in somatic tissues of the rat

PubMed Central

Singh, Deepak K.; Rath, Pramod C.

2012-01-01

We report strong somatic and germ line expression of LINE RNAs in eight different tissues of rat by using a novel ~2.8 kb genomic PstI-LINE DNA (P1-LINE) isolated from the rat brain. P1-LINE is present in a 93 kb LINE-SINE-cluster in sub-telomeric region of chromosome 12 (12p12) and as multiple truncated copies interspersed in all rat chromosomes. P1-LINEs occur as inverted repeats at multiple genomic loci in tissue-specific and mosaic patterns. P1-LINE RNAs are strongly expressed in brain, liver, lungs, heart, kidney, testes, spleen and thymus into large to small heterogeneous RNAs (~5.0 to 0.2 kb) in tissue-specific and dynamic patterns in individual rats. P1-LINE DNA is strongly methylated at CpG-dinucleotides in most genomic copies in all the tissues and weakly hypomethylated in few copies in some tissues. Small (700–75 nt) P1-LINE RNAs expressed in all tissues may be possible precursors for small regulatory RNAs (PIWI-interacting/piRNAs) bioinformatically derived from P1-LINE. The strong and dynamic expression of LINE RNAs from multiple chromosomal loci and the putative piRNAs in somatic tissues of rat under normal physiological conditions may define functional chromosomal domains marked by LINE RNAs as long noncoding RNAs (lncRNAs) unrestricted by DNA methylation. The tissue-specific, dynamic RNA expression and mosaic genomic distribution of LINEs representing a steady-state genomic flux of retrotransposon RNAs suggest for biological role of LINE RNAs as long ncRNAs and small piRNAs in mammalian tissues independent of their cellular fate for translation, reverse-transcription and retrotransposition. This may provide evolutionary advantages to LINEs and mammalian genomes. PMID:23064113

One Novel Multiple-Target Plasmid Reference Molecule Targeting Eight Genetically Modified Canola Events for Genetically Modified Canola Detection.

PubMed

Li, Zhuqing; Li, Xiang; Wang, Canhua; Song, Guiwen; Pi, Liqun; Zheng, Lan; Zhang, Dabing; Yang, Litao

2017-09-27

Multiple-target plasmid DNA reference materials have been generated and utilized as good substitutes of matrix-based reference materials in the analysis of genetically modified organisms (GMOs). Herein, we report the construction of one multiple-target plasmid reference molecule, pCAN, which harbors eight GM canola event-specific sequences (RF1, RF2, MS1, MS8, Topas 19/2, Oxy235, RT73, and T45) and a partial sequence of the canola endogenous reference gene PEP. The applicability of this plasmid reference material in qualitative and quantitative PCR assays of the eight GM canola events was evaluated, including the analysis of specificity, limit of detection (LOD), limit of quantification (LOQ), and performance of pCAN in the analysis of various canola samples, etc. The LODs are 15 copies for RF2, MS1, and RT73 assays using pCAN as the calibrator and 10 genome copies for the other events. The LOQ in each event-specific real-time PCR assay is 20 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and PEP assays are between 91% and 97%, and the squared regression coefficients (R 2 ) are all higher than 0.99. The quantification bias values varied from 0.47% to 20.68% with relative standard deviation (RSD) from 1.06% to 24.61% in the quantification of simulated samples. Furthermore, 10 practical canola samples sampled from imported shipments in the port of Shanghai, China, were analyzed employing pCAN as the calibrator, and the results were comparable with those assays using commercial certified materials as the calibrator. Concluding from these results, we believe that this newly developed pCAN plasmid is one good candidate for being a plasmid DNA reference material in the detection and quantification of the eight GM canola events in routine analysis.

Unique properties of multiple tandem copies of the M26 recombination hotspot in mitosis and meiosis in Schizosaccharomyces pombe.

PubMed

Steiner, Walter W; Recor, Chelsea L; Zakrzewski, Bethany M

2016-11-15

The M26 hotspot of the fission yeast Schizosaccharomyces pombe is one of the best-characterized eukaryotic hotspots of recombination. The hotspot requires a seven bp sequence, ATGACGT, that serves as a binding site for the Atf1-Pcr1 transcription factor, which is also required for activity. The M26 hotspot is active in meiosis but not mitosis and is active in some but not all chromosomal contexts and not on a plasmid. A longer palindromic version of M26, ATGACGTCAT, shows significantly greater activity than the seven bp sequence. Here, we tested whether the properties of the seven bp sequence were also true of the longer sequence by placing one, two, or three copies of the sequence into the ade6 gene, where M26 was originally discovered. These constructs were tested for activity when located on a plasmid or on a chromosome in mitosis and meiosis. We found that two copies of the 10bp M26 motif on a chromosome were significantly more active for meiotic recombination than one, but no further increase was observed with three copies. However, three copies of M26 on a chromosome created an Atf1-dependent mitotic recombination hotspot. When located on a plasmid, M26 also appears to behave as a mitotic recombination hotspot; however, this behavior most likely results from Atf1-dependent inter-allelic complementation between the plasmid and chromosomal ade6 alleles. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis on the correlation between temperature and discharge characteristic of cloud-to-ground lightning discharge plasma with multiple return strokes

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

Qu Haiyan; Chang Zhengshi; Yuan Ping

2011-01-15

The spectra of cloud-to-ground lightning with multiple return strokes have been obtained by using a slitless spectrograph on the Chinese Tibet plateau. Combining the spectra with synchronous electrical information, the correlation among spectral properties, channel temperatures and discharge characteristics, and thermal effects of current is discussed for the first time. The results show that the channel plasma temperature varies significantly from stroke to stroke within a given flash, and the total intensity of spectra is directly proportional to the amplitude of electric field change. Moreover, the positive correlation has been confirmed between the channel plasma temperature and the thermal effectmore » which shows the effect of the electric current accumulation. It is inferred that the total intensity of the spectra should be directly proportional to the intensity of discharge current, and channel temperature is correlated positively with the energy transmission in one return stroke.« less

Characteristics of return stroke electric fields produced by lightning flashes at distances of 1 to 15 kilometers

NASA Technical Reports Server (NTRS)

Hopf, CH.

1991-01-01

Electric field derivative signals from single and multiple lightning strokes are presented. For about 25 pct. of all acquired waveforms, produced by return strokes, stepped leaders or intracloud discharges, type and distance of the signal source are known from the observations by an all sky video camera system. The analysis of the electric field derivative waveforms in the time domain shows a significant difference in the impulse width between return stroke signals and those of stepped leaders and intracloud discharges. In addition, the computed amplitude density spectrum of return stroke waveforms lies by a factor of 10 above that of stepped leaders and intracloud discharges in the frequency range from 50 to 500 kHz.

Regression modeling and mapping of coniferous forest basal area and tree density from discrete-return lidar and multispectral data

Treesearch

Andrew T. Hudak; Nicholas L. Crookston; Jeffrey S. Evans; Michael K. Falkowski; Alistair M. S. Smith; Paul E. Gessler; Penelope Morgan

2006-01-01

We compared the utility of discrete-return light detection and ranging (lidar) data and multispectral satellite imagery, and their integration, for modeling and mapping basal area and tree density across two diverse coniferous forest landscapes in north-central Idaho. We applied multiple linear regression models subset from a suite of 26 predictor variables derived...

Return to work after severe multiple injuries: a multidimensional approach on status 1 and 2 years postinjury.

PubMed

Soberg, Helene Lundgaard; Finset, Arnstein; Bautz-Holter, Erik; Sandvik, Leiv; Roise, Olav

2007-02-01

The assessment of factors associated with return to work (RTW) after multiple trauma is important in trauma research. Goals in rehabilitation should comprise RTW. The purpose of this study was to examine the RTW rate and which factors predicted RTW for patients with severe multiple injuries using a prospective cohort design. In all, 100 patients with a New Injury Severity Score (NISS) >15, aged 18 to 67 years and admitted to a trauma referral center, were included starting January 2002 through June 2003. Outcomes were assessed 6 weeks after discharge and 1 and 2 years postinjury. Instruments were the Brief Approach/Avoidance Coping Questionnaire, Multidimensional Health Locus of Control, Short Form-36, the World Health Organization Disability Assessment Schedule II, and a cognitive function scale (COG). Mean age was 34.5 years (SD 13.5), 83% were male, and 66% were blue-collar workers. Mean NISS was 35.1 (SD 12.7). At 1 year, 28% achieved complete RTW, 43% at 2 years. Mean time back to work was 12.8 months (SD 5.9). Differences between the RTW and not complete RTW (NRTW) groups concerned personal and demographic variables, and physical and psychosocial functioning. Survival analysis showed that risk factors for NRTW were lower education, length of stay in hospital/rehabilitation >20 weeks, and low social functioning shortly after the return home. The majority of the patients had not completely returned to work 2 years postinjury. Demographic and injury related factors and social functioning were significant predictors of RTW status.

Use of a multi-level mixed methods approach to study the effectiveness of a primary care progressive return to activity protocol after acute mild traumatic brain injury/concussion in the military.

PubMed

Gregory, Emma; West, Therese A; Cole, Wesley R; Bailie, Jason M; McCulloch, Karen L; Ettenhofer, Mark L; Cecchini, Amy; Qashu, Felicia M

2017-01-01

The large number of U.S. service members diagnosed with concussion/mild traumatic brain injury each year underscores the necessity for clear and effective clinical guidance for managing concussion. Relevant research continues to emerge supporting a gradual return to pre-injury activity levels without aggravating symptoms; however, available guidance does not provide detailed standards for this return to activity process. To fill this gap, the Defense and Veterans Brain Injury Center released a recommendation for primary care providers detailing a step-wise return to unrestricted activity during the acute phase of concussion. This guidance was developed in collaboration with an interdisciplinary group of clinical, military, and academic subject matter experts using an evidence-based approach. Systematic evaluation of the guidance is critical to ensure positive patient outcomes, to discover barriers to implementation by providers, and to identify ways to improve the recommendation. Here we describe a multi-level, mixed-methods approach to evaluate the recommendation incorporating outcomes from both patients and providers. Procedures were developed to implement the study within complex but ecologically-valid settings at multiple military treatment facilities and operational medical units. Special consideration was given to anticipated challenges such as the frequent movement of military personnel, selection of appropriate design and measures, study implementation at multiple sites, and involvement of multiple service branches (Army, Navy, and Marine Corps). We conclude by emphasizing the need to consider contemporary approaches for evaluating the effectiveness of clinical guidance. Copyright © 2016 Elsevier Inc. All rights reserved.

A Case for More Multiple Scattering Lidar from Space: Analysis of Four LITE Pulses Returned from a Marine Stratocumulus Deck

NASA Technical Reports Server (NTRS)

Davis, Anthony B.; Winker, David M.

2011-01-01

Outline: (1) Signal Physics for Multiple-Scattering Cloud Lidar, (2) SNR Estimation (3) Cloud Property Retrievals (3a) several techniques (3b) application to Lidar-In-space Technology Experiment (LITE) data (3c) relation to O2 A-band

Multiple-Matrix Sampling: A Technique for Maximizing the Effectiveness of Lengthy Survey Instruments.

ERIC Educational Resources Information Center

Shemick, John M.

1983-01-01

In a project to identify and verify professional competencies for beginning industrial education teachers, researchers found a 173-item questionnaire unwieldy. Using multiple-matrix sampling, they distributed subsets of items to respondents, resulting in adequate returns as well as duplication, postage, and time savings. (SK)

Earth observation taken by the Expedition 43 crew

NASA Image and Video Library

2015-05-15

ISS043E194350 (05/15/2015) --- NASA astronaut Scott Kelly on the International Space Station tweeted this image out of an Earth observation image as part of his Space Geo trivia contest. Scott tweeted this comment and clue: "#SpaceGeo Four international borders in one photo from the International @Space_Station. Name them"! Two winners! Congrats to @TeacherWithTuba & @PC101!. The correct answer is :#SpaceGeo A: #Denmark #Norway #Sweden #Germany & #Poland. The winners will receive an autographed copy of this image when Scott returns to Earth in March 2016. Learn more about #SpaceGeo and play along every Wednesday for your chance to win: www.nasa.gov/feature/where-over-the-world-is-astronaut-sc...

Wilderness experience in Rocky Mountain National Park 2002: Report to RMNP

USGS Publications Warehouse

Schuster, Elke; Johnson, S. Shea; Taylor, Jonathan G.

2004-01-01

The social science technique of Visitor Employed Photography [VEP] was used to obtain information from visitors about wilderness experiences. Visitors were selected at random from Park-designated wilderness trails, in proportion to their use, and asked to participate in the survey. Respondents were given single-use, 10-exposure cameras and photo-log diaries to record experiences. A total of 293 cameras were distributed, with a response rate of 87%. Following the development of the photos, a copy of the photos, two pertinent pages from the photo-log, and a follow-up survey were mailed to respondents. Fifty six percent of the follow-up surveys were returned. Findings from the two surveys were analyzed and compared.

Implementation of the Recommendations of the Presidential Commission on the Space Shuttle Challenger Accident

NASA Technical Reports Server (NTRS)

1987-01-01

This final status report describes the actions taken by NASA in response to the recommendations of the Presidential Commission on the Space Shuttle Challenger Accident (Mission 51-L). The Commission recommendations and NASA's responses to them are summarized in the Executive Summary, which is accompanied by a schedule showing significant program milestones. A detailed discussion of the activities undertaken by NASA to implement each of the nine Commission recommendations is included and other related NASA actions required for safe return to flight are discussed. A copy of the interim plan submitted to the President one year ago and other significant reference documents are included as appendixes.

Rey-Osterrieth Complex Figure - copy and immediate recall: Normative data for the Latin American Spanish speaking adult population.

PubMed

Rivera, D; Perrin, P B; Morlett-Paredes, A; Galarza-Del-Angel, J; Martínez, C; Garza, M T; Saracho, C P; Rodríguez, W; Rodríguez-Agudelo, Y; Rábago, B; Aliaga, A; Schebela, S; Luna, M; Longoni, M; Ocampo-Barba, N; Fernández, E; Esenarro, L; García-Egan, P; Arango-Lasprilla, J C

2015-01-01

To generate normative data on the Rey-Osterrieth Complex Figure Test (ROCF) across 11 countries in Latin America, with country-specific adjustments for gender, age, and education, where appropriate. The sample consisted of 3,977 healthy adults who were recruited from Argentina, Bolivia, Chile, Cuba, El Salvador, Guatemala, Honduras, Mexico, Paraguay, Peru, and, Puerto Rico. Each subject was administered the ROCF as part of a larger neuropsychological battery. A standardized five-step statistical procedure was used to generate the norms. The final multiple linear regression models explained 7-34% of the variance in ROCF copy scores and 21-41% of the variance in immediate recall scores. Although t-tests showed significant differences between men and women on ROCF copy and immediate recall scores, none of the countries had an effect size larger than 0.3. As a result, gender-adjusted norms were not generated. The present study is the first to create norms for the ROCF in Latin America. As a result, this study will have important implications for the formation and practice of neuropsychology in this region.

Characterization of a complex context containing mecA but lacking genes encoding cassette chromosome recombinases in Staphylococcus haemolyticus

PubMed Central

2013-01-01

Background Methicillin resistance determinant mecA is generally transferred by SCCmec elements. However, the mecA gene might not be carried by a SCCmec in a Staphylococcus haemolyticus clinical isolate, WCH1, as no cassette chromosome recombinase genes were detected. Therefore, the genetic context of mecA in WCH1 was investigated. Results A 40-kb region containing mecA was obtained from WCH1, bounded by orfX at one end and several orfs of S. haemolyticus core chromosome at the other. This 40-kb region was very complex in structure with multiple genetic components that appeared to have different origins. For instance, the 3.7-kb structure adjacent to orfX was almost identical to that on the chromosome of Staphylococcus epidermidis RP62a but was absent from S. haemolyticus JCSC1435. Terminal inverted repeats of SCC were found but no ccr genes could be detected. mecA was bracketed by two copies of IS431, which was flanked by 8-bp direct target repeat sequence (DR). Conclusions The presence of 8-bp DR suggests that the two copies of IS431 might have formed a composite transposon for mobilizing mecA. This finding is of significance as multiple copies of IS431 are commonly present in the contexts of mecA, which might have the potential to form various composite transposons that could mediate the mobilization of mecA. This study also provides an explanation for the absence of ccr in some staphylococci isolates carrying mecA. PMID:23521926

Characterization of a complex context containing mecA but lacking genes encoding cassette chromosome recombinases in Staphylococcus haemolyticus.

PubMed

Zong, Zhiyong

2013-03-22

Methicillin resistance determinant mecA is generally transferred by SCCmec elements. However, the mecA gene might not be carried by a SCCmec in a Staphylococcus haemolyticus clinical isolate, WCH1, as no cassette chromosome recombinase genes were detected. Therefore, the genetic context of mecA in WCH1 was investigated. A 40-kb region containing mecA was obtained from WCH1, bounded by orfX at one end and several orfs of S. haemolyticus core chromosome at the other. This 40-kb region was very complex in structure with multiple genetic components that appeared to have different origins. For instance, the 3.7-kb structure adjacent to orfX was almost identical to that on the chromosome of Staphylococcus epidermidis RP62a but was absent from S. haemolyticus JCSC1435. Terminal inverted repeats of SCC were found but no ccr genes could be detected. mecA was bracketed by two copies of IS431, which was flanked by 8-bp direct target repeat sequence (DR). The presence of 8-bp DR suggests that the two copies of IS431 might have formed a composite transposon for mobilizing mecA. This finding is of significance as multiple copies of IS431 are commonly present in the contexts of mecA, which might have the potential to form various composite transposons that could mediate the mobilization of mecA. This study also provides an explanation for the absence of ccr in some staphylococci isolates carrying mecA.

Multiple bidirectional initiations and terminations of transcription in the Marek's disease virus long repeat regions.

PubMed Central

Chen, X B; Velicer, L F

1991-01-01

Marek's disease is an oncogenic disease of chickens caused by a herpesvirus, Marek's disease virus (MDV). Serial in vitro passage of pathogenic MDV results in amplification of a 132-bp direct repeat in the MDV genome's TRL and IRL repeat regions and loss of tumorigenicity. This led to the hypothesis that upon such expansion, one or more tumor-inducing genes fail to be expressed. In this report a group of cDNAs mapping in the expanded regions were isolated from a pathogenic MDV strain in which the 132-bp direct repeat number was found to range between one and seven. Partial cDNA sequencing and S1 nuclease protection analysis revealed that the corresponding transcripts are either initiated or terminated within or near the expanded regions at multiple sites in both rightward and leftward directions. Furthermore, each 132-bp repeat contains one TATA box and two polyadenylation consensus sequences in each direction. These RNAs contain a partial copy or one or more full copies of the 132-bp direct repeat at either their 5' or 3' end. Northern (RNA) blot analysis showed that the majority of transcripts are 1.8 kb in size, while the minor species range in size from 0.67 to 3.1 kb. Together, these data raise the possibility that the 132-bp direct repeat, and indirectly its copy number, may be involved in the regulation of transcriptional initiation and termination and therefore in the generation of four groups of transcripts from the TRL and IRL, although this remains to be demonstrated. Images PMID:1850022

SNPitty: An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data.

PubMed

van Riet, Job; Krol, Niels M G; Atmodimedjo, Peggy N; Brosens, Erwin; van IJcken, Wilfred F J; Jansen, Maurice P H M; Martens, John W M; Looijenga, Leendert H; Jenster, Guido; Dubbink, Hendrikus J; Dinjens, Winand N M; van de Werken, Harmen J G

2018-03-01

Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets of interest. SNPitty was validated for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, SNPitty is demonstrated in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations, or any combination thereof in regions or genes of interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. On the basis of these data, the authors demonstrate that SNPitty is robust and user friendly in a wide range of diagnostic scenarios. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Comparative Genomic Analysis Reveals Multiple Long Terminal Repeats, Lineage-Specific Amplification, and Frequent Interelement Recombination for Cassandra Retrotransposon in Pear (Pyrus bretschneideri Rehd.)

PubMed Central

Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

2014-01-01

Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. PMID:24899073

Effect of temperature shock and inventory surprises on natural gas and heating oil futures returns.

PubMed

Hu, John Wei-Shan; Hu, Yi-Chung; Lin, Chien-Yu

2014-01-01

The aim of this paper is to examine the impact of temperature shock on both near-month and far-month natural gas and heating oil futures returns by extending the weather and storage models of the previous study. Several notable findings from the empirical studies are presented. First, the expected temperature shock significantly and positively affects both the near-month and far-month natural gas and heating oil futures returns. Next, significant temperature shock has effect on both the conditional mean and volatility of natural gas and heating oil prices. The results indicate that expected inventory surprises significantly and negatively affects the far-month natural gas futures returns. Moreover, volatility of natural gas futures returns is higher on Thursdays and that of near-month heating oil futures returns is higher on Wednesdays than other days. Finally, it is found that storage announcement for natural gas significantly affects near-month and far-month natural gas futures returns. Furthermore, both natural gas and heating oil futures returns are affected more by the weighted average temperature reported by multiple weather reporting stations than that reported by a single weather reporting station.

Effect of Temperature Shock and Inventory Surprises on Natural Gas and Heating Oil Futures Returns

PubMed Central

Hu, John Wei-Shan; Lin, Chien-Yu

2014-01-01

The aim of this paper is to examine the impact of temperature shock on both near-month and far-month natural gas and heating oil futures returns by extending the weather and storage models of the previous study. Several notable findings from the empirical studies are presented. First, the expected temperature shock significantly and positively affects both the near-month and far-month natural gas and heating oil futures returns. Next, significant temperature shock has effect on both the conditional mean and volatility of natural gas and heating oil prices. The results indicate that expected inventory surprises significantly and negatively affects the far-month natural gas futures returns. Moreover, volatility of natural gas futures returns is higher on Thursdays and that of near-month heating oil futures returns is higher on Wednesdays than other days. Finally, it is found that storage announcement for natural gas significantly affects near-month and far-month natural gas futures returns. Furthermore, both natural gas and heating oil futures returns are affected more by the weighted average temperature reported by multiple weather reporting stations than that reported by a single weather reporting station. PMID:25133233

Sample Return from Small Solar System Bodies

NASA Astrophysics Data System (ADS)

Orgel, L.; A'Hearn, M.; Bada, J.; Baross, J.; Chapman, C.; Drake, M.; Kerridge, J.; Race, M.; Sogin, M.; Squyres, S.

With plans for multiple sample return missions in the next decade, NASA requested guidance from the National Research Council's SSB on how to treat samples returned from solar system bodies such as planetary satellites, asteroids and comets. A special Task Group assessed the potential for a living entity to be included in return samples from various bodies as well as the potential for large scale effects if such an entity were inadvertently introduced into the Earth's biosphere. The Group also assessed differences among solar system bodies, identified investigations that could reduce uncertainty about the bodies, and considered risks of returned samples compared to natural influx of material to the Earth in the form of interplanetary dust particles, meteorites and other small impactors. The final report (NRC, 1998) provides a decision making framework for future missions and makes recommendations on how to handle samples from different planetary satellites and primitive solar system bodies

Tecnologias mas nuevas para la seguridad escolar (Newer Technologies for School Security). ERIC Digest.

ERIC Educational Resources Information Center

Schneider, Tod

This digest in Spanish describes several technologies that can be used to control access to, and improve surveillance of, school grounds. Access can be controlled by using "smart" cards to control keyed entries. Many schools have problems with multiple copies of keys, and these card systems are integrated with computer software that…

Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages

USDA-ARS?s Scientific Manuscript database

Fungi that have the enzymes cyanase and carbonic anhydrase show a limited capacity to detoxify cyanate, a fungicide employed by both plants and humans. Here, we describe a novel two-gene cluster that comprises duplicated cyanase and carbonic anhydrase copies, which we name the CCA gene cluster, trac...

75 FR 82402 - Proposed Consolidated Vaccine Information Materials for Multiple Infant Vaccines

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-30

... number of shots your baby needs by combining several vaccines in one shot. These combination vaccines are... to any patient (or to the parent or legal representative in the case of a child) receiving vaccines... United States who intends to administer one of these covered vaccines is required to provide copies of...

Using Mouse Models to Explore Genotype-Phenotype Relationship in Down Syndrome

ERIC Educational Resources Information Center

Salehi, Ahmad; Faizi, Mehrdad; Belichenko, Pavel V.; Mobley, William C.

2007-01-01

Down Syndrome (DS) caused by trisomy 21 is characterized by a variety of phenotypes and involves multiple organs. Sequencing of human chromosome 21 (HSA21) and subsequently of its orthologues on mouse chromosome 16 have created an unprecedented opportunity to explore the complex relationship between various DS phenotypes and the extra copy of…

24 CFR 1710.15 - Regulatory exemption-multiple site subdivision-determination required.

Code of Federal Regulations, 2010 CFR

2010-04-01

... non-waivable provision in bold face type (which must be distinguished from the type used for the rest... contract or other document by requiring a specific type of notice or by requiring that notice be given at a... font. A copy of the acknowledgement will be maintained by the developer for three years and will be...

Better than Optimal by Taking a Limit?

ERIC Educational Resources Information Center

Betounes, David

2012-01-01

Designing an optimal Norman window is a standard calculus exercise. How much more difficult (or interesting) is its generalization to deploying multiple semicircles along the head (or along head and sill, or head and jambs)? What if we use shapes beside semi-circles? As the number of copies of the shape increases and the optimal Norman windows…

Genetic Structures of Copy Number Variants Revealed by Genotyping Single Sperm

PubMed Central

Luo, Minjie; Cui, Xiangfeng; Fredman, David; Brookes, Anthony J.; Azaro, Marco A.; Greenawalt, Danielle M.; Hu, Guohong; Wang, Hui-Yun; Tereshchenko, Irina V.; Lin, Yong; Shentu, Yue; Gao, Richeng; Shen, Li; Li, Honghua

2009-01-01

Background Copy number variants (CNVs) occupy a significant portion of the human genome and may have important roles in meiotic recombination, human genome evolution and gene expression. Many genetic diseases may be underlain by CNVs. However, because of the presence of their multiple copies, variability in copy numbers and the diploidy of the human genome, detailed genetic structure of CNVs cannot be readily studied by available techniques. Methodology/Principal Findings Single sperm samples were used as the primary subjects for the study so that CNV haplotypes in the sperm donors could be studied individually. Forty-eight CNVs characterized in a previous study were analyzed using a microarray-based high-throughput genotyping method after multiplex amplification. Seventeen single nucleotide polymorphisms (SNPs) were also included as controls. Two single-base variants, either allelic or paralogous, could be discriminated for all markers. Microarray data were used to resolve SNP alleles and CNV haplotypes, to quantitatively assess the numbers and compositions of the paralogous segments in each CNV haplotype. Conclusions/Significance This is the first study of the genetic structure of CNVs on a large scale. Resulting information may help understand evolution of the human genome, gain insight into many genetic processes, and discriminate between CNVs and SNPs. The highly sensitive high-throughput experimental system with haploid sperm samples as subjects may be used to facilitate detailed large-scale CNV analysis. PMID:19384415

Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

PubMed Central

Clouse, Ronald M.; Linchangco, Gregorio V.; Kerr, Alexander M.; Reid, Robert W.; Janies, Daniel A.

2015-01-01

Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms with variants from protostomes and chordates. We used multiple sequence alignment with various stringencies of alignment quality to cull highly divergent sequences and then conducted phylogenetic analyses using both nucleotide and amino acid sequences. Phylogenetic hypotheses consistently recovered TIMPs as diversifying in the ancestral deuterostome and these early lineages continuing to diversify in echinoderms. The four vertebrate TIMPs diversified from a single copy in the ancestral chordate, all other copies being lost. Consistent with greater MCT needs owing to body wall liquefaction, evisceration, autotomy and reproduction by fission, holothuroids had significantly more TIMPs and higher read depths per contig. Ten cysteine residues, an HPQ binding site and several other residues were conserved in at least 70% of all TIMPs. The conservation of binding sites and the placement of echinoderm TIMPs involved in MCT modification suggest that ECM regulation remains the primary function of TIMP genes, although within this role there are a large number of specialized copies. PMID:27017967

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies.

PubMed

Pohl, Nélida; Sison-Mangus, Marilou P; Yee, Emily N; Liswi, Saif W; Briscoe, Adriana D

2009-05-13

The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1 and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3-35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7-13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5-26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84-113 million years for the divergence of all butterfly families. These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.

A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2

PubMed Central

Didion, John P.; Morgan, Andrew P.; Clayshulte, Amelia M.-F.; Mcmullan, Rachel C.; Yadgary, Liran; Petkov, Petko M.; Bell, Timothy A.; Gatti, Daniel M.; Crowley, James J.; Hua, Kunjie; Aylor, David L.; Bai, Ling; Calaway, Mark; Chesler, Elissa J.; French, John E.; Geiger, Thomas R.; Gooch, Terry J.; Garland, Theodore; Harrill, Alison H.; Hunter, Kent; McMillan, Leonard; Holt, Matt; Miller, Darla R.; O'Brien, Deborah A.; Paigen, Kenneth; Pan, Wenqi; Rowe, Lucy B.; Shaw, Ginger D.; Simecek, Petr; Sullivan, Patrick F.; Svenson, Karen L; Weinstock, George M.; Threadgill, David W.; Pomp, Daniel; Churchill, Gary A.; Pardo-Manuel de Villena, Fernando

2015-01-01

Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 – 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2WSBdel1) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system. PMID:25679959

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

PubMed Central

2014-01-01

Background Of the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by the RepeatMasker program. RepeatMasker generates several output files, including the .out file, which provides annotations for all detected repeats in a query sequence. However, a remaining challenge consists of identifying the different copies of TEs that correspond to the identified hits. This step is essential for any evolutionary/comparative analysis of the different copies within a family. Different possibilities can lead to multiple hits corresponding to a unique copy of an element, such as the presence of large deletions/insertions or undetermined bases, and distinct consensus corresponding to a single full-length sequence (like for long terminal repeat (LTR)-retrotransposons). These possibilities must be taken into account to determine the exact number of TE copies. Results We have developed a perl tool that parses the RepeatMasker .out file to better determine the number and positions of TE copies in the query sequence, in addition to computing quantitative information for the different families. To determine the accuracy of the program, we tested it on several RepeatMasker .out files corresponding to two organisms (Drosophila melanogaster and Homo sapiens) for which the TE content has already been largely described and which present great differences in genome size, TE content, and TE families. Conclusions Our tool provides access to detailed information concerning the TE content in a genome at the family level from the .out file of RepeatMasker. This information includes the exact position and orientation of each copy, its proportion in the query sequence, and its quality compared to the reference element. In addition, our tool allows a user to directly retrieve the sequence of each copy and obtain the same detailed information at the family level when a local library with incomplete TE class/subclass information was used with RepeatMasker. We hope that this tool will be helpful for people working on the distribution and evolution of TEs within genomes.

Hard Copy Market Overview

NASA Astrophysics Data System (ADS)

Testan, Peter R.

1987-04-01

A number of Color Hard Copy (CHC) market drivers are currently indicating strong growth in the use of CHC technologies for the business graphics marketplace. These market drivers relate to product, software, color monitors and color copiers. The use of color in business graphics allows more information to be relayed than is normally the case in a monochrome format. The communicative powers of full-color computer generated output in the business graphics application area will continue to induce end users to desire and require color in their future applications. A number of color hard copy technologies will be utilized in the presentation graphics arena. Thermal transfer, ink jet, photographic and electrophotographic technologies are all expected to be utilized in the business graphics presentation application area in the future. Since the end of 1984, the availability of color application software packages has grown significantly. Sales revenue generated by business graphics software is expected to grow at a compound annual growth rate of just over 40 percent to 1990. Increased availability of packages to allow the integration of text and graphics is expected. Currently, the latest versions of page description languages such as Postscript, Interpress and DDL all support color output. The use of color monitors will also drive the demand for color hard copy in the business graphics market place. The availability of higher resolution screens is allowing color monitors to be easily used for both text and graphics applications in the office environment. During 1987, the sales of color monitors are expected to surpass the sales of monochrome monitors. Another major color hard copy market driver will be the color copier. In order to take advantage of the communications power of computer generated color output, multiple copies are required for distribution. Product introductions of a new generation of color copiers is now underway with additional introductions expected during 1987. The color hard copy market continues to be in a state of constant change, typical of any immature market. However, much of the change is positive. During 1985, the color hard copy market generated 1.2 billion. By 1990, total market revenue is expected to exceed 5.5 billion. The business graphics CHC application area is expected to grow at a compound annual growth rate greater than 40 percent to 1990.

Quantifying and modeling long-range cross correlations in multiple time series with applications to world stock indices

NASA Astrophysics Data System (ADS)

Wang, Duan; Podobnik, Boris; Horvatić, Davor; Stanley, H. Eugene

2011-04-01

We propose a modified time lag random matrix theory in order to study time-lag cross correlations in multiple time series. We apply the method to 48 world indices, one for each of 48 different countries. We find long-range power-law cross correlations in the absolute values of returns that quantify risk, and find that they decay much more slowly than cross correlations between the returns. The magnitude of the cross correlations constitutes “bad news” for international investment managers who may believe that risk is reduced by diversifying across countries. We find that when a market shock is transmitted around the world, the risk decays very slowly. We explain these time-lag cross correlations by introducing a global factor model (GFM) in which all index returns fluctuate in response to a single global factor. For each pair of individual time series of returns, the cross correlations between returns (or magnitudes) can be modeled with the autocorrelations of the global factor returns (or magnitudes). We estimate the global factor using principal component analysis, which minimizes the variance of the residuals after removing the global trend. Using random matrix theory, a significant fraction of the world index cross correlations can be explained by the global factor, which supports the utility of the GFM. We demonstrate applications of the GFM in forecasting risks at the world level, and in finding uncorrelated individual indices. We find ten indices that are practically uncorrelated with the global factor and with the remainder of the world indices, which is relevant information for world managers in reducing their portfolio risk. Finally, we argue that this general method can be applied to a wide range of phenomena in which time series are measured, ranging from seismology and physiology to atmospheric geophysics.

Quantifying and modeling long-range cross correlations in multiple time series with applications to world stock indices.

PubMed

Wang, Duan; Podobnik, Boris; Horvatić, Davor; Stanley, H Eugene

2011-04-01

We propose a modified time lag random matrix theory in order to study time-lag cross correlations in multiple time series. We apply the method to 48 world indices, one for each of 48 different countries. We find long-range power-law cross correlations in the absolute values of returns that quantify risk, and find that they decay much more slowly than cross correlations between the returns. The magnitude of the cross correlations constitutes "bad news" for international investment managers who may believe that risk is reduced by diversifying across countries. We find that when a market shock is transmitted around the world, the risk decays very slowly. We explain these time-lag cross correlations by introducing a global factor model (GFM) in which all index returns fluctuate in response to a single global factor. For each pair of individual time series of returns, the cross correlations between returns (or magnitudes) can be modeled with the autocorrelations of the global factor returns (or magnitudes). We estimate the global factor using principal component analysis, which minimizes the variance of the residuals after removing the global trend. Using random matrix theory, a significant fraction of the world index cross correlations can be explained by the global factor, which supports the utility of the GFM. We demonstrate applications of the GFM in forecasting risks at the world level, and in finding uncorrelated individual indices. We find ten indices that are practically uncorrelated with the global factor and with the remainder of the world indices, which is relevant information for world managers in reducing their portfolio risk. Finally, we argue that this general method can be applied to a wide range of phenomena in which time series are measured, ranging from seismology and physiology to atmospheric geophysics.

Impact of reproductive efficiency over time and mare financial value on economic returns among Thoroughbred mares in central Kentucky.

PubMed

Bosh, K A; Powell, D; Neibergs, J S; Shelton, B; Zent, W

2009-12-01

There have been no studies reporting the impact of reproductive efficiency and mare financial value on economic returns. To explore the economic consequences of differences in reproductive efficiency over time in the Thoroughbred mare. Complete production records for 1176 mares were obtained. Production history and drift in foaling date were calculated. Multiple logistic regression was used to identify factors influencing the probability of producing a registered foal in 2005. The 'net present value' and 'internal rate of return' were calculated for economic scenarios involving different initial mare financial values, levels of reproductive efficiency, and durations of investment. Among mares that did not produce a foal every year (63%), the mean time before failing to produce a registered foal was 3.4 years. The majority of mares drifted later in their foaling dates in subsequent foaling seasons. Increasing mare age, foaling after 1st April, needing to be mated multiple times during the season, and producing a lower number of foals in continuous sequence during previous years decreased the probability of producing a registered foal. Over a 7 year investment period, live foals must be produced in all but one year to yield a positive financial return. Profitability was highest among mares of greatest financial value. Mares are long-term investments due to the extended period before there is a return on the investment. Improving our understanding of mare, stallion and management factors that affect the likelihood of producing a live foal are critical to ensuring a positive financial return. Additional work is needed to test the robustness of the study's conclusions when the cost and revenue assumptions are varied. This information can assist in assessing mare profitability and developing management strategies to maximise profitability.

Biochemical analysis of DNA polymerase η fidelity in the presence of replication protein A.

PubMed

Suarez, Samuel C; Toffton, Shannon M; McCulloch, Scott D

2014-01-01

DNA polymerase η (pol η) synthesizes across from damaged DNA templates in order to prevent deleterious consequences like replication fork collapse and double-strand breaks. This process, termed translesion synthesis (TLS), is an overall positive for the cell, as cells deficient in pol η display higher mutation rates. This outcome occurs despite the fact that the in vitro fidelity of bypass by pol η alone is moderate to low, depending on the lesion being copied. One possible means of increasing the fidelity of pol η is interaction with replication accessory proteins present at the replication fork. We have previously utilized a bacteriophage based screening system to measure the fidelity of bypass using purified proteins. Here we report on the fidelity effects of a single stranded binding protein, replication protein A (RPA), when copying the oxidative lesion 7,8-dihydro-8-oxo-guanine(8-oxoG) and the UV-induced cis-syn thymine-thymine cyclobutane pyrimidine dimer (T-T CPD). We observed no change in fidelity dependent on RPA when copying these damaged templates. This result is consistent in multiple position contexts. We previously identified single amino acid substitution mutants of pol η that have specific effects on fidelity when copying both damaged and undamaged templates. In order to confirm our results, we examined the Q38A and Y52E mutants in the same full-length construct. We again observed no difference when RPA was added to the bypass reaction, with the mutant forms of pol η displaying similar fidelity regardless of RPA status. We do, however, observe some slight effects when copying undamaged DNA, similar to those we have described previously. Our results indicate that RPA by itself does not affect pol η dependent lesion bypass fidelity when copying either 8-oxoG or T-T CPD lesions.

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

PubMed Central

Mayer, Melanie G.; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J.

2015-01-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains´ pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for dauer regulation. We discuss the consequences of the novel vs. fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition. PMID:26087034

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

PubMed

Mayer, Melanie G; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J

2015-06-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for dauer regulation. We discuss the consequences of the novel vs. fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition.

An Alternative Humans to Mars Approach: Reducing Mission Mass with Multiple Mars Flyby Trajectories and Minimal Capability Investments

NASA Technical Reports Server (NTRS)

Whitley, Ryan J.; Jedrey, Richard; Landau, Damon; Ocampo, Cesar

2015-01-01

Mars flyby trajectories and Earth return trajectories have the potential to enable lower- cost and sustainable human exploration of Mars. Flyby and return trajectories are true minimum energy paths with low to zero post-Earth departure maneuvers. By emplacing the large crew vehicles required for human transit on these paths, the total fuel cost can be reduced. The traditional full-up repeating Earth-Mars-Earth cycler concept requires significant infrastructure, but a Mars only flyby approach minimizes mission mass and maximizes opportunities to build-up missions in a stepwise manner. In this paper multiple strategies for sending a crew of 4 to Mars orbit and back are examined. With pre-emplaced assets in Mars orbit, a transit habitat and a minimally functional Mars taxi, a complete Mars mission can be accomplished in 3 SLS launches and 2 Mars Flyby's, including Orion. While some years are better than others, ample opportunities exist within a given 15-year Earth-Mars alignment cycle. Building up a mission cadence over time, this approach can translate to Mars surface access. Risk reduction, which is always a concern for human missions, is mitigated by the use of flybys with Earth return (some of which are true free returns) capability.

THOR: Cloud Thickness from Off beam Lidar Returns

NASA Technical Reports Server (NTRS)

Cahalan, Robert F.; McGill, Matthew; Kolasinski, John; Varnai, Tamas; Yetzer, Ken

2004-01-01

Conventional wisdom is that lidar pulses do not significantly penetrate clouds having optical thickness exceeding about tau = 2, and that no returns are detectable from more than a shallow skin depth. Yet optically thicker clouds of tau much greater than 2 reflect a larger fraction of visible photons, and account for much of Earth s global average albedo. As cloud layer thickness grows, an increasing fraction of reflected photons are scattered multiple times within the cloud, and return from a diffuse concentric halo that grows around the incident pulse, increasing in horizontal area with layer physical thickness. The reflected halo is largely undetected by narrow field-of-view (FoV) receivers commonly used in lidar applications. THOR - Thickness from Off-beam Returns - is an airborne wide-angle detection system with multiple FoVs, capable of observing the diffuse halo, detecting wide-angle signal from which physical thickness of optically thick clouds can be retrieved. In this paper we describe the THOR system, demonstrate that the halo signal is stronger for thicker clouds, and validate physical thickness retrievals for clouds having z > 20, from NASA P-3B flights over the Department of Energy/Atmospheric Radiation Measurement/Southern Great Plains site, using the lidar, radar and other ancillary ground-based data.

Prevalence and Determinants of Bullying Among Health Care Workers in Portugal.

PubMed

Norton, Pedro; Costa, Viviana; Teixeira, Joel; Azevedo, Ana; Roma-Torres, António; Amaro, Joana; Cunha, Liliana

2017-05-01

Bullying is defined as systematic exposure to humiliation as well as hostile and violent behaviors against one or more individuals. These behaviors are a serious, growing problem, which affects a significant proportion of health care professionals. To support the hospital's risk management policy, a cross-sectional study was undertaken to determine the prevalence of bullying in this institution and identify the determinants of bullying. Bullying was measured using the Negative Acts Questionnaire-Revised, Portuguese version (NAQ-R), a self-administered tool. The questionnaire was made available in digital format on the hospital's internal network (Intranet) and in hard copy; questionnaires were returned via nonidentified internal mail addressed to the occupational health unit or deposited in suggestion boxes located throughout the hospital. Multiple questionnaire delivery methods guaranteed data anonymity and confidentiality. The prevalence of bullying in this hospital was 8% (95% confidence interval [CI] = [6.2, 10.2]). Reported bullying was predominantly vertical and more frequently occurring among nurses, clerical staff, and health care assistants (12.5%, 7.6%, 6.4%, respectively; p = .005). After adjusting for gender, age, occupation, type of contract, and work schedule, only type of contract was significantly associated with bullying in the workplace; the risk of bullying was twice as high among government employees compared to workers with indefinite duration employment contracts ( p = .038). This study identified a high prevalence of bullying among health professionals; hence a program to prevent and control this phenomenon was implemented in this institution.

Factors associated with playing football after anterior cruciate ligament reconstruction in female football players.

PubMed

Fältström, A; Hägglund, M; Kvist, J

2016-11-01

This study investigated whether player-related factors (demographic, personality, or psychological factors) or the characteristics of the anterior cruciate ligament (ACL) injury were associated with the return to playing football in females after ACL reconstruction (ACLR). We also compared current knee function, knee related quality of life and readiness to return to sport between females who returned to football and those who had not returned. Females who sustained a primary ACL rupture while playing football and underwent ACLR 6-36 months ago were eligible. Of the 460 contacted, 274 (60%) completed a battery of questionnaires, and 182 were included a median of 18 months (IQR 13) after ACLR. Of these, 94 (52%) returned to football and were currently playing, and 88 (48%) had not returned. Multiple logistic regression analysis identified two factors associated with returning to football: short time between injury and ACLR (0-3 months, OR 5.6; 3-12 months OR 4.7 vs reference group > 12 months) and high motivation. Current players showed higher ratings for current knee function, knee-related quality of life, and psychological readiness to return to sport (P < 0.001). Undergoing ACLR sooner after injury and high motivation to return to sports may impact a player's return to football after ACLR. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Common Peroneal Nerve Palsy with Multiple-Ligament Knee Injury and Distal Avulsion of the Biceps Femoris Tendon

PubMed Central

Oshima, Takeshi; Nakase, Junsuke; Numata, Hitoaki; Takata, Yasushi

2015-01-01

A multiple-ligament knee injury that includes posterolateral corner (PLC) disruption often causes palsy of the common peroneal nerve (CPN), which occurs in 44% of cases with PLC injury and biceps femoris tendon rupture or avulsion of the fibular head. Approximately half of these cases do not show functional recovery. This case report aims to present a criteria-based approach to the operation and postoperative management of CPN palsy that resulted from a multiple-ligament knee injury in a 22-year-old man that occurred during judo. We performed a two-staged surgery. The first stage was to repair the injuries to the PLC and biceps femoris. The second stage involved anterior cruciate ligament reconstruction. The outcomes were excellent, with a stable knee, excellent range of motion, and improvement in the palsy. The patient was able to return to judo competition 27 weeks after the injury. To the best of our knowledge, this is the first case report describing a return to sports following CPN palsy with multiple-ligament knee injury. PMID:26064740

Social Learning Strategies: Bridge-Building between Fields.

PubMed

Kendal, Rachel L; Boogert, Neeltje J; Rendell, Luke; Laland, Kevin N; Webster, Mike; Jones, Patricia L

2018-07-01

While social learning is widespread, indiscriminate copying of others is rarely beneficial. Theory suggests that individuals should be selective in what, when, and whom they copy, by following 'social learning strategies' (SLSs). The SLS concept has stimulated extensive experimental work, integrated theory, and empirical findings, and created impetus to the social learning and cultural evolution fields. However, the SLS concept needs updating to accommodate recent findings that individuals switch between strategies flexibly, that multiple strategies are deployed simultaneously, and that there is no one-to-one correspondence between psychological heuristics deployed and resulting population-level patterns. The field would also benefit from the simultaneous study of mechanism and function. SLSs provide a useful vehicle for bridge-building between cognitive psychology, neuroscience, and evolutionary biology. Copyright © 2018. Published by Elsevier Ltd.

Integrated Molecular Characterization of Uterine Carcinosarcoma.

PubMed

Cherniack, Andrew D; Shen, Hui; Walter, Vonn; Stewart, Chip; Murray, Bradley A; Bowlby, Reanne; Hu, Xin; Ling, Shiyun; Soslow, Robert A; Broaddus, Russell R; Zuna, Rosemary E; Robertson, Gordon; Laird, Peter W; Kucherlapati, Raju; Mills, Gordon B; Weinstein, John N; Zhang, Jiashan; Akbani, Rehan; Levine, Douglas A

2017-03-13

We performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified. Copyright © 2017 Elsevier Inc. All rights reserved.

Low copy numbers of complement C4 and homozygous deficiency of C4A may predispose to severe disease and earlier disease onset in patients with systemic lupus erythematosus.

PubMed

Jüptner, M; Flachsbart, F; Caliebe, A; Lieb, W; Schreiber, S; Zeuner, R; Franke, A; Schröder, J O

2018-04-01

Objectives Low copy numbers and deletion of complement C4 genes are potent risk factors for systemic lupus erythematosus (SLE). However, it is not known whether this genetic association affects the clinical outcome. We investigated C4 copy number variation and its relationship to clinical and serological features in a Northern European lupus cohort. Methods We genotyped the C4 gene locus using polymerase chain reaction (PCR)-based TaqMan assays in 169 patients with SLE classified according to the 1997 revised American College of Rheumatology (ACR) criteria and in 520 matched controls. In the patient group the mean C4 serum protein concentrations nephelometrically measured during a 12-month period prior to genetic analysis were compared to C4 gene copy numbers. Severity of disease was classified according to the intensity of the immunosuppressive regimens applied and compared to C4 gene copy numbers, too. In addition, we performed a TaqMan based analysis of three lupus-associated single-nucleotide polymorphisms (SNPs) located inside the major histocompatibility complex (MHC) to investigate the independence of complement C4 in association with SLE. Results Homozygous deficiency of the C4A isotype was identified as the strongest risk factor for SLE (odds ratio (OR) = 5.329; p = 7.7 × 10 -3 ) in the case-control comparison. Moreover, two copies of total C4 were associated with SLE (OR = 3.699; p = 6.8 × 10 -3 ). C4 serum levels were strongly related to C4 gene copy numbers in patients, the mean concentration ranging from 0.110 g/l (two copies) to 0.256 g/l (five to six copies; p = 4.9 × 10 -6 ). Two copies of total C4 and homozygous deletion of C4A were associated with a disease course requiring cyclophosphamide therapy (OR = 4.044; p = 0.040 and OR = 5.798; p = 0.034, respectively). Homozygous deletion of C4A was associated with earlier onset of SLE (median 24 vs. 34 years; p = 0.019) but not significant after correction for multiple testing. SNP analysis revealed a significant association of HLA-DRB1*0301 with SLE (OR = 2.231; p = 1.33 × 10 -5 ). Conclusions Our findings confirm the important role of complement C4 genes in the development of SLE. Beyond the impact on the susceptibility for lupus, C4 copy numbers may be related to earlier onset and a more severe course of the disease. The association of homozygous deletion of C4A and SLE is accompanied by the presence of HLA-DRB1*0301 without a proven pathophysiological mechanism.

Efficient Memory Access with NumPy Global Arrays using Local Memory Access

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

Daily, Jeffrey A.; Berghofer, Dan C.

This paper discusses the work completed working with Global Arrays of data on distributed multi-computer systems and improving their performance. The tasks completed were done at Pacific Northwest National Laboratory in the Science Undergrad Laboratory Internship program in the summer of 2013 for the Data Intensive Computing Group in the Fundamental and Computational Sciences DIrectorate. This work was done on the Global Arrays Toolkit developed by this group. This toolkit is an interface for programmers to more easily create arrays of data on networks of computers. This is useful because scientific computation is often done on large amounts of datamore » sometimes so large that individual computers cannot hold all of it. This data is held in array form and can best be processed on supercomputers which often consist of a network of individual computers doing their computation in parallel. One major challenge for this sort of programming is that operations on arrays on multiple computers is very complex and an interface is needed so that these arrays seem like they are on a single computer. This is what global arrays does. The work done here is to use more efficient operations on that data that requires less copying of data to be completed. This saves a lot of time because copying data on many different computers is time intensive. The way this challenge was solved is when data to be operated on with binary operations are on the same computer, they are not copied when they are accessed. When they are on separate computers, only one set is copied when accessed. This saves time because of less copying done although more data access operations were done.« less

Measures to facilitate the reintegration of returning migrant workers: international experiences.

PubMed

Lohrmann, R

1988-06-01

Bilateral and multilateral measures implemented to assist migrants who return to their country of origin have been designed to respond to a number of different but specific situations. 2 bilateral agreements are briefly described: 1) an agreement between the Federal Republic of Germany and the Republic of Turkey signed in the early 1970s, and 2) an agreement between France and Algeria signed in 1980. 3 different types of multilateral activities are described: 1) the operation of the so-called Return of Talent program by the Intergovernmental Committee for Migration, 2) the Transfer of KNow-how Through Expatriate Nationals program of the UN Development Programme, and 3) the elaboration of a model machinery on return migration by the Organization for Economic Cooperation and Development. While the 1st 2 activities are operational programs, by which annually between 1000-2000 professionals are assisted in their permanent return to or temporary sojourn in their developing countries of origin, with the financial support of both the developed and the developing countries concerned, the 3rd initiative is a conceptual effort aimed at assisting governments to implement policy measures designed to make return migration commensurate with national development goals. 3 recent proposals include 1) the proposal for an international labor compensatory facility, 2) an international fund for vocational training, and 3) an international fund for manpower resources. A common factor shared by all these programs is that they have all involved on 1 side industrial receiving countries which feel themselves obliged to observe a number of principles guaranteed by law and which govern employment conditions and working relations. The reintegration measures implemented or proposed in cooperation with them have been adopted in full consideration of the prevailing standards of these countries, as different as they may be from 1 country to another. A common consideration has been that the returning migrant should reintegrate in his country of origin as far as possible in conditions allowing the returnee to attain self-sufficiency and social security coverage. However, this underlying context does not necessarily prevail in all world regions where different forms of labor migration take place. Therefore the measures experienced in the relationship of specific countries cannot be easily copied for implementation in other countries. Multilateral measures benefited a rather limited number of individuals only, in many instances skilled and highly skilled migrants.

Mars Sample Return - Launch and Detection Strategies for Orbital Rendezvous

NASA Technical Reports Server (NTRS)

Woolley, Ryan C.; Mattingly, Richard L.; Riedel, Joseph E.; Sturm, Erick J.

2011-01-01

This study sets forth conceptual mission design strategies for the ascent and rendezvous phase of the proposed NASA/ESA joint Mars Sample Return Campaign. The current notional mission architecture calls for the launch of an acquisition/cache rover in 2018, an orbiter with an Earth return vehicle in 2022, and a fetch rover and ascent vehicle in 2024. Strategies are presented to launch the sample into a coplanar orbit with the Orbiter which facilitate robust optical detection, orbit determination, and rendezvous. Repeating ground track orbits exist at 457 and 572 km which provide multiple launch opportunities with similar geometries for detection and rendezvous.

Mars Sample Return: Launch and Detection Strategies for Orbital Rendezvous

NASA Technical Reports Server (NTRS)

Woolley, Ryan C.; Mattingly, Richard L.; Riedel, Joseph E.; Sturm, Erick J.

2011-01-01

This study sets forth conceptual mission design strategies for the ascent and rendezvous phase of the proposed NASA/ESA joint Mars Sample Return Campaign. The current notional mission architecture calls for the launch of an acquisition/ caching rover in 2018, an Earth return orbiter in 2022, and a fetch rover with ascent vehicle in 2024. Strategies are presented to launch the sample into a nearly coplanar orbit with the Orbiter which would facilitate robust optical detection, orbit determination, and rendezvous. Repeating ground track orbits existat 457 and 572 km which would provide multiple launch opportunities with similar geometries for detection and rendezvous.

Multiple output power supply circuit for an ion engine with shared upper inverter

NASA Technical Reports Server (NTRS)

Cardwell, Jr., Gilbert I. (Inventor); Phelps, Thomas K. (Inventor)

2001-01-01

A power supply circuit for an ion engine suitable for a spacecraft is coupled to a bus having a bus input and a bus return. The power supply circuit has a first primary winding of a first transformer. An upper inverter circuit is coupled to the bus input and the first primary winding. The power supply circuit further includes a first lower inverter circuit coupled to the bus return and the first primary winding. The second primary winding of a second transformer is coupled to the upper inverter circuit. A second lower inverter circuit is coupled to the bus return and the second primary winding.

The role of copy and paste function in orthopedic trauma progress notes.

PubMed

Winn, Wesley; Shakir, Irshad A; Israel, Heidi; Cannada, Lisa K

2017-01-01

The electronic medical record (EMR) is standard in institutions. While there is not concern for legibility of notes and access to charts, there is an ease of copy and paste for daily notes. This may not lead to accurate portrayal of patient's status. Our purpose was to evaluate the use of copy and paste functions in daily notes of patients with injuries at high risk for complications. IRB approval was obtained for a retrospective review. Inclusion criteria included patients aged 18 and older treated at our Level 1 Trauma Center after implementation of Epic Systems Corporation, Verona, WI, USA. Those who were surgically treated for bicondylar tibial plateau fracture, or open tibial shaft fracture type I or II were included. Manual comparison of daily progress to the previous day's note was carried out. Comparisons were made by evaluating the subjective, objective, and plan portions of the notes, coded nominally using 1 for a change 0 for remaining the same. 38 patients' charts were reviewed during a 10-month (July 2012-April 2013) period, and the average length of stay was 12 days (range: 2-35). A total of 418 notes were compared. The overall average of copied data was 85% daily. In the subjective portion, 85-97% of the data was copied on a daily basis and 71-92% of the data was copied within the objective portion of the notes. There were 15 medical complications necessitating intervention. Of these medical complications, the note the day after the complication reflected the event in 10 out of 15, or 70%, of the complications. Thus 5, or 30%, of the patients did not have notes reflecting the complication ( p  < 0.05). There were 7 complications related to the injuries: 4 cases of compartment syndrome, 1 case of foot drop, representing a change in neurologic status, an amputation, and a wound infection treated with antibiotics. Four of the 7 complications (57%) were not reflected in the notes the following day after the complication ( p  < 0.05). There were 54 planned returns to the operating room for procedures, yet 30 of the 54 (56%) notes regarding planned surgical procedures notes did not accurately report the plan for surgery ( p  < 0.05). There were 4 patients with unplanned trips to the operating room and 3 of the notes (75%) did not reflect this ( p  < 0.05). Twelve patients (32%) did not have notes accurately reflecting discharge plans and/or destination ( p  < 0.05). Our results demonstrated widespread use of copy and paste function. We encourage evaluation of the charts by comparing notes to check and a plan to minimize this practice. There needs to be consistent note writing guidelines and appropriate templates used. This will decrease the inaccuracies in the chart and provide a clear picture of the patient, their injuries, and current status.

Photocopying and the Law: A Guide for Librarians and Teachers and Other Suppliers and Users of Photocopies of Copyright Work.

ERIC Educational Resources Information Center

Australian Copyright Council, Sydney.

Some possible uses to which the photocopying of copyright works can be put under the Copyright Act of 1968 are explored. The topics considered are "substantial part," fair dealing in relation to research, private study and published criticisms or reviews, photocopying limitations, illustrations and multiple copies. The law, as…

Molecular Surveillance for Multidrug-Resistant Plasmodium falciparum, Cambodia

PubMed Central

Shah, Naman K.; Alker, Alisa P.; Sem, Rithy; Susanti, Agustina Ika; Muth, Sinuon; Maguire, Jason D.; Duong, Socheat; Ariey, Frederic; Meshnick, Steven R.

2008-01-01

We conducted surveillance for multidrug-resistant Plasmodium falciparum in Cambodia during 2004–2006 by assessing molecular changes in pfmdr1. The high prevalence of isolates with multiple pfmdr1 copies found in western Cambodia near the Thai border, where artesunate–mefloquine therapy failures occur, contrasts with isolates from eastern Cambodia, where this combination therapy remains highly effective. PMID:18826834

Networking CD-ROMs: The Decision Maker's Guide to Local Area Network Solutions.

ERIC Educational Resources Information Center

Elshami, Ahmed M.

In an era when patrons want access to CD-ROM resources but few libraries can afford to buy multiple copies, CD-ROM local area networks (LANs) are emerging as a cost-effective way to provide shared access. To help librarians make informed decisions, this manual offers information on: (1) the basics of LANs, a "local area network primer";…

catcher: A Software Program to Detect Answer Copying in Multiple-Choice Tests Based on Nominal Response Model

ERIC Educational Resources Information Center

Kalender, Ilker

2012-01-01

catcher is a software program designed to compute the [omega] index, a common statistical index for the identification of collusions (cheating) among examinees taking an educational or psychological test. It requires (a) responses and (b) ability estimations of individuals, and (c) item parameters to make computations and outputs the results of…

A New Integrative Conjugative Element Occurs in Mycoplasma agalactiae as Chromosomal and Free Circular Forms

PubMed Central

Marenda, Marc; Barbe, Valérie; Gourgues, Géraldine; Mangenot, Sophie; Sagne, Evelyne; Citti, Christine

2006-01-01

An integrative conjugative element, ICEA, was characterized in Mycoplasma agalactiae strain 5632, in which it occurs as multiple chromosomal copies and as a free circular form. The distribution of ICEA sequences in M. agalactiae strains and their occurrence in Mycoplasma bovis suggest the spreading of the element within or between species. PMID:16707706

Copyfitting Instructor: A Computer-Assisted Instructional Aid for the Dirtiest Job in Advertising Design and Production Courses.

ERIC Educational Resources Information Center

Wesson, David A.

Copyfitting is probably the least exciting portion of any course that deals with design and production of print advertising. Students find the transformation of manuscript copy into set type difficult to visualize. The math, though no more than multiplication and division, seems insurmountable to some--probably because the entities such as points,…

Using Pinochle to Motivate the Restricted Combinations with Repetitions Problem

ERIC Educational Resources Information Center

Gorman, Patrick S.; Kunkel, Jeffrey D.; Vasko, Francis J.

2011-01-01

A standard example used in introductory combinatoric courses is to count the number of five-card poker hands possible from a straight deck of 52 distinct cards. A more interesting problem is to count the number of distinct hands possible from a Pinochle deck in which there are multiple, but obviously limited, copies of each type of card (two…

Arnica (Asteraceae) phylogeny revisited using RPB2: complex patterns and multiple d-paralogues.

PubMed

Ekenäs, Catarina; Heidari, Nahid; Andreasen, Katarina

2012-08-01

The region coding for the second largest subunit of RNA polymerase II (RPB2) was explored for resolving interspecific relationships in Arnica and lower level taxa in general. The region between exons 17 and 23 was cloned and sequenced for 33 accessions of Arnica and four outgroup taxa. Three paralogues of the RPB2-d copy (RPB2-dA, B and C) were detected in Arnica and outgroup taxa, indicating that the duplications must have occurred before the divergence of Arnica. Parsimony and Bayesian analyses of separate alignments of the three copies reveal complex patterns in Arnica, likely reflecting a history of lineage sorting in combination with apomixis, polyploidization, and possibly hybridization. Cloned sequences of some taxa do not form monophyletic clades within paralogues, but form multiple strongly supported clades with sequences of other taxa. Some well supported groups are present in more than one paralogue and many groups are in line with earlier hypotheses regarding interspecific relationships within the genus. Low levels of homoplasy in combination with relatively high sequence variation indicates that the introns of the RPB2 region could be suitable for phylogenetic studies in low level taxonomy. Copyright © 2012. Published by Elsevier Inc.

KNQ1, a Kluyveromyces lactis gene encoding a transmembrane protein, may be involved in iron homeostasis.

PubMed

Marchi, Emmanuela; Lodi, Tiziana; Donnini, Claudia

2007-08-01

The original purpose of the experiments described in this article was to identify, in the biotechnologically important yeast Kluyveromyces lactis, gene(s) that are potentially involved in oxidative protein folding within the endoplasmic reticulum (ER), which often represents a bottleneck for heterologous protein production. Because treatment with the membrane-permeable reducing agent dithiothreitol inhibits disulfide bond formation and mimics the reducing effect that the normal transit of folding proteins has in the ER environment, the strategy was to search for genes that conferred higher levels of resistance to dithiothreitol when present in multiple copies. We identified a gene (KNQ1) encoding a drug efflux permease for several toxic compounds that in multiple copies conferred increased dithiothreitol resistance. However, the KNQ1 product is not involved in the excretion of dithiothreitol or in recombinant protein secretion. We generated a knq1 null mutant, and showed that both overexpression and deletion of the KNQ1 gene resulted in increased resistance to dithiothreitol. KNQ1 amplification and deletion resulted in enhanced transcription of iron transport genes, suggesting, for the membrane-associated protein Knq1p, a new, unexpected role in iron homeostasis on which dithiothreitol tolerance may depend.

Two methods for measuring Bell nonlocality via local unitary invariants of two-qubit systems in Hong-Ou-Mandel interferometers

NASA Astrophysics Data System (ADS)

Bartkiewicz, Karol; Chimczak, Grzegorz

2018-01-01

We describe a direct method to experimentally determine local two-qubit invariants by performing interferometric measurements on multiple copies of a given two-qubit state. We use this framework to analyze two different kinds of two-qubit invariants of Makhlin and Jing et al. These invariants allow us to fully reconstruct any two-qubit state up to local unitaries. We demonstrate that measuring three invariants is sufficient to find, e.g., the optimal Bell inequality violation. These invariants can be measured with local or nonlocal measurements. We show that the nonlocal strategy that follows from Makhlin's invariants is more resource efficient than local strategy following from the invariants of Jing et al. To measure all of the Makhlin's invariants directly one needs to use both two-qubit singlets and three-qubit W -state projections on multiple copies of the two-qubit state. This problem is equivalent to a coordinate system handedness measurement. We demonstrate that these three-qubit measurements can be performed by utilizing Hong-Ou-Mandel interference, which gives significant speedup in comparison to the classical handedness measurement. Finally, we point to potential applications of our results in quantum secret sharing.

Unified quantum no-go theorems and transforming of quantum pure states in a restricted set

NASA Astrophysics Data System (ADS)

Luo, Ming-Xing; Li, Hui-Ran; Lai, Hong; Wang, Xiaojun

2017-12-01

The linear superposition principle in quantum mechanics is essential for several no-go theorems such as the no-cloning theorem, the no-deleting theorem and the no-superposing theorem. In this paper, we investigate general quantum transformations forbidden or permitted by the superposition principle for various goals. First, we prove a no-encoding theorem that forbids linearly superposing of an unknown pure state and a fixed pure state in Hilbert space of a finite dimension. The new theorem is further extended for multiple copies of an unknown state as input states. These generalized results of the no-encoding theorem include the no-cloning theorem, the no-deleting theorem and the no-superposing theorem as special cases. Second, we provide a unified scheme for presenting perfect and imperfect quantum tasks (cloning and deleting) in a one-shot manner. This scheme may lead to fruitful results that are completely characterized with the linear independence of the representative vectors of input pure states. The upper bounds of the efficiency are also proved. Third, we generalize a recent superposing scheme of unknown states with a fixed overlap into new schemes when multiple copies of an unknown state are as input states.

Genome Wide Search for Biomarkers to Diagnose Yersinia Infections.

PubMed

Kalia, Vipin Chandra; Kumar, Prasun

2015-12-01

Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.

Techniques for Computing the DFT Using the Residue Fermat Number Systems and VLSI

NASA Technical Reports Server (NTRS)

Truong, T. K.; Chang, J. J.; Hsu, I. S.; Pei, D. Y.; Reed, I. S.

1985-01-01

The integer complex multiplier and adder over the direct sum of two copies of a finite field is specialized to the direct sum of the rings of integers modulo Fermat numbers. Such multiplications and additions can be used in the implementation of a discrete Fourier transform (DFT) of a sequence of complex numbers. The advantage of the present approach is that the number of multiplications needed for the DFT can be reduced substantially over the previous approach. The architectural designs using this approach are regular, simple, expandable and, therefore, naturally suitable for VLSI implementation.

EBR-II and TREAT Digitization Project

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

Griffith, George W.; Rabiti, Cristian

2015-09-01

Digitizing the technical drawings for EBR-II and TREAT provides multiple benefits. Moving the scanned or hard copy drawings to modern 3-D CAD (Computer Aided Drawing) format saves data that could be lost over time. The 3-D drawings produce models that can interface with other drawings to make complex assemblies. The 3-D CAD format can also include detailed material properties and parametric coding that can tie critical dimensions together allowing easier modification. Creating the new files from the old drawings has found multiple inconsistencies that are being flagged or corrected improving understanding of the reactor(s).

Duel between an ASAT with Multiple Kill Vehicles and a Space-Based Weapons Platform with Kinetic Energy Weapons

DTIC Science & Technology

1986-01-01

b~l~l Ec B-J COPYl OF 2 COPIES AD-A241 820 �liJiil I~ I III 111 r11 III lii II - IDA MEMORANDUM REPORT M-144 DUEL BETWEEN AN ASAT WITH MULTIPLE...20301-7100 ELEMENT NO. NO. NO. ACC3SSION NO. _____ ____ ____ ____ ____ _ ____ _ _T-3__187 I1I TITLE (include S*CuHWl CWia cetlonVi Duel Between an ASAT...neceuaiy andi identd by b~lock number) iA ,mathematical model is described for a duel beltween a ground-based anti-satellite (ASAT) and a space-based

Lightning channel current persists between strokes

NASA Astrophysics Data System (ADS)

Wendel, JoAnna

2014-09-01

The usual cloud-to-ground lightning occurs when a large negative charge contained in a "stepped leader" travels down toward the Earth's surface. It then meets a positive charge that comes up tens of meters from the ground, resulting in a powerful neutralizing explosion that begins the first return stroke of the lightning flash. The entire flash lasts only a few hundred milliseconds, but during that time, multiple subsequent stroke-return stroke sequences usually occur.

Detailed assessment of gene activation levels by multiple hypoxia-responsive elements under various hypoxic conditions.

PubMed

Takeuchi, Yasuto; Inubushi, Masayuki; Jin, Yong-Nan; Murai, Chika; Tsuji, Atsushi B; Hata, Hironobu; Kitagawa, Yoshimasa; Saga, Tsuneo

2014-12-01

HIF-1/HRE pathway is a promising target for the imaging and the treatment of intractable malignancy (HIF-1; hypoxia-inducible factor 1, HRE; hypoxia-responsive element). The purposes of our study are: (1) to assess the gene activation levels resulting from various numbers of HREs under various hypoxic conditions, (2) to evaluate the bidirectional activity of multiple HREs, and (3) to confirm whether multiple HREs can induce gene expression in vivo. Human colon carcinoma HCT116 cells were transiently transfected by the constructs containing a firefly luciferase reporter gene and various numbers (2, 4, 6, 8, 10, and 12) of HREs (nHRE+, nHRE-). The relative luciferase activities were measured under various durations of hypoxia (6, 12, 18, and 24 h), O2 concentrations (1, 2, 4, 8, and 16 %), and various concentrations of deferoxamine mesylate (20, 40, 80, 160, and 320 µg/mL growth medium). The bidirectional gene activation levels by HREs were examined in the constructs (dual-luc-nHREs) containing firefly and Renilla luciferase reporter genes at each side of nHREs. Finally, to test whether the construct containing 12HRE and the NIS reporter gene (12HRE-NIS) can induce gene expression in vivo, SPECT imaging was performed in a mouse xenograft model. (1) gene activation levels by HREs tended to increase with increasing HRE copy number, but a saturation effect was observed in constructs with more than 6 or 8 copies of an HRE, (2) gene activation levels by HREs increased remarkably during 6-12 h of hypoxia, but not beyond 12 h, (3) gene activation levels by HREs decreased with increasing O2 concentrations, but could be detected even under mild hypoxia at 16 % O2, (4) the bidirectionally proportional activity of the HRE was confirmed regardless of the hypoxic severity, and (5) NIS expression driven by 12 tandem copies of an HRE in response to hypoxia could be visualized on in vivo SPECT imaging. The results of this study will help in the understanding and assessment of the activity of multiple HREs under hypoxia and become the basis for hypoxia-targeted imaging and therapy in the future.

Dynamics of breast milk HIV-1 RNA with unilateral mastitis or abscess.

PubMed

Semrau, Katherine; Kuhn, Louise; Brooks, Daniel R; Cabral, Howard; Sinkala, Moses; Kankasa, Chipepo; Thea, Donald M; Aldrovandi, Grace M

2013-03-01

Mastitis and abscess in HIV-infected women increase the risk of breastfeeding transmission of HIV. Guidelines encourage women to stop breastfeeding on the affected breast and feed on the contralateral breast. However, impact of breast pathology on breast milk HIV dynamics is unknown. HIV RNA was quantified in 211 breast milk samples collected before, during, and after a clinical mastitis or an abscess diagnosis from 38 HIV-infected women participating in a Zambian breastfeeding study. HIV RNA quantity was compared between affected and unaffected breasts over time using generalized estimating equation models. A sample of 115 women without breast pathology was selected as a control group. In the affected breast, breast milk HIV RNA quantity increased from the pre- to during-pathology period by log(10) 0.45 copies per milliliter [95% confidence interval (CI): 0.16 to 0.74], and after symptom resolution, HIV RNA levels were no different from prepathology levels (log10 -0.04 copies per milliliter 95% CI: -0.33 to 0.25). In the contralateral, unaffected breast, HIV RNA quantity did not significantly increase (log(10) 0.15 copies per milliliter, 95% CI: -0.41 to 0.10). Increase was more marked in women with abscess or with a greater number of mastitis symptoms. HIV RNA was not significantly different between affected and unaffected women, except at the time of diagnosis. Breast milk HIV RNA increased modestly in the affected breast with unilateral mastitis or abscess and returned to prepathology levels with symptom resolution. Contralateral HIV RNA was not affected. Results support guidelines encouraging feeding from the contralateral breast to minimize the risk of HIV transmission associated with unilateral breast pathology.

Dynamics of breast milk HIV-1 RNA with unilateral mastitis or abscess

PubMed Central

Semrau, Katherine; Kuhn, Louise; Brooks, Daniel R.; Cabral, Howard; Sinkala, Moses; Kankasa, Chipepo; Thea, Donald M.; Aldrovandi, Grace M.

2013-01-01

Background Mastitis and abscess in HIV-infected women increase risk of breastfeeding transmission of HIV. Guidelines encourage women to stop breastfeeding on the affected breast and feed on the contralateral breast. However, impact of breast pathology on breast milk HIV dynamics is unknown. Methods HIV RNA was quantified in 211 breast milk samples collected before, during and after a clinical mastitis or abscess diagnosis from 38 HIV-infected women participating in a Zambian breastfeeding study. HIV RNA quantity was compared between affected and unaffected breasts over time using generalized estimating equation models. A sample of 115 women without breast pathology was selected as a control group. Results In the affected breast, breast milk HIV RNA quantity increased from the pre- to during-pathology period by log10 0.45 copies/mL (95% CI: 0.16, 0.74) and after symptom resolution, HIV RNA levels were no different from pre-pathology levels (log10 -0.04 copies/mL 95%CI: -0.33, 0.25). In the contralateral unaffected breast, HIV RNA quantity did not significantly increase (log10 0.15 copies/mL, 95% CI: -0.41, 0.10). Increase was more marked in women with abscess or with a greater number of mastitis symptoms. HIV RNA was not significantly different between affected and unaffected women, except at the time of diagnosis. Conclusions Breast milk HIV RNA increased modestly in the affected breast with unilateral mastitis or abscess and returned to pre-pathology levels with symptom resolution. Contralateral HIV RNA was not affected. Results support guidelines encouraging feeding from the contralateral breast to minimize risk of HIV transmission associated with unilateral breast pathology. PMID:23202812

A cure for the blues: opsin duplication and subfunctionalization for short-wavelength sensitivity in jewel beetles (Coleoptera: Buprestidae).

PubMed

Lord, Nathan P; Plimpton, Rebecca L; Sharkey, Camilla R; Suvorov, Anton; Lelito, Jonathan P; Willardson, Barry M; Bybee, Seth M

2016-05-18

Arthropods have received much attention as a model for studying opsin evolution in invertebrates. Yet, relatively few studies have investigated the diversity of opsin proteins that underlie spectral sensitivity of the visual pigments within the diverse beetles (Insecta: Coleoptera). Previous work has demonstrated that beetles appear to lack the short-wavelength-sensitive (SWS) opsin class that typically confers sensitivity to the "blue" region of the light spectrum. However, this is contrary to established physiological data in a number of Coleoptera. To explore potential adaptations at the molecular level that may compensate for the loss of the SWS opsin, we carried out an exploration of the opsin proteins within a group of beetles (Buprestidae) where short-wave sensitivity has been demonstrated. RNA-seq data were generated to identify opsin proteins from nine taxa comprising six buprestid species (including three male/female pairs) across four subfamilies. Structural analyses of recovered opsins were conducted and compared to opsin sequences in other insects across the main opsin classes-ultraviolet, short-wavelength, and long-wavelength. All nine buprestids were found to express two opsin copies in each of the ultraviolet and long-wavelength classes, contrary to the single copies recovered in all other molecular studies of adult beetle opsin expression. No SWS opsin class was recovered. Furthermore, the male Agrilus planipennis (emerald ash borer-EAB) expressed a third LWS opsin at low levels that is presumed to be a larval copy. Subsequent homology and structural analyses identified multiple amino acid substitutions in the UVS and LWS copies that could confer short-wavelength sensitivity. This work is the first to compare expressed opsin genes against known electrophysiological data that demonstrate multiple peak sensitivities in Coleoptera. We report the first instance of opsin duplication in adult beetles, which occurs in both the UVS and LWS opsin classes. Through structural comparisons of known insect opsins, we suggest that opsin duplication and amino acid variation within the chromophore binding pocket explains sensitivity in the short-wavelength portion of the visible light spectrum in these species. These findings are the first to reveal molecular complexity of the color vision system within beetles.

Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies.

PubMed

Bianchi, Diana W; Chudova, Darya; Sehnert, Amy J; Bhatt, Sucheta; Murray, Kathryn; Prosen, Tracy L; Garber, Judy E; Wilkins-Haug, Louise; Vora, Neeta L; Warsof, Stephen; Goldberg, James; Ziainia, Tina; Halks-Miller, Meredith

2015-07-14

Understanding the relationship between aneuploidy detection on noninvasive prenatal testing (NIPT) and occult maternal malignancies may explain results that are discordant with the fetal karyotype and improve maternal clinical care. To evaluate massively parallel sequencing data for patterns of copy-number variations that might prospectively identify occult maternal malignancies. Case series identified from 125,426 samples submitted between February 15, 2012, and September 30, 2014, from asymptomatic pregnant women who underwent plasma cell-free DNA sequencing for clinical prenatal aneuploidy screening. Analyses were conducted in a clinical laboratory that performs DNA sequencing. Among the clinical samples, abnormal results were detected in 3757 (3%); these were reported to the ordering physician with recommendations for further evaluation. NIPT for fetal aneuploidy screening (chromosomes 13, 18, 21, X, and Y). Detailed genome-wide bioinformatics analysis was performed on available sequencing data from 8 of 10 women with known cancers. Genome-wide copy-number changes in the original NIPT samples and in subsequent serial samples from individual patients when available are reported. Copy-number changes detected in NIPT sequencing data in the known cancer cases were compared with the types of aneuploidies detected in the overall cohort. From a cohort of 125,426 NIPT results, 3757 (3%) were positive for 1 or more aneuploidies involving chromosomes 13, 18, 21, X, or Y. From this set of 3757 samples, 10 cases of maternal cancer were identified. Detailed clinical and sequencing data were obtained in 8. Maternal cancers most frequently occurred with the rare NIPT finding of more than 1 aneuploidy detected (7 known cancers among 39 cases of multiple aneuploidies by NIPT, 18% [95% CI, 7.5%-33.5%]). All 8 cases that underwent further bioinformatics analysis showed unique patterns of nonspecific copy-number gains and losses across multiple chromosomes. In 1 case, blood was sampled after completion of treatment for colorectal cancer and the abnormal pattern was no longer evident. In this preliminary study, a small number of cases of occult malignancy were subsequently diagnosed among pregnant women whose noninvasive prenatal testing results showed discordance with the fetal karyotype. The clinical importance of these findings will require further research.

Acute respiratory infections among returning Hajj pilgrims-Jordan, 2014.

PubMed

Al-Abdallat, Mohammad Mousa; Rha, Brian; Alqasrawi, Sultan; Payne, Daniel C; Iblan, Ibrahim; Binder, Alison M; Haddadin, Aktham; Nsour, Mohannad Al; Alsanouri, Tarek; Mofleh, Jawad; Whitaker, Brett; Lindstrom, Stephen L; Tong, Suxiang; Ali, Sami Sheikh; Dahl, Rebecca Moritz; Berman, LaShondra; Zhang, Jing; Erdman, Dean D; Gerber, Susan I

2017-04-01

The emergence of Middle East Respiratory Syndrome coronavirus (MERS-CoV) has prompted enhanced surveillance for respiratory infections among pilgrims returning from the Hajj, one of the largest annual mass gatherings in the world. To describe the epidemiology and etiologies of respiratory illnesses among pilgrims returning to Jordan after the 2014 Hajj. Surveillance for respiratory illness among pilgrims returning to Jordan after the 2014 Hajj was conducted at sentinel health care facilities using epidemiologic surveys and molecular diagnostic testing of upper respiratory specimens for multiple respiratory pathogens, including MERS-CoV. Among the 125 subjects, 58% tested positive for at least one virus; 47% tested positive for rhino/enterovirus. No cases of MERS-CoV were detected. The majority of pilgrims returning to Jordan from the 2014 Hajj with respiratory illness were determined to have a viral etiology, but none were due to MERS-CoV. A greater understanding of the epidemiology of acute respiratory infections among returning travelers to other countries after Hajj should help optimize surveillance systems and inform public health response practices. Published by Elsevier B.V.

Mild traumatic brain injury: lessons learned from clinical, sports, and combat concussions.

PubMed

Kelly, Judy C; Amerson, Efland H; Barth, Jeffrey T

2012-01-01

Over the past forty years, a tremendous amount of information has been gained on the mechanisms and consequences of mild traumatic brain injuries. Using sports as a laboratory to study this phenomenon, a natural recovery curve emerged, along with standards for managing concussions and returning athletes back to play. Although advances have been made in this area, investigation into recovery and return to play continues. With the increase in combat-related traumatic brain injuries in the military setting, lessons learned from sports concussion research are being applied by the Department of Defense to the assessment of blast concussions and return to duty decision making. Concussion management and treatment for military personnel can be complicated by additional combat related stressors not present in the civilian environment. Cognitive behavioral therapy is one of the interventions that has been successful in treating symptoms of postconcussion syndrome. While we are beginning to have an understanding of the impact of multiple concussions and subconcussive blows in the sports world, much is still unknown about the impact of multiple blast injuries.

TEAM - Titan Exploration Atmospheric Microprobes

NASA Astrophysics Data System (ADS)

Nixon, Conor; Esper, Jaime; Aslam, Shahid; Quilligan, Gerald

2016-10-01

The astrobiological potential of Titan's surface hydrocarbon liquids and probable interior water ocean has led to its inclusion as a destination in NASA's "Ocean Worlds" initiative, and near-term investigation of these regions is a high-level scientific goal. TEAM is a novel initiative to investigate the lake and sea environs using multiple dropsondes -scientific probes derived from an existing cubesat bus architecture (CAPE - the Cubesat Application for Planetary Exploration) developed at NASA GSFC. Each 3U probe will parachute to the surface, making atmospheric structure and composition measurements during the descent, and photographing the surface - land, shoreline and seas - in detail. TEAM probes offer a low-cost, high-return means to explore multiple areas on Titan, yielding crucial data about the condensing chemicals, haze and cloud layers, winds, and surface features of the lakes and seas. These microprobes may be included on a near-term New Frontiers class mission to the Saturn system as additional payload, bringing increased scientific return and conducting reconnaissance for future landing zones. In this presentation we describe the probe architecture, baseline payload, flight profile and the unique engineering and science data that can be returned.

Simultaneously measuring multiple protein interactions and their correlations in a cell by Protein-interactome Footprinting

PubMed Central

Luo, Si-Wei; Liang, Zhi; Wu, Jia-Rui

2017-01-01

Quantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers. Using PiF, we quantitatively reveal dynamic patterns of PPIs and their correlation network in E. coli two-component systems. PMID:28338015

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

PubMed

Wilkinson, Shaun P; Fisher, Paul L; van Oppen, Madeleine J H; Davy, Simon K

2015-03-14

The symbiosis between corals and the dinoflagellate alga Symbiodinium is essential for the development and survival of coral reefs. Yet this fragile association is highly vulnerable to environmental disturbance. A coral's ability to tolerate temperature stress depends on the fitness of its resident symbionts, whose thermal optima vary extensively between lineages. However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis, and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations. Two distinct Symbiodinium ITS2 sequences (denoted C100 and C109) were retrieved from all P. damicornis colonies analysed. However, the symbiont assemblage consisted of three distinct Symbiodinium populations: cells featuring pure arrays of ITS2 type C109, near-homogeneous cells of type C100 (with trace ITS2 copies of type C109), and those with co-dominant C100 and C109 ITS2 repeats. The symbiont consortia of some colonies consisted almost entirely of these putative C100 × C109 recombinants. Our results are consistent with the occurrence of sexual recombination between Symbiodinium types C100 and C109. While the multiple-copy nature of the ITS2 dictates that the observed pattern of intra-genomic co-dominance may be a result of incomplete concerted evolution of intra-genomic polymorphisms, this is a less likely explanation given the occurrence of homogeneous cells of the C109 type. Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci.

27 CFR 478.126a - Reporting multiple sales or other disposition of pistols and revolvers.

Code of Federal Regulations, 2010 CFR

2010-04-01

... business days, two or more pistols, or revolvers, or any combination of pistols and revolvers totaling two..., or any combination thereof, are returned to the same person from whom they were received. The report.... Not later than the close of business on the day that the multiple sale or other disposition occurs...

On the behavior of return stroke current and the remotely detected electric field change waveform

NASA Astrophysics Data System (ADS)

Shao, Xuan-Min; Lay, Erin; Jacobson, Abram R.

2012-04-01

After accumulating a large number of remotely recorded negative return stroke electric field change waveforms, a subtle but persistent kink was found following the main return stroke peak by several microseconds. To understand the corresponding return stroke current properties behind the kink and the general return stroke radiation waveform, we analyze strokes occurring in triggered lightning flashes for which have been measured both the channel base current and simultaneous remote electric radiation field. In this study, the channel base current is assumed to propagate along the return stroke channel in a dispersive and lossy manner. The measured channel base current is band-pass filtered, and the higher-frequency component is assumed to attenuate faster than the lower-frequency component. The radiation electric field is computed for such a current behavior and is then propagated to distant sensors. It is found that such a return stroke model is capable of very closely reproducing the measured electric waveforms at multiple stations for the triggered return strokes, and such a model is considered applicable to the common behavior of the natural return stroke as well. On the basis of the analysis, a number of other observables are derived. The time-evolving current dispersion and attenuation compare well with previously reported optical observations. The observable speed tends to agree with optical and VHF observations. Line charge density that is removed or deposited by the return stroke is derived, and the implication of the charge density distribution on leader channel decay is discussed.

Motivating medical information system performance by system quality, service quality, and job satisfaction for evidence-based practice

PubMed Central

2012-01-01

Background No previous studies have addressed the integrated relationships among system quality, service quality, job satisfaction, and system performance; this study attempts to bridge such a gap with evidence-based practice study. Methods The convenience sampling method was applied to the information system users of three hospitals in southern Taiwan. A total of 500 copies of questionnaires were distributed, and 283 returned copies were valid, suggesting a valid response rate of 56.6%. SPSS 17.0 and AMOS 17.0 (structural equation modeling) statistical software packages were used for data analysis and processing. Results The findings are as follows: System quality has a positive influence on service quality (γ11= 0.55), job satisfaction (γ21= 0.32), and system performance (γ31= 0.47). Service quality (β31= 0.38) and job satisfaction (β32= 0.46) will positively influence system performance. Conclusions It is thus recommended that the information office of hospitals and developers take enhancement of service quality and user satisfaction into consideration in addition to placing b on system quality and information quality when designing, developing, or purchasing an information system, in order to improve benefits and gain more achievements generated by hospital information systems. PMID:23171394

Mars double-aeroflyby free returns

NASA Astrophysics Data System (ADS)

Jesick, Mark

2017-09-01

Mars double-flyby free-return trajectories that pass twice through the Martian atmosphere are documented. This class of trajectories is advantageous for potential Mars atmospheric sample return missions because of its low geocentric energy at departure and arrival, because it would enable two sample collections at unique locations during different Martian seasons, and because of its lack of deterministic maneuvers. Free return opportunities are documented over Earth departure dates ranging from 2015 through 2100, with viable missions available every Earth-Mars synodic period. After constraining the maximum lift-to-drag ratio to be less than one, the minimum observed Earth departure hyperbolic excess speed is 3.23 km/s, the minimum Earth atmospheric entry speed is 11.42 km/s, and the minimum round-trip flight time is 805 days. An algorithm using simplified dynamics is developed along with a method to derive an initial estimate for trajectories in a more realistic dynamic model. Multiple examples are presented, including free returns that pass outside and inside of Mars's appreciable atmosphere.

Preferential inclusion of extrachromosomal genetic elements in yeast meiotic spores.

PubMed

Brewer, B J; Fangman, W L

1980-09-01

During meiosis and sporulation in the yeast Saccharomyces cerevisiae, extrachromosomal traits are efficiently transmitted to haploid spores. Although the pattern of inheritance of chromosomal traits reflects the mechanism of regular chromosomal segregation in meiosis, it is not known what processes are reflected by the efficient inheritance of extrachromosomal traits. Because extrachromosomal genetic elements in yeast are present in multiple copies, perpetuation of an extrachromosomal trait could occur by the passive envelopment of a subset of copies or by an active sequestering of all or a subset of copies within the four spores. We show that only subsets of the four extrachromosomal nucleic acids commonly found in yeast are transmitted through meiosis--55% of mitochondrial DNA copies, 82% of the 2-micron DNA plasmids, and about 70% of the L and M double-stranded RNAs. However, electron micrographs of serial sections through yeast asci indicate that the four spore enclose only 30% of the total ascus material. Thus these extrachromosomal elements are preferentially included within the spores, indicating that their inheritance is not a random process. Transmission of mitochondrial DNA can be accounted for by the observed enclosure of 52% of the mitochondrial volume within the spores. The high transmission frequencies of the double-stranded RNAs (which exist as virus-like particles in the cytoplasm) and 2-micron DNA must indicate that either these nucleic acids are actively recruited from the cytoplasm by some mechanism or they are associated in some way with the nucleus during meiosis.

Copy Number Alterations Associated with Acute Lymphoblastic Leukemia in Mexican Children. A report from The Mexican Inter-Institutional Group for the identification of the causes of childhood leukemia.

PubMed

Rosales-Rodríguez, Beatriz; Fernández-Ramírez, Fernando; Núñez-Enríquez, Juan Carlos; Velázquez-Wong, Ana Claudia; Medina-Sansón, Aurora; Jiménez-Hernández, Elva; Flores-Lujano, Janet; Peñaloza-González, José Gabriel; Espinosa-Elizondo, Rosa Martha; Pérez-Saldívar, María Luisa; Torres-Nava, José Refugio; Martín-Trejo, Jorge Alfonso; Martínez-Morales, Gabriela Bibiana; Bekker-Méndez, Vilma Carolina; Mejía-Aranguré, Juan Manuel; Rosas-Vargas, Haydee

2016-11-01

B-cell precursor acute lymphocytic leukemia (B-ALL) represents a worldwide public health issue. Particularly, Mexico is one of the countries with the highest incidence of ALL in children. Between the multiple factors involved in ALL etiology, genetic alterations are clearly one of the most relevant features. In this work, a group of 24 B-ALL patients, all negative for the four most frequent gene fusions (ETV6-RUNX1, BCR-ABL1, TCF3-PBX1 and MLL-AF4), were included in a high-resolution microarray analysis in order to evaluate genomic copy-number alterations (CNAs). The results of this preliminary report showed a broad genomic heterogeneity among the studied samples; 58% of the patients were hyperdiploid and 33% displayed a chromosome 9p deletion of variable length affecting genes CDKN2A/B, two patients displayed genomic instability with a high number of focal CNAs, three patients presented unique duplications affecting 2q, 12p and 1q, respectively, and one patient displayed no copy number imbalances. The copy-number profile of 44 genes previously related to B-ALL was heterogeneous as well. Overall results highlight the need for a detailed description of the genetic alterations in ALL cancer cells in order to understand the molecular pathogenesis of the disease and to identify any prognostic markers with clinical significance. Copyright © 2016 IMSS. Published by Elsevier Inc. All rights reserved.

Gene amplification confers glyphosate resistance in Amaranthus palmeri

PubMed Central

Gaines, Todd A.; Zhang, Wenli; Wang, Dafu; Bukun, Bekir; Chisholm, Stephen T.; Shaner, Dale L.; Nissen, Scott J.; Patzoldt, William L.; Tranel, Patrick J.; Culpepper, A. Stanley; Grey, Timothy L.; Webster, Theodore M.; Vencill, William K.; Sammons, R. Douglas; Jiang, Jiming; Preston, Christopher; Leach, Jan E.; Westra, Philip

2009-01-01

The herbicide glyphosate became widely used in the United States and other parts of the world after the commercialization of glyphosate-resistant crops. These crops have constitutive overexpression of a glyphosate-insensitive form of the herbicide target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Increased use of glyphosate over multiple years imposes selective genetic pressure on weed populations. We investigated recently discovered glyphosate-resistant Amaranthus palmeri populations from Georgia, in comparison with normally sensitive populations. EPSPS enzyme activity from resistant and susceptible plants was equally inhibited by glyphosate, which led us to use quantitative PCR to measure relative copy numbers of the EPSPS gene. Genomes of resistant plants contained from 5-fold to more than 160-fold more copies of the EPSPS gene than did genomes of susceptible plants. Quantitative RT-PCR on cDNA revealed that EPSPS expression was positively correlated with genomic EPSPS relative copy number. Immunoblot analyses showed that increased EPSPS protein level also correlated with EPSPS genomic copy number. EPSPS gene amplification was heritable, correlated with resistance in pseudo-F2 populations, and is proposed to be the molecular basis of glyphosate resistance. FISH revealed that EPSPS genes were present on every chromosome and, therefore, gene amplification was likely not caused by unequal chromosome crossing over. This occurrence of gene amplification as an herbicide resistance mechanism in a naturally occurring weed population is particularly significant because it could threaten the sustainable use of glyphosate-resistant crop technology. PMID:20018685

Gaussian Decomposition of Laser Altimeter Waveforms

NASA Technical Reports Server (NTRS)

Hofton, Michelle A.; Minster, J. Bernard; Blair, J. Bryan

1999-01-01

We develop a method to decompose a laser altimeter return waveform into its Gaussian components assuming that the position of each Gaussian within the waveform can be used to calculate the mean elevation of a specific reflecting surface within the laser footprint. We estimate the number of Gaussian components from the number of inflection points of a smoothed copy of the laser waveform, and obtain initial estimates of the Gaussian half-widths and positions from the positions of its consecutive inflection points. Initial amplitude estimates are obtained using a non-negative least-squares method. To reduce the likelihood of fitting the background noise within the waveform and to minimize the number of Gaussians needed in the approximation, we rank the "importance" of each Gaussian in the decomposition using its initial half-width and amplitude estimates. The initial parameter estimates of all Gaussians ranked "important" are optimized using the Levenburg-Marquardt method. If the sum of the Gaussians does not approximate the return waveform to a prescribed accuracy, then additional Gaussians are included in the optimization procedure. The Gaussian decomposition method is demonstrated on data collected by the airborne Laser Vegetation Imaging Sensor (LVIS) in October 1997 over the Sequoia National Forest, California.

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma

PubMed Central

Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-01-01

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations. PMID:28533481

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma.

PubMed

Wu, Ren-Chin; Chao, An-Shine; Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-07-18

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations.

A Meta-Analysis of Multiple Matched Copy Number and Transcriptomics Data Sets for Inferring Gene Regulatory Relationships

PubMed Central

Newton, Richard; Wernisch, Lorenz

2014-01-01

Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments. PMID:25148247

Off-axis low coherence digital holographic interferometry for quantitative phase imaging with an LED

NASA Astrophysics Data System (ADS)

Guo, Rongli; Wang, Fan; Hu, Xiaoying; Yang, Wenqian

2017-11-01

Off-axis digital holographic interferometry with the light source of a light emitting diode (LED) is presented and its application for quantitative phase imaging in a large range with low noise is demonstrated. The scheme is implemented in a grating based Mach-Zehnder interferometer. To achieve off-axis interferometry, firstly, the collimated beam emitted from an LED is diffracted into multiple orders by a grating and they are split into two copies by a beam splitter; secondly, in the object arm the zero order of one copy is filtered in the Fourier plane and is reshaped to illuminate the sample, while in the reference arm one of its first order of another copy is selected to serve as the reference beam, and then an off-axis hologram can be obtained at the image plane. The main advantage stemming from an LED illumination is its high spatial phase resolution, due to the subdued speckle effect. The off-axis geometry enables one-shot recording of the hologram in the millisecond scale. The utility of the proposed setup is illustrated with measurements of a resolution target and part of a wing of green-lacewing, and dynamic evaporation process of an ethanol film.

cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate.

PubMed

Clevert, Djork-Arné; Mitterecker, Andreas; Mayr, Andreas; Klambauer, Günter; Tuefferd, Marianne; De Bondt, An; Talloen, Willem; Göhlmann, Hinrich; Hochreiter, Sepp

2011-07-01

Cost-effective oligonucleotide genotyping arrays like the Affymetrix SNP 6.0 are still the predominant technique to measure DNA copy number variations (CNVs). However, CNV detection methods for microarrays overestimate both the number and the size of CNV regions and, consequently, suffer from a high false discovery rate (FDR). A high FDR means that many CNVs are wrongly detected and therefore not associated with a disease in a clinical study, though correction for multiple testing takes them into account and thereby decreases the study's discovery power. For controlling the FDR, we propose a probabilistic latent variable model, 'cn.FARMS', which is optimized by a Bayesian maximum a posteriori approach. cn.FARMS controls the FDR through the information gain of the posterior over the prior. The prior represents the null hypothesis of copy number 2 for all samples from which the posterior can only deviate by strong and consistent signals in the data. On HapMap data, cn.FARMS clearly outperformed the two most prevalent methods with respect to sensitivity and FDR. The software cn.FARMS is publicly available as a R package at http://www.bioinf.jku.at/software/cnfarms/cnfarms.html.

Dilation of fusion pores by crowding of SNARE proteins

PubMed Central

Wu, Zhenyong; Bello, Oscar D; Thiyagarajan, Sathish; Auclair, Sarah Marie; Vennekate, Wensi; Krishnakumar, Shyam S; O'Shaughnessy, Ben; Karatekin, Erdem

2017-01-01

Hormones and neurotransmitters are released through fluctuating exocytotic fusion pores that can flicker open and shut multiple times. Cargo release and vesicle recycling depend on the fate of the pore, which may reseal or dilate irreversibly. Pore nucleation requires zippering between vesicle-associated v-SNAREs and target membrane t-SNAREs, but the mechanisms governing the subsequent pore dilation are not understood. Here, we probed the dilation of single fusion pores using v-SNARE-reconstituted ~23-nm-diameter discoidal nanolipoprotein particles (vNLPs) as fusion partners with cells ectopically expressing cognate, 'flipped' t-SNAREs. Pore nucleation required a minimum of two v-SNAREs per NLP face, and further increases in v-SNARE copy numbers did not affect nucleation rate. By contrast, the probability of pore dilation increased with increasing v-SNARE copies and was far from saturating at 15 v-SNARE copies per face, the NLP capacity. Our experimental and computational results suggest that SNARE availability may be pivotal in determining whether neurotransmitters or hormones are released through a transient ('kiss and run') or an irreversibly dilating pore (full fusion). DOI: http://dx.doi.org/10.7554/eLife.22964.001 PMID:28346138

Grassland agriculture

USDA-ARS?s Scientific Manuscript database

Agriculture in grassland environments is facing multiple stresses from: shifting demographics, declining and fragmented agricultural landscapes, declining environmental quality, variable and changing climate, volatile and increasing energy costs, marginal economic returns, and globalization. Degrad...

Modified general primer PCR system for sensitive detection of multiple types of oncogenic human papillomavirus.

PubMed

Söderlund-Strand, Anna; Carlson, Joyce; Dillner, Joakim

2009-03-01

Human papillomavirus (HPV) infection is a necessary cause of cervical cancer and cervical dysplasia. Accurate and sensitive genotyping of multiple oncogenic HPVs is essential for a multitude of both clinical and research uses. We developed a modified general primer (MGP) PCR system with five forward and five reverse consensus primers. The MGP system was compared to the classical HPV general primer system GP5+/6+ using a proficiency panel with HPV plasmid dilutions as well as cervical samples from 592 women with low-grade cytological abnormalities. The reference method (GP5+/6+) had the desirable high sensitivity (five copies/PCR) for five oncogenic HPV types (HPV type 16 [HPV-16], HPV-18, HPV-56, HPV-59, and HPV-66). The MGP system was able to detect all 14 oncogenic HPV types at five copies/PCR. In the clinical samples, the MGP system detected a significantly higher proportion of women with more than two concomitant HPV infections than did the GP5+/6+ system (102/592 women compared to 42/592 women). MGP detected a significantly greater number of infections with HPV-16, -18, -31, -33, -35, -39, -42, -43, -45, -51, -52, -56, -58, and -70 than did GP5+/6+. In summary, the MGP system primers allow a more sensitive amplification of most of the HPV types that are established as oncogenic and had an improved ability to detect multiple concomitant HPV infections.

Tracking Multiple People Online and in Real Time

DTIC Science & Technology

2015-12-21

NO. 0704-0188 3. DATES COVERED (From - To) - UU UU UU UU 21-12-2015 Approved for public release; distribution is unlimited. Tracking multiple people ...online and in real time We cast the problem of tracking several people as a graph partitioning problem that takes the form of an NP-hard binary...PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. Duke University 2200 West Main Street Suite 710 Durham, NC 27705 -4010 ABSTRACT Tracking multiple

Probability distribution of financial returns in a model of multiplicative Brownian motion with stochastic diffusion coefficient

NASA Astrophysics Data System (ADS)

Silva, Antonio

2005-03-01

It is well-known that the mathematical theory of Brownian motion was first developed in the Ph. D. thesis of Louis Bachelier for the French stock market before Einstein [1]. In Ref. [2] we studied the so-called Heston model, where the stock-price dynamics is governed by multiplicative Brownian motion with stochastic diffusion coefficient. We solved the corresponding Fokker-Planck equation exactly and found an analytic formula for the time-dependent probability distribution of stock price changes (returns). The formula interpolates between the exponential (tent-shaped) distribution for short time lags and the Gaussian (parabolic) distribution for long time lags. The theoretical formula agrees very well with the actual stock-market data ranging from the Dow-Jones index [2] to individual companies [3], such as Microsoft, Intel, etc. [] [1] Louis Bachelier, ``Th'eorie de la sp'eculation,'' Annales Scientifiques de l''Ecole Normale Sup'erieure, III-17:21-86 (1900).[] [2] A. A. Dragulescu and V. M. Yakovenko, ``Probability distribution of returns in the Heston model with stochastic volatility,'' Quantitative Finance 2, 443--453 (2002); Erratum 3, C15 (2003). [cond-mat/0203046] [] [3] A. C. Silva, R. E. Prange, and V. M. Yakovenko, ``Exponential distribution of financial returns at mesoscopic time lags: a new stylized fact,'' Physica A 344, 227--235 (2004). [cond-mat/0401225

Evidence of Large Fluctuations of Stock Return and Financial Crises from Turkey: Using Wavelet Coherency and Varma Modeling to Forecast Stock Return

NASA Astrophysics Data System (ADS)

Oygur, Tunc; Unal, Gazanfer

Shocks, jumps, booms and busts are typical large fluctuation markers which appear in crisis. Models and leading indicators vary according to crisis type in spite of the fact that there are a lot of different models and leading indicators in literature to determine structure of crisis. In this paper, we investigate structure of dynamic correlation of stock return, interest rate, exchange rate and trade balance differences in crisis periods in Turkey over the period between October 1990 and March 2015 by applying wavelet coherency methodologies to determine nature of crises. The time period includes the Turkeys currency and banking crises; US sub-prime mortgage crisis and the European sovereign debt crisis occurred in 1994, 2001, 2008 and 2009, respectively. Empirical results showed that stock return, interest rate, exchange rate and trade balance differences are significantly linked during the financial crises in Turkey. The cross wavelet power, the wavelet coherency, the multiple wavelet coherency and the quadruple wavelet coherency methodologies have been used to examine structure of dynamic correlation. Moreover, in consequence of quadruple and multiple wavelet coherence, strongly correlated large scales indicate linear behavior and, hence VARMA (vector autoregressive moving average) gives better fitting and forecasting performance. In addition, increasing the dimensions of the model for strongly correlated scales leads to more accurate results compared to scalar counterparts.

Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis

PubMed Central

2013-01-01

Background Colorectal cancer is the third leading cause of cancer deaths in the United States. The initial assessment of colorectal cancer involves clinical staging that takes into account the extent of primary tumor invasion, determining the number of lymph nodes with metastatic cancer and the identification of metastatic sites in other organs. Advanced clinical stage indicates metastatic cancer, either in regional lymph nodes or in distant organs. While the genomic and genetic basis of colorectal cancer has been elucidated to some degree, less is known about the identity of specific cancer genes that are associated with advanced clinical stage and metastasis. Methods We compiled multiple genomic data types (mutations, copy number alterations, gene expression and methylation status) as well as clinical meta-data from The Cancer Genome Atlas (TCGA). We used an elastic-net regularized regression method on the combined genomic data to identify genetic aberrations and their associated cancer genes that are indicators of clinical stage. We ranked candidate genes by their regression coefficient and level of support from multiple assay modalities. Results A fit of the elastic-net regularized regression to 197 samples and integrated analysis of four genomic platforms identified the set of top gene predictors of advanced clinical stage, including: WRN, SYK, DDX5 and ADRA2C. These genetic features were identified robustly in bootstrap resampling analysis. Conclusions We conducted an analysis integrating multiple genomic features including mutations, copy number alterations, gene expression and methylation. This integrated approach in which one considers all of these genomic features performs better than any individual genomic assay. We identified multiple genes that robustly delineate advanced clinical stage, suggesting their possible role in colorectal cancer metastatic progression. PMID:24308539

Quantum origin of quantum jumps: Breaking of unitary symmetry induced by information transfer in the transition from quantum to classical

NASA Astrophysics Data System (ADS)

Zurek, Wojciech Hubert

2007-11-01

Measurements transfer information about a system to the apparatus and then, further on, to observers and (often inadvertently) to the environment. I show that even imperfect copying essential in such situations restricts possible unperturbed outcomes to an orthogonal subset of all possible states of the system, thus breaking the unitary symmetry of its Hilbert space implied by the quantum superposition principle. Preferred outcome states emerge as a result. They provide a framework for “wave-packet collapse,” designating terminal points of quantum jumps and defining the measured observable by specifying its eigenstates. In quantum Darwinism, they are the progenitors of multiple copies spread throughout the environment—the fittest quantum states that not only survive decoherence, but subvert the environment into carrying information about them—into becoming a witness.

Optimal Information Processing in Biochemical Networks

NASA Astrophysics Data System (ADS)

Wiggins, Chris

2012-02-01

A variety of experimental results over the past decades provide examples of near-optimal information processing in biological networks, including in biochemical and transcriptional regulatory networks. Computing information-theoretic quantities requires first choosing or computing the joint probability distribution describing multiple nodes in such a network --- for example, representing the probability distribution of finding an integer copy number of each of two interacting reactants or gene products while respecting the `intrinsic' small copy number noise constraining information transmission at the scale of the cell. I'll given an overview of some recent analytic and numerical work facilitating calculation of such joint distributions and the associated information, which in turn makes possible numerical optimization of information flow in models of noisy regulatory and biochemical networks. Illustrating cases include quantification of form-function relations, ideal design of regulatory cascades, and response to oscillatory driving.

A Fluorescent G-quadruplex Sensor for Chemical RNA Copying.

PubMed

Giurgiu, Constantin; Wright, Tom; O'Flaherty, Derek; Szostak, Jack

2018-06-25

Non-enzymatic RNA replication may have been one of the processes involved in the appearance of life on Earth. Attempts to recreate this process in a laboratory setting have not been successful thus far, highlighting a critical need for finding prebiotic conditions that increase the rate and the yield. Here, we present a highly parallel assay for template directed RNA synthesis that relies on the intrinsic fluorescence of a 2-aminopurine modified G-quadruplex. We demonstrate the application of the assay to examine the combined influence of multiple variables including pH, divalent metal concentrations and ribonucleotide concentrations on the copying of RNA sequences. The assay enables a direct survey of physical and chemical conditions, potentially prebiotic, which could enable the chemical replication of RNA. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multivariable Control Laws for the AFTI/F-16

DTIC Science & Technology

1983-07-01

file prior to entering TOTAL. 296 CREATE, AKEY, COPY, AMAT, rIMATi COPY, HMAT, BMAT , 741 COPY, CMAT, BMAT , COPY, JMAT, AMATi 72, COPY, CMAT, NMAT...COPY, MMAT, AfIAT, COPY, IMAT, BMAT , 74, COPY, CMAT, BMAT , COPY, LMAT, AMAT, 72, COPY, CMAT, OMAT, BKEY CREATE, BKEY, COPY, OMAT, AMAT, 75, COPY, CMAT...AMAT, COPY, NMAT, BMAT , 74, COPY, CMAT, BMAT , COPY, IMAT, AMAT, 74, COPY, CMATi BMAT , COPY, HMAT, AMAT, 73,1 COPY, CMAT, AMAT, 71, COPY, AMAT, EMAT

Data article on disposition towards enhancing SMEs' performance through entrepreneurial orientations: Perspectives from a developing economy.

PubMed

Ibidunni, Ayodotun Stephen; Ibidunni, Oyebisi Mary; Olokundun, Maxwell Ayodele; Falola, Hezekiah Olubusayo; Salau, Odunayo Paul; Borishade, Taiye Tairat

2018-06-01

This article present data on the disposition of SME operators towards enhancing SMEs Performance through entrepreneurial orientations. Copies of structured questionnaire were administered to 102 SME owners/managers. Using descriptive and standard multiple regression statistical analysis, the data described how proactiveness, risk-taking and autonomy orientations significantly influenced SMEs' profitability, sales growth, customer satisfaction and new product success.

Repeating Patterns and Multiplicative Thinking: Analysis of Classroom Interactions with 9-Year-Old Students that Support the Transition from the Known to the Novel

ERIC Educational Resources Information Center

Warren, Elizabeth; Cooper, Tom

2007-01-01

In early years' (primary grade) classrooms in Australia repeated patterns are commonly explored as an early introductory activity to mathematics. Most young students have an extensive knowledge of and exhibit success in copying, continuing, creating and transferring patterns into other media. By contrast, research indicates one of the most…

17 CFR 240.14a-7 - Obligations of registrants to provide a list of, or mail soliciting material to, security holders.

Code of Federal Regulations, 2013 CFR

2013-04-01

... Internet Availability of Proxy Materials (as described in § 240.14a-16), furnished by the security holder... security holder shall be sent to that address, provided that if multiple copies of the Notice of Internet... 17 Commodity and Securities Exchanges 3 2013-04-01 2013-04-01 false Obligations of registrants to...

17 CFR 240.14a-7 - Obligations of registrants to provide a list of, or mail soliciting material to, security holders.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Internet Availability of Proxy Materials (as described in § 240.14a-16), furnished by the security holder... security holder shall be sent to that address, provided that if multiple copies of the Notice of Internet... 17 Commodity and Securities Exchanges 4 2014-04-01 2014-04-01 false Obligations of registrants to...

17 CFR 240.14a-7 - Obligations of registrants to provide a list of, or mail soliciting material to, security holders.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Internet Availability of Proxy Materials (as described in § 240.14a-16), furnished by the security holder... security holder shall be sent to that address, provided that if multiple copies of the Notice of Internet... 17 Commodity and Securities Exchanges 3 2011-04-01 2011-04-01 false Obligations of registrants to...

17 CFR 240.14a-7 - Obligations of registrants to provide a list of, or mail soliciting material to, security holders.

Code of Federal Regulations, 2012 CFR

2012-04-01

... Internet Availability of Proxy Materials (as described in § 240.14a-16), furnished by the security holder... security holder shall be sent to that address, provided that if multiple copies of the Notice of Internet... 17 Commodity and Securities Exchanges 3 2012-04-01 2012-04-01 false Obligations of registrants to...

Cloning and analysis of the positively acting regulatory gene amdR from Aspergillus nidulans.

PubMed Central

Andrianopoulos, A; Hynes, M J

1988-01-01

The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of four unlinked structural genes involved in acetamide (amdS), omega amino acid (gatA and gabA), and lactam (lamA) catabolism. By the use of DNA-mediated transformation of A. nidulans, the amdR regulatory gene was cloned from a genomic cosmid library. Southern blot analysis of DNA from various loss-of-function amdR mutants revealed the presence of four detectable DNA rearrangements, including a deletion, an insertion, and a translocation. No detectable DNA rearrangements were found in several constitutive amdRc mutants. Analysis of the fate of amdR-bearing plasmids in transformants showed that 10 to 20% of the transformation events were homologous integrations or gene conversions, and this phenomenon was exploited in developing a strategy by which amdRc and amdR- alleles can be readily cloned and analyzed. Examination of the transcription of amdR by Northern blot (RNA blot) analysis revealed the presence of two mRNAs (2.7 and 1.8 kilobases) which were constitutively synthesized at a very low level. In addition, amdR transcription did not appear to depend on the presence of a functional amdR product nor was it altered in amdRc mutants. The dosage effects of multiple copies of amdR in transformants were examined, and it was shown that such transformants exhibited stronger growth than did the wild type on acetamide and pyrrolidinone media, indicating increased expression of the amdS and lamA genes, respectively. These results were used to formulate a model for amdR-mediated regulation of gene expression in which the low constitutive level of amdR product sets the upper limits of basal and induced transcription of the structural genes. Multiple copies of 5' sequences from the amdS gene can result in reduced growth on substrates whose utilization is dependent on amdR-controlled genes. This has been attributed to titration of limiting amdR gene product. Strong support for this proposal was obtained by showing that multiple copies of the amdR gene can reverse this phenomenon (antititration). Images PMID:3062382

Comparative analysis of diguanylate cyclase and phosphodiesterase genes in Klebsiella pneumoniae.

PubMed

Cruz, Diana P; Huertas, Mónica G; Lozano, Marcela; Zárate, Lina; Zambrano, María Mercedes

2012-07-09

Klebsiella pneumoniae can be found in environmental habitats as well as in hospital settings where it is commonly associated with nosocomial infections. One of the factors that contribute to virulence is its capacity to form biofilms on diverse biotic and abiotic surfaces. The second messenger Bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) is a ubiquitous signal in bacteria that controls biofilm formation as well as several other cellular processes. The cellular levels of this messenger are controlled by c-di-GMP synthesis and degradation catalyzed by diguanylate cyclase (DGC) and phophodiesterase (PDE) enzymes, respectively. Many bacteria contain multiple copies of these proteins with diverse organizational structure that highlight the complex regulatory mechanisms of this signaling network. This work was undertaken to identify DGCs and PDEs and analyze the domain structure of these proteins in K. pneumoniae. A search for conserved GGDEF and EAL domains in three sequenced K. pneumoniae genomes showed that there were multiple copies of GGDEF and EAL containing proteins. Both single domain and hybrid GGDEF proteins were identified: 21 in K. pneumoniae Kp342, 18 in K. pneumoniae MGH 78578 and 17 in K. pneumoniae NTUH-K2044. The majority had only the GGDEF domain, most with the GGEEF motif, and hybrid proteins containing both GGDEF and EAL domains were also found. The I site for allosteric control was identified only in single GGDEF domain proteins and not in hybrid proteins. EAL-only proteins, containing either intact or degenerate domains, were also identified: 15 in Kp342, 15 in MGH 78578 and 10 in NTUH-K2044. Several input sensory domains and transmembrane segments were identified, which together indicate complex regulatory circuits that in many cases can be membrane associated. The comparative analysis of proteins containing GGDEF/EAL domains in K. pneumoniae showed that most copies were shared among the three strains and that some were unique to a particular strain. The multiplicity of these proteins and the diversity of structural characteristics suggest that the c-di-GMP network in this enteric bacterium is highly complex and reflects the importance of having diverse mechanisms to control cellular processes in environments as diverse as soils or plants and clinical settings.

A universal genomic coordinate translator for comparative genomics

PubMed Central

2014-01-01

Background Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Results Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species. Conclusions Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken. PMID:24976580

A universal genomic coordinate translator for comparative genomics.

PubMed

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species. Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.

Long-term return behavior of Chinese whole blood donors.

PubMed

Guo, Nan; Wang, Jingxing; Yu, Qilu; Yang, Tonghan; Dong, Xiangdong; Wen, Guoxin; Tiemuer, Mei-hei-li; Li, Julin; He, Weilan; Lv, Yunlai; Ma, Hongli; Wen, Xiuqiong; Huang, Mei; Ness, Paul; Liu, Jing; Wright, David J; Nelson, Kenrad; Shan, Hua

2013-09-01

It is important to understand donor return behavior to maintain sufficient numbers of blood donors in developing countries where blood supplies are often inadequate. A total of 54,267 whole blood (WB) donors who donated between January 1 and March 31, 2008, at the five blood centers in China were followed for 2.5 years. Logistic regression was conducted to identify factors associated with their return behavior. A recurrent-event Cox proportional-hazard model was used to evaluate the overall effect of demographic variables and return behavior among first-time donors. Donors with previous donation history were more likely to return and the number of previous returns was positively associated with future return (odds ratios, 3.31, 4.82, and 8.16 for one, two to three, and more than three times compared to none). Thirty-four percent of donors (first-time donor, 21%; repeat donor, 54%) made at least one return donation, with 14% returning in the first 9 months. The multivariable logistic regression model for all WB donors and the Cox proportional hazard model for first-time donors showed consistent predictors for return: female sex, older age (≥ 25 years), larger volume (300 or 400 mL), and donating in satellite collection site. Encouraging first-time donors to make multiple donations is important for keeping adequate blood supply. The finding that first-time and repeat donors shared the same predictors for return indicates that retention strategies on repeat donors may be effective on first-time donors. Studies on motivators and barriers to return are needed, so that successful retention strategies can be tailored. © 2013 American Association of Blood Banks.

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

PubMed Central

Pohl, Nélida; Sison-Mangus, Marilou P; Yee, Emily N; Liswi, Saif W; Briscoe, Adriana D

2009-01-01

Background The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Results Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1α and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3–35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7–13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5–26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84–113 million years for the divergence of all butterfly families. Conclusion These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation. PMID:19439087

Comet nucleus and asteroid sample return missions

NASA Technical Reports Server (NTRS)

Melton, Robert G.; Thompson, Roger C.; Starchville, Thomas F., Jr.; Adams, C.; Aldo, A.; Dobson, K.; Flotta, C.; Gagliardino, J.; Lear, M.; Mcmillan, C.

1992-01-01

During the 1991-92 academic year, the Pennsylvania State University has developed three sample return missions: one to the nucleus of comet Wild 2, one to the asteroid Eros, and one to three asteroids located in the Main Belt. The primary objective of the comet nucleus sample return mission is to rendezvous with a short period comet and acquire a 10 kg sample for return to Earth. Upon rendezvous with the comet, a tethered coring and sampler drill will contact the surface and extract a two-meter core sample from the target site. Before the spacecraft returns to Earth, a monitoring penetrator containing scientific instruments will be deployed for gathering long-term data about the comet. A single asteroid sample return mission to the asteroid 433 Eros (chosen for proximity and launch opportunities) will extract a sample from the asteroid surface for return to Earth. To limit overall mission cost, most of the mission design uses current technologies, except the sampler drill design. The multiple asteroid sample return mission could best be characterized through its use of future technology including an optical communications system, a nuclear power reactor, and a low-thrust propulsion system. A low-thrust trajectory optimization code (QuickTop 2) obtained from the NASA LeRC helped in planning the size of major subsystem components, as well as the trajectory between targets.

Informed actions: where to cost effectively manage multiple threats to species to maximize return on investment.

PubMed

Auerbach, Nancy A; Tulloch, Ayesha I T; Possingham, Hugh P

Conservation practitioners, faced with managing multiple threats to biodiversity and limited funding, must prioritize investment in different management actions. From an economic perspective, it is routine practice to invest where the highest rate of return is expected. This return-on-investment (ROI) thinking can also benefit species conservation, and researchers are developing sophisticated approaches to support decision-making for cost-effective conservation. However, applied use of these approaches is limited. Managers may be wary of “black-box” algorithms or complex methods that are difficult to explain to funding agencies. As an alternative, we demonstrate the use of a basic ROI analysis for determining where to invest in cost-effective management to address threats to species. This method can be applied using basic geographic information system and spreadsheet calculations. We illustrate the approach in a management action prioritization for a biodiverse region of eastern Australia. We use ROI to prioritize management actions for two threats to a suite of threatened species: habitat degradation by cattle grazing, and predation by invasive red foxes (Vulpes vulpes). We show how decisions based on cost-effective threat management depend upon how expected benefits to species are defined and how benefits and costs co-vary. By considering a combination of species richness, restricted habitats, species vulnerability, and costs of management actions, small investments can result in greater expected benefit compared with management decisions that consider only species richness. Furthermore, a landscape management strategy that implements multiple actions is more efficient than managing only for one threat, or more traditional approaches that don't consider ROI. Our approach provides transparent and logical decision support for prioritizing different actions intended to abate threats associated with multiple species; it is of use when managers need a justifiable and repeatable approach to investment.

Protecting Biodiversity when Money Matters: Maximizing Return on Investment

PubMed Central

Underwood, Emma C.; Shaw, M. Rebecca; Wilson, Kerrie A.; Kareiva, Peter; Klausmeyer, Kirk R.; McBride, Marissa F.; Bode, Michael; Morrison, Scott A.; Hoekstra, Jonathan M.; Possingham, Hugh P.

2008-01-01

Background Conventional wisdom identifies biodiversity hotspots as priorities for conservation investment because they capture dense concentrations of species. However, density of species does not necessarily imply conservation ‘efficiency’. Here we explicitly consider conservation efficiency in terms of species protected per dollar invested. Methodology/Principal Findings We apply a dynamic return on investment approach to a global biome and compare it with three alternate priority setting approaches and a random allocation of funding. After twenty years of acquiring habitat, the return on investment approach protects between 32% and 69% more species compared to the other priority setting approaches. To correct for potential inefficiencies of protecting the same species multiple times we account for the complementarity of species, protecting up to three times more distinct vertebrate species than alternate approaches. Conclusions/Significance Incorporating costs in a return on investment framework expands priorities to include areas not traditionally highlighted as priorities based on conventional irreplaceability and vulnerability approaches. PMID:18231601

Maternal perspectives on postpartum return to the workplace.

PubMed

Nichols, Mary R; Roux, Gayle M

2004-01-01

To describe maternal perceptions about postpartum return to the workplace. The research framework was McCubbin and McCubbin's Resiliency Model of Family Stress, Adjustment, and Adaptation. Employed, postpartum women, who resided in six different states, were recruited from day care and primary care settings to participate in this descriptive study. Seventy-four employed, married women, who returned to the workplace within one year after childbirth. As part of a larger study, perceptions about combining multiple roles after return to the workplace are the focus for this report. Participants responded to open-ended questions about their return to the workplace during the first months after giving birth. Content analysis of those responses resulted in two major categories, Resiliency Challenges: Negative Aspects (role conflict/overload, family stress, family/child issues, finances, psychosocial issues) and Resiliency Building: Positive Aspects (social support, maternal role satisfaction, positive adaptation, career role satisfaction). The data support the premise that employed women view returning to the workforce as having more challenges than they expected because the experience was viewed as being mostly negative. Preparing for return to the workplace is an important, but neglected, topic that needs to be addressed and defined more clearly in the literature. Therefore, future research is needed to identify resources and interventions that will help women experience fewer challenges associated with postpartum employment.

Application of a multiple scattering model to estimate optical depth, lidar ratio and ice crystal effective radius of cirrus clouds observed with lidar.

NASA Astrophysics Data System (ADS)

Gouveia, Diego; Baars, Holger; Seifert, Patric; Wandinger, Ulla; Barbosa, Henrique; Barja, Boris; Artaxo, Paulo; Lopes, Fabio; Landulfo, Eduardo; Ansmann, Albert

2018-04-01

Lidar measurements of cirrus clouds are highly influenced by multiple scattering (MS). We therefore developed an iterative approach to correct elastic backscatter lidar signals for multiple scattering to obtain best estimates of single-scattering cloud optical depth and lidar ratio as well as of the ice crystal effective radius. The approach is based on the exploration of the effect of MS on the molecular backscatter signal returned from above cloud top.

Return to Sports After Multiple Trauma: Which Factors Are Responsible?-Results From a 17-Year Follow-up.

PubMed

Weber, Christian D; Horst, Klemens; Nguyen, Anthony R; Bader, Magdalena J; Probst, Christian; Zelle, Boris; Pape, Hans-Christoph; Dienstknecht, Thomas

2017-09-01

We hypothesize that the majority of polytraumatised patients are unable to maintain their preinjury level of sporting activity, and that musculoskeletal injuries are a major contributing factor. We assessed the impact of such injuries on sporting prowess, with a focus on isolating, particularly debilitating musculoskeletal trauma. We conducted a cohort study of 637 patients at a level 1 trauma centre, to assess the long-term outcome of severe trauma on return to sporting activities (RTS). Data collated on the multiply injured patient included preinjury physical activity, standardized outcome scores (SF-12, GOS, HASPOC), and clinical follow-up of at least 10 years duration. The return to preinjury sports participation was defined as a primary outcome parameter. Regression analyses were performed to identify specific injuries interfering with the RTS. Prognostic study; Level of evidence, II. Mean follow-up was 17 ± 5 years. We included 465 patients, including 207 athletic and 258 nonathletic individuals. Mean age at the time of injury was 26 ± 11.5 years and injury severity was comparable between the 2 cohorts. The deleterious effects on quality of life and the total duration of the rehabilitation process were also similar in athletes and nonathletes. Athletes were more likely to be unable to return to preinjury activities, or to return to a lower level of sporting prowess posttrauma. We identified knee injuries as the type of musculoskeletal trauma most likely to be career ending for the athlete (odds ratio 3.4, 95% confidence interval, 1.4-8.3; P = 0.008). Our results demonstrate an enforced shift from high-impact and team sports to low-impact activities after multiple trauma. Injuries of the lower extremities, especially around the knee joint, seem to have the highest lifechanging potential, preventing individuals from returning to their previous sporting activities.

[Analysis of genomic copy number variations in two unrelated neonates with 8p deletion and duplication associated with congenital heart disease].

PubMed

Mei, Mei; Yang, Lin; Zhan, Guodong; Wang, Huijun; Ma, Duan; Zhou, Wenhao; Huang, Guoying

2014-06-01

To screen for genomic copy number variations (CNVs) in two unrelated neonates with multiple congenital abnormalities using Affymetrix SNP chip and try to find the critical region associated with congenital heart disease. Two neonates were tested for genomic copy number variations by using Cytogenetic SNP chip.Rare CNVs with potential clinical significance were selected of which deletion segments' size was larger than 50 kb and duplication segments' size was larger than 150 kb based on the analysis of ChAs software, without false positive CNVs and segments of normal population. The identified CNVs were compared with those of the cases in DECIPHER and ISCA databases. Eleven rare CNVs with size from 546.6-27 892 kb were identified in the 2 neonates. The deletion region and size of case 1 were 8p23.3-p23.1 (387 912-11 506 771 bp) and 11.1 Mb respectively, the duplication region and size of case 1 were 8p23.1-p11.1 (11 508 387-43 321 279 bp) and 31.8 Mb respectively. The deletion region and size of case 2 were 8p23.3-p23.1 (46 385-7 809 878 bp) and 7.8 Mb respectively, the duplication region and size of case 2 were 8p23.1-p11.21 (12 260 914-40 917 092 bp) and 28.7 Mb respectively. The comparison with Decipher and ISCA databases supported previous viewpoint that 8p23.1 had been associated with congenital heart disease and the region between 7 809 878-11 506 771 bp may play a role in the severe cardiac defects associated with 8p23.1 deletions. Case 1 had serious cardiac abnormalities whose GATA4 was located in the duplication segment and the copy number increased while SOX7 was located in the deletion segment and the copy number decreased. The region between 7 809 878-11 506 771 bp in 8p23.1 is associated with heart defects and copy number variants of SOX7 and GATA4 may result in congenital heart disease.

Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy

PubMed Central

Lohr, Jens G.; Stojanov, Petar; Carter, Scott L.; Cruz-Gordillo, Peter; Lawrence, Michael S.; Auclair, Daniel; Sougnez, Carrie; Knoechel, Birgit; Gould, Joshua; Saksena, Gordon; Cibulskis, Kristian; McKenna, Aaron; Chapman, Michael A.; Straussman, Ravid; Levy, Joan; Perkins, Louise M.; Keats, Jonathan J.; Schumacher, Steven E.; Rosenberg, Mara; Getz, Gad

2014-01-01

SUMMARY We performed massively parallel sequencing of paired tumor/normal samples from 203 multiple myeloma (MM) patients and identified significantly mutated genes and copy number alterations, and discovered putative tumor suppressor genes by determining homozygous deletions and loss-of-heterozygosity. We observed frequent mutations in KRAS (particularly in previously treated patients), NRAS, BRAF, FAM46C, TP53 and DIS3 (particularly in non-hyperdiploid MM). Mutations were often present in subclonal populations, and multiple mutations within the same pathway (e.g. KRAS, NRAS and BRAF) were observed in the same patient. In vitro modeling predicts only partial treatment efficacy of targeting subclonal mutations, and even growth promotion of non-mutated subclones in some cases. These results emphasize the importance of heterogeneity analysis for treatment decisions. PMID:24434212

Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy.

PubMed

Lohr, Jens G; Stojanov, Petar; Carter, Scott L; Cruz-Gordillo, Peter; Lawrence, Michael S; Auclair, Daniel; Sougnez, Carrie; Knoechel, Birgit; Gould, Joshua; Saksena, Gordon; Cibulskis, Kristian; McKenna, Aaron; Chapman, Michael A; Straussman, Ravid; Levy, Joan; Perkins, Louise M; Keats, Jonathan J; Schumacher, Steven E; Rosenberg, Mara; Getz, Gad; Golub, Todd R

2014-01-13

We performed massively parallel sequencing of paired tumor/normal samples from 203 multiple myeloma (MM) patients and identified significantly mutated genes and copy number alterations and discovered putative tumor suppressor genes by determining homozygous deletions and loss of heterozygosity. We observed frequent mutations in KRAS (particularly in previously treated patients), NRAS, BRAF, FAM46C, TP53, and DIS3 (particularly in nonhyperdiploid MM). Mutations were often present in subclonal populations, and multiple mutations within the same pathway (e.g., KRAS, NRAS, and BRAF) were observed in the same patient. In vitro modeling predicts only partial treatment efficacy of targeting subclonal mutations, and even growth promotion of nonmutated subclones in some cases. These results emphasize the importance of heterogeneity analysis for treatment decisions. Copyright © 2014 Elsevier Inc. All rights reserved.

Internal cycle modeling and environmental assessment of multiple cycle consumer products

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

Tsiliyannis, C.A., E-mail: anion@otenet.gr

2012-01-15

Highlights: Black-Right-Pointing-Pointer Dynamic flow models are presented for remanufactured, reused or recycled products. Black-Right-Pointing-Pointer Early loss and stochastic return are included for fast and slow cycling products. Black-Right-Pointing-Pointer The reuse-to-input flow ratio (Internal Cycle Factor, ICF) is determined. Black-Right-Pointing-Pointer The cycle rate, which is increasing with the ICF, monitors eco-performance. Black-Right-Pointing-Pointer Early internal cycle losses diminish the ICF, the cycle rate and performance. - Abstract: Dynamic annual flow models incorporating consumer discard and usage loss and featuring deterministic and stochastic end-of-cycle (EOC) return by the consumer are developed for reused or remanufactured products (multiple cycle products, MCPs), including fast andmore » slow cycling, short and long-lived products. It is shown that internal flows (reuse and overall consumption) increase proportionally to the dimensionless internal cycle factor (ICF) which is related to environmental impact reduction factors. The combined reuse/recycle (or cycle) rate is shown capable for shortcut, albeit effective, monitoring of environmental performance in terms of waste production, virgin material extraction and manufacturing impacts of all MCPs, a task, which physical variables (lifetime, cycling frequency, mean or total number of return trips) and conventional rates, via which environmental policy has been officially implemented (e.g. recycling rate) cannot accomplish. The cycle rate is shown to be an increasing (hyperbolic) function of ICF. The impact of the stochastic EOC return characteristics on total reuse and consumption flows, as well as on eco-performance, is assessed: symmetric EOC return has a small, positive effect on performance compared to deterministic, while early shifted EOC return is more beneficial. In order to be efficient, environmental policy should set higher minimum reuse targets for higher trippage MCPs. The results may serve for monitoring, flow accounting and comparative eco-assessment of MCPs. They may be useful in identifying reachable and efficient reuse/recycle targets for consumer products and in planning return via appropriate labelling and digital coding for enhancing environmental performance, while satisfying consumer demand.« less

Multivariate multiscale entropy of financial markets

NASA Astrophysics Data System (ADS)

Lu, Yunfan; Wang, Jun

2017-11-01

In current process of quantifying the dynamical properties of the complex phenomena in financial market system, the multivariate financial time series are widely concerned. In this work, considering the shortcomings and limitations of univariate multiscale entropy in analyzing the multivariate time series, the multivariate multiscale sample entropy (MMSE), which can evaluate the complexity in multiple data channels over different timescales, is applied to quantify the complexity of financial markets. Its effectiveness and advantages have been detected with numerical simulations with two well-known synthetic noise signals. For the first time, the complexity of four generated trivariate return series for each stock trading hour in China stock markets is quantified thanks to the interdisciplinary application of this method. We find that the complexity of trivariate return series in each hour show a significant decreasing trend with the stock trading time progressing. Further, the shuffled multivariate return series and the absolute multivariate return series are also analyzed. As another new attempt, quantifying the complexity of global stock markets (Asia, Europe and America) is carried out by analyzing the multivariate returns from them. Finally we utilize the multivariate multiscale entropy to assess the relative complexity of normalized multivariate return volatility series with different degrees.

[Sulfide ooze mud and sodium chloride baths in treating osteoarthrosis patients].

PubMed

Novikova, N V

1989-01-01

Humoral immunity initially affected in patients with osteoarthrosis returns to normal under the influence of a multiple-modality treatment involving application of sulphide moor in combination with sodium chloride baths.

Energy cost and return for hunting in African wild dogs and cheetahs.

PubMed

Hubel, Tatjana Y; Myatt, Julia P; Jordan, Neil R; Dewhirst, Oliver P; McNutt, J Weldon; Wilson, Alan M

2016-03-29

African wild dogs (Lycaon pictus) are reported to hunt with energetically costly long chase distances. We used high-resolution GPS and inertial technology to record 1,119 high-speed chases of all members of a pack of six adult African wild dogs in northern Botswana. Dogs performed multiple short, high-speed, mostly unsuccessful chases to capture prey, while cheetahs (Acinonyx jubatus) undertook even shorter, higher-speed hunts. We used an energy balance model to show that the energy return from group hunting and feeding substantially outweighs the cost of multiple short chases, which indicates that African wild dogs are more energetically robust than previously believed. Comparison with cheetah illustrates the trade-off between sheer athleticism and high individual kill rate characteristic of cheetahs, and the energetic robustness of frequent opportunistic group hunting and feeding by African wild dogs.

Hypnotically facilitated exposure response prevention therapy for an OIF veteran with OCD.

PubMed

Proescher, Eric J

2010-07-01

The highly stressful conditions of a war zone may exacerbate or trigger a wide variety of symptoms including Obsessive Compulsive Disorder (OCD) once a service member returns home. Service members and new veterans of the Iraq and Afghanistan wars present to treatment with multiple psychosocial concerns and co-morbid psychiatric conditions. Evidence-based treatments including exposure based therapies are commonly recommended for use with returning veterans. Although studies support the efficacy of Exposure Response Prevention (ERP) therapy for treating OCD, eligibility for these studies limits participation to subjects who self-report a well-defined, circumscribed complaint. This approach is not typical of clinic clients who, more often than not, report multiple psychological issues. The following individual case study demonstrates how integrating hypnosis facilitated the cognitive-behavioral ERP therapy and treatment for a patient suffering from OCD.

Sexual cognitive predictors of sexual communication in junior college adolescents: medical student perspectives.

PubMed

Lou, Jiunn-Horng; Chen, Sheng-Hwang; Yu, Hsing-Yi; Lin, Yen-Chin; Li, Ren-Hau

2010-12-01

Further understanding the relationship between sexual cognition and sexual communication in adolescents may facilitate sexual health promotion in this population. This study was designed to investigate associations between sexual cognitive variables and sexual communication in adolescents. This study used a cross-sectional research design with conventional sampling. Data were collected from one medical college in central Taiwan. A total of 900 questionnaires were dispatched, with 748 copies returned, giving a response rate of 83.1%. Structural questionnaires were designed to collect demographic data, sexual self-concept inventory, sexual risk cognition, sexual self-efficacy, and sexual communication scale. This study applied statistical methods, including descriptive statistics, Pearson product-moment correlation, and multiple regression analysis. Major findings revealed that (a) adolescents talked about sexual activity and sexual issues with their parents at a moderate level (mean = 2.52, SD = 1.24), (b) all sexual cognitive variables (sexual self-concept, sexual risk cognitions, and sexual self-efficacy) correlated positively with sexual communication, and (c) predictors of sexual communication were supported by demographic data (having heterosexual friends, satisfaction with heterosexual friends, and duration of relationships with heterosexual friends) and sexual cognitive variables, which accounted for 62.0% of variance. Study results can contribute to the development of safe sexual health programs and improve healthcare provider knowledge of sexual communication among adolescents. More sexual communication between adolescents and their parents is encouraged. Moreover, sexual health programs must give increased focus on the issue of adolescent sexual cognition to help encourage increased discussion between adolescents and their parents regarding sexual activity and issues.

Pessimistic orientation in relation to telomere length in older men: the VA Normative Aging Study

PubMed Central

Ikeda, Ai; Schwartz, Joel; Peters, Junenette L.; Baccarelli, Andrea A.; Hoxha, Mirjam; Dioni, Laura; Spiro, Avron; Sparrow, David; Vokonas, Pantel; Kubzansky, Laura D.

2014-01-01

Background Recent research suggests pessimistic orientation is associated with shorter leukocyte telomere length (LTL). However, this is the first study to look not only at effects of pessimistic orientation on average LTL at multiple time points, but also at effects on the rate of change in LTL over time. Methods Participants were older men from the VA Normative Aging Study (n=490). The Life Orientation Test (LOT) was used to measure optimistic and pessimistic orientations at study baseline, and relative LTL by telomere to single copy gene ratio (T:S ratio) was obtained repeatedly over the course of the study (1999-2008). A total of 1,010 observations were included in the analysis. Linear mixed effect models with a random subject intercept were used to estimate associations. Results Higher pessimistic orientation scores were associated with shorter average LTL (percent difference by 1-SD increase in pessimistic orientation (95% CI): -3.08 (-5.62, -0.46)), and the finding was maintained after adjusting for the higher likelihood that healthier individuals return for follow-up visits (-3.44 (-5.95,-0.86)). However, pessimistic orientation scores were not associated with rate of change in LTL over time. No associations were found between overall optimism and optimistic orientation subscale scores and LTL. Conclusion Higher pessimistic orientation scores were associated with shorter LTL in older men. While there was no evidence that pessimistic orientation was associated with rate of change in LTL over time, higher levels of pessimistic orientation were associated with shorter LTL at baseline and this association persisted over time. PMID:24636503

Genomic profiles of low-grade murine gliomas evolve during progression to glioblastoma. | Office of Cancer Genomics

Cancer.gov

Background: Gliomas are diverse neoplasms with multiple molecular subtypes. How tumor-initiating mutations relate to molecular subtypes as these tumors evolve during malignant progression remains unclear.Methods: We used genetically engineered mouse models, histopathology, genetic lineage tracing, expression profiling, and copy number analyses to examine how genomic tumor diversity evolves during the course of malignant progression from low- to high-grade disease.

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum

DOE PAGES

De León, Kara B.; Utturkar, Sagar M.; Camilleri, Laura B.; ...

2015-09-24

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Finally, nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.

Integration of multi-omics data for integrative gene regulatory network inference.

PubMed

Zarayeneh, Neda; Ko, Euiseong; Oh, Jung Hun; Suh, Sang; Liu, Chunyu; Gao, Jean; Kim, Donghyun; Kang, Mingon

2017-01-01

Gene regulatory networks provide comprehensive insights and indepth understanding of complex biological processes. The molecular interactions of gene regulatory networks are inferred from a single type of genomic data, e.g., gene expression data in most research. However, gene expression is a product of sequential interactions of multiple biological processes, such as DNA sequence variations, copy number variations, histone modifications, transcription factors, and DNA methylations. The recent rapid advances of high-throughput omics technologies enable one to measure multiple types of omics data, called 'multi-omics data', that represent the various biological processes. In this paper, we propose an Integrative Gene Regulatory Network inference method (iGRN) that incorporates multi-omics data and their interactions in gene regulatory networks. In addition to gene expressions, copy number variations and DNA methylations were considered for multi-omics data in this paper. The intensive experiments were carried out with simulation data, where iGRN's capability that infers the integrative gene regulatory network is assessed. Through the experiments, iGRN shows its better performance on model representation and interpretation than other integrative methods in gene regulatory network inference. iGRN was also applied to a human brain dataset of psychiatric disorders, and the biological network of psychiatric disorders was analysed.

Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder

PubMed Central

Elia, Josephine; Glessner, Joseph T; Wang, Kai; Takahashi, Nagahide; Shtir, Corina J; Hadley, Dexter; Sleiman, Patrick M A; Zhang, Haitao; Kim, Cecilia E; Robison, Reid; Lyon, Gholson J; Flory, James H; Bradfield, Jonathan P; Imielinski, Marcin; Hou, Cuiping; Frackelton, Edward C; Chiavacci, Rosetta M; Sakurai, Takeshi; Rabin, Cara; Middleton, Frank A; Thomas, Kelly A; Garris, Maria; Mentch, Frank; Freitag, Christine M; Steinhausen, Hans-Christoph; Todorov, Alexandre A; Reif, Andreas; Rothenberger, Aribert; Franke, Barbara; Mick, Eric O; Roeyers, Herbert; Buitelaar, Jan; Lesch, Klaus-Peter; Banaschewski, Tobias; Ebstein, Richard P; Mulas, Fernando; Oades, Robert D; Sergeant, Joseph; Sonuga-Barke, Edmund; Renner, Tobias J; Romanos, Marcel; Romanos, Jasmin; Warnke, Andreas; Walitza, Susanne; Meyer, Jobst; Pálmason, Haukur; Seitz, Christiane; Loo, Sandra K; Smalley, Susan L; Biederman, Joseph; Kent, Lindsey; Asherson, Philip; Anney, Richard J L; Gaynor, J William; Shaw, Philip; Devoto, Marcella; White, Peter S; Grant, Struan F A; Buxbaum, Joseph D; Rapoport, Judith L; Williams, Nigel M; Nelson, Stanley F; Faraone, Stephen V; Hakonarson, Hakon

2014-01-01

Attention deficit hyperactivity disorder (ADHD) is a common, heritable neuropsychiatric disorder of unknown etiology. We performed a whole-genome copy number variation (CNV) study on 1,013 cases with ADHD and 4,105 healthy children of European ancestry using 550,000 SNPs. We evaluated statistically significant findings in multiple independent cohorts, with a total of 2,493 cases with ADHD and 9,222 controls of European ancestry, using matched platforms. CNVs affecting metabotropic glutamate receptor genes were enriched across all cohorts (P = 2.1 × 10−9). We saw GRM5 (encoding glutamate receptor, metabotropic 5) deletions in ten cases and one control (P = 1.36 × 10−6). We saw GRM7 deletions in six cases, and we saw GRM8 deletions in eight cases and no controls. GRM1 was duplicated in eight cases. We experimentally validated the observed variants using quantitative RT-PCR. A gene network analysis showed that genes interacting with the genes in the GRM family are enriched for CNVs in ~10% of the cases (P = 4.38 × 10−10) after correction for occurrence in the controls. We identified rare recurrent CNVs affecting glutamatergic neurotransmission genes that were overrepresented in multiple ADHD cohorts. PMID:22138692

Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof.

PubMed

Nolden, T; Pfaff, F; Nemitz, S; Freuling, C M; Höper, D; Müller, T; Finke, Stefan

2016-04-05

Reverse genetics approaches are indispensable tools for proof of concepts in virus replication and pathogenesis. For negative strand RNA viruses (NSVs) the limited number of infectious cDNA clones represents a bottleneck as clones are often generated from cell culture adapted or attenuated viruses, with limited potential for pathogenesis research. We developed a system in which cDNA copies of complete NSV genomes were directly cloned into reverse genetics vectors by linear-to-linear RedE/T recombination. Rapid cloning of multiple rabies virus (RABV) full length genomes and identification of clones identical to field virus consensus sequence confirmed the approache's reliability. Recombinant viruses were recovered from field virus cDNA clones. Similar growth kinetics of parental and recombinant viruses, preservation of field virus characters in cell type specific replication and virulence in the mouse model were confirmed. Reduced titers after reporter gene insertion indicated that the low level of field virus replication is affected by gene insertions. The flexibility of the strategy was demonstrated by cloning multiple copies of an orthobunyavirus L genome segment. This important step in reverse genetics technology development opens novel avenues for the analysis of virus variability combined with phenotypical characterization of recombinant viruses at a clonal level.

Integration of multi-omics data for integrative gene regulatory network inference

PubMed Central

Zarayeneh, Neda; Ko, Euiseong; Oh, Jung Hun; Suh, Sang; Liu, Chunyu; Gao, Jean; Kim, Donghyun

2017-01-01

Gene regulatory networks provide comprehensive insights and indepth understanding of complex biological processes. The molecular interactions of gene regulatory networks are inferred from a single type of genomic data, e.g., gene expression data in most research. However, gene expression is a product of sequential interactions of multiple biological processes, such as DNA sequence variations, copy number variations, histone modifications, transcription factors, and DNA methylations. The recent rapid advances of high-throughput omics technologies enable one to measure multiple types of omics data, called ‘multi-omics data’, that represent the various biological processes. In this paper, we propose an Integrative Gene Regulatory Network inference method (iGRN) that incorporates multi-omics data and their interactions in gene regulatory networks. In addition to gene expressions, copy number variations and DNA methylations were considered for multi-omics data in this paper. The intensive experiments were carried out with simulation data, where iGRN’s capability that infers the integrative gene regulatory network is assessed. Through the experiments, iGRN shows its better performance on model representation and interpretation than other integrative methods in gene regulatory network inference. iGRN was also applied to a human brain dataset of psychiatric disorders, and the biological network of psychiatric disorders was analysed. PMID:29354189

A model-based approach to wildland fire reconstruction using sediment charcoal records

USGS Publications Warehouse

Itter, Malcolm S.; Finley, Andrew O.; Hooten, Mevin B.; Higuera, Philip E.; Marlon, Jennifer R.; Kelly, Ryan; McLachlan, Jason S.

2017-01-01

Lake sediment charcoal records are used in paleoecological analyses to reconstruct fire history, including the identification of past wildland fires. One challenge of applying sediment charcoal records to infer fire history is the separation of charcoal associated with local fire occurrence and charcoal originating from regional fire activity. Despite a variety of methods to identify local fires from sediment charcoal records, an integrated statistical framework for fire reconstruction is lacking. We develop a Bayesian point process model to estimate the probability of fire associated with charcoal counts from individual-lake sediments and estimate mean fire return intervals. A multivariate extension of the model combines records from multiple lakes to reduce uncertainty in local fire identification and estimate a regional mean fire return interval. The univariate and multivariate models are applied to 13 lakes in the Yukon Flats region of Alaska. Both models resulted in similar mean fire return intervals (100–350 years) with reduced uncertainty under the multivariate model due to improved estimation of regional charcoal deposition. The point process model offers an integrated statistical framework for paleofire reconstruction and extends existing methods to infer regional fire history from multiple lake records with uncertainty following directly from posterior distributions.

Continued Development of in Situ Geochronology for Planetary Using KArLE (Potassium-Argon Laser Experiment)

NASA Technical Reports Server (NTRS)

Devismes, D.; Cohen, B. A.

2016-01-01

Geochronology is a fundamental measurement for planetary samples, providing the ability to establish an absolute chronology for geological events, including crystallization history, magmatic evolution, and alteration events, and providing global and solar system context for such events. The capability for in situ geochronology will open up the ability for geochronology to be accomplished as part of lander or rover complement, on multiple samples rather than just those returned. An in situ geochronology package can also complement sample return missions by identifying the most interesting rocks to cache or return to Earth. The K-Ar radiometric dating approach to in situ dating has been validated by the Curiosity rover on Mars as well as several laboratories on Earth. Several independent projects developing in situ rock dating for planetary samples, based on the K-Ar method, are giving promising results. Among them, the Potassium (K)-Argon Laser Experiment (KArLE) at MSFC is based on techniques already in use for in planetary exploration, specifically, Laser-induced Breakdown Spectroscopy (LIBS, used on the Curiosity Chemcam), mass spectroscopy (used on multiple planetary missions, including Curiosity, ExoMars, and Rosetta), and optical imaging (used on most missions).

Finding Multiple Internal Rates of Return for a Project with Non-Conventional Cash Flows: Utilizing Popular Financial/Graphing Calculators and Spreadsheet Software

ERIC Educational Resources Information Center

Chen, Jeng-Hong

2008-01-01

This study demonstrates that a popular graphing calculator among students, TI-83 Plus, has a powerful function to draw the NPV profile and find the accurate multiple IRRs for a project with non-conventional cash flows. However, finance textbooks or related supplementary materials do not provide students instructions for this part. The detailed…

The dynamics of genome replication using deep sequencing

PubMed Central

Müller, Carolin A.; Hawkins, Michelle; Retkute, Renata; Malla, Sunir; Wilson, Ray; Blythe, Martin J.; Nakato, Ryuichiro; Komata, Makiko; Shirahige, Katsuhiko; de Moura, Alessandro P.S.; Nieduszynski, Conrad A.

2014-01-01

Eukaryotic genomes are replicated from multiple DNA replication origins. We present complementary deep sequencing approaches to measure origin location and activity in Saccharomyces cerevisiae. Measuring the increase in DNA copy number during a synchronous S-phase allowed the precise determination of genome replication. To map origin locations, replication forks were stalled close to their initiation sites; therefore, copy number enrichment was limited to origins. Replication timing profiles were generated from asynchronous cultures using fluorescence-activated cell sorting. Applying this technique we show that the replication profiles of haploid and diploid cells are indistinguishable, indicating that both cell types use the same cohort of origins with the same activities. Finally, increasing sequencing depth allowed the direct measure of replication dynamics from an exponentially growing culture. This is the first time this approach, called marker frequency analysis, has been successfully applied to a eukaryote. These data provide a high-resolution resource and methodological framework for studying genome biology. PMID:24089142

Writing Forces Associated With Four Pencil Grasp Patterns in Grade 4 Children

PubMed Central

Schwellnus, Heidi; Carnahan, Heather; Kushki, Azadeh; Polatajko, Helene; Missiuna, Cheryl

2013-01-01

OBJECTIVE. We investigated differences in handwriting kinetics, speed, and legibility among four pencil grasps after a 10-min copy task. METHOD. Seventy-four Grade 4 students completed a handwriting assessment before and after a copy task. Grip and axial forces were measured with an instrumented stylus and force-sensitive tablet. We used multiple linear regression to analyze the relationship between grasp pattern and grip and axial forces. RESULTS. We found no kinetic differences among grasps, whether considered individually or grouped by the number of fingers on the barrel. However, when grasps were grouped according to the thumb position, the adducted grasps exhibited higher mean grip and axial forces. CONCLUSION. Grip forces were generally similar across the different grasps. Kinetic differences resulting from thumb position seemed to have no bearing on speed and legibility. Interventions for handwriting difficulties should focus more on speed and letter formation than on grasp pattern. PMID:23433277

Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.

PubMed

Ostrovnaya, Irina; Seshan, Venkatraman E; Olshen, Adam B; Begg, Colin B

2011-06-15

If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called 'Clonality'. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results. Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

PubMed

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

PubMed Central

Artzy-Randrup, Yael; Rorick, Mary M; Day, Karen; Chen, Donald; Dobson, Andrew P; Pascual, Mercedes

2012-01-01

The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity. DOI: http://dx.doi.org/10.7554/eLife.00093.001 PMID:23251784

Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data.

PubMed

Gao, Jianing; Wan, Changlin; Zhang, Huan; Li, Ao; Zang, Qiguang; Ban, Rongjun; Ali, Asim; Yu, Zhenghua; Shi, Qinghua; Jiang, Xiaohua; Zhang, Yuanwei

2017-10-03

Copy number variations (CNVs) are the main genetic structural variations in cancer genome. Detecting CNVs in genetic exome region is efficient and cost-effective in identifying cancer associated genes. Many tools had been developed accordingly and yet these tools lack of reliability because of high false negative rate, which is intrinsically caused by genome exonic bias. To provide an alternative option, here, we report Anaconda, a comprehensive pipeline that allows flexible integration of multiple CNV-calling methods and systematic annotation of CNVs in analyzing WES data. Just by one command, Anaconda can generate CNV detection result by up to four CNV detecting tools. Associated with comprehensive annotation analysis of genes involved in shared CNV regions, Anaconda is able to deliver a more reliable and useful report in assistance with CNV-associate cancer researches. Anaconda package and manual can be freely accessed at http://mcg.ustc.edu.cn/bsc/ANACONDA/ .

Are referring doctors ready for enterprise and community wide immediate image and report access?

PubMed

Wadley, Brian D; Hayward, Ulrike; Trambert, Michael; Kywi, Alberto; Hartzman, Steve

2002-01-01

At most medical centers film-based radiology requires that single or multiple copies of patient exams and reports be distributed for results communication. A successful picture archiving and communication system (PACS) should provide a means to improve upon this inefficient paradigm, with universal access to imagery and exam results on demand at the user's convenience. Enterprise and community-wide experience with universal PACS access is reviewed. Referring physicians were surveyed about their experience with PACS, with regard to acceptance, productivity, frequency of usage, and impact on patient care. Web audit trails were used to assess physician usage. Film printing logs were reviewed. The filmless paradigm was highly regarded and frequently used by nearly all users. Significant productivity benefits were gleaned by all of the referring physicians. Patient quality of care benefitted from more efficient communication of results. Very small quantities of film were used for printing of exams, typically for patient copies.

Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data

PubMed Central

Xiong, Lie; Kuan, Pei-Fen; Tian, Jianan; Keles, Sunduz; Wang, Sijian

2015-01-01

In this paper, we propose a novel multivariate component-wise boosting method for fitting multivariate response regression models under the high-dimension, low sample size setting. Our method is motivated by modeling the association among different biological molecules based on multiple types of high-dimensional genomic data. Particularly, we are interested in two applications: studying the influence of DNA copy number alterations on RNA transcript levels and investigating the association between DNA methylation and gene expression. For this purpose, we model the dependence of the RNA expression levels on DNA copy number alterations and the dependence of gene expression on DNA methylation through multivariate regression models and utilize boosting-type method to handle the high dimensionality as well as model the possible nonlinear associations. The performance of the proposed method is demonstrated through simulation studies. Finally, our multivariate boosting method is applied to two breast cancer studies. PMID:26609213

Integrative Analysis Reveals an Outcome-associated and Targetable Pattern of p53 and Cell Cycle Deregulation in Diffuse Large B-cell Lymphoma

PubMed Central

Monti, Stefano; Chapuy, Bjoern; Takeyama, Kunihiko; Rodig, Scott J; Hao, Yangsheng; Yeda, Kelly T.; Inguilizian, Haig; Mermel, Craig; Curie, Treeve; Dogan, Ahmed; Kutok, Jeffery L; Beroukim, Rameen; Neuberg, Donna; Habermann, Thomas; Getz, Gad; Kung, Andrew L; Golub, Todd R; Shipp, Margaret A

2013-01-01

Summary Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease with a high proliferation rate. By integrating copy number data with transcriptional profiles and performing pathway analysis in primary DLBCLs, we identified a comprehensive set of copy number alterations (CNAs) that decreased p53 activity and perturbed cell cycle regulation. Primary tumors either had multiple complementary alterations of p53 and cell cycle components or largely lacked these lesions. DLBCLs with p53 and cell cycle pathway CNAs had decreased abundance of p53 target transcripts and increased expression of E2F target genes and the Ki67 proliferation marker. CNAs of the CDKN2A-TP53-RB-E2F axis provide a structural basis for increased proliferation in DLBCL, predict outcome with current therapy and suggest targeted treatment approaches. PMID:22975378

Using Pinochle to motivate the restricted combinations with repetitions problem

NASA Astrophysics Data System (ADS)

Gorman, Patrick S.; Kunkel, Jeffrey D.; Vasko, Francis J.

2011-07-01

A standard example used in introductory combinatoric courses is to count the number of five-card poker hands possible from a straight deck of 52 distinct cards. A more interesting problem is to count the number of distinct hands possible from a Pinochle deck in which there are multiple, but obviously limited, copies of each type of card (two copies for single-deck, four for double deck). This problem is more interesting because our only concern is to count the number of distinguishable hands that can be dealt. In this note, under various scenarios, we will discuss two combinatoric techniques for counting these hands; namely, the inclusion-exclusion principle and generating functions. We will then show that these Pinochle examples motivate a general counting formula for what are called 'regular' combinations by Riordan. Finally, we prove the correctness of this formula using generating functions.

Processing the Viking lander camera data

NASA Technical Reports Server (NTRS)

Levinthal, E. C.; Tucker, R.; Green, W.; Jones, K. L.

1977-01-01

Over 1000 camera events were returned from the two Viking landers during the Primary Mission. A system was devised for processing camera data as they were received, in real time, from the Deep Space Network. This system provided a flexible choice of parameters for three computer-enhanced versions of the data for display or hard-copy generation. Software systems allowed all but 0.3% of the imagery scan lines received on earth to be placed correctly in the camera data record. A second-order processing system was developed which allowed extensive interactive image processing including computer-assisted photogrammetry, a variety of geometric and photometric transformations, mosaicking, and color balancing using six different filtered images of a common scene. These results have been completely cataloged and documented to produce an Experiment Data Record.

Earth observation taken by the Expedition 43 crew

NASA Image and Video Library

2015-04-21

ISS043E128768 (04/21/2015) --- NASA astronaut Scott Kelly on the International Space Station May 6, 2015 tweeted this image out of an Earth observation as part of his Space Geo trivia contest. Scott tweeted this comment and clue: "#SpaceGeo! A serpent is known for deceptive traits, but don’t let this snake pull the wool over your eyes. Name it!” Congratulations to @splinesmith for correctly identifying this image first, : #BighornRiver Montana/Wyoming named in 1805 for Bighorn sheep along its banks. He will receive an autographed copy of this image when Scott returns to Earth in March 2016. Learn more about #SpaceGeo and play along every Wednesday for your chance to win: http://www.nasa.gov/feature/where-over-the-world-is-astronaut-scott-kelly

Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma

PubMed Central

Thomas, Rachael; Borst, Luke; Rotroff, Daniel; Motsinger-Reif, Alison; Lindblad-Toh, Kerstin; Modiano, Jaime F.; Breen, Matthew

2017-01-01

Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24 and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near two-fold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22% versus 40%). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly-distinct subtypes of canine hemangiosarcoma. PMID:24599718

Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma.

PubMed

Thomas, Rachael; Borst, Luke; Rotroff, Daniel; Motsinger-Reif, Alison; Lindblad-Toh, Kerstin; Modiano, Jaime F; Breen, Matthew

2014-09-01

Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.

Diverse Forms of RPS9 Splicing Are Part of an Evolving Autoregulatory Circuit

PubMed Central

Plocik, Alex M.; Guthrie, Christine

2012-01-01

Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and in that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit. To test for similar intron function in animals, we performed an experimental test and comparative analyses for autoregulation among distantly related animal RPS9 orthologs. Overexpression of an exogenous RpS9 copy in Drosophila melanogaster S2 cells induced alternative splicing and degradation of the endogenous copy by nonsense-mediated decay (NMD). Also, analysis of expressed sequence tag data from distantly related animals, including Homo sapiens and Ciona intestinalis, revealed diverse alternatively-spliced RPS9 isoforms predicted to elicit NMD. We propose that multiple forms of splicing regulation among RPS9 orthologs from various eukaryotes operate analogously to translational repression of the alpha operon by S4, the distant prokaryotic ortholog. Thus, RPS9 orthologs appear to have independently evolved variations on a fundamental autoregulatory circuit. PMID:22479208

Adapting Poisson-Boltzmann to the self-consistent mean field theory: Application to protein side-chain modeling

NASA Astrophysics Data System (ADS)

Koehl, Patrice; Orland, Henri; Delarue, Marc

2011-08-01

We present an extension of the self-consistent mean field theory for protein side-chain modeling in which solvation effects are included based on the Poisson-Boltzmann (PB) theory. In this approach, the protein is represented with multiple copies of its side chains. Each copy is assigned a weight that is refined iteratively based on the mean field energy generated by the rest of the protein, until self-consistency is reached. At each cycle, the variational free energy of the multi-copy system is computed; this free energy includes the internal energy of the protein that accounts for vdW and electrostatics interactions and a solvation free energy term that is computed using the PB equation. The method converges in only a few cycles and takes only minutes of central processing unit time on a commodity personal computer. The predicted conformation of each residue is then set to be its copy with the highest weight after convergence. We have tested this method on a database of hundred highly refined NMR structures to circumvent the problems of crystal packing inherent to x-ray structures. The use of the PB-derived solvation free energy significantly improves prediction accuracy for surface side chains. For example, the prediction accuracies for χ1 for surface cysteine, serine, and threonine residues improve from 68%, 35%, and 43% to 80%, 53%, and 57%, respectively. A comparison with other side-chain prediction algorithms demonstrates that our approach is consistently better in predicting the conformations of exposed side chains.

Tracking vaginal, anal and oral infection in a mouse papillomavirus infection model.

PubMed

Hu, Jiafen; Budgeon, Lynn R; Cladel, Nancy M; Balogh, Karla; Myers, Roland; Cooper, Timothy K; Christensen, Neil D

2015-12-01

Noninvasive and practical techniques to longitudinally track viral infection are sought after in clinical practice. We report a proof-of-principle study to monitor the viral DNA copy number using a newly established mouse papillomavirus (MmuPV1) mucosal infection model. We hypothesized that viral presence could be identified and quantified by collecting lavage samples from cervicovaginal, anal and oral sites. Nude mice infected at these sites with infectious MmuPV1 were tracked for up to 23 weeks starting at 6 weeks post-infection. Viral DNA copy number was determined by SYBR Green Q-PCR analysis. In addition, we tracked viral DNA load through three complete oestrous cycles to pinpoint whether there was a correlation between the DNA load and the four stages of the oestrous cycle. Our results showed that high viral DNA copy number was reproducibly detected from both anal and cervicovaginal lavage samples. The infection and disease progression were further confirmed by histology, cytology, in situ hybridization, immunohistochemistry and transmission electron microscopy. Interestingly, the viral copy number fluctuated over the oestrous cycle, with the highest level at the oestrus stage, implying that multiple sampling might be necessary to provide a reliable diagnosis. Virus DNA was detected in oral lavage samples at a later time after infection. Lower viral DNA load was found in oral samples when compared with those in anal and vaginal tracts. To our knowledge, our study is the first in vivo study to sequentially monitor papillomavirus infection from mucosal anal, oral and vaginal tracts in a preclinical model.

Penalized differential pathway analysis of integrative oncogenomics studies.

PubMed

van Wieringen, Wessel N; van de Wiel, Mark A

2014-04-01

Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study involving cancer patients. The two molecular levels involved are linked through the central dogma of molecular biology. DNA copy number aberrations abound in the cancer cell. Here we investigate how these aberrations affect gene expression levels within a pathway using observational integrative genomics data of cancer patients. In particular, we aim to identify differential edges between regulatory networks of two groups involving these molecular levels. Motivated by the rate equations, the regulatory mechanism between DNA copy number aberrations and gene expression levels within a pathway is modeled by a simultaneous-equations model, for the one- and two-group case. The latter facilitates the identification of differential interactions between the two groups. Model parameters are estimated by penalized least squares using the lasso (L1) penalty to obtain a sparse pathway topology. Simulations show that the inclusion of DNA copy number data benefits the discovery of gene-gene interactions. In addition, the simulations reveal that cis-effects tend to be over-estimated in a univariate (single gene) analysis. In the application to real data from integrative oncogenomic studies we show that inclusion of prior information on the regulatory network architecture benefits the reproducibility of all edges. Furthermore, analyses of the TP53 and TGFb signaling pathways between ER+ and ER- samples from an integrative genomics breast cancer study identify reproducible differential regulatory patterns that corroborate with existing literature.

Modified screening and ranking algorithm for copy number variation detection.

PubMed

Xiao, Feifei; Min, Xiaoyi; Zhang, Heping

2015-05-01

Copy number variation (CNV) is a type of structural variation, usually defined as genomic segments that are 1 kb or larger, which present variable copy numbers when compared with a reference genome. The screening and ranking algorithm (SaRa) was recently proposed as an efficient approach for multiple change-points detection, which can be applied to CNV detection. However, some practical issues arise from application of SaRa to single nucleotide polymorphism data. In this study, we propose a modified SaRa on CNV detection to address these issues. First, we use the quantile normalization on the original intensities to guarantee that the normal mean model-based SaRa is a robust method. Second, a novel normal mixture model coupled with a modified Bayesian information criterion is proposed for candidate change-point selection and further clustering the potential CNV segments to copy number states. Simulations revealed that the modified SaRa became a robust method for identifying change-points and achieved better performance than the circular binary segmentation (CBS) method. By applying the modified SaRa to real data from the HapMap project, we illustrated its performance on detecting CNV segments. In conclusion, our modified SaRa method improves SaRa theoretically and numerically, for identifying CNVs with high-throughput genotyping data. The modSaRa package is implemented in R program and freely available at http://c2s2.yale.edu/software/modSaRa. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Copy Number Variation of KIR Genes Influences HIV-1 Control

PubMed Central

Shianna, Kevin V.; Feng, Sheng; Urban, Thomas J.; Ge, Dongliang; De Luca, Andrea; Martinez-Picado, Javier; Wolinsky, Steven M.; Martinson, Jeremy J.; Jamieson, Beth D.; Bream, Jay H.; Martin, Maureen P.; Borrow, Persephone; Letvin, Norman L.; McMichael, Andrew J.; Haynes, Barton F.; Telenti, Amalio; Carrington, Mary; Goldstein, David B.; Alter, Galit

2011-01-01

A genome-wide screen for large structural variants showed that a copy number variant (CNV) in the region encoding killer cell immunoglobulin-like receptors (KIR) associates with HIV-1 control as measured by plasma viral load at set point in individuals of European ancestry. This CNV encompasses the KIR3DL1-KIR3DS1 locus, encoding receptors that interact with specific HLA-Bw4 molecules to regulate the activation of lymphocyte subsets including natural killer (NK) cells. We quantified the number of copies of KIR3DS1 and KIR3DL1 in a large HIV-1 positive cohort, and showed that an increase in KIR3DS1 count associates with a lower viral set point if its putative ligand is present (p = 0.00028), as does an increase in KIR3DL1 count in the presence of KIR3DS1 and appropriate ligands for both receptors (p = 0.0015). We further provide functional data that demonstrate that NK cells from individuals with multiple copies of KIR3DL1, in the presence of KIR3DS1 and the appropriate ligands, inhibit HIV-1 replication more robustly, and associated with a significant expansion in the frequency of KIR3DS1+, but not KIR3DL1+, NK cells in their peripheral blood. Our results suggest that the relative amounts of these activating and inhibitory KIR play a role in regulating the peripheral expansion of highly antiviral KIR3DS1+ NK cells, which may determine differences in HIV-1 control following infection. PMID:22140359

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

PubMed Central

Sun, Kun; Jiang, Peiyong; Chan, K. C. Allen; Wong, John; Cheng, Yvonne K. Y.; Liang, Raymond H. S.; Chan, Wai-kong; Ma, Edmond S. K.; Chan, Stephen L.; Cheng, Suk Hang; Chan, Rebecca W. Y.; Tong, Yu K.; Ng, Simon S. M.; Wong, Raymond S. M.; Hui, David S. C.; Leung, Tse Ngong; Leung, Tak Y.; Lai, Paul B. S.; Chiu, Rossa W. K.; Lo, Yuk Ming Dennis

2015-01-01

Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma. PMID:26392541

The Role of Copy Number Variation in Susceptibility to Amyotrophic Lateral Sclerosis: Genome-Wide Association Study and Comparison with Published Loci

PubMed Central

Wain, Louise V.; Pedroso, Inti; Landers, John E.; Breen, Gerome; Shaw, Christopher E.; Leigh, P. Nigel; Brown, Robert H.

2009-01-01

Background The genetic contribution to sporadic amyotrophic lateral sclerosis (ALS) has not been fully elucidated. There are increasing efforts to characterise the role of copy number variants (CNVs) in human diseases; two previous studies concluded that CNVs may influence risk of sporadic ALS, with multiple rare CNVs more important than common CNVs. A little-explored issue surrounding genome-wide CNV association studies is that of post-calling filtering and merging of raw CNV calls. We undertook simulations to define filter thresholds and considered optimal ways of merging overlapping CNV calls for association testing, taking into consideration possibly overlapping or nested, but distinct, CNVs and boundary estimation uncertainty. Methodology and Principal Findings In this study we screened Illumina 300K SNP genotyping data from 730 ALS cases and 789 controls for copy number variation. Following quality control filters using thresholds defined by simulation, a total of 11321 CNV calls were made across 575 cases and 621 controls. Using region-based and gene-based association analyses, we identified several loci showing nominally significant association. However, the choice of criteria for combining calls for association testing has an impact on the ranking of the results by their significance. Several loci which were previously reported as being associated with ALS were identified here. However, of another 15 genes previously reported as exhibiting ALS-specific copy number variation, only four exhibited copy number variation in this study. Potentially interesting novel loci, including EEF1D, a translation elongation factor involved in the delivery of aminoacyl tRNAs to the ribosome (a process which has previously been implicated in genetic studies of spinal muscular atrophy) were identified but must be treated with caution due to concerns surrounding genomic location and platform suitability. Conclusions and Significance Interpretation of CNV association findings must take into account the effects of filtering and combining CNV calls when based on early genome-wide genotyping platforms and modest study sizes. PMID:19997636

Detection of Sleeping Beauty transposition in the genome of host cells by non-radioactive Southern blot analysis

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

Aravalli, Rajagopal N., E-mail: aravalli@umn.edu; Park, Chang W.; Steer, Clifford J., E-mail: steer001@umn.edu

The Sleeping Beauty transposon (SB-Tn) system is being used widely as a DNA vector for the delivery of therapeutic transgenes, as well as a tool for the insertional mutagenesis in animal models. In order to accurately assess the insertional potential and properties related to the integration of SB it is essential to determine the copy number of SB-Tn in the host genome. Recently developed SB100X transposase has demonstrated an integration rate that was much higher than the original SB10 and that of other versions of hyperactive SB transposases, such as HSB3 or HSB17. In this study, we have constructed amore » series of SB vectors carrying either a DsRed or a human β-globin transgene that was encompassed by cHS4 insulator elements, and containing the SB100X transposase gene outside the SB-Tn unit within the same vector in cis configuration. These SB-Tn constructs were introduced into the K-562 erythroid cell line, and their presence in the genomes of host cells was analyzed by Southern blot analysis using non-radioactive probes. Many copies of SB-Tn insertions were detected in host cells regardless of transgene sequences or the presence of cHS4 insulator elements. Interestingly, the size difference of 2.4 kb between insulated SB and non-insulated controls did not reflect the proportional difference in copy numbers of inserted SB-Tns. We then attempted methylation-sensitive Southern blots to assess the potential influence of cHS4 insulator elements on the epigenetic modification of SB-Tn. Our results indicated that SB100X was able to integrate at multiple sites with the number of SB-Tn copies larger than 6 kb in size. In addition, the non-radioactive Southern blot protocols developed here will be useful to detect integrated SB-Tn copies in any mammalian cell type.« less