Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.

PubMed

Yip, W S Vincent; Shigematsu, Hideki; Taylor, David W; Baserga, Susan J

2016-10-14

Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2'-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effect of Crc and Hfq proteins on the transcription, processing, and stability of the Pseudomonas putida CrcZ sRNA

PubMed Central

Hernández-Arranz, Sofía; Sánchez-Hevia, Dione; Rojo, Fernando; Moreno, Renata

2016-01-01

In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. The effect of these two proteins is antagonized by the CrcZ and CrcY small RNAs (sRNAs), the levels of which vary greatly according to growth conditions. The crcZ and crcY genes are transcribed from promoters PcrcZ and PcrcY, respectively, a process that relies on the CbrB transcriptional activator and the RpoN σ factor. Here we show that crcZ can also be transcribed from the promoter of the immediate upstream gene, cbrB, a weak constitutive promoter. The cbrB-crcZ transcript was processed to render a sRNA very similar in size to the CrcZ produced from promoter PcrcZ. The processed sRNA, termed CrcZ*, was able to antagonize Hfq/Crc because, when provided in trans, it relieved the deregulated Hfq/Crc-dependent hyperrepressing phenotype of a ΔcrcZΔcrcY strain. CrcZ* may help in attaining basal levels of CrcZ/CrcZ* that are sufficient to protect the cell from an excessive Hfq/Crc-dependent repression. Since a functional sRNA can be produced from PcrcZ, an inducible strong promoter, or by cleavage of the cbrB-crcZ mRNA, crcZ can be considered a 3′-untranslated region of the cbrB-crcZ mRNA. In the absence of Hfq, the processed form of CrcZ was not observed. In addition, we show that Crc and Hfq increase CrcZ stability, which supports the idea that these proteins can form a complex with CrcZ and protect it from degradation by RNases. PMID:27777366

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria

PubMed Central

Vogel, Jörg; Bartels, Verena; Tang, Thean Hock; Churakov, Gennady; Slagter-Jäger, Jacoba G.; Hüttenhofer, Alexander; Wagner, E. Gerhart H.

2003-01-01

Recent bioinformatics-aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot-gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co-expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III-dependent cleavage. To the best of our knowledge, this represents the first case of two non-coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half-lives (<2 to >32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed. PMID:14602901

Regulation of a polyamine transporter by the conserved 3′ UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides

PubMed Central

Peng, Tao; Berghoff, Bork A.; Oh, Jeong-Il; Weber, Lennart; Schirmer, Jasmin; Schwarz, Johannes; Glaeser, Jens; Klug, Gabriele

2016-01-01

ABSTRACT Singlet oxygen is generated by bacteriochlorophylls when light and oxygen are simultaneously present in Rhodobacter sphaeroides. Singlet oxygen triggers a specific response that is partly regulated by the alternative sigma factor RpoHI/HII. The sRNA RSs2461 has previously been identified as an RpoHI/HII-dependent sRNA and is derived from the 3′ UTR of the mRNA for an OmpR-type transcriptional regulator. Similar to the RpoHI/HII-dependent CcsR and SorY sRNAs, RSs2461 affects the resistance of R. sphaeroides against singlet oxygen and was therefore renamed here SorX. Furthermore, SorX has a strong impact on resistance against organic hydroperoxides that usually occur as secondary damages downstream of singlet oxygen. The 75-nt SorX 3′ fragment, which is generated by RNase E cleavage and highly conserved among related species, represents the functional entity. A target search identified potA mRNA, which encodes a subunit of a polyamine transporter, as a direct SorX target and stress resistance via SorX could be linked to potA. The PotABCD transporter is an uptake system for spermidine in E. coli. While spermidine is generally described as beneficial during oxidative stress, we observed significantly increased sensitivity of R. sphaeroides to organic hydroperoxides in the presence of spermidine. We therefore propose that the diminished import of spermidine, due to down-regulation of potA by SorX, counteracts oxidative stress. Together with results from other studies this underlines the importance of regulated transport to bacterial stress defense. PMID:27420112

Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1.

PubMed

Georg, Jens; Kostova, Gergana; Vuorijoki, Linda; Schön, Verena; Kadowaki, Taro; Huokko, Tuomas; Baumgartner, Desirée; Müller, Maximilian; Klähn, Stephan; Allahverdiyeva, Yagut; Hihara, Yukako; Futschik, Matthias E; Aro, Eva-Mari; Hess, Wolfgang R

2017-05-22

Oxygenic photosynthesis crucially depends on proteins that possess Fe 2+ or Fe/S complexes as co-factors or prosthetic groups. Here, we show that the small regulatory RNA (sRNA) IsaR1 (Iron-Stress-Activated RNA 1) plays a pivotal role in acclimation to low-iron conditions. The IsaR1 regulon consists of more than 15 direct targets, including Fe 2+ -containing proteins involved in photosynthetic electron transfer, detoxification of anion radicals, citrate cycle, and tetrapyrrole biogenesis. IsaR1 is essential for maintaining physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (1) directly, via posttranscriptional repression of gene expression; (2) indirectly, via suppression of pigment; and (3) Fe/S cluster biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a critically important riboregulator. These findings provide a new perspective for understanding the regulation of iron homeostasis in photosynthetic organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ultra Deep Sequencing of Listeria monocytogenes sRNA Transcriptome Revealed New Antisense RNAs

PubMed Central

Behrens, Sebastian; Widder, Stefanie; Mannala, Gopala Krishna; Qing, Xiaoxing; Madhugiri, Ramakanth; Kefer, Nathalie; Mraheil, Mobarak Abu; Rattei, Thomas; Hain, Torsten

2014-01-01

Listeria monocytogenes, a gram-positive pathogen, and causative agent of listeriosis, has become a widely used model organism for intracellular infections. Recent studies have identified small non-coding RNAs (sRNAs) as important factors for regulating gene expression and pathogenicity of L. monocytogenes. Increased speed and reduced costs of high throughput sequencing (HTS) techniques have made RNA sequencing (RNA-Seq) the state-of-the-art method to study bacterial transcriptomes. We created a large transcriptome dataset of L. monocytogenes containing a total of 21 million reads, using the SOLiD sequencing technology. The dataset contained cDNA sequences generated from L. monocytogenes RNA collected under intracellular and extracellular condition and additionally was size fractioned into three different size ranges from <40 nt, 40–150 nt and >150 nt. We report here, the identification of nine new sRNAs candidates of L. monocytogenes and a reevaluation of known sRNAs of L. monocytogenes EGD-e. Automatic comparison to known sRNAs revealed a high recovery rate of 55%, which was increased to 90% by manual revision of the data. Moreover, thorough classification of known sRNAs shed further light on their possible biological functions. Interestingly among the newly identified sRNA candidates are antisense RNAs (asRNAs) associated to the housekeeping genes purA, fumC and pgi and potentially their regulation, emphasizing the significance of sRNAs for metabolic adaptation in L. monocytogenes. PMID:24498259

Effect of Crc and Hfq proteins on the transcription, processing, and stability of the Pseudomonas putida CrcZ sRNA.

PubMed

Hernández-Arranz, Sofía; Sánchez-Hevia, Dione; Rojo, Fernando; Moreno, Renata

2016-12-01

In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. The effect of these two proteins is antagonized by the CrcZ and CrcY small RNAs (sRNAs), the levels of which vary greatly according to growth conditions. The crcZ and crcY genes are transcribed from promoters PcrcZ and PcrcY, respectively, a process that relies on the CbrB transcriptional activator and the RpoN σ factor. Here we show that crcZ can also be transcribed from the promoter of the immediate upstream gene, cbrB, a weak constitutive promoter. The cbrB-crcZ transcript was processed to render a sRNA very similar in size to the CrcZ produced from promoter PcrcZ The processed sRNA, termed CrcZ*, was able to antagonize Hfq/Crc because, when provided in trans, it relieved the deregulated Hfq/Crc-dependent hyperrepressing phenotype of a ΔcrcZΔcrcY strain. CrcZ* may help in attaining basal levels of CrcZ/CrcZ* that are sufficient to protect the cell from an excessive Hfq/Crc-dependent repression. Since a functional sRNA can be produced from PcrcZ, an inducible strong promoter, or by cleavage of the cbrB-crcZ mRNA, crcZ can be considered a 3'-untranslated region of the cbrB-crcZ mRNA. In the absence of Hfq, the processed form of CrcZ was not observed. In addition, we show that Crc and Hfq increase CrcZ stability, which supports the idea that these proteins can form a complex with CrcZ and protect it from degradation by RNases. © 2016 Hernández-Arranz et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Integration Host Factor Is Required for RpoN-Dependent hrpL Gene Expression and Controls Motility by Positively Regulating rsmB sRNA in Erwinia amylovora.

PubMed

Lee, Jae Hoon; Zhao, Youfu

2016-01-01

Erwinia amylovora requires an hrp-type III secretion system (T3SS) to cause disease. It has been reported that HrpL, the master regulator of T3SS, is transcriptionally regulated by sigma factor 54 (RpoN), YhbH, and HrpS. In this study, the role of integration host factor (IHF) in regulating hrpL and T3SS gene expression was investigated. IHF is a nucleoid-associated protein that regulates gene expression by influencing nucleoid structure and DNA bending. Our results showed that both ihfA and ihfB mutants of E. amylovora did not induce necrotic lesions on pear fruits. Growth of both mutants was greatly reduced, and expression of the hrpL and T3SS genes was significantly down-regulated as compared with those of the wild type. In addition, expression of the ihfA, but not the ihfB gene, was under auto-suppression by IHF. Furthermore, both ihfA and ihfB mutants were hypermotile, due to significantly reduced expression of small RNA (sRNA) rsmB. Electrophoresis mobility shift assay further confirmed that IHF binds to the promoters of the hrpL and ihfA genes, as well as the rsmB sRNA gene. These results indicate that IHF is required for RpoN-dependent hrpL gene expression and virulence, and controls motility by positively regulating the rsmB sRNA in E. amylovora.

An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.

PubMed

Robledo, Marta; Schlüter, Jan-Philip; Loehr, Lars O; Linne, Uwe; Albaum, Stefan P; Jiménez-Zurdo, José I; Becker, Anke

2018-01-01

Adjustment of cell cycle progression is crucial for bacterial survival and adaptation under adverse conditions. However, the understanding of modulation of cell cycle control in response to environmental changes is rather incomplete. In α-proteobacteria, the broadly conserved cell cycle master regulator CtrA underlies multiple levels of control, including coupling of cell cycle and cell differentiation. CtrA levels are known to be tightly controlled through diverse transcriptional and post-translational mechanisms. Here, small RNA (sRNA)-mediated post-transcriptional regulation is uncovered as an additional level of CtrA fine-tuning. Computational predictions as well as transcriptome and proteome studies consistently suggested targeting of ctrA and the putative cold shock chaperone cspA5 mRNAs by the trans- encoded sRNA ( trans- sRNA) GspR (formerly SmelC775) in several Sinorhizobium species. GspR strongly accumulated in the stationary growth phase, especially in minimal medium (MM) cultures. Lack of the gspR locus confers a fitness disadvantage in competition with the wild type, while its overproduction hampers cell growth, suggesting that this riboregulator interferes with cell cycle progression. An eGFP-based reporter in vivo assay, involving wild-type and mutant sRNA and mRNA pairs, experimentally confirmed GspR-dependent post-transcriptional down-regulation of ctrA and cspA5 expression, which most likely occurs through base-pairing to the respective mRNA. The energetically favored secondary structure of GspR is predicted to comprise three stem-loop domains, with stem-loop 1 and stem-loop 3 targeting ctrA and cspA5 mRNA, respectively. Moreover, this work reports evidence for post-transcriptional control of ctrA by CspA5. Thus, this regulation and GspR-mediated post-transcriptional repression of ctrA and cspA5 expression constitute a coherent feed-forward loop, which may enhance the negative effect of GspR on CtrA levels. This novel regulatory circuit involving

An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA

PubMed Central

Robledo, Marta; Schlüter, Jan-Philip; Loehr, Lars O.; Linne, Uwe; Albaum, Stefan P.; Jiménez-Zurdo, José I.; Becker, Anke

2018-01-01

Adjustment of cell cycle progression is crucial for bacterial survival and adaptation under adverse conditions. However, the understanding of modulation of cell cycle control in response to environmental changes is rather incomplete. In α-proteobacteria, the broadly conserved cell cycle master regulator CtrA underlies multiple levels of control, including coupling of cell cycle and cell differentiation. CtrA levels are known to be tightly controlled through diverse transcriptional and post-translational mechanisms. Here, small RNA (sRNA)-mediated post-transcriptional regulation is uncovered as an additional level of CtrA fine-tuning. Computational predictions as well as transcriptome and proteome studies consistently suggested targeting of ctrA and the putative cold shock chaperone cspA5 mRNAs by the trans-encoded sRNA (trans-sRNA) GspR (formerly SmelC775) in several Sinorhizobium species. GspR strongly accumulated in the stationary growth phase, especially in minimal medium (MM) cultures. Lack of the gspR locus confers a fitness disadvantage in competition with the wild type, while its overproduction hampers cell growth, suggesting that this riboregulator interferes with cell cycle progression. An eGFP-based reporter in vivo assay, involving wild-type and mutant sRNA and mRNA pairs, experimentally confirmed GspR-dependent post-transcriptional down-regulation of ctrA and cspA5 expression, which most likely occurs through base-pairing to the respective mRNA. The energetically favored secondary structure of GspR is predicted to comprise three stem-loop domains, with stem-loop 1 and stem-loop 3 targeting ctrA and cspA5 mRNA, respectively. Moreover, this work reports evidence for post-transcriptional control of ctrA by CspA5. Thus, this regulation and GspR-mediated post-transcriptional repression of ctrA and cspA5 expression constitute a coherent feed-forward loop, which may enhance the negative effect of GspR on CtrA levels. This novel regulatory circuit involving

Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis.

PubMed

Mars, Ruben A T; Nicolas, Pierre; Ciccolini, Mariano; Reilman, Ewoud; Reder, Alexander; Schaffer, Marc; Mäder, Ulrike; Völker, Uwe; van Dijl, Jan Maarten; Denham, Emma L

2015-03-01

Isogenic bacterial populations can consist of cells displaying heterogeneous physiological traits. Small regulatory RNAs (sRNAs) could affect this heterogeneity since they act by fine-tuning mRNA or protein levels to coordinate the appropriate cellular behavior. Here we show that the sRNA RnaC/S1022 from the Gram-positive bacterium Bacillus subtilis can suppress exponential growth by modulation of the transcriptional regulator AbrB. Specifically, the post-transcriptional abrB-RnaC/S1022 interaction allows B. subtilis to increase the cell-to-cell variation in AbrB protein levels, despite strong negative autoregulation of the abrB promoter. This behavior is consistent with existing mathematical models of sRNA action, thus suggesting that induction of protein expression noise could be a new general aspect of sRNA regulation. Importantly, we show that the sRNA-induced diversity in AbrB levels generates heterogeneity in growth rates during the exponential growth phase. Based on these findings, we hypothesize that the resulting subpopulations of fast- and slow-growing B. subtilis cells reflect a bet-hedging strategy for enhanced survival of unfavorable conditions.

Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.

PubMed

Carroll, Ronan K; Weiss, Andy; Broach, William H; Wiemels, Richard E; Mogen, Austin B; Rice, Kelly C; Shaw, Lindsey N

2016-02-09

In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. Despite a large number of studies identifying regulatory or small RNA (sRNA) genes in Staphylococcus aureus, their annotation is notably lacking in available genome files. In addition to this, there has been a considerable lack of cross-referencing in the wealth of studies identifying these elements, often leading to the same sRNA being identified multiple times and bearing multiple names. In this work

Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq

PubMed Central

Wang, Lijun; Wang, Weiwei; Li, Fudong; Zhang, Jiahai; Wu, Jihui; Gong, Qingguo; Shi, Yunyu

2015-01-01

Small RNA OxyS is induced during oxidative stress in Escherichia coli and it is an Hfq-dependent negative regulator of mRNA translation. OxyS represses the translation of fhlA and rpoS mRNA, which encode the transcriptional activator and σs subunit of RNA polymerase, respectively. However, little is known regarding how Hfq, an RNA chaperone, interacts with OxyS at the atomic level. Here, using fluorescence polarization and tryptophan fluorescence quenching assays, we verified that the A-rich linker region of OxyS sRNA binds Hfq at its distal side. We also report two crystal structures of Hfq in complex with A-rich RNA fragments from this linker region. Both of these RNA fragments bind to the distal side of Hfq and adopt a different conformation compared with those previously reported for the (A-R-N)n tripartite recognition motif. Furthermore, using fluorescence polarization, electrophoresis mobility shift assays and in vivo translation assays, we found that an Hfq mutant, N48A, increases the binding affinity of OxyS for Hfq in vitro but is defective in the negative regulation of fhlA translation in vivo, suggesting that the normal function of OxyS depends on the details of the interaction with Hfq that may be related to the rapid recycling of Hfq in the cell. PMID:25670676

quenched-smFISH: Counting small RNA in Pathogenic Bacteria

NASA Astrophysics Data System (ADS)

Shepherd, Douglas; Li, Nan; Micheva-Viteva, Sofiya; Munsky, Brian; Hong-Geller, Elizabeth; Werner, James

2014-03-01

Here, we present a modification to single-molecule fluorescence in situ hybridization, quenched smFISH (q-smFISH), that enables quantitative detection and analysis of small RNA (sRNA) expressed in bacteria. We show that short nucleic acid targets can be detected when the background of unbound singly dye-labeled DNA oligomers is reduced through hybridization with a set of complementary DNA oligomers labeled with a fluorescence quencher. Exploiting an automated, multi-color wide-field microscope and GPU-accelerated data analysis package, we analyzed the statistics of sRNA expression in thousands of individual Yersinia pseudotuberculosis and Yersinia pestis bacteria before and during a simulated infection. Before infection, we find only a small fraction of either bacteria express the small RNAs YSR35 or YSP8. The copy numbers of these RNA are increased during simulated infection, suggesting a role in pathogenesis. The ability to directly quantify expression level changes of sRNA in single cells as a function of external stimuli provides key information on the role of sRNA in bacterial regulatory networks.

Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs

PubMed Central

Morita, Teppei; Nishino, Ryo; Aiba, Hiroji

2017-01-01

Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of seven or more T residues at the 3′ end, as noted in previous studies. Here, we have studied the role of the terminator hairpin in the biogenesis of sRNAs focusing on SgrS and RyhB in Escherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the poly(U) tail is shortened. The transcripts with shortened poly(U) tails no longer bind to Hfq and lose the ability to repress the target mRNAs. The shortened transcripts are generated in an in vitro transcription system with purified RNA polymerase, indicating that the generation of shortened transcripts is caused by premature transcription termination. We conclude that the terminator structure of sRNA genes is optimized to generate functional sRNAs. Thus, the Rho-independent terminators of sRNA genes possess two common features: a long T residue stretch that is a prerequisite for generation of functional sRNAs and a moderate strength of hairpin structure that ensures the termination at the seventh or longer position within the consecutive T stretch. The modulation of the termination position at the Rho-independent terminators is critical for biosynthesis of functional sRNAs. PMID:28606943

Disclosure of Incidental Findings From Next-Generation Sequencing in Pediatric Genomic Research

PubMed Central

Abdul-Karim, Ruqayyah; Berkman, Benjamin E.; Wendler, David; Rid, Annette; Khan, Javed; Badgett, Tom

2013-01-01

Next-generation sequencing technologies will likely be used with increasing frequency in pediatric research. One consequence will be the increased identification of individual genomic research findings that are incidental to the aims of the research. Although researchers and ethicists have raised theoretical concerns about incidental findings in the context of genetic research, next-generation sequencing will make this once largely hypothetical concern an increasing reality. Most commentators have begun to accept the notion that there is some duty to disclose individual genetic research results to research subjects; however, the scope of that duty remains unclear. These issues are especially complicated in the pediatric setting, where subjects cannot currently but typically will eventually be able to make their own medical decisions at the age of adulthood. This article discusses the management of incidental findings in the context of pediatric genomic research. We provide an overview of the current literature and propose a framework to manage incidental findings in this unique context, based on what we believe is a limited responsibility to disclose. We hope this will be a useful source of guidance for investigators, institutional review boards, and bioethicists that anticipates the complicated ethical issues raised by advances in genomic technology. PMID:23400601

The Phosphorolytic Exoribonucleases Polynucleotide Phosphorylase and RNase PH Stabilize sRNAs and Facilitate Regulation of Their mRNA Targets

PubMed Central

2016-01-01

ABSTRACT Gene regulation by base pairing between small noncoding RNAs (sRNAs) and their mRNA targets is an important mechanism that allows bacteria to maintain homeostasis and respond to dynamic environments. In Gram-negative bacteria, sRNA pairing and regulation are mediated by several RNA-binding proteins, including the sRNA chaperone Hfq and polynucleotide phosphorylase (PNPase). PNPase and its homolog RNase PH together represent the two 3′ to 5′ phosphorolytic exoribonucleases found in Escherichia coli; however, the role of RNase PH in sRNA regulation has not yet been explored and reported. Here, we have examined in detail how PNPase and RNase PH interact to support sRNA stability, activity, and base pairing in exponential and stationary growth conditions. Our results indicate that these proteins facilitate the stability and regulatory function of the sRNAs RyhB, CyaR, and MicA during exponential growth. PNPase further appears to contribute to pairing between RyhB and its mRNA targets. During stationary growth, each sRNA responded differently to the absence or presence of PNPase and RNase PH. Finally, our results suggest that PNPase and RNase PH stabilize only Hfq-bound sRNAs. Taken together, these results confirm and extend previous findings that PNPase participates in sRNA regulation and reveal that RNase PH serves a similar, albeit more limited, role as well. These proteins may, therefore, act to protect sRNAs from spurious degradation while also facilitating regulatory pairing with their targets. IMPORTANCE In many bacteria, Hfq-dependent base-pairing sRNAs facilitate rapid changes in gene expression that are critical for maintaining homeostasis and responding to stress and environmental changes. While a role for Hfq in this process was identified more than 2 decades ago, the identity and function of the other proteins required for Hfq-dependent regulation by sRNAs have not been resolved. Here, we demonstrate that PNPase and RNase PH, the two

Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya

PubMed Central

2012-01-01

findings open a new avenue for further investigation of the sRNA silencing pathway in plants. PMID:23216749

Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya.

PubMed

Aryal, Rishi; Yang, Xiaozeng; Yu, Qingyi; Sunkar, Ramanjulu; Li, Lei; Ming, Ray

2012-12-05

The small RNAs (sRNA) are a regulatory class of RNA mainly represented by the 21 and 24-nucleotide size classes. The cellular sRNAs are processed by RNase III family enzyme dicer (Dicer like in plant) from a self-complementary hairpin loop or other type of RNA duplexes. The papaya genome has been sequenced, but its microRNAs and other regulatory RNAs are yet to be analyzed. We analyzed the genomic features of the papaya sRNA population from three sRNA deep sequencing libraries made from leaves, flowers, and leaves infected with Papaya Ringspot Virus (PRSV). We also used the deep sequencing data to annotate the micro RNA (miRNA) in papaya. We identified 60 miRNAs, 24 of which were conserved in other species, and 36 of which were novel miRNAs specific to papaya. In contrast to the Chargaff's purine-pyrimidine equilibrium, cellular sRNA was significantly biased towards a purine rich population. Of the two purine bases, higher frequency of adenine was present in 23nt or longer sRNAs, while 22nt or shorter sRNAs were over represented by guanine bases. However, this bias was not observed in the annotated miRNAs in plants. The 21nt species were expressed from fewer loci but expressed at higher levels relative to the 24nt species. The highly expressed 21nt species were clustered in a few isolated locations of the genome. The PRSV infected leaves showed higher accumulation of 21 and 22nt sRNA compared to uninfected leaves. We observed higher accumulation of miRNA* of seven annotated miRNAs in virus-infected tissue, indicating the potential function of miRNA* under stressed conditions. We have identified 60 miRNAs in papaya. Our study revealed the asymmetric purine-pyrimidine distribution in cellular sRNA population. The 21nt species of sRNAs have higher expression levels than 24nt sRNA. The miRNA* of some miRNAs shows higher accumulation in PRSV infected tissues, suggesting that these strands are not totally functionally redundant. The findings open a new avenue for further

Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

PubMed Central

Weiss, Andy; Broach, William H.; Wiemels, Richard E.; Mogen, Austin B.; Rice, Kelly C.

2016-01-01

ABSTRACT In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. PMID:26861020

Comparative analysis among the small RNA populations of source, sink and conductive tissues in two different plant-virus pathosystems.

PubMed

Herranz, Mari Carmen; Navarro, Jose Antonio; Sommen, Evelien; Pallas, Vicente

2015-02-22

In plants, RNA silencing plays a fundamental role as defence mechanism against viruses. During last years deep-sequencing technology has allowed to analyze the sRNA profile of a large variety of virus-infected tissues. Nevertheless, the majority of these studies have been restricted to a unique tissue and no comparative analysis between phloem and source/sink tissues has been conducted. In the present work, we compared the sRNA populations of source, sink and conductive (phloem) tissues in two different plant virus pathosystems. We chose two cucurbit species infected with two viruses very different in genome organization and replication strategy; Melon necrotic spot virus (MNSV) and Prunus necrotic ringspot virus (PNRSV). Our findings showed, in both systems, an increase of the 21-nt total sRNAs together with a decrease of those with a size of 24-nt in all the infected tissues, except for the phloem where the ratio of 21/24-nt sRNA species remained constant. Comparing the vsRNAs, both PNRSV- and MNSV-infected plants share the same vsRNA size distribution in all the analyzed tissues. Similar accumulation levels of sense and antisense vsRNAs were observed in both systems except for roots that showed a prevalence of (+) vsRNAs in both pathosystems. Additionally, the presence of overrepresented discrete sites along the viral genome, hot spots, were identified and validated by stem-loop RT-PCR. Despite that in PNRSV-infected plants the presence of vsRNAs was scarce both viruses modulated the host sRNA profile. We compare for the first time the sRNA profile of four different tissues, including source, sink and conductive (phloem) tissues, in two plant-virus pathosystems. Our results indicate that antiviral silencing machinery in melon and cucumber acts mainly through DCL4. Upon infection, the total sRNA pattern in phloem remains unchanged in contrast to the rest of the analyzed tissues indicating a certain tissue-tropism to this polulation. Independently of the

Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR.

PubMed

Nithya, Ravichantar; Ahmed, Siti Aminah; Hoe, Chee-Hock; Gopinath, Subash C B; Citartan, Marimuthu; Chinni, Suresh V; Lee, Li Pin; Rozhdestvensky, Timofey S; Tang, Thean-Hock

2015-01-01

Salmonellosis, a communicable disease caused by members of the Salmonella species, transmitted to humans through contaminated food or water. It is of paramount importance, to generate accurate detection methods for discriminating the various Salmonella species that cause severe infection in humans, including S. Typhi and S. Paratyphi A. Here, we formulated a strategy of detection and differentiation of salmonellosis by a multiplex polymerase chain reaction assay using S. Typhi non-protein coding RNA (sRNA) genes. With the designed sequences that specifically detect sRNA genes from S. Typhi and S. Paratyphi A, a detection limit of up to 10 pg was achieved. Moreover, in a stool-seeding experiment with S. Typhi and S. Paratyphi A, we have attained a respective detection limit of 15 and 1.5 CFU/mL. The designed strategy using sRNA genes shown here is comparatively sensitive and specific, suitable for clinical diagnosis and disease surveillance, and sRNAs represent an excellent molecular target for infectious disease.

Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs.

PubMed

Morita, Teppei; Nishino, Ryo; Aiba, Hiroji

2017-09-01

Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of seven or more T residues at the 3' end, as noted in previous studies. Here, we have studied the role of the terminator hairpin in the biogenesis of sRNAs focusing on SgrS and RyhB in Escherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the poly(U) tail is shortened. The transcripts with shortened poly(U) tails no longer bind to Hfq and lose the ability to repress the target mRNAs. The shortened transcripts are generated in an in vitro transcription system with purified RNA polymerase, indicating that the generation of shortened transcripts is caused by premature transcription termination. We conclude that the terminator structure of sRNA genes is optimized to generate functional sRNAs. Thus, the Rho-independent terminators of sRNA genes possess two common features: a long T residue stretch that is a prerequisite for generation of functional sRNAs and a moderate strength of hairpin structure that ensures the termination at the seventh or longer position within the consecutive T stretch. The modulation of the termination position at the Rho-independent terminators is critical for biosynthesis of functional sRNAs. © 2017 Morita et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Management of Incidental Findings in the Era of Next-generation Sequencing

PubMed Central

Blackburn, Heather L.; Schroeder, Bradley; Turner, Clesson; Shriver, Craig D.; Ellsworth, Darrell L.; Ellsworth, Rachel E.

2015-01-01

Next-generation sequencing (NGS) technologies allow for the generation of whole exome or whole genome sequencing data, which can be used to identify novel genetic alterations associated with defined phenotypes or to expedite discovery of functional variants for improved patient care. Because this robust technology has the ability to identify all mutations within a genome, incidental findings (IF)- genetic alterations associated with conditions or diseases unrelated to the patient’s present condition for which current tests are being performed- may have important clinical ramifications. The current debate among genetic scientists and clinicians focuses on the following questions: 1) should any IF be disclosed to patients, and 2) which IF should be disclosed – actionable mutations, variants of unknown significance, or all IF? Policies for disclosure of IF are being developed for when and how to convey these findings and whether adults, minors, or individuals unable to provide consent have the right to refuse receipt of IF. In this review, we detail current NGS technology platforms, discuss pressing issues regarding disclosure of IF, and how IF are currently being handled in prenatal, pediatric, and adult patients. PMID:26069456

Sub-cellular mRNA localization modulates the regulation of gene expression by small RNAs in bacteria

NASA Astrophysics Data System (ADS)

Teimouri, Hamid; Korkmazhan, Elgin; Stavans, Joel; Levine, Erel

2017-10-01

Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that demonstrate that families of mRNAs show non-trivial sub-cellular distributions raise the question of how localization may affect the regulatory activity of sRNAs. Here we address this question within a simple mathematical model. We show that the non-uniform spatial distributions of mRNA can alter the threshold-linear response that characterizes sRNAs that act stoichiometrically, and modulate the hierarchy among targets co-regulated by the same sRNA. We also identify conditions where the sub-cellular organization of cofactors in the sRNA pathway can induce spatial heterogeneity on sRNA targets. Our results suggest that under certain conditions, interpretation and modeling of natural and synthetic gene regulatory circuits need to take into account the spatial organization of the transcripts of participating genes.

Identification and expression profiles of sRNAs and their biogenesis and action-related genes in male and female cones of Pinus tabuliformis.

PubMed

Niu, Shi-Hui; Liu, Chang; Yuan, Hu-Wei; Li, Pei; Li, Yue; Li, Wei

2015-09-15

Small RNA (sRNA) play pivotal roles in reproductive development, and their biogenesis and action mechanisms are well characterised in angiosperm plants; however, corresponding studies in conifers are very limited. To improve our understanding of the roles of sRNA pathways in the reproductive development of conifers, the genes associated with sRNA biogenesis and action pathways were identified and analysed, and sRNA sequencing and parallel analysis of RNA ends (PARE) were performed in male and female cones of the Chinese pine (Pinus tabuliformis). Based on high-quality reference transcriptomic sequences, 21 high-confidence homologues involved in sRNA biogenesis and action in P. tabuliformis were identified, including two different DCL3 genes and one AGO4 gene. More than 75 % of genes involved in sRNA biogenesis and action have higher expression levels in female than in male cones. Twenty-six microRNA (miRNA) families and 74 targets, including 46 24-nt sRNAs with a 5' A, which are specifically expressed in male cones or female cones and probably bind to AGO4, were identified. The sRNA pathways have higher activity in female than in male cones, and the miRNA pathways are the main sRNA pathways in P. tabuliformis. The low level of 24-nt short-interfering RNAs in conifers is not caused by the absence of biogenesis-related genes or AGO-binding proteins, but most likely caused by the low accumulation of these key components. The identification of sRNAs and their targets, as well as genes associated with sRNA biogenesis and action, will provide a good starting point for investigations into the roles of sRNA pathways in cone development in conifers.

A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.

PubMed

Chao, Yanjie; Vogel, Jörg

2016-02-04

Small RNAs (sRNAs) from conserved noncoding genes are crucial regulators in bacterial signaling pathways but have remained elusive in the Cpx response to inner membrane stress. Here we report that an alternative biogenesis pathway releasing the conserved mRNA 3' UTR of stress chaperone CpxP as an ∼60-nt sRNA provides the noncoding arm of the Cpx response. This so-called CpxQ sRNA, generated by general mRNA decay through RNase E, acts as an Hfq-dependent repressor of multiple mRNAs encoding extracytoplasmic proteins. Both CpxQ and the Cpx pathway are required for cell survival under conditions of dissipation of membrane potential. Our discovery of CpxQ illustrates how the conversion of a transcribed 3' UTR into an sRNA doubles the output of a single mRNA to produce two factors with spatially segregated functions during inner membrane stress: a chaperone that targets problematic proteins in the periplasm and a regulatory RNA that dampens their synthesis in the cytosol. Copyright © 2016 Elsevier Inc. All rights reserved.

Spot 42 Small RNA Regulates Arabinose-Inducible araBAD Promoter Activity by Repressing Synthesis of the High-Affinity Low-Capacity Arabinose Transporter

PubMed Central

Chen, Jiandong

2016-01-01

ABSTRACT The l-arabinose-inducible araBAD promoter (PBAD) enables tightly controlled and tunable expression of genes of interest in a broad range of bacterial species. It has been used successfully to study bacterial sRNA regulation, where PBAD drives expression of target mRNA translational fusions. Here we report that in Escherichia coli, Spot 42 sRNA regulates PBAD promoter activity by affecting arabinose uptake. We demonstrate that Spot 42 sRNA represses araF, a gene encoding the AraF subunit of the high-affinity low-capacity arabinose transporter AraFGH, through direct base-pairing interactions. We further show that endogenous Spot 42 sRNA is sufficient to repress araF expression under various growth conditions. Finally, we demonstrate this posttranscriptional repression has a biological consequence, decreasing the induction of PBAD at low levels of arabinose. This problem can be circumvented using strategies reported previously for avoiding all-or-none induction behavior, such as through constitutive expression of the low-affinity high-capacity arabinose transporter AraE or induction with a higher concentration of inducers. This work adds araF to the set of Spot 42-regulated genes, in agreement with previous studies suggesting that Spot 42, itself negatively regulated by the cyclic AMP (cAMP) receptor protein-cAMP complex, reinforces the catabolite repression network. IMPORTANCE The bacterial arabinose-inducible system is widely used for titratable control of gene expression. We demonstrate here that a posttranscriptional mechanism mediated by Spot 42 sRNA contributes to the functionality of the PBAD system at subsaturating inducer concentrations by affecting inducer uptake. Our finding extends the inputs into the known transcriptional control for the PBAD system and has implications for improving its usage for tunable gene expression. PMID:27849174

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7.

PubMed

Klähn, Stephan; Schaal, Christoph; Georg, Jens; Baumgartner, Desirée; Knippen, Gernot; Hagemann, Martin; Muro-Pastor, Alicia M; Hess, Wolfgang R

2015-11-10

Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5'UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor (IF)7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus [Formula: see text] assimilation via GS. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4 KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis toward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.

Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species

PubMed Central

Bernick, David L.; Dennis, Patrick P.; Lui, Lauren M.; Lowe, Todd M.

2012-01-01

A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea is limited. We employed RNA-seq to identify novel sRNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense sRNAs encoded opposite to key regulatory (ferric uptake regulator), metabolic (triose-phosphate isomerase), and core transcriptional apparatus genes (transcription factor B). We also found a large increase in the number of conserved C/D box sRNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these sRNAs indicates they are relatively recent, stable adaptations. PMID:22783241

Characterization of acid‑tolerance‑associated small RNAs in clinical isolates of Streptococcus mutans: Potential biomarkers for caries prevention.

PubMed

Zhu, Wenhui; Liu, Shanshan; Zhuang, Peilin; Liu, Jia; Wang, Yan; Lin, Huancai

2017-12-01

Streptococcus mutans is a cariogenic bacterium that contributes to dental caries due to its ability to produce lactic acid, which acidifies the local environment. The potential of S. mutans to respond to environmental stress and tolerate low pH is essential for its survival and predominance in caries lesions. Small noncoding RNAs (sRNAs) have been reported to be involved in bacterial stress and virulence. Few studies have investigated the sRNAs of S. mutans and the function of these sRNAs remains to be elucidated. In the present study, the association between sRNA133474 and acid tolerance, including potential underlying mechanisms, were investigated within clinical strains of S. mutans. From pediatric dental plaques, 20 strains of S. mutans were isolated. An acid killing assay was performed to analyze acid tolerance of S. mutans. Expression patterns of sRNA133474 were investigated during various growth phases under various acidic conditions via reverse transcription‑quantitative polymerase chain reaction. RNA predator and Kyoto Encyclopedia of Genes and Genomes analyses were performed to predict target mRNAs of sRNA133474 and to examine the involvement of putative pathways of target mRNAs, respectively. The results of the present study demonstrated that sRNA133474 activity was growth phase‑dependent, and two distinct expression patterns were identified in 10 clinical strains. At pH 5.5 and 7.5 the expression levels of sRNA133474 were significantly different, and high‑acid tolerant strains exhibited reduced expression levels of sRNA133474 compared with low‑acid tolerant strains. A correlation between sRNA133474 expression levels and acid tolerance was observed in 20 clinical isolates of S. mutans (r=‑0.6298, P<0.01). Finally, five target mRNAs (liaS, liaR, comE, covR and ciaR) involved in the two‑component system (TCS) were selected for further evaluation; the expression levels of three target mRNAs (liaR, ciaR and covR) were negatively

Sex specific expression and distribution of small RNAs in papaya.

PubMed

Aryal, Rishi; Jagadeeswaran, Guru; Zheng, Yun; Yu, Qingyi; Sunkar, Ramanjulu; Ming, Ray

2014-01-13

Regulatory function of small non-coding RNAs (sRNA) in response to environmental and developmental cues has been established. Additionally, sRNA, also plays an important role in maintaining the heterochromatin and centromere structures of the chromosome. Papaya, a trioecious species with recently evolved sex chromosomes, has emerged as an excellent model system to study sex determination and sex chromosome evolution in plants. However, role of small RNA in papaya sex determination is yet to be explored. We analyzed the high throughput sRNAs reads in the Illumina libraries prepared from male, female, and hermaphrodite flowers of papaya. Using the sRNA reads, we identified 29 miRNAs that were not previously reported from papaya. Including this and two previous studies, a total of 90 miRNAs has been identified in papaya. We analyzed the expression of these miRNAs in each sex types. A total of 65 miRNAs, including 31 conserved and 34 novel mirNA, were detected in at least one library. Fourteen of the 65 miRNAs were differentially expressed among different sex types. Most of the miRNA expressed higher in male flowers were related to the auxin signaling pathways, whereas the miRNAs expressed higher in female flowers were the potential regulators of the apical meristem identity genes. Aligning the sRNA reads identified the sRNA hotspots adjacent to the gaps of the X and Y chromosomes. The X and Y chromosomes sRNA hotspots has a 7.8 and 4.4 folds higher expression of sRNA, respectively, relative to the chromosome wide average. Approximately 75% of the reads aligned to the X chromosome hotspot was identical to that of the Y chromosome hotspot. By analyzing the large-scale sRNA sequences from three sex types, we identified the sRNA hotspots flanking the gaps of papaya X, Y, and Yh chromosome. The sRNAs expression patterns in these regions were reminiscent of the pericentromeric region indicating that the only remaining gap in each of these chromosomes is likely the

Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture.

PubMed

Chan, Stephen Y; Snow, Jonathan W

2017-04-03

The putative transfer and gene regulatory activities of diet-derived small RNAs (sRNAs) in ingesting animals are still debated. The existence of natural uptake of diet-derived sRNA by invertebrate species could have significant implication for our understanding of ecological relationships and could synergize with efforts to use RNA interference (RNAi) technology in agriculture. Here, we synthesize information gathered from studies in invertebrates using natural or artificial dietary delivery of sRNA and from studies of sRNA in vertebrate animals and plants to review our current understanding of uptake and impact of natural diet-derived sRNA on invertebrates. Our understanding has been influenced and sometimes confounded by the diversity of invertebrates and ingested plants studied, our limited insights into how gene expression may be modulated by dietary sRNAs at the mechanistic level, and the paucity of studies focusing directly on natural uptake of sRNA. As such, we suggest 2 strategies to investigate this phenomenon more comprehensively and thus facilitate the realization of its potentially broad impact on ecology and agriculture in the future.

Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture

PubMed Central

Chan, Stephen Y.; Snow, Jonathan W.

2017-01-01

ABSTRACT The putative transfer and gene regulatory activities of diet-derived small RNAs (sRNAs) in ingesting animals are still debated. The existence of natural uptake of diet-derived sRNA by invertebrate species could have significant implication for our understanding of ecological relationships and could synergize with efforts to use RNA interference (RNAi) technology in agriculture. Here, we synthesize information gathered from studies in invertebrates using natural or artificial dietary delivery of sRNA and from studies of sRNA in vertebrate animals and plants to review our current understanding of uptake and impact of natural diet-derived sRNA on invertebrates. Our understanding has been influenced and sometimes confounded by the diversity of invertebrates and ingested plants studied, our limited insights into how gene expression may be modulated by dietary sRNAs at the mechanistic level, and the paucity of studies focusing directly on natural uptake of sRNA. As such, we suggest 2 strategies to investigate this phenomenon more comprehensively and thus facilitate the realization of its potentially broad impact on ecology and agriculture in the future. PMID:27763816

Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize.

PubMed

Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Motta, Mariana Romeiro; Vieira, Tauan; Regulski, Michael; Martienssen, Robert A; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

2014-09-06

Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays-hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription. Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.

Construction of new synthetic biology tools for the control of gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002.

PubMed

Zess, Erin K; Begemann, Matthew B; Pfleger, Brian F

2016-02-01

Predictive control of gene expression is an essential tool for developing synthetic biological systems. The current toolbox for controlling gene expression in cyanobacteria is a barrier to more in-depth genetic analysis and manipulation. Towards relieving this bottleneck, this work describes the use of synthetic biology to construct an anhydrotetracycline-based induction system and adapt a trans-acting small RNA (sRNA) system for use in the cyanobacterium Synechococcus sp. strain PCC 7002. An anhydrotetracycline-inducible promoter was developed to maximize intrinsic strength and dynamic range. The resulting construct, PEZtet , exhibited tight repression and a maximum 32-fold induction upon addition of anhydrotetracycline. Additionally, a sRNA system based on the Escherichia coli IS10 RNA-IN/OUT regulator was adapted for use in Synechococcus sp. strain PCC 7002. This system exhibited 70% attenuation of target gene expression, providing a demonstration of the use of sRNAs for differential gene expression in cyanobacteria. These systems were combined to produce an inducible sRNA system, which demonstrated 59% attenuation of target gene expression. Lastly, the role of Hfq, a critical component of sRNA systems in E. coli, was investigated. Genetic studies showed that the Hfq homolog in Synechococcus sp. strain PCC 7002 did not impact repression by the engineered sRNA system. In summary, this work describes new synthetic biology tools that can be applied to physiological studies, metabolic engineering, or sRNA platforms in Synechococcus sp. strain PCC 7002. © 2015 Wiley Periodicals, Inc.

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213

PubMed Central

2012-01-01

Background Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demarcating overlapping gene boundaries, and identifying regulatory elements such as small RNA are not accurate using these approaches. In this study, we re-visit the structural annotation of Mannheimia haemolytica PHL213, a bovine respiratory disease pathogen. M. haemolytica is one of the causative agents of bovine respiratory disease that results in about $3 billion annual losses to the cattle industry. We used RNA-Seq and analyzed the data using freely-available computational methods and resources. The aim was to identify previously unannotated regions of the genome using RNA-Seq based expression profile to complement the existing annotation of this pathogen. Results Using the Illumina Genome Analyzer, we generated 9,055,826 reads (average length ~76 bp) and aligned them to the reference genome using Bowtie. The transcribed regions were analyzed using SAMTOOLS and custom Perl scripts in conjunction with BLAST searches and available gene annotation information. The single nucleotide resolution map enabled the identification of 14 novel protein coding regions as well as 44 potential novel sRNA. The basal transcription profile revealed that 2,506 of the 2,837 annotated regions were expressed in vitro, at 95.25% coverage, representing all broad functional gene categories in the genome. The expression profile also helped identify 518 potential operon structures involving 1,086 co-expressed pairs. We also identified 11 proteins with mutated/alternate start codons. Conclusions The application of RNA-Seq based transcriptome profiling to structural gene annotation helped correct existing annotation errors and identify potential novel protein coding regions and sRNA. We used computational tools to predict regulatory elements such as promoters and terminators

An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.

PubMed

Pichon, Christophe; du Merle, Laurence; Caliot, Marie Elise; Trieu-Cuot, Patrick; Le Bouguénec, Chantal

2012-04-01

Characterization of small non-coding ribonucleic acids (sRNA) among the large volume of data generated by high-throughput RNA-seq or tiling microarray analyses remains a challenge. Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. After years of effort, dedicated software were developed based on comparative genomic analyses or mathematical/statistical models. Although these genomic analyses enabled sRNAs in intergenic regions to be efficiently identified, they all failed to predict antisense sRNA genes (asRNA), i.e. RNA genes located on the DNA strand complementary to that which encodes the protein. The statistical models enabled any genomic region to be analyzed theorically but not efficiently. We present a new model for in silico identification of sRNA and asRNA candidates within an entire bacterial genome. This model was successfully used to analyze the Gram-negative Escherichia coli and Gram-positive Streptococcus agalactiae. In both bacteria, numerous asRNAs are transcribed from the complementary strand of genes located in pathogenicity islands, strongly suggesting that these asRNAs are regulators of the virulence expression. In particular, we characterized an asRNA that acted as an enhancer-like regulator of the type 1 fimbriae production involved in the virulence of extra-intestinal pathogenic E. coli.

An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains

PubMed Central

Pichon, Christophe; du Merle, Laurence; Caliot, Marie Elise; Trieu-Cuot, Patrick; Le Bouguénec, Chantal

2012-01-01

Characterization of small non-coding ribonucleic acids (sRNA) among the large volume of data generated by high-throughput RNA-seq or tiling microarray analyses remains a challenge. Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. After years of effort, dedicated software were developed based on comparative genomic analyses or mathematical/statistical models. Although these genomic analyses enabled sRNAs in intergenic regions to be efficiently identified, they all failed to predict antisense sRNA genes (asRNA), i.e. RNA genes located on the DNA strand complementary to that which encodes the protein. The statistical models enabled any genomic region to be analyzed theorically but not efficiently. We present a new model for in silico identification of sRNA and asRNA candidates within an entire bacterial genome. This model was successfully used to analyze the Gram-negative Escherichia coli and Gram-positive Streptococcus agalactiae. In both bacteria, numerous asRNAs are transcribed from the complementary strand of genes located in pathogenicity islands, strongly suggesting that these asRNAs are regulators of the virulence expression. In particular, we characterized an asRNA that acted as an enhancer-like regulator of the type 1 fimbriae production involved in the virulence of extra-intestinal pathogenic E. coli. PMID:22139924

RNA-Seq analysis uncovers non-coding small RNA system of Mycobacterium neoaurum in the metabolism of sterols to accumulate steroid intermediates.

PubMed

Liu, Min; Zhu, Zhan-Tao; Tao, Xin-Yi; Wang, Feng-Qing; Wei, Dong-Zhi

2016-04-25

Understanding the metabolic mechanism of sterols to produce valuable steroid intermediates in mycobacterium by a noncoding small RNA (sRNA) view is still limited. In the work, RNA-seq was implemented to investigate the noncoding transcriptome of Mycobacterium neoaurum (Mn) in the transformation process of sterols to valuable steroid intermediates, including 9α-hydroxy-4-androstene-3,17-dione (9OHAD), 1,4-androstadiene-3,17-dione (ADD), and 22-hydroxy-23, 24-bisnorchola-1,4-dien-3-one (1,4-BNA). A total of 263 sRNA candidates were predicted from the intergenic regions in Mn. Differential expression of sRNA candidates was explored in the wide type Mn with vs without sterol addition, and the steroid intermediate producing Mn strains vs wide type Mn with sterol addition, respectively. Generally, sRNA candidates were differentially expressed in various strains, but there were still some shared candidates with outstandingly upregulated or downregulated expression in these steroid producing strains. Accordingly, four regulatory networks were constructed to reveal the direct and/or indirect interactions between sRNA candidates and their target genes in four groups, including wide type Mn with vs without sterol addition, 9OHAD, ADD, and BNA producing strains vs wide type Mn with sterol addition, respectively. Based on these constructed networks, several highly focused sRNA candidates were discovered to be prevalent in the networks, which showed comprehensive regulatory roles in various cellular processes, including lipid transport and metabolism, amino acid transport and metabolism, signal transduction, cell envelope biosynthesis and ATP synthesis. To explore the functional role of sRNA candidates in Mn cells, we manipulated the overexpression of candidates 131 and 138 in strain Mn-9OHAD, which led to enhanced production of 9OHAD from 1.5- to 2.3-fold during 6 d' fermentation and a slight effect on growth rate. This study revealed the complex and important regulatory

Twenty-four-nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids.

PubMed

Greaves, Ian K; Eichten, Steven R; Groszmann, Michael; Wang, Aihua; Ying, Hua; Peacock, W James; Dennis, Elizabeth S

2016-11-01

Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24-nt siRNAs and altered patterns of DNA methylation that can affect gene expression. Driving the changes in methylation are the processes trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). In TCM/TCdM the methylation state of one allele is altered to resemble the other allele. We show that Pol IV-dependent sRNAs are required to establish TCM events. The changes in DNA methylation and the associated changes in sRNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome. The inheritance of these altered epigenetic states varies in F2 individuals, resulting in individuals with genetically identical loci displaying different epigenetic states and gene expression profiles. The change in methylation at these regions is associated with the presence of sRNAs. Loci without any sRNA activity can have altered methylation states, suggesting that a sRNA-independent mechanism may also contribute to the altered methylation state of the F1 and F2 generations.

Twenty-four–nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids

PubMed Central

Greaves, Ian K.; Eichten, Steven R.; Groszmann, Michael; Wang, Aihua; Ying, Hua; Peacock, W. James; Dennis, Elizabeth S.

2016-01-01

Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24-nt siRNAs and altered patterns of DNA methylation that can affect gene expression. Driving the changes in methylation are the processes trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). In TCM/TCdM the methylation state of one allele is altered to resemble the other allele. We show that Pol IV-dependent sRNAs are required to establish TCM events. The changes in DNA methylation and the associated changes in sRNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome. The inheritance of these altered epigenetic states varies in F2 individuals, resulting in individuals with genetically identical loci displaying different epigenetic states and gene expression profiles. The change in methylation at these regions is associated with the presence of sRNAs. Loci without any sRNA activity can have altered methylation states, suggesting that a sRNA-independent mechanism may also contribute to the altered methylation state of the F1 and F2 generations. PMID:27791153

Finding exact constants in a Markov model of Zipfs law generation

NASA Astrophysics Data System (ADS)

Bochkarev, V. V.; Lerner, E. Yu.; Nikiforov, A. A.; Pismenskiy, A. A.

2017-12-01

According to the classical Zipfs law, the word frequency is a power function of the word rank with an exponent -1. The objective of this work is to find multiplicative constant in a Markov model of word generation. Previously, the case of independent letters was mathematically strictly investigated in [Bochkarev V V and Lerner E Yu 2017 International Journal of Mathematics and Mathematical Sciences Article ID 914374]. Unfortunately, the methods used in this paper cannot be generalized in case of Markov chains. The search of the correct formulation of the Markov generalization of this results was performed using experiments with different ergodic matrices of transition probability P. Combinatory technique allowed taking into account all the words with probability of more than e -300 in case of 2 by 2 matrices. It was experimentally proved that the required constant in the limit is equal to the value reciprocal to conditional entropy of matrix row P with weights presenting the elements of the vector π of the stationary distribution of the Markov chain.

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

PubMed

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

2016-01-22

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

CoLIde

PubMed Central

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-01-01

Small RNAs (sRNAs) are 20–25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci.   To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk. PMID:23851377

CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.

PubMed

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-07-01

Small RNAs (sRNAs) are 20-25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci. To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk.

Small RNA-based prediction of hybrid performance in maize.

PubMed

Seifert, Felix; Thiemann, Alexander; Schrag, Tobias A; Rybka, Dominika; Melchinger, Albrecht E; Frisch, Matthias; Scholten, Stefan

2018-05-21

Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program. Correlation of genomic differences and messenger RNA (mRNA) or sRNA expression differences between parental lines with hybrid performance of their hybrids revealed that sRNAs showed an inverse relationship in contrast to the other two data types. We associated differences for SNPs, mRNA and sRNA expression between parental inbred lines with the performance of their hybrid combinations and developed two prediction approaches using distance measures based on associated markers. Cross-validations revealed parental differences in sRNA expression to be strong predictors for hybrid performance for grain yield in maize, comparable to genomic and mRNA data. The integration of both positively and negatively associated markers in the prediction approaches enhanced the prediction accurary. The associated sRNAs belong predominantly to the canonical size classes of 22- and 24-nt that show specific genomic mapping characteristics. Expression profiles of sRNA are a promising alternative to SNPs or mRNA expression profiles for hybrid prediction, especially for plant species without reference genome or transcriptome information. The characteristics of the sRNAs we identified suggest that association studies based on breeding populations facilitate the identification of sRNAs involved in hybrid performance.

Determination of in vivo regulation kinetics of small non-coding RNA in bacteria

NASA Astrophysics Data System (ADS)

Fei, Jingyi

Small RNAs (sRNAs) play important roles in regulating gene expression through a variety of mechanisms. As one of the most common strategies, sRNA induced target messenger RNA (mRNA) includes two major steps: target search by base-pairing interactions with the and downstream execution by modulating translation or the stability of the mRNA. Here we describe a new imaging and analysis platform based on super-resolution fluorescence microscopy, which enabled the first in vivo kinetic measurement of sRNA-mediated gene regulation. Specifically, this platform was used to investigate a sugar-phosphate stress-induced bacterial sRNA that induces the degradation of target mRNAs. The data reveal that the sRNA binds to a primary target mRNA in a reversible and dynamic fashion, and that formation of the sRNA-mRNA complexes is the rate-limiting step, dictating the overall efficiency of regulation in vivo; whereas the downstream co-degradation of sRNA-mRNA complex can kinetically compete with the fast complex disassembly. Examination of a secondary target of this sRNA indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other sRNA systems and other target search processes.

Modeling sRNA-Regulated Plasmid Maintenance

PubMed Central

Klumpp, Stefan

2017-01-01

We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid. Key to their function is the tight regulation of expression of a protein toxin by an sRNA antitoxin. Here, we focus on the nonlinear nature of the regulatory circuit dynamics of the toxin-antitoxin mechanism. The mechanism relies on a transient increase in protein concentration rather than on the steady state of the genetic circuit. Through a systematic analysis of the parameter dependence of this transient increase, we confirm some known design features of this system and identify new ones: for an efficient toxin-antitoxin mechanism, the synthesis rate of the toxin’s mRNA template should be lower that of the sRNA antitoxin, the mRNA template should be more stable than the sRNA antitoxin, and the mRNA-sRNA complex should be more stable than the sRNA antitoxin. Moreover, a short half-life of the protein toxin is also beneficial to the function of the toxin-antitoxin system. In addition, we study a therapeutic scenario in which a competitor mRNA is introduced to sequester the sRNA antitoxin, causing the toxic protein to be expressed. PMID:28085919

StarScan: a web server for scanning small RNA targets from degradome sequencing data.

PubMed

Liu, Shun; Li, Jun-Hao; Wu, Jie; Zhou, Ke-Ren; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2015-07-01

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Insights into transcription termination of Hfq-binding sRNAs of Escherichia coli and characterization of readthrough products

PubMed Central

Morita, Teppei; Ueda, Masaki; Kubo, Kento; Aiba, Hiroji

2015-01-01

The genes encoding Hfq-dependent sRNAs possess a typical Rho-independent transcription terminator. Here, we have studied the molecular events occurring at Rho-independent terminators of sRNA genes, focusing on two well-characterized Hfq-binding sRNAs, SgrS and RyhB. We constructed several hybrid genes in which the DNA sequence corresponding to a strong Rho-independent terminator was placed just downstream from the Rho-independent terminators of sRNA genes. By using this system, we demonstrate that transcripts frequently read through the Rho-independent terminators of sgrS and ryhB in normally growing cells. We show that Hfq does not affect the transcriptional readthrough event itself. We also find that the readthrough products no longer bind to Hfq in vivo. We have developed a competition assay based on a biotin–streptavidin system to analyze the interaction of Hfq and a particular RNA molecule in vitro. By using this method, we verify that the 3′-extended form of SgrS does not bind to Hfq in vitro. Finally, we demonstrate that transcription termination is significantly enhanced under stress conditions where transcription initiation of sRNA genes on the chromosome is induced. We conclude that the production of sRNAs is regulated not only at the step of transcription initiation but also at the step of transcription termination. The mechanism by which transcription termination is enhanced under stress conditions remains to be understood. PMID:26106215

Random number generation in bilingual Balinese and German students: preliminary findings from an exploratory cross-cultural study.

PubMed

Strenge, Hans; Lesmana, Cokorda Bagus Jaya; Suryani, Luh Ketut

2009-08-01

Verbal random number generation is a procedurally simple task to assess executive function and appears ideally suited for the use under diverse settings in cross-cultural research. The objective of this study was to examine ethnic group differences between young adults in Bali (Indonesia) and Kiel (Germany): 50 bilingual healthy students, 30 Balinese and 20 Germans, attempted to generate a random sequence of the digits 1 to 9. In Balinese participants, randomization was done in Balinese (native language L1) and Indonesian (first foreign language L2), in German subjects in the German (L1) and English (L2) languages. 10 of 30 Balinese (33%), but no Germans, were unable to inhibit habitual counting in more than half of the responses. The Balinese produced significantly more nonrandom responses than the Germans with higher rates of counting and significantly less occurrence of the digits 2 and 3 in L1 compared with L2. Repetition and cycling behavior did not differ between the four languages. The findings highlight the importance of taking into account culture-bound psychosocial factors for Balinese individuals when administering and interpreting a random number generation test.

The Seventh Generation: Native Students Speak about Finding the Good Path.

ERIC Educational Resources Information Center

Bergstrom, Amy; Cleary, Linda Miller; Peacock, Thomas D.

Many American Indian, First Nations, and Alaska Native cultures have prophecies about the "Seventh Generation"--young people who will have a spiritual and cultural awakening and lead the regeneration of the nations and the earth. This book honors the Seventh Generation. It draws on the words of 120 Native youth, interviewed in the United States…

Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories

PubMed Central

Liu, Yang; El-Kassaby, Yousry A.

2017-01-01

While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18–24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration. We applied diverse profiling methods to examine sRNA and miRNA features, including size distribution, sequence conservation and reproduction-specific regulation, as well as to predict their putative targets. The top 27 most abundant miRNAs were highly overlapped between the two species (e.g., miR166,−319 and−396), but in P. glauca, they were less abundant and significantly less correlated with seed-set phases. The most abundant sRNAs in libraries were deeply conserved miRNAs in the plant kingdom for Arabidopsis but long sRNAs (24-nt) for P. glauca. We also found significant difference in normalized expression between populations for population-specific sRNAs but not for lineage-specific ones. Moreover, lineage-specific sRNAs were enriched in the 21-nt size class. This pattern is consistent in both species and alludes to a specific type of sRNAs (e.g., miRNA, tasiRNA) being selected for. In addition, we deemed 24 and 9 sRNAs in P. glauca and Arabidopsis, respectively, as sRNA candidates targeting known adaptive genes. Temperature had significant influence on selected gene and miRNA expression at seed development in both species. This study increases our integrated understanding of sRNA evolution and its potential link to genomic architecture (e.g., sRNA derivation from genome and sRNA-mediated genomic events) and organismal complexity (e.g., association between

Biotechnological uses of RNAi in plants: risk assessment considerations.

PubMed

Casacuberta, Josep M; Devos, Yann; du Jardin, Patrick; Ramon, Matthew; Vaucheret, Hervé; Nogué, Fabien

2015-03-01

RNAi offers opportunities to generate new traits in genetically modified (GM) plants. Instead of expressing novel proteins, RNAi-based GM plants reduce target gene expression. Silencing of off-target genes may trigger unintended effects, and identifying these genes would facilitate risk assessment. However, using bioinformatics alone is not reliable, due to the lack of genomic data and insufficient knowledge of mechanisms governing mRNA-small (s)RNA interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improving Mathematics Learning by Integrating Curricular Activities with Innovative and Developmentally Appropriate Digital Apps: Findings from the Next Generation Preschool Math Evaluation

ERIC Educational Resources Information Center

Presser, Ashley Lewis; Vahey, Philip; Dominguez, Ximena

2015-01-01

This paper describes findings from a blocked randomized design (BRD) field study conducted to examine the "Next Generation Preschool Math" (NGPM) program's implementation in preschool classrooms and promise in improving young children's mathematic learning. NGPM integrates traditional preschool activities with developmentally appropriate…

Trans-kingdom small RNA transfer during host-pathogen interactions: The case of P. falciparum and erythrocytes.

PubMed

Walzer, Katelyn A; Chi, Jen-Tsan

2017-04-03

This review focuses on the role of trans-kingdom movement of small RNA (sRNA) molecules between parasites, particularly Plasmodium falciparum, and their respective host cells. While the intercellular transfer of sRNAs within organisms is well recognized, recent studies illustrate many examples of trans-kingdom sRNA exchange within the context of host-parasite interactions. These interactions are predominantly found in the transfer of host sRNAs between erythrocytes and the invading P. falciparum, as well as other host cell types. In addition, parasite-encoded sRNAs can also be transferred to host cells to evade the immune system. The transport of these parasite sRNAs in the body fluids of the host may also offer means to detect and monitor the parasite infection. These isolated examples may only represent the tip of the iceberg in which the transfer of sRNA between host and parasites is a critical aspect of host-pathogen interactions. In addition, the levels of these sRNAs and their speed of transfer may vary dramatically under different contexts to push the biologic equilibrium toward the benefit of hosts vs. parasites. Therefore, these sRNA transfers may offer potential strategies to detect, prevent or treat parasite infections. Here, we review a brief history of the discovery of host erythrocyte sRNAs, their transfers and interactions in the context of P. falciparum infection. We also provide examples and discuss the functional significance of the reciprocal transfer of parasite-encoded sRNAs into hosts. These understandings of sRNA exchanges are put in the context of their implications for parasite pathogenesis, host defenses and the evolution of host polymorphisms driven by host interactions with these parasites.

Theoretical studies on sRNA-mediated regulation in bacteria

NASA Astrophysics Data System (ADS)

Chang, Xiao-Xue; Xu, Liu-Fang; Shi, Hua-Lin

2015-12-01

Small RNA(sRNA)-mediated post-transcriptional regulation differs from protein-mediated regulation. Through base-pairing, sRNA can regulate the target mRNA in a catalytic or stoichiometric manner. Some theoretical models were built for comparison of the protein-mediated and sRNA-mediated modes in the steady-state behaviors and noise properties. Many experiments demonstrated that a single sRNA can regulate several mRNAs, which causes crosstalk between the targets. Here, we focus on some models in which two target mRNAs are silenced by the same sRNA to discuss their crosstalk features. Additionally, the sequence-function relationship of sRNA and its role in the kinetic process of base-pairing have been highlighted in model building. Project supported by the National Basic Research Program of China (Grant No. 2013CB834100), the National Natural Science Foundation of China (Grant Nos. 11121403 and 11274320), the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y4KF171CJ1), the National Natural Science Foundation for Young Scholar of China (Grant No. 11304115), and the China Postdoctoral Science Foundation (Grant No. 2013M541282).

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets

PubMed Central

Paicu, Claudia; Mohorianu, Irina; Stocks, Matthew; Xu, Ping; Coince, Aurore; Billmeier, Martina; Dalmay, Tamas; Moulton, Vincent; Moxon, Simon

2017-01-01

Abstract Motivation MicroRNAs are a class of ∼21–22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. Results We test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. Availability and Implementation miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. Contact v.moulton@uea.ac.uk or s.moxon@uea.ac.uk Supplementary information Supplementary data are available at Bioinformatics online. PMID:28407097

Retiring the Generation Gap: How Employees Young and Old Can Find Common Ground

ERIC Educational Resources Information Center

Deal, Jennifer J.

2007-01-01

How different are the generations, really? Everybody knows that the "generation gap" between younger and older people causes stress and frustration at work. Are the differences people complain about just a big misunderstanding, or are they real? And most important, how can one use similarities and differences among the generations to be more…

Reflecting on Earlier Experiences with Unsolicited Findings: Points to Consider for Next-Generation Sequencing and Informed Consent in Diagnostics

PubMed Central

Rigter, Tessel; Henneman, Lidewij; Kristoffersson, Ulf; Hall, Alison; Yntema, Helger G; Borry, Pascal; Tönnies, Holger; Waisfisz, Quinten; Elting, Mariet W; Dondorp, Wybo J; Cornel, Martina C

2013-01-01

High-throughput nucleotide sequencing (often referred to as next-generation sequencing; NGS) is increasingly being chosen as a diagnostic tool for cases of expected but unresolved genetic origin. When exploring a higher number of genetic variants, there is a higher chance of detecting unsolicited findings. The consequential increased need for decisions on disclosure of these unsolicited findings poses a challenge for the informed consent procedure. This article discusses the ethical and practical dilemmas encountered when contemplating informed consent for NGS in diagnostics from a multidisciplinary point of view. By exploring recent similar experiences with unsolicited findings in other settings, an attempt is made to describe what can be learned so far for implementing NGS in standard genetic diagnostics. The article concludes with a set of points to consider in order to guide decision-making on the extent of return of results in relation to the mode of informed consent. We hereby aim to provide a sound basis for developing guidelines for optimizing the informed consent procedure. PMID:23784691

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

PubMed Central

Dalmay, Tamas

2018-01-01

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues. PMID:29474379

Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies.

PubMed

Goddard, Katrina A B; Whitlock, Evelyn P; Berg, Jonathan S; Williams, Marc S; Webber, Elizabeth M; Webster, Jennifer A; Lin, Jennifer S; Schrader, Kasmintan A; Campos-Outcalt, Doug; Offit, Kenneth; Feigelson, Heather Spencer; Hollombe, Celine

2013-09-01

The aim of this study was to develop, operationalize, and pilot test a transparent, reproducible, and evidence-informed method to determine when to report incidental findings from next-generation sequencing technologies. Using evidence-based principles, we proposed a three-stage process. Stage I "rules out" incidental findings below a minimal threshold of evidence and is evaluated using inter-rater agreement and comparison with an expert-based approach. Stage II documents criteria for clinical actionability using a standardized approach to allow experts to consistently consider and recommend whether results should be routinely reported (stage III). We used expert opinion to determine the face validity of stages II and III using three case studies. We evaluated the time and effort for stages I and II. For stage I, we assessed 99 conditions and found high inter-rater agreement (89%), and strong agreement with a separate expert-based method. Case studies for familial adenomatous polyposis, hereditary hemochromatosis, and α1-antitrypsin deficiency were all recommended for routine reporting as incidental findings. The method requires <3 days per topic. We establish an operational definition of clinically actionable incidental findings and provide documentation and pilot testing of a feasible method that is scalable to the whole genome.

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF-YA2 and YUC2.

PubMed

Gyula, Péter; Baksa, Ivett; Tóth, Tamás; Mohorianu, Irina; Dalmay, Tamás; Szittya, György

2018-06-01

Plants substantially alter their developmental program upon changes in the ambient temperature. The 21-24 nt small RNAs (sRNAs) are important gene expression regulators, which play a major role in development and adaptation. However, little is known about how the different sRNA classes respond to changes in the ambient temperature. We profiled the sRNA populations in four different tissues of Arabidopsis thaliana plants grown at 15, 21 and 27 °C. We found that only a small fraction (0.6%) of the sRNA loci are ambient temperature-controlled. We identified thermoresponsive miRNAs and identified their target genes using degradome libraries. We verified that the target of the thermoregulated miR169, NF-YA2, is also ambient temperature-regulated. NF-YA2, as the component of the conserved transcriptional regulator NF-Y complex, binds the promoter of the flowering time regulator FT and the auxin biosynthesis gene YUC2. Other differentially expressed loci include thermoresponsive phased siRNA loci that target various auxin pathway genes and tRNA fragments. Furthermore, a temperature dependent 24-nt heterochromatic siRNA locus in the promoter of YUC2 may contribute to the epigenetic regulation of auxin homeostasis. This holistic approach facilitated a better understanding of the role of different sRNA classes in ambient temperature adaptation of plants. This article is protected by copyright. All rights reserved.

Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility.

PubMed

Leistra, Abigail N; Amador, Paul; Buvanendiran, Aishwarya; Moon-Walker, Alex; Contreras, Lydia M

2017-12-15

Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering. We then modularly recombine the selected substructures, differentially representing those of presumed high or low functional contribution, to build a library of 21 CsrB variants. Using fluorescent translational reporter assays, we demonstrate that the CsrB variants achieve a 5-fold gradient of control of well-characterized Csr network targets. Interestingly, results suggest that less conserved local structures within long, multisubstrate sRNAs may represent better targets for rational engineering than their well-conserved counterparts. Lastly, mapping the impact of sRNA variants on a signature Csr network phenotype indicates the potential of this approach for tuning the activity of global sRNA regulators in the context of metabolic engineering applications.

Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia

PubMed Central

Liao, Jian-You; Guo, Yan-Hua; Zheng, Ling-Ling; Li, Yan; Xu, Wen-Li; Zhang, Yu-Chan; Zhou, Hui; Lun, Zhao-Rong; Ayala, Francisco J.; Qu, Liang-Hu

2014-01-01

Small RNAs (sRNAs), including microRNAs and endogenous siRNAs (endo-siRNAs), regulate most important biologic processes in eukaryotes, such as cell division and differentiation. Although sRNAs have been extensively studied in various eukaryotes, the role of sRNAs in the early emergence of eukaryotes is unclear. To address these questions, we deep sequenced the sRNA transcriptome of four different stages in the differentiation of Giardia lamblia, one of the most primitive eukaryotes. We identified a large number of endo-siRNAs in this fascinating parasitic protozoan and found that they were produced from live telomeric retrotransposons and three genomic regions (i.e., endo-siRNA generating regions [eSGRs]). eSGR-derived endo-siRNAs were proven to target mRNAs in trans. Gradual up-regulation of endo-siRNAs in the differentiation of Giardia suggested that they might be involved in the regulation of this process. This hypothesis was supported by the impairment of the differentiation ability of Giardia when GLDICER, essential for the biogenesis of endo-siRNAs, was knocked down. Endo-siRNAs are not the only sRNA regulators in Giardia differentiation, because a great number of tRNAs-derived sRNAs showed more dramatic expression changes than endo-siRNAs in this process. We totally identified five novel kinds of tRNAs-derived sRNAs and found that the biogenesis in four of them might be correlated with that of stress-induced tRNA-derived RNA (sitRNA), which was discovered in our previous studies. Our studies reveal an unexpected complex panorama of sRNA in G. lamblia and shed light on the origin and functional evolution of eukaryotic sRNAs. PMID:25225396

An Efficient Strategy of Screening for Pathogens in Wild-Caught Ticks and Mosquitoes by Reusing Small RNA Deep Sequencing Data

PubMed Central

An, Xiaoping; Fan, Hang; Ma, Maijuan; Anderson, Benjamin D.; Jiang, Jiafu; Liu, Wei; Cao, Wuchun; Tong, Yigang

2014-01-01

This paper explored our hypothesis that sRNA (18∼30 bp) deep sequencing technique can be used as an efficient strategy to identify microorganisms other than viruses, such as prokaryotic and eukaryotic pathogens. In the study, the clean reads derived from the sRNA deep sequencing data of wild-caught ticks and mosquitoes were compared against the NCBI nucleotide collection (non-redundant nt database) using Blastn. The blast results were then analyzed with in-house Python scripts. An empirical formula was proposed to identify the putative pathogens. Results showed that not only viruses but also prokaryotic and eukaryotic species of interest can be screened out and were subsequently confirmed with experiments. Specially, a novel Rickettsia spp. was indicated to exist in Haemaphysalis longicornis ticks collected in Beijing. Our study demonstrated the reuse of sRNA deep sequencing data would have the potential to trace the origin of pathogens or discover novel agents of emerging/re-emerging infectious diseases. PMID:24618575

Structural model of an mRNA in complex with the bacterial chaperone Hfq

DOE PAGES

Peng, Yi; Curtis, Joseph E.; Fang, Xianyang; ...

2014-11-17

The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. In this paper, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different sRNAs. Selective 2'-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Monte Carlo molecular dynamics simulations show that the distal face and lateral rim of Hfq interact with three sites in the rpoS leader, folding the RNA into a compact tertiary structure. These interactions are needed for sRNAmore » regulation of rpoS translation and position the sRNA target adjacent to an sRNA binding region on the proximal face of Hfq. Finally, our results show how Hfq specifically distorts the structure of the rpoS mRNA to enable sRNA base pairing and translational control.« less

Revisiting the Archival Finding Aid

ERIC Educational Resources Information Center

Cox, Richard J.

2007-01-01

Archivists have been creating finding aids for generations, and in the last three decades they have done this work via a succession of standardized formats. However, like many other disciplines, they have carried out such work in violation of systems analysis. Although purporting to have the users of finding aids systems first and foremost in…

WHATIF: an open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data

PubMed Central

Ye, Zhan; Kadolph, Christopher; Strenn, Robert; Wall, Daniel; McPherson, Elizabeth; Lin, Simon

2015-01-01

Background Identification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reportable incidental genetic findings. However, no informatics tools are currently available to support evaluation of incidental findings in next-generation sequencing data. Methods The Wisconsin Hierarchical Analysis Tool for Incidental Findings (WHATIF), was developed as a stand-alone Windows-based desktop executable, to support the interactive analysis of incidental findings in the context of the ACMG recommendations. WHATIF integrates the European Bioinformatics Institute Variant Effect Predictor (VEP) tool for biological interpretation and the National Center for Biotechnology Information ClinVar tool for clinical interpretation. Results An open-source desktop program was created to annotate incidental findings and present the results with a user-friendly interface. Further, a meaningful index (WHATIF Index) was devised for each gene to facilitate ranking of the relative importance of the variants and estimate the potential workload associated with further evaluation of the variants. Our WHATIF application is available at: http://tinyurl.com/WHATIF-SOFTWARE Conclusions The WHATIF application offers a user-friendly interface and allows users to investigate the extracted variant information efficiently and intuitively while always accessing the up to date information on variants via application programming interfaces (API) connections. WHATIF’s highly flexible design and straightforward implementation aids users in customizing the source code to meet their own special needs. PMID:25890833

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes

PubMed Central

Le Rhun, Anaïs; Beer, Yan Yan; Reimegård, Johan; Chylinski, Krzysztof; Charpentier, Emmanuelle

2016-01-01

ABSTRACT Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation. PMID:26580233

Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response.

PubMed

Gerrick, Elias R; Barbier, Thibault; Chase, Michael R; Xu, Raylin; François, Josie; Lin, Vincent H; Szucs, Matthew J; Rock, Jeremy M; Ahmad, Rushdy; Tjaden, Brian; Livny, Jonathan; Fortune, Sarah M

2018-06-19

One key to the success of Mycobacterium tuberculosis as a pathogen is its ability to reside in the hostile environment of the human macrophage. Bacteria adapt to stress through a variety of mechanisms, including the use of small regulatory RNAs (sRNAs), which posttranscriptionally regulate bacterial gene expression. However, very little is currently known about mycobacterial sRNA-mediated riboregulation. To date, mycobacterial sRNA discovery has been performed primarily in log-phase growth, and no direct interaction between any mycobacterial sRNA and its targets has been validated. Here, we performed large-scale sRNA discovery and expression profiling in M. tuberculosis during exposure to five pathogenically relevant stresses. From these data, we identified a subset of sRNAs that are highly induced in multiple stress conditions. We focused on one of these sRNAs, ncRv11846, here renamed mycobacterial regulatory sRNA in iron (MrsI). We characterized the regulon of MrsI and showed in mycobacteria that it regulates one of its targets, bfrA , through a direct binding interaction. MrsI mediates an iron-sparing response that is required for optimal survival of M. tuberculosis under iron-limiting conditions. However, MrsI is induced by multiple host-like stressors, which appear to trigger MrsI as part of an anticipatory response to impending iron deprivation in the macrophage environment. Copyright © 2018 the Author(s). Published by PNAS.

Experimental approaches to identify small RNAs and their diverse roles in bacteria--what we have learnt in one decade of MicA research.

PubMed

Van Puyvelde, Sandra; Vanderleyden, Jozef; De Keersmaecker, Sigrid C J

2015-10-01

Nowadays the identification of small RNAs (sRNAs) and characterization of their role within regulatory networks takes a prominent place in deciphering complex bacterial phenotypes. Compared to the study of other components of bacterial cells, this is a relatively new but fast-growing research field. Although reports on new sRNAs appear regularly, some sRNAs are already subject of research for a longer time. One of such sRNAs is MicA, a sRNA best described for its role in outer membrane remodeling, but probably having a much broader function than anticipated. An overview of what we have learnt from MicA led to the conclusion that even for this well-described sRNA, we still do not have the overall picture. More general, the story of MicA might become an experimental lead for unraveling the many sRNAs with unknown functions. In this review, three important topics in the sRNA field are covered, exemplified from the perspective of MicA: (i) identification of new sRNAs, (ii) target identification and unraveling the biological function, (iii) structural analysis. The complex mechanisms of action of MicA deliver some original insights in the sRNA field which includes the existence of dimer formation or simultaneous cis and trans regulation, and might further inspire the understanding of the function of other sRNAs. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

PubMed Central

Zheng, Yun; Ji, Bo; Song, Renhua; Wang, Shengpeng; Li, Ting; Zhang, Xiaotuo; Chen, Kun; Li, Tianqing; Li, Jinyan

2016-01-01

Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required. We propose a novel method (named MiRME) for an accurate and fast detection of miRNA M/E sites using a progressive sequence alignment approach which refines sensitivity and improves FPR step-by-step. From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3′-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical editing sites. We demonstrated that a few non-canonical editing sites were not resulted from mutations in genome by integrating the analysis of genome HTS profiles of two human cell lines, suggesting the existence of new editing types to further diversify the functions of miRNAs. Compared with six existing studies or methods, MiRME has shown much superior performance for the identification and visualization of the M/E sites of miRNAs from the ever-increasing sRNA HTS profiles. PMID:27229138

The box C/D sRNP dimeric architecture is conserved across domain Archaea

PubMed Central

Bower-Phipps, Kathleen R.; Taylor, David W.; Wang, Hong-Wei; Baserga, Susan J.

2012-01-01

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2′-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species—Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus—indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain. PMID:22753779

The box C/D sRNP dimeric architecture is conserved across domain Archaea.

PubMed

Bower-Phipps, Kathleen R; Taylor, David W; Wang, Hong-Wei; Baserga, Susan J

2012-08-01

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

PubMed

Le Rhun, Anaïs; Beer, Yan Yan; Reimegård, Johan; Chylinski, Krzysztof; Charpentier, Emmanuelle

2016-01-01

Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.

Cue generation and memory construction in direct and generative autobiographical memory retrieval.

PubMed

Harris, Celia B; O'Connor, Akira R; Sutton, John

2015-05-01

Theories of autobiographical memory emphasise effortful, generative search processes in memory retrieval. However recent research suggests that memories are often retrieved directly, without effortful search. We investigated whether direct and generative retrieval differed in the characteristics of memories recalled, or only in terms of retrieval latency. Participants recalled autobiographical memories in response to cue words. For each memory, they reported whether it was retrieved directly or generatively, rated its visuo-spatial perspective, and judged its accompanying recollective experience. Our results indicated that direct retrieval was commonly reported and was faster than generative retrieval, replicating recent findings. The characteristics of directly retrieved memories differed from generatively retrieved memories: directly retrieved memories had higher field perspective ratings and lower observer perspective ratings. However, retrieval mode did not influence recollective experience. We discuss our findings in terms of cue generation and content construction, and the implication for reconstructive models of autobiographical memory. Copyright © 2015 Elsevier Inc. All rights reserved.

Waking Up the Mind: Qualitative Study Findings About the Process Through Which Programs Combining Income Generation and Health Education Can Empower Indigenous Guatemalan Women.

PubMed

Gurman, Tilly A; Ballard, Anne; Kerr, Samantha; Walsh, Janée; Petrocy, Amy

2016-01-01

We explored the process through which two income-generation programs that include health education empower indigenous Guatemalan women artisans. Both artisans (n = 44) and program staff (n = 11) participated in semistructured interviews. Respondents expressed that women gained support about personal issues and experienced an awakening of the mind (despertar la mente). Through active participation, women's fear of strangers and speaking in public decreased. Women also gained mobility, awareness of their rights as women, and self-confidence from earning and managing their own income. Given our findings, we suggest that programs combining income generation and health education have the potential to empower women.

GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans.

PubMed

Almeida, Miguel Vasconcelos; Dietz, Sabrina; Redl, Stefan; Karaulanov, Emil; Hildebrandt, Andrea; Renz, Christian; Ulrich, Helle D; König, Julian; Butter, Falk; Ketting, René F

2018-05-16

Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro , that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities. © 2018 The Authors.

Metasynthesis findings: potential versus reality.

PubMed

Finfgeld-Connett, Deborah

2014-11-01

Early on, qualitative researchers predicted that metasynthesis research had the potential to significantly push knowledge development forward. More recently, scholars have questioned whether this is actually occurring. To examine this concern, a randomly selected sample of metasynthesis articles was systematically reviewed to identify the types of findings that have been produced. Based on this systematic examination, it appears that findings from metasynthesis investigations might not be reaching their full potential. Metasynthesis investigations frequently result in isolated findings rather than findings in relationship, and opportunities to generate research hypotheses and theoretical models are not always fully realized. With this in mind, methods for moving metasynthesis findings into relationship are discussed. © The Author(s) 2014.

Transcriptome sequencing analysis of novel sRNAs of Kineococcus radiotolerans in response to ionizing radiation.

PubMed

Chen, Zhouwei; Li, Lufeng; Shan, Zhan; Huang, Hannian; Chen, Huan; Ding, Xianfeng; Guo, Jiangfeng; Liu, Lili

2016-11-01

Kineococcus radiotolerans is a Gram-positive, radio-resistant bacterium isolated from a radioactive environment. The small noncoding RNAs (sRNAs) in bacteria are reported to play roles in the immediate response to stress and/or the recovery from stress. The analysis of K. radiotolerans transcriptome sequencing results can identify these sRNAs in a genome-wide detection, using RNA sequencing (RNA-seq) by the deep sequencing technique. In this study, the raw data of radiation-exposed samples (RS) and control samples (CS) were acquired separately from the sequencing platform. There were 217 common sRNA candidates in the two samples screened in the genome-wide scale by bioinformatics analysis. There were 43 differentially expressed sRNA candidates, including 28 up-regulated and 15 down-regulated ones. The down-regulated sRNAs were selected for the sRNA target prediction, of which 12 sRNAs that may modulate the genes related to the transcription regulation and DNA repair were considered as the candidates involved in the radio-resistance regulation system. Copyright © 2016 Elsevier GmbH. All rights reserved.

GRIL-Seq, a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation

PubMed Central

Han, Kook; Tjaden, Brian; Lory, Stephen

2017-01-01

The first step in the post-transcriptional regulatory function of most bacterial small non-coding RNAs (sRNAs) is base-pairing with partially complementary sequences of targeted transcripts. We present a simple method for identifying sRNA targets in vivo and defining processing sites of the regulated transcripts. The technique (referred to as GRIL-Seq) is based on preferential ligation of sRNAs to ends of base-paired targets in bacteria co-expressing T4 RNA ligase, followed by sequencing to identify the chimeras. In addition to the RNA chaperone Hfq, the GRIL-Seq method depends on the activity of the pyrophosphorylase RppH. Using PrrF1, an iron-regulated sRNA in Pseudomonas aeruginosa, we demonstrate that direct regulatory targets of this sRNA can be readily identified. Therefore, GRIL-Seq represents a powerful tool not only for identifying direct targets of sRNAs in a variety of environments, but can also result in uncovering novel roles for sRNAs and their targets in complex regulatory networks. PMID:28005055

GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation.

PubMed

Han, Kook; Tjaden, Brian; Lory, Stephen

2016-12-22

The first step in the post-transcriptional regulatory function of most bacterial small non-coding RNAs (sRNAs) is base pairing with partially complementary sequences of targeted transcripts. We present a simple method for identifying sRNA targets in vivo and defining processing sites of the regulated transcripts. The technique, referred to as global small non-coding RNA target identification by ligation and sequencing (GRIL-seq), is based on preferential ligation of sRNAs to the ends of base-paired targets in bacteria co-expressing T4 RNA ligase, followed by sequencing to identify the chimaeras. In addition to the RNA chaperone Hfq, the GRIL-seq method depends on the activity of the pyrophosphorylase RppH. Using PrrF1, an iron-regulated sRNA in Pseudomonas aeruginosa, we demonstrated that direct regulatory targets of this sRNA can readily be identified. Therefore, GRIL-seq represents a powerful tool not only for identifying direct targets of sRNAs in a variety of environments, but also for uncovering novel roles for sRNAs and their targets in complex regulatory networks.

Sensitivity of Small RNA-Based Detection of Plant Viruses.

PubMed

Santala, Johanna; Valkonen, Jari P T

2018-01-01

Plants recognize unrelated viruses by the antiviral defense system called RNA interference (RNAi). RNAi processes double-stranded viral RNA into small RNAs (sRNAs) of 21-24 nucleotides, the reassembly of which into longer strands in silico allows virus identification by comparison with the sequences available in databases. The aim of this study was to compare the virus detection sensitivity of sRNA-based virus diagnosis with the established virus species-specific polymerase chain reaction (PCR) approach. Viruses propagated in tobacco plants included three engineered, infectious clones of Potato virus A (PVA), each carrying a different marker gene, and an infectious clone of Potato virus Y (PVY). Total RNA (containing sRNA) was isolated and subjected to reverse-transcription real-time PCR (RT-RT-PCR) and sRNA deep-sequencing at different concentrations. RNA extracted from various crop plants was included in the reactions to normalize RNA concentrations. Targeted detection of selected viruses showed a similar threshold for the sRNA and reverse-transcription quantitative PCR (RT-qPCR) analyses. The detection limit for PVY and PVA by RT-qPCR in this study was 3 and 1.5 fg of viral RNA, respectively, in 50 ng of total RNA per PCR reaction. When knowledge was available about the viruses likely present in the samples, sRNA-based virus detection was 10 times more sensitive than RT-RT-PCR. The advantage of sRNA analysis is the detection of all tested viruses without the need for virus-specific primers or probes.

Generative Perspectives on Language Acquisition: Empirical Findings, Theoretical Considerations, and Crosslinguistic Comparisons.

ERIC Educational Resources Information Center

Clahsen, Harald, Ed.

The collection of essays and studies concerning generative grammar and first and second language acquisition includes: "The Optional-Infinitive Stage in Child English: Evidence from Negation" (Tony Harris, Ken Wexler); "Towards a Structure-Building Model of Acquisition" (Andrew Radford); "The Underspecification of…

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. Results To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. Conclusions This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni.

PubMed

Mandhan, Vibha; Kaur, Jagdeep; Singh, Kashmir

2012-11-01

MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to understand their roles in key

Plant Responses to Pathogen Attack: Small RNAs in Focus.

PubMed

Islam, Waqar; Noman, Ali; Qasim, Muhammad; Wang, Liande

2018-02-08

Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.

Plant Responses to Pathogen Attack: Small RNAs in Focus

PubMed Central

2018-01-01

Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases. PMID:29419801

Dealing with the incidental finding of secondary variants by the example of SRNS patients undergoing targeted next-generation sequencing.

PubMed

Weber, Stefanie; Büscher, Anja K; Hagmann, Henning; Liebau, Max C; Heberle, Christian; Ludwig, Michael; Rath, Sabine; Alberer, Martin; Beissert, Antje; Zenker, Martin; Hoyer, Peter F; Konrad, Martin; Klein, Hanns-Georg; Hoefele, Julia

2016-01-01

Steroid-resistant nephrotic syndrome (SRNS) is a severe cause of progressive renal disease. Genetic forms of SRNS can present with autosomal recessive or autosomal dominant inheritance. Recent studies have identified mutations in multiple podocyte genes responsible for SRNS. Improved sequencing methods (next-generation sequencing, NGS) now promise rapid mutational testing of SRNS genes. In the present study, a simultaneous screening of ten SRNS genes in 37 SRNS patients was performed by NGS. In 38 % of the patients, causative mutations in one SRNS gene were found. In 22 % of the patients, in addition to these mutations, a secondary variant in a different gene was identified. This high incidence of accumulating sequence variants was unexpected but, although they might have modifier effects, the pathogenic potential of these additional sequence variants seems unclear so far. The example of molecular diagnostics by NGS in SRNS patients shows that these new sequencing technologies might provide further insight into molecular pathogenicity in genetic disorders but will also generate results, which will be difficult to interpret and complicate genetic counseling. Although NGS promises more frequent identification of disease-causing mutations, the identification of causative mutations, the interpretation of incidental findings and possible pitfalls might pose problems, which hopefully will decrease by further experience and elucidation of molecular interactions.

The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

PubMed

Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

2017-01-01

RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed

Small RNA Regulators of Plant-Hemipteran Interactions: Micromanagers with Versatile Roles

PubMed Central

Sattar, Sampurna; Thompson, Gary A.

2016-01-01

Non-coding small RNAs (sRNAs) in plants have important roles in regulating biological processes, including development, reproduction, and stress responses. Recent research indicates significant roles for sRNA-mediated gene silencing during plant-hemipteran interactions that involve all three of these biological processes. Plant responses to hemipteran feeding are determined by changes in the host transcriptome that appear to be fine-tuned by sRNAs. The role of sRNA in plant defense responses is complex. Different forms of sRNAs, with specific modes of action, regulate changes in the host transcriptome primarily through post-transcriptional gene silencing and occasionally through translational repression. Plant genetic resistance against hemipterans provides a model to explore the regulatory roles of sRNAs in plant defense. Aphid-induced sRNA expression in resistance genotypes delivers a new paradigm in understanding the regulation of R gene-mediated resistance in host plants. Unique sRNA profiles, including changes in sRNA biogenesis and expression can also provide insights into susceptibility to insect herbivores. Activation of phytohormone-mediated defense responses against insect herbivory is another hallmark of this interaction, and recent studies have shown that regulation of phytohormone signaling is under the control of sRNAs. Hemipterans feeding on resistant plants also show changes in insect sRNA profiles, possibly influencing insect development and reproduction. Changes in insect traits such as fecundity, host range, and resistance to insecticides are impacted by sRNAs and can directly contribute to the success of certain insect biotypes. In addition to causing direct damage to the host plant, hemipteran insects are often vectors of viral pathogens. Insect anti-viral RNAi machinery is activated to limit virus accumulation, suggesting a role in insect immunity. Virus-derived long sRNAs strongly resemble insect piRNAs, leading to the speculation that the pi

Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense

PubMed Central

2011-01-01

Background Small RNA (sRNA) regulatory pathways (SRRPs) are important to anti-viral defence in mosquitoes. To identify critical features of the virus infection process in Dengue serotype 2 (DENV2)-infected Ae. aegypti, we deep-sequenced small non-coding RNAs. Triplicate biological replicates were used so that rigorous statistical metrics could be applied. Results In addition to virus-derived siRNAs (20-23 nts) previously reported for other arbovirus-infected mosquitoes, we show that PIWI pathway sRNAs (piRNAs) (24-30 nts) and unusually small RNAs (usRNAs) (13-19 nts) are produced in DENV-infected mosquitoes. We demonstrate that a major catalytic enzyme of the siRNA pathway, Argonaute 2 (Ago2), co-migrates with a ~1 megadalton complex in adults prior to bloodfeeding. sRNAs were cloned and sequenced from Ago2 immunoprecipitations. Viral sRNA patterns change over the course of infection. Host sRNAs were mapped to the published aedine transcriptome and subjected to analysis using edgeR (Bioconductor). We found that sRNA profiles are altered early in DENV2 infection, and mRNA targets from mitochondrial, transcription/translation, and transport functional categories are affected. Moreover, small non-coding RNAs (ncRNAs), such as tRNAs, spliceosomal U RNAs, and snoRNAs are highly enriched in DENV-infected samples at 2 and 4 dpi. Conclusions These data implicate the PIWI pathway in anti-viral defense. Changes to host sRNA profiles indicate that specific cellular processes are affected during DENV infection, such as mitochondrial function and ncRNA levels. Together, these data provide important progress in understanding the DENV2 infection process in Ae. aegypti. PMID:21356105

Analysis of plant-derived miRNAs in animal small RNA datasets

PubMed Central

2012-01-01

Background Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA is considered to be unstable within the gastrointestinal tract of many animals, thus limiting potential for any adverse effects from consumption of dietary RNA. A recent paper reported that putative plant miRNAs were detected in animal plasma and serum, presumably acquired through ingestion, and may have a functional impact in the consuming organisms. Results To address the question of how common this phenomenon could be, we searched for plant miRNAs sequences in public sRNA datasets from various tissues of mammals, chicken and insects. Our analyses revealed that plant miRNAs were present in the animal sRNA datasets, and significantly miR168 was extremely over-represented. Furthermore, all or nearly all (>96%) miR168 sequences were monocot derived for most datasets, including datasets for two insects reared on dicot plants in their respective experiments. To investigate if plant-derived miRNAs, including miR168, could accumulate and move systemically in insects, we conducted insect feeding studies for three insects including corn rootworm, which has been shown to be responsive to plant-produced long double-stranded RNAs. Conclusions Our analyses suggest that the observed plant miRNAs in animal sRNA datasets can originate in the process of sequencing, and that accumulation of plant miRNAs via dietary exposure is not universal in animals. PMID:22873950

Global assessment of small RNAs reveals a non-coding transcript involved in biofilm formation and attachment in Acinetobacter baumannii ATCC 17978

PubMed Central

Pérez, Astrid; Gómez, Manuel J.; Gayoso, Carmen; Vallejo, Juan A.; Ohneck, Emily J.; Valle, Jaione; Actis, Luis A.; Beceiro, Alejandro; Bou, Germán

2017-01-01

Many strains of Acinetobacter baumannii have been described as being able to form biofilm. Small non-coding RNAs (sRNAs) control gene expression in many regulatory circuits in bacteria. The aim of the present work was to provide a global description of the sRNAs produced both by planktonic and biofilm-associated (sessile) cells of A. baumannii ATCC 17978, and to compare the corresponding gene expression profiles to identify sRNAs molecules associated to biofilm formation and virulence. sRNA was extracted from both planktonic and sessile cells and reverse transcribed. cDNA was subjected to 454-pyrosequencing using the GS-FLX Titanium chemistry. The global analysis of the small RNA transcriptome revealed different sRNA expression patterns in planktonic and biofilm associated cells, with some of the transcripts only expressed or repressed in sessile bacteria. A total of 255 sRNAs were detected, with 185 of them differentially expressed in the different types of cells. A total of 9 sRNAs were expressed only in biofilm cells, while the expression of other 21 coding regions were repressed only in biofilm cells. Strikingly, the expression level of the sRNA 13573 was 120 times higher in biofilms than in planktonic cells, an observation that prompted us to further investigate the biological role of this non-coding transcript. Analyses of an isogenic mutant and over-expressing strains revealed that the sRNA 13573 gene is involved in biofilm formation and attachment to A549 human alveolar epithelial cells. The present work serves as a basis for future studies examining the complex regulatory network that regulate biofilm biogenesis and attachment to eukaryotic cells in A. baumannii ATCC 17978. PMID:28763494

The Regulatory Small RNA MarS Supports Virulence of Streptococcus pyogenes.

PubMed

Pappesch, Roberto; Warnke, Philipp; Mikkat, Stefan; Normann, Jana; Wisniewska-Kucper, Aleksandra; Huschka, Franziska; Wittmann, Maja; Khani, Afsaneh; Schwengers, Oliver; Oehmcke-Hecht, Sonja; Hain, Torsten; Kreikemeyer, Bernd; Patenge, Nadja

2017-09-25

Small regulatory RNAs (sRNAs) play a role in the control of bacterial virulence gene expression. In this study, we investigated an sRNA that was identified in Streptococcus pyogenes (group A Streptococcus, GAS) but is conserved throughout various streptococci. In a deletion strain, expression of mga, the gene encoding the multiple virulence gene regulator, was reduced. Accordingly, transcript and proteome analyses revealed decreased expression of several Mga-activated genes. Therefore, and because the sRNA was shown to interact with the 5' UTR of the mga transcript in a gel-shift assay, we designated it MarS for m ga-activating regulatory sRNA. Down-regulation of important virulence factors, including the antiphagocytic M-protein, led to increased susceptibility of the deletion strain to phagocytosis and reduced adherence to human keratinocytes. In a mouse infection model, the marS deletion mutant showed reduced dissemination to the liver, kidney, and spleen. Additionally, deletion of marS led to increased tolerance towards oxidative stress. Our in vitro and in vivo results indicate a modulating effect of MarS on virulence gene expression and on the pathogenic potential of GAS.

The Use of Backscattered Electron Imaging and Transmission Electron Microscopy to Assess Bone Architecture and Mineral Loci: Effect of Intermittent Slow-Release Sodium Fluoride Therapy

NASA Astrophysics Data System (ADS)

Zerwekh, Joseph E.; Bellotto, Dennis; Prostak, Kenneth S.; Hagler, Herbert K.; Pak, Charles Y. C.

1996-04-01

Backscattered electron imaging (BEI) and transmission electron microscopy (TEM) were used to examine the effects of treatment with intermittent slow-release sodium fluoride (SRNaF) and continuous calcium citrate on bone architecture and crystallinity. Examination was performed in nondecalcified biopsies obtained from patients following up to four years of therapy (placebo or SRNaF) and compared to pretreatment biopsies from each patient, as well as to bone from young, normal subjects. BEI images disclosed increased areas of recent bone formation following fluoride administration. There was no evidence of a mineralization defect in any biopsy and both cortical and trabecular architecture remained normal. TEM analysis demonstrated intrafibrillar platelike crystals and extrafibrillar needlelike crystals for both the pre- and post-treatment biopsies as well as for the bone from young normal subjects. There was no evidence of increased crystal size or of an increase in extrafibrillar mineral deposition. These observations suggest that intermittent SRNaF and continuous calcium therapy exerts an anabolic action on the skeleton not accompanied by a mineralization defect or an alteration of bone mineral deposition. The use of BEI and TEM holds promise for the study of the pathophysiology and treatment of metabolic bone diseases.

Looking ahead to our next generation of nurse leaders: Generation X Nurse Managers.

PubMed

Keys, Yolanda

2014-01-01

The present inquiry identifies elements of professional success, and personal and professional fulfilment as defined by Generation X Nurse Managers. Although work concerning Nurse Manager preparation has been documented, there is a paucity of research specific to the generation of nurses next in line to assume leadership roles. For the purposes of this study, a qualitative approach was used to develop insight regarding Generation X Nurse Managers and their perspectives on professional success, personal and professional fulfilment, and organisational environments that are conducive to loyalty and long-term professional commitment. Findings from this study reinforced those identified in the original study in that inflexible organisational cultures, a lack of opportunities for upward mobility, the need to be available at all times, feeling stereotyped or undervalued can all be barriers to members of Generation X perceptions of professional success and professional and personal fulfilment. Study findings suggest that Generation X Nurse Managers would benefit from initiatives focused on better preparation for the Nurse Manager role, openness to innovative scheduling alternatives and tailored support and feedback. © 2014 John Wiley & Sons Ltd.

psRNATarget: a plant small RNA target analysis server (2017 release).

PubMed

Dai, Xinbin; Zhuang, Zhaohong; Zhao, Patrick Xuechun

2018-04-30

Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility. This update enhances its analytical performance by developing a new scoring schema that is capable of discovering miRNA-mRNA interactions at higher 'recall rates' without significantly increasing total prediction output. The scoring procedure is customizable for the users to search both canonical and non-canonical targets. This update also enables transmitting and analyzing 'big' data empowered by (a) the implementation of multi-threading chunked file uploading, which can be paused and resumed, using HTML5 APIs and (b) the allocation of significantly more computing nodes to its back-end Linux cluster. The updated psRNATarget server has clear, compelling and user-friendly interfaces that enhance user experiences and present data clearly and concisely. The psRNATarget is freely available at http://plantgrn.noble.org/psRNATarget/.

Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression.

PubMed

Moreno, Renata; Fonseca, Pilar; Rojo, Fernando

2012-01-01

The Crc protein is a translational repressor that recognizes a specific target at some mRNAs, controlling catabolite repression and co-ordinating carbon metabolism in pseudomonads. In Pseudomonas aeruginosa, the levels of free Crc protein are controlled by CrcZ, a sRNA that sequesters Crc, acting as an antagonist. We show that, in Pseudomonas putida, the levels of free Crc are controlled by CrcZ and by a novel 368 nt sRNA named CrcY. CrcZ and CrcY, which contain six potential targets for Crc, were able to bind Crc specifically in vitro. The levels of CrcZ and CrcY were low under conditions generating a strong catabolite repression, and increased strongly when catabolite repression was absent. Deletion of either crcZ or crcY had no effect on catabolite repression, but the simultaneous absence of both sRNAs led to constitutive catabolite repression that compromised growth on some carbon sources. Overproduction of CrcZ or CrcY significantly reduced repression. We propose that CrcZ and CrcY act in concert, sequestering and modulating the levels of free Crc according to metabolic conditions. The CbrA/CbrB two-component system activated crcZ transcription, but had little effect on crcY. CrcY was detected in P. putida, Pseudomonas fluorescens and Pseudomonas syringae, but not in P. aeruginosa. © 2011 Blackwell Publishing Ltd.

Generativity does not necessarily satisfy all your needs: Associations among cultural demand for generativity, generative concern, generative action, and need satisfaction in the elderly in four cultures.

PubMed

Hofer, Jan; Busch, Holger; Au, Alma; Poláčková Šolcová, Iva; Tavel, Peter; Wong, Teresa Tsien

2016-03-01

The present study examines the association between various facets of generativity, that is, cultural demand for generativity, generative concern, and generative action, with the satisfaction of the needs for relatedness, competence, and autonomy in samples of elderly from Cameroon, China (Hong Kong), the Czech Republic, and Germany. Participants provided information on self-transcendence values (internalized cultural demand), generative concern and action, and need satisfaction. Results suggest, first, that internalized cultural demand affects generative action indirectly through generative concern, second, that generative concern has a positive direct effect on need satisfaction, but that, third, there is also an indirect effect of generative concern on need satisfaction through generative action, which, fourth, is positive for the needs for relatedness and competence but negative for the need for autonomy. These findings were culture-invariant in our study, suggesting generalizability to other cultures. They are discussed with respect to the role of values in generativity and a possible trade-off of generative action for the satisfaction of needs at least in the elderly. (c) 2016 APA, all rights reserved).

Small RNAs Reflect Grandparental Environments in Apomictic Dandelion

PubMed Central

Morgado, Lionel; Preite, Veronica; Oplaat, Carla; Anava, Sarit; Ferreira de Carvalho, Julie; Rechavi, Oded; Johannes, Frank; Verhoeven, Koen J.F.

2017-01-01

Abstract Plants can show long-term effects of environmental stresses and in some cases a stress “memory” has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation. PMID:28472380

Small RNAs as important regulators for the hybrid vigour of super-hybrid rice.

PubMed

Zhang, Lei; Peng, Yonggang; Wei, Xiaoli; Dai, Yan; Yuan, Dawei; Lu, Yufei; Pan, Yangyang; Zhu, Zhen

2014-11-01

Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

SRD: a Staphylococcus regulatory RNA database.

PubMed

Sassi, Mohamed; Augagneur, Yoann; Mauro, Tony; Ivain, Lorraine; Chabelskaya, Svetlana; Hallier, Marc; Sallou, Olivier; Felden, Brice

2015-05-01

An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The "Staphylococcal Regulatory RNA Database" (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA's genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNA-seq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature. © 2015 Sassi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Beyond Genomic Prediction: Combining Different Types of omics Data Can Improve Prediction of Hybrid Performance in Maize.

PubMed

Schrag, Tobias A; Westhues, Matthias; Schipprack, Wolfgang; Seifert, Felix; Thiemann, Alexander; Scholten, Stefan; Melchinger, Albrecht E

2018-04-01

The ability to predict the agronomic performance of single-crosses with high precision is essential for selecting superior candidates for hybrid breeding. With recent technological advances, thousands of new parent lines, and, consequently, millions of new hybrid combinations are possible in each breeding cycle, yet only a few hundred can be produced and phenotyped in multi-environment yield trials. Well established prediction approaches such as best linear unbiased prediction (BLUP) using pedigree data and whole-genome prediction using genomic data are limited in capturing epistasis and interactions occurring within and among downstream biological strata such as transcriptome and metabolome. Because mRNA and small RNA (sRNA) sequences are involved in transcriptional, translational and post-translational processes, we expect them to provide information influencing several biological strata. However, using sRNA data of parent lines to predict hybrid performance has not yet been addressed. Here, we gathered genomic, transcriptomic (mRNA and sRNA) and metabolomic data of parent lines to evaluate the ability of the data to predict the performance of untested hybrids for important agronomic traits in grain maize. We found a considerable interaction for predictive ability between predictor and trait, with mRNA data being a superior predictor for grain yield and genomic data for grain dry matter content, while sRNA performed relatively poorly for both traits. Combining mRNA and genomic data as predictors resulted in high predictive abilities across both traits and combining other predictors improved prediction over that of the individual predictors alone. We conclude that downstream "omics" can complement genomics for hybrid prediction, and, thereby, contribute to more efficient selection of hybrid candidates. Copyright © 2018 by the Genetics Society of America.

A Transgenic Transcription Factor (TaDREB3) in Barley Affects the Expression of MicroRNAs and Other Small Non-Coding RNAs

PubMed Central

Hackenberg, Michael; Shi, Bu-Jun; Gustafson, Perry; Langridge, Peter

2012-01-01

Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley over-expressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (|log2| >1). Furthermore, TaDREB3-derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley. PMID:22870277

Genome-Wide Identification of Different Dormant Medicago sativa L. MicroRNAs in Response to Fall Dormancy

PubMed Central

Du, Hongqi; Sun, Xiaoge; Shi, Yinghua; Wang, Chengzhang

2014-01-01

Background MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that regulate gene post-transcriptional expression in plants and animals. High-throughput sequencing technology is capable of identifying small RNAs in plant species. Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide, and fall dormancy is an adaptive characteristic related to the biomass production and winter survival in alfalfa. Here, we applied high-throughput sRNA sequencing to identify some miRNAs that were responsive to fall dormancy in standard variety (Maverick and CUF101) of alfalfa. Results Four sRNA libraries were generated and sequenced from alfalfa leaves in two typical varieties at distinct seasons. Through integrative analysis, we identified 51 novel miRNA candidates of 206 families. Additionally, we identified 28 miRNAs associated with fall dormancy in standard variety (Maverick and CUF101), including 20 known miRNAs and eight novel miRNAs. Both high-throughput sequencing and RT-qPCR confirmed that eight known miRNA members were up-regulated and six known miRNA members were down-regulated in response to fall dormancy in standard variety (Maverick and CUF101). Among the 51 novel miRNA candidates, five miRNAs were up-regulated and three miRNAs were down-regulated in response to fall dormancy in standard variety (Maverick and CUF101), and five of them were confirmed by Northern blot analysis. Conclusion We identified 20 known miRNAs and eight new miRNA candidates that were responsive to fall dormancy in standard variety (Maverick and CUF101) by high-throughput sequencing of small RNAs from Medicago sativa. Our data provide a useful resource for investigating miRNA-mediated regulatory mechanisms of fall dormancy in alfalfa, and these findings are important for our understanding of the roles played by miRNAs in the response of plants to abiotic stress in general and fall dormancy in alfalfa. PMID:25473944

Genome-wide identification of different dormant Medicago sativa L. MicroRNAs in response to fall dormancy.

PubMed

Fan, Wenna; Zhang, Senhao; Du, Hongqi; Sun, Xiaoge; Shi, Yinghua; Wang, Chengzhang

2014-01-01

MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that regulate gene post-transcriptional expression in plants and animals. High-throughput sequencing technology is capable of identifying small RNAs in plant species. Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide, and fall dormancy is an adaptive characteristic related to the biomass production and winter survival in alfalfa. Here, we applied high-throughput sRNA sequencing to identify some miRNAs that were responsive to fall dormancy in standard variety (Maverick and CUF101) of alfalfa. Four sRNA libraries were generated and sequenced from alfalfa leaves in two typical varieties at distinct seasons. Through integrative analysis, we identified 51 novel miRNA candidates of 206 families. Additionally, we identified 28 miRNAs associated with fall dormancy in standard variety (Maverick and CUF101), including 20 known miRNAs and eight novel miRNAs. Both high-throughput sequencing and RT-qPCR confirmed that eight known miRNA members were up-regulated and six known miRNA members were down-regulated in response to fall dormancy in standard variety (Maverick and CUF101). Among the 51 novel miRNA candidates, five miRNAs were up-regulated and three miRNAs were down-regulated in response to fall dormancy in standard variety (Maverick and CUF101), and five of them were confirmed by Northern blot analysis. We identified 20 known miRNAs and eight new miRNA candidates that were responsive to fall dormancy in standard variety (Maverick and CUF101) by high-throughput sequencing of small RNAs from Medicago sativa. Our data provide a useful resource for investigating miRNA-mediated regulatory mechanisms of fall dormancy in alfalfa, and these findings are important for our understanding of the roles played by miRNAs in the response of plants to abiotic stress in general and fall dormancy in alfalfa.

75 FR 33656 - Exelon Generation Company, LLC Oyster Creek Nuclear Generating Station Environmental Assessment...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-14

... Oyster Creek Nuclear Generating Station Environmental Assessment and Finding of No Significant Impact The... Company, LLC (the licensee), for operation of the Oyster Creek Nuclear Generating Station (Oyster Creek), located in Ocean County, New Jersey. Therefore, as required by 10 CFR Section 51.21, the NRC performed an...

Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci.

PubMed

Polydore, Seth; Axtell, Michael J

2018-06-01

Plant small RNAs (sRNAs) modulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. Small RNAs fall into two major categories: those are reliant on RNA-dependent RNA polymerases (RDRs) for biogenesis and those that are not. Known RDR1/2/6-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR1/2/6-independent sRNAs are primarily microRNAs (miRNA) and other hairpin-derived sRNAs. In this study we produced and analyzed sRNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. We found 58 previously annotated miRNA loci that were reliant on RDR1, -2, or -6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent sRNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for sRNA biogenesis. These 38 sRNA-producing loci have as-yet-undescribed biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggests that these 38 loci represent one or more undescribed types of sRNA in Arabidopsis thaliana. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Why Do First-Generation Students Fail?

ERIC Educational Resources Information Center

Mehta, Sanjay S.; Newbold, John J.; O'Rourke, Matthew A.

2011-01-01

Previous studies have determined factors contributing to first-generation student success. This study finds that first-generation students are less involved, have less social and financial support, and do not show a preference for active coping strategies. First-generation students report less social and academic satisfaction as well as lower…

Knowing Generation Y: a new generation of nurses in practice.

PubMed

Chung, Stephanie M

Generation Y is commonly defined as those people born between 1980 and 2000, now aged in their 20s and 30s. Their grandparents experienced post-World War II reconstruction, their parents the economic boom of the 1980s. There are currently 81 million individuals in the Generation Y cohort in the USA, making it the second-largest, and possibly most influential, cohort since World War II (Manion, 2009). Members of Generation Y are diverse, technologically advanced and vocal about their opinions. They tend to resist traditional hierarchy, want recognition/reward for achievements and distrust institutions. Knowing these characteristics is useful for nurse managers, preceptors and team members working with members of Generation Y. Studies have proven that Generation Y is challenging the nursing workforce through rapid turnover (Cogin, 2012). This article explores a theoretical model that predicts retention and/or turnover of nurses in light of Generation Y behaviours and motivators-for example, moving from agency to agency rather than devoting many years to a single practice. Further research is needed to find out whether these behaviours and motivators are unique to Generation Y alone.

Affective neuroscience of self-generated thought.

PubMed

Fox, Kieran C R; Andrews-Hanna, Jessica R; Mills, Caitlin; Dixon, Matthew L; Markovic, Jelena; Thompson, Evan; Christoff, Kalina

2018-05-12

Despite increasing scientific interest in self-generated thought-mental content largely independent of the immediate environment-there has yet to be any comprehensive synthesis of the subjective experience and neural correlates of affect in these forms of thinking. Here, we aim to develop an integrated affective neuroscience encompassing many forms of self-generated thought-normal and pathological, moderate and excessive, in waking and in sleep. In synthesizing existing literature on this topic, we reveal consistent findings pertaining to the prevalence, valence, and variability of emotion in self-generated thought, and highlight how these factors might interact with self-generated thought to influence general well-being. We integrate these psychological findings with recent neuroimaging research, bringing attention to the neural correlates of affect in self-generated thought. We show that affect in self-generated thought is prevalent, positively biased, highly variable (both within and across individuals), and consistently recruits many brain areas implicated in emotional processing, including the orbitofrontal cortex, amygdala, insula, and medial prefrontal cortex. Many factors modulate these typical psychological and neural patterns, however; the emerging affective neuroscience of self-generated thought must endeavor to link brain function and subjective experience in both everyday self-generated thought as well as its dysfunctions in mental illness. © 2018 New York Academy of Sciences.

Generativity in Elderly Oblate Sisters of Providence

PubMed Central

Black, Helen K.; Hannum, Susan M.; Rubinstein, Robert L.; de Medeiros, Kate

2016-01-01

Purpose of the Study: We explored how generativity and well-being merged in a group of childless older women: African and Hispanic Roman Catholic Religious Sisters, linking two minority identity characteristics. Design and Methods: We qualitatively interviewed 8 Oblate Sisters of Providence (OSP), by providing a framework for examining the range of the women’s generativity—cultural spheres in which generativity is rooted and outlets for generativity. Results: Early negative experiences, such as fleeing despotism in Haiti and Cuba and racism within the Catholic Church, occurred alongside positive experiences—families who stressed education, and Caucasian Religious who taught children of color. This became a foundation for the Sister’s generative commitment. Implications: Findings highlight that research gains from a phenomenological understanding of how religious faith promotes generative cognitions and emotions. Findings also reveal that the experiences of a subculture in society—African-American elderly women religious—add to theories and definitions of generativity. PMID:25352535

Elaborative encoding through self-generation enhances outcomes with errorless learning: Findings from the Skypekids memory study.

PubMed

Haslam, Catherine; Wagner, Joseph; Wegener, Signy; Malouf, Tania

2017-01-01

Errorless learning has demonstrated efficacy in the treatment of memory impairment in adults and older adults with acquired brain injury. In the same population, use of elaborative encoding through supported self-generation in errorless paradigms has been shown to further enhance memory performance. However, the evidence base relevant to application of both standard and self-generation forms of errorless learning in children is far weaker. We address this limitation in the present study to examine recall performance in children with brain injury (n = 16) who were taught novel age-appropriate science and social science facts through the medium of Skype. All participants were taught these facts under conditions of standard errorless learning, errorless learning with self-generation, and trial-and-error learning after which memory was tested at 5-minute, 30-minute, 1-hour and 24-hour delays. Analysis revealed no main effect of time, with participants retaining most information acquired over the 24-hour testing period, but a significant effect of condition. Notably, self-generation proved more effective than both standard errorless and trial-and-error learning. Further analysis of the data revealed that severity of attentional impairment was less detrimental to recall performance under errorless conditions. This study extends the literature to provide further evidence of the value of errorless learning methods in children with ABI and the first demonstration of the effectiveness of self-generation when delivered via the Internet.

Generativity in Elderly Oblate Sisters of Providence.

PubMed

Black, Helen K; Hannum, Susan M; Rubinstein, Robert L; de Medeiros, Kate

2016-06-01

We explored how generativity and well-being merged in a group of childless older women: African and Hispanic Roman Catholic Religious Sisters, linking two minority identity characteristics. We qualitatively interviewed 8 Oblate Sisters of Providence (OSP), by providing a framework for examining the range of the women's generativity-cultural spheres in which generativity is rooted and outlets for generativity. Early negative experiences, such as fleeing despotism in Haiti and Cuba and racism within the Catholic Church, occurred alongside positive experiences-families who stressed education, and Caucasian Religious who taught children of color. This became a foundation for the Sister's generative commitment. Findings highlight that research gains from a phenomenological understanding of how religious faith promotes generative cognitions and emotions. Findings also reveal that the experiences of a subculture in society-African-American elderly women religious-add to theories and definitions of generativity. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Next Generation of Risk Assessment Multi-Year Study-Highlights of Findings, Applications to Risk Assessment, and Future Directions.

PubMed

Cote, Ila; Andersen, Melvin E; Ankley, Gerald T; Barone, Stanley; Birnbaum, Linda S; Boekelheide, Kim; Bois, Frederic Y; Burgoon, Lyle D; Chiu, Weihsueh A; Crawford-Brown, Douglas; Crofton, Kevin M; DeVito, Michael; Devlin, Robert B; Edwards, Stephen W; Guyton, Kathryn Z; Hattis, Dale; Judson, Richard S; Knight, Derek; Krewski, Daniel; Lambert, Jason; Maull, Elizabeth Anne; Mendrick, Donna; Paoli, Gregory M; Patel, Chirag Jagdish; Perkins, Edward J; Poje, Gerald; Portier, Christopher J; Rusyn, Ivan; Schulte, Paul A; Simeonov, Anton; Smith, Martyn T; Thayer, Kristina A; Thomas, Russell S; Thomas, Reuben; Tice, Raymond R; Vandenberg, John J; Villeneuve, Daniel L; Wesselkamper, Scott; Whelan, Maurice; Whittaker, Christine; White, Ronald; Xia, Menghang; Yauk, Carole; Zeise, Lauren; Zhao, Jay; DeWoskin, Robert S

2016-11-01

The Next Generation (NexGen) of Risk Assessment effort is a multi-year collaboration among several organizations evaluating new, potentially more efficient molecular, computational, and systems biology approaches to risk assessment. This article summarizes our findings, suggests applications to risk assessment, and identifies strategic research directions. Our specific objectives were to test whether advanced biological data and methods could better inform our understanding of public health risks posed by environmental exposures. New data and methods were applied and evaluated for use in hazard identification and dose-response assessment. Biomarkers of exposure and effect, and risk characterization were also examined. Consideration was given to various decision contexts with increasing regulatory and public health impacts. Data types included transcriptomics, genomics, and proteomics. Methods included molecular epidemiology and clinical studies, bioinformatic knowledge mining, pathway and network analyses, short-duration in vivo and in vitro bioassays, and quantitative structure activity relationship modeling. NexGen has advanced our ability to apply new science by more rapidly identifying chemicals and exposures of potential concern, helping characterize mechanisms of action that influence conclusions about causality, exposure-response relationships, susceptibility and cumulative risk, and by elucidating new biomarkers of exposure and effects. Additionally, NexGen has fostered extensive discussion among risk scientists and managers and improved confidence in interpreting and applying new data streams. While considerable uncertainties remain, thoughtful application of new knowledge to risk assessment appears reasonable for augmenting major scope assessments, forming the basis for or augmenting limited scope assessments, and for prioritization and screening of very data limited chemicals. Citation: Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K

The Next Generation of Risk Assessment Multi-Year Study—Highlights of Findings, Applications to Risk Assessment, and Future Directions

PubMed Central

Cote, Ila; Andersen, Melvin E.; Ankley, Gerald T.; Barone, Stanley; Birnbaum, Linda S.; Boekelheide, Kim; Bois, Frederic Y.; Burgoon, Lyle D.; Chiu, Weihsueh A.; Crawford-Brown, Douglas; Crofton, Kevin M.; DeVito, Michael; Devlin, Robert B.; Edwards, Stephen W.; Guyton, Kathryn Z.; Hattis, Dale; Judson, Richard S.; Knight, Derek; Krewski, Daniel; Lambert, Jason; Maull, Elizabeth Anne; Mendrick, Donna; Paoli, Gregory M.; Patel, Chirag Jagdish; Perkins, Edward J.; Poje, Gerald; Portier, Christopher J.; Rusyn, Ivan; Schulte, Paul A.; Simeonov, Anton; Smith, Martyn T.; Thayer, Kristina A.; Thomas, Russell S.; Thomas, Reuben; Tice, Raymond R.; Vandenberg, John J.; Villeneuve, Daniel L.; Wesselkamper, Scott; Whelan, Maurice; Whittaker, Christine; White, Ronald; Xia, Menghang; Yauk, Carole; Zeise, Lauren; Zhao, Jay; DeWoskin, Robert S.

2016-01-01

Background: The Next Generation (NexGen) of Risk Assessment effort is a multi-year collaboration among several organizations evaluating new, potentially more efficient molecular, computational, and systems biology approaches to risk assessment. This article summarizes our findings, suggests applications to risk assessment, and identifies strategic research directions. Objective: Our specific objectives were to test whether advanced biological data and methods could better inform our understanding of public health risks posed by environmental exposures. Methods: New data and methods were applied and evaluated for use in hazard identification and dose–response assessment. Biomarkers of exposure and effect, and risk characterization were also examined. Consideration was given to various decision contexts with increasing regulatory and public health impacts. Data types included transcriptomics, genomics, and proteomics. Methods included molecular epidemiology and clinical studies, bioinformatic knowledge mining, pathway and network analyses, short-duration in vivo and in vitro bioassays, and quantitative structure activity relationship modeling. Discussion: NexGen has advanced our ability to apply new science by more rapidly identifying chemicals and exposures of potential concern, helping characterize mechanisms of action that influence conclusions about causality, exposure–response relationships, susceptibility and cumulative risk, and by elucidating new biomarkers of exposure and effects. Additionally, NexGen has fostered extensive discussion among risk scientists and managers and improved confidence in interpreting and applying new data streams. Conclusions: While considerable uncertainties remain, thoughtful application of new knowledge to risk assessment appears reasonable for augmenting major scope assessments, forming the basis for or augmenting limited scope assessments, and for prioritization and screening of very data limited chemicals. Citation: Cote I

PmiRExAt: plant miRNA expression atlas database and web applications

PubMed Central

Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

2016-01-01

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

Assessment of small RNA sorting into different extracellular fractions revealed by high-throughput sequencing of breast cell lines

PubMed Central

Tosar, Juan Pablo; Gámbaro, Fabiana; Sanguinetti, Julia; Bonilla, Braulio; Witwer, Kenneth W.; Cayota, Alfonso

2015-01-01

Intercellular communication can be mediated by extracellular small regulatory RNAs (sRNAs). Circulating sRNAs are being intensively studied for their promising use as minimally invasive disease biomarkers. To date, most attention is centered on exosomes and microRNAs as the vectors and the secreted species, respectively. However, this field would benefit from an increased understanding of the plethora of sRNAs secreted by different cell types in different extracellular fractions. It is still not clear if specific sRNAs are selected for secretion, or if sRNA secretion is mostly passive. We sequenced the intracellular sRNA content (19–60 nt) of breast epithelial cell lines (MCF-7 and MCF-10A) and compared it with extracellular fractions enriched in microvesicles, exosomes and ribonucleoprotein complexes. Our results are consistent with a non-selective secretion model for most microRNAs, although a few showed secretion patterns consistent with preferential secretion. On the contrary, 5′ tRNA halves and 5′ RNA Y4-derived fragments of 31–33 were greatly and significantly enriched in the extracellular space (even in non-mammary cell lines), where tRNA halves were detected as part of ∼45 kDa ribonucleoprotein complexes. Overall, we show that different sRNA families have characteristic secretion patterns and open the question of the role of these sRNAs in the extracellular space. PMID:25940616

Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida.

PubMed

Bojanovič, Klara; D'Arrigo, Isotta; Long, Katherine S

2017-04-01

Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and small RNAs (sRNAs). A total of 440 sRNA transcripts were detected, of which 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts, and 50% to novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed under at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings. IMPORTANCE This study maps the complete transcriptional response of P. putida KT2440 to osmotic, oxidative, and imipenem stress conditions at short and long exposure times. Over 400 sRNA transcripts, consisting of both intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous knowledge of stress response mechanisms due to the depth of the RNA sequencing data. Almost half of the sRNAs exhibit significant expression changes under at least one

Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida

PubMed Central

Bojanovič, Klara; D'Arrigo, Isotta

2017-01-01

ABSTRACT Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and small RNAs (sRNAs). A total of 440 sRNA transcripts were detected, of which 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts, and 50% to novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed under at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings. IMPORTANCE This study maps the complete transcriptional response of P. putida KT2440 to osmotic, oxidative, and imipenem stress conditions at short and long exposure times. Over 400 sRNA transcripts, consisting of both intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous knowledge of stress response mechanisms due to the depth of the RNA sequencing data. Almost half of the sRNAs exhibit significant expression changes under at least

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR

PubMed Central

Lagares, Antonio; Borella, Germán Ceizel; Linne, Uwe; Becker, Anke

2017-01-01

ABSTRACT Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for Makes more granules Regulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR (mmgRΔ33–51). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti. IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans-encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR.

PubMed

Lagares, Antonio; Ceizel Borella, Germán; Linne, Uwe; Becker, Anke; Valverde, Claudio

2017-04-15

Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans -encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti , over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for M akes m ore g ranules R egulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR ( mmgR Δ33-51 ). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans -encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti

How generation affects source memory.

PubMed

Geghman, Kindiya D; Multhaup, Kristi S

2004-07-01

Generation effects (better memory for self-produced items than for provided items) typically occur in item memory. Jurica and Shimamura (1999) reported a negative generation effect in source memory, but their procedure did not test participants on the items they had generated. In Experiment 1, participants answered questions and read statements made by a face on a computer screen. The target word was unscrambled, or letters were filled in. Generation effects were found for target recall and source recognition (which person did which task). Experiment 2 extended these findings to a condition in which the external sources were two different faces. Generation had a positive effect on source memory, supporting an overlap in the underlying mechanisms of item and source memory.

Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks

PubMed Central

Adamson, David N.; Lim, Han N.

2011-01-01

Bacteria possess networks of small RNAs (sRNAs) that are important for modulating gene expression. At the center of many of these sRNA networks is the Hfq protein. Hfq's role is to quickly match cognate sRNAs and target mRNAs from among a large number of possible combinations and anneal them to form duplexes. Here we show using a kinetic model that Hfq can efficiently and robustly achieve this difficult task by minimizing the sequestration of sRNAs and target mRNAs in Hfq complexes. This sequestration can be reduced by two non-mutually exclusive kinetic mechanisms. The first mechanism involves heterotropic cooperativity (where sRNA and target mRNA binding to Hfq is influenced by other RNAs bound to Hfq); this cooperativity can selectively decrease singly-bound Hfq complexes and ternary complexes with non-cognate sRNA-target mRNA pairs while increasing cognate ternary complexes. The second mechanism relies on frequent RNA dissociation enabling the rapid cycling of sRNAs and target mRNAs among different Hfq complexes; this increases the probability the cognate ternary complex forms before the sRNAs and target mRNAs degrade. We further demonstrate that the performance of sRNAs in isolation is not predictive of their performance within a network. These findings highlight the importance of experimentally characterizing duplex formation in physiologically relevant contexts with multiple RNAs competing for Hfq. The model will provide a valuable framework for guiding and interpreting these experiments. PMID:21876666

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection.

PubMed

Åsman, Anna K M; Vetukuri, Ramesh R; Jahan, Sultana N; Fogelqvist, Johan; Corcoran, Pádraic; Avrova, Anna O; Whisson, Stephen C; Dixelius, Christina

2014-12-10

The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans.

Target surface finding using 3D SAR data

NASA Astrophysics Data System (ADS)

Ruiter, Jason R.; Burns, Joseph W.; Subotic, Nikola S.

2005-05-01

Methods of generating more literal, easily interpretable imagery from 3-D SAR data are being studied to provide all weather, near-visual target identification and/or scene interpretation. One method of approaching this problem is to automatically generate shape-based geometric renderings from the SAR data. In this paper we describe the application of the Marching Tetrahedrons surface finding algorithm to 3-D SAR data. The Marching Tetrahedrons algorithm finds a surface through the 3-D data cube, which provides a recognizable representation of the target surface. This algorithm was applied to the public-release X-patch simulations of a backhoe, which provided densely sampled 3-D SAR data sets. The performance of the algorithm to noise and spatial resolution were explored. Surface renderings were readily recognizable over a range of spatial resolution, and maintained their fidelity even under relatively low Signal-to-Noise Ratio (SNR) conditions.

tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.

PubMed

Zheng, Ling-Ling; Xu, Wei-Lin; Liu, Shun; Sun, Wen-Ju; Li, Jun-Hao; Wu, Jie; Yang, Jian-Hua; Qu, Liang-Hu

2016-07-08

tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers. The binomial test was introduced to evaluate whether reads from a small RNA-seq data set represent tRFs or degraded fragments. A classification method was then used to annotate the types of tRFs based on their sites of origin in pre-tRNA or mature tRNA. We applied the pipeline to analyze 10 991 data sets from 32 types of cancers and identified thousands of expressed tRFs. A tool called 'tRFinCancer' was developed to facilitate the users to inspect the expression of tRFs across different types of cancers. Another tool called 'tRFBrowser' shows both the sites of origin and the distribution of chemical modification sites in tRFs on their source tRNA. The tRF2Cancer web server is available at http://rna.sysu.edu.cn/tRFfinder/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida

PubMed Central

2012-01-01

Background Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio salmonicida, causes cold-water vibriosis in farmed Atlantic salmon. Its genome encodes Spot 42 with 84% identity to E. coli Spot 42. Results We generated a A. salmonicida spf deletion mutant. We then used microarray and Northern blot analyses to monitor global effects on the transcriptome in order to provide insights into the biological roles of Spot 42 in this bacterium. In the presence of glucose, we found a surprisingly large number of ≥ 2X differentially expressed genes, and several major cellular processes were affected. A gene encoding a pirin-like protein showed an on/off expression pattern in the presence/absence of Spot 42, which suggests that Spot 42 plays a key regulatory role in the central metabolism by regulating the switch between fermentation and respiration. Interestingly, we discovered an sRNA named VSsrna24, which is encoded immediately downstream of spf. This new sRNA has an expression pattern opposite to that of Spot 42, and its expression is repressed by glucose. Conclusions We hypothesize that Spot 42 plays a key role in the central metabolism, in part by regulating the pyruvat dehydrogenase enzyme complex via pirin. PMID:22272603

The 5΄ UTR of the type I toxin ZorO can both inhibit and enhance translation

PubMed Central

Wen, Jia; Harp, John R.

2017-01-01

Abstract Many bacterial type I toxin mRNAs possess a long 5΄ untranslated region (UTR) that serves as the target site of the corresponding antitoxin sRNA. This is the case for the zorO-orzO type I system where the OrzO antitoxin base pairs to the 174-nucleotide zorO 5΄ UTR. Here, we demonstrate that the full-length 5΄ UTR of the zorO type I toxin hinders its own translation independent of the sRNA whereas a processed 5΄ UTR (zorO Δ28) promotes translation. The full-length zorO 5΄ UTR folds into an extensive secondary structure sequestering the ribosome binding site (RBS). Processing of the 5΄ UTR does not alter the RBS structure, but opens a large region (EAP region) located upstream of the RBS. Truncation of this EAP region impairs zorO translation, but this defect can be rescued upon exposing the RBS. Additionally, the region spanning +35 to +50 of the zorO mRNA is needed for optimal translation of zorO. Importantly, the positive and negative effects on translation imparted by the 5΄ UTR can be transferred onto a reporter gene, indicative that the 5΄ UTR can solely drive regulation. Moreover, we show that the OrzO sRNA can inhibit zorO translation via base pairing to the of the EAP region. PMID:27903909

High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)

PubMed Central

Donaire, Livia; Pedrola, Laia; de la Rosa, Raúl; Llave, César

2011-01-01

Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive. PMID:22140484

The small regulatory RNA FasX enhances group A Streptococcus virulence and inhibits pilus expression via serotype-specific targets

PubMed Central

Danger, Jessica L.; Cao, Tram N.; Cao, Tran H.; Sarkar, Poulomee; Treviño, Jeanette; Pflughoeft, Kathryn J.; Sumby, Paul

2015-01-01

Summary Bacterial pathogens commonly show intra-species variation in virulence factor expression and often this correlates with pathogenic potential. The group A Streptococcus (GAS) produces a small regulatory RNA (sRNA), FasX, which regulates the expression of pili and the thrombolytic agent streptokinase. As GAS serotypes are polymorphic regarding (a) FasX abundance, (b) the fibronectin, collagen, T-antigen (FCT) region of the genome, which contains the pilus genes (nine different FCT-types), and (c) the streptokinase-encoding gene (ska) sequence (two different alleles), we sought to test whether FasX regulates pilus and streptokinase expression in a serotype-specific manner. Parental, fasX mutant, and complemented derivatives of serotype M1 (ska-2, FCT-2), M2 (ska-1, FCT-6), M6 (ska-2, FCT-1), and M28 (ska-1, FCT-4) isolates were compared. While FasX reduced pilus expression in each serotype, the molecular basis differed, as FasX bound, and inhibited the translation of, different FCT-region mRNAs. FasX enhanced streptokinase expression in each serotype, although the degree of regulation varied. Finally, we established that the regulation afforded by FasX enhances GAS virulence, assessed by a model of bacteremia using human plasminogen-expressing mice. Our data are the first to identify and characterize serotype-specific regulation by an sRNA in GAS, and to show an sRNA directly contributes to GAS virulence. PMID:25586884

Identification and validation of sRNAs in Edwardsiella tarda S08.

PubMed

Sun, Yuying; Zhang, Jiquan; Qin, Lei; Yan, Cui; Zhang, Xiaojun; Liu, Dandan

2017-01-01

Bacterial small non-coding RNAs (sRNAs) are known as novel regulators involved in virulence, stress responsibility, and so on. Recently, a lot of new researches have highlighted the critical roles of sRNAs in fine-tune gene regulation in both prokaryotes and eukaryotes. Edwardsiella tarda (E. tarda) is a gram-negative, intracellular pathogen that causes edwardsiellosis in fish. Thus far, no sRNA has been reported in E. tarda. The present study represents the first attempt to identify sRNAs in E. tarda S08. Ten sRNAs were validated by RNA sequencing and quantitative PCR (qPCR). ET_sRNA_1 and ET_sRNA_2 were homolous to tmRNA and GcvB, respectively. However, the other candidate sRNAs have not been reported till now. The cellular abundance of 10 validated sRNA was detected by qPCR at different growth phases to monitor their biosynthesis. Nine candidate sRNAs were expressed in the late-stage of exponential growth and stationary stages of growth (36~60 h). And the expression of the nine sRNAs was growth phase-dependent. But ET_sRNA_10 was almost expressed all the time and reached the highest peak at 48 h. Their targets were predicted by TargetRNA2 and each sRNA target contains some genes that directly or indirectly relate to virulence. These results preliminary showed that sRNAs probably play a regulatory role of virulence in E. tarda.

First-Generation Students' Academic Engagement and Retention

ERIC Educational Resources Information Center

Soria, Krista M.; Stebleton, Michael J.

2012-01-01

This study investigates differences in academic engagement and retention between first-generation and non-first-generation undergraduate students. Utilizing the Student Experience in the Research University survey of 1864 first-year students at a large, public research university located in the United States, this study finds that first-generation…

Leveraging Rigorous Local Evaluations to Understand Contradictory Findings

ERIC Educational Resources Information Center

Boulay, Beth; Martin, Carlos; Zief, Susan; Granger, Robert

2013-01-01

Contradictory findings from "well-implemented" rigorous evaluations invite researchers to identify the differences that might explain the contradictions, helping to generate testable hypotheses for new research. This panel will examine efforts to ensure that the large number of local evaluations being conducted as part of four…

75 FR 6223 - PSEG Nuclear LLC; Hope Creek Generating Station and Salem Nuclear Generating Station, Unit Nos. 1...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-08

... NUCLEAR REGULATORY COMMISSION [Docket Nos. 50-272, 50-311 and 50-354; NRC-2010-0043] PSEG Nuclear LLC; Hope Creek Generating Station and Salem Nuclear Generating Station, Unit Nos. 1 and 2; Environmental Assessment and Finding of No Significant Impact The U.S. Nuclear Regulatory Commission (NRC) is considering issuance of an Exemption, pursuant...

Advanced Stirling Radioisotope Generator EU2 Anomaly Investigation

NASA Technical Reports Server (NTRS)

Lewandowski, Edward J.; Dobbs, Michael W.; Oriti, Salvatore M.

2016-01-01

The Advanced Stirling Radioisotope Generator (ASRG) Engineering Unit 2 (EU2) is the highest fidelity electrically-heated Stirling radioisotope generator built to date. NASA Glenn Research Center (GRC) completed the assembly of the ASRG EU2 in September, 2014 using hardware from the now cancelled ASRG flight development project. The ASRG EU2 integrated the first pair of Sunpower's ASC-E3 Stirling convertors (ASC-E3 #1 and #2) in an aluminum generator housing with Lockheed Martin's Engineering Development Unit (EDU) 4 controller. After just 179 hours of EU2 generator operation, the first power fluctuation occurred on ASC-E3 #1. The first power fluctuation occurred 175 hours later on ASC-E3 #2. Over time, the power fluctuations became more frequent on both convertors and larger in magnitude. Eventually the EU2 was shut down in January, 2015. An anomaly investigation was chartered to determine root cause of the power fluctuations and other anomalous observations. A team with members from GRC, Sunpower, and Lockheed Martin conducted a thorough investigation of the EU2 anomalies. Findings from the EU2 disassembly identified proximate causes of the anomalous observations. Discussion of the team's assessment of the primary possible failure theories, root cause, and conclusions is provided. Recommendations are made for future Stirling generator development to address the findings from the anomaly investigation. Additional findings from the investigation are also discussed.

For a Dialogue on Relations between the Generations

ERIC Educational Resources Information Center

Lisovskii, Vladimir Timofeevich

2004-01-01

This article reports the findings of a study examining how young people in Russia rate themselves and their parents' generation. The sociological survey was carried out in 1999 and 2001 in a number of big and small towns of Russia. The focus of the study was on three generations: the "generation of the 1960s" (children of the thaw);…

Using Qualitative Metasummary to Synthesize Qualitative and Quantitative Descriptive Findings

PubMed Central

Sandelowski, Margarete; Barroso, Julie; Voils, Corrine I.

2008-01-01

The new imperative in the health disciplines to be more methodologically inclusive has generated a growing interest in mixed research synthesis, or the integration of qualitative and quantitative research findings. Qualitative metasummary is a quantitatively oriented aggregation of qualitative findings originally developed to accommodate the distinctive features of qualitative surveys. Yet these findings are similar in form and mode of production to the descriptive findings researchers often present in addition to the results of bivariate and multivariable analyses. Qualitative metasummary, which includes the extraction, grouping, and formatting of findings, and the calculation of frequency and intensity effect sizes, can be used to produce mixed research syntheses and to conduct a posteriori analyses of the relationship between reports and findings. PMID:17243111

Finding Purpose in Pain: Using Logotherapy as a Method for Addressing Survivor Guilt in First-Generation College Students

ERIC Educational Resources Information Center

Tate, Kevin A.; Williams, Cyrus, III; Harden, Dia

2013-01-01

First-generation college students face a variety of academic and personal challenges, including survivor guilt (Piorkowski, 1983). Survivor guilt for these students involves negative emotions related to leaving family and friends "behind" in difficult contexts and lived experiences. This article provides (a) an overview of first-generation college…

EPA's Endangerment Finding: Paving the Way Toward the Next Generation of Cars and Trucks

EPA Pesticide Factsheets

View a fact sheet on how the Final Endangerment Finding will allow EPA to finalize the first greenhouse gas standards for new light-duty vehicles as part of the joint rulemaking with the Department of Transportation.

Electricity Generation Baseline Report

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

Logan, Jeffrey; Marcy, Cara; McCall, James

This report was developed by a team of national laboratory analysts over the period October 2015 to May 2016 and is part of a series of studies that provide background material to inform development of the second installment of the Quadrennial Energy Review (QER 1.2). The report focuses specifically on U.S. power sector generation. The report limits itself to the generation sector and does not address in detail parallel issues in electricity end use, transmission and distribution, markets and policy design, and other important segments. The report lists 15 key findings about energy system needs of the future.

Double-blind comparison of first- and second-generation antipsychotics in early-onset schizophrenia and schizo-affective disorder: findings from the treatment of early-onset schizophrenia spectrum disorders (TEOSS) study.

PubMed

Sikich, Linmarie; Frazier, Jean A; McClellan, Jon; Findling, Robert L; Vitiello, Benedetto; Ritz, Louise; Ambler, Denisse; Puglia, Madeline; Maloney, Ann E; Michael, Emily; De Jong, Sandra; Slifka, Karen; Noyes, Nancy; Hlastala, Stefanie; Pierson, Leslie; McNamara, Nora K; Delporto-Bedoya, Denise; Anderson, Robert; Hamer, Robert M; Lieberman, Jeffrey A

2008-11-01

and schizoaffective disorder. The safety findings related to weight gain and metabolic problems raise important public health concerns, given the widespread use of second-generation antipsychotics in youth for nonpsychotic disorders.

Generational Differences in Academic Achievement among Immigrant Youths: A Meta-Analytic Review

ERIC Educational Resources Information Center

Duong, Mylien T.; Badaly, Daryaneh; Liu, Freda F.; Schwartz, David; McCarty, Carolyn A.

2016-01-01

Research on generational differences in immigrant youths' academic achievement has yielded conflicting findings. This meta-analysis reconciles discrepant findings by testing meta-analytic moderators. Fifty-three studies provided 74 comparisons on academic outcomes. First- and second-generation youths did not significantly differ on academic…

Lupus Nephritis: An Overview of Recent Findings

PubMed Central

de Zubiria Salgado, Alberto; Herrera-Diaz, Catalina

2012-01-01

Lupus nephritis (LN) is one of the most serious complications of systemic lupus erythematosus (SLE) since it is the major predictor of poor prognosis. In susceptible individuals suffering of SLE, in situ formation and deposit of immune complexes (ICs) from apoptotic bodies occur in the kidneys as a result of an amplified epitope immunological response. IC glomerular deposits generate release of proinflammatory cytokines and cell adhesion molecules causing inflammation. This leads to monocytes and polymorphonuclear cells chemotaxis. Subsequent release of proteases generates endothelial injury and mesangial proliferation. Presence of ICs promotes adaptive immune response and causes dendritic cells to release type I interferon. This induces maturation and activation of infiltrating T cells, and amplification of Th2, Th1 and Th17 lymphocytes. Each of them, amplify B cells and activates macrophages to release more proinflammatory molecules, generating effector cells that cannot be modulated promoting kidney epithelial proliferation and fibrosis. Herein immunopathological findings of LN are reviewed. PMID:22536486

High Harmonic Radiation Generation and Attosecond pulse generation from Intense Laser-Solid Interactions

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

Thomas, Alexander Roy; Krushelnick, Karl

2016-09-08

We have studied ion motion effects in high harmonic generation, including shifts to the harmonics which result in degradation of the attosecond pulse train, and how to mitigate them. We have examined the scaling with intensity of harmonic emission. We have also switched the geometry of the interaction to measure, for the first time, harmonics from a normal incidence interaction. This was performed by using a special parabolic reflector with an on axis hole and is to allow measurements of the attosecond pulses using standard techniques. Here is a summary of the findings: First high harmonic generation in laser-solid interactionsmore » at 10 21 Wcm -2, demonstration of harmonic focusing, study of ion motion effects in high harmonic generation in laser-solid interactions, and demonstration of harmonic amplification.« less

Next-Generation Tools For Next-Generation Surveys

NASA Astrophysics Data System (ADS)

Murray, S. G.

2017-04-01

The next generation of large-scale galaxy surveys, across the electromagnetic spectrum, loom on the horizon as explosively game-changing datasets, in terms of our understanding of cosmology and structure formation. We are on the brink of a torrent of data that is set to both confirm and constrain current theories to an unprecedented level, and potentially overturn many of our conceptions. One of the great challenges of this forthcoming deluge is to extract maximal scientific content from the vast array of raw data. This challenge requires not only well-understood and robust physical models, but a commensurate network of software implementations with which to efficiently apply them. The halo model, a semi-analytic treatment of cosmological spatial statistics down to nonlinear scales, provides an excellent mathematical framework for exploring the nature of dark matter. This thesis presents a next-generation toolkit based on the halo model formalism, intended to fulfil the requirements of next-generation surveys. Our toolkit comprises three tools: (i) hmf, a comprehensive and flexible calculator for halo mass functions (HMFs) within extended Press-Schechter theory, (ii) the MRP distribution for extremely efficient analytic characterisation of HMFs, and (iii) halomod, an extension of hmf which provides support for the full range of halo model components. In addition to the development and technical presentation of these tools, we apply each to the task of physical modelling. With hmf, we determine the precision of our knowledge of the HMF, due to uncertainty in our knowledge of the cosmological parameters, over the past decade of cosmic microwave background (CMB) experiments. We place rule-of-thumb uncertainties on the predicted HMF for the Planck cosmology, and find that current limits on the precision are driven by modeling uncertainties rather than those from cosmological parameters. With the MRP, we create and test a method for robustly fitting the HMF to observed

Being part of a multi-generational medical practice team.

PubMed

Hills, Laura

2010-01-01

What happens when you find yourself working in your medical practice every day with co-workers who are the ages of your parents or children? Do you find yourself reverting to age-related roles? Do you become exasperated with or bewildered by the values and behaviors of older or younger colleagues? This article explores the challenges and opportunities the medical practice staff member faces when he or she is part of a multi-generational medical practice team. It describes the tensions that often occur when a medical practice staff runs the gamut from those who remember using a library card catalog and those who can't remember the days before Google. It describes the core values, career goals, key formative events, and attitudes that may have shaped the thinking and behavior of the four generations that may work in the medical practice today: Traditionalists, Baby Boomers, Generation X, and Generation Y. It suggests preferred communication and learning methods for staff members of different generations. Finally, this article offers 10 best practices for working in a multi-generational staff and for creating a supportive multi-generational medical practice culture.

Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design.

PubMed

Hu, Chelsea Y; Takahashi, Melissa K; Zhang, Yan; Lucks, Julius B

2018-05-22

RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs. Using parameter sensitivity analysis, we design a simple set of experiments that allow us to accurately predict NAR function in TX-TL. We transfer successful network designs into Escherichia coli and show that our sRNA transcriptional network reduces both network response time and steady-state gene expression. This work broadens our ability to construct increasingly sophisticated RNA genetic networks with predictable function.

Pathways from childhood abuse to prospective revictimization: depression, sex to reduce negative affect, and forecasted sexual behavior.

PubMed

Miron, Lynsey R; Orcutt, Holly K

2014-11-01

Research suggests that adverse events in childhood, such as childhood physical, sexual, and emotional abuse, confer risk for later sexual assault. Psychological distress, coping strategies, and sexual behavior may help explain the path from childhood abuse to revictimization. The present study explored how the use of sex to regulate negative affect (SRNA) operates independently, and in combination with other psychosocial factors to increase college women's (N=541) risk of experiencing prospective adult sexual assault (ASA). Sequential multiple mediator models in Mplus were used to assess the effect of three different forms of childhood abuse on prospective ASA, both independently and while controlling for other forms of childhood abuse. The indirect effect of adolescent sexual assault (AdolSA), depressive symptoms, SRNA, and participants' response to a sex-related vignette was tested using bias-corrected bootstrapping. In the full path model, childhood emotional abuse and AdolSA predicted ASA, while childhood physical and sexual abuse were directly associated with AdolSA, but not ASA. Additionally, depressive symptoms and participants' estimate of their likely behavior in a sex-related vignette directly predicted prospective ASA. Results using bootstrapping revealed that a history of childhood abuse predicted prospective ASA via diverse direct and indirect paths, as well as through a similar multiple mediator path. Overall, findings suggest that a combination of affective, coping, and sexual expectancy factors contribute to risk for revictimization in adult survivors of childhood abuse. Future research directions and targets for risk-reduction programming are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pathways from Childhood Abuse to Prospective Revictimization: Depression, Sex to Reduce Negative Affect, and Forecasted Sexual Behavior

PubMed Central

Miron, Lynsey R.; Orcutt, Holly K.

2014-01-01

Research suggests that adverse events in childhood, such as childhood physical, sexual, and emotional abuse, confer risk for later sexual assault. Psychological distress, coping strategies, and sexual behavior may help explain the path from childhood abuse to revictimization. The present study explored how the use of sex to regulate negative affect (SRNA) operates independently, and in combination with other psychosocial factors to increase college women’s (N = 541) risk of experiencing prospective adult sexual assault (ASA). Sequential multiple mediator models in Mplus were used to assess the effect of three different forms of childhood abuse on prospective ASA, both independently and while controlling for other forms of childhood abuse. The indirect effect of adolescent sexual assault (AdolSA), depressive symptoms, SRNA, and participants’ response to a sex-related vignette was tested using bias-corrected bootstrapping. In the full path model, childhood emotional abuse and AdolSA predicted ASA, while childhood physical and sexual abuse were directly associated with AdolSA, but not ASA. Additionally, depressive symptoms and participants’ estimate of their likely behavior in a sex-related vignette directly predicted prospective ASA. Results using bootstrapping revealed that a history of childhood abuse predicted prospective ASA via diverse direct and indirect paths, as well as through a similar multiple mediator path. Overall, findings suggest that a combination of affective, coping, and sexual expectancy factors contribute to risk for revictimization in adult survivors of childhood abuse. Future research directions and targets for risk-reduction programming will be discussed. PMID:25455965

Electromechanically generating electricity with a gapped-graphene electric generator

NASA Astrophysics Data System (ADS)

Dressen, Donald; Golovchenko, Jene

2015-03-01

We demonstrate the fabrication and operation of a gapped-graphene electric generator (G-GEG) device. The G-GEG generates electricity from the mechanical oscillation of droplets of electrolytes and ionic liquids. The spontaneous adsorption of ionic species on graphene charges opposing electric double-layer capacitors (EDLCs) on each half of the device. Modulating the area of contact between the droplet and graphene leads to adsorption/desorption of ions, effectively charging/discharging each EDLC and generating a current. The flow of current supports a potential difference across the G-GEG due to the device's internal impedance. Both the magnitude and polarity of the induced current and voltage show a strong dependence on the type of ionic species used, suggesting that certain ions interact more strongly with graphene than others. We find that a simple model circuit consisting of an AC current source in series with a resistor and a time-varying capacitor accurately predicts the device's dynamic behavior. Additionally, we discuss the effect of graphene's intrinsic quantum capacitance on the G-GEG's performance and speculate on the utility of the device in the context of energy harvesting.

High flexible Hydropower Generation concepts for future grids

NASA Astrophysics Data System (ADS)

Hell, Johann

2017-04-01

The ongoing changes in electric power generation are resulting in new requirements for the classical generating units. In consequence a paradigm change in operation of power systems is necessary and a new approach in finding solutions is needed. The presented paper is dealing with the new requirements on current and future energy systems with the focus on hydro power generation. A power generation landscape for some European regions is shown and generation and operational flexibility is explained. Based on the requirements from the Transmission System Operator in UK, the transient performance of a Pumped Storage installation is discussed.

The effects of learner-generated representations versus computer-generated representations on physics problem solving

NASA Astrophysics Data System (ADS)

Price, Gwyneth A.

In this study, multiple external representations and Generative Learning Theory were used to design instruction that would facilitate physics learning. Specifically, the study looks at the learning differences that may occur when students are engaged in generating a graphical representation as compared to being presented with a computer-generated graph. It is hypothesized that by generating the graphical representation students will be able to overcome obstacles to integration and determine the relationships involved within a representation. In doing so, students will build a more complete mental model of the situation and be able to more readily use this information in transfer situations, thus improving their problem solving ability. Though the results of this study do not lend strong support for the hypothesis, the results are still informative and encouraging. Though several of the obstacles associated with learning from multiple representations such as cognitive load were cause for concern, those students with appropriate prior knowledge and familiarity with graphical representations were able to benefit from the generative activity. This finding indicates that if the issues are directly addressed within instruction, it may be that all students may be able to benefit from being actively engaged in generating representations.

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

PubMed Central

Mank, Nils N.; Berghoff, Bork A.; Hermanns, Yannick N.; Klug, Gabriele

2012-01-01

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA. PMID:22988125

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ.

PubMed

Mank, Nils N; Berghoff, Bork A; Hermanns, Yannick N; Klug, Gabriele

2012-10-02

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.

Advanced Stirling Radioisotope Generator Engineering Unit 2 Anomaly Investigation

NASA Technical Reports Server (NTRS)

Lewandowski, Edward J.; Dobbs, Michael W.; Oriti, Salvatore M.

2018-01-01

The Advanced Stirling Radioisotope Generator (ASRG) Engineering Unit 2 (EU2) is the highest fidelity electrically heated Stirling radioisotope generator built to date. NASA Glenn Research Center completed the assembly of the ASRG EU2 in September 2014 using hardware from the now cancelled ASRG flight development project. The ASRG EU2 integrated the first pair of Sunpower's Advanced Stirling Convertors (ASC-E3 #1 and #2) in an aluminum generator housing with Lockheed Martin's (LM's) Engineering Development Unit (EDU) 4 controller. After just 179 hr of EU2 generator operation, the first power fluctuation occurred on ASC-E3 #1. The first power fluctuation occurred 175 hr later on ASC-E3 #2. Over time, the power fluctuations became more frequent on both convertors and larger in magnitude. Eventually the EU2 was shut down in January 2015. An anomaly investigation was chartered to determine root cause of the power fluctuations and other anomalous observations. A team with members from Glenn, Sunpower, and LM conducted a thorough investigation of the EU2 anomalies. Findings from the EU2 disassembly identified proximate causes of the anomalous observations. Discussion of the team's assessment of the primary possible failure theories, root cause, and conclusions is provided. Recommendations are made for future Stirling generator development to address the findings from the anomaly investigation. Additional findings from the investigation are also discussed.

Modular synthetic inverters from zinc finger proteins and small RNAs

DOE PAGES

Hsia, Justin; Holtz, William J.; Maharbiz, Michel M.; ...

2016-02-17

Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosenmore » parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.« less

Expanding the histological findings in postvaccinial non-viral folliculitis

PubMed Central

Bunick, Christopher G.; Mariwalla, Kavita; Ibrahim, Omer; Modi, Badri; Imaeda, Suguru; McNiff, Jennifer

2014-01-01

Postvaccinial non-viral folliculitis has been recognized in the past decade as a new adverse cutaneous reaction to the smallpox vaccination. Contrary to more serious smallpox vaccine reactions, postvaccinial non-viral folliculitis has a benign course resolving spontaneously within approximately seven days. We describe additional histopathological findings associated with postvaccinial non-viral folliculitis, which has only been described once previously. New findings include the presence of neutrophilic or lymphohistiocytic infiltrates that concentrate around the hair follicles. We compare our findings to the follicular nature of varicella and herpes zoster infections, generating the hypothesis of deposition of vaccinia protein within folliculosebaceous units as a potential pathophysiologic mechanism behind postvaccinial non-viral folliculitis. PMID:23278890

Constraining dynamical neutrino mass generation with cosmological data

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

Koksbang, S.M.; Hannestad, S., E-mail: koksbang@phys.au.dk, E-mail: sth@phys.au.dk

We study models in which neutrino masses are generated dynamically at cosmologically late times. Our study is purely phenomenological and parameterized in terms of three effective parameters characterizing the redshift of mass generation, the width of the transition region, and the present day neutrino mass. We also study the possibility that neutrinos become strongly self-interacting at the time where the mass is generated. We find that in a number of cases, models with large present day neutrino masses are allowed by current CMB, BAO and supernova data. The increase in the allowed mass range makes it possible that a non-zeromore » neutrino mass could be measured in direct detection experiments such as KATRIN. Intriguingly we also find that there are allowed models in which neutrinos become strongly self-interacting around the epoch of recombination.« less

Using Self-Generated Drawings to Solve Arithmetic Word Problems.

ERIC Educational Resources Information Center

Van Essen, Gerard; Hamaker, Christiaan

1990-01-01

Results are presented from two intervention studies which investigate whether encouraging elementary students to generate drawings of arithmetic word problems facilitates problem-solving performance. Findings indicate that fifth graders (N=50) generated many drawings of word problems and improved problem solutions after the intervention, whereas…

An efficient and high fidelity method for amplification, cloning and sequencing of complete tospovirus genomic RNA segments

USDA-ARS?s Scientific Manuscript database

Amplification and sequencing of the complete M- and S-RNA segments of Tomato spotted wilt virus and Impatiens necrotic spot virus as a single fragment is useful for whole genome sequencing of tospoviruses co-infecting a single host plant. It avoids issues associated with overlapping amplicon-based ...

Nontechnical Teaching Skills Education for Certified Registered Nurse Anesthetist Clinical Instructors and the Impact on the Clinical Education of Student Registered Nurse Anesthetists

ERIC Educational Resources Information Center

Welch, Gena M.

2017-01-01

Purpose: The purpose of this Scholarly project was to improve Student Registered Nurse Anesthetist (SRNA) clinical education consistency and quality by enhancing communication between Certified Registered Nurse Anesthetists (CRNAs) clinical instructors and SRNAs. This was accomplished by educating CRNA clinical instructors on non-technical skills,…

Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for Citrus Huanglongbing Disease

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB) is a devastating citrus disease that is associated with bacteria of the genus Candidatus Liberibacter(Ca. L.). Powerful diagnostic tools and management strategies are desired to control HLB. Host small Ribonucleic acid (sRNA) play a vital role in regulating host responses to pa...

SoMART, a web server for miRNA, tasiRNA and target gene analysis in Solanaceae plants

USDA-ARS?s Scientific Manuscript database

Plant micro(mi)RNAs and trans-acting small interfering (tasi)RNAs mediate posttranscriptional silencing of genes and play important roles in a variety of biological processes. Although bioinformatics prediction and small (s)RNA cloning are the key approaches used for identification of miRNAs, tasiRN...

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs.

PubMed

Chávez Montes, Ricardo A; de Fátima Rosas-Cárdenas, Flor; De Paoli, Emanuele; Accerbi, Monica; Rymarquis, Linda A; Mahalingam, Gayathri; Marsch-Martínez, Nayelli; Meyers, Blake C; Green, Pamela J; de Folter, Stefan

2014-04-23

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.

Searching RNA motifs and their intermolecular contacts with constraint networks.

PubMed

Thébault, P; de Givry, S; Schiex, T; Gaspin, C

2006-09-01

Searching RNA gene occurrences in genomic sequences is a task whose importance has been renewed by the recent discovery of numerous functional RNA, often interacting with other ligands. Even if several programs exist for RNA motif search, none exists that can represent and solve the problem of searching for occurrences of RNA motifs in interaction with other molecules. We present a constraint network formulation of this problem. RNA are represented as structured motifs that can occur on more than one sequence and which are related together by possible hybridization. The implemented tool MilPat is used to search for several sRNA families in genomic sequences. Results show that MilPat allows to efficiently search for interacting motifs in large genomic sequences and offers a simple and extensible framework to solve such problems. New and known sRNA are identified as H/ACA candidates in Methanocaldococcus jannaschii. http://carlit.toulouse.inra.fr/MilPaT/MilPat.pl.

Destination memory for self-generated actions.

PubMed

El Haj, Mohamad

2016-10-01

There is a substantial body of literature showing memory enhancement for self-generated information in normal aging. The present paper investigated this outcome for destination memory or memory for outputted information. In Experiment 1, younger adults and older adults had to place (self-generated actions) and observe an experimenter placing (experiment-generated actions) items into two different destinations (i.e., a black circular box and a white square box). On a subsequent recognition task, the participants had to decide into which box each item had originally been placed. These procedures showed better destination memory for self- than experimenter-generated actions. In Experiment 2, destination and source memory were assessed for self-generated actions. Younger adults and older adults had to place items into the two boxes (self-generated actions), take items out of the boxes (self-generated actions), and observe an experimenter taking items out of the boxes (experiment-generated actions). On a subsequent recognition task, they had to decide into which box (destination memory)/from which box (source memory) each item had originally been placed/taken. For both populations, source memory was better than destination memory for self-generated actions, and both were better than source memory for experimenter-generated actions. Taken together, these findings highlight the beneficial effect of self-generation on destination memory in older adults.

Generative Contexts

NASA Astrophysics Data System (ADS)

Lyles, Dan Allen

Educational research has identified how science, technology, engineering, and mathematics (STEM) practice and education have underperforming metrics in racial and gender diversity, despite decades of intervention. These disparities are part of the construction of a culture of science that is alienating to these populations. Recent studies in a social science framework described as "Generative Justice" have suggested that the context of social and scientific practice might be modified to bring about more just and equitable relations among the disenfranchised by circulating the value they and their non-human allies create back to them in unalienated forms. What is not known are the underlying principles of social and material space that makes a system more or less generative. I employ an autoethnographic method at four sites: a high school science class; a farm committed to "Black and Brown liberation"; a summer program geared towards youth environmental mapping; and a summer workshop for Harlem middle school students. My findings suggest that by identifying instances where material affinity, participatory voice, and creative solidarity are mutually reinforcing, it is possible to create educational contexts that generate unalienated value, and circulate it back to the producers themselves. This cycle of generation may help explain how to create systems of justice that strengthen and grow themselves through successive iterations. The problem of lack of diversity in STEM may be addressed not merely by recruiting the best and the brightest from underrepresented populations, but by changing the context of STEM education to provide tools for its own systematic restructuring.

Holocaust exposure and disordered eating: a study of multi-generational transmission.

PubMed

Zohar, Ada H; Giladi, Lotem; Givati, Timor

2007-01-01

To test the hypothesis that disordered eating in second- and third-generation women would be related to their levels of Holocaust exposure and family dysfunction. One hundred eight mother-daughter dyads were ascertained through the daughters, all Israeli college students 18-35 years of age. Mothers and daughters assessed themselves on family function, Holocaust exposure and disordered eating. The disordered eating of women of the third generation was partially predicted by their mothers' disordered eating and by their mothers' Holocaust exposure. The second generation reported more maternal over-protection and emotional over-involvement than did the third generation. Contrary to expectation, the third-generation women were more Holocaust exposed than were the second generation. The nature of Holocaust exposure for second and third generations needs further study and clarification in relation to disordered eating. There is considerable disparity between the results of clinical and qualitative studies which tend to find a strong relationship between Holocaust exposure and psychopathology, and population-based quantitative studies which tend to find a much weaker relationship. 2006 John Wiley & Sons, Ltd and Eating Disorders Association

Radiative B decays with four generations

NASA Astrophysics Data System (ADS)

Hewett, Joanne L.

1987-07-01

We study the decay b-->sγ in the four-generation model including the effects of QCD corrections. We find the fourth-generation contributions to be quite significant, extending the range of allowed branching ratios, BR(b-->sγ), to lie both above and below the three-generation standard model value. The existence of a fourth family of quarks would make a prediction for the top-quark mass difficult to obtain from this process. The author would like to thank T. Rizzo and J. Trampetic for discussions on QCD corrections, G. Eilam for introducing the author to the subject of rare B decays, and the Center for Particle Theory for its hospitality while this work was completed.

Critical litter moisture maximizes ammonia generation

USDA-ARS?s Scientific Manuscript database

The natural breakdown of litter (bedding material mixed with deposits of feces, feathers, spilled feed and water) generates ammonia in poultry houses. Good management practices can reduce ammonia concentrations in poultry houses. Findings from a recent publication indicate there is a critical litt...

Characterization of small RNAs and their targets of Fusarium oxysporum infected and non-infected cotton seedlings

USDA-ARS?s Scientific Manuscript database

In this study, we characterized small RNA (sRNA) or microRNA (miRNA) profiles during Fusarium oxysporum f.sp. vasinfectum (FOV) race 3 pathogenesis in cotton (Gossypium hirsutum L.) seedlings. sRNAs or miRNA are known to play important roles in gene expression, including stress responses, influencin...

Adult congenital heart disease imaging with second-generation dual-source computed tomography: initial experiences and findings.

PubMed

Ghoshhajra, Brian B; Sidhu, Manavjot S; El-Sherief, Ahmed; Rojas, Carlos; Yeh, Doreen Defaria; Engel, Leif-Christopher; Liberthson, Richard; Abbara, Suhny; Bhatt, Ami

2012-01-01

Adult congenital heart disease patients present a unique challenge to the cardiac imager. Patients may present with both acute and chronic manifestations of their complex congenital heart disease and also require surveillance for sequelae of their medical and surgical interventions. Multimodality imaging is often required to clarify their anatomy and physiology. Radiation dose is of particular concern in these patients with lifelong imaging needs for their chronic disease. The second-generation dual-source scanner is a recently available advanced clinical cardiac computed tomography (CT) scanner. It offers a combination of the high-spatial resolution of modern CT, the high-temporal resolution of dual-source technology, and the wide z-axis coverage of modern cone-beam geometry CT scanners. These advances in technology allow novel protocols that markedly reduce scan time, significantly reduce radiation exposure, and expand the physiologic imaging capabilities of cardiac CT. We present a case series of complicated adult congenital heart disease patients imaged by the second-generation dual-source CT scanner with extremely low-radiation doses and excellent image quality. © 2012 Wiley Periodicals, Inc.

An empirical generative framework for computational modeling of language acquisition.

PubMed

Waterfall, Heidi R; Sandbank, Ben; Onnis, Luca; Edelman, Shimon

2010-06-01

This paper reports progress in developing a computer model of language acquisition in the form of (1) a generative grammar that is (2) algorithmically learnable from realistic corpus data, (3) viable in its large-scale quantitative performance and (4) psychologically real. First, we describe new algorithmic methods for unsupervised learning of generative grammars from raw CHILDES data and give an account of the generative performance of the acquired grammars. Next, we summarize findings from recent longitudinal and experimental work that suggests how certain statistically prominent structural properties of child-directed speech may facilitate language acquisition. We then present a series of new analyses of CHILDES data indicating that the desired properties are indeed present in realistic child-directed speech corpora. Finally, we suggest how our computational results, behavioral findings, and corpus-based insights can be integrated into a next-generation model aimed at meeting the four requirements of our modeling framework.

An Intelligent CAI Monitor and Generative Tutor. Final Report.

ERIC Educational Resources Information Center

Koffman, Elliot B.; Perry, James

This final report summarizes research findings and presents a model for generative computer assisted instruction (CAI) with respect to its usefulness in the classroom environment. Methods used to individualize instruction, and the evolution of a procedure used to select a concept for presentation to a student with the generative CAI system are…

Expertise-Based Differences in Search and Option-Generation Strategies

ERIC Educational Resources Information Center

Raab, Markus; Johnson, Joseph G.

2007-01-01

The current work builds on option-generation research using experts of various skill levels in a realistic task. We extend previous findings that relate an athlete's performance strategy to generated options and subsequent choices in handball. In a 2-year longitudinal study, we present eye-tracking data to independently verify decision strategies…

Generation SMH (shaking my head): Work-Life Balance and Generational Realities

NASA Astrophysics Data System (ADS)

Jones, M. B.

2012-12-01

Many Federal Agencies have 'workforce development' programs that focus on preparing the next generation of scientists and engineers at the graduate and undergraduate level. Several of the science Agencies (e.g., NASA, NOAA, EPA, etc.), have programs that support students in many of the diverse disciplines that are unique to those Agency missions. While financial support certainly is critical to assist students in the STEM and other fields, professional development is just as important to equip students with a balanced arsenal of tactics to be successful professionals in the STEM workforce of today. Finding life balance as one moves through a STEM career path poses unique challenges that require a certain skill set that is not always intuitive. Some of those challenges include: selecting grad or post doc positions (negotiating to a family's advantage); balancing work and family commitments; and dealing with employer/advisor perceptions and expectations. For current and future generations in STEM, many of the above mentioned challenges require additional skill in negotiating interactions with individuals from other generations. Understanding perceptions and managing expectations are learnable skills that do not necessarily come with project funding.

The Small RNA GcvB Promotes Mutagenic Break Repair by Opposing the Membrane Stress Response

PubMed Central

Barreto, Brittany; Rogers, Elizabeth; Xia, Jun; Frisch, Ryan L.; Richters, Megan; Fitzgerald, Devon M.

2016-01-01

ABSTRACT Microbes and human cells possess mechanisms of mutagenesis activated by stress responses. Stress-inducible mutagenesis mechanisms may provide important models for mutagenesis that drives host-pathogen interactions, antibiotic resistance, and possibly much of evolution generally. In Escherichia coli, repair of DNA double-strand breaks is switched to a mutagenic mode, using error-prone DNA polymerases, via the SOS DNA damage and general (σS) stress responses. We investigated small RNA (sRNA) clients of Hfq, an RNA chaperone that promotes mutagenic break repair (MBR), and found that GcvB promotes MBR by allowing a robust σS response, achieved via opposing the membrane stress (σE) response. Cells that lack gcvB were MBR deficient and displayed reduced σS-dependent transcription but not reduced σS protein levels. The defects in MBR and σS-dependent transcription in ΔgcvB cells were alleviated by artificially increasing σS levels, implying that GcvB promotes mutagenesis by allowing a normal σS response. ΔgcvB cells were highly induced for the σE response, and blocking σE response induction restored both mutagenesis and σS-promoted transcription. We suggest that GcvB may promote the σS response and mutagenesis indirectly, by promoting membrane integrity, which keeps σE levels lower. At high levels, σE might outcompete σS for binding RNA polymerase and so reduce the σS response and mutagenesis. The data show the delicate balance of stress response modulation of mutagenesis. IMPORTANCE Mutagenesis mechanisms upregulated by stress responses promote de novo antibiotic resistance and cross-resistance in bacteria, antifungal drug resistance in yeasts, and genome instability in cancer cells under hypoxic stress. This paper describes the role of a small RNA (sRNA) in promoting a stress-inducible-mutagenesis mechanism, mutagenic DNA break repair in Escherichia coli. The roles of many sRNAs in E. coli remain unknown. This study shows that ΔgcvB cells

The Small RNA GcvB Promotes Mutagenic Break Repair by Opposing the Membrane Stress Response.

PubMed

Barreto, Brittany; Rogers, Elizabeth; Xia, Jun; Frisch, Ryan L; Richters, Megan; Fitzgerald, Devon M; Rosenberg, Susan M

2016-12-15

Microbes and human cells possess mechanisms of mutagenesis activated by stress responses. Stress-inducible mutagenesis mechanisms may provide important models for mutagenesis that drives host-pathogen interactions, antibiotic resistance, and possibly much of evolution generally. In Escherichia coli, repair of DNA double-strand breaks is switched to a mutagenic mode, using error-prone DNA polymerases, via the SOS DNA damage and general (σ S ) stress responses. We investigated small RNA (sRNA) clients of Hfq, an RNA chaperone that promotes mutagenic break repair (MBR), and found that GcvB promotes MBR by allowing a robust σ S response, achieved via opposing the membrane stress (σ E ) response. Cells that lack gcvB were MBR deficient and displayed reduced σ S -dependent transcription but not reduced σ S protein levels. The defects in MBR and σ S -dependent transcription in ΔgcvB cells were alleviated by artificially increasing σ S levels, implying that GcvB promotes mutagenesis by allowing a normal σ S response. ΔgcvB cells were highly induced for the σ E response, and blocking σ E response induction restored both mutagenesis and σ S -promoted transcription. We suggest that GcvB may promote the σ S response and mutagenesis indirectly, by promoting membrane integrity, which keeps σ E levels lower. At high levels, σ E might outcompete σ S for binding RNA polymerase and so reduce the σ S response and mutagenesis. The data show the delicate balance of stress response modulation of mutagenesis. Mutagenesis mechanisms upregulated by stress responses promote de novo antibiotic resistance and cross-resistance in bacteria, antifungal drug resistance in yeasts, and genome instability in cancer cells under hypoxic stress. This paper describes the role of a small RNA (sRNA) in promoting a stress-inducible-mutagenesis mechanism, mutagenic DNA break repair in Escherichia coli The roles of many sRNAs in E. coli remain unknown. This study shows that ΔgcvB cells

First complete genome sequence of an emerging cucumber green mottle mosaic virus isolate in North America

USDA-ARS?s Scientific Manuscript database

The complete genome sequence (6,423 nt) of an emerging Cucumber green mottle mosaic virus (CGMMV) isolate on cucumber in North America was determined through deep sequencing of sRNA and rapid amplification of cDNA ends. It shares 99% nucleotide sequence identity to the Asian genotype, but only 90% t...

Novel meiotic miRNAs and indications for a role of phasiRNAs in meiosis

USDA-ARS?s Scientific Manuscript database

Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and miRNAs directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolate...

Women’s Empowerment across Generations in Bangladesh

PubMed Central

Schuler, Sidney Ruth; Rottach, Elisabeth

2010-01-01

This study uses qualitative data to examine young women’s relationships with their mothers and mothers-in-law to understand how these relationships foster empowerment in the younger generation or fail to do so. The data consist of ethnographic interviews with 20 triads of women—young married women, their mothers and their mothers-in-law. Findings show that the influence of empowerment across generations was greater in the sphere of economic empowerment and education than in relation to marriage and childbearing. The study illustrates how patriarchal institutions resistant to change can limit the effects of women’s empowerment on the next generation. PMID:20847904

Transformational leadership to promote cross-generational retention.

PubMed

Lobo, Vanessa M

2010-05-01

As the current nursing shortage intensifies under the weight of an aging population, retention of front-line staff is becoming paramount. Studies have consistently demonstrated that the leadership style of nurse managers plays a significant role to this end. This paper describes some of the challenges that managers encounter in their dealings with the contemporary multigenerational workforce - including the baby boomers, generation X and generation Y (the "millennials"). A review of research findings suggests the insufficiency of a single leadership approach to nurse management compared to more tailored generational strategies. Application of the transformational leadership model provides the background and tenets from which solutions are proposed for multigenerational management.

Quantum mechanical energy-based screening of combinatorially generated library of tautomers. TauTGen: a tautomer generator program.

PubMed

Harańczyk, Maciej; Gutowski, Maciej

2007-01-01

We describe a procedure of finding low-energy tautomers of a molecule. The procedure consists of (i) combinatorial generation of a library of tautomers, (ii) screening based on the results of geometry optimization of initial structures performed at the density functional level of theory, and (iii) final refinement of geometry for the top hits at the second-order Möller-Plesset level of theory followed by single-point energy calculations at the coupled cluster level of theory with single, double, and perturbative triple excitations. The library of initial structures of various tautomers is generated with TauTGen, a tautomer generator program. The procedure proved to be successful for these molecular systems for which common chemical knowledge had not been sufficient to predict the most stable structures.

An empirical assessment of generational differences in basic human values.

PubMed

Lyons, Sean T; Duxbury, Linda; Higgins, Christopher

2007-10-01

This study assessed generational differences in human values as measured by the Schwartz Value Survey. It was proposed that the two most recent generations, Millennials and Generation Xers, would value Self-enhancement and Openness to Change more than the two older generations, Baby Boomers and Matures, while the two older generations would value Self-transcendence and Conservation more. The hypotheses were tested with a combined sample of Canadian knowledge workers and undergraduate business students (N = 1,194). Two hypotheses were largely supported, although an unexpectedly large difference was observed between Millennials and Generation Xers with respect to Openness to Change and Self-enhancement. The findings suggest that generation is a useful variable in examining differences in social values.

Generativity: Lived Experience as Curricular Content.

ERIC Educational Resources Information Center

Wallin, Jason; Graham, Tanya

2002-01-01

Modern educational practice, inspired by the scientific rationalism of the 17th and 18th centuries, focuses on control, certainty, and order, thus rendering students' experiences superficial. Generativity "finds" the curriculum in students' life experiences, giving them relevance and the opportunity to be explored. Where life is not the…

Iterative Authoring Using Story Generation Feedback: Debugging or Co-creation?

NASA Astrophysics Data System (ADS)

Swartjes, Ivo; Theune, Mariët

We explore the role that story generation feedback may play within the creative process of interactive story authoring. While such feedback is often used as 'debugging' information, we explore here a 'co-creation' view, in which the outcome of the story generator influences authorial intent. We illustrate an iterative authoring approach in which each iteration consists of idea generation, implementation and simulation. We find that the tension between authorial intent and the partially uncontrollable story generation outcome may be relieved by taking such a co-creation approach.

A genome-wide identification of the miRNAome in response to salinity stress in date palm (Phoenix dactylifera L.).

PubMed

Yaish, Mahmoud W; Sunkar, Ramanjulu; Zheng, Yun; Ji, Bo; Al-Yahyai, Rashid; Farooq, Sardar A

2015-01-01

Although date palm is relatively salt-tolerant, little is known about the underlying molecular mechanisms that contribute to its salt tolerance. Only recently, investigators have uncovered microRNA-mediated post-transcriptional gene regulation, which is critical for typical plant development and adaptation to stress conditions such as salinity. To identify conserved and novel miRNAs in date palm and to characterize miRNAs that could play a role in salt tolerance, we have generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm. Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of some miRNAs in date palm. In leaves, 54 of the identified miRNAs were significantly affected and the majority (70%) of them were upregulated, whereas in roots, 25 of the identified miRNAs were significantly affected and 76% of them were upregulated by the salinity stress. The salt-responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world that can tolerate a wide range of abiotic stresses, date palm contains a large population of conserved and non-conserved miRNAs that function at the post-transcriptional level. This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.

Construction of FuzzyFind Dictionary using Golay Coding Transformation for Searching Applications

NASA Astrophysics Data System (ADS)

Kowsari, Kamram

2015-03-01

searching through a large volume of data is very critical for companies, scientists, and searching engines applications due to time complexity and memory complexity. In this paper, a new technique of generating FuzzyFind Dictionary for text mining was introduced. We simply mapped the 23 bits of the English alphabet into a FuzzyFind Dictionary or more than 23 bits by using more FuzzyFind Dictionary, and reflecting the presence or absence of particular letters. This representation preserves closeness of word distortions in terms of closeness of the created binary vectors within Hamming distance of 2 deviations. This paper talks about the Golay Coding Transformation Hash Table and how it can be used on a FuzzyFind Dictionary as a new technology for using in searching through big data. This method is introduced by linear time complexity for generating the dictionary and constant time complexity to access the data and update by new data sets, also updating for new data sets is linear time depends on new data points. This technique is based on searching only for letters of English that each segment has 23 bits, and also we have more than 23-bit and also it could work with more segments as reference table.

Quark ACM with topologically generated gluon mass

NASA Astrophysics Data System (ADS)

Choudhury, Ishita Dutta; Lahiri, Amitabha

2016-03-01

We investigate the effect of a small, gauge-invariant mass of the gluon on the anomalous chromomagnetic moment (ACM) of quarks by perturbative calculations at one-loop level. The mass of the gluon is taken to have been generated via a topological mass generation mechanism, in which the gluon acquires a mass through its interaction with an antisymmetric tensor field Bμν. For a small gluon mass ( < 10 MeV), we calculate the ACM at momentum transfer q2 = -M Z2. We compare those with the ACM calculated for the gluon mass arising from a Proca mass term. We find that the ACM of up, down, strange and charm quarks vary significantly with the gluon mass, while the ACM of top and bottom quarks show negligible gluon mass dependence. The mechanism of gluon mass generation is most important for the strange quarks ACM, but not so much for the other quarks. We also show the results at q2 = -m t2. We find that the dependence on gluon mass at q2 = -m t2 is much less than at q2 = -M Z2 for all quarks.

Does the generation effect occur for pictures?

PubMed

Kinjo, H; Snodgrass, J G

2000-01-01

The generation effect is the finding that self-generated stimuli are recalled and recognized better than read stimuli. The effect has been demonstrated primarily with words. This article examines the effect for pictures in two experiments: Subjects named complete pictures (name condition) and fragmented pictures (generation condition). In Experiment 1, memory was tested in 3 explicit tasks: free recall, yes/no recognition, and a source-monitoring task on whether each picture was complete or fragmented (the complete/incomplete task). The generation effect was found for all 3 tasks. However, in the recognition and source-monitoring tasks, the generation effect was observed only in the generation condition. We hypothesized that absence of the effect in the name condition was due to the sensory or process match effect between study and test pictures and the superior identification of pictures in the name condition. Therefore, stimuli were changed from pictures to their names in Experiment 2. Memory was tested in the recognition task, complete/incomplete task, and second source-monitoring task (success/failure) on whether each picture had been identified successfully. The generation effect was observed for all 3 tasks. These results suggest that memory of structural and semantic characteristics and of success in identification of generated pictures may contribute to the generation effect.

Generational Attitudes and Teacher ICT Use

ERIC Educational Resources Information Center

Pegler, Karen; Kollewyn, Joan; Crichton, Susan

2010-01-01

This paper explores the impact of generational attitudes on teachers' ICT use. Findings from the preliminary research suggest that when applications have a use or purpose that extends beyond the classroom and into their social or personal sphere, younger teachers demonstrate noticeable confidence and a higher potential for technology integration…

High Renewable Generation | Energy Analysis | NREL

Science.gov Websites

and water use. Featured Studies Eastern Renewable Generation Integration Study Renewable Electricity Futures Study North American Renewable Integration Study Data and Tools Find out more about NREL's Grid are documented in Transparent Cost Database/Open Energy Information. Publications SunShot Vision Study

An Algorithm for Finding Candidate Synaptic Sites in Computer Generated Networks of Neurons with Realistic Morphologies

PubMed Central

van Pelt, Jaap; Carnell, Andrew; de Ridder, Sander; Mansvelder, Huibert D.; van Ooyen, Arjen

2010-01-01

Neurons make synaptic connections at locations where axons and dendrites are sufficiently close in space. Typically the required proximity is based on the dimensions of dendritic spines and axonal boutons. Based on this principle one can search those locations in networks formed by reconstructed neurons or computer generated neurons. Candidate synapses are then located where axons and dendrites are within a given criterion distance from each other. Both experimentally reconstructed and model generated neurons are usually represented morphologically by piecewise-linear structures (line pieces or cylinders). Proximity tests are then performed on all pairs of line pieces from both axonal and dendritic branches. Applying just a test on the distance between line pieces may result in local clusters of synaptic sites when more than one pair of nearby line pieces from axonal and dendritic branches is sufficient close, and may introduce a dependency on the length scale of the individual line pieces. The present paper describes a new algorithm for defining locations of candidate synapses which is based on the crossing requirement of a line piece pair, while the length of the orthogonal distance between the line pieces is subjected to the distance criterion for testing 3D proximity. PMID:21160548

Mother and Grandmother Parenting in Low-Income Three-Generation Rural Households

PubMed Central

Barnett, Melissa A.

2009-01-01

This study draws data from the Family Life Project to examine parenting behaviors observed for 105 mothers and grandmothers raising an infant in rural low-income multigenerational households. Multilevel models are used to examine the relationships between maternal age and psychological distress and parenting of the infant by both generations. The findings indicate that young maternal age is a risk factor for less sensitive parenting in the presence of other risks, including psychological distress. Further, young maternal age is associated with negative parenting behaviors by grandmothers only. Grandmothers and mothers displayed similar levels of negative intrusive parenting, but different factors were linked to the observed parenting of each generation. These findings contribute to understanding the benefits and risks of three-generation households. PMID:19946461

Do researchers have an obligation to actively look for genetic incidental findings?

PubMed

Gliwa, Catherine; Berkman, Benjamin E

2013-01-01

The rapid growth of next-generation genetic sequencing has prompted debate about the responsibilities of researchers toward genetic incidental findings. Assuming there is a duty to disclose significant incidental findings, might there be an obligation for researchers to actively look for these findings? We present an ethical framework for analyzing whether there is a positive duty to look for genetic incidental findings. Using the ancillary care framework as a guide, we identify three main criteria that must be present to give rise to an obligation to look: high benefit to participants, lack of alternative access for participants, and reasonable burden on researchers. Our analysis indicates that there is no obligation to look for incidental findings today, but during the ongoing translation of genomic analysis from research to clinical care, this obligation may arise.

Do Researchers Have an Obligation to Actively Look for Genetic Incidental Findings?

PubMed Central

Gliwa, Catherine; Berkman, Benjamin E.

2014-01-01

The rapid growth of next-generation genetic sequencing has prompted debate about the responsibilities of researchers toward genetic incidental findings. Assuming there is a duty to disclose significant incidental findings, might there be an obligation for researchers to actively look for these findings? We present an ethical framework for analyzing whether there is a positive duty to look for genetic incidental findings. Using the ancillary care framework as a guide, we identify three main criteria that must be present to give rise to an obligation to look: high benefit to participants, lack of alternative access for participants, and reasonable burden on researchers. Our analysis indicates that there is no obligation to look for incidental findings today, but during the ongoing translation of genomic analysis from research to clinical care, this obligation may arise. PMID:23391059

Nonlinear spin current generation in noncentrosymmetric spin-orbit coupled systems

NASA Astrophysics Data System (ADS)

Hamamoto, Keita; Ezawa, Motohiko; Kim, Kun Woo; Morimoto, Takahiro; Nagaosa, Naoto

2017-06-01

Spin current plays a central role in spintronics. In particular, finding more efficient ways to generate spin current has been an important issue and has been studied actively. For example, representative methods of spin-current generation include spin-polarized current injections from ferromagnetic metals, the spin Hall effect, and the spin battery. Here, we theoretically propose a mechanism of spin-current generation based on nonlinear phenomena. By using Boltzmann transport theory, we show that a simple application of the electric field E induces spin current proportional to E2 in noncentrosymmetric spin-orbit coupled systems. We demonstrate that the nonlinear spin current of the proposed mechanism is supported in the surface state of three-dimensional topological insulators and two-dimensional semiconductors with the Rashba and/or Dresselhaus interaction. In the latter case, the angular dependence of the nonlinear spin current can be manipulated by the direction of the electric field and by the ratio of the Rashba and Dresselhaus interactions. We find that the magnitude of the spin current largely exceeds those in the previous methods for a reasonable magnitude of the electric field. Furthermore, we show that application of ac electric fields (e.g., terahertz light) leads to the rectifying effect of the spin current, where dc spin current is generated. These findings will pave a route to manipulate the spin current in noncentrosymmetric crystals.

Transformation-aware Exploit Generation using a HI-CFG

DTIC Science & Technology

2013-05-16

testing has many limitations of its own: it can require significant target -specific setup to perform well; it is unlikely to trigger vulnerabilities...check fails represents a potential vulnerability, but a conservative analysis can produce false positives , so we can use exploit generation to find...warnings that correspond to true positives . We can also find potentially vulnerable instructions in the course of a manual binary- level security audit

CRISPRi-sRNA: Transcriptional-Translational Regulation of Extracellular Electron Transfer in Shewanella oneidensis.

PubMed

Cao, Yingxiu; Li, Xiaofei; Li, Feng; Song, Hao

2017-09-15

Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i.e., clustered regularly interspaced short palindromic repeats interference (CRISPRi), in S. oneidensis MR-1 using green fluorescent protein (GFP) as a reporter. We used this CRISPRi technology to repress the expression levels of target genes, individually and in combination, in the EET pathways (e.g., the MtrCAB pathway and genes affecting the formation of electroactive biofilms in S. oneidensis), which in turn enabled the efficient regulation of EET efficiency. We then established a translational regulation technology, i.e., Hfq-dependent small regulatory RNA (sRNA), in S. oneidensis by repressing the GFP reporter and mtrA, which is a critical gene in the EET pathways in S. oneidensis. To achieve coordinated transcriptional and translational regulation at the genomic level, the CRISPRi and Hfq-dependent sRNA systems were incorporated into a single plasmid harbored in a recombinant S. oneidensis strain, which enabled an even higher efficiency of mtrA gene repression in the EET pathways than that achieved by the CRISPRi and Hfq-dependent sRNA system alone, as exhibited by the reduced electricity output. Overall, we developed a combined CRISPRi-sRNA method that enabled the synergistic transcriptional and translational regulation of target genes in S. oneidensis. This technology involving CRISPRi-sRNA transcriptional-translational regulation of gene expression at the genomic level could be applied to other microorganisms.

Small RNA-mediated regulation in bacteria: A growing palette of diverse mechanisms.

PubMed

Dutta, Tanmay; Srivastava, Shubhangi

2018-05-20

Small RNAs (sRNAs) in bacteria have evolved with diverse mechanisms to balance their target gene expression in response to changes in the environment. Accumulating studies on bacterial regulatory processes firmly established that sRNAs modulate their target gene expression generally at the posttranscriptional level. Identification of large number of sRNAs by advanced technologies, like deep sequencing, tilling microarray, indicates the existence of a plethora of distinctive sRNA-mediated regulatory mechanisms in bacteria. Types of the novel mechanisms are increasing with the discovery of new sRNAs. Complementary base pairing between sRNAs and target RNAs assisted by RNA chaperones like Hfq and ProQ, in many occasions, to regulate the cognate gene expression is prevalent in sRNA mechanisms. sRNAs, in most studied cases, can directly base pair with target mRNA to remodel its expression. Base pairing can happen either in the untranslated regions or in the coding regions of mRNA to activate/repress its translation. sRNAs also act as target mimic to titrate away different regulatory RNAs from its target. Other mechanism includes the sequestration of regulatory proteins, especially transcription factors, by sRNAs. Numerous sRNAs, following analogous mechanism, are widespread in bacteria, and thus, has drawn immense attention for the development of RNA-based technologies. Nevertheless, typical sRNA mechanisms are also discovered to be confined in some bacteria. Analysis of the sRNA mechanisms unravels their existence in both the single step processes and the complex regulatory networks with a global effect on cell physiology. This review deals with the diverse array of mechanisms, which sRNAs follow to maintain bacterial lifestyle. Copyright © 2018 Elsevier B.V. All rights reserved.

Does war contribute to family violence against children? Findings from a two-generational multi-informant study in Northern Uganda.

PubMed

Saile, Regina; Ertl, Verena; Neuner, Frank; Catani, Claudia

2014-01-01

After 20 years of civil war in Northern Uganda, the continuity of violence within the family constitutes a major challenge to children's healthy development in the post-conflict era. Previous exposure to trauma and ongoing psychopathology in guardians potentially contribute to parental perpetration against children and dysfunctional interactions in the child's family ecology that increase children's risk of maltreatment. In order to investigate distal and proximal risk factors of child victimization, we first aimed to identify factors leading to more self-reported perpetration in guardians. Second, we examined factors in the child's family environment that promote child-reported experiences of maltreatment. Using a two-generational design we interviewed 368 children, 365 female guardians, and 304 male guardians from seven war-affected rural communities in Northern Uganda on the basis of standardized questionnaires. We found that the strongest predictors of self-reported aggressive parenting behaviors toward the child were guardians' own experiences of childhood maltreatment, followed by female guardians' victimization experiences in their intimate relationship and male guardians' posttrautmatic stress disorder (PTSD) symptoms and alcohol-related problems. Regarding children's self-report of victimization in the family, proximal factors including violence between adults in the household and male guardians' PTSD symptom severity level predicted higher levels of maltreatment. Distal variables such as female guardians' history of childhood victimization and female guardians' exposure to traumatic war events also increased children's report of maltreatment. The current findings suggest that in the context of organized violence, an intergenerational cycle of violence persists that is exacerbated by female guardians' re-victimization experiences and male guardians' psychopathological symptoms. Copyright © 2013 Elsevier Ltd. All rights reserved.

Generation of hollow Gaussian beams by spatial filtering

NASA Astrophysics Data System (ADS)

Liu, Zhengjun; Zhao, Haifa; Liu, Jianlong; Lin, Jie; Ashfaq Ahmad, Muhammad; Liu, Shutian

2007-08-01

We demonstrate that hollow Gaussian beams can be obtained from Fourier transform of the differentials of a Gaussian beam, and thus they can be generated by spatial filtering in the Fourier domain with spatial filters that consist of binomial combinations of even-order Hermite polynomials. A typical 4f optical system and a Michelson interferometer type system are proposed to implement the proposed scheme. Numerical results have proved the validity and effectiveness of this method. Furthermore, other polynomial Gaussian beams can also be generated by using this scheme. This approach is simple and may find significant applications in generating the dark hollow beams for nanophotonic technology.

Generation of hollow Gaussian beams by spatial filtering.

PubMed

Liu, Zhengjun; Zhao, Haifa; Liu, Jianlong; Lin, Jie; Ahmad, Muhammad Ashfaq; Liu, Shutian

2007-08-01

We demonstrate that hollow Gaussian beams can be obtained from Fourier transform of the differentials of a Gaussian beam, and thus they can be generated by spatial filtering in the Fourier domain with spatial filters that consist of binomial combinations of even-order Hermite polynomials. A typical 4f optical system and a Michelson interferometer type system are proposed to implement the proposed scheme. Numerical results have proved the validity and effectiveness of this method. Furthermore, other polynomial Gaussian beams can also be generated by using this scheme. This approach is simple and may find significant applications in generating the dark hollow beams for nanophotonic technology.

Generation of Path-Encoded Greenberger-Horne-Zeilinger States

NASA Astrophysics Data System (ADS)

Bergamasco, N.; Menotti, M.; Sipe, J. E.; Liscidini, M.

2017-11-01

We study the generation of Greenberger-Horne-Zeilinger (GHZ) states of three path-encoded photons. Inspired by the seminal work of Bouwmeester et al. [Phys. Rev. Lett. 82, 1345 (1999), 10.1103/PhysRevLett.82.1345] on polarization-entangled GHZ states, we find a corresponding path representation for the photon states of an optical circuit, identify the elements required for the state generation, and propose a possible implementation of our strategy. Besides the practical advantage of employing an integrated system that can be fabricated with proven lithographic techniques, our example suggests that it is possible to enhance the generation efficiency by using microring resonators.

How the millennial generation is transforming employee benefits.

PubMed

Howe, Neil

2014-01-01

According to a number of recent studies, the millennial generation, today's incoming young-adult employees, shows far more interest than older generations in a broad spectrum of employee bene its to protect them from various life risks. They are more cautious than boomers or Gen Xers in choosing their financial portfolios and more focused on planning for their long-term future. Millennials even value health insurance almost as much as older adults--despite the fact they're much less likely to use it. These findings are in broad alignment with broader millennial generational traits that LifeCourse Associates has been studying fo many years.

Thriving Children, Successful Parents: A Two-Generation Approach to Policy

ERIC Educational Resources Information Center

Schmit, Stephanie; Matthews, Hannah; Golden, Olivia

2014-01-01

A two-generation approach to public policies brings together worlds that are often separated (focusing only on children or only on parents) to modify or create new policies that focus on the needs of parents and children together. Two-generation policies reflect strong research findings that the well-being of parents is a crucial ingredient in…

Aldehyde levels in e-cigarette aerosol: Findings from a replication study and from use of a new-generation device.

PubMed

Farsalinos, Konstantinos E; Kistler, Kurt A; Pennington, Alexander; Spyrou, Alketa; Kouretas, Dimitris; Gillman, Gene

2018-01-01

A recent study identified high aldehyde emissions from e-cigarettes (ECs), that when converted to reasonable daily human EC liquid consumption, 5 g/day, gave formaldehyde exposure equivalent to 604-3257 tobacco cigarettes. We replicated this study and also tested a new-generation atomizer under verified realistic (no dry puff) conditions. CE4v2 atomizers were tested at 3.8 V and 4.8 V, and a Nautilus Mini atomizer was tested at 9.0 W and 13.5 W. All measurements were performed in a laboratory ISO-accredited for EC aerosol collection and aldehyde measurements. CE4v2 generated dry puffs at both voltage settings. Formaldehyde levels were >10-fold lower, acetaldehyde 6-9-fold lower and acrolein 16-26-fold lower than reported in the previous study. Nautilus Mini did not generate dry puffs, and minimal aldehydes were emitted despite >100% higher aerosol production per puff compared to CE4v2 (formaldehyde: 16.7 and 16.5 μg/g; acetaldehyde: 9.6 and 10.3 μg/g; acrolein: 8.6 and 11.7 μg/g at 9.0 W and 13.5 W, respectively). EC liquid consumption of 5 g/day reduces aldehyde exposure by 94.4-99.8% compared to smoking 20 tobacco cigarettes. Checking for dry puffs is essential for EC emission testing. Under realistic conditions, new-generation ECs emit minimal aldehydes/g liquid at both low and high power. Validated methods should be used when analyzing EC aerosol. Copyright © 2017 Elsevier Ltd. All rights reserved.

Magnetic field generation in core-sheath jets via the kinetic Kelvin-Helmholtz instability

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

Nishikawa, K.-I.; Hardee, P. E.; Duţan, I.

2014-09-20

We have investigated magnetic field generation in velocity shears via the kinetic Kelvin-Helmholtz instability (kKHI) using a relativistic plasma jet core and stationary plasma sheath. Our three-dimensional particle-in-cell simulations consider plasma jet cores with Lorentz factors of 1.5, 5, and 15 for both electron-proton and electron-positron plasmas. For electron-proton plasmas, we find generation of strong large-scale DC currents and magnetic fields that extend over the entire shear surface and reach thicknesses of a few tens of electron skin depths. For electron-positron plasmas, we find generation of alternating currents and magnetic fields. Jet and sheath plasmas are accelerated across the shearmore » surface in the strong magnetic fields generated by the kKHI. The mixing of jet and sheath plasmas generates a transverse structure similar to that produced by the Weibel instability.« less

The impact of intuition and supervisor-nurse relationships on empowerment and affective commitment by generation.

PubMed

Farr-Wharton, Rod; Brunetto, Yvonne; Shacklock, Kate

2012-06-01

  This article reports a generational cohort and leader-member exchange theoretical frameworks-guided study of the influence of the supervisor-subordinate relationship on three generational nurse cohorts' use of intuition, perceptions of empowerment and affective commitment.   Within a global context of nurse shortages, knowledge about factors influencing nurse retention is urgently sought. We postulated that nurses' use of intuition is the key to their empowerment and consequent commitment to the organization, and that impact would vary among the three large nurse generations.   A self-report survey was used to gather data in 2008, which were then analysed using correlations, regression analysis, manova and path analysis. Data were obtained from 900 Baby Boomer and Generations X and Y nurses, randomly chosen from seven private hospitals across Australia.   The findings confirm the important impact of supervisor-nurse relationships upon all three generations' use of intuition. The findings add new knowledge about the differing importance of using intuition for Generation X, Generation Y and Baby Boomer nurses' perceptions of empowerment, suggesting it is more important to Baby Boomers and Generation X than to Generation Y. Further, the impact of using intuition differs significantly among the generational cohorts. The findings suggest the need for a more differentiated tailored style - sensitive to varying needs of the generations. Improving supervisor-nurse relationships is also critical, because of their impact upon nurses' use of intuition, perceptions of empowerment and affective commitment. Poor relationships lead to increased nurse replacement costs. © 2011 Blackwell Publishing Ltd.

Religious Homogamy and Marital Quality: Historical and Generational Patterns, 1980-1997

ERIC Educational Resources Information Center

Myers, Scott M.

2006-01-01

Despite significant social changes in the past 50 years, research continues to find a strong and enduring link between religious homogamy and marital quality. Yet, research has not explicitly examined whether this link has changed over time or over generations. To address historical and generational trends, I use national, longitudinal data…

Educating the Next Generation of Agricultural Scientists.

ERIC Educational Resources Information Center

National Academy of Sciences - National Research Council, Washington, DC. Board on Agriculture.

The Committee on Evaluation of Trends in Agricultural Research at the Doctoral and Postdoctoral Level was established to analyze issues related to the next generation of agricultural scientists. This report contains the findings, conclusions, and recommendations regarding the status and future needs of agricultural scientists. This report focuses…

Expression of Small RNA in Aphis gossypii and Its Potential Role in the Resistance Interaction with Melon

PubMed Central

Sattar, Sampurna; Anstead, James A.; Sunkar, Ramanjulu; Thompson, Gary A.

2012-01-01

Background The regulatory role of small RNAs (sRNAs) in various biological processes is an active area of investigation; however, there has been limited information available on the role of sRNAs in plant-insect interactions. This study was designed to identify sRNAs in cotton-melon aphid (Aphis gossypii) during the Vat-mediated resistance interaction with melon (Cucumis melo). Methodology/Principal Findings The role of miRNAs was investigated in response to aphid herbivory, during both resistant and susceptible interactions. sRNA libraries made from A. gossypii tissues feeding on Vat+ and Vat− plants revealed an unexpected abundance of 27 nt long sRNA sequences in the aphids feeding on Vat+ plants. Eighty-one conserved microRNAs (miRNAs), twelve aphid-specific miRNAs, and nine novel candidate miRNAs were also identified. Plant miRNAs found in the aphid libraries were most likely ingested during phloem feeding. The presence of novel miRNAs was verified by qPCR experiments in both resistant Vat+ and susceptible Vat− interactions. The comparative analyses revealed that novel miRNAs were differentially regulated during the resistant and susceptible interactions. Gene targets predicted for the miRNAs identified in this study by in silico analyses revealed their involvement in morphogenesis and anatomical structure determination, signal transduction pathways, cell differentiation and catabolic processes. Conclusion/Significance In this study, conserved and novel miRNAs were reported in A. gossypii. Deep sequencing data showed differences in the abundance of miRNAs and piRNA-like sequences in A. gossypii. Quantitative RT-PCR revealed that A. gossypii miRNAs were differentially regulated during resistant and susceptible interactions. Aphids can also ingest plant miRNAs during phloem feeding that are stable in the insect. PMID:23173035

Important imaging finding e-mail alert system: experience after 3 years of implementation.

PubMed

Abujudeh, Hani H; Kaewlai, Rathachai; Choy, Garry; Whelton, Dianne G; Rosenthal, Daniel I

2009-09-01

To evaluate the effectiveness of an important finding alert (IFA) system that uses e-mail technology to alert referring physicians to an important but nonurgent imaging finding. The institutional review board approved the study; the requirement for informed consent was waived. The authors retrospectively reviewed the radiology reports generated from January 2005 to December 2007 to determine how many reports contained an IFA statement, how many IFA messages were sent, and how many such messages were viewed by referring physicians. They reviewed 1000 randomly selected radiology reports that contained the IFA statement to identify the imaging modalities and findings that triggered the radiologists' use of the IFA system. A total of 1540254 radiology reports were generated during the 3-year period. A total of 56 691 (3.7%) reports contained the IFA statement. IFA e-mail messages were sent for 52 883 (93.3%) of the 56 691 reports, and 42 285 (74.6%) of the 56 691 reports were viewed by the referring physicians. The most common important but nonurgent findings were definitive (449 [44.9%] of 1000 reports) and indeterminate (260 [26.0%] of 1000 reports) abnormalities. More than half (n = 503) of the alerts were related to computed tomographic examinations, and the majority (n = 677, 67.7%) of them were initiated by thoracic and abdominal radiologists. The IFA system is a potentially useful method of communicating nonurgent but important imaging findings with use of e-mail technology.

Developing Methodologies to Find Abbreviated Laboratory Test Names in Narrative Clinical Documents by Generating High Quality Q-Grams.

PubMed

Kim, Kyungmo; Choi, Jinwook

2017-01-01

Laboratory test names are used as basic information to diagnose diseases. However, this kind of medical information is usually written in a natural language. To find this information, lexicon based methods have been good solutions but they cannot find terms that do not have abbreviated expressions, such as "neuts" that means "neutrophils". To address this issue, similar word matching can be used; however, it can be disadvantageous because of significant false positives. Moreover, processing time is longer as the size of terms is bigger. Therefore, we suggest a novel q-gram based algorithm, named modified triangular area filtering, to find abbreviated laboratory test terms in clinical documents, minimizing the possibility to impair the lexicons' precision. In addition, we found the terms using the methodology with reasonable processing time. The results show that this method can achieve 92.54 precision, 87.72 recall, 90.06 f1-score in test sets when edit distance threshold(τ) = 3.

Theoretical analysis of tsunami generation by pyroclastic flows

USGS Publications Warehouse

Watts, P.; Waythomas, C.F.

2003-01-01

Pyroclastic flows are a common product of explosive volcanism and have the potential to initiate tsunamis whenever thick, dense flows encounter bodies of water. We evaluate the process of tsunami generation by pyroclastic flow by decomposing the pyroclastic flow into two components, the dense underflow portion, which we term the pyroclastic debris flow, and the plume, which includes the surge and coignimbrite ash cloud parts of the flow. We consider five possible wave generation mechanisms. These mechanisms consist of steam explosion, pyroclastic debris flow, plume pressure, plume shear, and pressure impulse wave generation. Our theoretical analysis of tsunami generation by these mechanisms provides an estimate of tsunami features such as a characteristic wave amplitude and wavelength. We find that in most situations, tsunami generation is dominated by the pyroclastic debris flow component of a pyroclastic flow. This work presents information sufficient to construct tsunami sources for an arbitrary pyroclastic flow interacting with most bodies of water. Copyright 2003 by the American Geophysical Union.

A Unique cis-Encoded Small Noncoding RNA Is Regulating Legionella pneumophila Hfq Expression in a Life Cycle-Dependent Manner.

PubMed

Oliva, Giulia; Sahr, Tobias; Rolando, Monica; Knoth, Maike; Buchrieser, Carmen

2017-01-10

Legionella pneumophila is an environmental bacterium that parasitizes protozoa, but it may also infect humans, thereby causing a severe pneumonia called Legionnaires' disease. To cycle between the environment and a eukaryotic host, L. pneumophila is regulating the expression of virulence factors in a life cycle-dependent manner: replicating bacteria do not express virulence factors, whereas transmissive bacteria are highly motile and infective. Here we show that Hfq is an important regulator in this network. Hfq is highly expressed in transmissive bacteria but is expressed at very low levels in replicating bacteria. A L. pneumophila hfq deletion mutant exhibits reduced abilities to infect and multiply in Acanthamoeba castellanii at environmental temperatures. The life cycle-dependent regulation of Hfq expression depends on a unique cis-encoded small RNA named Anti-hfq that is transcribed antisense of the hfq transcript and overlaps its 5' untranslated region. The Anti-hfq sRNA is highly expressed only in replicating L. pneumophila where it regulates hfq expression through binding to the complementary regions of the hfq transcripts. This results in reduced Hfq protein levels in exponentially growing cells. Both the small noncoding RNA (sRNA) and hfq mRNA are bound and stabilized by the Hfq protein, likely leading to the cleavage of the RNA duplex by the endoribonuclease RNase III. In contrast, after the switch to transmissive bacteria, the sRNA is not expressed, allowing now an efficient expression of the hfq gene and consequently Hfq. Our results place Hfq and its newly identified sRNA anti-hfq in the center of the regulatory network governing L. pneumophila differentiation from nonvirulent to virulent bacteria. The abilities of L. pneumophila to replicate intracellularly and to cause disease depend on its capacity to adapt to different extra- and intracellular environmental conditions. Therefore, a timely and fine-tuned expression of virulence factors and

Intergenerational Relationship Quality Across Three Generations

PubMed Central

Tighe, Lauren A.; Fingerman, Karen L.; Zarit, Steven H.

2012-01-01

Objectives. Studies of intergenerational relationship quality often include one or two generations. This study examined within-family differences and similarities or transmission of positive and negative relationship quality across three generations. Method. Participants included 633 middle-aged individuals (G2; 52% women, ages 40–60 years), 592 of their offspring (G3; 53% daughters; ages 18–41 years), and 337 of their parents (i.e., grandparents; G1; 69% women; ages 59–96 years). Results. Multilevel models revealed differences and similarities in relationship quality across generations. The oldest generation (G1) reported greater positive and less negative quality relationships than the middle (G2) and the younger (G3) generations. There was limited evidence of transmission. Middle-aged respondents who reported more positive and less negative ties with their parents (G1) reported more positive and less negative ties with their own children (G3). Grandmother (G1) reports of more positive relationship quality were associated with G3 reports of more positive relationship quality with G2. Discussion. Findings are consistent with the intergenerational stake hypothesis and only partially consistent with the theory of intergenerational transmission. Overall, this study suggests that there is greater within-family variability than similarities in how family members feel about one another. PMID:22628478

Ontology-Based Multiple Choice Question Generation

PubMed Central

Al-Yahya, Maha

2014-01-01

With recent advancements in Semantic Web technologies, a new trend in MCQ item generation has emerged through the use of ontologies. Ontologies are knowledge representation structures that formally describe entities in a domain and their relationships, thus enabling automated inference and reasoning. Ontology-based MCQ item generation is still in its infancy, but substantial research efforts are being made in the field. However, the applicability of these models for use in an educational setting has not been thoroughly evaluated. In this paper, we present an experimental evaluation of an ontology-based MCQ item generation system known as OntoQue. The evaluation was conducted using two different domain ontologies. The findings of this study show that ontology-based MCQ generation systems produce satisfactory MCQ items to a certain extent. However, the evaluation also revealed a number of shortcomings with current ontology-based MCQ item generation systems with regard to the educational significance of an automatically constructed MCQ item, the knowledge level it addresses, and its language structure. Furthermore, for the task to be successful in producing high-quality MCQ items for learning assessments, this study suggests a novel, holistic view that incorporates learning content, learning objectives, lexical knowledge, and scenarios into a single cohesive framework. PMID:24982937

A Simple Syllogism-Solving Test: Empirical Findings and Implications for "g" Research

ERIC Educational Resources Information Center

Shikishima, Chizuru; Yamagata, Shinji; Hiraishi, Kai; Sugimoto, Yutaro; Murayama, Kou; Ando, Juko

2011-01-01

It has been reported that the ability to solve syllogisms is highly "g"-loaded. In the present study, using a self-administered shortened version of a syllogism-solving test, the "BAROCO Short," we examined whether robust findings generated by previous research regarding IQ scores were also applicable to "BAROCO…

Estimating evaporative vapor generation from automobiles based on parking activities.

PubMed

Dong, Xinyi; Tschantz, Michael; Fu, Joshua S

2015-07-01

A new approach is proposed to quantify the evaporative vapor generation based on real parking activity data. As compared to the existing methods, two improvements are applied in this new approach to reduce the uncertainties: First, evaporative vapor generation from diurnal parking events is usually calculated based on estimated average parking duration for the whole fleet, while in this study, vapor generation rate is calculated based on parking activities distribution. Second, rather than using the daily temperature gradient, this study uses hourly temperature observations to derive the hourly incremental vapor generation rates. The parking distribution and hourly incremental vapor generation rates are then adopted with Wade-Reddy's equation to estimate the weighted average evaporative generation. We find that hourly incremental rates can better describe the temporal variations of vapor generation, and the weighted vapor generation rate is 5-8% less than calculation without considering parking activity. Copyright © 2015 Elsevier Ltd. All rights reserved.

A New Generation of Russian College Students

ERIC Educational Resources Information Center

Lisauskene, M.

2006-01-01

This article reports the findings of a study examining the values, life stereotypes, and models of behavior of the so-called "next generation" of the Russian youth. The study was titled "From Secondary School Graduate to College Student to Graduate" and was carried out in seven higher educational institutions and two secondary specialized…

Finding My Way: Perceptions of Institutional Support and Belonging in Low-Income, First-Generation, First-Year College Students

ERIC Educational Resources Information Center

Means, Darris R.; Pyne, Kimberly B.

2017-01-01

For this qualitative case study we explored students' perceptions of institutional support and sense of belonging within the college environment. Following 10 low-income, first-generation college students out of a college access program and through their first year of college, we examined institutional support structures that have been reported to…

Asymptotics of bivariate generating functions with algebraic singularities

NASA Astrophysics Data System (ADS)

Greenwood, Torin

Flajolet and Odlyzko (1990) derived asymptotic formulae the coefficients of a class of uni- variate generating functions with algebraic singularities. Gao and Richmond (1992) and Hwang (1996, 1998) extended these results to classes of multivariate generating functions, in both cases by reducing to the univariate case. Pemantle and Wilson (2013) outlined new multivariate ana- lytic techniques and used them to analyze the coefficients of rational generating functions. After overviewing these methods, we use them to find asymptotic formulae for the coefficients of a broad class of bivariate generating functions with algebraic singularities. Beginning with the Cauchy integral formula, we explicity deform the contour of integration so that it hugs a set of critical points. The asymptotic contribution to the integral comes from analyzing the integrand near these points, leading to explicit asymptotic formulae. Next, we use this formula to analyze an example from current research. In the following chapter, we apply multivariate analytic techniques to quan- tum walks. Bressler and Pemantle (2007) found a (d + 1)-dimensional rational generating function whose coefficients described the amplitude of a particle at a position in the integer lattice after n steps. Here, the minimal critical points form a curve on the (d + 1)-dimensional unit torus. We find asymptotic formulae for the amplitude of a particle in a given position, normalized by the number of steps n, as n approaches infinity. Each critical point contributes to the asymptotics for a specific normalized position. Using Groebner bases in Maple again, we compute the explicit locations of peak amplitudes. In a scaling window of size the square root of n near the peaks, each amplitude is asymptotic to an Airy function.

Dopamine Modulates Option Generation for Behavior.

PubMed

Ang, Yuen-Siang; Manohar, Sanjay; Plant, Olivia; Kienast, Annika; Le Heron, Campbell; Muhammed, Kinan; Hu, Michele; Husain, Masud

2018-05-21

Animals make innumerable decisions every day, each of which involves evaluating potential options for action. But how are options generated? Although much is now known about decision making when a fixed set of potential options is provided, surprisingly little progress has been made on self-generated options. Some researchers have proposed that such abilities might be modulated by dopamine. Here, we used a new measure of option generation that is quantitative, objective, and culture fair to investigate how humans generate different behavioral options. Participants were asked to draw as many different paths (options) as they could between two points within a fixed time. Healthy individuals (n = 96) exhibited a trade-off between uniqueness (how individually different their options were) and fluency (number of options), generating either many similar or few unique options. To assess influence of dopamine, we first examined patients with Parkinson's disease (n = 35) ON and OFF their dopaminergic medication and compared them to elderly healthy controls (n = 34). Then we conducted a double-blind, placebo-controlled crossover study of the D2 agonist cabergoline in healthy older people (n = 29). Across both studies, dopamine increased fluency but diminished overall uniqueness of options generated, due to the effect of fluency trading off with uniqueness. Crucially, however, when this trade-off was corrected for, dopamine was found to increase uniqueness for any given fluency. Three carefully designed control studies showed that performance on our option-generation task was not related to executing movements, planning actions, or selecting between generated options. These findings show that dopamine plays an important role in modulating option generation. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Straight from the Source: What Works for First-Generation College Students

ERIC Educational Resources Information Center

Engle, Jennifer; Bermeo, Adolfo; O'Brien, Colleen

2006-01-01

This report presents the findings from focus groups with first-generation students in Texas. The students shared what works to help them make the transition from high school to college, as well as what didn't work or what could work better to get more first-generation students into college. Pre-college services and programs can ease the transition…

Solid-State Thermionic Power Generators: An Analytical Analysis in the Nonlinear Regime

NASA Astrophysics Data System (ADS)

Zebarjadi, M.

2017-07-01

Solid-state thermionic power generators are an alternative to thermoelectric modules. In this paper, we develop an analytical model to investigate the performance of these generators in the nonlinear regime. We identify dimensionless parameters determining their performance and provide measures to estimate an acceptable range of thermal and electrical resistances of thermionic generators. We find the relation between the optimum load resistance and the internal resistance and suggest guidelines for the design of thermionic power generators. Finally, we show that in the nonlinear regime, thermionic power generators can have efficiency values higher than the state-of-the-art thermoelectric modules.

Experimental generation of optical coherence lattices

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

Chen, Yahong; Cai, Yangjian, E-mail: serpo@dal.ca, E-mail: yangjiancai@suda.edu.cn; Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province and Key Lab of Modern Optical Technologies of Education Ministry of China, Soochow University, Suzhou 215006

2016-08-08

We report experimental generation and measurement of recently introduced optical coherence lattices. The presented optical coherence lattice realization technique hinges on a superposition of mutually uncorrelated partially coherent Schell-model beams with tailored coherence properties. We show theoretically that information can be encoded into and, in principle, recovered from the lattice degree of coherence. Our results can find applications to image transmission and optical encryption.

Disorganizing experiences in second- and third-generation holocaust survivors.

PubMed

Scharf, Miri; Mayseless, Ofra

2011-11-01

Second-generation Holocaust survivors might not show direct symptoms of posttraumatic stress disorder or attachment disorganization, but are at risk for developing high levels of psychological distress. We present themes of difficult experiences of second-generation Holocaust survivors, arguing that some of these aversive experiences might have disorganizing qualities even though they do not qualify as traumatic. Based on in-depth interviews with 196 second-generation parents and their adolescent children, three themes of disorganizing experiences carried across generations were identified: focus on survival issues, lack of emotional resources, and coercion to please the parents and satisfy their needs. These themes reflect the frustration of three basic needs: competence, relatedness, and autonomy, and this frustration becomes disorganizing when it involves stability, potency, incomprehensibility, and helplessness. The findings shed light on the effect of trauma over the generations and, as such, equip therapists with a greater understanding of the mechanisms involved.

Electrical power generation by mechanically modulating electrical double layers.

PubMed

Moon, Jong Kyun; Jeong, Jaeki; Lee, Dongyun; Pak, Hyuk Kyu

2013-01-01

Since Michael Faraday and Joseph Henry made their great discovery of electromagnetic induction, there have been continuous developments in electrical power generation. Most people today get electricity from thermal, hydroelectric, or nuclear power generation systems, which use this electromagnetic induction phenomenon. Here we propose a new method for electrical power generation, without using electromagnetic induction, by mechanically modulating the electrical double layers at the interfacial areas of a water bridge between two conducting plates. We find that when the height of the water bridge is mechanically modulated, the electrical double layer capacitors formed on the two interfacial areas are continuously charged and discharged at different phases from each other, thus generating an AC electric current across the plates. We use a resistor-capacitor circuit model to explain the results of this experiment. This observation could be useful for constructing a micro-fluidic power generation system in the near future.

Assessment of Indoor Route-finding Technology for People with Visual Impairment

PubMed Central

Kalia, Amy A.; Legge, Gordon E.; Roy, Rudrava; Ogale, Advait

2010-01-01

This study investigated navigation with route instructions generated by digital-map software and synthetic speech. Participants, either visually impaired or sighted wearing blind folds, successfully located rooms in an unfamiliar building. Users with visual impairment demonstrated better route-finding performance when the technology provided distance information in number of steps rather than walking time or number of feet. PMID:21869851

A computer method of finding valuations forcing validity of LC formulae

NASA Astrophysics Data System (ADS)

Godlewski, Łukasz; Świetorzecka, Kordula; Mulawka, Jan

2014-11-01

The purpose of this paper is to present the computer implementation of a system known as LC temporal logic [1]. Firstly, to become familiar with some theoretical issues, a short introduction to this logic is discussed. The algorithms allowing a deep analysis of the formulae of LC logic are considered. In particular we discuss how to determine if a formula is a tautology, contrtautology or it is satisfable. Next, we show how to find all valuations to satisfy the formula. Finally, we consider finding histories generated by the formula and transforming these histories into the state machine. Moreover, a description of the experiments that verify the implementation are briefly presented.

Direct mass limits for chiral fourth-generation quarks in all mixing scenarios.

PubMed

Flacco, Christian J; Whiteson, Daniel; Tait, Tim M P; Bar-Shalom, Shaouly

2010-09-10

Present limits on chiral fourth-generation quark masses mb' and mt' are broadly generalized and strengthened by combining both t' and b' decays and considering a full range of t' and b' flavor-mixing scenarios with the lighter generations (to 1-‖V44‖2≈10(-13)). Various characteristic mass-splitting choices are considered. With mt'>mb' we find that CDF Collaboration limits on the b' mass vary by no more than 10%-20% with any choice of flavor mixing, while for the t' mass, we typically find stronger bounds, in some cases up to mt'>430  GeV. For mb'>mt', we find mb'>380-430  GeV, depending on the flavor mixing and the size of the mt'-mb' mass splitting.

Sharing Patient-Generated Data in Clinical Practices: An Interview Study.

PubMed

Zhu, Haining; Colgan, Joanna; Reddy, Madhu; Choe, Eun Kyoung

2016-01-01

Patients are tracking and generating an increasingly large volume of personal health data outside the clinic due to an explosion of wearable sensing and mobile health (mHealth) apps. The potential usefulness of these data is enormous as they can provide good measures of everyday behavior and lifestyle. However, how we can fully leverage patient-generated data (PGD) and integrate them in clinical practice is less clear. In this interview study, we aim to understand how patients and clinicians currently share patient-generated data in clinical care practice. From the study, we identified technical, social, and organizational challenges in sharing and fully leveraging patient-generated data in clinical practices. Our findings can provide researchers potential avenues for enablers and barriers in sharing patient-generated data in clinical settings.

Comprehension and Generation of Metaphoric Language in Children, Adolescents, and Adults with Dyslexia.

PubMed

Kasirer, Anat; Mashal, Nira

2017-05-01

Difficulties with figurative language comprehension were documented in adult dyslexia (DYS). In the present research, we investigated the comprehension and generation of metaphors in 37 children, 35 adolescents, and 34 adults with and without DYS. We also tested the contribution of executive function to metaphor processing. A multiple-choice questionnaire with conventional and novel metaphors was used to assess comprehension; a concept-explanation task was used to test conventional and novel metaphor generation (verbal creativity). The findings indicated differences between the dyslexic children and the control group in conventional metaphor comprehension. However, both groups performed similarly in the novel metaphor comprehension test. Furthermore, although children and adolescents with DYS showed similar performance in metaphor generation as their typically developing peers, adults with DYS generated more metaphors than controls. While scores on tests of verbal knowledge and mental flexibility contributed to the prediction of conventional metaphor comprehension, scores on non-verbal tests and mental flexibility contributed to the prediction of novel metaphor generation. Our findings suggest that individuals with DYS are not impaired in novel metaphor comprehension and metaphor generation and that metaphor comprehension and generation utilize different cognitive resources. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Profile of students’ generated representations and creative thinking skill in problem solving in vocational school

NASA Astrophysics Data System (ADS)

Fikri, P. M.; Sinaga, P.; Hasanah, L.; Solehat, D.

2018-05-01

This study aims to determine profile of students’ generated representations and creative thinking skill on problem solving in vocational school. This research is a descriptive research to get an idea of comprehend students’ generated representations and creative thinking skill on problem solving of vocational school in Bandung. Technique of collecting data is done by test method, observation, and interview. Representation is something that represents, describes or symbolizes an object or process. To evaluate the multi-representation skill used essay test with rubric of scoring was used to assess multi-depressant student skills. While creative thinking skill on problem solving used essay test which contains the components of skills in finding facts, problem finding skills, idea finding skills and solution finding skills. The results showed generated representations is still relatively low, this is proven by average student answers explanation is mathematically correct but there is no explanation verbally or graphically. While creative thinking skill on problem solving is still relatively low, this is proven by average score for skill indicator in finding the student problem is 1.52 including the non-creative category, average score for the skill indicator in finding the student idea is 1.23 including the non-creative category, and the average score of the students skill in finding this solution is 0.72 belongs to a very uncreative category.

How Visuo-Spatial Mental Imagery Develops: Image Generation and Maintenance

PubMed Central

Wimmer, Marina C.; Maras, Katie L.; Robinson, Elizabeth J; Doherty, Martin J; Pugeault, Nicolas

2015-01-01

Two experiments examined the nature of visuo-spatial mental imagery generation and maintenance in 4-, 6-, 8-, 10-year old children and adults (N = 211). The key questions were how image generation and maintenance develop (Experiment 1) and how accurately children and adults coordinate mental and visually perceived images (Experiment 2). Experiment 1 indicated that basic image generation and maintenance abilities are present at 4 years of age but the precision with which images are generated and maintained improves particularly between 4 and 8 years. In addition to increased precision, Experiment 2 demonstrated that generated and maintained mental images become increasingly similar to visually perceived objects. Altogether, findings suggest that for simple tasks demanding image generation and maintenance, children attain adult-like precision younger than previously reported. This research also sheds new light on the ability to coordinate mental images with visual images in children and adults. PMID:26562296

Mining a clinical data warehouse to discover disease-finding associations using co-occurrence statistics

PubMed Central

Cao, Hui; Markatou, Marianthi; Melton, Genevieve B.; Chiang, Michael F.; Hripcsak, George

2005-01-01

This paper applies co-occurrence statistics to discover disease-finding associations in a clinical data warehouse. We used two methods, χ2 statistics and the proportion confidence interval (PCI) method, to measure the dependence of pairs of diseases and findings, and then used heuristic cutoff values for association selection. An intrinsic evaluation showed that 94 percent of disease-finding associations obtained by χ2 statistics and 76.8 percent obtained by the PCI method were true associations. The selected associations were used to construct knowledge bases of disease-finding relations (KB-χ2, KB-PCI). An extrinsic evaluation showed that both KB-χ2 and KB-PCI could assist in eliminating clinically non-informative and redundant findings from problem lists generated by our automated problem list summarization system. PMID:16779011

Mining a clinical data warehouse to discover disease-finding associations using co-occurrence statistics.

PubMed

Cao, Hui; Markatou, Marianthi; Melton, Genevieve B; Chiang, Michael F; Hripcsak, George

2005-01-01

This paper applies co-occurrence statistics to discover disease-finding associations in a clinical data warehouse. We used two methods, chi2 statistics and the proportion confidence interval (PCI) method, to measure the dependence of pairs of diseases and findings, and then used heuristic cutoff values for association selection. An intrinsic evaluation showed that 94 percent of disease-finding associations obtained by chi2 statistics and 76.8 percent obtained by the PCI method were true associations. The selected associations were used to construct knowledge bases of disease-finding relations (KB-chi2, KB-PCI). An extrinsic evaluation showed that both KB-chi2 and KB-PCI could assist in eliminating clinically non-informative and redundant findings from problem lists generated by our automated problem list summarization system.

Transgenerational effects of childhood conditions on third generation health and education outcomes.

PubMed

van den Berg, Gerard J; Pinger, Pia R

2016-12-01

This paper examines the extent to which pre-puberty nutritional conditions in one generation affect productivity-related outcomes in later generations. Recent findings from the biological literature suggest that the so-called slow growth period around age 9 is a sensitive period for male germ cell development. We build on this evidence and investigate whether undernutrition at those ages transmits to children and grandchildren. Our findings indicate that third generation males (females) tend to have higher mental health scores if their paternal grandfather (maternal grandmother) was exposed to a famine during the slow growth period. These effects appear to reflect biological responses to adaptive expectations about scarcity in the environment, and as such they can be seen as an economic correctional mechanism in evolution, with marked socio-economic implications for the offspring. Copyright © 2016 Elsevier B.V. All rights reserved.

Does changing from a first generation antipsychotic (perphenazin) to a second generation antipsychotic (risperidone) alter brain activation and motor activity? A case report

PubMed Central

2013-01-01

Background In patients with schizophrenia, altered brain activation and motor activity levels are central features, reflecting cognitive impairments and negative symptoms, respectively. Newer studies using nonlinear methods have addressed the severe disturbances in neurocognitive functioning that is regarded as one of the core features of schizophrenia. Our aim was to compare brain activation and motor activity in a patient during pharmacological treatment that was switched from a first- to a second-generation antipsychotic drug. We hypothesised that this change of medication would increase level of responding in both measures. Case presentation We present the case of a 53-year-old male with onset of severe mental illness in adolescence, ICD-10 diagnosed as schizophrenia of paranoid type, chronic form. We compared brain activation and motor activity in this patient during pharmacological treatment with a first-generation (perphenazin), and later switched to a second-generation (risperidone) antipsychotic drug. We used functional magnetic resonance imaging (fMRI) to measure brain activation and wrist worn actigraphy to measure motor activity. Conclusion Our study showed that brain activation decreased in areas critical for cognitive functioning in this patient, when changing from a first to a second generation antipsychotic drug. However the mean motor activity level was unchanged, although risperidone reduced variability, particularly short-term variability from minute to minute. Compared to the results from previous studies, the present findings indicate that changing to a second-generation antipsychotic alters variability measures towards that seen in a control group, but with reduced brain activation, which was an unexpected finding. PMID:23648137

Does changing from a first generation antipsychotic (perphenazin) to a second generation antipsychotic (risperidone) alter brain activation and motor activity? A case report.

PubMed

Berle, Jan Øystein; Løberg, Else-Marie; Fasmer, Ole Bernt

2013-05-06

In patients with schizophrenia, altered brain activation and motor activity levels are central features, reflecting cognitive impairments and negative symptoms, respectively. Newer studies using nonlinear methods have addressed the severe disturbances in neurocognitive functioning that is regarded as one of the core features of schizophrenia. Our aim was to compare brain activation and motor activity in a patient during pharmacological treatment that was switched from a first- to a second-generation antipsychotic drug. We hypothesised that this change of medication would increase level of responding in both measures. We present the case of a 53-year-old male with onset of severe mental illness in adolescence, ICD-10 diagnosed as schizophrenia of paranoid type, chronic form. We compared brain activation and motor activity in this patient during pharmacological treatment with a first-generation (perphenazin), and later switched to a second-generation (risperidone) antipsychotic drug. We used functional magnetic resonance imaging (fMRI) to measure brain activation and wrist worn actigraphy to measure motor activity. Our study showed that brain activation decreased in areas critical for cognitive functioning in this patient, when changing from a first to a second generation antipsychotic drug. However the mean motor activity level was unchanged, although risperidone reduced variability, particularly short-term variability from minute to minute. Compared to the results from previous studies, the present findings indicate that changing to a second-generation antipsychotic alters variability measures towards that seen in a control group, but with reduced brain activation, which was an unexpected finding.

Understanding variations in secondary findings reporting practices across U.S. genome sequencing laboratories.

PubMed

Ackerman, Sara L; Koenig, Barbara A

2018-01-01

Increasingly used for clinical purposes, genome and exome sequencing can generate clinically relevant information that is not directly related to the reason for testing (incidental or secondary findings). Debates about the ethical implications of secondary findings were sparked by the American College of Medical Genetics (ACMG) 2013 policy statement, which recommended that laboratories report pathogenic alterations in 56 genes. Although wide variation in laboratories' secondary findings policies has been reported, little is known about its causes. We interviewed 18 laboratory directors and genetic counselors at 10 U.S. laboratories to investigate the motivations and interests shaping secondary findings reporting policies for clinical exome sequencing. Analysis of interview transcripts and laboratory documents was informed by sociological theories of standardization. Laboratories varied widely in terms of the types of secondary findings reported, consent-form language, and choices offered to patients. In explaining their adaptation of the ACMG report, our participants weighed genetic information's clinical, moral, professional, and commercial value in an attempt to maximize benefits for patients and families, minimize the costs of sequencing and analysis, adhere to professional norms, attract customers, and contend with the uncertain clinical implications of much of the genetic information generated. Nearly all laboratories in our study voluntarily adopted ACMG's recommendations, but their actual practices varied considerably and were informed by laboratory-specific judgments about clinical utility and patient benefit. Our findings offer a compelling example of standardization as a complex process that rarely leads simply to uniformity of practice. As laboratories take on a more prominent role in decisions about the return of genetic information, strategies are needed to inform patients, families, and clinicians about the differences between laboratories' practices

Solar thermoelectric generators

NASA Technical Reports Server (NTRS)

1977-01-01

The methods, the findings and the conclusions of a study for the design of a Solar Thermoelectric Generator (STG) intended for use as a power source for a spacecraft orbiting the planet Mercury are discussed. Several state-of-the-art thermoelectric technologies in the intended application were considered. The design of various STG configurations based on the thermoelectric technology selected from among the various technologies was examined in detail and a recommended STG design was derived. The performance characteristics of the selected STG technology and associated design were studied in detail as a function of the orbital characteristics of the STG in Mercury and throughout the orbit of Mercury around the sun.

The Korean American Family: Assimilation and Its Toll on the First and Second Generation Relationship.

ERIC Educational Resources Information Center

Hong, Joann J.; Hong, Steve

Over the last 15 years researchers have taken an increased interest in studying the large pool of recent Korean immigrants. This analysis concentrates on finding how first generation Korean Americans relate and interact with their second generation counterparts. Using studies on the adjustment of first generation Korean immigrants and the levels…

An algebra for spatio-temporal information generation

NASA Astrophysics Data System (ADS)

Pebesma, Edzer; Scheider, Simon; Gräler, Benedikt; Stasch, Christoph; Hinz, Matthias

2016-04-01

When we accept the premises of James Frew's laws of metadata (Frew's first law: scientists don't write metadata; Frew's second law: any scientist can be forced to write bad metadata), but also assume that scientists try to maximise the impact of their research findings, can we develop our information infrastructures such that useful metadata is generated automatically? Currently, sharing of data and software to completely reproduce research findings is becoming standard, e.g. in the Journal of Statistical Software [1]. The reproduction (e.g. R) scripts however convey correct syntax, but still limited semantics. We propose [2] a new, platform-neutral way to algebraically describe how data is generated, e.g. by observation, and how data is derived, e.g. by processing observations. It starts with forming functions composed of four reference system types (space, time, quality, entity), which express for instance continuity of objects over time, and continuity of fields over space and time. Data, which is discrete by definition, is generated by evaluating such functions at discrete space and time instances, or by evaluating a convolution (aggregation) over them. Derived data is obtained by inputting data to data derivation functions, which for instance interpolate, estimate, aggregate, or convert fields into objects and vice versa. As opposed to the traditional when, where and what semantics of data sets, our algebra focuses on describing how a data set was generated. We argue that it can be used to discover data sets that were derived from a particular source x, or derived by a particular procedure y. It may also form the basis for inferring meaningfulness of derivation procedures [3]. Current research focuses on automatically generating provenance documentation from R scripts. [1] http://www.jstatsoft.org/ (open access) [2] http://www.meaningfulspatialstatistics.org has the full paper (in review) [3] Stasch, C., S. Scheider, E. Pebesma, W. Kuhn, 2014. Meaningful

Dynamics of myosin-driven skeletal muscle contraction: I. Steady-state force generation.

PubMed

Lan, Ganhui; Sun, Sean X

2005-06-01

Skeletal muscle contraction is a canonical example of motor-driven force generation. Despite the long history of research in this topic, a mechanistic explanation of the collective myosin force generation is lacking. We present a theoretical model of muscle contraction based on the conformational movements of individual myosins and experimentally measured chemical rate constants. Detailed mechanics of the myosin motor and the geometry of the sarcomere are taken into account. Two possible scenarios of force generation are examined. We find only one of the scenarios can give rise to a plausible contraction mechanism. We propose that the synchrony in muscle contraction is due to a force-dependent ADP release step. Computational results of a half sarcomere with 150 myosin heads can explain the experimentally measured force-velocity relationship and efficiency data. We predict that the number of working myosin motors increases as the load force is increased, thus showing synchrony among myosin motors during muscle contraction. We also find that titin molecules anchoring the thick filament are passive force generators in assisting muscle contraction.

Dynamics of Myosin-Driven Skeletal Muscle Contraction: I. Steady-State Force Generation

PubMed Central

Lan, Ganhui; Sun, Sean X.

2005-01-01

Skeletal muscle contraction is a canonical example of motor-driven force generation. Despite the long history of research in this topic, a mechanistic explanation of the collective myosin force generation is lacking. We present a theoretical model of muscle contraction based on the conformational movements of individual myosins and experimentally measured chemical rate constants. Detailed mechanics of the myosin motor and the geometry of the sarcomere are taken into account. Two possible scenarios of force generation are examined. We find only one of the scenarios can give rise to a plausible contraction mechanism. We propose that the synchrony in muscle contraction is due to a force-dependent ADP release step. Computational results of a half sarcomere with 150 myosin heads can explain the experimentally measured force-velocity relationship and efficiency data. We predict that the number of working myosin motors increases as the load force is increased, thus showing synchrony among myosin motors during muscle contraction. We also find that titin molecules anchoring the thick filament are passive force generators in assisting muscle contraction. PMID:15778440

Photocurrent generation in a metallic transition-metal dichalcogenide

NASA Astrophysics Data System (ADS)

Mehmood, Naveed; Rasouli, Hamid Reza; ćakıroǧlu, Onur; Kasırga, T. Serkan

2018-05-01

Photocurrent generation is unexpected in metallic 2D layered materials unless a photothermal mechanism is prevalent. Yet, typical high thermal conductivity and low absorption of the visible spectrum prevent photothermal current generation in metals. Here, we report photoresponse from two-terminal devices of mechanically exfoliated metallic 3R-Nb S2 thin crystals using scanning photocurrent microscopy (SPCM) both at zero and finite bias. SPCM measurements reveal that the photocurrent predominantly emerges from metal/Nb S2 junctions of the two-terminal device at zero bias. At finite biases, along with the photocurrent generated at metal/Nb S2 junctions, now a negative photoresponse from all over the Nb S2 crystal is evident. Among our results, we realized that the observed photocurrent can be explained by the local heating caused by the laser excitation. These findings show that Nb S2 is among a few metallic materials in which photocurrent generation is possible.

Thermoelectric Generation Of Current - Theoretical And Experimental Analysis

NASA Astrophysics Data System (ADS)

Ruciński, Adam; Rusowicz, Artur

2017-12-01

This paper provides some information about thermoelectric technology. Some new materials with improved figures of merit are presented. These materials in Peltier modules make it possible to generate electric current thanks to a temperature difference. The paper indicates possible applications of thermoelectric modules as interesting tools for using various waste heat sources. Some zero-dimensional equations describing the conditions of electric power generation are given. Also, operating parameters of Peltier modules, such as voltage and electric current, are analyzed. The paper shows chosen characteristics of power generation parameters. Then, an experimental stand for ongoing research and experimental measurements are described. The authors consider the resistance of a receiver placed in the electric circuit with thermoelectric elements. Finally, both the analysis of experimental results and conclusions drawn from theoretical findings are presented. Voltage generation of about 1.5 to 2.5 V for the temperature difference from 65 to 85 K was observed when a bismuth telluride thermoelectric couple (traditionally used in cooling technology) was used.

Anatomy education for the YouTube generation.

PubMed

Barry, Denis S; Marzouk, Fadi; Chulak-Oglu, Kyrylo; Bennett, Deirdre; Tierney, Paul; O'Keeffe, Gerard W

2016-01-01

Anatomy remains a cornerstone of medical education despite challenges that have seen a significant reduction in contact hours over recent decades; however, the rise of the "YouTube Generation" or "Generation Connected" (Gen C), offers new possibilities for anatomy education. Gen C, which consists of 80% Millennials, actively interact with social media and integrate it into their education experience. Most are willing to merge their online presence with their degree programs by engaging with course materials and sharing their knowledge freely using these platforms. This integration of social media into undergraduate learning, and the attitudes and mindset of Gen C, who routinely creates and publishes blogs, podcasts, and videos online, has changed traditional learning approaches and the student/teacher relationship. To gauge this, second year undergraduate medical and radiation therapy students (n = 73) were surveyed regarding their use of online social media in relation to anatomy learning. The vast majority of students had employed web-based platforms to source information with 78% using YouTube as their primary source of anatomy-related video clips. These findings suggest that the academic anatomy community may find value in the integration of social media into blended learning approaches in anatomy programs. This will ensure continued connection with the YouTube generation of students while also allowing for academic and ethical oversight regarding the use of online video clips whose provenance may not otherwise be known. © 2015 American Association of Anatomists.

A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics.

PubMed

Feng, Lihui; Rutherford, Steven T; Papenfort, Kai; Bagert, John D; van Kessel, Julia C; Tirrell, David A; Wingreen, Ned S; Bassler, Bonnie L

2015-01-15

Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA. We show that a representative Qrr, Qrr3, uses four distinct mechanisms to control its particular targets: the Qrr3 sRNA represses luxR through catalytic degradation, represses luxM through coupled degradation, represses luxO through sequestration, and activates aphA by revealing the ribosome binding site while the sRNA itself is degraded. Qrr3 forms different base-pairing interactions with each mRNA target, and the particular pairing strategy determines which regulatory mechanism occurs. Combined mathematical modeling and experiments show that the specific Qrr regulatory mechanism employed governs the potency, dynamics, and competition of target mRNA regulation, which in turn, defines the overall quorum-sensing response. Copyright © 2015 Elsevier Inc. All rights reserved.

Methods of automatic nucleotide-sequence analysis. Multicomponent spectrophotometric analysis of mixtures of nucleic acid components by a least-squares procedure

PubMed Central

Lee, Sheila; McMullen, D.; Brown, G. L.; Stokes, A. R.

1965-01-01

1. A theoretical analysis of the errors in multicomponent spectrophotometric analysis of nucleoside mixtures, by a least-squares procedure, has been made to obtain an expression for the error coefficient, relating the error in calculated concentration to the error in extinction measurements. 2. The error coefficients, which depend only on the `library' of spectra used to fit the experimental curves, have been computed for a number of `libraries' containing the following nucleosides found in s-RNA: adenosine, guanosine, cytidine, uridine, 5-ribosyluracil, 7-methylguanosine, 6-dimethylaminopurine riboside, 6-methylaminopurine riboside and thymine riboside. 3. The error coefficients have been used to determine the best conditions for maximum accuracy in the determination of the compositions of nucleoside mixtures. 4. Experimental determinations of the compositions of nucleoside mixtures have been made and the errors found to be consistent with those predicted by the theoretical analysis. 5. It has been demonstrated that, with certain precautions, the multicomponent spectrophotometric method described is suitable as a basis for automatic nucleotide-composition analysis of oligonucleotides containing nine nucleotides. Used in conjunction with continuous chromatography and flow chemical techniques, this method can be applied to the study of the sequence of s-RNA. PMID:14346087

Characterization of ribonuclease III from Brucella.

PubMed

Wu, Chang-Xian; Xu, Xian-Jin; Zheng, Ke; Liu, Fang; Yang, Xu-Dong; Chen, Chuang-Fu; Chen, Huan-Chun; Liu, Zheng-Fei

2016-04-01

Bacterial ribonuclease III (RNase III) is a highly conserved endonuclease, which plays pivotal roles in RNA maturation and decay pathways by cleaving double-stranded structure of RNAs. Here we cloned rncS gene from the genomic DNA of Brucella melitensis, and analyzed the cleavage properties of RNase III from Brucella. We identified Brucella-encoding small RNA (sRNA) by high-throughput sequencing and northern blot, and found that sRNA of Brucella and Homo miRNA precursor (pre-miRNA) can be bound and cleaved by B.melitensis ribonuclease III (Bm-RNase III). Cleavage activity of Bm-RNase III is bivalent metal cations- and alkaline buffer-dependent. We constructed several point mutations in Bm-RNase III, whose cleavage activity indicated that the 133th Glutamic acid residue was required for catalytic activity. Western blot revealed that Bm-RNase III was differently expressed in Brucella virulence strain 027 and vaccine strain M5-90. Collectively, our data suggest that Brucella RNase III can efficiently bind and cleave stem-loop structure of small RNA, and might participate in regulation of virulence in Brucella. Copyright © 2016 Elsevier B.V. All rights reserved.

The RNA methyltransferase Dnmt2 is required for efficient Dicer-2-dependent siRNA pathway activity in Drosophila.

PubMed

Durdevic, Zeljko; Mobin, Mehrpouya Balaghy; Hanna, Katharina; Lyko, Frank; Schaefer, Matthias

2013-09-12

Transfer RNA (tRNA) fragmentation in response to stress conditions has been described in many organisms. tRNA fragments have been found in association with small interfering RNA (siRNA) components, but the biological role of these interactions remains unclear. We report here that the tRNA methyltransferase Dnmt2 is essential for efficient Dicer-2 (Dcr-2) function in Drosophila. Using small RNA (sRNA) sequencing, we confirmed that Dnmt2 limits the extent of tRNA fragmentation during the heat-shock response. tRNAs as well as tRNA fragments serve as Dcr-2 substrates, and Dcr-2 degrades tRNA-derived sequences, especially under heat-shock conditions. tRNA-derived RNAs are able to inhibit Dcr-2 activity on long double-stranded RNAs (dsRNAs). Consequently, heat-shocked Dnmt2 mutant animals accumulate dsRNAs, produce fewer siRNAs, and show misregulation of siRNA pathway-dependent genes. These results reveal the impact of tRNA fragmentation on siRNA pathways and implicate tRNA modifications in the regulation of sRNA homeostasis during the heat-shock response. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes

PubMed Central

Yu, Dongliang; Meng, Yijun; Zuo, Ziwei; Xue, Jie; Wang, Huizhong

2016-01-01

Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip. PMID:26858106

Trans-generational desensitization and within-generational resensitization of a sucrose-best neuron in the polyphagous herbivore Helicoverpa armigera (Lepidoptera: Noctuidae)

PubMed Central

Ma, Ying; Li, Jingjing; Tang, Qingbo; Zhang, Xuening; Zhao, Xincheng; Yan, Fengming; van Loon, Joop J. A.

2016-01-01

Dietary exposure of insects to a feeding deterrent substance for hours to days can induce habituation and concomitant desensitization of the response of peripheral gustatory neurons to such a substance. In the present study, larvae of the herbivore Helicoverpa armigera were fed on diets containing either a high, medium or low concentration of sucrose, a major feeding stimulant. The responsiveness of the sucrose-best neuron in the lateral sensilla styloconica on the galea was quantified. Results showed the response of the sucrose-best neuron exposed to high-sucrose diets decreased gradually over successive generations, resulting in complete desensitization in the 5th and subsequent generations. However, the sensitivity was completely restored in the ninth generation after neonate larvae were exposed to low-sucrose diet. These findings demonstrate phenotypic plasticity and exclude inadvertent artificial selection for low sensitivity to sucrose. No significant changes were found in the sensitivity of caterpillars which experienced low- or medium-sucrose diets over the same generations. Such desensitization versus re-sensitization did not generalise to the phagosimulant myo-inositol-sensitive neuron or the feeding deterrent-sensitive neuron. Our results demonstrate that under conditions of high sucrose availability trans-generational desensitization of a neuron sensitive to this feeding stimulant becomes more pronounced whereas re-sensitization occurs within one generation. PMID:27966640

Overexpression of MicA induces production of OmpC-enriched outer membrane vesicles that protect against Salmonella challenge.

PubMed

Choi, Hyun-Il; Kim, Moonjeong; Jeon, Jinseong; Han, Jin Kwan; Kim, Kwang-Sun

2017-08-26

Outer membrane vesicles (OMVs) derived from bacteria are promising candidates for subunit vaccines. Stresses that modulate the composition of outer membrane proteins (OMPs) are important for OMV synthesis. Small RNAs (sRNAs) expressed in response to stress regulate OMPs, although the mechanism underlying sRNA-mediated OMV biogenesis and its utility for developing vaccine platforms remains to be elucidated. Here, we characterized the role of a sRNA, MicA, which regulates OmpA, a major OMP involved in both production of OMVs and reactive immunity against Salmonella challenge. A Salmonella strain overexpressing MicA generated more OMVs than a control strain. In addition, OmpC was the major component of MicA-derived OMV proteins. MicA-derived OMVs induced Th1- and Th17-type immune responses in vitro and reduced Salmonella-mediated lethality in a mouse model. Thus, OmpA-regulatory sRNA-derived OMVs may facilitate production of Salmonella-protective vaccines. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification and bioinformatics analysis of microRNAs from the sporophyte and gametophyte of Pyropia haitanensis

NASA Astrophysics Data System (ADS)

Huang, Aiyou; Wang, Guangce

2016-05-01

Pyropia haitanensis (T. J. Chang et B. F. Zheng) N. Kikuchi et M. Miyata ( Porphyra haitanensis) is an economically important genus that is cultured widely in China. P. haitanensis is cultured on a larger scale than Pyropia yezoensis, making up an important part of the total production of cultivated Pyropia in China. However, the majority of molecular mechanisms underlying the physiological processes of P. haitanensis remain unknown. P. haitanensis could utilize inorganic carbon and the sporophytes of P. haitanensis might possess a PCK-type C4-like carbon-fixation pathway. To identify microRNAs and their probable roles in sporophyte and gametophyte development, we constructed and sequenced small RNA libraries from sporophytes and gametophytes of P. haitanensis. Five microRNAs were identified that shared no sequence homology with known microRNAs. Our results indicated that P. haitanensis might posses a complex sRNA processing system in which the novel microRNAs act as important regulators of the development of different generations of P. haitanensis.

Assessing Adolescents' Communicative Self-Efficacy to Discuss Controversial Issues: Findings from a Randomized Study of the Word Generation Program

ERIC Educational Resources Information Center

Lin, Alex R.; Lawrence, Joshua F.; Snow, Catherine E.; Taylor, Karen S.

2016-01-01

Communicative self-efficacy serves as an important link between discussing controversial issues and civic engagement because confidence in one's discourse skills is important to managing conflicting perspectives and developing solutions to community-based problems. Freely available to schools, "Word Generation" is a cross-content…

A novel sub-shot segmentation method for user-generated video

NASA Astrophysics Data System (ADS)

Lei, Zhuo; Zhang, Qian; Zheng, Chi; Qiu, Guoping

2018-04-01

With the proliferation of the user-generated videos, temporal segmentation is becoming a challengeable problem. Traditional video temporal segmentation methods like shot detection are not able to work on unedited user-generated videos, since they often only contain one single long shot. We propose a novel temporal segmentation framework for user-generated video. It finds similar frames with a tree partitioning min-Hash technique, constructs sparse temporal constrained affinity sub-graphs, and finally divides the video into sub-shot-level segments with a dense-neighbor-based clustering method. Experimental results show that our approach outperforms all the other related works. Furthermore, it is indicated that the proposed approach is able to segment user-generated videos at an average human level.

Do-it-yourself networks: a novel method of generating weighted networks.

PubMed

Shanafelt, D W; Salau, K R; Baggio, J A

2017-11-01

Network theory is finding applications in the life and social sciences for ecology, epidemiology, finance and social-ecological systems. While there are methods to generate specific types of networks, the broad literature is focused on generating unweighted networks. In this paper, we present a framework for generating weighted networks that satisfy user-defined criteria. Each criterion hierarchically defines a feature of the network and, in doing so, complements existing algorithms in the literature. We use a general example of ecological species dispersal to illustrate the method and provide open-source code for academic purposes.

Actualizing the Seventh Generation Prophecy: A Case Study in Teacher Education at a Tribal College

ERIC Educational Resources Information Center

Azure, Lisa Benz

2016-01-01

The present generation of American Indian, college-aged young adults are by their own accord fulfilling the "prophecy of the Seventh Generation." According to this prophecy, after seven generations of living in close contact with Europeans, young tribal descendants who are growing up today will find ways to bring back their culture and…

Visual Thinking Styles and Idea Generation Strategies Employed in Visual Brainstorming Sessions

ERIC Educational Resources Information Center

Börekçi, Naz A. G. Z.

2017-01-01

This paper presents the findings of visual analyses conducted on 369 sketch ideas generated in three 6-3-5 visual brainstorming sessions by a total of 25 participants, following the same design brief. The motivation for the study was an interest in the thematic content of the ideas generated as groups, and the individual representation styles used…

Strong ground motions generated by earthquakes on creeping faults

USGS Publications Warehouse

Harris, Ruth A.; Abrahamson, Norman A.

2014-01-01

A tenet of earthquake science is that faults are locked in position until they abruptly slip during the sudden strain-relieving events that are earthquakes. Whereas it is expected that locked faults when they finally do slip will produce noticeable ground shaking, what is uncertain is how the ground shakes during earthquakes on creeping faults. Creeping faults are rare throughout much of the Earth's continental crust, but there is a group of them in the San Andreas fault system. Here we evaluate the strongest ground motions from the largest well-recorded earthquakes on creeping faults. We find that the peak ground motions generated by the creeping fault earthquakes are similar to the peak ground motions generated by earthquakes on locked faults. Our findings imply that buildings near creeping faults need to be designed to withstand the same level of shaking as those constructed near locked faults.

Expanding the histologic findings in smallpox-related post-vaccinial non-viral folliculitis.

PubMed

Bunick, Christopher G; Mariwalla, Kavita; Ibrahim, Omer; Modi, Badri; Imaeda, Suguru; McNiff, Jennifer M

2013-03-01

Post-vaccinial non-viral folliculitis has been recognized in the past decade as a new adverse cutaneous reaction to smallpox vaccination. Contrary to more serious smallpox vaccine reactions, post-vaccinial non-viral folliculitis has a benign course and resolves spontaneously within approximately 7 days. We describe additional histopathologic findings associated with post-vaccinial non-viral folliculitis, which has only been described once previously. New findings include the presence of a neutrophilic or lymphohistiocytic infiltrate that is concentrated around the hair follicles. We compare our findings to the follicular nature of varicella and herpes zoster infections, generating the hypothesis of deposition of vaccinia protein within folliculosebaceous units as a potential pathophysiologic mechanism behind post-vaccinial non-viral folliculitis. © 2012 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.

Clinical decision-making and secondary findings in systems medicine.

PubMed

Fischer, T; Brothers, K B; Erdmann, P; Langanke, M

2016-05-21

Systems medicine is the name for an assemblage of scientific strategies and practices that include bioinformatics approaches to human biology (especially systems biology); "big data" statistical analysis; and medical informatics tools. Whereas personalized and precision medicine involve similar analytical methods applied to genomic and medical record data, systems medicine draws on these as well as other sources of data. Given this distinction, the clinical translation of systems medicine poses a number of important ethical and epistemological challenges for researchers working to generate systems medicine knowledge and clinicians working to apply it. This article focuses on three key challenges: First, we will discuss the conflicts in decision-making that can arise when healthcare providers committed to principles of experimental medicine or evidence-based medicine encounter individualized recommendations derived from computer algorithms. We will explore in particular whether controlled experiments, such as comparative effectiveness trials, should mediate the translation of systems medicine, or if instead individualized findings generated through "big data" approaches can be applied directly in clinical decision-making. Second, we will examine the case of the Riyadh Intensive Care Program Mortality Prediction Algorithm, pejoratively referred to as the "death computer," to demonstrate the ethical challenges that can arise when big-data-driven scoring systems are applied in clinical contexts. We argue that the uncritical use of predictive clinical algorithms, including those envisioned for systems medicine, challenge basic understandings of the doctor-patient relationship. Third, we will build on the recent discourse on secondary findings in genomics and imaging to draw attention to the important implications of secondary findings derived from the joint analysis of data from diverse sources, including data recorded by patients in an attempt to realize their

Problem Generation in the Mission to Mars Curriculum.

ERIC Educational Resources Information Center

Czarnik, John C., Jr.; Hickey, Daniel T.

This paper will explore a problem finding task the authors developed as one component of the Mission to Mars curriculum, an inquiry-based science unit developed by Petrosino & The Cognition and Technology Group at Vanderbilt (CTGV). The paper also attempts to address evolving conceptions of the problem generation task, primarily from that of…

Electron dynamics in high energy density plasma bunch generation driven by intense picosecond laser pulse

NASA Astrophysics Data System (ADS)

Li, M.; Yuan, T.; Xu, Y. X.; Luo, S. N.

2018-05-01

When an intense picosecond laser pulse is loaded upon a dense plasma, a high energy density plasma bunch, including electron bunch and ion bunch, can be generated in the target. We simulate this process through one-dimensional particle-in-cell simulation and find that the electron bunch generation is mainly due to a local high energy density electron sphere originated in the plasma skin layer. Once generated the sphere rapidly expands to compress the surrounding electrons and induce high density electron layer, coupled with that, hot electrons are efficiently triggered in the local sphere and traveling in the whole target. Under the compressions of light pressure, forward-running and backward-running hot electrons, a high energy density electron bunch generates. The bunch energy density is as high as TJ/m3 order of magnitude in our conditions, which is significant in laser driven dynamic high pressure generation and may find applications in high energy density physics.

Instructional Methods for Human Anatomy and Cell Biology in Nurse Anesthesia Graduate Programs: A Survey with a Focus on Regional Anesthesia

DTIC Science & Technology

1997-09-01

undergraduate nursing students . They concluded that students who did well in this course tended to perform better in nursing school overall...curriculum for the medical student of the 21st century: Gross anatomy. Clinical Anatomy. 9 (2), 71-99. Fitzgerald, M.J.T. (1992). Undergraduate medical...Road, Bethesda, MD 20814-4799. Student Registered Nurse Anesthetist (SRNA). 1991 -1995 1 st Medical Group, Langley Air Force Base, Virginia

Instructional Methods for Human Anatomy and Cell Biology in Nurse Anesthesia Graduate Programs: A Survey With a Focus on Regional Anesthesia

DTIC Science & Technology

1997-07-14

and Wieland (1995) examined Anatomy and Physiology as a predictor of success in undergraduate nursing students . They concluded that students who did... Student Registered Nurse Anesthetist (SRNA). 1991 -1995 1 st Medical Group, Langley Air Force Base, Virginia. Clinical Nurse, Special Care Unit...anesthetic techniques in situ, and 3 (4%) of the programs afford the students the opportunity to practice regional anesthetic techniques on the specimens

A preliminary design for flight testing the FINDS algorithm

NASA Technical Reports Server (NTRS)

Caglayan, A. K.; Godiwala, P. M.

1986-01-01

This report presents a preliminary design for flight testing the FINDS (Fault Inferring Nonlinear Detection System) algorithm on a target flight computer. The FINDS software was ported onto the target flight computer by reducing the code size by 65%. Several modifications were made to the computational algorithms resulting in a near real-time execution speed. Finally, a new failure detection strategy was developed resulting in a significant improvement in the detection time performance. In particular, low level MLS, IMU and IAS sensor failures are detected instantaneously with the new detection strategy, while accelerometer and the rate gyro failures are detected within the minimum time allowed by the information generated in the sensor residuals based on the point mass equations of motion. All of the results have been demonstrated by using five minutes of sensor flight data for the NASA ATOPS B-737 aircraft in a Microwave Landing System (MLS) environment.

Experimental Study of Lift-Generated Vortices

NASA Technical Reports Server (NTRS)

Rossow, Vernon J.; Nixon, David (Technical Monitor)

1998-01-01

The flow fields of vortices, whether bouyancy-driven or lift-generated, are fascinating fluid-dynamic phenomena which often possess intense swirl velocities and complex time-dependent behavior. As part of the on-going study of vortex behavior, this paper presents a historical overview of the research conducted on the structure and modification of the vortices generated by the lifting surfaces of subsonic transport aircraft. It is pointed out that the characteristics of lift-generated vortices are related to the aerodynamic shapes that produce them and that various arrangements of surfaces can be used to produce different vortex structures. The primary purpose of the research to be described is to find a way to reduce the hazard potential of lift-generated vortices shed by subsonic transport aircraft in the vicinity of airports during landing and takeoff operations. It is stressed that lift-generated vortex wakes are so complex that progress towards a solution requires application of a combined theoretical and experimental research program because either alone often leads to incorrect conclusions. It is concluded that a satisfactory aerodynamic solution to the wake-vortex problem at airports has not yet been found but a reduction in the impact of the wake-vortex hazard on airport capacity may become available in the foreseeable future through wake-vortex avoidance concepts currently under study. The material to be presented in this overview is drawn from aerospace journals that are available publicly.

Deep Generative Models of Galaxy Images for the Calibration of the Next Generation of Weak Lensing Surveys

NASA Astrophysics Data System (ADS)

Lanusse, Francois; Ravanbakhsh, Siamak; Mandelbaum, Rachel; Schneider, Jeff; Poczos, Barnabas

2017-01-01

Weak gravitational lensing has long been identified as one of the most powerful probes to investigate the nature of dark energy. As such, weak lensing is at the heart of the next generation of cosmological surveys such as LSST, Euclid or WFIRST.One particularly crititcal source of systematic errors in these surveys comes from the shape measurement algorithms tasked with estimating galaxy shapes. GREAT3, the last community challenge to assess the quality of state-of-the-art shape measurement algorithms has in particular demonstrated that all current methods are biased to various degrees and, more importantly, that these biases depend on the details of the galaxy morphologies. These biases can be measured and calibrated by generating mock observations where a known lensing signal has been introduced and comparing the resulting measurements to the ground-truth. Producing these mock observations however requires input galaxy images of higher resolution and S/N than the simulated survey, which typically implies acquiring extremely expensive space-based observations.The goal of this work is to train a deep generative model on already available Hubble Space Telescope data which can then be used to sample new galaxy images conditioned on parameters such as magnitude, size or redshift and exhibiting complex morphologies. Such model can allow us to inexpensively produce large set of realistic realistic images for calibration purposes.We implement a conditional generative model based on state-of-the-art deep learning methods and fit it to deep galaxy images from the COSMOS survey. The quality of the model is assessed by computing an extensive set of galaxy morphology statistics on the generated images. Beyond simple second moment statistics such as size and ellipticity, we apply more complex statistics specifically designed to be sensitive to disturbed galaxy morphologies. We find excellent agreement between the morphologies of real and model generated galaxies.Our results

Exploring generational cohort work satisfaction in hospital nurses.

PubMed

Gordon, Pamela Ann

2017-07-03

Purpose Although extensive research exists regarding job satisfaction, many previous studies used a more restrictive, quantitative methodology. The purpose of this qualitative study is to capture the perceptions of hospital nurses within generational cohorts regarding their work satisfaction. Design/methodology/approach A preliminary qualitative, phenomenological study design explored hospital nurses' work satisfaction within generational cohorts - Baby Boomers (1946-1964), Generation X (1965-1980) and Millennials (1981-2000). A South Florida hospital provided the venue for the research. In all, 15 full-time staff nurses, segmented into generational cohorts, participated in personal interviews to determine themes related to seven established factors of work satisfaction: pay, autonomy, task requirements, administration, doctor-nurse relationship, interaction and professional status. Findings An analysis of the transcribed interviews confirmed the importance of the seven factors of job satisfaction. Similarities and differences between the generational cohorts related to a combination of stages of life and generational attributes. Practical implications The results of any qualitative research relate only to the specific venue studied and are not generalizable. However, the information gleaned from this study is transferable and other organizations are encouraged to conduct their own research and compare the results. Originality/value This study is unique, as the seven factors from an extensively used and highly respected quantitative research instrument were applied as the basis for this qualitative inquiry into generational cohort job satisfaction in a hospital setting.

Mathematical modeling to predict residential solid waste generation.

PubMed

Benítez, Sara Ojeda; Lozano-Olvera, Gabriela; Morelos, Raúl Adalberto; Vega, Carolina Armijo de

2008-01-01

One of the challenges faced by waste management authorities is determining the amount of waste generated by households in order to establish waste management systems, as well as trying to charge rates compatible with the principle applied worldwide, and design a fair payment system for households according to the amount of residential solid waste (RSW) they generate. The goal of this research work was to establish mathematical models that correlate the generation of RSW per capita to the following variables: education, income per household, and number of residents. This work was based on data from a study on generation, quantification and composition of residential waste in a Mexican city in three stages. In order to define prediction models, five variables were identified and included in the model. For each waste sampling stage a different mathematical model was developed, in order to find the model that showed the best linear relation to predict residential solid waste generation. Later on, models to explore the combination of included variables and select those which showed a higher R(2) were established. The tests applied were normality, multicolinearity and heteroskedasticity. Another model, formulated with four variables, was generated and the Durban-Watson test was applied to it. Finally, a general mathematical model is proposed to predict residential waste generation, which accounts for 51% of the total.

Modelling municipal solid waste generation: a review.

PubMed

Beigl, Peter; Lebersorger, Sandra; Salhofer, Stefan

2008-01-01

The objective of this paper is to review previously published models of municipal solid waste generation and to propose an implementation guideline which will provide a compromise between information gain and cost-efficient model development. The 45 modelling approaches identified in a systematic literature review aim at explaining or estimating the present or future waste generation using economic, socio-demographic or management-orientated data. A classification was developed in order to categorise these highly heterogeneous models according to the following criteria--the regional scale, the modelled waste streams, the hypothesised independent variables and the modelling method. A procedural practice guideline was derived from a discussion of the underlying models in order to propose beneficial design options concerning regional sampling (i.e., number and size of observed areas), waste stream definition and investigation, selection of independent variables and model validation procedures. The practical application of the findings was demonstrated with two case studies performed on different regional scales, i.e., on a household and on a city level. The findings of this review are finally summarised in the form of a relevance tree for methodology selection.

Trip generation characteristics of special generators

DOT National Transportation Integrated Search

2010-03-01

Special generators are introduced in the sequential four-step modeling procedure to represent certain types of facilities whose trip generation characteristics are not fully captured by the standard trip generation module. They are also used in the t...

Evaluating approaches to find exon chains based on long reads.

PubMed

Kuosmanen, Anna; Norri, Tuukka; Mäkinen, Veli

2018-05-01

Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions. We survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity/precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long-read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy. The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.

Biology Question Generation from a Semantic Network

NASA Astrophysics Data System (ADS)

Zhang, Lishan

Science instructors need questions for use in exams, homework assignments, class discussions, reviews, and other instructional activities. Textbooks never have enough questions, so instructors must find them from other sources or generate their own questions. In order to supply instructors with biology questions, a semantic network approach was developed for generating open response biology questions. The generated questions were compared to professional authorized questions. To boost students' learning experience, adaptive selection was built on the generated questions. Bayesian Knowledge Tracing was used as embedded assessment of the student's current competence so that a suitable question could be selected based on the student's previous performance. A between-subjects experiment with 42 participants was performed, where half of the participants studied with adaptive selected questions and the rest studied with mal-adaptive order of questions. Both groups significantly improved their test scores, and the participants in adaptive group registered larger learning gains than participants in the control group. To explore the possibility of generating rich instructional feedback for machine-generated questions, a question-paragraph mapping task was identified. Given a set of questions and a list of paragraphs for a textbook, the goal of the task was to map the related paragraphs to each question. An algorithm was developed whose performance was comparable to human annotators. A multiple-choice question with high quality distractors (incorrect answers) can be pedagogically valuable as well as being much easier to grade than open-response questions. Thus, an algorithm was developed to generate good distractors for multiple-choice questions. The machine-generated multiple-choice questions were compared to human-generated questions in terms of three measures: question difficulty, question discrimination and distractor usefulness. By recruiting 200 participants from

Concatenated shift registers generating maximally spaced phase shifts of PN-sequences

NASA Technical Reports Server (NTRS)

Hurd, W. J.; Welch, L. R.

1977-01-01

A large class of linearly concatenated shift registers is shown to generate approximately maximally spaced phase shifts of pn-sequences, for use in pseudorandom number generation. A constructive method is presented for finding members of this class, for almost all degrees for which primitive trinomials exist. The sequences which result are not normally characterized by trinomial recursions, which is desirable since trinomial sequences can have some undesirable randomness properties.

Reflection enhances creativity: Beneficial effects of idea evaluation on idea generation.

PubMed

Hao, Ning; Ku, Yixuan; Liu, Meigui; Hu, Yi; Bodner, Mark; Grabner, Roland H; Fink, Andreas

2016-03-01

The present study aimed to explore the neural correlates underlying the effects of idea evaluation on idea generation in creative thinking. Participants were required to generate original uses of conventional objects (alternative uses task) during EEG recording. A reflection task (mentally evaluating the generated ideas) or a distraction task (object characteristics task) was inserted into the course of idea generation. Behavioral results revealed that participants generated ideas with higher originality after evaluating the generated ideas than after performing the distraction task. The EEG results revealed that idea evaluation was accompanied with upper alpha (10-13 Hz) synchronization, most prominent at frontal cortical sites. Moreover, upper alpha activity in frontal cortices during idea generation was enhanced after idea evaluation. These findings indicate that idea evaluation may elicit a state of heightened internal attention or top-down activity that facilitates efficient retrieval and integration of internal memory representations. Copyright © 2016 Elsevier Inc. All rights reserved.

Developing the Persian version of the homophone meaning generation test

PubMed Central

Ebrahimipour, Mona; Motamed, Mohammad Reza; Ashayeri, Hassan; Modarresi, Yahya; Kamali, Mohammad

2016-01-01

Background: Finding the right word is a necessity in communication, and its evaluation has always been a challenging clinical issue, suggesting the need for valid and reliable measurements. The Homophone Meaning Generation Test (HMGT) can measure the ability to switch between verbal concepts, which is required in word retrieval. The purpose of this study was to adapt and validate the Persian version of the HMGT. Methods: The first phase involved the adaptation of the HMGT to the Persian language. The second phase concerned the psychometric testing. The word-finding performance was assessed in 90 Persian-speaking healthy individuals (20-50 year old; 45 males and 45 females) through three naming tasks: Semantic Fluency, Phonemic Fluency, and Homophone Meaning Generation Test. The participants had no history of neurological or psychiatric diseases, alcohol abuse, severe depression, or history of speech, language, or learning problems. Results: The internal consistency coefficient was larger than 0.8 for all the items with a total Cronbach’s alpha of 0.80. Interrater and intrarater reliability were also excellent. The validity of all items was above 0.77, and the content validity index (0.99) was appropriate. The Persian HMGT had strong convergent validity with semantic and phonemic switching and adequate divergent validity with semantic and phonemic clustering. Conclusion: The Persian version of the Homophone Meaning Generation Test is an appropriate, valid, and reliable test to evaluate the ability to switch between verbal concepts in the assessment of word-finding performance. PMID:27390705

Developing the Persian version of the homophone meaning generation test.

PubMed

Ebrahimipour, Mona; Motamed, Mohammad Reza; Ashayeri, Hassan; Modarresi, Yahya; Kamali, Mohammad

2016-01-01

Finding the right word is a necessity in communication, and its evaluation has always been a challenging clinical issue, suggesting the need for valid and reliable measurements. The Homophone Meaning Generation Test (HMGT) can measure the ability to switch between verbal concepts, which is required in word retrieval. The purpose of this study was to adapt and validate the Persian version of the HMGT. The first phase involved the adaptation of the HMGT to the Persian language. The second phase concerned the psychometric testing. The word-finding performance was assessed in 90 Persian-speaking healthy individuals (20-50 year old; 45 males and 45 females) through three naming tasks: Semantic Fluency, Phonemic Fluency, and Homophone Meaning Generation Test. The participants had no history of neurological or psychiatric diseases, alcohol abuse, severe depression, or history of speech, language, or learning problems. The internal consistency coefficient was larger than 0.8 for all the items with a total Cronbach's alpha of 0.80. Interrater and intrarater reliability were also excellent. The validity of all items was above 0.77, and the content validity index (0.99) was appropriate. The Persian HMGT had strong convergent validity with semantic and phonemic switching and adequate divergent validity with semantic and phonemic clustering. The Persian version of the Homophone Meaning Generation Test is an appropriate, valid, and reliable test to evaluate the ability to switch between verbal concepts in the assessment of word-finding performance.

Lessons learned in transit efficiencies, revenue generation and cost reductions

DOT National Transportation Integrated Search

1997-01-01

The purpose of this research project was to gather and redistribute information : on how transit agencies are finding ways to either generate new revenues or : reduce costs without harming the best interests of their passengers. This : research proje...

The Valence of Self-Generated (Status Updates) and Other-Generated (Wall-Posts) Information Determines Impression Formation on Facebook

PubMed Central

Rosenthal-Stott, Harriet E. S.; Dicks, Rea E.; Fielding, Lois S.

2015-01-01

We examined whether self-generated (status updates) or other-generated (wall-posts) information on Facebook influenced the impression formed of the target individual. Along with examining reliance on particular types of information, we explored the valence (positive/ neutral/ negative) of the information, as reliance on self-generated or other-generated information may depend on whether self-presentation is perceived (i.e., presenting oneself positively / not negatively). Self-presentation may be perceived if the targets have positive/ neutral statuses, while negative statuses would indicate a lack of self-presentation. In line with previous research, participants should rely on other-generated information (wall-posts) to form an impression when participants are viewed to have self-presented (positive / neutral status updates), as this information could be viewed as unreliable. Forty participants rated nine Facebook profiles where statuses and wall-posts portrayed personality traits varying in valence. Each profile consisted of a neutral profile photo, three status updates (all positive, negative, or neutral) and three wall-posts (all positive, negative, or neutral). Materials were established in two pilots. Impression formation was measured as perceived social, task, and physical attractiveness of the target individual. Participants also ranked the profiles for likeability. Supporting our expectations, other-generated information (wall-posts) dominated impression formation for social attractiveness when self-generated information (status updates) was positive/ neutral. Task attractiveness was affected by information valence, regardless of source (self or other). Despite the inclusion of neutral photos, physical attractiveness was affected by self-generated information, with negative statuses lowering physical attractiveness. We suggest that these findings have implications for impression formation beyond the Facebook setting. The 557 traits analyzed in Pilot 1 are

Effectiveness of self-generated cues in early Alzheimer's disease.

PubMed

Lipinska, B; Bäckman, L; Mäntylä, T; Viitanen, M

1994-12-01

The ability to utilize cognitive support in the form of self-generated cues in mild Alzheimer's disease (AD), and the factors promoting efficient cue utilization in this group of patients, were examined in two experiments on memory for words. Results from both experiments showed that normal old adults as well as AD patients performed better with self-generated cues than with experimenter-provided cues, although the latter type of cues resulted in gains relative to free recall. The findings indicate no qualitative differences in patterns of performance between the normal old and the AD patients. For both groups of subjects, cue effectiveness was optimized when (a) there was self-generation activity at encoding, and (b) encoding and retrieval conditions were compatible.

Mushrooms as Efficient Solar Steam-Generation Devices.

PubMed

Xu, Ning; Hu, Xiaozhen; Xu, Weichao; Li, Xiuqiang; Zhou, Lin; Zhu, Shining; Zhu, Jia

2017-07-01

Solar steam generation is emerging as a promising technology, for its potential in harvesting solar energy for various applications such as desalination and sterilization. Recent studies have reported a variety of artificial structures that are designed and fabricated to improve energy conversion efficiencies by enhancing solar absorption, heat localization, water supply, and vapor transportation. Mushrooms, as a kind of living organism, are surprisingly found to be efficient solar steam-generation devices for the first time. Natural and carbonized mushrooms can achieve ≈62% and ≈78% conversion efficiencies under 1 sun illumination, respectively. It is found that this capability of high solar steam generation is attributed to the unique natural structure of mushroom, umbrella-shaped black pileus, porous context, and fibrous stipe with a small cross section. These features not only provide efficient light absorption, water supply, and vapor escape, but also suppress three components of heat losses at the same time. These findings not only reveal the hidden talent of mushrooms as low-cost materials for solar steam generation, but also provide inspiration for the future development of high-performance solar thermal conversion devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulating the Effects of Cross-Generational Cultural Transmission on Language Change

NASA Astrophysics Data System (ADS)

Gong, Tao; Shuai, Lan

Language evolves in a socio-cultural environment. Apart from biological evolution and individual learning, cultural transmission also casts important influence on many aspects of language evolution. In this paper, based on the lexicon-syntax coevolution model, we extend the acquisition framework in our previous work to examine the roles of three forms of cultural transmission spanning the offspring, parent, and grandparent generations in language change. These transmissions are: those between the parent and offspring generations (PO), those within the offspring generation (OO), and those between the grandparent and offspring generations (GO). The simulation results of the considered model and relevant analyses illustrate not only the necessity of PO and OO transmissions for language change, thus echoing our previous findings, but also the importance of GO transmission, a form of cross-generational cultural transmission, on preserving the mutual understandability of the communal language across generations of individuals.

77 FR 25131 - Turning Point Solar LLC: Notice of Finding of No Significant Impact

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-27

... monocrystalline photovoltaic panels mounted on fixed solar racking equipment and the construction of access roads... DEPARTMENT OF AGRICULTURE Rural Utilities Service Turning Point Solar LLC: Notice of Finding of No... Environmental Assessment (EA) associated with a solar generation project. The EA was prepared in accordance with...

Physics of frequency-modulated comb generation in quantum-well diode lasers

NASA Astrophysics Data System (ADS)

Dong, Mark; Cundiff, Steven T.; Winful, Herbert G.

2018-05-01

We investigate the physical origin of frequency-modulated combs generated from single-section semiconductor diode lasers based on quantum wells, isolating the essential physics necessary for comb generation. We find that the two effects necessary for comb generation—spatial hole burning (leading to multimode operation) and four-wave mixing (leading to phase locking)—are indeed present in some quantum-well systems. The physics of comb generation in quantum wells is similar to that in quantum dot and quantum cascade lasers. We discuss the nature of the spectral phase and some important material parameters of these diode lasers.

Scales of mass generation for quarks, leptons, and majorana neutrinos.

PubMed

Dicus, Duane A; He, Hong-Jian

2005-06-10

We study 2-->n inelastic fermion-(anti)fermion scattering into multiple longitudinal weak gauge bosons and derive universal upper bounds on the scales of fermion mass generation by imposing unitarity of the S matrix. We place new upper limits on the scales of fermion mass generation, independent of the electroweak symmetry breaking scale. Strikingly, we find that the strongest 2-->n limits fall in a narrow range, 3-170 TeV (with n=2-24), depending on the observed fermion masses.

sRNA antitoxins: more than one way to repress a toxin.

PubMed

Wen, Jia; Fozo, Elizabeth M

2014-08-04

Bacterial toxin-antitoxin loci consist of two genes: one encodes a potentially toxic protein, and the second, an antitoxin to repress its function or expression. The antitoxin can either be an RNA or a protein. For type I and type III loci, the antitoxins are RNAs; however, they have very different modes of action. Type I antitoxins repress toxin protein expression through interacting with the toxin mRNA, thereby targeting the mRNA for degradation or preventing its translation or both; type III antitoxins directly bind to the toxin protein, sequestering it. Along with these two very different modes of action for the antitoxin, there are differences in the functions of the toxin proteins and the mobility of these loci between species. Within this review, we discuss the major differences as to how the RNAs repress toxin activity, the potential consequences for utilizing different regulatory strategies, as well as the confirmed and potential biological roles for these loci across bacterial species.

Associating ground magnetometer observations with current or voltage generators

NASA Astrophysics Data System (ADS)

Hartinger, M. D.; Xu, Z.; Clauer, C. R.; Yu, Y.; Weimer, D. R.; Kim, H.; Pilipenko, V.; Welling, D. T.; Behlke, R.; Willer, A. N.

2017-07-01

A circuit analogy for magnetosphere-ionosphere current systems has two extremes for drivers of ionospheric currents: ionospheric electric fields/voltages constant while current/conductivity vary—the "voltage generator"—and current constant while electric field/conductivity vary—the "current generator." Statistical studies of ground magnetometer observations associated with dayside Transient High Latitude Current Systems (THLCS) driven by similar mechanisms find contradictory results using this paradigm: some studies associate THLCS with voltage generators, others with current generators. We argue that most of this contradiction arises from two assumptions used to interpret ground magnetometer observations: (1) measurements made at fixed position relative to the THLCS field-aligned current and (2) negligible auroral precipitation contributions to ionospheric conductivity. We use observations and simulations to illustrate how these two assumptions substantially alter expectations for magnetic perturbations associated with either a current or a voltage generator. Our results demonstrate that before interpreting ground magnetometer observations of THLCS in the context of current/voltage generators, the location of a ground magnetometer station relative to the THLCS field-aligned current and the location of any auroral zone conductivity enhancements need to be taken into account.

Gaussian entanglement generation from coherence using beam-splitters

PubMed Central

Wang, Zhong-Xiao; Wang, Shuhao; Ma, Teng; Wang, Tie-Jun; Wang, Chuan

2016-01-01

The generation and quantification of quantum entanglement is crucial for quantum information processing. Here we study the transition of Gaussian correlation under the effect of linear optical beam-splitters. We find the single-mode Gaussian coherence acts as the resource in generating Gaussian entanglement for two squeezed states as the input states. With the help of consecutive beam-splitters, single-mode coherence and quantum entanglement can be converted to each other. Our results reveal that by using finite number of beam-splitters, it is possible to extract all the entanglement from the single-mode coherence even if the entanglement is wiped out before each beam-splitter. PMID:27892537

Microturbine and Thermoelectric Generator Combined System: A Case Study.

PubMed

Miozzo, Alvise; Boldrini, Stefano; Ferrario, Alberto; Fabrizio, Monica

2017-03-01

Waste heat recovery is one of the suitable industrial applications of thermoelectrics. Thermoelectric generators (TEG) are used, commonly, only for low-mid size power generation systems. The low efficiency of thermoelectric modules generally does not encourage their combination with high power and temperature sources, such as gas turbines. Nevertheless, the particular features of thermoelectric technology (no moving parts, scalability, reliability, low maintenance costs) are attractive for many applications. In this work, the feasibility of the integration of a TE generator into a cogeneration system is evaluated. The cogeneration system consists of a microturbine and heat exchangers for the production of electrical and thermal energy. The aim is to improve electric power generation by using TE modules and the “free” thermal energy supplied by the cogeneration system, through the exhaust pipe of the microturbine. Three different solutions for waste heat recovery from the exhausts gas are evaluated, from the fluid dynamics and heat transfer point of view, to find out a suitable design strategy for a combined power generation system.

Evaluation of a binary optimization approach to find the optimum locations of energy storage devices in a power grid with stochastically varying loads and wind generation

NASA Astrophysics Data System (ADS)

Dar, Zamiyad

The prices in the electricity market change every five minutes. The prices in peak demand hours can be four or five times more than the prices in normal off peak hours. Renewable energy such as wind power has zero marginal cost and a large percentage of wind energy in a power grid can reduce the price significantly. The variability of wind power prevents it from being constantly available in peak hours. The price differentials between off-peak and on-peak hours due to wind power variations provide an opportunity for a storage device owner to buy energy at a low price and sell it in high price hours. In a large and complex power grid, there are many locations for installation of a storage device. Storage device owners prefer to install their device at locations that allow them to maximize profit. Market participants do not possess much information about the system operator's dispatch, power grid, competing generators and transmission system. The publicly available data from the system operator usually consists of Locational Marginal Prices (LMP), load, reserve prices and regulation prices. In this thesis, we develop a method to find the optimum location of a storage device without using the grid, transmission or generator data. We formulate and solve an optimization problem to find the most profitable location for a storage device using only the publicly available market pricing data such as LMPs, and reserve prices. We consider constraints arising due to storage device operation limitations in our objective function. We use binary optimization and branch and bound method to optimize the operation of a storage device at a given location to earn maximum profit. We use two different versions of our method and optimize the profitability of a storage unit at each location in a 36 bus model of north eastern United States and south eastern Canada for four representative days representing four seasons in a year. Finally, we compare our results from the two versions of our

Commanding Generation Y: How Generation X Military Leaders Can Better Utilize Generational Tendencies

DTIC Science & Technology

2013-03-21

leadership style between the generations may not differ, defining characteristics of how a leader communicates and overcoming generational stereotypes become...in command, is not immune to generational stereotypes and must maintain a professional tradition of arms while appreciating the nuances of Generation...6 DEFINING GENERATIONAL TRAITS AND STEREOTYPES …………...…...........................6 Defining Baby Boomer Stereotypes …………………………………..…..…..…………..8

Generation Rx.com. What are young people really doing online?

PubMed

Rideout, Victoria

2002-01-01

The Kaiser Family Foundation examined the ways Generation Xers use the Web to find health information and found some surprising results. Not only do young adults access online health information, but they seek it more often than they check sports scores, purchase merchandise, or participate in a chat room. They're also likely to be influenced by what they find online, and many report that they've changed their behavior based on what they've learned.

Scope of Algae as Third Generation Biofuels

PubMed Central

Behera, Shuvashish; Singh, Richa; Arora, Richa; Sharma, Nilesh Kumar; Shukla, Madhulika; Kumar, Sachin

2015-01-01

An initiative has been taken to develop different solid, liquid, and gaseous biofuels as the alternative energy resources. The current research and technology based on the third generation biofuels derived from algal biomass have been considered as the best alternative bioresource that avoids the disadvantages of first and second generation biofuels. Algal biomass has been investigated for the implementation of economic conversion processes producing different biofuels such as biodiesel, bioethanol, biogas, biohydrogen, and other valuable co-products. In the present review, the recent findings and advance developments in algal biomass for improved biofuel production have been explored. This review discusses about the importance of the algal cell contents, various strategies for product formation through various conversion technologies, and its future scope as an energy security. PMID:25717470

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

Floating Choices: A Generational Perspective on Intentions of Rural-Urban Migrants in China

PubMed Central

Yue, Zhongshan; Li, Shuzhuo; Feldman, Marcus W.; Du, Haifeng

2013-01-01

Using data from a 2005 Survey of rural-urban migrants in Shenzhen, this paper investigates intentions of two groups of migrants. We use the birth years from 1970 to 1980 as a reasonable range of dividing lines to separate the two groups. For each year we divide the sample into those born before that year and those born in or after that year. These are referred to as the old and the new generation, respectively. Three possible development trajectories are considered: settling in cities, returning home to seek a nonagricultural job, and returning home to farm. We find that members of the new generation have stronger desires to do non-farm work, and returning to seek a nonagricultural job has become the most important planned trajectory for this generation. Sharp differences exist between the two generations in the reasons that underlie their intentions. For the old generation, conditions such as age, family responsibility, and type of job are important determinants of intentions, while other conditions such as initial migration motives, social capital, and socioeconomic conditions of origin areas are important for the intentions of the new generation. Thus the new generation is more likely to view migration as a form of investment with the accumulation of human capital and social capital. Those migrants from the old generation who have higher education levels also intend to seek non-farm jobs. However, because of the combined effects of life cycle and the market transition in China, these intentions are not as strong as those of the new generation. We discuss economic and policy implications of our findings. PMID:24151348

Cellular generators of the cortical auditory evoked potential initial component.

PubMed

Steinschneider, M; Tenke, C E; Schroeder, C E; Javitt, D C; Simpson, G V; Arezzo, J C; Vaughan, H G

1992-01-01

Cellular generators of the initial cortical auditory evoked potential (AEP) component were determined by analyzing laminar profiles of click-evoked AEPs, current source density, and multiple unit activity (MUA) in primary auditory cortex of awake monkeys. The initial AEP component is a surface-negative wave, N8, that peaks at 8-9 msec and inverts in polarity below lamina 4. N8 is generated by a lamina 4 current sink and a deeper current source. Simultaneous MUA is present from lower lamina 3 to the subjacent white matter. Findings indicate that thalamocortical afferents are a generator of N8 and support a role for lamina 4 stellate cells. Relationships to the human AEP are discussed.

Ancestral Exposure to Stress Generates New Behavioral Traits and a Functional Hemispheric Dominance Shift.

PubMed

Ambeskovic, Mirela; Soltanpour, Nasrin; Falkenberg, Erin A; Zucchi, Fabiola C R; Kolb, Bryan; Metz, Gerlinde A S

2017-03-01

In a continuously stressful environment, the effects of recurrent prenatal stress (PS) accumulate across generations and generate new behavioral traits in the absence of genetic variation. Here, we investigated if PS or multigenerational PS across 4 generations differentially affect behavioral traits, laterality, and hemispheric dominance in male and female rats. Using skilled reaching and skilled walking tasks, 3 findings support the formation of new behavioral traits and shifted laterality by multigenerational stress. First, while PS in the F1 generation did not alter paw preference, multigenerational stress in the F4 generation shifted paw preference to favor left-handedness only in males. Second, multigenerational stress impaired skilled reaching and skilled walking movement abilities in males, while improving these abilities in females beyond the levels of controls. Third, the shift toward left-handedness in multigenerationally stressed males was accompanied by increased dendritic complexity and greater spine density in the right parietal cortex. Thus, cumulative multigenerational stress generates sexually dimorphic left-handedness and dominance shift toward the right hemisphere in males. These findings explain the origins of apparently heritable behavioral traits and handedness in the absence of DNA sequence variations while proposing epigenetic mechanisms. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Issues on generating primordial anisotropies at the end of inflation

NASA Astrophysics Data System (ADS)

Emami, Razieh; Firouzjahi, Hassan

2012-01-01

We revisit the idea of generating primordial anisotropies at the end of inflation in models of inflation with gauge fields. To be specific we consider the charged hybrid inflation model where the waterfall field is charged under a U(1) gauge field so the surface of end of inflation is controlled both by inflaton and the gauge fields. Using δN formalism properly we find that the anisotropies generated at the end of inflation from the gauge field fluctuations are exponentially suppressed on cosmological scales. This is because the gauge field evolves exponentially during inflation while in order to generate appreciable anisotropies at the end of inflation the spectator gauge field has to be frozen. We argue that this is a generic feature, that is, one can not generate observable anisotropies at the end of inflation within an FRW background.

Generational diversity in associate degree nursing students: Teaching styles and preferences in Pennsylvania

NASA Astrophysics Data System (ADS)

Kitko, Jennifer V.

2011-12-01

Nursing educators face the challenge of meeting the needs of a multi-generational classroom. The reality of having members from the Veteran and Baby Boomer generations in a classroom with Generation X and Y students provides an immediate need for faculty to examine students' teaching method preferences as well as their own use of teaching methods. Most importantly, faculty must facilitate an effective multi-generational learning environment. Research has shown that the generation to which a person belongs is likely to affect the ways in which he/she learns (Hammill, 2005). Characterized by its own attitudes, behaviors, beliefs, and motivational needs, each generation also has distinct educational expectations. It is imperative, therefore, that nurse educators be aware of these differences and develop skills through which to communicate with the different generations, thereby reducing teaching/learning problems in the classroom. This is a quantitative, descriptive study that compared the teaching methods preferred by different generations of associate degree nursing students with the teaching methods that the instructors actually use. The research study included 289 participants; 244 nursing student participants and 45 nursing faculty participants from four nursing departments in colleges in Pennsylvania. Overall, the results of the study found many statistically significant findings. The results of the ANOVA test revealed eight statistically significant findings among Generation Y, Generation X and Baby boomers. The preferred teaching methods included: lecture, self-directed learning, web-based course with no class meetings, important for faculty to know my name, classroom structure, know why I am learning what I am learning, learning for the sake of learning and grade is all that matters. Lecture was found to be the most frequently used teaching method by faculty as well as the most preferred teaching methods by students. Overall, the support for a variety of

75 FR 52045 - Arizona Public Service Company, Palo Verde Nuclear Generating Station, Unit 3; Environmental...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-24

... Company, Palo Verde Nuclear Generating Station, Unit 3; Environmental Assessment and Finding of No.... NPF-74, issued to Arizona Public Service Company (APS, the licensee), for operation of Palo Verde... Statement for the Palo Verde Nuclear Generating Station, NUREG-0841, dated February 1982. Agencies and...

Workplace-related generational characteristics of nurses: A mixed-method systematic review.

PubMed

Stevanin, Simone; Palese, Alvisa; Bressan, Valentina; Vehviläinen-Julkunen, Katri; Kvist, Tarja

2018-06-01

The aim of this study was to describe and summarize workplace characteristics of three nursing generations: Baby Boomers, Generations X and Y. Generational differences affect occupational well-being, nurses' performance, patient outcomes and safety; therefore, nurse managers, administrators and educators are interested increasingly in making evidence-based decisions about the multigenerational nursing workforce. Mixed-method systematic review. Medline, CINAHL, PsycINFO and Scopus (January 1991-January 2017). (1) The Joanna Briggs Institute's method for conducting mixed-method systematic reviews; (2) the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and (3) the Enhancing Transparency in Reporting the Synthesis of Qualitative Research guidelines. The studies' methodological quality was assessed with the Mixed-Methods Appraisal Tool. Quantitative and mixed-method studies were transformed into qualitative methods using a convergent qualitative synthesis and qualitative findings were combined with a narrative synthesis. Thirty-three studies were included with three main themes and 11 subthemes: (1) Job attitudes (work engagement; turnover intentions, reasons for leaving; reasons, incentives/disincentives to continue nursing); (2) Emotion-related job aspects (stress/resilience; well-being/job satisfaction; affective commitment; unit climate; work ethic) and (3) Practice and leadership-related aspects (autonomy; perceived competence; leadership relationships and perceptions). Baby Boomers reported lower levels of stress and burnout than did Generations X and Y, different work engagement, factors affecting workplace well-being and retention and greater intention to leave compared with Generation Y, which was less resilient, but more cohesive. Although several studies reported methodological limitations and conflicting findings, generational differences in nurses' job attitudes, emotional, practice and leadership factors should be considered to enhance

Effects of Combining Na and Sr additions on Eutectic Modification in Al-Si alloy

NASA Astrophysics Data System (ADS)

Zhu, G. L.; Gu, N. J.; Zhou, B. J.

2017-09-01

Experiments were designed to investigate the effects of strontium and sodium modified on the eutectic silicon for Al-Si alloy. It was found that combining addition of Na and Sr did not appear to cause deleterious interactions of modification, at at the same time, Sr-Na was fairly constant with holding time and without obvious modification fading. Addition of Na-Sr modifier could take effect quickly and decrease incubation period.

Radiographic findings in late-presenting congenital diaphragmatic hernia: helpful imaging findings.

PubMed

Muzzafar, Sofia; Swischuk, Leonard E; Jadhav, Siddharth P

2012-03-01

Imaging findings in delayed presentation of congenital diaphragmatic hernia can be confusing and misleading, resulting in a delay in diagnosis. To evaluate the often puzzling plain film findings of late-presenting CDH in an effort to determine whether any of the findings could be helpful in arriving at an early diagnosis. We reviewed and documented the plain film findings and clinical data in eight patients seen during the last 20 years with late-presenting CDH. IRB exempt status was obtained in this study. There were five boys and three girls. The age range was 4 months to 12 years with a mean of 2.4 years. Five children presented with acute respiratory problems while three presented with acute abdominal pain. Two children presented with both respiratory and abdominal findings and one also presented with hematemesis. Two children had radiographic findings that were not difficult to analyze while the remaining six had findings that posed initial diagnostic problems. Although not common, late-presenting CDH can result in confusing plain film radiographic findings and a delay in diagnosis. We found that the most important finding in analyzing these radiographs is in evaluating the location and position of the gastric bubble with the more common left-side hernias.

Internal Wave Generation by Convection

NASA Astrophysics Data System (ADS)

Lecoanet, Daniel Michael

In nature, it is not unusual to find stably stratified fluid adjacent to convectively unstable fluid. This can occur in the Earth's atmosphere, where the troposphere is convective and the stratosphere is stably stratified; in lakes, where surface solar heating can drive convection above stably stratified fresh water; in the oceans, where geothermal heating can drive convection near the ocean floor, but the water above is stably stratified due to salinity gradients; possible in the Earth's liquid core, where gradients in thermal conductivity and composition diffusivities maybe lead to different layers of stable or unstable liquid metal; and, in stars, as most stars contain at least one convective and at least one radiative (stably stratified) zone. Internal waves propagate in stably stratified fluids. The characterization of the internal waves generated by convection is an open problem in geophysical and astrophysical fluid dynamics. Internal waves can play a dynamically important role via nonlocal transport. Momentum transport by convectively excited internal waves is thought to generate the quasi-biennial oscillation of zonal wind in the equatorial stratosphere, an important physical phenomenon used to calibrate global climate models. Angular momentum transport by convectively excited internal waves may play a crucial role in setting the initial rotation rates of neutron stars. In the last year of life of a massive star, convectively excited internal waves may transport even energy to the surface layers to unbind them, launching a wind. In each of these cases, internal waves are able to transport some quantity--momentum, angular momentum, energy--across large, stable buoyancy gradients. Thus, internal waves represent an important, if unusual, transport mechanism. This thesis advances our understanding of internal wave generation by convection. Chapter 2 provides an underlying theoretical framework to study this problem. It describes a detailed calculation of the

Problem Solving as an Encoding Task: A Special Case of the Generation Effect

ERIC Educational Resources Information Center

Kizilirmak, Jasmin M.; Wiegmann, Berit; Richardson-Klavehn, Alan

2016-01-01

Recent evidence suggests that solving problems through insight can enhance long-term memory for the problem and its solution. Previous findings have shown that generation of the solution as well as experiencing a feeling of Aha! can have a beneficial relationship to later memory. These findings lead to the question of how learning in…

Finding Minimum-Power Broadcast Trees for Wireless Networks

NASA Technical Reports Server (NTRS)

Arabshahi, Payman; Gray, Andrew; Das, Arindam; El-Sharkawi, Mohamed; Marks, Robert, II

2004-01-01

Some algorithms have been devised for use in a method of constructing tree graphs that represent connections among the nodes of a wireless communication network. These algorithms provide for determining the viability of any given candidate connection tree and for generating an initial set of viable trees that can be used in any of a variety of search algorithms (e.g., a genetic algorithm) to find a tree that enables the network to broadcast from a source node to all other nodes while consuming the minimum amount of total power. The method yields solutions better than those of a prior algorithm known as the broadcast incremental power algorithm, albeit at a slightly greater computational cost.

Range and stability of structural colors generated by Morpho-inspired color reflectors.

PubMed

Chung, Kyungjae; Shin, Jung H

2013-05-01

The range and stability of structural colors generated by Morpho-inspired color reflectors are investigated. We find that despite the internal randomness of such structures that gives rise to their Morpho-like angle-independent iridescence, their colors under ambient lighting condition can be predicted by simple transfer-matrix calculations of corresponding planar multilayer structures. By calculating the possible range of colors generated by multilayers of different structures and material combinations using such transfer-matrix methods, we find that low-refractive index multilayers with intrastructure absorption, such as the melanin-containing chitin/air multilayer structure from the Morpho butterflies, can provide not only the most pure structural colors with the largest color gamut, but also the highest stability of color against variations in multilayer structure.

The comparative effect of individually-generated vs. collaboratively-generated computer-based concept mapping on science concept learning

NASA Astrophysics Data System (ADS)

Kwon, So Young

Using a quasi-experimental design, the researcher investigated the comparative effects of individually-generated and collaboratively-generated computer-based concept mapping on middle school science concept learning. Qualitative data were analyzed to explain quantitative findings. One hundred sixty-one students (74 boys and 87 girls) in eight, seventh grade science classes at a middle school in Southeast Texas completed the entire study. Using prior science performance scores to assure equivalence of student achievement across groups, the researcher assigned the teacher's classes to one of the three experimental groups. The independent variable, group, consisted of three levels: 40 students in a control group, 59 students trained to individually generate concept maps on computers, and 62 students trained to collaboratively generate concept maps on computers. The dependent variables were science concept learning as demonstrated by comprehension test scores, and quality of concept maps created by students in experimental groups as demonstrated by rubric scores. Students in the experimental groups received concept mapping training and used their newly acquired concept mapping skills to individually or collaboratively construct computer-based concept maps during study time. The control group, the individually-generated concept mapping group, and the collaboratively-generated concept mapping group had equivalent learning experiences for 50 minutes during five days, excepting that students in a control group worked independently without concept mapping activities, students in the individual group worked individually to construct concept maps, and students in the collaborative group worked collaboratively to construct concept maps during their study time. Both collaboratively and individually generated computer-based concept mapping had a positive effect on seventh grade middle school science concept learning but neither strategy was more effective than the other. However

Radiative Effects of Atmospheric Aerosols and Impacts on Solar Photovoltaic Electricity Generation

NASA Astrophysics Data System (ADS)

Lund, Cory Christopher

Atmospheric aerosols, by scattering and absorbing radiation, perturbs the Earth's energy balance and reduces the amount of insolation reaching the surface. This dissertation first studies the radiative effects of aerosols by analyzing the internal mixing of various aerosol species. It then examines the aerosol impact on solar PV efficiency and the resulting influence on power systems, including both atmospheric aerosols and deposition of particulate matter (PM) on PV surfaces,. Chapter 2 studies the radiative effects of black carbon (BC), sulfate and organic carbon (OC) internal mixing using a simple radiative transfer model. I find that internal mixing may not result in a positive radiative forcing compared to external mixing, but blocks additional shortwave radiation from the surface, enhancing the surface dimming effect. Chapter 3 estimates the impact of atmospheric aerosol attenuation on solar PV resources in China using a PV performance model with satellite-derived long-term surface irradiance data. I find that, in Eastern China, annual average reductions of solar resources due to aerosols are more than 20%, with comparable impacts to clouds in winter. Improving air quality in China would increase efficiency of solar PV generation. As a positive feedback, increased PV efficiency and deployment would further reduce air pollutant emissions too. Chapter 4 further quantifies the total aerosol impact on PV efficiency globally, including both atmospheric aerosols and the deposition of PM on PV surfaces. I find that, if panels are uncleaned and soiling is only removed by precipitation, deposition of PM accounts for more than two-thirds of the total aerosol impact in most regions. Cleaning the panels, even every few months, would largely increase PV efficiency in resource-abundant regions. Chapter 5 takes a further step to evaluate the impact of PV generation reduction due to aerosols on a projected 2030 power system in China with 400GW of PV. I find that aerosols

Message passing for integrating and assessing renewable generation in a redundant power grid

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

Zdeborova, Lenka; Backhaus, Scott; Chertkov, Michael

2009-01-01

A simplified model of a redundant power grid is used to study integration of fluctuating renewable generation. The grid consists of large number of generator and consumer nodes. The net power consumption is determined by the difference between the gross consumption and the level of renewable generation. The gross consumption is drawn from a narrow distribution representing the predictability of aggregated loads, and we consider two different distributions representing wind and solar resources. Each generator is connected to D consumers, and redundancy is built in by connecting R {le} D of these consumers to other generators. The lines are switchablemore » so that at any instance each consumer is connected to a single generator. We explore the capacity of the renewable generation by determining the level of 'firm' generation capacity that can be displaced for different levels of redundancy R. We also develop message-passing control algorithm for finding switch sellings where no generator is overloaded.« less

Left and right basal ganglia and frontal activity during language generation: contributions to lexical, semantic, and phonological processes.

PubMed

Crosson, Bruce; Benefield, Hope; Cato, M Allison; Sadek, Joseph R; Moore, Anna Bacon; Wierenga, Christina E; Gopinath, Kaundinya; Soltysik, David; Bauer, Russell M; Auerbach, Edward J; Gökçay, Didem; Leonard, Christiana M; Briggs, Richard W

2003-11-01

fMRI was used to determine the frontal, basal ganglia, and thalamic structures engaged by three facets of language generation: lexical status of generated items, the use of semantic vs. phonological information during language generation, and rate of generation. During fMRI, 21 neurologically normal subjects performed four tasks: generation of nonsense syllables given beginning and ending consonant blends, generation of words given a rhyming word, generation of words given a semantic category at a fast rate (matched to the rate of nonsense syllable generation), and generation of words given a semantic category at a slow rate (matched to the rate of generating of rhyming words). Components of a left pre-SMA-dorsal caudate nucleus-ventral anterior thalamic loop were active during word generation from rhyming or category cues but not during nonsense syllable generation. Findings indicate that this loop is involved in retrieving words from pre-existing lexical stores. Relatively diffuse activity in the right basal ganglia (caudate nucleus and putamen) also was found during word-generation tasks but not during nonsense syllable generation. Given the relative absence of right frontal activity during the word generation tasks, we suggest that the right basal ganglia activity serves to suppress right frontal activity, preventing right frontal structures from interfering with language production. Current findings establish roles for the left and the right basal ganglia in word generation. Hypotheses are discussed for future research to help refine our understanding of basal ganglia functions in language generation.

A portable infrasound generator.

PubMed

Park, Joseph; Robertson, James

2009-04-01

The rotary subwoofer is a novel low frequency transducer capable of efficiently generating infrasound from a compact source. A field-deployable version of this device may find application as a calibration source for infrasound arrays of the International Monitoring System (IMS) [(2001). The Global Verification Regime and the International Monitoring System (CTBTO Preparatory Commission Vienna International Centre, Vienna, Austria)]. A prototype tested at the IMS infrasound array I59US demonstrated the ability to insonify all elements of the array from a standoff distance of 3.8 km. Signal-to-noise ratios of continuous wave signals ranged from 5 to 15 dB, indicating the utility of this source to transmit controllable infrasound signals over distances of 5 km.

Automatic generation of Web mining environments

NASA Astrophysics Data System (ADS)

Cibelli, Maurizio; Costagliola, Gennaro

1999-02-01

The main problem related to the retrieval of information from the world wide web is the enormous number of unstructured documents and resources, i.e., the difficulty of locating and tracking appropriate sources. This paper presents a web mining environment (WME), which is capable of finding, extracting and structuring information related to a particular domain from web documents, using general purpose indices. The WME architecture includes a web engine filter (WEF), to sort and reduce the answer set returned by a web engine, a data source pre-processor (DSP), which processes html layout cues in order to collect and qualify page segments, and a heuristic-based information extraction system (HIES), to finally retrieve the required data. Furthermore, we present a web mining environment generator, WMEG, that allows naive users to generate a WME specific to a given domain by providing a set of specifications.

Fluidic Active Transducer for Electricity Generation

PubMed Central

Yang, YoungJun; Park, Junwoo; Kwon, Soon-Hyung; Kim, Youn Sang

2015-01-01

Flows in small size channels have been studied for a long time over multidisciplinary field such as chemistry, biology and medical through the various topics. Recently, the attempts of electricity generation from the small flows as a new area for energy harvesting in microfluidics have been reported. Here, we propose for the first time a new fluidic electricity generator (FEG) by modulating the electric double layer (EDL) with two phase flows of water and air without external power sources. We find that an electric current flowed by the forming/deforming of the EDL with a simple separated phase flow of water and air at the surface of the FEG. Electric signals between two electrodes of the FEG are checked from various water/air passing conditions. Moreover, we verify the possibility of a self-powered air slug sensor by applying the FEG in the detection of an air slug. PMID:26511626

Generational differences in distress, attitudes and incivility among nurses.

PubMed

Leiter, Michael P; Price, Sheri L; Spence Laschinger, Heather K

2010-11-01

The first research objective was to replicate the finding of Leiter et al. [(2008)Journal of Nursing Management, 16, 100-109.] of Generation X nurses (n=338) reporting higher levels of distress than Baby Boomer nurses (n=139). The second objective was to test whether Generation X nurses reported more negative social environments at work than did Baby Boomer nurses. Negative social environments can influence the quality of work and the experience of distress for nurses. Generational differences in the experience of distress and collegiality have implications for the establishment of healthy workplaces, recruitment and retention. A questionnaire survey of nurses was organized by generation. Analyses of variance contrasted the scores on burnout, turnover intention, physical symptoms, supervisor incivility, coworker incivility and team civility. The results confirmed the hypotheses of Generation X nurses reporting more negative experiences than did Baby Boomer nurses on all measures. The negative quality of social encounters at work contributes to nurses' experience of distress and suggest conflicts of values with the dominant culture of their workplaces. Proactive initiatives to enhance the quality of collegiality can contribute to retention strategies. Building collegiality across generations can be especially useful. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

Refrigeration generation using expander-generator units

NASA Astrophysics Data System (ADS)

Klimenko, A. V.; Agababov, V. S.; Koryagin, A. V.; Baidakova, Yu. O.

2016-05-01

The problems of using the expander-generator unit (EGU) to generate refrigeration, along with electricity were considered. It is shown that, on the level of the temperatures of refrigeration flows using the EGU, one can provide the refrigeration supply of the different consumers: ventilation and air conditioning plants and industrial refrigerators and freezers. The analysis of influence of process parameters on the cooling power of the EGU, which depends on the parameters of the gas expansion process in the expander and temperatures of cooled environment, was carried out. The schematic diagram of refrigeration generation plant based on EGU is presented. The features and advantages of EGU to generate refrigeration compared with thermotransformer of steam compressive and absorption types were shown, namely: there is no need to use the energy generated by burning fuel to operate the EGU; beneficial use of the heat delivered to gas from the flow being cooled in equipment operating on gas; energy production along with refrigeration generation, which makes it possible to create, using EGU, the trigeneration plants without using the energy power equipment. It is shown that the level of the temperatures of refrigeration flows, which can be obtained by using the EGU on existing technological decompression stations of the transported gas, allows providing the refrigeration supply of various consumers. The information that the refrigeration capacity of an expander-generator unit not only depends on the parameters of the process of expansion of gas flowing in the expander (flow rate, temperatures and pressures at the inlet and outlet) but it is also determined by the temperature needed for a consumer and the initial temperature of the flow of the refrigeration-carrier being cooled. The conclusion was made that the expander-generator units can be used to create trigeneration plants both at major power plants and at small energy.

Option generation in decision making: ideation beyond memory retrieval

PubMed Central

Del Missier, Fabio; Visentini, Mimì; Mäntylä, Timo

2015-01-01

According to prescriptive decision theories, the generation of options for choice is a central aspect of decision making. A too narrow representation of the problem may indeed limit the opportunity to evaluate promising options. However, despite the theoretical and applied significance of this topic, the cognitive processes underlying option generation are still unclear. In particular, while a cued recall account of option generation emphasizes the role of memory and executive control, other theoretical proposals stress the importance of ideation processes based on various search and thinking processes. Unfortunately, relevant behavioral evidence on the cognitive processes underlying option generation is scattered and inconclusive. In order to reach a better understanding, we carried out an individual-differences study employing a wide array of cognitive predictors, including measures of episodic memory, semantic memory, cognitive control, and ideation fluency. The criterion tasks consisted of three different poorly-structured decision-making scenarios, and the participants were asked to generate options to solve these problems. The main criterion variable of the study was the number of valid options generated, but also the diversity and the quality of generated options were examined. The results showed that option generation fluency and diversity in the context of ill-structured decision making are supported by ideation ability even after taking into account the effects of individual differences in several other aspects of cognitive functioning. Thus, ideation processes, possibly supported by search and thinking processes, seem to contribute to option generation beyond basic associative memory retrieval. The findings of the study also indicate that generating more options may have multifaceted consequences for choice, increasing the quality of the best option generated but decreasing the mean quality of the options in the generated set. PMID:25657628

Option generation in decision making: ideation beyond memory retrieval.

PubMed

Del Missier, Fabio; Visentini, Mimì; Mäntylä, Timo

2014-01-01

According to prescriptive decision theories, the generation of options for choice is a central aspect of decision making. A too narrow representation of the problem may indeed limit the opportunity to evaluate promising options. However, despite the theoretical and applied significance of this topic, the cognitive processes underlying option generation are still unclear. In particular, while a cued recall account of option generation emphasizes the role of memory and executive control, other theoretical proposals stress the importance of ideation processes based on various search and thinking processes. Unfortunately, relevant behavioral evidence on the cognitive processes underlying option generation is scattered and inconclusive. In order to reach a better understanding, we carried out an individual-differences study employing a wide array of cognitive predictors, including measures of episodic memory, semantic memory, cognitive control, and ideation fluency. The criterion tasks consisted of three different poorly-structured decision-making scenarios, and the participants were asked to generate options to solve these problems. The main criterion variable of the study was the number of valid options generated, but also the diversity and the quality of generated options were examined. The results showed that option generation fluency and diversity in the context of ill-structured decision making are supported by ideation ability even after taking into account the effects of individual differences in several other aspects of cognitive functioning. Thus, ideation processes, possibly supported by search and thinking processes, seem to contribute to option generation beyond basic associative memory retrieval. The findings of the study also indicate that generating more options may have multifaceted consequences for choice, increasing the quality of the best option generated but decreasing the mean quality of the options in the generated set.

Generation of high-density biskyrmions by electric current

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

Peng, Licong; Zhang, Ying; He, Min

Much interest has been focused on the manipulation of magnetic skyrmions, including the generation, annihilation, and motion behaviors, for potential applications in spintronics. We experimentally demonstrate that a high-density Bloch-type biskyrmion lattice in MnNiGa can be generated by applying electric current. It is revealed that the density of biskyrmions can be remarkably increased by increasing the electric current, in contrast to the scattered biskyrmions induced by a magnetic field alone. Furthermore, the transition from the ferromagnetic state to the stripe domain structure can be terminated by the electric current, leading to the biskyrmions dominated residual domain pattern. These biskyrmions inmore » such residual domain structure are extremely stable at zero magnetic and electric fields and can further evolve into the high-density biskyrmion lattice over a temperature range from 100 to 330 K. Finally, our experimental findings open up a new pathway for the generation of skyrmion lattice by electric current manipulation.« less

Generation of high-density biskyrmions by electric current

DOE PAGES

Peng, Licong; Zhang, Ying; He, Min; ...

2017-06-16

Much interest has been focused on the manipulation of magnetic skyrmions, including the generation, annihilation, and motion behaviors, for potential applications in spintronics. We experimentally demonstrate that a high-density Bloch-type biskyrmion lattice in MnNiGa can be generated by applying electric current. It is revealed that the density of biskyrmions can be remarkably increased by increasing the electric current, in contrast to the scattered biskyrmions induced by a magnetic field alone. Furthermore, the transition from the ferromagnetic state to the stripe domain structure can be terminated by the electric current, leading to the biskyrmions dominated residual domain pattern. These biskyrmions inmore » such residual domain structure are extremely stable at zero magnetic and electric fields and can further evolve into the high-density biskyrmion lattice over a temperature range from 100 to 330 K. Finally, our experimental findings open up a new pathway for the generation of skyrmion lattice by electric current manipulation.« less

Spectrum of intracranial incidental findings on pediatric brain magnetic resonance imaging: What clinician should know?

PubMed Central

Gupta, Surya N; Gupta, Vikash S; White, Andrew C

2016-01-01

Intracranial incidental findings on magnetic resonance imaging (MRI) of the brain continue to generate interest in healthy control, research, and clinical subjects. However, in clinical practice, the discovery of incidental findings acts as a “distractor”. This review is based on existing heterogeneous reports, their clinical implications, and how the results of incidental findings influence clinical management. This draws attention to the followings: (1) the prevalence of clinically significant incidental findings is low; (2) there is a lack of a systematic approach to classification; and discusses (3) how to deal with the detected incidental findings based a proposed common clinical profile. Individualized neurological care requires an active discussion regarding the need for neuroimaging. Clinical significance of incidental findings should be decided based on lesion’s neuroradiologic characteristics in the given clinical context. Available evidence suggests that the outcome of an incidentally found “serious lesion in children” is excellent. Future studies of intracranial incidental findings on pediatric brain MRI should be focused on a homogeneous population. The study should address this clinical knowledge based review powered by the statistical analyses. PMID:27610341

Theoretical predictions for hot-carrier generation from surface plasmon decay

PubMed Central

Sundararaman, Ravishankar; Narang, Prineha; Jermyn, Adam S.; Goddard III, William A.; Atwater, Harry A.

2014-01-01

Decay of surface plasmons to hot carriers finds a wide variety of applications in energy conversion, photocatalysis and photodetection. However, a detailed theoretical description of plasmonic hot-carrier generation in real materials has remained incomplete. Here we report predictions for the prompt distributions of excited ‘hot’ electrons and holes generated by plasmon decay, before inelastic relaxation, using a quantized plasmon model with detailed electronic structure. We find that carrier energy distributions are sensitive to the electronic band structure of the metal: gold and copper produce holes hotter than electrons by 1–2 eV, while silver and aluminium distribute energies more equitably between electrons and holes. Momentum-direction distributions for hot carriers are anisotropic, dominated by the plasmon polarization for aluminium and by the crystal orientation for noble metals. We show that in thin metallic films intraband transitions can alter the carrier distributions, producing hotter electrons in gold, but interband transitions remain dominant. PMID:25511713

The impacts of renewable energy policies on renewable energy sources for electricity generating capacity

NASA Astrophysics Data System (ADS)

Koo, Bryan Bonsuk

Electricity generation from non-hydro renewable sources has increased rapidly in the last decade. For example, Renewable Energy Sources for Electricity (RES-E) generating capacity in the U.S. almost doubled for the last three year from 2009 to 2012. Multiple papers point out that RES-E policies implemented by state governments play a crucial role in increasing RES-E generation or capacity. This study examines the effects of state RES-E policies on state RES-E generating capacity, using a fixed effects model. The research employs panel data from the 50 states and the District of Columbia, for the period 1990 to 2011, and uses a two-stage approach to control endogeneity embedded in the policies adopted by state governments, and a Prais-Winsten estimator to fix any autocorrelation in the panel data. The analysis finds that Renewable Portfolio Standards (RPS) and Net-metering are significantly and positively associated with RES-E generating capacity, but neither Public Benefit Funds nor the Mandatory Green Power Option has a statistically significant relation to RES-E generating capacity. Results of the two-stage model are quite different from models which do not employ predicted policy variables. Analysis using non-predicted variables finds that RPS and Net-metering policy are statistically insignificant and negatively associated with RES-E generating capacity. On the other hand, Green Energy Purchasing policy is insignificant in the two-stage model, but significant in the model without predicted values.

Rock Finding

ERIC Educational Resources Information Center

Rommel-Esham, Katie; Constable, Susan D.

2006-01-01

In this article, the authors discuss a literature-based activity that helps students discover the importance of making detailed observations. In an inspiring children's classic book, "Everybody Needs a Rock" by Byrd Baylor (1974), the author invites readers to go "rock finding," laying out 10 rules for finding a "perfect" rock. In this way, the…

Characterisation of mouse epididymosomes reveals a complex profile of microRNAs and a potential mechanism for modification of the sperm epigenome

PubMed Central

Reilly, Jackson N.; McLaughlin, Eileen A.; Stanger, Simone J.; Anderson, Amanda L.; Hutcheon, Kate; Church, Kiralee; Mihalas, Bettina P.; Tyagi, Sonika; Holt, Janet E.; Eamens, Andrew L.; Nixon, Brett

2016-01-01

Recent evidence has shown that the sperm epigenome is vulnerable to dynamic modifications arising from a variety of paternal environment exposures and that this legacy can serve as an important determinant of intergenerational inheritance. It has been postulated that such exchange is communicated to maturing spermatozoa via the transfer of small non-protein-coding RNAs (sRNAs) in a mechanism mediated by epididymosomes; small membrane bound vesicles released by the soma of the male reproductive tract (epididymis). Here we confirm that mouse epididymosomes encapsulate an impressive cargo of >350 microRNAs (miRNAs), a developmentally important sRNA class, the majority (~60%) of which are also represented by the miRNA signature of spermatozoa. This includes >50 miRNAs that were found exclusively in epididymal sperm and epididymosomes, but not in the surrounding soma. We also documented substantial changes in the epididymosome miRNA cargo, including significant fold changes in almost half of the miRNAs along the length of the epididymis. Finally, we provide the first direct evidence for the transfer of several prominent miRNA species between mouse epididymosomes and spermatozoa to afford novel insight into a mechanism of intercellular communication by which the sRNA payload of sperm can be selectively modified during their post-testicular maturation. PMID:27549865

A novel small RNA S042 increases acid tolerance in Lactococcus lactis F44.

PubMed

Wu, Hao; Song, Shunyi; Tian, Kairen; Zhou, Dandan; Wang, Binbin; Liu, Jiaheng; Zhu, Hongji; Qiao, Jianjun

2018-06-07

Lactococcus lactis, a gram-positive bacterium, encounters various environmental stresses, especially acid stress, during fermentation. Small RNAs (sRNAs) that serve as regulators at post-transcriptional level play important roles in acid stress response. Here, a novel sRNA S042 was identified by RNA-Seq, RT-PCR and Northern blot. The transcription level of s042 was upregulated 2.29-fold under acid stress by Quantitative RT-PCR (qRT-PCR) analysis. Acid tolerance assay showed that overexpressing s042 increased the survival rate of L. lactis F44 and deleting s042 significantly inhibited the viability under acidic conditions. Moreover, the targets were predicted by online software and four genes were chosen as candidates. Among them, argR (arginine regulator) and accD (acetyl-CoA carboxylase carboxyl transferase subunit beta) were validated to be the direct targets activated by S042 through reporter fusion assay. The regulatory mechanism between S042 and its targets was further investigated through Bioinformatics and qRT-PCR. This study served to highlight the role of the novel sRNA S042 in acid resistance of L. lactis and provided new insights into the response mechanism of acid stress. Copyright © 2018 Elsevier Inc. All rights reserved.

Bacteria of leg atheromatous arteries responsible for inflammation.

PubMed

Olszewski, Waldemar Lech; Rutkowska, Joanna; Moscicka-Wesolowska, Maria; Swoboda-Kopec, Ewa; Stelmach, Ewa; Zaleska, Marzanna; Zagozda, Malgorzata

2016-09-01

Ischaemia of the lower limbs is frequently followed by inflammation and, in advanced cases, necrosis of peripheral tissues. Whether this is caused by arterial hypoperfusion only or by the presence of bacteria in the arterial walI as well remains unclear. The aim of the study was to prove the presence and source of bacteria in arterial specimens and evaluate their chemotactic properties resulting in the formation of periarterial cellular infiltrates. Bacterial culture and testing for 16sRNA were performed in fragments of popliteal artery harvested from amputated limbs. Carotid artery plaques served as controls. Fragments of arteries were transplanted into scid mice to evaluate their chemotactic activity for macrophages. a) higher prevalence of isolates and 16sRNA in atherosclerotic popliteal than carotid arteries, b) high density of plaque and periarterial infiltrates and mRNA level for pro-inflammatory cytokines in popliteal arteries, c) prevalent microbes were Staphylococcus aureus, S. epidermidis and Enterococci, d) foot skin and arterial bacterial phenotypes and DNA revealed evident similarities, and e) more intensive mouse macrophage accumulation in popliteal than carotid implants into scid mice. The presence of bacteria in the lower limb arterial wall was documented. They may predispose to inflammation secondary to ischaemic changes.

Power Generation for River and Tidal Generators

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

Muljadi, Eduard; Wright, Alan; Gevorgian, Vahan

Renewable energy sources are the second largest contributor to global electricity production, after fossil fuels. The integration of renewable energy continued to grow in 2014 against a backdrop of increasing global energy consumption and a dramatic decline in oil prices during the second half of the year. As renewable generation has become less expensive during recent decades, and it becomes more accepted by the global population, the focus on renewable generation has expanded from primarily wind and solar to include new types with promising future applications, such as hydropower generation, including river and tidal generation. Today, hydropower is considered onemore » of the most important renewable energy sources. In river and tidal generation, the input resource flow is slower but also steadier than it is in wind or solar generation, yet the level of water turbulent flow may vary from one place to another. This report focuses on hydrokinetic power conversion.« less

Immersed finger-type indium tin oxide ohmic contacts on p-GaN photoelectrodes for photoelectrochemical hydrogen generation.

PubMed

Liu, Shu-Yen; Sheu, J K; Lee, M L; Lin, Yu-Chuan; Tu, S J; Huang, F W; Lai, W C

2012-03-12

In this study, we demonstrated photoelectrochemical (PEC) hydrogen generation using p-GaN photoelectrodes associated with immersed finger-type indium tin oxide (IF-ITO) ohmic contacts. The IF-ITO/p-GaN photoelectrode scheme exhibits higher photocurrent and gas generation rate compared with p-GaN photoelectrodes without IF-ITO ohmic contacts. In addition, the critical external bias for detectable hydrogen generation can be effectively reduced by the use of IF-ITO ohmic contacts. This finding can be attributed to the greatly uniform distribution of the IF-ITO/p-GaN photoelectrode applied fields over the whole working area. As a result, the collection efficiency of photo-generated holes by electrode contacts is higher than that of p-GaN photoelectrodes without IF-ITO contacts. Microscopy revealed a tiny change on the p-GaN surfaces before and after hydrogen generation. In contrast, photoelectrodes composed of n-GaN have a short lifetime due to n-GaN corrosion during hydrogen generation. Findings of this study indicate that the ITO finger contacts on p-GaN layer is a potential candidate as photoelectrodes for PEC hydrogen generation.

Synergistic Effect of Auto-Activation and Small RNA Regulation on Gene Expression

NASA Astrophysics Data System (ADS)

Xiong, Li-Ping; Ma, Yu-Qiang; Tang, Lei-Han

2010-09-01

Auto-activation and small ribonucleic acid (RNA)-mediated regulation are two important mechanisms in controlling gene expression. We study the synergistic effect of these two regulations on gene expression. It is found that under this combinatorial regulation, gene expression exhibits bistable behaviors at the transition regime, while each of these two regulations, if working solely, only leads to monostability. Within the stochastic framework, the base pairing strength between sRNA and mRNA plays an important role in controlling the transition time between on and off states. The noise strength of protein number in the off state approaches 1 and is smaller than that in the on state. The noise strength also depends on which parameters, the feedback strength or the synthesis rate of small RNA, are tuned in switching the gene expression on and off. Our findings may provide a new insight into gene-regulation mechanism and can be applied in synthetic biology.

Incidental findings in imaging research: evaluating incidence, benefit, and burden.

PubMed

Orme, Nicholas M; Fletcher, Joel G; Siddiki, Hassan A; Harmsen, W Scott; O'Byrne, Megan M; Port, John D; Tremaine, William J; Pitot, Henry C; McFarland, Elizabeth G; Robinson, Marguerite E; Koenig, Barbara A; King, Bernard F; Wolf, Susan M

2010-09-27

Little information exists concerning the frequency and medical significance of incidental findings (IFs) in imaging research. Medical records of research participants undergoing a research imaging examination interpreted by a radiologist during January through March 2004 were reviewed, with 3-year clinical follow-up. An expert panel reviewed all IFs generating clinical action to determine medical benefit/burden on the basis of predefined criteria. The frequency of IFs that generated further clinical action was estimated by modality, body part, age, and sex, along with net medical benefit or burden. Of 1426 research imaging examinations, 567 (39.8%) had at least 1 IF (1055 total). Risk of an IF increased significantly by age (odds ratio [OR], 1.5; 95% confidence interval, 1.4-1.7 per decade increase). Abdominopelvic computed tomography generated more IFs than other examinations (OR, 18.9 vs ultrasonography; 9.2% with subsequent clinical action), with computed tomography of the thorax and magnetic resonance imaging of the head next (OR, 11.9 and 5.9; 2.8% and 2.2% with action, respectively). Of the 567 examinations with an IF, 35 (6.2%) generated clinical action, resulting in clear medical benefit in 1.1% (6 of 567) and clear medical burden in 0.5% (3 of 567). Medical benefit/burden was usually unclear (26 of 567 [4.6%]). Frequency of IFs in imaging research examinations varies significantly by imaging modality, body region, and age. Research imaging studies at high risk for generating IFs can be identified. Routine evaluation of research images by radiologists may result in identification of IFs in a high number of cases and subsequent clinical action to address them in a small but significant minority. Such clinical action can result in medical benefit to a small number of patients.

Enhanced second-harmonic generation from resonant GaAs gratings.

PubMed

de Ceglia, D; D'Aguanno, G; Mattiucci, N; Vincenti, M A; Scalora, M

2011-03-01

We theoretically study second harmonic generation in nonlinear, GaAs gratings. We find large enhancement of conversion efficiency when the pump field excites the guided mode resonances of the grating. Under these circumstances the spectrum near the pump wavelength displays sharp resonances characterized by dramatic enhancements of local fields and favorable conditions for second-harmonic generation, even in regimes of strong linear absorption at the harmonic wavelength. In particular, in a GaAs grating pumped at 1064 nm, we predict second-harmonic conversion efficiencies approximately 5 orders of magnitude larger than conversion rates achievable in either bulk or etalon structures of the same material.

Incidental Findings in Imaging Research: Evaluating Incidence, Benefit and Burden

PubMed Central

Orme, Nicholas M.; Fletcher, Joel G.; Siddiki, Hassan A.; Harmsen, W. Scott; O’Byrne, Megan M.; Port, John D.; Tremaine, William J.; Pitot, Henry C.; McFarland, Beth; Robinson, Marguerite E.; Koenig, Barabara A.; King, Bernard F.; Wolf, Susan M.

2013-01-01

Context Little information exists concerning the frequency of clinically significant incidental findings (IFs) identified in the course of imaging research across a broad spectrum of imaging modalities and body regions. Objective To estimate the frequency with which research imaging IFs generate further clinical action, and the medical benefit/burden of identifying these IFs. Design, Setting, and Participants Retrospective review of subjects undergoing a research imaging exam that was interpreted by a radiologist for IFs in the first quarter of 2004, with 3-year clinical follow-up. An expert panel reviewed IFs generating clinical action to determine medical benefit/burden based on predefined criteria. Main Outcome Measures Frequency of (1) IFs that generated further clinical action by modality, body part, age, gender, and (2) IFs resulting in clear medical benefit or burden. Results 1376 patients underwent 1426 research imaging studies. 40% (567/1426) of exams had at least one IF (1055 total). Risk of an IF increased significantly by age (OR=1.5; [1.4–1.7=95% C.I.] per decade increase). Abdominopelvic CT generated more IFs than other exams (OR=18.9 compared with ultrasound; 9.2% with subsequent clinical action), with CT Thorax and MR brain next (OR=11.9 and 5.9; 2.8% and 2.2% with action, respectively). Overall 6.2% of exams (35/567) with an IF generated clinical action, resulting in clear medical benefit in 1.1% (6/567) and clear medical burden in 0.5% (3/567). In most instances, medical benefit/burden was unclear (4.6%; 26/567). Conclusions The frequency of IFs in imaging research exams varies significantly by imaging modality, body region and age. Research imaging studies at high risk for generating IFs can be identified. Routine evaluation of research images by radiologists may result in identification of IFs in a substantial number of cases and subsequent clinical action to address them in much smaller number. Such clinical action can result in medical

Marital Satisfaction Among African Americans and Black Caribbeans: Findings From the National Survey of American Life*

PubMed Central

Bryant, Chalandra M.; Taylor, Robert Joseph; Lincoln, Karen D.; Chatters, Linda M.; Jackson, James S.

2010-01-01

This study examines the correlates of marital satisfaction using data from a national probability sample of African Americans (N = 962) and Black Caribbeans (N = 560). Findings reveal differences between African Americans and Black Caribbeans, and men and women within those groups, in the predictors of marital satisfaction. Black Caribbean women reported overall higher levels of marital satisfaction than African American women. The findings amply demonstrate the significance of ethnic diversity within the Black population in the United States. Difficulties with finances (budgeting, credit issues, and debt management) are one of the key issues that generate conflict in marriages; stress generated as a result of financial problems can lower marital satisfaction. Because these issues are salient for couples at any given time in the family life cycle, counseling at critical points in the marriage (birth of children, launching of children from home, and retirement) may be helpful. PMID:21151891

The MEarth Project: Finding the Best Targets for Atmospheric Characterization with JWST

NASA Astrophysics Data System (ADS)

Berta-Thompson, Z.

2014-04-01

If we want to directly observe the radius, orbit, mass, and atmosphere of a small, cool, habitable exoplanet, our best opportunity is to find such a planet transiting a small, cool, nearby M dwarf star. The MEarth Project is an ongoing all-sky survey for Earth-like planets transiting the closest, smallest M dwarfs in the Galaxy. MEarth aims to find good targets for atmospheric characterization with JWST and the next generation of enormous ground-based telescopes. This poster provides a status update on the MEarth Project, including the progress we've made over the past five years with 8 telescopes in the Northern hemisphere and promising early results from our new installation of 8 more telescopes in the Southern hemisphere.

The First Ones: Three Studies on First-Generation College Students

ERIC Educational Resources Information Center

Longwell-Grice, Rob; Adsitt, Nicole Zervas; Mullins, Kathleen; Serrata, William

2016-01-01

The findings from 3 qualitative research studies related to first-generation college students show themes of strains in family relationships and lack of practical familial support. One study reveals sources of resiliency and persistence of graduate students; another explores sense of belonging for undergraduates attending 3 types of private…

Factors Influencing the Academic Achievement of First-Generation College Students

ERIC Educational Resources Information Center

Strayhorn, Terrell L.

2006-01-01

First-generation college students face a number of unique challenges in college. These obstacles may have a disparate effect on educational outcomes such as academic achievement. This study presents findings from an analysis of the Baccalaureate & Beyond Longitudinal Study using hierarchical multiple regression techniques to measure the influence…

Probing cooperative force generation in collective cancer invasion

NASA Astrophysics Data System (ADS)

Alobaidi, Amani A.; Xu, Yaopengxiao; Chen, Shaohua; Jiao, Yang; Sun, Bo

2017-08-01

Collective cellular dynamics in the three-dimensional extracellular matrix (ECM) plays a crucial role in many physiological processes such as cancer invasion. Both chemical and mechanical signaling support cell-cell communications on a variety of length scales, leading to collective migratory behaviors. Here we conduct experiments using 3D in vitro tumor models and develop a phenomenological model in order to probe the cooperativity of force generation in the collective invasion of breast cancer cells. In our model, cell-cell communication is characterized by a single parameter that quantifies the correlation length of cellular migration cycles. We devise a stochastic reconstruction method to generate realizations of cell colonies with specific contraction phase correlation functions and correlation length a. We find that as a increases, the characteristic size of regions containing cells with similar contraction phases grows. For small a values, the large fluctuations in individual cell contraction phases smooth out the temporal fluctuations in the time-dependent deformation field in the ECM. For large a values, the periodicity of an individual cell contraction cycle is clearly manifested in the temporal variation of the overall deformation field in the ECM. Through quantitative comparisons of the simulated and experimentally measured deformation fields, we find that the correlation length for collective force generation in the breast cancer diskoid in geometrically micropatterned ECM (DIGME) system is a≈ 25~μ \\text{m} , which is roughly twice the linear size of a single cell. One possible mechanism for this intermediate cell correlation length is the fiber-mediated stress propagation in the 3D ECM network in the DIGME system.

A fast ergodic algorithm for generating ensembles of equilateral random polygons

NASA Astrophysics Data System (ADS)

Varela, R.; Hinson, K.; Arsuaga, J.; Diao, Y.

2009-03-01

Knotted structures are commonly found in circular DNA and along the backbone of certain proteins. In order to properly estimate properties of these three-dimensional structures it is often necessary to generate large ensembles of simulated closed chains (i.e. polygons) of equal edge lengths (such polygons are called equilateral random polygons). However finding efficient algorithms that properly sample the space of equilateral random polygons is a difficult problem. Currently there are no proven algorithms that generate equilateral random polygons with its theoretical distribution. In this paper we propose a method that generates equilateral random polygons in a 'step-wise uniform' way. We prove that this method is ergodic in the sense that any given equilateral random polygon can be generated by this method and we show that the time needed to generate an equilateral random polygon of length n is linear in terms of n. These two properties make this algorithm a big improvement over the existing generating methods. Detailed numerical comparisons of our algorithm with other widely used algorithms are provided.

Viewpoints of working sandwich generation women and occupational therapists on role balance strategies.

PubMed

Evans, Kiah L; Girdler, Sonya J; Falkmer, Torbjorn; Richmond, Janet E; Wagman, Petra; Millsteed, Jeannine; Falkmer, Marita

2017-09-01

Occupational therapists need to be cognizant of evidence-based role balance advice and strategies that women with multigenerational caring responsibilities can implement independently or with minimal assistance, as role balance may not be the primary goal during many encounters with this population. Hence, this study aimed to identify the viewpoints on the most helpful role balance strategies for working sandwich generation women, both from their own perspectives and from the perspective of occupational therapists. This was achieved through a Q methodology study, where 54 statements were based on findings from interviews, sandwich generation literature and occupational therapy literature. In total, 31 working sandwich generation women and 42 occupational therapists completed the Q sort through either online or paper administration. The data were analysed using factor analysis with varimax rotation and were interpreted through collaboration with experts in the field. The findings revealed similarities between working sandwich generation women and occupational therapists, particularly in terms of advocating strategies related to sleep, rest and seeking practical assistance from support networks. Differences were also present, with working sandwich generation women viewpoints tending to emphasize strategies related to coping with a busy lifestyle attending to multiple responsibilities. In contrast, occupational therapy viewpoints prioritized strategies related to the occupational therapy process, such as goal setting, activity focused interventions, monitoring progress and facilitating sustainable outcomes.

Comparison of Control Group Generating Methods.

PubMed

Szekér, Szabolcs; Fogarassy, György; Vathy-Fogarassy, Ágnes

2017-01-01

Retrospective studies suffer from drawbacks such as selection bias. As the selection of the control group has a significant impact on the evaluation of the results, it is very important to find the proper method to generate the most appropriate control group. In this paper we suggest two nearest neighbors based control group selection methods that aim to achieve good matching between the individuals of case and control groups. The effectiveness of the proposed methods is evaluated by runtime and accuracy tests and the results are compared to the classical stratified sampling method.

SUNQUAKE GENERATION BY CORONAL MAGNETIC RESTRUCTURING

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

Russell, A. J. B.; Mooney, M. K.; Leake, J. E.

2016-11-01

Sunquakes are the surface signatures of acoustic waves in the Sun’s interior that are produced by some but not all flares and coronal mass ejections (CMEs). This paper explores a mechanism for sunquake generation by the changes in magnetic field that occur during flares and CMEs, using MHD simulations with a semiempirical FAL-C atmosphere to demonstrate the generation of acoustic waves in the interior in response to changing magnetic tilt in the corona. We find that Alfvén–sound resonance combined with the ponderomotive force produces acoustic waves in the interior with sufficient energy to match sunquake observations when the magnetic fieldmore » angle changes of the order of 10° in a region where the coronal field strength is a few hundred gauss or more. The most energetic sunquakes are produced when the coronal field is strong, while the variation of magnetic field strength with height and the timescale of the change in tilt are of secondary importance.« less

Generating equilateral random polygons in confinement

NASA Astrophysics Data System (ADS)

Diao, Y.; Ernst, C.; Montemayor, A.; Ziegler, U.

2011-10-01

One challenging problem in biology is to understand the mechanism of DNA packing in a confined volume such as a cell. It is known that confined circular DNA is often knotted and hence the topology of the extracted (and relaxed) circular DNA can be used as a probe of the DNA packing mechanism. However, in order to properly estimate the topological properties of the confined circular DNA structures using mathematical models, it is necessary to generate large ensembles of simulated closed chains (i.e. polygons) of equal edge lengths that are confined in a volume such as a sphere of certain fixed radius. Finding efficient algorithms that properly sample the space of such confined equilateral random polygons is a difficult problem. In this paper, we propose a method that generates confined equilateral random polygons based on their probability distribution. This method requires the creation of a large database initially. However, once the database has been created, a confined equilateral random polygon of length n can be generated in linear time in terms of n. The errors introduced by the method can be controlled and reduced by the refinement of the database. Furthermore, our numerical simulations indicate that these errors are unbiased and tend to cancel each other in a long polygon.

Future requirements in surface modeling and grid generation

NASA Technical Reports Server (NTRS)

Cosner, Raymond R.

1995-01-01

The past ten years have seen steady progress in surface modeling procedures, and wholesale changes in grid generation technology. Today, it seems fair to state that a satisfactory grid can be developed to model nearly any configuration of interest. The issues at present focus on operational concerns such as cost and quality. Continuing evolution of the engineering process is placing new demands on the technologies of surface modeling and grid generation. In the evolution toward a multidisciplinary analysis-bascd design environment, methods developed for Computational Fluid Dynamics are finding acceptance in many additional applications. These two trends, the normal evolution of the process and a watershed shift toward concurrent and multidisciplinary analysis, will be considered in assessing current capabilities and needed technological improvements.

Field-enhanced route to generating anti-Frenkel pairs in HfO2

NASA Astrophysics Data System (ADS)

Schie, Marcel; Menzel, Stephan; Robertson, John; Waser, Rainer; De Souza, Roger A.

2018-03-01

The generation of anti-Frenkel pairs (oxygen vacancies and oxygen interstitials) in monoclinic and cubic HfO2 under an applied electric field is examined. A thermodynamic model is used to derive an expression for the critical field strength required to generate an anti-Frenkel pair. The critical field strength of EaFcr˜101GVm-1 obtained for HfO2 exceeds substantially the field strengths routinely employed in the forming and switching operations of resistive switching HfO2 devices, suggesting that field-enhanced defect generation is negligible. Atomistic simulations with molecular static (MS) and molecular dynamic (MD) approaches support this finding. The MS calculations indicated a high formation energy of Δ EaF≈8 eV for the infinitely separated anti-Frenkel pair, and only a decrease to Δ EaF≈6 eV for the adjacent anti-Frenkel pair. The MD simulations showed no defect generation in either phase for E <3 GVm-1 , and only sporadic defect generation in the monoclinic phase (at E =3 GVm-1 ) with fast (trec<4 ps ) recombination. At even higher E but below EaFcr both monoclinic and cubic structures became unstable as a result of field-induced deformation of the ionic potential wells. Further MD investigations starting with preexisting anti-Frenkel pairs revealed recombination of all pairs within trec<1 ps , even for the case of neutral vacancies and charged interstitials, for which formally there is no electrostatic attraction between the defects. In conclusion, we find no physically reasonable route to generating point-defects in HfO2 by an applied field.

Generational Recruiting: Applying Generational Theory to Tactical Level Recruiting

DTIC Science & Technology

2013-04-24

Development Command Quantico, Virginia 22134-5068 MASTER OF MILITARY STUDIES TITLE: GENERATIONAL RECRUITING: APPLYING GENERATIONAL THEORY TO TACTICAL...MAIN SECTION 1:The Three Generations: Their Development , Traits, Values, and How Best to Communicate With Them...evaluation of the present young adult generation of Americans to determine how to most effectively recruit and efficiently recruit this generation for

A generative model for scientific concept hierarchies.

PubMed

Datta, Srayan; Adar, Eytan

2018-01-01

In many scientific disciplines, each new 'product' of research (method, finding, artifact, etc.) is often built upon previous findings-leading to extension and branching of scientific concepts over time. We aim to understand the evolution of scientific concepts by placing them in phylogenetic hierarchies where scientific keyphrases from a large, longitudinal academic corpora are used as a proxy of scientific concepts. These hierarchies exhibit various important properties, including power-law degree distribution, power-law component size distribution, existence of a giant component and less probability of extending an older concept. We present a generative model based on preferential attachment to simulate the graphical and temporal properties of these hierarchies which helps us understand the underlying process behind scientific concept evolution and may be useful in simulating and predicting scientific evolution.

Terahertz generation by beating two Langmuir waves in a warm and collisional plasma

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

Zhang, Xiao-Bo; Qiao, Xin; Cheng, Li-Hong

2015-09-15

Terahertz (THz) radiation generated by beating of two Langmuir waves in a warm and collisional plasma is discussed theoretically. The critical angle between the two Langmuir waves and the critical wave-length (wave vector) of Langmuir waves for generating THz radiation are obtained analytically. Furthermore, the maximum radiation energy is obtained. We find that the critical angle, the critical wave-length, and the generated radiation energy strongly depend on plasma temperature and wave-length of the Langmuir waves. That is, the THz radiation generated by beating of two Langmuir waves in a warm and collisional plasma can be controlled by adjusting the plasmamore » temperature and the Langmuir wave-length.« less

Generating Multi-Destination Maps.

PubMed

Zhang, Junsong; Fan, Jiepeng; Luo, Zhenshan

2017-08-01

Multi-destination maps are a kind of navigation maps aimed to guide visitors to multiple destinations within a region, which can be of great help to urban visitors. However, they have not been developed in the current online map service. To address this issue, we introduce a novel layout model designed especially for generating multi-destination maps, which considers the global and local layout of a multi-destination map. We model the layout problem as a graph drawing that satisfies a set of hard and soft constraints. In the global layout phase, we balance the scale factor between ROIs. In the local layout phase, we make all edges have good visibility and optimize the map layout to preserve the relative length and angle of roads. We also propose a perturbation-based optimization method to find an optimal layout in the complex solution space. The multi-destination maps generated by our system are potential feasible on the modern mobile devices and our result can show an overview and a detail view of the whole map at the same time. In addition, we perform a user study to evaluate the effectiveness of our method, and the results prove that the multi-destination maps achieve our goals well.

Apigenin promotes TRAIL-mediated apoptosis regardless of ROS generation.

PubMed

Kang, Chang-Hee; Molagoda, Ilandarage Menu Neelaka; Choi, Yung Hyun; Park, Cheol; Moon, Dong-Oh; Kim, Gi-Young

2018-01-01

Apigenin is a bioactive flavone in several herbs including parsley, thyme, and peppermint. Apigenin possesses anti-cancer and anti-inflammatory properties; however, whether apigenin enhances TRAIL-mediated apoptosis in cancer cells is unknown. In the current study, we found that apigenin enhanced TRAIL-induced apoptosis by promoting caspase activation and death receptor 5 (DR5) expression and a chimeric antibody against DR5 completely blocked the apoptosis. Apigenin also upregulated reactive oxygen species (ROS) generation; however, intriguingly, ROS inhibitors, glutathione (GSH) or N-acetyl-l-cysteine (NAC), moderately increased apigenin/TRAIL-induced apoptosis. Additional results showed that an autophagy inducer, rapamycin, enhanced apigenin/TRAIL-mediated apoptosis by a slight increase of ROS generation. Accordingly, NAC and GSH rather decreased apigenin-induced autophagy formation, suggesting that apigenin-induced ROS generation increased autophagy formation. However, autophagy inhibitors, bafilomycin (BAF) and 3-methyladenine (3-MA), showed different result in apigenin/TRAIL-mediated apoptosis without ROS generation. 3-MA upregulated the apoptosis but remained ROS levels; however, no changes on apoptosis and ROS generation were observed by BAF treatment. Taken together, these findings reveal that apigenin enhances TRAIL-induced apoptosis by activating apoptotic caspases by upregulating DR5 expression regardless of ROS generation, which may be a promising strategy for an adjuvant of TRAIL. Copyright © 2017 Elsevier Ltd. All rights reserved.

Indoor Fast Neutron Generator for Biophysical and Electronic Applications

NASA Astrophysics Data System (ADS)

Cannuli, A.; Caccamo, M. T.; Marchese, N.; Tomarchio, E. A.; Pace, C.; Magazù, S.

2018-05-01

This study focuses the attention on an indoor fast neutron generator for biophysical and electronic applications. More specifically, the findings obtained by several simulations with the MCNP Monte Carlo code, necessary for the realization of a shield for indoor measurements, are presented. Furthermore, an evaluation of the neutron spectrum modification caused by the shielding is reported. Fast neutron generators are a valid and interesting available source of neutrons, increasingly employed in a wide range of research fields, such as science and engineering. The employed portable pulsed neutron source is a MP320 Thermo Scientific neutron generator, able to generate 2.5 MeV neutrons with a neutron yield of 2.0 x 106 n/s, a pulse rate of 250 Hz to 20 KHz and a duty factor varying from 5% to 100%. The neutron generator, based on Deuterium-Deuterium nuclear fusion reactions, is employed in conjunction with a solid-state photon detector, made of n-type high-purity germanium (PINS-GMX by ORTEC) and it is mainly addressed to biophysical and electronic studies. The present study showed a proposal for the realization of a shield necessary for indoor applications for MP320 neutron generator, with a particular analysis of the transport of neutrons simulated with Monte Carlo code and described the two main lines of research in which the source will be used.

Generation and Initial Characterization of FDD Knock In Mice

PubMed Central

Giliberto, Luca; Matsuda, Shuji; Vidal, Ruben; D'Adamio, Luciano

2009-01-01

Background Mutations in the integral membrane protein 2B [1], also known as BRI2 [2], a type II trans-membrane domain protein cause two autosomal dominant neurodegenerative diseases, Familial British and Danish Dementia [3]. In these conditions, accumulation of a C-terminal peptide (ABri and ADan) cleaved off from the mutated precursor protein by the pro-protein convertase furin [4], leads to amyloid deposition in the walls of blood vessels and parenchyma of the brain. Recent advances in the understanding of the generation of amyloid in Alzheimer's disease has lead to the finding that BRI2 interacts with the Amyloid Precursor Protein (APP), decreasing the efficiency of APP processing to generate Aβ [5], [6], [7]. The interaction between the two precursors, APP and BRI2, and possibly between Aβ and ABri or ADan, could be important in influencing the rate of amyloid production or the tendency of these peptides to aggregate. Methodology/Principal Findings We have generated the first BRI2 Danish Knock-In (FDDKI) murine model of FDD, expressing the pathogenic decamer duplication in exon 6 of the BRI2 gene. FDDKI mice do not show any evident abnormal phenotype, with normal brain histology and no detectable amyloid deposition in blood vessel walls or parenchyma. Conclusions/Significance This new murine mouse model will be important to further understand the interaction between APP and BRI2, and to provide insights into the molecular basis of FDD. PMID:19924302

Consulting communities on feedback of genetic findings in international health research: sharing sickle cell disease and carrier information in coastal Kenya

PubMed Central

2013-01-01

Background International health research in malaria-endemic settings may include screening for sickle cell disease, given the relationship between this important genetic condition and resistance to malaria, generating questions about whether and how findings should be disclosed. The literature on disclosing genetic findings in the context of research highlights the role of community consultation in understanding and balancing ethically important issues from participants’ perspectives, including social forms of benefit and harm, and the influence of access to care. To inform research practice locally, and contribute to policy more widely, this study aimed to explore the views of local residents in Kilifi County in coastal Kenya on how researchers should manage study-generated information on sickle cell disease and carrier status. Methods Between June 2010 and July 2011, we consulted 62 purposively selected Kilifi residents on how researchers should manage study-generated sickle cell disease findings. Methods drew on a series of deliberative informed small group discussions. Data were analysed thematically, using charts, to describe participants’ perceptions of the importance of disclosing findings, including reasoning, difference and underlying values. Themes were derived from the underlying research questions and from issues emerging from discussions. Data interpretation drew on relevant areas of social science and bioethics literature. Results Perceived health and social benefits generated strong support for disclosing findings on sickle cell disease, but the balance of social benefits and harms was less clear for sickle cell trait. Many forms of health and social benefits and harms of information-sharing were identified, with important underlying values related to family interests and the importance of openness. The influence of micro and macro level contextual features and prioritization of values led to marked diversity of opinion. Conclusions The approach

Consulting communities on feedback of genetic findings in international health research: sharing sickle cell disease and carrier information in coastal Kenya.

PubMed

Marsh, Vicki; Kombe, Francis; Fitzpatrick, Raymond; Williams, Thomas N; Parker, Michael; Molyneux, Sassy

2013-10-14

International health research in malaria-endemic settings may include screening for sickle cell disease, given the relationship between this important genetic condition and resistance to malaria, generating questions about whether and how findings should be disclosed. The literature on disclosing genetic findings in the context of research highlights the role of community consultation in understanding and balancing ethically important issues from participants' perspectives, including social forms of benefit and harm, and the influence of access to care. To inform research practice locally, and contribute to policy more widely, this study aimed to explore the views of local residents in Kilifi County in coastal Kenya on how researchers should manage study-generated information on sickle cell disease and carrier status. Between June 2010 and July 2011, we consulted 62 purposively selected Kilifi residents on how researchers should manage study-generated sickle cell disease findings. Methods drew on a series of deliberative informed small group discussions. Data were analysed thematically, using charts, to describe participants' perceptions of the importance of disclosing findings, including reasoning, difference and underlying values. Themes were derived from the underlying research questions and from issues emerging from discussions. Data interpretation drew on relevant areas of social science and bioethics literature. Perceived health and social benefits generated strong support for disclosing findings on sickle cell disease, but the balance of social benefits and harms was less clear for sickle cell trait. Many forms of health and social benefits and harms of information-sharing were identified, with important underlying values related to family interests and the importance of openness. The influence of micro and macro level contextual features and prioritization of values led to marked diversity of opinion. The approach demonstrates a high ethical importance in

Towards an automated intelligence product generation capability

NASA Astrophysics Data System (ADS)

Smith, Alison M.; Hawes, Timothy W.; Nolan, James J.

2015-05-01

Creating intelligence information products is a time consuming and difficult process for analysts faced with identifying key pieces of information relevant to a complex set of information requirements. Complicating matters, these key pieces of information exist in multiple modalities scattered across data stores, buried in huge volumes of data. This results in the current predicament analysts find themselves; information retrieval and management consumes huge amounts of time that could be better spent performing analysis. The persistent growth in data accumulation rates will only increase the amount of time spent on these tasks without a significant advance in automated solutions for information product generation. We present a product generation tool, Automated PrOduct Generation and Enrichment (APOGEE), which aims to automate the information product creation process in order to shift the bulk of the analysts' effort from data discovery and management to analysis. APOGEE discovers relevant text, imagery, video, and audio for inclusion in information products using semantic and statistical models of unstructured content. APOGEEs mixed-initiative interface, supported by highly responsive backend mechanisms, allows analysts to dynamically control the product generation process ensuring a maximally relevant result. The combination of these capabilities results in significant reductions in the time it takes analysts to produce information products while helping to increase the overall coverage. Through evaluation with a domain expert, APOGEE has been shown the potential to cut down the time for product generation by 20x. The result is a flexible end-to-end system that can be rapidly deployed in new operational settings.

Teaching Millennials and Generation Z: Bridging the Generational Divide.

PubMed

Shatto, Bobbi; Erwin, Kelly

2017-02-01

Most undergraduate students today are part of the millennial generation. However, the next wave of students-Generation Z-are just beginning to enter universities. Although these groups share many similarities, they each have unique characteristics that create challenges in the classroom. Incorporating technology, engaging students with adaptive learning activities, and understanding basic generational differences are ways to limit the effects of generational conflict while keeping both millennials and Generation Z students engaged in learning. It is important to understand basic differences and distinctions across generations for developing pedagogy that reaches these unique student populations.

Findings

MedlinePlus

... Issue All Issues Explore Findings by Topic Cell Biology Cellular Structures, Functions, Processes, Imaging, Stress Response Chemistry ... Glycobiology, Synthesis, Natural Products, Chemical Reactions Computers in Biology Bioinformatics, Modeling, Systems Biology, Data Visualization Diseases Cancer, ...

Durational and generational differences in Mexican immigrant obesity: Is acculturation the explanation?

PubMed Central

Creighton, Mathew J.; Goldman, Noreen; Pebley, Anne R.; Chung, Chang Y.

2012-01-01

Using the Los Angeles Family and Neighborhood Survey (L.A.FANS-2; n = 1610), we explore the link between Mexican immigrant acculturation, diet, exercise and obesity. We distinguish Mexican immigrants and 2nd generation Mexicans from 3rd+ generation whites, blacks and Mexicans. First, we examine variation in social and linguistic measures by race/ethnicity, duration of residence and immigrant generation. Second, we consider the association between acculturation, diet and exercise. Third, we evaluate the degree to which acculturation, diet, exercise, and socioeconomic status explain the association between race/ethnicity, immigrant exposure to the US (duration since immigration/generation), and adult obesity. Among immigrants, we find a clear relationship between acculturation measures, exposure to the US, and obesity-related behaviors (diet and exercise). However, the acculturation measures do not clearly account for the link between adult obesity, immigrant duration and generation, and race/ethnicity. PMID:22575698

Are Generation Y Nurses Satisfied on the Job? Understanding Their Lived Experiences.

PubMed

Anselmo-Witzel, Sonia; Orshan, Susan A; Heitner, Keri L; Bachand, Jeanie

2017-04-01

The purpose of this study was to explore the lived experiences of job satisfaction among Generation Y nurses in the workplace. Job satisfaction in nursing is at an all-time low. With an increasing shortage of nurses, there is a need for more awareness and understanding of job satisfaction and intent to stay among Generation Y nurses who are the future generation of nurses. Descriptive phenomenology-guided, in-depth semistructured interviews were conducted to explore the lived experiences of job satisfaction among 10 Generation Y nurses. Four main themes and 6 subthemes that emerged brought meaning to the nurses' experiences. The 4 main themes were experiences of feeling good, relationships, job strain, and having choices. Findings indicated Generation Y nurses want to fulfill inner feelings of job satisfaction. If these inner feelings are not met, they will seek other opportunities to fulfill job satisfaction.

Identity, prosocial behavior, and generative concern in German and Cameroonian Nso adolescents.

PubMed

Busch, Holger; Hofer, Jan

2011-08-01

Little is known about whether ego identity statuses have the same developmental concomitants in different cultural contexts. Thus, 159 German and 158 Cameroonian Nso adolescents aged 15-18 were recruited to test if associations between identity and generativity (i.e. the desire to create a positive legacy) and prosocial behavior (i.e. helpful and supportive behavior), respectively, are comparable. In both cultural samples, only identity achievement was positively linked with generative concern and prosocial tendencies. Integrating these and previous findings on the association between prosocial behavior and generativity, a partial mediation of the relation between identity achievement and generative concern through prosocial tendencies was hypothesized and confirmed for both cultural groups. Thus, there is an equivalent association between identity achievement, prosocial behavior, and generative concern in adolescents with widely different cultural background. Copyright © 2010 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

High-order-harmonic generation from H2+ molecular ions near plasmon-enhanced laser fields

NASA Astrophysics Data System (ADS)

Yavuz, I.; Tikman, Y.; Altun, Z.

2015-08-01

Simulations of plasmon-enhanced high-order-harmonic generation are performed for a H2+ molecular cation near the metallic nanostructures. We employ the numerical solution of the time-dependent Schrödinger equation in reduced coordinates. We assume that the main axis of H2+ is aligned perfectly with the polarization direction of the plasmon-enhanced field. We perform systematic calculations on plasmon-enhanced harmonic generation based on an infinite-mass approximation, i.e., pausing nuclear vibrations. Our simulations show that molecular high-order-harmonic generation from plasmon-enhanced laser fields is possible. We observe the dispersion of a plateau of harmonics when the laser field is plasmon enhanced. We find that the maximum kinetic energy of the returning electron follows 4 Up . We also find that when nuclear vibrations are enabled, the efficiency of the harmonics is greatly enhanced relative to that of static nuclei. However, the maximum kinetic energy 4 Up is largely maintained.

Cirrus cloud model parameterizations: Incorporating realistic ice particle generation

NASA Technical Reports Server (NTRS)

Sassen, Kenneth; Dodd, G. C.; Starr, David OC.

1990-01-01

Recent cirrus cloud modeling studies have involved the application of a time-dependent, two dimensional Eulerian model, with generalized cloud microphysical parameterizations drawn from experimental findings. For computing the ice versus vapor phase changes, the ice mass content is linked to the maintenance of a relative humidity with respect to ice (RHI) of 105 percent; ice growth occurs both with regard to the introduction of new particles and the growth of existing particles. In a simplified cloud model designed to investigate the basic role of various physical processes in the growth and maintenance of cirrus clouds, these parametric relations are justifiable. In comparison, the one dimensional cloud microphysical model recently applied to evaluating the nucleation and growth of ice crystals in cirrus clouds explicitly treated populations of haze and cloud droplets, and ice crystals. Although these two modeling approaches are clearly incompatible, the goal of the present numerical study is to develop a parametric treatment of new ice particle generation, on the basis of detailed microphysical model findings, for incorporation into improved cirrus growth models. For example, the relation between temperature and the relative humidity required to generate ice crystals from ammonium sulfate haze droplets, whose probability of freezing through the homogeneous nucleation mode are a combined function of time and droplet molality, volume, and temperature. As an example of this approach, the results of cloud microphysical simulations are presented showing the rather narrow domain in the temperature/humidity field where new ice crystals can be generated. The microphysical simulations point out the need for detailed CCN studies at cirrus altitudes and haze droplet measurements within cirrus clouds, but also suggest that a relatively simple treatment of ice particle generation, which includes cloud chemistry, can be incorporated into cirrus cloud growth.

The analysis of harmonic generation coefficients in the ablative Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Lu, Yan; Fan, Zhengfeng; Lu, Xinpei; Ye, Wenhua; Zou, Changlin; Zhang, Ziyun; Zhang, Wen

2017-10-01

In this research, we use the numerical simulation method to investigate the generation coefficients of the first three harmonics and the zeroth harmonic in the Ablative Rayleigh-Taylor Instability. It is shown that the interface shifts to the low temperature side during the ablation process. In consideration of the third-order perturbation theory, the first three harmonic amplitudes of the weakly nonlinear regime are calculated and then the harmonic generation coefficients are obtained by curve fitting. The simulation results show that the harmonic generation coefficients changed with time and wavelength. Using the higher-order perturbation theory, we find that more and more harmonics are generated in the later weakly nonlinear stage, which is caused by the negative feedback of the later higher harmonics. Furthermore, extending the third-order theory to the fifth-order theory, we find that the second and the third harmonics coefficients linearly depend on the wavelength, while the feedback coefficients are almost constant. Further analysis also shows that when the fifth-order theory is considered, the normalized effective amplitudes of second and third harmonics can reach about 25%-40%, which are only 15%-25% in the frame of the previous third-order theory. Therefore, the third order perturbation theory is needed to be modified by the higher-order theory when ηL reaches about 20% of the perturbation wavelength.

Psychological empowerment and job satisfaction between Baby Boomer and Generation X nurses.

PubMed

Sparks, Amy M

2012-05-01

This paper is a report of a study of differences in nurses' generational psychological empowerment and job satisfaction. Generations differ in work styles such as autonomy, work ethics, involvement, views on leadership, and primary views on what constitutes innovation, quality, and service. A secondary analysis was conducted from two data sets resulting in a sample of 451 registered nurses employed at five hospitals in West Virginia. One data set was gathered from a convenience sample and one from a randomly selected sample. Data were collected from 2000 to 2004. Baby Boomer nurses reported higher mean total psychological empowerment scores than Generation X nurses. There were no differences in total job satisfaction scores between the generations. There were significant differences among the generations' psychological empowerment scores. Generational differences related to psychological empowerment could provide insight into inconsistent findings related to nurse job satisfaction. Nurse administrators may consider this evidence when working on strategic plans to motivate and entice Generation X nurses and retain Baby Boomers. Although implications based on this study are tentative, the results indicate the need for administrators to consider the differences between Baby Boomer and Generation X nurses. © 2011 Blackwell Publishing Ltd.

In vitro comparison of noise levels produced by different CPAP generators.

PubMed

Kirchner, Lieselotte; Wald, Martin; Jeitler, Valerie; Pollak, Arnold

2012-01-01

Minimization of noise exposure is an important aim of modern neonatal intensive care medicine. Binasal continuous positive airway pressure (CPAP) generators are among the most important sources of continuous noise in neonatal wards. The aim of this study was to find out which CPAP generator creates the least noise. In an experimental setup, two jet CPAP generators (Infant Flow® generator and MediJet®) and two conventional CPAP generators (Bubble CPAP® and Baby Flow®) were compared. Noise production was measured in decibels in an A-weighted scale [dB(A)] in a closed incubator at 2 mm lateral distance from the end of the nasal prongs. Reproduction of constant airway pressure and air leak was achieved by closure of the nasal prongs with a type of adhesive tape that is semipermeable to air. The noise levels produced by the four generators were significantly different (p < 0.001). Values measured at a continuous constant flow rate of 8 l/min averaged 83 dB(A) for the Infant Flow® generator with or without sound absorber, 72 dB(A) for the MediJet®, 62 dB(A) for the Bubble CPAP® and 55 dB(A) for the Baby Flow®. Conventional CPAP generators work more quietly than the currently available jet CPAP generators. Copyright © 2011 S. Karger AG, Basel.

Inertial effects on the stress generation of active fluids

NASA Astrophysics Data System (ADS)

Takatori, S. C.; Brady, J. F.

2017-09-01

Suspensions of self-propelled bodies generate a unique mechanical stress owing to their motility that impacts their large-scale collective behavior. For microswimmers suspended in a fluid with negligible particle inertia, we have shown that the virial swim stress is a useful quantity to understand the rheology and nonequilibrium behaviors of active soft matter systems. For larger self-propelled organisms such as fish, it is unclear how particle inertia impacts their stress generation and collective movement. Here we analyze the effects of finite particle inertia on the mechanical pressure (or stress) generated by a suspension of self-propelled bodies. We find that swimmers of all scales generate a unique swim stress and Reynolds stress that impact their collective motion. We discover that particle inertia plays a similar role as confinement in overdamped active Brownian systems, where the reduced run length of the swimmers decreases the swim stress and affects the phase behavior. Although the swim and Reynolds stresses vary individually with the magnitude of particle inertia, the sum of the two contributions is independent of particle inertia. This points to an important concept when computing stresses in computer simulations of nonequilibrium systems: The Reynolds and the virial stresses must both be calculated to obtain the overall stress generated by a system.

Control of mobility in molecular organic semiconductors by dendrimer generation

NASA Astrophysics Data System (ADS)

Lupton, J. M.; Samuel, I. D.; Beavington, R.; Frampton, M. J.; Burn, P. L.; Bässler, H.

2001-04-01

Conjugated dendrimers are of interest as novel materials for light-emitting diodes. They consist of a luminescent chromophore at the core with highly branched conjugated dendron sidegroups. In these materials, light emission occurs from the core and is independent of generation. The dendron branching controls the separation between the chromophores. We present here a family of conjugated dendrimers and investigate the effect of dendron branching on light emission and charge transport. We apply a number of transport measurement techniques to thin films of a conjugated dendrimer in a light-emitting diode configuration to determine the effect of chromophore spacing on charge transport. We find that the mobility is reduced by two orders of magnitude as the size of the molecule doubles with increased branching or dendrimer generation. The degree of branching allows a unique control of mobility by molecular structure. An increase in chromophore separation also results in a reduction of intermolecular interactions, which reduces the red emission tail in film photoluminescence. We find that the steady-state charge transport is well described by a simple device model incorporating the effect of generation, and use the materials to shed light on the interpretation of transient electroluminescence data. We demonstrate the significance of the ability to tune the mobility in bilayer devices, where a more balanced charge transport can be achieved.

Finding Hidden Location Patterns of Two Competitive Supermarkets in Thailand

NASA Astrophysics Data System (ADS)

Khumsri, Jinattaporn; Fujihara, Akihiro

There are two famous supermarkets in Thailand: Big C and Lotus. They are the highest competitive supermarkets whose hold the most market share by lots of promotions and also gather all convenience services including banking, restaurant, and others. In recent years, they gradually expand their stores and they take a similar strategy to determine where to locate a store. It is important for them to consider store allocation to obtain new customers efficiently. To consider this, we gather geographical locations of these supermarkets from Twitter using Twitter API. We gathered tweets having these supermarket names and geotags for seven months. To extract hidden location patterns from gathered data, we introduce location motif which is a directed subgraph whose edges are linked to every pair of the shortest-distance opponent node. We investigate every possible configuration of location motif when they have a small number of nodes and find that the configuration increases exponentially. We also visualize location motifs generated from gathered data on the map of Thailand and count the frequency of observed location motifs. As a result, we find that even if the possible location motifs exponentially increase as the number of nodes grows, limited location motifs can be observed. Using location motif, we successfully find an evidence of biased store allocation in reality.

Stress Generation, Avoidance Coping, and Depressive Symptoms: A 10-Year Model

PubMed Central

Holahan, Charles J.; Moos, Rudolf H.; Holahan, Carole K.; Brennan, Penny L.; Schutte, Kathleen K.

2011-01-01

This study examined (a) the role of avoidance coping in prospectively generating both chronic and acute life stressors and (b) the stress-generating role of avoidance coping as a prospective link to future depressive symptoms. Participants were 1,211 late-middle-aged individuals (500 women and 711 men) assessed 3 times over a 10-year period. As predicted, baseline avoidance coping was prospectively associated with both more chronic and more acute life stressors 4 years later. Furthermore, as predicted, these intervening life stressors linked baseline avoidance coping and depressive symptoms 10 years later, controlling for the influence of initial depressive symptoms. These findings broaden knowledge about the stress-generation process and elucidate a key mechanism through which avoidance coping is linked to depressive symptoms. PMID:16173853

Finding Direction in the Search for Selection.

PubMed

Thiltgen, Grant; Dos Reis, Mario; Goldstein, Richard A

2017-01-01

Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the species. Recently, a few methods have been developed to detect and characterize directional selection on a molecular level. Using the results of evolutionary simulations as well as HIV drug resistance data as models of directional selection, we compare two such methods with each other, as well as against a standard method for detecting diversifying selection. We find that the method to detect diversifying selection also detects directional selection under certain conditions. One method developed for detecting directional selection is powerful and accurate for a wide range of conditions, while the other can generate an excessive number of false positives.

The Generation R Study: A Review of Design, Findings to Date, and a Study of the 5-HTTLPR by Environmental Interaction from Fetal Life Onward

ERIC Educational Resources Information Center

Tiemeier, Henning; Velders, Fleur P.; Szekely, Eszter; Roza, Sabine J.; Dieleman, Gwen; Jaddoe, Vincent W. V.; Uitterlinden, Andre G.; White, Tonya J. H.; Bakermans-Kranenburg, Marian J.; Hofman, Albert; Van IJzendoorn, Marinus H.; Hudziak, James J.; Verhulst, Frank C.

2012-01-01

Objective: First, we give an overview of child psychiatric research in the Generation R Study, a population-based cohort from fetal life forward. Second, we examine within Generation R whether the functional polymorphism (5-HTTLPR) in the promoter of the serotonin transporter gene interacts with prenatal maternal chronic difficulties, prenatal…

Adapting Training to Meet the Preferred Learning Styles of Different Generations

ERIC Educational Resources Information Center

Urick, Michael

2017-01-01

This article considers how training professionals can respond to differences in training preferences between generational groups. It adopts two methods. First, it surveys the existing research and finds generally that preferences for training approaches can differ between groups and specifically that younger employees are perceived to leverage…

Crossing the Generational Divide: Supporting Generational Differences at Work

ERIC Educational Resources Information Center

Berl, Patricia Scallan

2006-01-01

Differences in attitudes and behaviors, regularly exhibited between youth and their elders, are frequently referred to as the "generation gap". On the job, these generational distinctions are becoming increasingly complex as "multi-generation gaps" emerge, with three or more generations defining roles and expectations, each vying for positions in…

Thermoelectric Generators Based on Ionic Liquids

NASA Astrophysics Data System (ADS)

Laux, Edith; Uhl, Stefanie; Jeandupeux, Laure; López, Pilar Pérez; Sanglard, Pauline; Vanoli, Ennio; Marti, Roger; Keppner, Herbert

2018-06-01

Looking at energy harvesting using body or waste heat for portable electronic or on-board devices, Ionic liquids are interesting candidates as thermoactive materials in thermoelectric generators (TEGs) because of their outstanding properties. Two different kinds of ionic liquid, with alkylammonium and choline as cations, were studied, whereby different anions and redox couples were combined. This study focussed on the intention to find non-hazardous and environmentally friendly ionic liquids for TEGs to be selected among the thousands that can potentially be used. Seebeck coefficients (SEs) as high as - 15 mV/K were measured, in a particular case for an electrode temperature difference of 20 K. The bottleneck of our TEG device is still the abundance of negative SE liquids matching the internal resistance with the existing positive SE-liquids at series connections. In this paper, we show further progress in finding increased negative SE liquids. For current extraction from the TEG, the ionic liquid must be blended with a redox couple, allowing carrier exchange in a cyclic process under a voltage which is incuced by the asymmetry of the generator in terms of hot and cold electrodes. In our study, two types of redox pairs were tested. It was observed that a high SE of an ionic liquid/redox blend is not a sufficient condition for high power output. It appears that more complex effects between the ionic liquid and the electrode determine the magnitude of the final current/power output. The physico-chemical understanding of such a TEG cell is not yet available.

Thermoelectric Generators Based on Ionic Liquids

NASA Astrophysics Data System (ADS)

Laux, Edith; Uhl, Stefanie; Jeandupeux, Laure; López, Pilar Pérez; Sanglard, Pauline; Vanoli, Ennio; Marti, Roger; Keppner, Herbert

2018-03-01

Looking at energy harvesting using body or waste heat for portable electronic or on-board devices, Ionic liquids are interesting candidates as thermoactive materials in thermoelectric generators (TEGs) because of their outstanding properties. Two different kinds of ionic liquid, with alkylammonium and choline as cations, were studied, whereby different anions and redox couples were combined. This study focussed on the intention to find non-hazardous and environmentally friendly ionic liquids for TEGs to be selected among the thousands that can potentially be used. Seebeck coefficients (SEs) as high as - 15 mV/K were measured, in a particular case for an electrode temperature difference of 20 K. The bottleneck of our TEG device is still the abundance of negative SE liquids matching the internal resistance with the existing positive SE-liquids at series connections. In this paper, we show further progress in finding increased negative SE liquids. For current extraction from the TEG, the ionic liquid must be blended with a redox couple, allowing carrier exchange in a cyclic process under a voltage which is incuced by the asymmetry of the generator in terms of hot and cold electrodes. In our study, two types of redox pairs were tested. It was observed that a high SE of an ionic liquid/redox blend is not a sufficient condition for high power output. It appears that more complex effects between the ionic liquid and the electrode determine the magnitude of the final current/power output. The physico-chemical understanding of such a TEG cell is not yet available.

Generational diversity.

PubMed

Kramer, Linda W

2010-01-01

Generational diversity has proven challenges for nurse leaders, and generational values may influence ideas about work and career planning. This article discusses generational gaps, influencing factors and support, and the various generational groups present in today's workplace as well as the consequences of need addressing these issues. The article ends with a discussion of possible solutions.

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

PubMed Central

Melckenbeeck, Ine; Audenaert, Pieter; Michoel, Tom; Colle, Didier; Pickavet, Mario

2016-01-01

Graphlets are small subgraphs, usually containing up to five vertices, that can be found in a larger graph. Identification of the graphlets that a vertex in an explored graph touches can provide useful information about the local structure of the graph around that vertex. Actually finding all graphlets in a large graph can be time-consuming, however. As the graphlets grow in size, more different graphlets emerge and the time needed to find each graphlet also scales up. If it is not needed to find each instance of each graphlet, but knowing the number of graphlets touching each node of the graph suffices, the problem is less hard. Previous research shows a way to simplify counting the graphlets: instead of looking for the graphlets needed, smaller graphlets are searched, as well as the number of common neighbors of vertices. Solving a system of equations then gives the number of times a vertex is part of each graphlet of the desired size. However, until now, equations only exist to count graphlets with 4 or 5 nodes. In this paper, two new techniques are presented. The first allows to generate the equations needed in an automatic way. This eliminates the tedious work needed to do so manually each time an extra node is added to the graphlets. The technique is independent on the number of nodes in the graphlets and can thus be used to count larger graphlets than previously possible. The second technique gives all graphlets a unique ordering which is easily extended to name graphlets of any size. Both techniques were used to generate equations to count graphlets with 4, 5 and 6 vertices, which extends all previous results. Code can be found at https://github.com/IneMelckenbeeck/equation-generator and https://github.com/IneMelckenbeeck/graphlet-naming. PMID:26797021

Primitive erythrocytes are generated from hemogenic endothelial cells.

PubMed

Stefanska, Monika; Batta, Kiran; Patel, Rahima; Florkowska, Magdalena; Kouskoff, Valerie; Lacaud, Georges

2017-07-25

Primitive erythroblasts are the first blood cells generated during embryonic hematopoiesis. Tracking their emergence both in vivo and in vitro has remained challenging due to the lack of specific cell surface markers. To selectively investigate primitive erythropoiesis, we have engineered a new transgenic embryonic stem (ES) cell line, where eGFP expression is driven by the regulatory sequences of the embryonic βH1 hemoglobin gene expressed specifically in primitive erythroid cells. Using this ES cell line, we observed that the first primitive erythroblasts are detected in vitro around day 1.5 of blast colony differentiation, within the cell population positive for the early hematopoietic progenitor marker CD41. Moreover, we establish that these eGFP + cells emerge from a hemogenic endothelial cell population similarly to their definitive hematopoietic counterparts. We further generated a corresponding βH1-eGFP transgenic mouse model and demonstrated the presence of a primitive erythroid primed hemogenic endothelial cell population in the developing embryo. Taken together, our findings demonstrate that both in vivo and in vitro primitive erythrocytes are generated from hemogenic endothelial cells.

Models of Consent to Return of Incidental Findings in Genomic Research

PubMed Central

Appelbaum, Paul S.; Parens, Erik; Waldman, Cameron R.; Klitzman, Robert; Fyer, Abby; Martinez, Josue; Price, W. Nicholson; Chung, Wendy K.

2014-01-01

Genomic research has the capacity to generate a wide array of findings that go beyond the goals of the study—usually referred to as “incidental findings.” The evolving consensus of researchers, participants, and expert panels is that at least some incidental results should be made available to participants. However, there are a number of challenges to discussing these issues with participants and ascertaining their preferences, including the complexity and magnitude of the relevant information. Believing that usual models of informed consent are not likely to be effective in this context, we identify four approaches that investigators and IRBs might consider: traditional consent, staged consent, mandatory return, and outsourcing. Each has advantages and disadvantages compared with the other options, and which one is selected for a given project will depend on a mix of practical and normative considerations that are described in this paper. PMID:24919982

Statistical Analysis of Complexity Generators for Cost Estimation

NASA Technical Reports Server (NTRS)

Rowell, Ginger Holmes

1999-01-01

Predicting the cost of cutting edge new technologies involved with spacecraft hardware can be quite complicated. A new feature of the NASA Air Force Cost Model (NAFCOM), called the Complexity Generator, is being developed to model the complexity factors that drive the cost of space hardware. This parametric approach is also designed to account for the differences in cost, based on factors that are unique to each system and subsystem. The cost driver categories included in this model are weight, inheritance from previous missions, technical complexity, and management factors. This paper explains the Complexity Generator framework, the statistical methods used to select the best model within this framework, and the procedures used to find the region of predictability and the prediction intervals for the cost of a mission.

Working Sandwich Generation Women Utilize Strategies within and between Roles to Achieve Role Balance.

PubMed

Evans, Kiah L; Millsteed, Jeannine; Richmond, Janet E; Falkmer, Marita; Falkmer, Torbjorn; Girdler, Sonya J

2016-01-01

Increasingly, women simultaneously balance the roles of mother, parental carer and worker. However, individual role balance strategies among these working 'sandwich' generation women have not been thoroughly explored. Eighteen women combining these three roles were interviewed about their individual role balance strategies. Findings were identified through the framework analysis technique, underpinned by the Model of Juggling Occupations. Achieving and maintaining role balance was explained as a complex process accomplished through a range of strategies. Findings revealed the women used six within-role balance strategies: living with integrity, being the best you can, doing what you love, loving what you do, remembering why and searching for signs of success. The women also described six between-role balance strategies: maintaining health and wellbeing, repressing perfectionism, managing time and energy, releasing responsibility, nurturing social connection and reciprocating. These findings provide a basis for health care providers to understand and potentially support working 'sandwich' generation women.

Working Sandwich Generation Women Utilize Strategies within and between Roles to Achieve Role Balance

PubMed Central

Girdler, Sonya J.

2016-01-01

Increasingly, women simultaneously balance the roles of mother, parental carer and worker. However, individual role balance strategies among these working ‘sandwich’ generation women have not been thoroughly explored. Eighteen women combining these three roles were interviewed about their individual role balance strategies. Findings were identified through the framework analysis technique, underpinned by the Model of Juggling Occupations. Achieving and maintaining role balance was explained as a complex process accomplished through a range of strategies. Findings revealed the women used six within-role balance strategies: living with integrity, being the best you can, doing what you love, loving what you do, remembering why and searching for signs of success. The women also described six between-role balance strategies: maintaining health and wellbeing, repressing perfectionism, managing time and energy, releasing responsibility, nurturing social connection and reciprocating. These findings provide a basis for health care providers to understand and potentially support working ‘sandwich’ generation women. PMID:27305074

Motor/generator

DOEpatents

Hickam, Christopher Dale [Glasford, IL

2008-05-13

A motor/generator is provided for connecting between a transmission input shaft and an output shaft of a prime mover. The motor/generator may include a motor/generator housing, a stator mounted to the motor/generator housing, a rotor mounted at least partially within the motor/generator housing and rotatable about a rotor rotation axis, and a transmission-shaft coupler drivingly coupled to the rotor. The transmission-shaft coupler may include a clamp, which may include a base attached to the rotor and a plurality of adjustable jaws.

Expect the unexpected: screening for secondary findings in clinical genomics research.

PubMed

Mackley, Michael P; Capps, Benjamin

2017-06-01

Due to decreasing cost, and increasing speed and precision, genomic sequencing in research is resulting in the generation of vast amounts of genetic data. The question of how to manage that information has been an area of significant debate. In particular, there has been much discussion around the issue of 'secondary findings' (SF)-findings unrelated to the research that have diagnostic significance. The following includes ethical commentaries, guidelines and policies in respect to large-scale clinical genomics studies. Research participant autonomy and their informed consent are paramount-policies around SF must be made clear and participants must have the choice as to which results they wish to receive, if any. While many agree that clinically 'actionable' findings should be returned, some question whether they should be actively sought within a research protocol. SF present challenges to a growing field; diverse policies around their management have the potential to hinder collaboration and future research. The impact of returning SF and accurate estimates of their clinical utility are needed to inform future protocol design. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Quantitative Comparison of Photothermal Heat Generation between Gold Nanospheres and Nanorods.

PubMed

Qin, Zhenpeng; Wang, Yiru; Randrianalisoa, Jaona; Raeesi, Vahid; Chan, Warren C W; Lipiński, Wojciech; Bischof, John C

2016-07-21

Gold nanoparticles (GNPs) are widely used for biomedical applications due to unique optical properties, established synthesis methods, and biological compatibility. Despite important applications of plasmonic heating in thermal therapy, imaging, and diagnostics, the lack of quantification in heat generation leads to difficulties in comparing the heating capability for new plasmonic nanostructures and predicting the therapeutic and diagnostic outcome. This study quantifies GNP heat generation by experimental measurements and theoretical predictions for gold nanospheres (GNS) and nanorods (GNR). Interestingly, the results show a GNP-type dependent agreement between experiment and theory. The measured heat generation of GNS matches well with theory, while the measured heat generation of GNR is only 30% of that predicted theoretically at peak absorption. This then leads to a surprising finding that the polydispersity, the deviation of nanoparticle size and shape from nominal value, significantly influences GNR heat generation (>70% reduction), while having a limited effect for GNS (<10% change). This work demonstrates that polydispersity is an important metric in quantitatively predicting plasmonic heat generation and provides a validated framework to quantitatively compare the heating capabilities between gold and other plasmonic nanostructures.

Quantitative Comparison of Photothermal Heat Generation between Gold Nanospheres and Nanorods

NASA Astrophysics Data System (ADS)

Qin, Zhenpeng; Wang, Yiru; Randrianalisoa, Jaona; Raeesi, Vahid; Chan, Warren C. W.; Lipiński, Wojciech; Bischof, John C.

2016-07-01

Gold nanoparticles (GNPs) are widely used for biomedical applications due to unique optical properties, established synthesis methods, and biological compatibility. Despite important applications of plasmonic heating in thermal therapy, imaging, and diagnostics, the lack of quantification in heat generation leads to difficulties in comparing the heating capability for new plasmonic nanostructures and predicting the therapeutic and diagnostic outcome. This study quantifies GNP heat generation by experimental measurements and theoretical predictions for gold nanospheres (GNS) and nanorods (GNR). Interestingly, the results show a GNP-type dependent agreement between experiment and theory. The measured heat generation of GNS matches well with theory, while the measured heat generation of GNR is only 30% of that predicted theoretically at peak absorption. This then leads to a surprising finding that the polydispersity, the deviation of nanoparticle size and shape from nominal value, significantly influences GNR heat generation (>70% reduction), while having a limited effect for GNS (<10% change). This work demonstrates that polydispersity is an important metric in quantitatively predicting plasmonic heat generation and provides a validated framework to quantitatively compare the heating capabilities between gold and other plasmonic nanostructures.

Experimental Verification of Entanglement Generated in a Plasmonic System.

PubMed

Dieleman, F; Tame, M S; Sonnefraud, Y; Kim, M S; Maier, S A

2017-12-13

A core process in many quantum tasks is the generation of entanglement. It is being actively studied in a variety of physical settings-from simple bipartite systems to complex multipartite systems. In this work we experimentally study the generation of bipartite entanglement in a nanophotonic system. Entanglement is generated via the quantum interference of two surface plasmon polaritons in a beamsplitter structure, i.e., utilizing the Hong-Ou-Mandel (HOM) effect, and its presence is verified using quantum state tomography. The amount of entanglement is quantified by the concurrence and we find values of up to 0.77 ± 0.04. Verifying entanglement in the output state from HOM interference is a nontrivial task and cannot be inferred from the visibility alone. The techniques we use to verify entanglement could be applied to other types of photonic system and therefore may be useful for the characterization of a range of different nanophotonic quantum devices.

Spontaneous Generation of Infectious Prion Disease in Transgenic Mice

PubMed Central

Castilla, Joaquín; Pintado, Belén; Gutiérrez-Adan, Alfonso; Andréoletti, Olivier; Aguilar-Calvo, Patricia; Arroba, Ana-Isabel; Parra-Arrondo, Beatriz; Ferrer, Isidro; Manzanares, Jorge; Espinosa, Juan-Carlos

2013-01-01

We generated transgenic mice expressing bovine cellular prion protein (PrPC) with a leucine substitution at codon 113 (113L). This protein is homologous to human protein with mutation 102L, and its genetic link with Gerstmann–Sträussler–Scheinker syndrome has been established. This mutation in bovine PrPC causes a fully penetrant, lethal, spongiform encephalopathy. This genetic disease was transmitted by intracerebral inoculation of brain homogenate from ill mice expressing mutant bovine PrP to mice expressing wild-type bovine PrP, which indicated de novo generation of infectious prions. Our findings demonstrate that a single amino acid change in the PrPC sequence can induce spontaneous generation of an infectious prion disease that differs from all others identified in hosts expressing the same PrPC sequence. These observations support the view that a variety of infectious prion strains might spontaneously emerge in hosts displaying random genetic PrPC mutations. PMID:24274622

Wind Generators

NASA Technical Reports Server (NTRS)

1989-01-01

When Enerpro, Inc. president, Frank J. Bourbeau, attempted to file a patent on a system for synchronizing a wind generator to the electric utility grid, he discovered Marshall Space Flight Center's Frank Nola's power factor controller. Bourbeau advanced the technology and received a NASA license and a patent for his Auto Synchronous Controller (ASC). The ASC reduces generator "inrush current," which occurs when large generators are abruptly brought on line. It controls voltage so the generator is smoothly connected to the utility grid when it reaches its synchronous speed, protecting the components from inrush current damage. Generator efficiency is also increased in light winds by applying lower than rated voltage. Wind energy is utilized to drive turbines to generate electricity for utility companies.

Generating Customized Verifiers for Automatically Generated Code

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2008-01-01

Program verification using Hoare-style techniques requires many logical annotations. We have previously developed a generic annotation inference algorithm that weaves in all annotations required to certify safety properties for automatically generated code. It uses patterns to capture generator- and property-specific code idioms and property-specific meta-program fragments to construct the annotations. The algorithm is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, this is difficult since it involves tedious and error-prone low-level term manipulations. Here, we describe an annotation schema compiler that largely automates this customization task using generative techniques. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all customized analysis functions and glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator, and we demonstrate this by customizing it to certify frame safety of space flight navigation code that was automatically generated from Simulink models by MathWorks' Real-Time Workshop.

Age Moderates the Relationship Between Generativity Concern and Understanding of Wealth.

PubMed

Li, Tianyuan; Tsang, Vivian Hiu-Ling

2016-01-01

Wealth can be considered as resource to promote either public welfare (i.e. through altruistic understanding) or personal well-being (i.e. through egoistic understanding). How people understand wealth can influence the distribution of valuable materialistic resources within a society. The current study examined how generativity concern, the concern for next generation and social welfare in the future, influenced people's understanding of wealth and whether age moderated the relationship. A total of 133 participants ranging from 18 to 78 years old were interviewed with four open-ended questions regarding their understanding of wealth. Their generativity concern and demographical information were also recorded. Findings showed that generativity concern was related to a less egoistic and more altruistic understanding of wealth. Moreover, the effect of generativity concern was especially salient for younger adults, but not significant for older adults. The results suggest that generativity concern is a construct that applies to both young and older adults. It can even be more influential to young adults' cognitive conceptualization in certain aspects (e.g., understanding of wealth) than that of older adults. Future studies can further investigate the general impact of generativity concern as well as the behavioral consequences of people's understanding of wealth. The results were also discussed in the context of lifelong learning.

Automatic Generation of Supervisory Control System Software Using Graph Composition

NASA Astrophysics Data System (ADS)

Nakata, Hideo; Sano, Tatsuro; Kojima, Taizo; Seo, Kazuo; Uchida, Tomoyuki; Nakamura, Yasuaki

This paper describes the automatic generation of system descriptions for SCADA (Supervisory Control And Data Acquisition) systems. The proposed method produces various types of data and programs for SCADA systems from equipment definitions using conversion rules. At first, this method makes directed graphs, which represent connections between the equipment, from equipment definitions. System descriptions are generated using the conversion rules, by analyzing these directed graphs, and finding the groups of equipment that involve similar operations. This method can make the conversion rules multi levels by using the composition of graphs, and can reduce the number of rules. The developer can define and manage these rules efficiently.

Luteolin as reactive oxygen generator by X-ray and UV irradiation

NASA Astrophysics Data System (ADS)

Toyama, Michiru; Mori, Takashi; Takahashi, Junko; Iwahashi, Hitoshi

2018-05-01

Non-toxic X-ray-responsive substances can be used in the radiosensitization of cancer, like porphyrin mediated radiotherapy. However, most X-ray-responsive substances are toxic. To find novel non-toxic X-ray-responsive substances, we studied the X-ray and UV reactivity of 40 non-toxic compounds extracted from plants. Dihydroethidium was used as an indicator to detect reactive oxygen species (ROS) generated by the compounds under X-ray or UV irradiation. We found that 13 of the investigated compounds generated ROS under X-ray irradiation and 17 generated ROS under UV irradiation. Only 4 substances generated ROS under both X-ray and UV. In particular, luteolin exhibited the highest activity among the investigated compounds; therefore, the ROS generated by luteolin were thoroughly characterized. To identify the ROS, we employed a combination of ROS detection reagents and their quenchers. O2·- generation by luteolin was monitored using dihydroethidium and superoxide dismutase (as an O2·- quencher). OH· and 1O2 generation was determined using aminophenyl fluorescein with ethanol (OH· quencher) and Singlet Oxygen Sensor Green® with NaN3 (1O2 quencher), respectively. Generation of O2·- under X-ray and UV irradiation was observed; however, no OH· or 1O2 was detected. The production of ROS from luteolin is surprising, because luteolin is a well-known antioxidant.

Family Finding Evaluations: A Summary of Recent Findings--Appendix. Publication #2015-01A

ERIC Educational Resources Information Center

Vandivere, Sharon; Malm, Karin

2015-01-01

This document was produced by the authors based on their research for the report, "Family Finding Evaluations: A Summary of Recent Findings. Publication #2015-01," and is an added resource for further information. The report reviews the results from 13 evaluations of Family Finding. The Family Finding model provides child welfare…

Species Profiles: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (South Atlantic) Hard Clam,

DTIC Science & Technology

1987-08-01

C.E., and R.F. Srna. 1975 Shallow-water marine benthic macro- Toxicity of ammonia, n itite ion, invertebrates of South Carolina: nitrate ion, anI...to iden- Proc. Gulf Caribb. Fish. Inst. 26: tification of marine and estuarine 59-74. invertebrates : Cape Hatteras to the Bay of Fundy. Wiley...Ma is. Mileikovsky, S.A. 1973. Speed of 7;-pWT-ihtsville Beach. 17 pp. active movement of pelagic larvae of marine bottom invertebrates and Pearse

Does the stress generation hypothesis apply to eating disorders?: an examination of stress generation in eating, depressive, and anxiety symptoms.

PubMed

Bodell, Lindsay P; Hames, Jennifer L; Holm-Denoma, Jill M; Smith, April R; Gordon, Kathryn H; Joiner, Thomas E

2012-12-15

The stress generation hypothesis posits that individuals actively contribute to stress in their lives. Although stress generation has been studied frequently in the context of depression, few studies have examined whether this stress generation process is unique to depression or whether it occurs in other disorders. Although evidence suggests that stress contributes to the development of eating disorders, it is unclear whether eating disorders contribute to subsequent stress. A prospective design was used to examine the influence of eating disorder symptoms on negative life stressors. Two hundred and ninety female undergraduates completed questionnaires at two time points that examined eating disorder, depressive and anxiety symptoms and the presence of negative life events. Regression analyses found that while eating disorder symptoms (i.e. bulimic symptoms and drive for thinness) were independent, significant predictors of negative life events, they did not predict negative life events above and beyond symptoms of depression. Limitations include the use of self-report measures and a college-based sample, which may limit generalizability of the results. Findings suggest that if stress generation is present in individuals with symptoms of eating disorders, it is likely attributable to symptoms of depression. Thus, it may be important for clinicians to target depressive symptoms in order to reduce the frequency of negative life stressors among individuals with eating disorders. Copyright © 2012 Elsevier B.V. All rights reserved.

High-order harmonic generation from a two-dimensional band structure

NASA Astrophysics Data System (ADS)

Jin, Jian-Zhao; Xiao, Xiang-Ru; Liang, Hao; Wang, Mu-Xue; Chen, Si-Ge; Gong, Qihuang; Peng, Liang-You

2018-04-01

In the past few years, harmonic generation in solids has attracted tremendous attention. Recently, some experiments of two-dimensional (2D) monolayer or few-layer materials have been carried out. These studies demonstrated that harmonic generation in the 2D case shows a strong dependence on the laser's orientation and ellipticity, which calls for a quantitative theoretical interpretation. In this work, we carry out a systematic study on the harmonic generation from a 2D band structure based on a numerical solution to the time-dependent Schrödinger equation. By comparing with the 1D case, we find that the generation dynamics can have a significant difference due to the existence of many crossing points in the 2D band structure. In particular, the higher conduction bands can be excited step by step via these crossing points and the total contribution of the harmonic is given by the mixing of transitions between different clusters of conduction bands to the valence band. We also present the orientation dependence of the harmonic yield on the laser polarization direction.

Generational differences of baccalaureate nursing students' preferred teaching methods and faculty use of teaching methods

NASA Astrophysics Data System (ADS)

Delahoyde, Theresa

Nursing education is experiencing a generational phenomenon with student enrollment spanning three generations. Classrooms of the 21st century include the occasional Baby Boomer and a large number of Generation X and Generation Y students. Each of these generations has its own unique set of characteristics that have been shaped by values, trends, behaviors, and events in society. These generational characteristics create vast opportunities to learn, as well as challenges. One such challenge is the use of teaching methods that are congruent with nursing student preferences. Although there is a wide range of studies conducted on student learning styles within the nursing education field, there is little research on the preferred teaching methods of nursing students. The purpose of this quantitative, descriptive study was to compare the preferred teaching methods of multi-generational baccalaureate nursing students with faculty use of teaching methods. The research study included 367 participants; 38 nursing faculty and 329 nursing students from five different colleges within the Midwest region. The results of the two-tailed t-test found four statistically significant findings between Generation X and Y students and their preferred teaching methods including; lecture, listening to the professor lecture versus working in groups; actively participating in group discussion; and the importance of participating in group assignments. The results of the Analysis of Variance (ANOVA) found seventeen statistically significant findings between levels of students (freshmen/sophomores, juniors, & seniors) and their preferred teaching methods. Lecture was found to be the most frequently used teaching method by faculty as well as the most preferred teaching method by students. Overall, the support for a variety of teaching methods was also found in the analysis of data.

The Role of Generational Status, Self-Esteem, Academic Self-Efficacy, and Perceived Social Support in College Students' Psychological Well-Being

ERIC Educational Resources Information Center

Wang, Chia-Chih D. C.; Castaneda-Sound, Carrie

2008-01-01

This study examined the influences of generational status, self-esteem, academic self-efficacy, and perceived social support on 367 undergraduate college students' well-being. Findings showed that 1st-generation students reported significantly more somatic symptoms and lower levels of academic self-efficacy than did non-1st-generation students. In…

Ultrasound-driven Megahertz Faraday Waves for Generation of Monodisperse Micro Droplets and Applications

NASA Astrophysics Data System (ADS)

Tsai, Chen S.; Mao, Rong W.; Lin, Shih K.; Tsai, Shirley C.; Boss, Gerry; Brenner, Matt; Smaldone, Gerry; Mahon, Sari; Shahverdi, Kaveh; Zhu, Yun

Our theoretical findings on instability of Faraday waves at megahertz (MHz) drive frequency and realization of silicon-based MHz multiple-Fourier horn ultrasonic nozzles (MFHUNs) together have enabled generation of mono-disperse droplets of controllable diameter (2.5-6.0 μm) at very low electrical drive power (<0.5 Watt). The resulting battery-run clogging-free droplet generator has imminent application to pulmonary (inhalation) drug delivery and other potential applications. Here an update of advances on analysis and design of the MHz MFHUNs and the underlying physical mechanism for generation of mono-disperse micro droplets, and the nebulizer platform for application to detoxification of cyanide poisoning are presented.

Generative inference for cultural evolution.

PubMed

Kandler, Anne; Powell, Adam

2018-04-05

One of the major challenges in cultural evolution is to understand why and how various forms of social learning are used in human populations, both now and in the past. To date, much of the theoretical work on social learning has been done in isolation of data, and consequently many insights focus on revealing the learning processes or the distributions of cultural variants that are expected to have evolved in human populations. In population genetics, recent methodological advances have allowed a greater understanding of the explicit demographic and/or selection mechanisms that underlie observed allele frequency distributions across the globe, and their change through time. In particular, generative frameworks-often using coalescent-based simulation coupled with approximate Bayesian computation (ABC)-have provided robust inferences on the human past, with no reliance on a priori assumptions of equilibrium. Here, we demonstrate the applicability and utility of generative inference approaches to the field of cultural evolution. The framework advocated here uses observed population-level frequency data directly to establish the likely presence or absence of particular hypothesized learning strategies. In this context, we discuss the problem of equifinality and argue that, in the light of sparse cultural data and the multiplicity of possible social learning processes, the exclusion of those processes inconsistent with the observed data might be the most instructive outcome. Finally, we summarize the findings of generative inference approaches applied to a number of case studies.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Prolonged photo-carriers generated in a massive-and-anisotropic Dirac material.

PubMed

Nurmamat, Munisa; Ishida, Yukiaki; Yori, Ryohei; Sumida, Kazuki; Zhu, Siyuan; Nakatake, Masashi; Ueda, Yoshifumi; Taniguchi, Masaki; Shin, Shik; Akahama, Yuichi; Kimura, Akio

2018-06-13

Transient electron-hole pairs generated in semiconductors can exhibit unconventional excitonic condensation. Anisotropy in the carrier mass is considered as the key to elongate the life time of the pairs, and hence to stabilize the condensation. Here we employ time- and angle-resolved photoemission spectroscopy to explore the dynamics of photo-generated carriers in black phosphorus. The electronic structure above the Fermi level has been successfully observed, and a massive-and-anisotropic Dirac-type dispersions are confirmed; more importantly, we directly observe that the photo-carriers generated across the direct band gap have the life time exceeding 400 ps. Our finding confirms that black phosphorus is a suitable platform for excitonic condensations, and also open an avenue for future applications in broadband mid-infrared BP-based optoelectronic devices.

The method of generating functions in exact scalar field inflationary cosmology

NASA Astrophysics Data System (ADS)

Chervon, Sergey V.; Fomin, Igor V.; Beesham, Aroonkumar

2018-04-01

The construction of exact solutions in scalar field inflationary cosmology is of growing interest. In this work, we review the results which have been obtained with the help of one of the most effective methods, viz., the method of generating functions for the construction of exact solutions in scalar field cosmology. We also include in the debate the superpotential method, which may be considered as the bridge to the slow roll approximation equations. Based on the review, we suggest a classification for the generating functions, and find a connection for all of them with the superpotential.

Expanding Stress Generation Theory: Test of a Transdiagnostic Model

PubMed Central

Conway, Christopher C.; Hammen, Constance; Brennan, Patricia A.

2016-01-01

Originally formulated to understand the recurrence of depressive disorders, the stress generation hypothesis has recently been applied in research on anxiety and externalizing disorders. Results from these investigations, in combination with findings of extensive comorbidity between depression and other mental disorders, suggest the need for an expansion of stress generation models to include the stress generating effects of transdiagnostic pathology as well as those of specific syndromes. Employing latent variable modeling techniques to parse the general and specific elements of commonly co-occurring Axis I syndromes, the current study examined the associations of transdiagnostic internalizing and externalizing dimensions with stressful life events over time. Analyses revealed that, after adjusting for the covariation between the dimensions, internalizing was a significant predictor of interpersonal dependent stress, whereas externalizing was a significant predictor of noninterpersonal dependent stress. Neither latent dimension was associated with the occurrence of independent, or fateful, stressful life events. At the syndrome level, once variance due to the internalizing factor was partialled out, unipolar depression contributed incrementally to the generation of interpersonal dependent stress. In contrast, the presence of panic disorder produced a “stress inhibition” effect, predicting reduced exposure to interpersonal dependent stress. Additionally, dysthymia was associated with an excess of noninterpersonal dependent stress. The latent variable modeling framework used here is discussed in terms of its potential as an integrative model for stress generation research. PMID:22428789

New Horizons Finds Blue Skies and Water Ice on Pluto

NASA Image and Video Library

2017-12-08

Pluto’s Blue Sky: Pluto’s haze layer shows its blue color in this picture taken by the New Horizons Ralph/Multispectral Visible Imaging Camera (MVIC). The high-altitude haze is thought to be similar in nature to that seen at Saturn’s moon Titan. The source of both hazes likely involves sunlight-initiated chemical reactions of nitrogen and methane, leading to relatively small, soot-like particles (called tholins) that grow as they settle toward the surface. This image was generated by software that combines information from blue, red and near-infrared images to replicate the color a human eye would perceive as closely as possible. Credits: NASA/JHUAPL/SwRI Read more: www.nasa.gov/nh/nh-finds-blue-skies-and-water-ice-on-pluto NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Examining Associations between Reading Motivation and Inference Generation beyond Reading Comprehension Skill

ERIC Educational Resources Information Center

Clinton, Virginia

2015-01-01

The purpose of this study was to examine the associations between reading motivation and inference generation while reading. Undergraduate participants (N = 69) read two science articles while thinking aloud, completed a standardized reading comprehension assessment, and self reported their habitual reading motivation. Findings indicate that…

Finding Patterns

ERIC Educational Resources Information Center

Mulvey, Bridget

2016-01-01

Students best learn science through a combination of science inquiry and language learning. This article presents a series of chemistry lessons on the naming of compounds. The weeklong unit focuses on patterns across compound names and chemical formulas and addresses several of the "Next Generation Science Standards" (NGSS Lead States…

Air Emission Reduction Benefits of Biogas Electricity Generation at Municipal Wastewater Treatment Plants.

PubMed

Gingerich, Daniel B; Mauter, Meagan S

2018-02-06

Conventional processes for municipal wastewater treatment facilities are energy and materially intensive. This work quantifies the air emission implications of energy consumption, chemical use, and direct pollutant release at municipal wastewater treatment facilities across the U.S. and assesses the potential to avoid these damages by generating electricity and heat from the combustion of biogas produced during anaerobic sludge digestion. We find that embedded and on-site air emissions from municipal wastewater treatment imposed human health, environmental, and climate (HEC) damages on the order of $1.63 billion USD in 2012, with 85% of these damages attributed to the estimated consumption of 19 500 GWh of electricity by treatment processes annually, or 0.53% of the US electricity demand. An additional 11.8 million tons of biogenic CO 2 are directly emitted by wastewater treatment and sludge digestion processes currently installed at plants. Retrofitting existing wastewater treatment facilities with anaerobic sludge digestion for biogas production and biogas-fueled heat and electricity generation has the potential to reduce HEC damages by up to 24.9% relative to baseline emissions. Retrofitting only large plants (>5 MGD), where biogas generation is more likely to be economically viable, would generate HEC benefits of $254 annually. These findings reinforce the importance of accounting for use-phase embedded air emissions and spatially resolved marginal damage estimates when designing sustainable infrastructure systems.

Prediction and generation of binary Markov processes: Can a finite-state fox catch a Markov mouse?

NASA Astrophysics Data System (ADS)

Ruebeck, Joshua B.; James, Ryan G.; Mahoney, John R.; Crutchfield, James P.

2018-01-01

Understanding the generative mechanism of a natural system is a vital component of the scientific method. Here, we investigate one of the fundamental steps toward this goal by presenting the minimal generator of an arbitrary binary Markov process. This is a class of processes whose predictive model is well known. Surprisingly, the generative model requires three distinct topologies for different regions of parameter space. We show that a previously proposed generator for a particular set of binary Markov processes is, in fact, not minimal. Our results shed the first quantitative light on the relative (minimal) costs of prediction and generation. We find, for instance, that the difference between prediction and generation is maximized when the process is approximately independently, identically distributed.

The Generation of Antiphase Oscillations and Synchrony by a Rebound-Based Vertebrate Central Pattern Generator

PubMed Central

Merrison-Hort, Robert; Zhang, Hong-Yan; Borisyuk, Roman

2014-01-01

Many neural circuits are capable of generating multiple stereotyped outputs after different sensory inputs or neuromodulation. We have previously identified the central pattern generator (CPG) for Xenopus tadpole swimming that involves antiphase oscillations of activity between the left and right sides. Here we analyze the cellular basis for spontaneous left–right motor synchrony characterized by simultaneous bursting on both sides at twice the swimming frequency. Spontaneous synchrony bouts are rare in most tadpoles, and they instantly emerge from and switch back to swimming, most frequently within the first second after skin stimulation. Analyses show that only neurons that are active during swimming fire action potentials in synchrony, suggesting both output patterns derive from the same neural circuit. The firing of excitatory descending interneurons (dINs) leads that of other types of neurons in synchrony as it does in swimming. During synchrony, the time window between phasic excitation and inhibition is 7.9 ± 1 ms, shorter than that in swimming (41 ± 2.3 ms). The occasional, extra midcycle firing of dINs during swimming may initiate synchrony, and mismatches of timing in the left and right activity can switch synchrony back to swimming. Computer modeling supports these findings by showing that the same neural network, in which reciprocal inhibition mediates rebound firing, can generate both swimming and synchrony without circuit reconfiguration. Modeling also shows that lengthening the time window between phasic excitation and inhibition by increasing dIN synaptic/conduction delay can improve the stability of synchrony. PMID:24760866

A method to generate soft shadows using a layered depth image and warping.

PubMed

Im, Yeon-Ho; Han, Chang-Young; Kim, Lee-Sup

2005-01-01

We present an image-based method for propagating area light illumination through a Layered Depth Image (LDI) to generate soft shadows from opaque and nonrefractive transparent objects. In our approach, using the depth peeling technique, we render an LDI from a reference light sample on a planar light source. Light illumination of all pixels in an LDI is then determined for all the other sample points via warping, an image-based rendering technique, which approximates ray tracing in our method. We use an image-warping equation and McMillan's warp ordering algorithm to find the intersections between rays and polygons and to find the order of intersections. Experiments for opaque and nonrefractive transparent objects are presented. Results indicate our approach generates soft shadows fast and effectively. Advantages and disadvantages of the proposed method are also discussed.

Determination of LEDs degradation with entropy generation rate

NASA Astrophysics Data System (ADS)

Cuadras, Angel; Yao, Jiaqiang; Quilez, Marcos

2017-10-01

We propose a method to assess the degradation and aging of light emitting diodes (LEDs) based on irreversible entropy generation rate. We degraded several LEDs and monitored their entropy generation rate ( S ˙ ) in accelerated tests. We compared the thermoelectrical results with the optical light emission evolution during degradation. We find a good relationship between aging and S ˙ (t), because S ˙ is both related to device parameters and optical performance. We propose a threshold of S ˙ (t) as a reliable damage indicator of LED end-of-life that can avoid the need to perform optical measurements to assess optical aging. The method lays beyond the typical statistical laws for lifetime prediction provided by manufacturers. We tested different LED colors and electrical stresses to validate the electrical LED model and we analyzed the degradation mechanisms of the devices.

Next generation of weather generators on web service framework

NASA Astrophysics Data System (ADS)

Chinnachodteeranun, R.; Hung, N. D.; Honda, K.; Ines, A. V. M.

2016-12-01

Weather generator is a statistical model that synthesizes possible realization of long-term historical weather in future. It generates several tens to hundreds of realizations stochastically based on statistical analysis. Realization is essential information as a crop modeling's input for simulating crop growth and yield. Moreover, they can be contributed to analyzing uncertainty of weather to crop development stage and to decision support system on e.g. water management and fertilizer management. Performing crop modeling requires multidisciplinary skills which limit the usage of weather generator only in a research group who developed it as well as a barrier for newcomers. To improve the procedures of performing weather generators as well as the methodology to acquire the realization in a standard way, we implemented a framework for providing weather generators as web services, which support service interoperability. Legacy weather generator programs were wrapped in the web service framework. The service interfaces were implemented based on an international standard that was Sensor Observation Service (SOS) defined by Open Geospatial Consortium (OGC). Clients can request realizations generated by the model through SOS Web service. Hierarchical data preparation processes required for weather generator are also implemented as web services and seamlessly wired. Analysts and applications can invoke services over a network easily. The services facilitate the development of agricultural applications and also reduce the workload of analysts on iterative data preparation and handle legacy weather generator program. This architectural design and implementation can be a prototype for constructing further services on top of interoperable sensor network system. This framework opens an opportunity for other sectors such as application developers and scientists in other fields to utilize weather generators.

Lexicon generation methods, lexicon generation devices, and lexicon generation articles of manufacture

DOEpatents

Carter, Richard J [Richland, WA; McCall, Jonathon D [West Richland, WA; Whitney, Paul D [Richland, WA; Gregory, Michelle L [Richland, WA; Turner, Alan E [Kennewick, WA; Hetzler, Elizabeth G [Kennewick, WA; White, Amanda M [Kennewick, WA; Posse, Christian [Seattle, WA; Nakamura, Grant C [Kennewick, WA

2010-10-26

Lexicon generation methods, computer implemented lexicon editing methods, lexicon generation devices, lexicon editors, and articles of manufacture are described according to some aspects. In one aspect, a lexicon generation method includes providing a seed vector indicative of occurrences of a plurality of seed terms within a plurality of text items, providing a plurality of content vectors indicative of occurrences of respective ones of a plurality of content terms within the text items, comparing individual ones of the content vectors with respect to the seed vector, and responsive to the comparing, selecting at least one of the content terms as a term of a lexicon usable in sentiment analysis of text.

Force generation by groups of migrating bacteria

PubMed Central

Koch, Matthias D.; Liu, Guannan; Stone, Howard A.; Shaevitz, Joshua W.

2017-01-01

From colony formation in bacteria to wound healing and embryonic development in multicellular organisms, groups of living cells must often move collectively. Although considerable study has probed the biophysical mechanisms of how eukaryotic cells generate forces during migration, little such study has been devoted to bacteria, in particular with regard to the question of how bacteria generate and coordinate forces during collective motion. This question is addressed here using traction force microscopy. We study two distinct motility mechanisms of Myxococcus xanthus, namely, twitching and gliding. For twitching, powered by type-IV pilus retraction, we find that individual cells exert local traction in small hotspots with forces on the order of 50 pN. Twitching bacterial groups also produce traction hotspots, but with forces around 100 pN that fluctuate rapidly on timescales of <1.5 min. Gliding, the second motility mechanism, is driven by lateral transport of substrate adhesions. When cells are isolated, gliding produces low average traction on the order of 1 Pa. However, traction is amplified approximately fivefold in groups. Advancing protrusions of gliding cells push, on average, in the direction of motion. Together, these results show that the forces generated during twitching and gliding have complementary characters, and both forces have higher values when cells are in groups. PMID:28655845

Force generation by groups of migrating bacteria.

PubMed

Sabass, Benedikt; Koch, Matthias D; Liu, Guannan; Stone, Howard A; Shaevitz, Joshua W

2017-07-11

From colony formation in bacteria to wound healing and embryonic development in multicellular organisms, groups of living cells must often move collectively. Although considerable study has probed the biophysical mechanisms of how eukaryotic cells generate forces during migration, little such study has been devoted to bacteria, in particular with regard to the question of how bacteria generate and coordinate forces during collective motion. This question is addressed here using traction force microscopy. We study two distinct motility mechanisms of Myxococcus xanthus , namely, twitching and gliding. For twitching, powered by type-IV pilus retraction, we find that individual cells exert local traction in small hotspots with forces on the order of 50 pN. Twitching bacterial groups also produce traction hotspots, but with forces around 100 pN that fluctuate rapidly on timescales of <1.5 min. Gliding, the second motility mechanism, is driven by lateral transport of substrate adhesions. When cells are isolated, gliding produces low average traction on the order of 1 Pa. However, traction is amplified approximately fivefold in groups. Advancing protrusions of gliding cells push, on average, in the direction of motion. Together, these results show that the forces generated during twitching and gliding have complementary characters, and both forces have higher values when cells are in groups.

Squeezed-light generation in a nonlinear planar waveguide with a periodic corrugation

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

Perina, Jan Jr.; Haderka, Ondrej; Sibilia, Concita

Two-mode nonlinear interaction (second-harmonic and second-subharmonic generation) in a planar waveguide with a small periodic corrugation at the surface is studied. Scattering of the interacting fields on the corrugation leads to constructive interference that enhances the nonlinear process provided that all the interactions are phase matched. Conditions for the overall phase matching are found. Compared with a perfectly quasi-phase-matched waveguide, better values of squeezing as well as higher intensities are reached under these conditions. Procedure for finding optimum values of parameters for squeezed-light generation is described.

Finding the Center of Volume of the Forearm

NASA Astrophysics Data System (ADS)

Klein, Stacy S.; Roselli, Robert J.

2008-04-01

A typical first-year physics course teaches students about the center of mass using both regular and irregularly shaped objects. Students often suspend an object in each of two dimensions from a string with the intersection determining the center of mass of the object. While these methods can be effective, they are not particularly exciting or motivating. Wouldn't it be more interesting to find the center of mass of a body part, such as the forearm? Through a series of simple measurements and assumptions, students can generate a first-order approximation of the center of volume and center of mass of their forearm. Comparisons can be made between the muscular forearm of the football player in the class with the scrawniest arm in the room, creating a deeper understanding of center of mass and how it relates to the human body.

Insert Tidal Here: Finding Stability of Galilean Satellite Interiors

NASA Astrophysics Data System (ADS)

Walker, M.; Bills, B. G.; Mitchell, J.; Rhoden, A.

2017-12-01

The tidal environment is often hypothesized as a cause of surface expression in the satellites of the outer solar system. In two notable cases, Io's volcanism is thought to be driven by tidal heating of its mantle while the shattered surface of Europa's ice shell is said to be generated by tidal stresses in that ice. Being adjacent moons of Jupiter, these satellites give us a unique opportunity to apply a single set of general coupled models at each body to predict how one model can predict the heat generation and flow, strain and stress states, and structural parameters for each body. We include the effects of interior evolution into the tidal environment in addition to an evolving orbit. We find that the interiors of Io and Europa will evolve, as a consequence of the heat transfer from interior to surface, and stable structural and heat flow conditions are found. Then as their orbits evolve, perturbed by the mutual interactions of the Laplace mean motion resonance, those conditions of structural and heat stability also change. In particular, we find that at current orbital conditions there is sufficient heat to completely melt Io models for which a convecting interior is capped by a conducting lid. This argues for the presence of a non dissipating (or barely dissipating) core below the mantle, which future Io structure models should include. For the Europa model at current orbit, we use a silicate interior under an ocean capped by a two layer ice; convecting below with a conducting surface. We find stability in heat and structure occurs when the lower ice melts and recedes until the shell is roughly 50km thick. We present a variety of plausible structures for these bodies, and track how the stability of those structures trend as the orbit (in particular the orbital eccentricity, mean motion, and obliquity) change. We show how the Love numbers, layer thicknesses, surface heat flow, and orbital parameters are all linked. For Europa, upcoming measurements from

Encouragement of Enzyme Reaction Utilizing Heat Generation from Ferromagnetic Particles Subjected to an AC Magnetic Field.

PubMed

Suzuki, Masashi; Aki, Atsushi; Mizuki, Toru; Maekawa, Toru; Usami, Ron; Morimoto, Hisao

2015-01-01

We propose a method of activating an enzyme utilizing heat generation from ferromagnetic particles under an ac magnetic field. We immobilize α-amylase on the surface of ferromagnetic particles and analyze its activity. We find that when α-amylase/ferromagnetic particle hybrids, that is, ferromagnetic particles, on which α-amylase molecules are immobilized, are subjected to an ac magnetic field, the particles generate heat and as a result, α-amylase on the particles is heated up and activated. We next prepare a solution, in which α-amylase/ferromagnetic particle hybrids and free, nonimmobilized chitinase are dispersed, and analyze their activities. We find that when the solution is subjected to an ac magnetic field, the activity of α-amylase immobilized on the particles increases, whereas that of free chitinase hardly changes; in other words, only α-amylase immobilized on the particles is selectively activated due to heat generation from the particles.

Crossing Borders: Generation 1.5's Journey from Alien to Master

ERIC Educational Resources Information Center

Yu, Eunjyu

2016-01-01

This paper identifies various challenges that a 1.5 generation immigrant faced in a mainstream college composition class and reports on how he constructed his social presence and became a successful multilingual writer. The findings of this study would help higher education institutions more effectively serve the growing population of ESL students…

Generating Spatiotemporal Joint Torque Patterns from Dynamical Synchronization of Distributed Pattern Generators

PubMed Central

Pitti, Alexandre; Lungarella, Max; Kuniyoshi, Yasuo

2009-01-01

Pattern generators found in the spinal cord are no more seen as simple rhythmic oscillators for motion control. Indeed, they achieve flexible and dynamical coordination in interaction with the body and the environment dynamics giving to rise motor synergies. Discovering the mechanisms underlying the control of motor synergies constitutes an important research question not only for neuroscience but also for robotics: the motors coordination of high dimensional robotic systems is still a drawback and new control methods based on biological solutions may reduce their overall complexity. We propose to model the flexible combination of motor synergies in embodied systems via partial phase synchronization of distributed chaotic systems; for specific coupling strength, chaotic systems are able to phase synchronize their dynamics to the resonant frequencies of one external force. We take advantage of this property to explore and exploit the intrinsic dynamics of one specified embodied system. In two experiments with bipedal walkers, we show how motor synergies emerge when the controllers phase synchronize to the body's dynamics, entraining it to its intrinsic behavioral patterns. This stage is characterized by directed information flow from the sensors to the motors exhibiting the optimal situation when the body dynamics drive the controllers (mutual entrainment). Based on our results, we discuss the relevance of our findings for modeling the modular control of distributed pattern generators exhibited in the spinal cord, and for exploring the motor synergies in robots. PMID:20011216

Instant Generation

ERIC Educational Resources Information Center

Loveland, Elaina

2017-01-01

Generation Z students (born between 1995-2010) have replaced millennials on college campuses. Generation Z students are entrepreneurial, desire practical skills with their education, and are concerned about the cost of college. This article presents what need to be known about this new generation of students.

Generation of referring expressions: assessing the Incremental Algorithm.

PubMed

van Deemter, Kees; Gatt, Albert; van der Sluis, Ielka; Power, Richard

2012-07-01

A substantial amount of recent work in natural language generation has focused on the generation of ''one-shot'' referring expressions whose only aim is to identify a target referent. Dale and Reiter's Incremental Algorithm (IA) is often thought to be the best algorithm for maximizing the similarity to referring expressions produced by people. We test this hypothesis by eliciting referring expressions from human subjects and computing the similarity between the expressions elicited and the ones generated by algorithms. It turns out that the success of the IA depends substantially on the ''preference order'' (PO) employed by the IA, particularly in complex domains. While some POs cause the IA to produce referring expressions that are very similar to expressions produced by human subjects, others cause the IA to perform worse than its main competitors; moreover, it turns out to be difficult to predict the success of a PO on the basis of existing psycholinguistic findings or frequencies in corpora. We also examine the computational complexity of the algorithms in question and argue that there are no compelling reasons for preferring the IA over some of its main competitors on these grounds. We conclude that future research on the generation of referring expressions should explore alternatives to the IA, focusing on algorithms, inspired by the Greedy Algorithm, which do not work with a fixed PO. Copyright © 2011 Cognitive Science Society, Inc.

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes.

PubMed

Sittka, Alexandra; Sharma, Cynthia M; Rolle, Katarzyna; Vogel, Jörg

2009-01-01

The bacterial Sm-like protein, Hfq, is a key factor for the stability and function of small non-coding RNAs (sRNAs) in Escherichia coli. Homologues of this protein have been predicted in many distantly related organisms yet their functional conservation as sRNA-binding proteins has not entirely been clear. To address this, we expressed in Salmonella the Hfq proteins of two eubacteria (Neisseria meningitides, Aquifex aeolicus) and an archaeon (Methanocaldococcus jannaschii), and analyzed the associated RNA by deep sequencing. This in vivo approach identified endogenous Salmonella sRNAs as a major target of the foreign Hfq proteins. New Salmonella sRNA species were also identified, and some of these accumulated specifically in the presence of a foreign Hfq protein. In addition, we observed specific RNA processing defects, e.g., suppression of precursor processing of SraH sRNA by Methanocaldococcus Hfq, or aberrant accumulation of extracytoplasmic target mRNAs of the Salmonella GcvB, MicA or RybB sRNAs. Taken together, our study provides evidence of a conserved inherent sRNA-binding property of Hfq, which may facilitate the lateral transmission of regulatory sRNAs among distantly related species. It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo.

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.

PubMed

Celton, Jean-Marc; Gaillard, Sylvain; Bruneau, Maryline; Pelletier, Sandra; Aubourg, Sébastien; Martin-Magniette, Marie-Laure; Navarro, Lionel; Laurens, François; Renou, Jean-Pierre

2014-07-01

Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants. © 2014 INRA. New Phytologist © 2014 New Phytologist Trust.

Oasis 2: improved online analysis of small RNA-seq data.

PubMed

Rahman, Raza-Ur; Gautam, Abhivyakti; Bethune, Jörn; Sattar, Abdul; Fiosins, Maksims; Magruder, Daniel Sumner; Capece, Vincenzo; Shomroni, Orr; Bonn, Stefan

2018-02-14

Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing. Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module. Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment. Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.

Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization

PubMed Central

Capel, Elena; Zomer, Aldert L.; Nussbaumer, Thomas; Bole, Christine; Izac, Brigitte; Frapy, Eric; Meyer, Julie; Bouzinba-Ségard, Haniaa; Bille, Emmanuelle; Jamet, Anne; Cavau, Anne; Letourneur, Franck; Bourdoulous, Sandrine; Rattei, Thomas; Coureuil, Mathieu

2016-01-01

ABSTRACT Neisseria meningitidis is a leading cause of bacterial meningitis and septicemia, affecting infants and adults worldwide. N. meningitidis is also a common inhabitant of the human nasopharynx and, as such, is highly adapted to its niche. During bacteremia, N. meningitidis gains access to the blood compartment, where it adheres to endothelial cells of blood vessels and causes dramatic vascular damage. Colonization of the nasopharyngeal niche and communication with the different human cell types is a major issue of the N. meningitidis life cycle that is poorly understood. Here, highly saturated random transposon insertion libraries of N. meningitidis were engineered, and the fitness of mutations during routine growth and that of colonization of endothelial and epithelial cells in a flow device were assessed in a transposon insertion site sequencing (Tn-seq) analysis. This allowed the identification of genes essential for bacterial growth and genes specifically required for host cell colonization. In addition, after having identified the small noncoding RNAs (sRNAs) located in intergenic regions, the phenotypes associated with mutations in those sRNAs were defined. A total of 383 genes and 8 intergenic regions containing sRNA candidates were identified to be essential for growth, while 288 genes and 33 intergenic regions containing sRNA candidates were found to be specifically required for host cell colonization. PMID:27486197

A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb

PubMed Central

Meng, Yijun; Yu, Dongliang; Xue, Jie; Lu, Jiangjie; Feng, Shangguo; Shen, Chenjia; Wang, Huizhong

2016-01-01

Dendrobium officinale is an important traditional Chinese herb. Here, we did a transcriptome-wide, organ-specific study on this valuable plant by combining RNA, small RNA (sRNA) and degradome sequencing. RNA sequencing of four organs (flower, root, leaf and stem) of Dendrobium officinale enabled us to obtain 536,558 assembled transcripts, from which 2,645, 256, 42 and 54 were identified to be highly expressed in the four organs respectively. Based on sRNA sequencing, 2,038, 2, 21 and 24 sRNAs were identified to be specifically accumulated in the four organs respectively. A total of 1,047 mature microRNA (miRNA) candidates were detected. Based on secondary structure predictions and sequencing, tens of potential miRNA precursors were identified from the assembled transcripts. Interestingly, phase-distributed sRNAs with degradome-based processing evidences were discovered on the long-stem structures of two precursors. Target identification was performed for the 1,047 miRNA candidates, resulting in the discovery of 1,257 miRNA--target pairs. Finally, some biological meaningful subnetworks involving hormone signaling, development, secondary metabolism and Argonaute 1-related regulation were established. All of the sequencing data sets are available at NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/). Summarily, our study provides a valuable resource for the in-depth molecular and functional studies on this important Chinese orchid herb. PMID:26732614

Preparing for what might happen: An episodic specificity induction impacts the generation of alternative future events.

PubMed

Jing, Helen G; Madore, Kevin P; Schacter, Daniel L

2017-12-01

A critical adaptive feature of future thinking involves the ability to generate alternative versions of possible future events. However, little is known about the nature of the processes that support this ability. Here we examined whether an episodic specificity induction - brief training in recollecting details of a recent experience that selectively impacts tasks that draw on episodic retrieval - (1) boosts alternative event generation and (2) changes one's initial perceptions of negative future events. In Experiment 1, an episodic specificity induction significantly increased the number of alternative positive outcomes that participants generated to a series of standardized negative events, compared with a control induction not focused on episodic specificity. We also observed larger decreases in the perceived plausibility and negativity of the original events in the specificity condition, where participants generated more alternative outcomes, relative to the control condition. In Experiment 2, we replicated and extended these findings using a series of personalized negative events. Our findings support the idea that episodic memory processes are involved in generating alternative outcomes to anticipated future events, and that boosting the number of alternative outcomes is related to subsequent changes in the perceived plausibility and valence of the original events, which may have implications for psychological well-being. Published by Elsevier B.V.

Cylindrical neutron generator

DOEpatents

Leung, Ka-Ngo [Hercules, CA

2008-04-22

A cylindrical neutron generator is formed with a coaxial RF-driven plasma ion source and target. A deuterium (or deuterium and tritium) plasma is produced by RF excitation in a cylindrical plasma ion generator using an RF antenna. A cylindrical neutron generating target is coaxial with the ion generator, separated by plasma and extraction electrodes which contain many slots. The plasma generator emanates ions radially over 360.degree. and the cylindrical target is thus irradiated by ions over its entire circumference. The plasma generator and target may be as long as desired. The plasma generator may be in the center and the neutron target on the outside, or the plasma generator may be on the outside and the target on the inside. In a nested configuration, several concentric targets and plasma generating regions are nested to increase the neutron flux.

Cylindrical neutron generator

DOEpatents

Leung, Ka-Ngo

2005-06-14

A cylindrical neutron generator is formed with a coaxial RF-driven plasma ion source and target. A deuterium (or deuterium and tritium) plasma is produced by RF excitation in a cylindrical plasma ion generator using an RF antenna. A cylindrical neutron generating target is coaxial with the ion generator, separated by plasma and extraction electrodes which contain many slots. The plasma generator emanates ions radially over 360.degree. and the cylindrical target is thus irradiated by ions over its entire circumference. The plasma generator and target may be as long as desired. The plasma generator may be in the center and the neutron target on the outside, or the plasma generator may be on the outside and the target on the inside. In a nested configuration, several concentric targets and plasma generating regions are nested to increase the neutron flux.

Cylindrical neutron generator

DOEpatents

Leung, Ka-Ngo [Hercules, CA

2009-12-29

A cylindrical neutron generator is formed with a coaxial RF-driven plasma ion source and target. A deuterium (or deuterium and tritium) plasma is produced by RF excitation in a cylindrical plasma ion generator using an RF antenna. A cylindrical neutron generating target is coaxial with the ion generator, separated by plasma and extraction electrodes which contain many slots. The plasma generator emanates ions radially over 360.degree. and the cylindrical target is thus irradiated by ions over its entire circumference. The plasma generator and target may be as long as desired. The plasma generator may be in the center and the neutron target on the outside, or the plasma generator may be on the outside and the target on the inside. In a nested configuration, several concentric targets and plasma generating regions are nested to increase the neutron flux.

The self in action effects: selective attenuation of self-generated sounds.

PubMed

Weiss, Carmen; Herwig, Arvid; Schütz-Bosbach, Simone

2011-11-01

The immediate experience of self-agency, that is, the experience of generating and controlling our actions, is thought to be a key aspect of selfhood. It has been suggested that this experience is intimately linked to internal motor signals associated with the ongoing actions. These signals should lead to an attenuation of the sensory consequences of one's own actions and thereby allow classifying them as self-generated. The discovery of shared representations of actions between self and other, however, challenges this idea and suggests similar attenuation of one's own and other's sensory action effects. Here, we tested these assumptions by comparing sensory attenuation of self-generated and observed sensory effects. More specifically, we compared the loudness perception of sounds that were either self-generated, generated by another person or a computer. In two experiments, we found a reduced perception of loudness intensity specifically related to self-generation. Furthermore, the perception of sounds generated by another person and a computer did not differ from each other. These findings indicate that one's own agentive influence upon the outside world has a special perceptual quality which distinguishes it from any sort of external influence, including human and non-human sources. This suggests that a real sense of self-agency is not a socially shared but rather a unique and private experience. Copyright © 2011 Elsevier B.V. All rights reserved.

78 FR 52987 - Entergy Nuclear Operations, Inc., Indian Point Nuclear Generating Unit 3

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-27

... NUCLEAR REGULATORY COMMISSION [Docket No. 50-286; NRC-2013-0063] Entergy Nuclear Operations, Inc., Indian Point Nuclear Generating Unit 3 AGENCY: Nuclear Regulatory Commission. ACTION: Environmental assessment and finding of no significant impact; issuance. SUMMARY: The U.S. Nuclear Regulatory Commission...

Imaging with Second-Harmonic Generation Nanoparticles

NASA Astrophysics Data System (ADS)

Hsieh, Chia-Lung

Second-harmonic generation nanoparticles show promise as imaging probes due to their coherent and stable signal with a broad flexibility in the choice of excitation wavelength. In this thesis, we developed and demonstrated barium titanate nanoparticles as second-harmonic radiation imaging probes. We studied the absolute second-harmonic generation efficiency of the nanoparticles on single-particle level. The polarization dependent second-harmonic signal of single nanoparticles was studied in detail. From the measured polar response, we were able to find the orientation of the nanoparticle. We developed a biochemical interface for using the second-harmonic nanoprobes as biomarkers, including in vitro cellular imaging and in vivo live animal imaging. The nanoparticles were surface functionalized with primary amine groups for stable colloidal dispersion. We achieved specific labeling of the second-harmonic nanoprobes via immunostaining where the antibodies were covalently conjugated onto the nanoparticles. We observed no toxicity of the functionalized nanoparticles to biological cells. The coherent second-harmonic signal radiated from the nanoparticles offers opportunities for new imaging techniques. Using interferometric detection, namely harmonic holography, both amplitude and phase of the second-harmonic field can be captured. Through digital beam propagation, three-dimensional field distribution, reflecting three-dimensional distribution of the nanoparticles, can be reconstructed. We achieved a scan-free three-dimensional imaging of nanoparticles in biological cells with sub-micron spatial resolution by using the harmonic holographic microscope. We further exploited the coherent second-harmonic signal for imaging through scattering media by performing optical phase conjugation of the second-harmonic signal. We demonstrated an all-digital optical phase conjugation of the second-harmonic signal originated from a nanoparticle by combining harmonic holography and

Wavelength-dependence of double optical gating for attosecond pulse generation

NASA Astrophysics Data System (ADS)

Tian, Jia; Li, Min; Yu, Ji-Zhou; Deng, Yong-Kai; Liu, Yun-Quan

2014-10-01

Both polarization gating (PG) and double optical gating (DOG) are productive methods to generate single attosecond (as) pulses. In this paper, considering the ground-state depletion effect, we investigate the wavelength-dependence of the DOG method in order to optimize the generation of single attosecond pulses for the future application. By calculating the ionization probabilities of the leading edge of the pulse at different driving laser wavelengths, we obtain the upper limit of duration for the driving laser pulse for the DOG setup. We find that the upper limit duration increases with the increase of laser wavelength. We further describe the technical method of choosing and calculating the thickness values of optical components for the DOG setup.

A simplified analytic form for generation of axisymmetric plasma boundaries

DOE PAGES

Luce, Timothy C.

2017-02-23

An improved method has been formulated for generating analytic boundary shapes as input for axisymmetric MHD equilibria. This method uses the family of superellipses as the basis function, as previously introduced. The improvements are a simplified notation, reduction of the number of simultaneous nonlinear equations to be solved, and the realization that not all combinations of input parameters admit a solution to the nonlinear constraint equations. The method tests for the existence of a self-consistent solution and, when no solution exists, it uses a deterministic method to find a nearby solution. As a result, examples of generation of boundaries, includingmore » tests with an equilibrium solver, are given.« less

A simplified analytic form for generation of axisymmetric plasma boundaries

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

Luce, Timothy C.

An improved method has been formulated for generating analytic boundary shapes as input for axisymmetric MHD equilibria. This method uses the family of superellipses as the basis function, as previously introduced. The improvements are a simplified notation, reduction of the number of simultaneous nonlinear equations to be solved, and the realization that not all combinations of input parameters admit a solution to the nonlinear constraint equations. The method tests for the existence of a self-consistent solution and, when no solution exists, it uses a deterministic method to find a nearby solution. As a result, examples of generation of boundaries, includingmore » tests with an equilibrium solver, are given.« less

Development of a consensus approach for return of pathology incidental findings in the Genotype-Tissue Expression (GTEx) project.

PubMed

Lockhart, Nicole C; Weil, Carol J; Carithers, Latarsha J; Koester, Susan E; Little, A Roger; Volpi, Simona; Moore, Helen M; Berkman, Benjamin E

2018-06-14

The active debate about the return of incidental or secondary findings in research has primarily focused on return to research participants, or in some cases, family members. Particular attention has been paid to return of genomic findings. Yet, research may generate other types of findings that warrant consideration for return, including findings related to the pathology of donated biospecimens. In the case of deceased biospecimen donors who are also organ and/or tissue transplant donors, pathology incidental findings may be relevant not to family members, but to potential organ or tissue transplant recipients. This paper will describe the ethical implications of pathology incidental findings in the Genotype-Tissue Expression (GTEx) project, the process for developing a consensus approach as to if/when such findings should be returned, possible implications for other research projects collecting postmortem tissues and how the scenario encountered in GTEx fits into the larger return of results/incidental findings debate. © 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.

Adolescent Black Holes May be Hard to Find

NASA Astrophysics Data System (ADS)

Elvis, Martin; Chakravorty, Susmita

2017-08-01

Finding adolescent black holes that are growing rapidly from their seed masses is a major goal of the next generation of large observatories. We have examined how these early quasars may appear in terms of their broad emission lines (BELs) in the optical and ultraviolet. We find that below 10**6 Msol, the equivalent widths of the BELs drop precipitously. Moreover, if the BELs originate in clouds that form as the cool phase of a multi-phase medium, then for metallicities Z/Zsol ~< 3, the thermal instabilities that create them will not exist. However, in observed quasars at high redshift Z/Zsol is >> 3, so quasars are preferentially found in special environments, perhaps with deep potential wells. The population that we see though could be biased by the Z/Zsol > 3 requirement. A stronger argument is that the thermal instability leading to cool clouds is predominantly due to line emission by iron. Iron comes primarily from type 1a supernovae, which take of order 1 billion years to ignite. Hence iron should be under-abundant relative to other elements until z ~ 6 - 7. That the highest redshift quasar is at z = 7.1 may be a consequence of this requirement. Quasars above z ~ 7 could still be found by their rest-frame ultraviolet or X-ray continuum.

First-generation Korean-American parents' perceptions of discipline.

PubMed

Kim, Eunjung; Hong, Seunghye

2007-01-01

Nurses not only need to be familiar with professional guidelines of discipline and but also need to be aware of variances in styles of acceptable discipline across cultural groups. The goal of this study was to explore cultural influences in relation to (1) first-generation Korean-American parents' perceptions of common discipline strategies in the United States, and (2) discipline strategies commonly used among first-generation Korean-American parents. Inductive content analysis was used to analyze interview data from seven first-generation Korean-American parents. Derived themes indicated that parents considered spanking/hitting and less hugging/kissing as Korean style, and time-out, use of sticker charts, hugging/kissing, removing/adding privileges, and giving chores as American style. Recent immigrant parents were not familiar with common positive discipline strategies in the United States. As they adapted to mainstream society, they discontinued what they perceived to be negative aspects of Korean style and adopted positive aspects of American style. They were sensitive to children's views on discipline, and they experienced communication difficulties with children. These findings indicated that Korean-American parents' perceptions of discipline strategies were shaped by living in two cultures and were different from western viewpoints.

Towards multifocal ultrasonic neural stimulation: pattern generation algorithms

NASA Astrophysics Data System (ADS)

Hertzberg, Yoni; Naor, Omer; Volovick, Alexander; Shoham, Shy

2010-10-01

Focused ultrasound (FUS) waves directed onto neural structures have been shown to dynamically modulate neural activity and excitability, opening up a range of possible systems and applications where the non-invasiveness, safety, mm-range resolution and other characteristics of FUS are advantageous. As in other neuro-stimulation and modulation modalities, the highly distributed and parallel nature of neural systems and neural information processing call for the development of appropriately patterned stimulation strategies which could simultaneously address multiple sites in flexible patterns. Here, we study the generation of sparse multi-focal ultrasonic distributions using phase-only modulation in ultrasonic phased arrays. We analyse the relative performance of an existing algorithm for generating multifocal ultrasonic distributions and new algorithms that we adapt from the field of optical digital holography, and find that generally the weighted Gerchberg-Saxton algorithm leads to overall superior efficiency and uniformity in the focal spots, without significantly increasing the computational burden. By combining phased-array FUS and magnetic-resonance thermometry we experimentally demonstrate the simultaneous generation of tightly focused multifocal distributions in a tissue phantom, a first step towards patterned FUS neuro-modulation systems and devices.

Reliable steam generators: how KWU solved beginning problems for its customers

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

Eggers, B.; Engl, G.; Froehlich, K.

This paper describes improvements in inspection and maintenance techniques, the adaptation of a secondary-side concept, and the optimization of water chemistry to achieve the highest possible operational reliability of steam generator performance. In the late 1970s and the early 1980s steam generators of several pressurized water reactors delivered by Kraftwerk Union (KWU) experienced corrosion-induced tube-wall degradation. As a result of these findings and the similar experience in US plants, KWU initiated a systematic program to retain the operational history of the plants at their historically outstanding level. By a combination of improvement in the balance of plant, reduction of themore » phosphate conditioning, and even a change to an all-volatile treatment as well as by the performance of tubesheet lancing, the tube degradation in KWU steam generators is nearly halted and no other known corrosion mechanisms exist that could impair the life expectancy of the steam generators. Nevertheless, repair and cleaning techniques have been developed and are available for application, if necessary, such as tube plugging, tube sleeving, or even partial tube replacement as well as chemical cleaning of the steam generator's secondary side.« less

The Age Parameters of the Starting Demographic Events across Russian Generations

ERIC Educational Resources Information Center

Mitrofanova, E. S.

2016-01-01

This article presents comparisons of the ages and facts of starting demographic events in Russia based on the findings of three large-scale surveys: the European Social Survey, 2006; the Generations and Gender Survey, 2004, 2007, and 2011; and Person, Family, Society, 2013. This study focuses on the intergenerational and gender differences in the…

Examining causal components and a mediating process underlying self-generated health arguments for exercise and smoking cessation.

PubMed

Baldwin, Austin S; Rothman, Alexander J; Vander Weg, Mark W; Christensen, Alan J

2013-12-01

Self-persuasion-generating one's own arguments for engaging in a specific behavior-can be an effective strategy to promote health behavior change, yet the causal processes that explain why it is effective are not well-specified. We sought to elucidate specific causal components and a mediating process of self-persuasion in two health behavior domains: physical activity and smoking. In two experiments, participants were randomized to write or read arguments about regular exercise (Study 1: N = 76; college students) or smoking cessation (Study 2: N = 107; daily smokers). In Study 2, we also manipulated the argument content (matched vs. mismatched participants' own concerns about smoking) to isolate its effect from the effect of argument source (self vs. other). Study outcomes included participants' reports of argument ratings, attitudes, behavioral intentions (Studies 1 & 2), and cessation attempts at 1 month (Study 2). In Study 1, self-generated arguments about exercise were evaluated more positively than other arguments (p = .01, d = .63), and this biased processing mediated the self-generated argument effect on attitudes toward exercise (β = .08, 95% CI = .01, .18). In Study 2, the findings suggested that biased processing occurs because self-generated argument content matches people's own health concerns and not because of the argument source (self vs. other). In addition, self-generated arguments indirectly led to greater behavior change intentions (Studies 1 & 2) and a greater likelihood of a smoking cessation attempt (Study 2). The findings elucidate a causal component and a mediating process that explain why self-persuasion and related behavior change interventions, such as motivational interviewing, are effective. Findings also suggest that self-generated arguments may be an efficient way to deliver message interventions aimed at changing health behaviors.

Generation Z: Educating and Engaging the Next Generation of Students

ERIC Educational Resources Information Center

Seemiller, Corey; Grace, Meghan

2017-01-01

In 1995, the Internet was born. So, too, was Generation Z. The oldest of this post-Millennial generation arrived to college in 2013, and more than four years later, Generation Z students fill the nation's classrooms, campus programs, and residence halls. In order to recruit, educate, and graduate this new generational cohort effectively, educators…

Does dynamic stability govern propulsive force generation in human walking?

PubMed Central

Browne, Michael G.

2017-01-01

Before succumbing to slower speeds, older adults may walk with a diminished push-off to prioritize stability over mobility. However, direct evidence for trade-offs between push-off intensity and balance control in human walking, independent of changes in speed, has remained elusive. As a critical first step, we conducted two experiments to investigate: (i) the independent effects of walking speed and propulsive force (FP) generation on dynamic stability in young adults, and (ii) the extent to which young adults prioritize dynamic stability in selecting their preferred combination of walking speed and FP generation. Subjects walked on a force-measuring treadmill across a range of speeds as well as at constant speeds while modulating their FP according to a visual biofeedback paradigm based on real-time force measurements. In contrast to improvements when walking slower, walking with a diminished push-off worsened dynamic stability by up to 32%. Rather, we find that young adults adopt an FP at their preferred walking speed that maximizes dynamic stability. One implication of these findings is that the onset of a diminished push-off in old age may independently contribute to poorer balance control and precipitate slower walking speeds. PMID:29291129

Does dynamic stability govern propulsive force generation in human walking?

PubMed

Browne, Michael G; Franz, Jason R

2017-11-01

Before succumbing to slower speeds, older adults may walk with a diminished push-off to prioritize stability over mobility. However, direct evidence for trade-offs between push-off intensity and balance control in human walking, independent of changes in speed, has remained elusive. As a critical first step, we conducted two experiments to investigate: (i) the independent effects of walking speed and propulsive force ( F P ) generation on dynamic stability in young adults, and (ii) the extent to which young adults prioritize dynamic stability in selecting their preferred combination of walking speed and F P generation. Subjects walked on a force-measuring treadmill across a range of speeds as well as at constant speeds while modulating their F P according to a visual biofeedback paradigm based on real-time force measurements. In contrast to improvements when walking slower, walking with a diminished push-off worsened dynamic stability by up to 32%. Rather, we find that young adults adopt an F P at their preferred walking speed that maximizes dynamic stability. One implication of these findings is that the onset of a diminished push-off in old age may independently contribute to poorer balance control and precipitate slower walking speeds.

Double heterojunction nanowire photocatalysts for hydrogen generation.

PubMed

Tongying, P; Vietmeyer, F; Aleksiuk, D; Ferraudi, G J; Krylova, G; Kuno, M

2014-04-21

Charge separation and charge transfer across interfaces are key aspects in the design of efficient photocatalysts for solar energy conversion. In this study, we investigate the hydrogen generating capabilities and underlying photophysics of nanostructured photocatalysts based on CdSe nanowires (NWs). Systems studied include CdSe, CdSe/CdS core/shell nanowires and their Pt nanoparticle-decorated counterparts. Femtosecond transient differential absorption measurements reveal how semiconductor/semiconductor and metal/semiconductor heterojunctions affect the charge separation and hydrogen generation efficiencies of these hybrid photocatalysts. In turn, we unravel the role of surface passivation, charge separation at semiconductor interfaces and charge transfer to metal co-catalysts in determining photocatalytic H2 generation efficiencies. This allows us to rationalize why Pt nanoparticle decorated CdSe/CdS NWs, a double heterojunction system, performs best with H2 generation rates of ∼434.29 ± 27.40 μmol h(-1) g(-1) under UV/Visible irradiation. In particular, we conclude that the CdS shell of this double heterojunction system serves two purposes. The first is to passivate CdSe NW surface defects, leading to long-lived charges at the CdSe/CdS interface capable of carrying out reduction chemistries. Upon photoexcitation, we also find that CdS selectively injects charges into Pt NPs, enabling simultaneous reduction chemistries at the Pt NP/solvent interface. Pt nanoparticle decorated CdSe/CdS NWs thus enable reduction chemistries at not one, but rather two interfaces, taking advantage of each junction's optimal catalytic activities.

The law of incidental findings in human subjects research: establishing researchers' duties.

PubMed

Wolf, Susan M; Paradise, Jordan; Caga-anan, Charlisse

2008-01-01

Research technologies can now produce so much information that there is significant potential for incidental findings (IFs). These are findings generated in research that are beyond the aims of the study. Current law and federal regulations offer no direct guidance on how to deal with IFs in research, nor is there adequate professional or institutional guidance. We advocate a defined set of researcher duties based on law and ethics and recommend a pathway to be followed in handling IFs in research. This article traces the underlying ethical and legal theories supporting researcher duties to manage IFs, including duties to develop a plan for management in the research protocol, to discuss the possibility of and management plan for IFs in the informed consent process, and to address, evaluate, and ultimately offer to disclose IFs of potential clinical or reproductive significance to research participants when they arise.

Cluster size dependence of high-order harmonic generation

NASA Astrophysics Data System (ADS)

Tao, Y.; Hagmeijer, R.; Bastiaens, H. M. J.; Goh, S. J.; van der Slot, P. J. M.; Biedron, S. G.; Milton, S. V.; Boller, K.-J.

2017-08-01

We investigate high-order harmonic generation (HHG) from noble gas clusters in a supersonic gas jet. To identify the contribution of harmonic generation from clusters versus that from gas monomers, we measure the high-order harmonic output over a broad range of the total atomic number density in the jet (from 3×1016 to 3 × 1018 {{cm}}-3) at two different reservoir temperatures (303 and 363 K). For the first time in the evaluation of the harmonic yield in such measurements, the variation of the liquid mass fraction, g, versus pressure and temperature is taken into consideration, which we determine, reliably and consistently, to be below 20% within our range of experimental parameters. By comparing the measured harmonic yield from a thin jet with the calculated corresponding yield from monomers alone, we find an increased emission of the harmonics when the average cluster size is less than 3000. Using g, under the assumption that the emission from monomers and clusters add up coherently, we calculate the ratio of the average single-atom response of an atom within a cluster to that of a monomer and find an enhancement of around 100 for very small average cluster size (∼200). We do not find any dependence of the cut-off frequency on the composition of the cluster jet. This implies that HHG in clusters is based on electrons that return to their parent ions and not to neighboring ions in the cluster. To fully employ the enhanced average single-atom response found for small average cluster sizes (∼200), the nozzle producing the cluster jet must provide a large liquid mass fraction at these small cluster sizes for increasing the harmonic yield. Moreover, cluster jets may allow for quasi-phase matching, as the higher mass of clusters allows for a higher density contrast in spatially structuring the nonlinear medium.

TECHNICAL SUPPORT DOCUMENT: NATIONAL-SCALE MERCURY RISK ASSESSMENT SUPPORTING THE APPROPRIATE AND NECESSARY FINDING FOR COAL- AND OIL-FIRED ELECTRIC GENERATING UNITS

EPA Science Inventory

The EPA has completed a national-scale risk assessment for mercury to inform the appropriate and necessary determination for electric utility steam generating unites in the United States (U.S. EGU's), persuant to Section 112(n)(1)(A) of the Clean Air Act. This document describes...

Characterization of a deuterium-deuterium plasma fusion neutron generator

NASA Astrophysics Data System (ADS)

Lang, R. F.; Pienaar, J.; Hogenbirk, E.; Masson, D.; Nolte, R.; Zimbal, A.; Röttger, S.; Benabderrahmane, M. L.; Bruno, G.

2018-01-01

We characterize the neutron output of a deuterium-deuterium plasma fusion neutron generator, model 35-DD-W-S, manufactured by NSD/Gradel-Fusion. The measured energy spectrum is found to be dominated by neutron peaks at 2.2 MeV and 2.7 MeV. A detailed GEANT4 simulation accurately reproduces the measured energy spectrum and confirms our understanding of the fusion process in this generator. Additionally, a contribution of 14 . 1 MeV neutrons from deuterium-tritium fusion is found at a level of 3 . 5%, from tritium produced in previous deuterium-deuterium reactions. We have measured both the absolute neutron flux as well as its relative variation on the operational parameters of the generator. We find the flux to be proportional to voltage V 3 . 32 ± 0 . 14 and current I 0 . 97 ± 0 . 01. Further, we have measured the angular dependence of the neutron emission with respect to the polar angle. We conclude that it is well described by isotropic production of neutrons within the cathode field cage.

Distributed state-space generation of discrete-state stochastic models

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Gluckman, Joshua; Nicol, David

1995-01-01

High-level formalisms such as stochastic Petri nets can be used to model complex systems. Analysis of logical and numerical properties of these models of ten requires the generation and storage of the entire underlying state space. This imposes practical limitations on the types of systems which can be modeled. Because of the vast amount of memory consumed, we investigate distributed algorithms for the generation of state space graphs. The distributed construction allows us to take advantage of the combined memory readily available on a network of workstations. The key technical problem is to find effective methods for on-the-fly partitioning, so that the state space is evenly distributed among processors. In this paper we report on the implementation of a distributed state-space generator that may be linked to a number of existing system modeling tools. We discuss partitioning strategies in the context of Petri net models, and report on performance observed on a network of workstations, as well as on a distributed memory multi-computer.

Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization (LNA flow-FISH): A Method for Bacterial Small RNA Detection

DTIC Science & Technology

2012-01-10

flow cytometry, locked nucleic acid, sRNA, Vibrio , Date Published: 1/10/2012 This is an open-access article distributed under the terms of the Creative...solubilization process to maintain a 10 mL volume. Aliquot the 60% dextran sulfate solution and store at -20 °C until use. 1. Harvest 1x108 cells of...bioluminescent Vibrio campbellii or your bacteria of interest and transfer them into a 1.5 mL microcentrifuge tube. This quantity of cells provides

Study on THz wave generation from air plasma induced by quasi-square Airy beam

NASA Astrophysics Data System (ADS)

Zhang, Shijing; Zhang, Liangliang; Jiang, Guangtong; Zhang, Cunlin; Zhao, Yuejin

2018-01-01

Terahertz (THz) wave has attracted considerable attention in recent years because of its potential applications. The intense THz waves generated from air plasma induced by two-color femtosecond laser are widely used due to its high generation efficiency and broad frequency bandwidth. The parameters of the laser change the distribution of the air plasma, and then affect the generation of THz wave. In this research, we investigate the THz wave generation from air plasma induced by quasi-square Airy beam. Unlike the common Gauss beam, the quasi-square Airy beam has ability to autofocus and to increase the maximum intensity at the focus. By using the spatial light modulator (SLM), we can change the parameters of phase map to control the shape of the Airy beam. We obtain the two-color laser field by a 100-um-thick BBO crystal, then use a Golay detector to record THz wave energy. By comparing terahertz generation at different modulation depths, we find that terahertz energy produced by quasi-square Airy beam is up to 3.1 times stronger than that of Gauss beam with identical laser energy. In order to understand the influence of quasi-square Airy beam on the BBO crystal, we record THz wave energy by changing the azimuthal angle of BBO crystal with Gauss beam and Airy beam at different modulation depths. We find that the trend of terahertz energy with respect to the azimuthal angle of the BBO crystal keeps the same for different laser beams. We believe that the quasi-square Airy beam or other auto focusing beam can significantly improve the efficiency of terahertz wave generation and pave the way for its applications.

Where's Wally: the influence of visual salience on referring expression generation.

PubMed

Clarke, Alasdair D F; Elsner, Micha; Rohde, Hannah

2013-01-01

REFERRING EXPRESSION GENERATION (REG) PRESENTS THE CONVERSE PROBLEM TO VISUAL SEARCH: given a scene and a specified target, how does one generate a description which would allow somebody else to quickly and accurately locate the target?Previous work in psycholinguistics and natural language processing has failed to find an important and integrated role for vision in this task. That previous work, which relies largely on simple scenes, tends to treat vision as a pre-process for extracting feature categories that are relevant to disambiguation. However, the visual search literature suggests that some descriptions are better than others at enabling listeners to search efficiently within complex stimuli. This paper presents a study testing whether participants are sensitive to visual features that allow them to compose such "good" descriptions. Our results show that visual properties (salience, clutter, area, and distance) influence REG for targets embedded in images from the Where's Wally? books. Referring expressions for large targets are shorter than those for smaller targets, and expressions about targets in highly cluttered scenes use more words. We also find that participants are more likely to mention non-target landmarks that are large, salient, and in close proximity to the target. These findings identify a key role for visual salience in language production decisions and highlight the importance of scene complexity for REG.

An automated framework for hypotheses generation using literature.

PubMed

Abedi, Vida; Zand, Ramin; Yeasin, Mohammed; Faisal, Fazle Elahi

2012-08-29

In bio-medicine, exploratory studies and hypothesis generation often begin with researching existing literature to identify a set of factors and their association with diseases, phenotypes, or biological processes. Many scientists are overwhelmed by the sheer volume of literature on a disease when they plan to generate a new hypothesis or study a biological phenomenon. The situation is even worse for junior investigators who often find it difficult to formulate new hypotheses or, more importantly, corroborate if their hypothesis is consistent with existing literature. It is a daunting task to be abreast with so much being published and also remember all combinations of direct and indirect associations. Fortunately there is a growing trend of using literature mining and knowledge discovery tools in biomedical research. However, there is still a large gap between the huge amount of effort and resources invested in disease research and the little effort in harvesting the published knowledge. The proposed hypothesis generation framework (HGF) finds "crisp semantic associations" among entities of interest - that is a step towards bridging such gaps. The proposed HGF shares similar end goals like the SWAN but are more holistic in nature and was designed and implemented using scalable and efficient computational models of disease-disease interaction. The integration of mapping ontologies with latent semantic analysis is critical in capturing domain specific direct and indirect "crisp" associations, and making assertions about entities (such as disease X is associated with a set of factors Z). Pilot studies were performed using two diseases. A comparative analysis of the computed "associations" and "assertions" with curated expert knowledge was performed to validate the results. It was observed that the HGF is able to capture "crisp" direct and indirect associations, and provide knowledge discovery on demand. The proposed framework is fast, efficient, and robust in

Modeling long correlation times using additive binary Markov chains: Applications to wind generation time series.

PubMed

Weber, Juliane; Zachow, Christopher; Witthaut, Dirk

2018-03-01