CBC bound proteins and RNA fate
DEFF Research Database (Denmark)
Giacometti, Simone
) complex (CBCN), were recently shown to target capped RNA either toward export or degradation, but the mechanisms by which they can discriminate between different RNA families and route them toward different metabolic pathways still remain unclear. A major question to be answered is how and when...... the different CBC subcomplexes are recruited to the RNP. Here, we used an individual nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP) approach to identify the transcriptome-wide targets for 5 different components of the CBCAP and CBCN complexes, and compared results to the previously...... analysed NEXT-component RBM7. We report that: (i) CBP20, ARS2, PHAX and ZC3H18 bind close to the cap, while RBM7 and MTR4 bind throughout the mRNA body; (ii) CBP20, ARS2, PHAX and ZC3H18 associate with a broad set of RNA polymerase II (PolII)-derived RNAs and have only mild species preferences; (iii...
Structure of Escherichia coli Hfq bound to polyriboadenylate RNA
DEFF Research Database (Denmark)
Link, Todd M; Valentin-Hansen, Poul; Brennan, Richard G
2009-01-01
(A) RNA, A(15). The structure reveals a unique RNA binding mechanism. Unlike uridine-containing sequences, which bind to the "proximal" face, the poly(A) tract binds to the "distal" face of Hfq using 6 tripartite binding motifs. Each motif consists of an adenosine specificity site (A site), which......Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRNAs) to their target mRNAs, typically resulting...... in the down-regulation of gene expression. Hfq also plays a key role in bacterial RNA decay by binding tightly to polyadenylate [poly(A)] tracts. The structural mechanism by which Hfq recognizes and binds poly(A) is unknown. Here, we report the crystal structure of Escherichia coli Hfq bound to the poly...
Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins
de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin
2016-01-01
Abstract Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins. PMID:27131381
Class-specific Error Bounds for Ensemble Classifiers
Energy Technology Data Exchange (ETDEWEB)
Prenger, R; Lemmond, T; Varshney, K; Chen, B; Hanley, W
2009-10-06
The generalization error, or probability of misclassification, of ensemble classifiers has been shown to be bounded above by a function of the mean correlation between the constituent (i.e., base) classifiers and their average strength. This bound suggests that increasing the strength and/or decreasing the correlation of an ensemble's base classifiers may yield improved performance under the assumption of equal error costs. However, this and other existing bounds do not directly address application spaces in which error costs are inherently unequal. For applications involving binary classification, Receiver Operating Characteristic (ROC) curves, performance curves that explicitly trade off false alarms and missed detections, are often utilized to support decision making. To address performance optimization in this context, we have developed a lower bound for the entire ROC curve that can be expressed in terms of the class-specific strength and correlation of the base classifiers. We present empirical analyses demonstrating the efficacy of these bounds in predicting relative classifier performance. In addition, we specify performance regions of the ROC curve that are naturally delineated by the class-specific strengths of the base classifiers and show that each of these regions can be associated with a unique set of guidelines for performance optimization of binary classifiers within unequal error cost regimes.
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
Konevega, Andrey L; Fischer, Niels; Semenkov, Yuri P; Stark, Holger; Wintermeyer, Wolfgang; Rodnina, Marina V
2007-04-01
During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement.
Chromatin-bound RNA and the neurobiology of psychiatric disease.
Tushir, J S; Akbarian, S
2014-04-04
A large, and still rapidly expanding literature on epigenetic regulation in the nervous system has provided fundamental insights into the dynamic regulation of DNA methylation and post-translational histone modifications in the context of neuronal plasticity in health and disease. Remarkably, however, very little is known about the potential role of chromatin-bound RNAs, including many long non-coding transcripts and various types of small RNAs. Here, we provide an overview on RNA-mediated regulation of chromatin structure and function, with focus on histone lysine methylation and psychiatric disease. Examples of recently discovered chromatin-bound long non-coding RNAs important for neuronal health and function include the brain-derived neurotrophic factor antisense transcript (Bdnf-AS) which regulates expression of the corresponding sense transcript, and LOC389023 which is associated with human-specific histone methylation signatures at the chromosome 2q14.1 neurodevelopmental risk locus by regulating expression of DPP10, an auxillary subunit for voltage-gated K(+) channels. We predict that the exploration of chromatin-bound RNA will significantly advance our current knowledge base in neuroepigenetics and biological psychiatry. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.
Bounds on the performance of a class of digital communication systems
Polk, D. R.; Gupta, S. C.; Cohn, D. L.
1973-01-01
Bounds on the capacity of a class of digital communication channels are derived. Equating the bounds on capacity to rate-distortion functions of (typical) sources in turn produces bounds on the performance of a class of digital communication systems. For ratios of squared quantization level to noise variance much less than one, the power requirements for this class of digital communication systems are shown to be within approximately 3 dB of the theoretical optimum.
Lower bounds for protrusion replacement by counting equivalence classes
Jansen, B.M.P.; Wulms, J.J.H.M.; Guo, J.; Hermelin, D.
2017-01-01
Garnero et al. [SIAM J. Discrete Math. 2015, 29(4):1864-1894] recently introduced a framework based on dynamic programming to make applications of the protrusion replacement technique constructive and to obtain explicit upper bounds on the involved constants. They show that for several graph
Lower bounds for protrusion replacement by counting equivalence classes
Jansen, B.M.P.; Wulms, J.J.H.M.
2016-01-01
Garnero et al. [SIAM J. Discrete Math. 2015, 29(4):1864--1894] recently introduced a framework based on dynamic programming to make applications of the protrusion replacement technique constructive and to obtain explicit upper bounds on the involved constants. They show that for several graph
Bounded Delay Timing Analysis of a Class of CSP Programs
DEFF Research Database (Denmark)
Hulgaard, Henrik; Burns, Steven M.
1997-01-01
We describe an algebraic technique for performing timing analysis of a class of asynchronous circuits described as CSP programs (including Martin's probe operator) with the restrictions that there is no OR-causality and that guard selection is either completely free or mutually exclusive...
A Branch and Bound Algorithm for a Class of Biobjective Mixed Integer Programs
DEFF Research Database (Denmark)
Stidsen, Thomas Riis; Andersen, Kim Allan; Dammann, Bernd
2014-01-01
there is the complicating factor that some of the variables are required to be integral. The resulting class of problems is named multiobjective mixed integer programming (MOMIP) problems. Solving these kinds of optimization problems exactly requires a method that can generate the whole set of nondominated points (the...... Pareto-optimal front). In this paper, we first give a survey of the newly developed branch and bound methods for solving MOMIP problems. After that, we propose a new branch and bound method for solving a subclass of MOMIP problems, where only two objectives are allowed, the integer variables are binary......, and one of the two objectives has only integer variables. The proposed method is able to find the full set of nondominated points. It is tested on a large number of problem instances, from six different classes of MOMIP problems. The results reveal that the developed biobjective branch and bound method...
Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA.
Wahba, Amy; Ryan, Michael C; Shankavaram, Uma T; Camphausen, Kevin; Tofilon, Philip J
2018-01-02
Alternative splicing is a critical event in the posttranscriptional regulation of gene expression. To investigate whether this process influences radiation-induced gene expression we defined the effects of ionizing radiation on the generation of alternative transcripts in total cellular mRNA (the transcriptome) and polysome-bound mRNA (the translatome) of the human glioblastoma stem-like cell line NSC11. For these studies, RNA-Seq profiles from control and irradiated cells were compared using the program SpliceSeq to identify transcripts and splice variations induced by radiation. As compared to the transcriptome (total RNA) of untreated cells, the radiation-induced transcriptome contained 92 splice events suggesting that radiation induced alternative splicing. As compared to the translatome (polysome-bound RNA) of untreated cells, the radiation-induced translatome contained 280 splice events of which only 24 were overlapping with the radiation-induced transcriptome. These results suggest that radiation not only modifies alternative splicing of precursor mRNA, but also results in the selective association of existing mRNA isoforms with polysomes. Comparison of radiation-induced alternative transcripts to radiation-induced gene expression in total RNA revealed little overlap (about 3%). In contrast, in the radiation-induced translatome, about 38% of the induced alternative transcripts corresponded to genes whose expression level was affected in the translatome. This study suggests that whereas radiation induces alternate splicing, the alternative transcripts present at the time of irradiation may play a role in the radiation-induced translational control of gene expression and thus cellular radioresponse.
ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool
Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.
2012-01-01
Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases
Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk
2018-01-01
The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563
Explicit Bounds and Sharp Results for the Composition Operators Preserving the Exponential Class
Directory of Open Access Journals (Sweden)
Fernando Farroni
2016-01-01
Full Text Available Let f:Ω⊂Rn→Rn be a quasiconformal mapping whose Jacobian is denoted by Jf and let EXP(Ω be the space of exponentially integrable functions on Ω. We give an explicit bound for the norm of the composition operator Tf: u∈EXP(Ω↦u∘f-1∈EXP(f(Ω and, as a related question, we study the behaviour of the norm of logJf in the exponential class. The A∞ property of Jf is the counterpart in higher dimensions of the area distortion formula due to Astala in the plane and it is the key tool to prove the sharpness of our results.
Plant plasma membrane-bound staphylococcal-like DNases as a novel class of eukaryotic nucleases
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Leśniewicz Krzysztof
2012-10-01
Full Text Available Abstract Background The activity of degradative nucleases responsible for genomic DNA digestion has been observed in all kingdoms of life. It is believed that the main function of DNA degradation occurring during plant programmed cell death is redistribution of nucleic acid derived products such as nitrogen, phosphorus and nucleotide bases. Plant degradative nucleases that have been studied so far belong mainly to the S1-type family and were identified in cellular compartments containing nucleic acids or in the organelles where they are stored before final application. However, the explanation of how degraded DNA components are exported from the dying cells for further reutilization remains open. Results Bioinformatic and experimental data presented in this paper indicate that two Arabidopsis staphylococcal-like nucleases, named CAN1 and CAN2, are anchored to the cell membrane via N-terminal myristoylation and palmitoylation modifications. Both proteins possess a unique hybrid structure in their catalytic domain consisting of staphylococcal nuclease-like and tRNA synthetase anticodon binding-like motifs. They are neutral, Ca2+-dependent nucleaces showing a different specificity toward the ssDNA, dsDNA and RNA substrates. A study of microarray experiments and endogenous nuclease activity revealed that expression of CAN1 gene correlates with different forms of programmed cell death, while the CAN2 gene is constitutively expressed. Conclusions In this paper we present evidence showing that two plant staphylococcal-like nucleases belong to a new, as yet unidentified class of eukaryotic nucleases, characterized by unique plasma membrane localization. The identification of this class of nucleases indicates that plant cells possess additional, so far uncharacterized, mechanisms responsible for DNA and RNA degradation. The potential functions of these nucleases in relation to their unique intracellular location are discussed.
Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA
DEFF Research Database (Denmark)
Andersen, Christian Brix Folsted; Ballut, Lionel; Johansen, Jesper Sanderhoff
2006-01-01
exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic. eIF4AIII interacts with the phosphate-ribose backbone of six consecutive nucleotides...... and prevents part of the bound RNA from being double stranded. The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I....
MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action
DEFF Research Database (Denmark)
Wen, Jiayu; Parker, Brian J; Jacobsen, Anders
2011-01-01
the predictive effect of target flanking features. We observe distinct target determinants between expression-based and CLIP-based data. Target flanking features such as flanking region conservation are an important AGO-binding determinant-we hypothesize that CLIP experiments have a preference for strongly bound......Microarray expression analyses following miRNA transfection/inhibition and, more recently, Argonaute cross-linked immunoprecipitation (CLIP)-seq assays have been used to detect miRNA target sites. CLIP and expression approaches measure differing stages of miRNA functioning-initial binding of the mi...... miRNP-target interactions involving adjacent RNA-binding proteins that increase the strength of cross-linking. In contrast, seed-related features are major determinants in expression-based studies, but less so for CLIP-seq studies, and increased miRNA concentrations typical of transfection studies...
Class 2 CRISPR-Cas RNA-guided endonucleases
DEFF Research Database (Denmark)
Stella, Stefano; Alcón, Pablo; Montoya, Guillermo
2017-01-01
CRISPR-Cas is a bacterial defense system against phage infection and nucleic acid invasion. Class 2 type II CRISPR-Cas9 has also been widely used for genome engineering. Here, we review novel insights into the CRISPR class 2 type V enzymes, specifically Cpf1 and C2c1, which display different DNA-...
Targeting of a chimeric human histone fusion mRNA to membrane-bound polysomes in HeLa cells
International Nuclear Information System (INIS)
Zambetti, G.; Stein, J.; Stein, G.
1987-01-01
The subcellular location of histone mRNA-containing polysomes may play a key role in the posttranscriptional events that mediate histone mRNA turnover following inhibition of DNA synthesis. Previously, it has been shown that histone mRNA is found primarily on free polysomes that are associated with the cytoskeleton. The authors report here the construction of an Escherichia coli pBR322 β-lactamase signal peptide-human H3 histone fusion gene. The fusion transcript is targeted to membrane-bound polysomes and remains stable following interruption of DNA replication. Relocating mRNA within the cell may provide a procedure for studying the posttranscriptional regulation of gene expression
Upper and Lower Bounds of Frequency Interval Gramians for a Class of Perturbed Linear Systems
DEFF Research Database (Denmark)
Shaker, Hamid Reza
2012-01-01
if the system is controllable or observable, but also it is required to know the degree of controllability or observability of the system. Gramian matrices were introduced to address this issue by providing a quantitative measure for controllability and observability. In many applications, the information...... of uncertain systems. In this paper, we derive upper and lower bounds of frequency interval gramians under perturbations of an A-matrix in the state-space form. These bounds are obtained by solving algebraic Riccati equations. The results are further used to obtain upper and lower bounds of the frequency...
Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target
Energy Technology Data Exchange (ETDEWEB)
Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)
2014-09-19
In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.
Directory of Open Access Journals (Sweden)
Anna Lundin
2014-05-01
Full Text Available Coronaviruses raise serious concerns as emerging zoonotic viruses without specific antiviral drugs available. Here we screened a collection of 16671 diverse compounds for anti-human coronavirus 229E activity and identified an inhibitor, designated K22, that specifically targets membrane-bound coronaviral RNA synthesis. K22 exerts most potent antiviral activity after virus entry during an early step of the viral life cycle. Specifically, the formation of double membrane vesicles (DMVs, a hallmark of coronavirus replication, was greatly impaired upon K22 treatment accompanied by near-complete inhibition of viral RNA synthesis. K22-resistant viruses contained substitutions in non-structural protein 6 (nsp6, a membrane-spanning integral component of the viral replication complex implicated in DMV formation, corroborating that K22 targets membrane bound viral RNA synthesis. Besides K22 resistance, the nsp6 mutants induced a reduced number of DMVs, displayed decreased specific infectivity, while RNA synthesis was not affected. Importantly, K22 inhibits a broad range of coronaviruses, including Middle East respiratory syndrome coronavirus (MERS-CoV, and efficient inhibition was achieved in primary human epithelia cultures representing the entry port of human coronavirus infection. Collectively, this study proposes an evolutionary conserved step in the life cycle of positive-stranded RNA viruses, the recruitment of cellular membranes for viral replication, as vulnerable and, most importantly, druggable target for antiviral intervention. We expect this mode of action to serve as a paradigm for the development of potent antiviral drugs to combat many animal and human virus infections.
Dutertre, Martin; Vagner, Stéphan
2017-10-27
Upon DNA damage, cells trigger an early DNA-damage response (DDR) involving DNA repair and cell cycle checkpoints, and late responses involving gene expression regulation that determine cell fate. Screens for genes involved in the DDR have found many RNA-binding proteins (RBPs), while screens for novel RBPs have identified DDR proteins. An increasing number of RBPs are involved in early and/or late DDR. We propose to call this new class of actors of the DDR, which contain an RNA-binding activity, DNA-damage response RNA-binding proteins (DDRBPs). We then discuss how DDRBPs contribute not only to gene expression regulation in the late DDR but also to early DDR signaling, DNA repair, and chromatin modifications at DNA-damage sites through interactions with both long and short noncoding RNAs. Copyright © 2016 Elsevier Ltd. All rights reserved.
Cytoskeleton and Cytoskeleton-Bound RNA Visualization in Frog and Insect Oocytes.
Kloc, Malgorzata; Bilinski, Szczepan; Kubiak, Jacek Z
2016-01-01
The majority of oocyte functions involves and depends on the cytoskeletal elements, which include microtubules and actin and cytokeratin filaments. Various structures and molecules are temporarily or permanently bound to the cytoskeletal elements and their functions rely on cytoskeleton integrity and its timely assembly. Thus the accurate visualization of cytoskeleton is often crucial for studies and analyses of oocyte structure and functions. Here we describe several reliable methods for microtubule and/or microfilaments preservation and visualization in Xenopus oocyte extracts, and in situ in live and fixed insect and frog (Xenopus) oocytes. In addition, we describe visualization of cytoskeleton-bound RNAs using molecular beacons in live Xenopus oocytes.
Al-Hashimi, Hashim M; Gosser, Yuying; Gorin, Andrey; Hu, Weidong; Majumdar, Ananya; Patel, Dinshaw J
2002-01-11
Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture. Copyright 2001 Academic Press.
Stress induction of Bm1 RNA in silkworm larvae: SINEs, an unusual class of stress genes
Kimura, Richard H.; Choudary, Prabhakara V.; Stone, Koni K.; Schmid, Carl W.
2001-01-01
This study surveys the induction of RNA polymerase III (Pol III)–directed expression of short interspersed element (SINE) transcripts by various stresses in an animal model, silkworm larvae. Sublethal heat shock and exposure to several toxic compounds increase the level of Bm1 RNA, the silkworm SINE transcript, while also transiently increasing expression of a well-characterized stress-induced transcript, Hsp70 messenger RNA (mRNA). In certain cases, the Bm1 RNA response coincides with that of Hsp70 mRNA, but more often Bm1 RNA responds later in recovery. Baculovirus infection and exposure to certain toxic compounds increase Bm1 RNA but not Hsp70 mRNA, showing that SINE induction is not necessarily coupled to transcription of this particular heat shock gene. SINEs behave as an additional class of stress-inducible genes in living animals but are unusual as stress genes because of their high copy number, genomic dispersion, and Pol III–directed transcription. PMID:11599568
Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP
Wickramasinghe, Vihandha O.; Andrews, Robert; Ellis, Peter; Langford, Cordelia; Gurdon, John B.; Stewart, Murray; Venkitaraman, Ashok R.; Laskey, Ronald A.
2014-01-01
The nuclear phase of the gene expression pathway culminates in the export of mature messenger RNAs (mRNAs) to the cytoplasm through nuclear pore complexes. GANP (germinal- centre associated nuclear protein) promotes the transfer of mRNAs bound to the transport factor NXF1 to nuclear pore complexes. Here, we demonstrate that GANP, subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex, promotes selective nuclear export of a specific subset of mRNAs whose transport depends on NXF1. Genome-wide gene expression profiling showed that half of the transcripts whose nuclear export was impaired following NXF1 depletion also showed reduced export when GANP was depleted. GANP-dependent transcripts were highly expressed, yet short-lived, and were highly enriched in those encoding central components of the gene expression machinery such as RNA synthesis and processing factors. After injection into Xenopus oocyte nuclei, representative GANP-dependent transcripts showed faster nuclear export kinetics than representative transcripts that were not influenced by GANP depletion. We propose that GANP promotes the nuclear export of specific classes of mRNAs that may facilitate rapid changes in gene expression. PMID:24510098
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, Bernd; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Slaymaker, Ian M.; Makarova, Kira S.; Essletzbichler, Patrick; Volz, Sara E.; Joung, Julia; Oost, van der John; Regev, Aviv; Koonin, Eugene V.; Zhang, Feng
2015-01-01
The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized
Directory of Open Access Journals (Sweden)
Jie Chen
Full Text Available BACKGROUND: Trehalase, an enzyme that hydrolyzes trehalose to yield two glucose molecules, plays a pivotal role in various physiological processes. In recent years, trehalase proteins have been purified from several insect species and are divided into soluble (Tre-1 and membrane-bound (Tre-2 trehalases. However, no functions of the two trehalases in chitin biosynthesis in insects have yet been reported. PRINCIPAL FINDINGS: The membrane-bound trehalase of Spodoptera exigua (SeTre-2 was characterized in our laboratory previously. In this study, we cloned the soluble trehalase gene (SeTre-1 and investigated the tissue distribution and developmental expression pattern of the two trehalase genes. SeTre-1 was expressed highly in cuticle and Malpighian tubules, while SeTre-2 was expressed in tracheae and fat body. In the midgut, the two trehalase genes were expressed in different locations. Additionally, the expression profiles of both trehalase mRNAs and their enzyme activities suggest that they may play different roles in chitin biosynthesis. The RNA interference (RNAi of either SeTre-1 or SeTre-2 was gene-specific and effective, with efficiency rates up to 83% at 72 h post injection. After RNAi of SeTre-1 and SeTre-2, significant higher mortality rates were observed during the larva-pupa stage and pupa-adult stage, and the lethal phenotypes were classified and analyzed. Additionally, the change trends of concentration of trehalose and glucose appeared reciprocally in RNAi-mutants. Moreover, knockdown of SeTre-1 gene largely inhibited the expression of chitin synthase gene A (CHSA and reduced the chitin content in the cuticle to two-thirds relative to the control insects. The chitin synthase gene B (CHSB expression, however, was inhibited more by the injection of dsRNA for SeTre-2, and the chitin content in the midgut decreased by about 25%. CONCLUSIONS: SeTre-1 plays a major role in CHSA expression and chitin synthesis in the cuticle, and SeTre-2
High Class-Imbalance in pre-miRNA Prediction: A Novel Approach Based on deepSOM.
Stegmayer, Georgina; Yones, Cristian; Kamenetzky, Laura; Milone, Diego H
2017-01-01
The computational prediction of novel microRNA within a full genome involves identifying sequences having the highest chance of being a miRNA precursor (pre-miRNA). These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are usually only a few in comparison to the hundreds of thousands of potential candidates to miRNA that have to be analyzed, which makes this task a high class-imbalance classification problem. The classical way of approaching it has been training a binary classifier in a supervised manner, using well-known pre-miRNAs as positive class and artificially defining the negative class. However, although the selection of positive labeled examples is straightforward, it is very difficult to build a set of negative examples in order to obtain a good set of training samples for a supervised method. In this work, we propose a novel and effective way of approaching this problem using machine learning, without the definition of negative examples. The proposal is based on clustering unlabeled sequences of a genome together with well-known miRNA precursors for the organism under study, which allows for the quick identification of the best candidates to miRNA as those sequences clustered with known precursors. Furthermore, we propose a deep model to overcome the problem of having very few positive class labels. They are always maintained in the deep levels as positive class while less likely pre-miRNA sequences are filtered level after level. Our approach has been compared with other methods for pre-miRNAs prediction in several species, showing effective predictivity of novel miRNAs. Additionally, we will show that our approach has a lower training time and allows for a better graphical navegability and interpretation of the results. A web-demo interface to try deepSOM is available at http://fich.unl.edu.ar/sinc/web-demo/deepsom/.
López-Carrasco, Amparo; Flores, Ricardo
2017-07-01
Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.
Fleming, Damarius S; Miller, Laura C
2018-04-01
It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs have emerged as having an important role in the immune system in humans. The study uses transcriptomic read counts to profile the type and quantity of both well and lesser characterized sncRNAs, such as microRNAs and small nucleolar RNAs to identify and quantify the classes of sncRNA expressed in whole blood between healthy and highly pathogenic PRRSV-infected pigs. Our results returned evidence on nine classes of sncRNA, four of which were consistently statistically significantly different based on Fisher's Exact Test, that can be detected and possibly interrogated for their effect on host dysregulation during PRRSV infections. Published by Elsevier Inc.
Directory of Open Access Journals (Sweden)
Stacia L. Phillips
2016-01-01
Full Text Available Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Due to the limited coding capacity of the viral genome and the complexity of the viral life cycle, host cell proteins play essential roles throughout the course of viral infection. Host RNA-binding proteins mediate various aspects of virus replication through their physical interactions with viral RNA. Here we describe a technique designed to identify such interactions in the context of infected cells using UV cross-linking followed by antisense-mediated affinity purification and mass spectrometry. Using this approach, we identified interactions, several of them novel, between host proteins and dengue viral RNA in infected Huh7 cells. Most of these interactions were subsequently validated using RNA immunoprecipitation. Using small interfering RNA (siRNA-mediated gene silencing, we showed that more than half of these host proteins are likely involved in regulating virus replication, demonstrating the utility of this method in identifying biologically relevant interactions that may not be identified using traditional in vitro approaches.
The optimization of peptide cargo bound to MHC class I molecules by the peptide-loading complex.
Elliott, Tim; Williams, Anthony
2005-10-01
Major histocompatibility complex (MHC) class I complexes present peptides from both self and foreign intracellular proteins on the surface of most nucleated cells. The assembled heterotrimeric complexes consist of a polymorphic glycosylated heavy chain, non-polymorphic beta(2) microglobulin, and a peptide of typically nine amino acids in length. Assembly of the class I complexes occurs in the endoplasmic reticulum and is assisted by a number of chaperone molecules. A multimolecular unit termed the peptide-loading complex (PLC) is integral to this process. The PLC contains a peptide transporter (transporter associated with antigen processing), a thiooxido-reductase (ERp57), a glycoprotein chaperone (calreticulin), and tapasin, a class I-specific chaperone. We suggest that class I assembly involves a process of optimization where the peptide cargo of the complex is edited by the PLC. Furthermore, this selective peptide loading is biased toward peptides that have a longer off-rate from the assembled complex. We suggest that tapasin is the key chaperone that directs this action of the PLC with secondary contributions from calreticulin and possibly ERp57. We provide a framework model for how this may operate at the molecular level and draw parallels with the proposed mechanism of action of human leukocyte antigen-DM for MHC class II complex optimization.
Structure of the Epstein-Barr virus gp42 protein bound to the MHC class II recepter HLA-DR1
Energy Technology Data Exchange (ETDEWEB)
Mullen, M.; Haan, K.M.; Longnecker, R.; Jardetzky, T.
2010-03-08
Epstein-Barr virus (EBV) causes infectious mononucleosis, establishes long-term latent infections, and is associated with a variety of human tumors. The EBV gp42 glycoprotein binds MHC class II molecules, playing a critical role in infection of B lymphocytes. EBV gp42 belongs to the C-type lectin superfamily, with homology to NK receptors of the immune system. We report the crystal structure of gp42 bound to the human MHC class II molecule HLA-DR1. The gp42 binds HLA-DR1 using a surface site that is distinct from the canonical lectin and NK receptor ligand binding sites. At the canonical ligand binding site, gp42 forms a large hydrophobic groove, which could interact with other ligands necessary for EBV entry, providing a mechanism for coupling MHC recognition and membrane fusion.
International Nuclear Information System (INIS)
Narendrula, Rashmi; Mispel-Beyer, Kyle; Guo, Baoqing; Parissenti, Amadeo M.; Pritzker, Laura B.; Pritzker, Ken; Masilamani, Twinkle; Wang, Xiaohui; Lannér, Carita
2016-01-01
Cellular stressors and apoptosis-inducing agents have been shown to induce ribosomal RNA (rRNA) degradation in eukaryotic cells. Recently, RNA degradation in vivo was observed in patients with locally advanced breast cancer, where mid-treatment tumor RNA degradation was associated with complete tumor destruction and enhanced patient survival. However, it is not clear how widespread chemotherapy induced “RNA disruption” is, the extent to which it is associated with drug response or what the underlying mechanisms are. Ovarian (A2780, CaOV3) and breast (MDA-MB-231, MCF-7, BT474, SKBR3) cancer cell lines were treated with several cytotoxic chemotherapy drugs and total RNA was isolated. RNA was also prepared from docetaxel resistant A2780DXL and carboplatin resistant A2780CBN cells following drug exposure. Disruption of RNA was analyzed by capillary electrophoresis. Northern blotting was performed using probes complementary to the 28S and 18S rRNA to determine the origins of degradation bands. Apoptosis activation was assessed by flow cytometric monitoring of annexin-V and propidium iodide (PI) binding to cells and by measuring caspase-3 activation. The link between apoptosis and RNA degradation (disruption) was investigated using a caspase-3 inhibitor. All chemotherapy drugs tested were capable of inducing similar RNA disruption patterns. Docetaxel treatment of the resistant A2780DXL cells and carboplatin treatment of the A2780CBN cells did not result in RNA disruption. Northern blotting indicated that two RNA disruption bands were derived from the 3’-end of the 28S rRNA. Annexin-V and PI staining of docetaxel treated cells, along with assessment of caspase-3 activation, showed concurrent initiation of apoptosis and RNA disruption, while inhibition of caspase-3 activity significantly reduced RNA disruption. Supporting the in vivo evidence, our results demonstrate that RNA disruption is induced by multiple chemotherapy agents in cell lines from different tissues
Evidence for a Complex Class of Nonadenylated mRNA in Drosophila
Zimmerman, J. Lynn; Fouts, David L.; Manning, Jerry E.
1980-01-01
The amount, by mass, of poly(A+) mRNA present in the polyribosomes of third-instar larvae of Drosophila melanogaster, and the relative contribution of the poly(A+) mRNA to the sequence complexity of total polysomal RNA, has been determined. Selective removal of poly(A+) mRNA from total polysomal RNA by use of either oligo-dT-cellulose, or poly(U)-sepharose affinity chromatography, revealed that only 0.15% of the mass of the polysomal RNA was present as poly(A+) mRNA. The present study shows that this RNA hybridized at saturation with 3.3% of the single-copy DNA in the Drosophila genome. After correction for asymmetric transcription and reactability of the DNA, 7.4% of the single-copy DNA in the Drosophila genome is represented in larval poly(A+) mRNA. This corresponds to 6.73 x 106 nucleotides of mRNA coding sequences, or approximately 5,384 diverse RNA sequences of average size 1,250 nucleotides. However, total polysomal RNA hybridizes at saturation to 10.9% of the single-copy DNA sequences. After correcting this value for asymmetric transcription and tracer DNA reactability, 24% of the single-copy DNA in Drosophila is represented in total polysomal RNA. This corresponds to 2.18 x 107 nucleotides of RNA coding sequences or 17,440 diverse RNA molecules of size 1,250 nucleotides. This value is 3.2 times greater than that observed for poly(A+) mRNA, and indicates that ≃69% of the polysomal RNA sequence complexity is contributed by nonadenylated RNA. Furthermore, if the number of different structural genes represented in total polysomal RNA is ≃1.7 x 104, then the number of genes expressed in third-instar larvae exceeds the number of chromomeres in Drosophila by about a factor of three. This numerology indicates that the number of chromomeres observed in polytene chromosomes does not reflect the number of structural gene sequences in the Drosophila genome. PMID:6777246
Narendrula, Rashmi; Mispel-Beyer, Kyle; Guo, Baoqing; Parissenti, Amadeo M; Pritzker, Laura B; Pritzker, Ken; Masilamani, Twinkle; Wang, Xiaohui; Lannér, Carita
2016-02-24
Cellular stressors and apoptosis-inducing agents have been shown to induce ribosomal RNA (rRNA) degradation in eukaryotic cells. Recently, RNA degradation in vivo was observed in patients with locally advanced breast cancer, where mid-treatment tumor RNA degradation was associated with complete tumor destruction and enhanced patient survival. However, it is not clear how widespread chemotherapy induced "RNA disruption" is, the extent to which it is associated with drug response or what the underlying mechanisms are. Ovarian (A2780, CaOV3) and breast (MDA-MB-231, MCF-7, BT474, SKBR3) cancer cell lines were treated with several cytotoxic chemotherapy drugs and total RNA was isolated. RNA was also prepared from docetaxel resistant A2780DXL and carboplatin resistant A2780CBN cells following drug exposure. Disruption of RNA was analyzed by capillary electrophoresis. Northern blotting was performed using probes complementary to the 28S and 18S rRNA to determine the origins of degradation bands. Apoptosis activation was assessed by flow cytometric monitoring of annexin-V and propidium iodide (PI) binding to cells and by measuring caspase-3 activation. The link between apoptosis and RNA degradation (disruption) was investigated using a caspase-3 inhibitor. All chemotherapy drugs tested were capable of inducing similar RNA disruption patterns. Docetaxel treatment of the resistant A2780DXL cells and carboplatin treatment of the A2780CBN cells did not result in RNA disruption. Northern blotting indicated that two RNA disruption bands were derived from the 3'-end of the 28S rRNA. Annexin-V and PI staining of docetaxel treated cells, along with assessment of caspase-3 activation, showed concurrent initiation of apoptosis and RNA disruption, while inhibition of caspase-3 activity significantly reduced RNA disruption. Supporting the in vivo evidence, our results demonstrate that RNA disruption is induced by multiple chemotherapy agents in cell lines from different tissues and is
Darnell, James E., Jr.
1985-01-01
Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…
A New Class of SINEs with snRNA Gene-Derived Heads.
Kojima, Kenji K
2015-05-27
Eukaryotic genomes are colonized by various transposons including short interspersed elements (SINEs). The 5' region (head) of the majority of SINEs is derived from one of the three types of RNA genes--7SL RNA, transfer RNA (tRNA), or 5S ribosomal RNA (rRNA)--and the internal promoter inside the head promotes the transcription of the entire SINEs. Here I report a new group of SINEs whose heads originate from either the U1 or U2 small nuclear RNA gene. These SINEs, named SINEU, are distributed among crocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of a U1- or U2-derived sequence onto the 5' end of SINEU-1 elements. SINEU-1 and SINEU-3 are ancient and shared among alligators, crocodiles, and gharials, while SINEU-2 is absent in the alligator genome. SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials. All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi. A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Screening nylon-3 polymers, a new class of cationic amphiphiles, for siRNA delivery.
Nadithe, Venkatareddy; Liu, Runhui; Killinger, Bryan A; Movassaghian, Sara; Kim, Na Hyung; Moszczynska, Anna B; Masters, Kristyn S; Gellman, Samuel H; Merkel, Olivia M
2015-02-02
Amphiphilic nucleic acid carriers have attracted strong interest. Three groups of nylon-3 copolymers (poly-β-peptides) possessing different cationic/hydrophobic content were evaluated as siRNA delivery agents in this study. Their ability to condense siRNA was determined in SYBR Gold assays. Their cytotoxicity was tested by MTT assays, their efficiency of delivering Alexa Fluor-488-labeled siRNA intracellularly in the presence and absence of uptake inhibitors was assessed by flow cytometry, and their transfection efficacies were studied by luciferase knockdown in a cell line stably expressing luciferase (H1299/Luc). Endosomal release was determined by confocal laser scanning microscopy and colocalization with lysotracker. All polymers efficiently condensed siRNA at nitrogen-to-phosphate (N/P) ratios of 5 or lower, as reflected in hydrodynamic diameters smaller than that at N/P 1. Although several formulations had negative zeta potentials at N/P 1, G2C and G2D polyplexes yielded >80% uptake in H1299/Luc cells, as determined by flow cytometry. Luciferase knockdown (20-65%) was observed after transfection with polyplexes made of the high molecular weight polymers that were the most hydrophobic. The ability of nylon-3 polymers to deliver siRNA intracellularly even at negative zeta potential implies that they mediate transport across cell membranes based on their amphiphilicity. The cellular uptake route was determined to strongly depend on the presence of cholesterol in the cell membrane. These polymers are, therefore, very promising for siRNA delivery at reduced surface charge and toxicity. Our study identified nylon-3 formulations at low N/P ratios for effective gene knockdown, indicating that nylon-3 polymers are a new, promising type of gene delivery agent.
Screening Nylon-3 Polymers, a New Class of Cationic Amphiphiles, for siRNA Delivery
2015-01-01
Amphiphilic nucleic acid carriers have attracted strong interest. Three groups of nylon-3 copolymers (poly-β-peptides) possessing different cationic/hydrophobic content were evaluated as siRNA delivery agents in this study. Their ability to condense siRNA was determined in SYBR Gold assays. Their cytotoxicity was tested by MTT assays, their efficiency of delivering Alexa Fluor-488-labeled siRNA intracellularly in the presence and absence of uptake inhibitors was assessed by flow cytometry, and their transfection efficacies were studied by luciferase knockdown in a cell line stably expressing luciferase (H1299/Luc). Endosomal release was determined by confocal laser scanning microscopy and colocalization with lysotracker. All polymers efficiently condensed siRNA at nitrogen-to-phosphate (N/P) ratios of 5 or lower, as reflected in hydrodynamic diameters smaller than that at N/P 1. Although several formulations had negative zeta potentials at N/P 1, G2C and G2D polyplexes yielded >80% uptake in H1299/Luc cells, as determined by flow cytometry. Luciferase knockdown (20–65%) was observed after transfection with polyplexes made of the high molecular weight polymers that were the most hydrophobic. The ability of nylon-3 polymers to deliver siRNA intracellularly even at negative zeta potential implies that they mediate transport across cell membranes based on their amphiphilicity. The cellular uptake route was determined to strongly depend on the presence of cholesterol in the cell membrane. These polymers are, therefore, very promising for siRNA delivery at reduced surface charge and toxicity. Our study identified nylon-3 formulations at low N/P ratios for effective gene knockdown, indicating that nylon-3 polymers are a new, promising type of gene delivery agent. PMID:25437915
Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus
International Nuclear Information System (INIS)
Pleshe, Elizabeth; Truesdell, John; Batey, Robert T.
2005-01-01
The crystal structure of Aquifex aeolicus TrmH, a member of the a/b-knot superfamily responsible for O methylation of G18 of tRNAs, was determined to 1.85 Å resolution using the molecular-replacement method. Biological RNAs contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. One of the two most common forms of modification is methylation of the 2′-hydroxyl group of the ribose sugar, which is performed by a number of S-adenosylmethionine (SAM) dependent methyltransferases. In bacteria, many of these modifications in tRNA and rRNA are carried out by the α/β-knot superfamily of enzymes, whose SAM-binding pocket is created by a characteristic deep trefoil knot. TrmH, an enzyme found throughout all three kingdoms of life, modifies the universally conserved guanosine 18 position of tRNA. The crystal structure of TrmH from the thermophilic bacterium Aquifex aeolicus has been determined at 1.85 Å resolution using data collected from a synchrotron-radiation source. The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the α/β-knot superfamily, with α-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding
MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data.
Lee, Sangseon; Park, Youngjune; Kim, Sun
2017-07-15
Pathway based analysis of high throughput transcriptome data is a widely used approach to investigate biological mechanisms. Since a pathway consists of multiple functions, the recent approach is to determine condition specific sub-pathways or subpaths. However, there are several challenges. First, few existing methods utilize explicit gene expression information from RNA-seq. More importantly, subpath activity is usually an average of statistical scores, e.g., correlations, of edges in a candidate subpath, which fails to reflect gene expression quantity information. In addition, none of existing methods can handle multiple phenotypes. To address these technical problems, we designed and implemented an algorithm, MIDAS, that determines condition specific subpaths, each of which has different activities across multiple phenotypes. MIDAS utilizes gene expression quantity information fully and the network centrality information to determine condition specific subpaths. To test performance of our tool, we used TCGA breast cancer RNA-seq gene expression profiles with five molecular subtypes. 36 differentially activate subpaths were determined. The utility of our method, MIDAS, was demonstrated in four ways. All 36 subpaths are well supported by the literature information. Subsequently, we showed that these subpaths had a good discriminant power for five cancer subtype classification and also had a prognostic power in terms of survival analysis. Finally, in a performance comparison of MIDAS to a recent subpath prediction method, PATHOME, our method identified more subpaths and much more genes that are well supported by the literature information. http://biohealth.snu.ac.kr/software/MIDAS/. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Haga, K; Lemp, N A; Logg, C R; Nagashima, J; Faure-Kumar, E; Gomez, G G; Kruse, C A; Mendez, R; Stripecke, R; Kasahara, N; Kasahara, N A; Cicciarelli, J C
2006-12-01
Transplantation of many tissues requires histocompatibility matching of human leukocyte antigens (HLA) to prevent graft rejection, to reduce the level of immunosuppression needed to maintain graft survival, and to minimize the risk of graft-versus-host disease, particularly in the case of bone marrow transplantation. However, recent advances in fields of gene delivery and genetic regulation technologies have opened the possibility of engineering grafts that display reduced levels of HLA expression. Suppression of HLA expression could help to overcome the limitations imposed by extensive HLA polymorphisms that restrict the availability of suitable donors, necessitate the maintenance of large donor registries, and complicate the logistics of procuring and delivering matched tissues and organs to the recipient. Accordingly, we investigated whether knockdown of HLA by RNA interference (RNAi), a ubiquitous regulatory system that can efficiently and selectively inhibit the expression of specific gene products, would enable allogeneic cells to evade immune recognition. For efficient and stable delivery of short hairpin-type RNAi constructs (shRNA), we employed lentivirus-based gene transfer vectors, which provide a delivery system that can achieve integration into genomic DNA, thereby permanently modifying transduced graft cells. Our results show that lentivirus-mediated delivery of shRNA targeting pan-Class I and allele-specific HLA can achieve efficient and dose-dependent reduction in surface expression of HLA in human cells, associated with enhanced resistance to alloreactive T lymphocyte-mediated cytotoxicity, while avoiding MHC-non-restricted killing. We hypothesize that RNAi-induced silencing of HLA expression has the potential to create histocompatibility-enhanced, and, eventually, perhaps "universally" compatible cellular grafts.
Directory of Open Access Journals (Sweden)
Elkin Navarro-Quiroz
Full Text Available Renal involvement in Systemic Lupus Erythematous (SLE patients is one of the leading causes of morbidity and a significant contributor to mortality. It's estimated that nearly 50% of SLE individuals develop kidney disease in the first year of the diagnosis. Class IV lupus nephritis (LN-IV is the class of lupus nephritis most common in Colombian patients with SLE. Altered miRNAs expression levels have been reported in human autoimmune diseases including lupus. Variations in the expression pattern of peripheral blood circulating miRNAs specific for this class of lupus nephritis could be correlated with the pathophysiological status of this group of individuals. The aim of this study was to evaluate the relative abundance of circulating microRNAs in peripheral blood from Colombian patients with LN-IV. Circulating miRNAs in plasma of patients with diagnosis of LN-IV were compared with individuals without renal involvement (LNN group and healthy individuals (CTL group. Total RNA was extracted from 10 ml of venous blood and subsequently sequenced using Illumina. The sequences were processed and these were analyzed using miRBase and Ensembl databases. Differential gene expression analysis was carried out with edgeR and functional analysis were done with DIANA-miRPath. Analysis was carried out using as variables of selection fold change (≥2 o ≤-2 and false discovery rate (0.05. We identified 24 circulating microRNAs with differential abundance between LN-IV and CTL groups, fourteen of these microRNAs are described for the first time to lupus nephritis (hsa-miR-589-3p, hsa-miR-1260b, hsa-miR-4511, hsa-miR-485-5p, hsa-miR-584-5p, hsa-miR-543, hsa-miR-153-3p, hsa-miR-6087, hsa-miR-3942-5p, hsa-miR-7977, hsa-miR-323b-3p, hsa-miR-4732-3p and hsa-miR-6741-3p. These changes in the abundance of miRNAs could be interpreted as alterations in the miRNAs-mRNA regulatory network in the pathogenesis of LN, preceding the clinical onset of the disease. The findings
DEFF Research Database (Denmark)
Pedersen, Lasse Eggers; Harndahl, M.; Nielsen, Morten
2013-01-01
within the structural proteins of foot‐and‐mouth disease virus (FMDV), strain A24 were analyzed as candidate T‐cell epitopes. Peptides predicted by the NetMHCpan were tested in ELISA for binding to the SLA‐1*0401 and SLA‐2*0401 major histocompatibility complex class I proteins. Four of the 10 predicted...... FMDV peptides bound to SLA‐2*0401, whereas five of the nine predicted FMDV peptides bound to SLA‐1*0401. These methods provide the characterization of T‐cell epitopes in response to pathogens in more detail. The development of such approaches to analyze vaccine performance will contribute to a more...
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.
Hountondji, Codjo; Bulygin, Konstantin; Créchet, Jean-Bernard; Woisard, Anne; Tuffery, Pierre; Nakayama, Jun-Ichi; Frolova, Ludmila; Nierhaus, Knud H; Karpova, Galina; Baouz, Soria
2014-01-01
We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2',3'-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.
Universal bounds on current fluctuations.
Pietzonka, Patrick; Barato, Andre C; Seifert, Udo
2016-05-01
For current fluctuations in nonequilibrium steady states of Markovian processes, we derive four different universal bounds valid beyond the Gaussian regime. Different variants of these bounds apply to either the entropy change or any individual current, e.g., the rate of substrate consumption in a chemical reaction or the electron current in an electronic device. The bounds vary with respect to their degree of universality and tightness. A universal parabolic bound on the generating function of an arbitrary current depends solely on the average entropy production. A second, stronger bound requires knowledge both of the thermodynamic forces that drive the system and of the topology of the network of states. These two bounds are conjectures based on extensive numerics. An exponential bound that depends only on the average entropy production and the average number of transitions per time is rigorously proved. This bound has no obvious relation to the parabolic bound but it is typically tighter further away from equilibrium. An asymptotic bound that depends on the specific transition rates and becomes tight for large fluctuations is also derived. This bound allows for the prediction of the asymptotic growth of the generating function. Even though our results are restricted to networks with a finite number of states, we show that the parabolic bound is also valid for three paradigmatic examples of driven diffusive systems for which the generating function can be calculated using the additivity principle. Our bounds provide a general class of constraints for nonequilibrium systems.
Qiu, Shanwen; Abdelaziz, Mohamed Ewis; Abdel Latif, Fadl Hicham Fadl; Claudel, Christian G.
2013-01-01
In this article, we propose a new exact and grid-free numerical scheme for computing solutions associated with an hybrid traffic flow model based on the Lighthill-Whitham-Richards (LWR) partial differential equation, for a class of fundamental
Computational Lower Bounds Using Diagonalization
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 7. Computational Lower Bounds Using Diagonalization - Languages, Turing Machines and Complexity Classes. M V Panduranga Rao. General Article Volume 14 Issue 7 July 2009 pp 682-690 ...
Grossmann, K; Friedrich, H; Seitz, U
1980-01-01
The isolation and purification of DNA-dependent RNA polymerase I (EC 2.7.7.6) from parsley (Petroselinum crispum) callus cells grown in suspension culture is described. The enzyme was solubilized from isolated chromatin. Purification was achieved by using DEAE- and phospho-cellulose in batches, followed by column chromatography on DEAE- and phospho-cellulose (two columns) and density-gradient centrifugation. The highly purified enzyme was stable over several months. The properties of purified parsley RNA polymerase I were investigated. Optimum concentration for Mn2+ was 1 mM, and for Mg2+ 4-6 mM, Mn2+ was slightly more stimulatory than Mg2+. The enzyme was most active at low ionic strengths [10-20 mM-(NH4)SO4]. The influence of various phosphates was tested: pyrophosphate inhibited RNA polymerase at low concentrations, whereas orthophosphate had no effect on the enzyme activity. ADP was slightly inhibitory, and AMP had no effect on the enzyme reaction. Nucleoside triphosphates and bivalent cations in equimolar concentrations in the range 4-11 mM did not influence the RNA synthesis in vitro. Free nucleoside triphosphates in excess of this 1:1 ratio inhibited the enzyme activity, unlike free bivalent cations, which stimulated RNA polymerase I. PMID:7470092
DEFF Research Database (Denmark)
Stranzl, Thomas; Larsen, Mette Voldby; Lund, Ole
2012-01-01
Several studies have shown that cancers actively regulate alternative splicing. Altered splicing mechanisms in cancer lead to cancer-specific transcripts different from the pool of transcripts occurring only in healthy tissue. At the same time, altered presentation of HLA class I epitopes...... is frequently observed in various types of cancer. Down-regulation of genes related to HLA class I antigen processing has been observed in several cancer types, leading to fewer HLA class I antigens on the cell surface. Here, we use a peptidome wide analysis of predicted alternative splice forms, based...... on a publicly available database, to show that peptides over-represented in cancer splice variants comprise significantly fewer predicted HLA class I epitopes compared to peptides from normal transcripts. Peptides over-represented in cancer transcripts are in the case of the three most common HLA class I...
International Nuclear Information System (INIS)
Prunele, E de
2003-01-01
Conditions for bound states for a periodic linear chain are given within the framework of an exactly solvable non-relativistic quantum-mechanical model in three-dimensional space. These conditions express the strength parameter in terms of the distance between two consecutive centres of the chain, and of the range interaction parameter. This expression can be formulated in terms of polylogarithm functions, and, in some particular cases, in terms of the Riemann zeta function. An interesting mathematical result is that these expressions also correspond to the spectra of Toeplitz complex symmetric operators. The non-trivial zeros of the Riemann zeta function are interpreted as multiple points, at the origin, of the spectra of these Toeplitz operators
Unconditional lower bounds against advice
Buhrman, H.; Fortnow, L.; Santhanam, R.
2009-01-01
We show several unconditional lower bounds for exponential time classes against polynomial time classes with advice, including: (1) For any constant c, NEXP not in P^{NP[n^c]} (2) For any constant c, MAEXP not in MA/n^c (3) BPEXP not in BPP/n^{o(1)}. It was previously unknown even whether NEXP in
Nguyen, T. N.
2012-10-26
Trypanosoma brucei is the only organism known to have evolved a multifunctional RNA polymerase I (pol I) system that is used to express the parasite\\'s ribosomal RNAs, as well as its major cell surface antigens, namely, the variant surface glycoprotein (VSG) and procyclin, which are vital for establishing successful infections in the mammalian host and the tsetse vector, respectively. Thus far, biochemical analyses of the T. brucei RNA pol I transcription machinery have elucidated the subunit structure of the enzyme and identified the class I transcription factor A (CITFA). CITFA binds to RNA pol I promoters, and its CITFA-2 subunit was shown to be absolutely essential for RNA pol I transcription in the parasite. Tandem affinity purification (TAP) of CITFA revealed the subunits CITFA-1 to -6, which are conserved only among kinetoplastid organisms, plus the dynein light chain DYNLL1. Here, by tagging CITFA-6 instead of CITFA-2, a complex was purified that contained all known CITFA subunits, as well as a novel proline-rich protein. Functional studies carried out in vivo and in vitro, as well as a colocalization study, unequivocally demonstrated that this protein is a bona fide CITFA subunit, essential for parasite viability and indispensable for RNA pol I transcription of ribosomal gene units and the active VSG expression site in the mammalian-infective life cycle stage of the parasite. Interestingly, CITFA-7 function appears to be species specific, because expression of an RNA interference (RNAi)-resistant CITFA-7 transgene from Trypanosoma cruzi could not rescue the lethal phenotype of silencing endogenous CITFA-7.
It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...
Qiu, Shanwen
2013-09-01
In this article, we propose a new exact and grid-free numerical scheme for computing solutions associated with an hybrid traffic flow model based on the Lighthill-Whitham-Richards (LWR) partial differential equation, for a class of fundamental diagrams. In this hybrid flow model, the vehicles satisfy the LWR equation whenever possible, and have a constant acceleration otherwise. We first propose a mathematical definition of the solution as a minimization problem. We use this formulation to build a grid-free solution method for this model based on the minimization of component function. We then derive these component functions analytically for triangular fundamental diagrams, which are commonly used to model traffic flow. We also show that the proposed computational method can handle fixed or moving bottlenecks. A toolbox implementation of the resulting algorithm is briefly discussed, and posted at https://dl.dropbox.com/u/1318701/Toolbox.zip. © 2013 Elsevier Ltd.
Matusov, Eugene; Smith, Mark Philip
2012-09-01
We consider identity as a historically emerging discourse that requires genealogical analysis - not to discover the roots of our identity but to commit [ourselves] to its dissipation (Foucault 1977, p. 162). We suggest analyzing identity through the history of socio-economic classes, their life struggles, ambitions, development, and reproduction. We see learning not as a project of transformation of identity, but rather as developing access to socially valuable practices and developing one's own voice within these practices (through addressing and responding to other voices). The access and voice projects free agents from unnecessary finalization and objectivization by oneself and others (Bakhtin 1999; Bakhtin 1990). In education, we should develop indigenous discourses of learning and develop a conceptual framework that makes analysis of diverse discourses possible. We argue that learning, as transformation of participation in a sociocultural practice to gain more access, is a better conceptual framework than learning as transformation of identity.
Directory of Open Access Journals (Sweden)
Howard Amanda
2005-03-01
Full Text Available Abstract Amino acid sequence analyses indicate that the Soilborne wheat mosaic virus (SBWMV 19K protein is a cysteine-rich protein (CRP and shares sequence homology with CRPs derived from furo-, hordei-, peclu- and tobraviruses. Since the hordei- and pecluvirus CRPs were shown to be pathogenesis factors and/or suppressors of RNA silencing, experiments were conducted to determine if the SBWMV 19K CRP has similar activities. The SBWMV 19K CRP was introduced into the Potato virus X (PVX viral vector and inoculated to tobacco plants. The SBWMV 19K CRP aggravated PVX-induced symptoms and restored green fluorescent protein (GFP expression to GFP silenced tissues. These observations indicate that the SBWMV 19K CRP is a pathogenicity determinant and a suppressor of RNA silencing.
Directory of Open Access Journals (Sweden)
Ashish Lal
2011-11-01
Full Text Available A simple biochemical method to isolate mRNAs pulled down with a transfected, biotinylated microRNA was used to identify direct target genes of miR-34a, a tumor suppressor gene. The method reidentified most of the known miR-34a regulated genes expressed in K562 and HCT116 cancer cell lines. Transcripts for 982 genes were enriched in the pull-down with miR-34a in both cell lines. Despite this large number, validation experiments suggested that ~90% of the genes identified in both cell lines can be directly regulated by miR-34a. Thus miR-34a is capable of regulating hundreds of genes. The transcripts pulled down with miR-34a were highly enriched for their roles in growth factor signaling and cell cycle progression. These genes form a dense network of interacting gene products that regulate multiple signal transduction pathways that orchestrate the proliferative response to external growth stimuli. Multiple candidate miR-34a-regulated genes participate in RAS-RAF-MAPK signaling. Ectopic miR-34a expression reduced basal ERK and AKT phosphorylation and enhanced sensitivity to serum growth factor withdrawal, while cells genetically deficient in miR-34a were less sensitive. Fourteen new direct targets of miR-34a were experimentally validated, including genes that participate in growth factor signaling (ARAF and PIK3R2 as well as genes that regulate cell cycle progression at various phases of the cell cycle (cyclins D3 and G2, MCM2 and MCM5, PLK1 and SMAD4. Thus miR-34a tempers the proliferative and pro-survival effect of growth factor stimulation by interfering with growth factor signal transduction and downstream pathways required for cell division.
Lal, Ashish; Thomas, Marshall P; Altschuler, Gabriel; Navarro, Francisco; O'Day, Elizabeth; Li, Xiao Ling; Concepcion, Carla; Han, Yoon-Chi; Thiery, Jerome; Rajani, Danielle K; Deutsch, Aaron; Hofmann, Oliver; Ventura, Andrea; Hide, Winston; Lieberman, Judy
2011-11-01
A simple biochemical method to isolate mRNAs pulled down with a transfected, biotinylated microRNA was used to identify direct target genes of miR-34a, a tumor suppressor gene. The method reidentified most of the known miR-34a regulated genes expressed in K562 and HCT116 cancer cell lines. Transcripts for 982 genes were enriched in the pull-down with miR-34a in both cell lines. Despite this large number, validation experiments suggested that ~90% of the genes identified in both cell lines can be directly regulated by miR-34a. Thus miR-34a is capable of regulating hundreds of genes. The transcripts pulled down with miR-34a were highly enriched for their roles in growth factor signaling and cell cycle progression. These genes form a dense network of interacting gene products that regulate multiple signal transduction pathways that orchestrate the proliferative response to external growth stimuli. Multiple candidate miR-34a-regulated genes participate in RAS-RAF-MAPK signaling. Ectopic miR-34a expression reduced basal ERK and AKT phosphorylation and enhanced sensitivity to serum growth factor withdrawal, while cells genetically deficient in miR-34a were less sensitive. Fourteen new direct targets of miR-34a were experimentally validated, including genes that participate in growth factor signaling (ARAF and PIK3R2) as well as genes that regulate cell cycle progression at various phases of the cell cycle (cyclins D3 and G2, MCM2 and MCM5, PLK1 and SMAD4). Thus miR-34a tempers the proliferative and pro-survival effect of growth factor stimulation by interfering with growth factor signal transduction and downstream pathways required for cell division.
Directory of Open Access Journals (Sweden)
Zhili Ding
2016-01-01
Full Text Available The scavenger receptor class B, type I (SR-BI, is a member of the CD36 superfamily comprising transmembrane proteins involved in mammalian and fish lipid homeostasis regulation. We hypothesize that this receptor plays an important role in Macrobrachium nipponense lipid metabolism. However, little attention has been paid to SR-BI in commercial crustaceans. In the present study, we report a cDNA encoding M. nipponense scavenger receptor class B, type I (designated as MnSR-BI, obtained from a hepatopancreas cDNA library. The complete MnSR-BI coding sequence was 1545 bp, encoding 514 amino acid peptides. The MnSR-BI primary structure consisted of a CD36 domain that contained two transmembrane regions at the N- and C-terminals of the protein. SR-BI mRNA expression was specifically detected in muscle, gill, ovum, intestine, hepatopancreas, stomach, and ovary tissues. Furthermore, its expression in the hepatopancreas was regulated by dietary lipid sources, with prawns fed soybean and linseed oils exhibiting higher expression levels. RNAi-based SR-BI silencing resulted in the suppression of its expression in the hepatopancreas and variation in the expression of lipid metabolism-related genes. This is the first report of SR-BI in freshwater prawns and provides the basis for further studies on SR-BI in crustaceans.
On topological RNA interaction structures.
Qin, Jing; Reidys, Christian M
2013-07-01
Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.
International Nuclear Information System (INIS)
Ciesiolka, J.; Nurse, K.; Klein, J.; Ofengand, J.
1985-01-01
The complex of Artemia salina ribosomes and Escherichia coli acetylvalyl-tRNA could be cross-linked by irradiation with near-UV light. Cross-linking required the presence of the codon GUU, GUA being ineffective. The acetylvalyl group could be released from the cross-linked tRNA by treatment with puromycin, demonstrating that cross-linking had occurred at the P site. This was true both for pGUU- and also for poly(U2,G)-dependent cross-linking. All of the cross-linking was to the 18S rRNA of the small ribosomal subunit. Photolysis of the cross-link at 254 nm occurred with the same kinetics as that for the known cyclobutane dimer between this tRNA and Escherichia coli 16S rRNA. T1 RNase digestion of the cross-linked tRNA yielded an oligonucleotide larger in molecular weight than any from un-cross-linked rRNA or tRNA or from a prephotolyzed complex. Extended electrophoresis showed this material to consist of two oligomers of similar mobility, a faster one-third component and a slower two-thirds component. Each oligomer yielded two components on 254-nm photolysis. The slower band from each was the tRNA T1 oligomer CACCUCCCUVACAAGp, which includes the anticodon. The faster band was the rRNA 9-mer UACACACCGp and its derivative UACACACUG. Unexpectedly, the dephosphorylated and slower moving 9-mer was derived from the faster moving dimer. Deamination of the penultimate C to U is probably due to cyclobutane dimer formation and was evidence for that nucleotide being the site of cross-linking. Direct confirmation of the cross-linking site was obtained by Z-gel analysis
Mohri, Mehryar; Rostamizadeh, Afshin
2013-01-01
We present a brief survey of existing mistake bounds and introduce novel bounds for the Perceptron or the kernel Perceptron algorithm. Our novel bounds generalize beyond standard margin-loss type bounds, allow for any convex and Lipschitz loss function, and admit a very simple proof.
Circuit lower bounds in bounded arithmetics
Czech Academy of Sciences Publication Activity Database
Pich, Ján
2015-01-01
Roč. 166, č. 1 (2015), s. 29-45 ISSN 0168-0072 R&D Projects: GA AV ČR IAA100190902 Keywords : bounded arithmetic * circuit lower bounds Subject RIV: BA - General Mathematics Impact factor: 0.582, year: 2015 http://www.sciencedirect.com/science/article/pii/S0168007214000888
Reducing Conservatism of Analytic Transient Response Bounds via Shaping Filters
Kwan, Aiyueh; Bedrossian, Nazareth; Jan, Jiann-Woei; Grigoriadis, Karolos; Hua, Tuyen (Technical Monitor)
1999-01-01
Recent results show that the peak transient response of a linear system to bounded energy inputs can be computed using the energy-to-peak gain of the system. However, analytically computed peak response bound can be conservative for a class of class bounded energy signals, specifically pulse trains generated from jet firings encountered in space vehicles. In this paper, shaping filters are proposed as a Methodology to reduce the conservatism of peak response analytic bounds. This Methodology was applied to a realistic Space Station assembly operation subject to jet firings. The results indicate that shaping filters indeed reduce the predicted peak response bounds.
International Nuclear Information System (INIS)
Tezuka, Hirokazu.
1984-10-01
Scattering of a particle by bound nucleons is discussed. Effects of nucleons that are bound in a nucleus are taken as a structure function. The way how to calculate the structure function is given. (author)
RNA modifications by oxidation
DEFF Research Database (Denmark)
Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper
2012-01-01
to encompass various classes of novel regulatory RNAs, including, e.g., microRNAs. It is well known that DNA is constantly oxidized and repaired by complex genome maintenance mechanisms. Analogously, RNA also undergoes significant oxidation, and there are now convincing data suggesting that oxidation......The past decade has provided exciting insights into a novel class of central (small) RNA molecules intimately involved in gene regulation. Only a small percentage of our DNA is translated into proteins by mRNA, yet 80% or more of the DNA is transcribed into RNA, and this RNA has been found......, and the consequent loss of integrity of RNA, is a mechanism for disease development. Oxidized RNA is found in a large variety of diseases, and interest has been especially devoted to degenerative brain diseases such as Alzheimer disease, in which up to 50-70% of specific mRNA molecules are reported oxidized, whereas...
Automatic bounding estimation in modified NLMS algorithm
International Nuclear Information System (INIS)
Shahtalebi, K.; Doost-Hoseini, A.M.
2002-01-01
Modified Normalized Least Mean Square algorithm, which is a sign form of Nlm based on set-membership (S M) theory in the class of optimal bounding ellipsoid (OBE) algorithms, requires a priori knowledge of error bounds that is unknown in most applications. In a special but popular case of measurement noise, a simple algorithm has been proposed. With some simulation examples the performance of algorithm is compared with Modified Normalized Least Mean Square
DEFF Research Database (Denmark)
Oleksiewicz, M.B.; Kristensen, B.; Ladekjaer-Mikkelsen, A.S.
2002-01-01
The extracellular domains of swine leukocyte antigen class I (SLA-I, major histocompatibility complex protein class 1) were cloned and sequenced for two haplotypes (114 and H7) which do not share any alleles based on serological typing, and which are the most important in Danish farmed pigs...
Nguyen, T. N.; Nguyen, B. N.; Lee, J. H.; Panigrahi, A. K.; Gunzl, A.
2012-01-01
Trypanosoma brucei is the only organism known to have evolved a multifunctional RNA polymerase I (pol I) system that is used to express the parasite's ribosomal RNAs, as well as its major cell surface antigens, namely, the variant surface
Physical Uncertainty Bounds (PUB)
Energy Technology Data Exchange (ETDEWEB)
Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-03-19
This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.
International Nuclear Information System (INIS)
Inoue, J.; Ohtaka, K.
2004-01-01
We study virtual bound states in photonics, which are a vectorial extension of electron virtual bound states. The condition for these states is derived. It is found that the Mie resonant state which satisfies the condition that the size parameter is less than the angular momentum should be interpreted as a photon virtual bound state. In order to confirm the validity of the concept, we compare the photonic density of states, the width of which represents the lifetime of the photon virtual bound states, with numerical results
DEFF Research Database (Denmark)
Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias
2010-01-01
) resultant by means of mixed volume, as well as recent advances on aggregate root bounds for univariate polynomials, and are applicable to arbitrary positive dimensional systems. We improve upon Canny's gap theorem [7] by a factor of O(dn-1), where d bounds the degree of the polynomials, and n is the number...... bound on the number of steps that subdivision-based algorithms perform in order to isolate all real roots of a polynomial system. This leads to the first complexity bound of Milne's algorithm [22] in 2D....
Combinatorics of RNA-RNA interaction
DEFF Research Database (Denmark)
Li, Thomas J X; Reidys, Christian
2012-01-01
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...
Directory of Open Access Journals (Sweden)
Schraga Schwartz
2014-07-01
Full Text Available N6-methyladenosine (m6A is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429 are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing “basal” degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.
Bounded Gaussian process regression
DEFF Research Database (Denmark)
Jensen, Bjørn Sand; Nielsen, Jens Brehm; Larsen, Jan
2013-01-01
We extend the Gaussian process (GP) framework for bounded regression by introducing two bounded likelihood functions that model the noise on the dependent variable explicitly. This is fundamentally different from the implicit noise assumption in the previously suggested warped GP framework. We...... with the proposed explicit noise-model extension....
Bounded Intention Planning Revisited
Sievers Silvan; Wehrle Martin; Helmert Malte
2014-01-01
Bounded intention planning provides a pruning technique for optimal planning that has been proposed several years ago. In addition partial order reduction techniques based on stubborn sets have recently been investigated for this purpose. In this paper we revisit bounded intention planning in the view of stubborn sets.
Bounding species distribution models
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Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE
2011-10-01
Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].
Bounding Species Distribution Models
Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.
2011-01-01
Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].
International Nuclear Information System (INIS)
Diabate, S.; Strack, S.
1993-01-01
Tritium released into the environment may be incorporated into organic matter. Organically bound tritium in that case will show retention times in organisms that are considerably longer than those of tritiated water which has significant consequences on dose estimates. This article reviews the most important processes of organically bound tritium production and transport through food networks. Metabolic reactions in plant and animal organisms with tritiated water as a reaction partner are of great importance in this respect. The most important production process, in quantitative terms, is photosynthesis in green plants. The translocation of organically bound tritium from the leaves to edible parts of crop plants should be considered in models of organically bound tritium behavior. Organically bound tritium enters the human body on several pathways, either from the primary producers (vegetable food) or at a higher tropic level (animal food). Animal experiments have shown that the dose due to ingestion of organically bound tritium can be up to twice as high as a comparable intake of tritiated water in gaseous or liquid form. In the environment, organically bound tritium in plants and animals is often found to have higher specific tritium concentrations than tissue water. This is not due to some tritium enrichment effects but to the fact that no equilibrium conditions are reached under natural conditions. 66 refs
International Nuclear Information System (INIS)
Toki, Hiroshi; Yamazaki, Toshimitsu
1989-01-01
The standard method of pionic atom formation does not produce deeply bound pionic atoms. A study is made on the properties of deeply bound pionic atom states by using the standard pion-nucleus optical potential. Another study is made to estimate the cross sections of the formation of ls pionic atom states by various methods. The pion-nucleus optical potential is determined by weakly bound pionic atom states and pion nucleus scattering. Although this potential may not be valid for deeply bound pionic atoms, it should provide some hint on binding energies and level widths of deeply bound states. The width of the ls state comes out to be 0.3 MeV and is well separated from the rest. The charge dependence of the ls state is investigated. The binding energies and the widths increase linearly with Z azbove a Z of 30. The report then discusses various methods to populate deeply bound pionic atoms. In particular, 'pion exchange' reactions are proposed. (n, pπ) reaction is discussed first. The cross section is calculated by assuming the in- and out-going nucleons on-shell and the produced pion in (n1) pionic atom states. Then, (n, dπ - ) cross sections are estimated. (p, 2 Heπ - ) reaction would have cross sections similar to the cross section of (n, dπ - ) reaction. In conclusion, it seems best to do (n, p) experiment on heavy nuclei for deeply bound pionic atom. (Nogami, K.)
DEFF Research Database (Denmark)
Oleksiewicz, M.B.; Kristensen, B.; Ladekjaer-Mikkelsen, A.S.
2002-01-01
The extracellular domains of swine leukocyte antigen class I (SLA-I, major histocompatibility complex protein class 1) were cloned and sequenced for two haplotypes (114 and H7) which do not share any alleles based on serological typing, and which are the most important in Danish farmed pigs....... The extracellular domain of SLA-I was connected to porcine beta2 microglobulin by glycine-rich linkers. The engineered sin.-le-chain proteins, consisting of fused SLA-I and beta2 microglobulin, were overexpressed as inclusion bodies in Escherichia coli. Also, variants were made of the single-chain proteins......, by linking them through glycine-rich linkers to peptides representing T-cell epitopes from classical swine fever virus (CSFV) and foot-and-mouth disease virus (FMDV). An in vitro refold assay was developed, using a monoclonal anti-SLA antibody (PT85A) to gauge refolding. The single best-defined, SLA...
Bounded Rationality and Budgeting
Ibrahim, Mukdad
2016-01-01
This article discusses the theory of bounded rationality which had been introduced by Herbert Simon in the 1950s. Simon introduced the notion of bounded rationality stating that while decision-makers strive for rationality, they are limited by the effect of the environment, their information process capacity and by the constraints on their information storage and retrieval capabilities. Moreover, this article tries to specifically blend this notion into budgeting, using the foundations of inc...
Tate, Stephen James
2013-10-01
In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.
International Nuclear Information System (INIS)
Orzalesi, C.A.
1979-01-01
In relativistic quantum theory, bound states generate forces in the crossed channel; such forces can affect the binding and self-consistent solutions should be sought for the bound-state problem. The author investigates how self-consistency can be achieved by successive approximations, in a simple scalar model and with successive relativistic eikonal approximations (EAs). Within the generalized ladder approximation, some exact properties of the resulting ''first generation'' bound states are discussed. The binding energies in this approximation are rather small even for rather large values of the primary coupling constant. The coupling of the constituent particles to the first-generation reggeon is determined by a suitable EA and a new generalized ladder amplitude is constructed with rungs given either by the primary gluons or by the first-generation reggeons. The resulting new (second-generation) bound states are found in a reggeized EA. The size of the corrections to the binding energies due to the rebinding effects is surprisingly large. The procedure is then iterated, so as to find - again in an EA - the third-generation bound states. The procedure is found to be self-consistent already at this stage: the third-generation bound states coincide with those of second generation, and no further rebinding takes place in the higher iterations of the approximation method. Features - good and bad - of the model are discussed, as well as the possible relevance of rebinding mechanisms in hadron dynamics. (author)
Directory of Open Access Journals (Sweden)
Nussinov Ruth
2006-03-01
Full Text Available Abstract Background While the premise that lateral gene transfer (LGT is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS is no longer contentious. aaRSs are ancient enzymes, guarding the fidelity of the genetic code. They are clustered in two structurally unrelated classes. Only lysine aminoacyl-tRNA synthetase (LysRS is found both as a class 1 and a class 2 enzyme (LysRS1-2. Remarkably, in several extant prokaryotes both classes of the enzyme coexist, a unique phenomenon that has yet to receive its due attention. Results We applied a phylogenetic approach for determining the extent and origin of LGT in prokaryotic LysRS. Reconstructing species trees for Archaea and Bacteria, and inferring that their last common ancestors encoded LysRS1 and LysRS2, respectively, we studied the gains and losses of both classes. A complex pattern of LGT events emerged. In specific groups of organisms LysRS1 was replaced by LysRS2 (and vice versa. In one occasion, within the alpha proteobacteria, a LysRS2 to LysRS1 LGT was followed by reversal to LysRS2. After establishing the most likely LGT paths, we studied the possible origins of the laterally transferred genes. To this end, we reconstructed LysRS gene trees and evaluated the likely origins of the laterally transferred genes. While the sources of LysRS1 LGTs were readily identified, those for LysRS2 remain, for now, uncertain. The replacement of one LysRS by another apparently transits through a stage simultaneously coding for both synthetases, probably conferring a selective advantage to the affected organisms. Conclusion The family of LysRSs features complex LGT events. The currently available data were sufficient for identifying unambiguously the origins of LysRS1 but not of LysRS2 gene transfers. A selective advantage is suggested to organisms encoding simultaneously LysRS1-2.
The algebras of bounded and essentially bounded Lebesgue measurable functions
Directory of Open Access Journals (Sweden)
Mortini Raymond
2017-04-01
Full Text Available Let X be a set in ℝn with positive Lebesgue measure. It is well known that the spectrum of the algebra L∞(X of (equivalence classes of essentially bounded, complex-valued, measurable functions on X is an extremely disconnected compact Hausdorff space.We show, by elementary methods, that the spectrum M of the algebra ℒb(X, ℂ of all bounded measurable functions on X is not extremely disconnected, though totally disconnected. Let ∆ = { δx : x ∈ X} be the set of point evaluations and let g be the Gelfand topology on M. Then (∆, g is homeomorphic to (X, Τdis,where Tdis is the discrete topology. Moreover, ∆ is a dense subset of the spectrum M of ℒb(X, ℂ. Finally, the hull h(I, (which is homeomorphic to M(L∞(X, of the ideal of all functions in ℒb(X, ℂ vanishing almost everywhere on X is a nowhere dense and extremely disconnected subset of the Corona M \\ ∆ of ℒb(X, ℂ.
Musiu, Simone; Pürstinger, Gerhard; Stallinger, Sylvia; Vrancken, Robert; Haegeman, Andy; Koenen, Frank; Leyssen, Pieter; Froeyen, Mathy; Neyts, Johan; Paeshuyse, Jan
2014-06-01
2,6-Bis(benzimidazol-2-yl)pyridine (BBP/CSFA-0) was identified in a CPE-based screening as a selective inhibitor of the in vitro bovine viral diarrhea virus (BVDV) replication. The EC50-values for the inhibition of BVDV-induced cytopathic (CPE) effect, viral RNA synthesis and the production of infectious virus were 0.3±0.1μM, 0.05±0.01μM and 0.3±0.04μM, respectively. Furthermore, BBP/CSFA-0 inhibits the in vitro replication of the classical swine fever virus (CSFV) with an EC50 of 0.33±0.25μM. BBP/CSFA-0 proved in vitro inactive against the hepatitis C virus, that belongs like BVDV and CSFV to the family of Flaviviridae. Modification of the substituents on the two 1H-benzimidazole groups of BBP resulted in analogues equipotent in anti-BVDV activity (EC50=0.7±0.1μM), devoid of cytotoxicity (S.I.=142). BBP resistant BVDV was selected for and was found to carry the I261M mutation in the viral RNA-dependent RNA polymerase (RdRp). Likewise, BBP-resistant CSFV was selected for; this variant carries either an I261N or a P262A mutation in NS5B. Molecular modeling revealed that I261 and P262 are located in a small cavity near the fingertip domain of the pestivirus polymerase. BBP-resistant BVDV and CSFV proved to be cross-resistant to earlier reported pestivirus inhibitors (BPIP, AG110 and LZ37) that are known to target the same region of the RdRp. BBP did not inhibit the in vitro activity of recombinant BVDV RdRp but inhibited the activity of BVDV replication complexes (RCs). BBP interacts likely with the fingertip of the pestivirus RdRp at the same position as BPIP, AG110 and LZ37. This indicates that this region is a "hot spot" for inhibition of pestivirus replication. Copyright © 2014 Elsevier B.V. All rights reserved.
A note on BPS vortex bound states
Directory of Open Access Journals (Sweden)
A. Alonso-Izquierdo
2016-02-01
Full Text Available In this note we investigate bound states, where scalar and vector bosons are trapped by BPS vortices in the Abelian Higgs model with a critical ratio of the couplings. A class of internal modes of fluctuation around cylindrically symmetric BPS vortices is characterized mathematically, analyzing the spectrum of the second-order fluctuation operator when the Higgs and vector boson masses are equal. A few of these bound states with low values of quantized magnetic flux are described fully, and their main properties are discussed.
A note on BPS vortex bound states
Energy Technology Data Exchange (ETDEWEB)
Alonso-Izquierdo, A., E-mail: alonsoiz@usal.es [Departamento de Matematica Aplicada, Universidad de Salamanca (Spain); Garcia Fuertes, W., E-mail: wifredo@uniovi.es [Departamento de Fisica, Universidad de Oviedo (Spain); Mateos Guilarte, J., E-mail: guilarte@usal.es [Departamento de Fisica Fundamental, Universidad de Salamanca (Spain)
2016-02-10
In this note we investigate bound states, where scalar and vector bosons are trapped by BPS vortices in the Abelian Higgs model with a critical ratio of the couplings. A class of internal modes of fluctuation around cylindrically symmetric BPS vortices is characterized mathematically, analyzing the spectrum of the second-order fluctuation operator when the Higgs and vector boson masses are equal. A few of these bound states with low values of quantized magnetic flux are described fully, and their main properties are discussed.
Bounds for nonlinear composites via iterated homogenization
Ponte Castañeda, P.
2012-09-01
Improved estimates of the Hashin-Shtrikman-Willis type are generated for the class of nonlinear composites consisting of two well-ordered, isotropic phases distributed randomly with prescribed two-point correlations, as determined by the H-measure of the microstructure. For this purpose, a novel strategy for generating bounds has been developed utilizing iterated homogenization. The general idea is to make use of bounds that may be available for composite materials in the limit when the concentration of one of the phases (say phase 1) is small. It then follows from the theory of iterated homogenization that it is possible, under certain conditions, to obtain bounds for more general values of the concentration, by gradually adding small amounts of phase 1 in incremental fashion, and sequentially using the available dilute-concentration estimate, up to the final (finite) value of the concentration (of phase 1). Such an approach can also be useful when available bounds are expected to be tighter for certain ranges of the phase volume fractions. This is the case, for example, for the "linear comparison" bounds for porous viscoplastic materials, which are known to be comparatively tighter for large values of the porosity. In this case, the new bounds obtained by the above-mentioned "iterated" procedure can be shown to be much improved relative to the earlier "linear comparison" bounds, especially at low values of the porosity and high triaxialities. Consistent with the way in which they have been derived, the new estimates are, strictly, bounds only for the class of multi-scale, nonlinear composites consisting of two well-ordered, isotropic phases that are distributed with prescribed H-measure at each stage in the incremental process. However, given the facts that the H-measure of the sequential microstructures is conserved (so that the final microstructures can be shown to have the same H-measure), and that H-measures are insensitive to length scales, it is conjectured
Absolute Lower Bound on the Bounce Action
Sato, Ryosuke; Takimoto, Masahiro
2018-03-01
The decay rate of a false vacuum is determined by the minimal action solution of the tunneling field: bounce. In this Letter, we focus on models with scalar fields which have a canonical kinetic term in N (>2 ) dimensional Euclidean space, and derive an absolute lower bound on the bounce action. In the case of four-dimensional space, we show the bounce action is generically larger than 24 /λcr, where λcr≡max [-4 V (ϕ )/|ϕ |4] with the false vacuum being at ϕ =0 and V (0 )=0 . We derive this bound on the bounce action without solving the equation of motion explicitly. Our bound is derived by a quite simple discussion, and it provides useful information even if it is difficult to obtain the explicit form of the bounce solution. Our bound offers a sufficient condition for the stability of a false vacuum, and it is useful as a quick check on the vacuum stability for given models. Our bound can be applied to a broad class of scalar potential with any number of scalar fields. We also discuss a necessary condition for the bounce action taking a value close to this lower bound.
Observational Bounds on Cosmic Doomsday
Energy Technology Data Exchange (ETDEWEB)
Shmakova, Marina
2003-07-11
Recently it was found, in a broad class of models, that the dark energy density may change its sign during the evolution of the universe. This may lead to a global collapse of the universe within the time t{sub c} {approx} 10{sup 10}-10{sup 11} years. Our goal is to find what bounds on the future lifetime of the universe can be placed by the next generation of cosmological observations. As an example, we investigate the simplest model of dark energy with a linear potential V({phi}) = V{sub 0}(1 + {alpha}{phi}). This model can describe the present stage of acceleration of the universe if {alpha} is small enough. However, eventually the field {phi} rolls down, V({phi}) becomes negative, and the universe collapses. The existing observational data indicate that the universe described by this model will collapse not earlier than t{sub c} {approx_equal} 10 billion years from the present moment. We show that the data from SNAP and Planck satellites may extend the bound on the ''doomsday'' time to tc 40 billion years at the 95% confidence level.
DEFF Research Database (Denmark)
Damgård, Ivan Bjerre; Faust, Sebastian; Mukherjee, Pratyay
2013-01-01
Related key attacks (RKAs) are powerful cryptanalytic attacks where an adversary can change the secret key and observe the effect of such changes at the output. The state of the art in RKA security protects against an a-priori unbounded number of certain algebraic induced key relations, e.......g., affine functions or polynomials of bounded degree. In this work, we show that it is possible to go beyond the algebraic barrier and achieve security against arbitrary key relations, by restricting the number of tampering queries the adversary is allowed to ask for. The latter restriction is necessary......-protocols (including the Okamoto scheme, for instance) are secure even if the adversary can arbitrarily tamper with the prover’s state a bounded number of times and obtain some bounded amount of leakage. Interestingly, for the Okamoto scheme we can allow also independent tampering with the public parameters. We show...
Massive Galileon positivity bounds
de Rham, Claudia; Melville, Scott; Tolley, Andrew J.; Zhou, Shuang-Yong
2017-09-01
The EFT coefficients in any gapped, scalar, Lorentz invariant field theory must satisfy positivity requirements if there is to exist a local, analytic Wilsonian UV completion. We apply these bounds to the tree level scattering amplitudes for a massive Galileon. The addition of a mass term, which does not spoil the non-renormalization theorem of the Galileon and preserves the Galileon symmetry at loop level, is necessary to satisfy the lowest order positivity bound. We further show that a careful choice of successively higher derivative corrections are necessary to satisfy the higher order positivity bounds. There is then no obstruction to a local UV completion from considerations of tree level 2-to-2 scattering alone. To demonstrate this we give an explicit example of such a UV completion.
LENUS (Irish Health Repository)
Foy, Niall
2010-07-22
Abstract Background Lysyl-tRNA synthetase (LysRS) is unique within the aminoacyl-tRNA synthetase family in that both class I (LysRS1) and class II (LysRS2) enzymes exist. LysRS1 enzymes are found in Archaebacteria and some eubacteria while all other organisms have LysRS2 enzymes. All sequenced strains of Bacillus cereus (except AH820) and Bacillus thuringiensis however encode both a class I and a class II LysRS. The lysK gene (encoding LysRS1) of B. cereus strain 14579 has an associated T box element, the first reported instance of potential T box control of LysRS expression. Results A global study of 891 completely sequenced bacterial genomes identified T box elements associated with control of LysRS expression in only four bacterial species: B. cereus, B. thuringiensis, Symbiobacterium thermophilum and Clostridium beijerinckii. Here we investigate the T box element found in the regulatory region of the lysK gene in B. cereus strain 14579. We show that this T box element is functional, responding in a canonical manner to an increased level of uncharged tRNALys but, unusually, also responding to an increased level of uncharged tRNAAsn. We also show that B. subtilis strains with T box regulated expression of the endogenous lysS or the heterologous lysK genes are viable. Conclusions The T box element controlling lysK (encoding LysRS1) expression in B. cereus strain 14579 is functional, but unusually responds to depletion of charged tRNALys and tRNAAsn. This may have the advantage of making LysRS1 expression responsive to a wider range of nutritional stresses. The viability of B. subtilis strains with a single LysRS1 or LysRS2, whose expression is controlled by this T box element, makes the rarity of the occurrence of such control of LysRS expression puzzling.
Chloroplast protein synthesis: thylakoid bound polysomes synthesize thylakoid proteins
International Nuclear Information System (INIS)
Hurewitz, J.; Jagendorf, A.T.
1986-01-01
Previous work indicated more polysomes bound to pea thylakoids in light than in the dark, in vivo. With isolated intact chloroplasts incubated in darkness, 24 to 74% more RNA was thylakoid-bound at pH 8.3 than at pH 7. Thus the major effect of light in vivo may be due to higher stroma pH. In isolated pea chloroplasts, initiation inhibitors (pactamycin and kanamycin) decreased the extent of RNA binding, and elongation inhibitors (lincomycin and streptomycin) increased it. Thus translation initiation and termination probably control the cycling of bound ribosomes. While only 3 to 6% of total RNA is in bound polysomes the incorporation of 3 H-Leu into thylakoids was proportional to the amount of this bound RNA. When Micrococcal nuclease-treated thylakoids were added to labeled runoff translation products of stroma ribosomes, less than 1% of the label adhered to the added membranes; but 37% of the labeled products made by thylakoid polysomes were bound. These data support the concept that stroma ribosomes are recruited into thylakoid proteins
On the Applicability of Lower Bounds for Solving Rectilinear
DEFF Research Database (Denmark)
Clausen, Jens; Karisch, Stefan E.; Perregaard, M.
1998-01-01
. Recently, lower bounds based on decomposition were proposed for the so called rectilinear QAP that proved to be the strongest for a large class of problem instances. We investigate the strength of these bounds when applied not only at the root node of a search tree but as the bound function used......The quadratic assignment problem (QAP) belongs to the hard core of NP-hard optimization problems. After almost forty years of research only relatively small instances can be solved to optimality. The reason is that the quality of the lower bounds available for exact methods is not sufficient...
Bound entangled states violate a nonsymmetric local uncertainty relation
International Nuclear Information System (INIS)
Hofmann, Holger F.
2003-01-01
As a consequence of having a positive partial transpose, bound entangled states lack many of the properties otherwise associated with entanglement. It is therefore interesting to identify properties that distinguish bound entangled states from separable states. In this paper, it is shown that some bound entangled states violate a nonsymmetric class of local uncertainty relations [H. F. Hofmann and S. Takeuchi, Phys. Rev. A 68, 032103 (2003)]. This result indicates that the asymmetry of nonclassical correlations may be a characteristic feature of bound entanglement
Bounded Gaps between Products of Special Primes
Directory of Open Access Journals (Sweden)
Ping Ngai Chung
2014-03-01
Full Text Available In their breakthrough paper in 2006, Goldston, Graham, Pintz and Yıldırım proved several results about bounded gaps between products of two distinct primes. Frank Thorne expanded on this result, proving bounded gaps in the set of square-free numbers with r prime factors for any r ≥ 2, all of which are in a given set of primes. His results yield applications to the divisibility of class numbers and the triviality of ranks of elliptic curves. In this paper, we relax the condition on the number of prime factors and prove an analogous result using a modified approach. We then revisit Thorne’s applications and give a better bound in each case.
Kitamura, Masaru
2002-02-15
Clostridium botulinum type E toxin was isolated in the form of a complex with RNA(s) from bacterial cells. Characterization of the complexed RNA remains to be elucidated. The RNA is identified here as ribosomal RNA (rRNA) having 23S and 16S components. The RNA-toxin complexes were found to be made up of three types with different molecular sizes. The three types of RNA-toxin complex are toxin bound to both the 23S and 16S rRNA, toxin bound to the 16S rRNA and a small amount of 23S rRNA, and toxin bound only to the 16S rRNA. ©2002 Elsevier Science (USA).
Appell, Jürgen; Merentes Díaz, Nelson José
2013-01-01
This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements
Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da
2006-01-01
Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...
Multipartite secret key distillation and bound entanglement
International Nuclear Information System (INIS)
Augusiak, Remigiusz; Horodecki, Pawel
2009-01-01
Recently it has been shown that quantum cryptography beyond pure entanglement distillation is possible and a paradigm for the associated protocols has been established. Here we systematically generalize the whole paradigm to the multipartite scenario. We provide constructions of new classes of multipartite bound entangled states, i.e., those with underlying twisted Greenberger-Horne-Zeilinger (GHZ) structure and nonzero distillable cryptographic key. We quantitatively estimate the key from below with the help of the privacy squeezing technique.
Kahneman, Daniel
2002-01-01
The work cited by the Nobel committee was done jointly with the late Amos Tversky (1937-1996) during a long and unusually close collaboration. Together, we explored the psychology of intuitive beliefs and choices and examined their bounded rationality. This essay presents a current perspective on the three major topics of our joint work: heuristics of judgment, risky choice, and framing effects. In all three domains we studied intuitions - thoughts and preferences that come to mind quickly an...
Bounded Satisfiability for PCTL
Bertrand, Nathalie; Fearnley, John; Schewe, Sven
2012-01-01
While model checking PCTL for Markov chains is decidable in polynomial-time, the decidability of PCTL satisfiability, as well as its finite model property, are long standing open problems. While general satisfiability is an intriguing challenge from a purely theoretical point of view, we argue that general solutions would not be of interest to practitioners: such solutions could be too big to be implementable or even infinite. Inspired by bounded synthesis techniques, we turn to the more appl...
Topology and prediction of RNA pseudoknots
DEFF Research Database (Denmark)
Reidys, Christian; Huang, Fenix; Andersen, Jørgen Ellegaard
2011-01-01
Motivation: Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered. Results: Here, we use the natural topological classification of RNA structures in terms...
Detection Performance of Signals in Dependent Noise From a Gaussian Mixture Uncertainty Class
National Research Council Canada - National Science Library
Gerlach, K
1998-01-01
... (correlated) multivariate noise from a Gaussian mixture uncertainty class. This uncertainty class is defined using upper and lower bounding functions on the univariate Gaussian mixing distribution function...
Explicit formula for a fundamental class of functions
Avdispahić, Muharem; Smajlović, Lejla
2005-01-01
The purpose of this paper is to prove an analogue of A. Weil's explicit formula for a fundamental class of functions, i.e. the class of meromorphic functions that have an Euler sum representation and satisfy certain a functional equation. The advance of this explicit formula is that it enlarges the class of allowed test functions, from the class of functions with bounded Jordan variation to the class of functions of $\\phi $-bounded variation. A condition posed to the test fu...
Signatures of RNA binding proteins globally coupled to effective microRNA target sites
DEFF Research Database (Denmark)
Jacobsen, Anders; Wen, Jiayu; Marks, Debora S
2010-01-01
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs), bound to Argonaute proteins (RISC), destabilize mRNAs through base-pairing with the mRNA. However, the gene expression changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting...
Energy Technology Data Exchange (ETDEWEB)
Maldacena, Juan [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States); Shenker, Stephen H. [Stanford Institute for Theoretical Physics and Department of Physics, Stanford University,382 Via Pueblo Mall, Stanford, CA (United States); Stanford, Douglas [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States)
2016-08-17
We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent λ{sub L}≤2πk{sub B}T/ℏ. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.
International Nuclear Information System (INIS)
Kim, Yongbae; Olivi, Luisa; Cheong, Jae Hoon; Maertens, Alex; Bressler, Joseph P.
2007-01-01
Aluminum and other trivalent metals were shown to stimulate uptake of transferrin bound iron and nontransferrin bound iron in erytholeukemia and hepatoma cells. Because of the association between aluminum and Alzheimer's Disease, and findings of higher levels of iron in Alzheimer's disease brains, the effects of aluminum on iron homeostasis were examined in a human glial cell line. Aluminum stimulated dose- and time-dependent uptake of nontransferrin bound iron and iron bound to transferrin. A transporter was likely involved in the uptake of nontransferrin iron because uptake reached saturation, was temperature-dependent, and attenuated by inhibitors of protein synthesis. Interestingly, the effects of aluminum were not blocked by inhibitors of RNA synthesis. Aluminum also decreased the amount of iron bound to ferritin though it did not affect levels of divalent metal transporter 1. These results suggest that aluminum disrupts iron homeostasis in Brain by several mechanisms including the transferrin receptor, a nontransferrin iron transporter, and ferritin
DEFF Research Database (Denmark)
Gasiunas, Vaidas; Mezini, Mira; Ostermann, Klaus
2007-01-01
of dependent classes and a machine-checked type soundness proof in Isabelle/HOL [29], the first of this kind for a language with virtual classes and path-dependent types. [29] T.Nipkow, L.C. Poulson, and M. Wenzel. Isabelle/HOL -- A Proof Assistant for Higher-Order Logic, volume 2283 of LNCS, Springer, 2002......Virtual classes allow nested classes to be refined in subclasses. In this way nested classes can be seen as dependent abstractions of the objects of the enclosing classes. Expressing dependency via nesting, however, has two limitations: Abstractions that depend on more than one object cannot...... be modeled and a class must know all classes that depend on its objects. This paper presents dependent classes, a generalization of virtual classes that expresses similar semantics by parameterization rather than by nesting. This increases expressivity of class variations as well as the flexibility...
Directory of Open Access Journals (Sweden)
Haifeng eChen
2015-11-01
Full Text Available RNA polymerase catalyzes transcription with a high fidelity. If DNA/RNA mismatch or DNA damage occurs downstream, a backtracked RNA polymerase can proofread this situation. However, the backtracked mechanism is still poorly understood. Here we have performed multiple explicit-solvent molecular dynamics (MD simulations on bound and apo DNA/RNA hybrid to study backtracked recognition. MD simulations at room temperature suggest that specific electrostatic interactions play key roles in the backtracked recognition between the polymerase and DNA/RNA hybrid. Kinetics analysis at high temperature shows that bound and apo DNA/RNA hybrid unfold via a two-state process. Both kinetics and free energy landscape analyses indicate that bound DNA/RNA hybrid folds in the order of DNA/RNA contracting, the tertiary folding and polymerase binding. The predicted Φ-values suggest that C7, G9, dC12, dC15 and dT16 are key bases for the backtracked recognition of DNA/RNA hybrid. The average RMSD values between the bound structures and the corresponding apo ones and Kolmogorov-Smirnov (KS P test analyses indicate that the recognition between DNA/RNA hybrid and polymerase might follow an induced fit mechanism for DNA/RNA hybrid and conformation selection for polymerase. Furthermore, this method could be used to relative studies of specific recognition between nucleic acid and protein.
Golden, Barbara L.; Kundrot, Craig E.
2003-01-01
RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.
International Nuclear Information System (INIS)
Ritchie, Burke
2006-01-01
The Hamiltonian for Dirac's second-order equation depends nonlinearly on the potential V and the energy E. For this reason the magnetic contribution to the Hamiltonian for s-waves, which has a short range, is attractive for a repulsive Coulomb potential (V>0) and repulsive for an attractive Coulomb potential (V 2 . Usually solutions are found in the regime E=mc 2 +ε , where except for high Z, ε 2 . Here it is shown that for V>0 the attractive magnetic term and the linear repulsive term combine to support a bound state near E=0.5mc 2 corresponding to a binding energy E b =-ε =0.5mc 2
Inequalities and bounds for nucleon-nucleon scattering
International Nuclear Information System (INIS)
Ramandurai, K.S.
1979-08-01
The objective of this work is to derive model-independent inequalities and bounds for nucleon-nucleon elastic scattering amplitudes based on well-established theoretical principles and symmetries. Two classes of methods are used: algebraic and variational. In the algebraic part, the author derives inequalities and bounds for NN amplitudes and observables using their mutual relations and x symmetries. In the variational part, he employs Lagrange's method of undetermined multipliers to evaluate the bounds. He tests the predictions of a sample of proposed phase shifts at three different energies using the results obtained
On the Feng-Rao bound for generalized hamming weights
DEFF Research Database (Denmark)
Geil, Hans Olav; Thommesen, Christian
2006-01-01
The Feng-Rao bound gives good estimates of the minimum distance of a large class of codes. In this work we are concerned with the problem of how to extend the Feng-Rao bound so that it deals with all the generalized Hamming weights. The problem was solved by Heijnen and Pellikaan in [7] for a large...... family of codes that includes the duals of one-point geometric Goppa codes and the q-ary Reed-Muller codes, but not the Feng-Rao improved such ones. We show that Heijnen and Pellikaan's results holds for the more general class of codes for which the traditional Feng-Rao bound can be applied. We also...... establish the connection to the Shibuya-Sakaniwa bound for generalized Hamming weights ([15], [16], [17], [18], [19] and [20]). More precisely we show that the Shibuya-Sakaniwa bound is a consequence of the extended Feng-Rao bound. In particular the extended Feng-Rao bound gives always at least as good...
On the Feng-Rao bound for generalized Hamming weights
DEFF Research Database (Denmark)
Geil, Olav; Thommesen, Christian
2005-01-01
The Feng-Rao bound gives good estimates of the minimum distance of a large class of codes. In this work we are concerned with the problem of how to extend the Feng-Rao bound so that it deals with all the generalized Hamming weights. The problem was solved by Heijnen and Pellikaan in [7] for a large...... family of codes that includes the duals of one-point geometric Goppa codes and the q-ary Reed-Muller codes, but not the Feng-Rao improved such ones. We show that Heijnen and Pellikaan’s results holds for the more general class of codes for which the traditional Feng-Rao bound can be applied. We also...... establish the connection to the Shibuya-Sakaniwa bound for generalized Hamming weights ([15], [16], [17], [18], [19] and [20]). More precisely we show that the Shibuya-Sakaniwa bound is a consequence of the extended Feng-Rao bound. In particular the extended Feng-Rao bound gives always at least as good...
Contribution of granule bound starch synthase in kernel modification ...
African Journals Online (AJOL)
The role of gbssI and gbssII genes, encoding granule bound starch synthase enzyme I and II, respectively, in quality protein maize (QPM) were studied at different days after pollination (DAP). Total RNA was used for first strand cDNA synthesis using the ImpromIISriptTM reverse transcriptase. No detectable levels of gbssI ...
DEFF Research Database (Denmark)
Sparvath, Steffen Lynge
introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...
Hacker, Andrew
1976-01-01
Provides critical reviews of three books, "The Political Economy of Social Class", "Ethnicity: Theory and Experience," and "Ethnicity in the United States," focusing on the political economy of social class and ethnicity. (Author/AM)
Bounding approaches to system identification
Norton, John; Piet-Lahanier, Hélène; Walter, Éric
1996-01-01
In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.
Tapping the RNA world for therapeutics.
Lieberman, Judy
2018-04-16
A recent revolution in RNA biology has led to the identification of new RNA classes with unanticipated functions, new types of RNA modifications, an unexpected multiplicity of alternative transcripts and widespread transcription of extragenic regions. This development in basic RNA biology has spawned a corresponding revolution in RNA-based strategies to generate new types of therapeutics. Here, I review RNA-based drug design and discuss barriers to broader applications and possible ways to overcome them. Because they target nucleic acids rather than proteins, RNA-based drugs promise to greatly extend the domain of 'druggable' targets beyond what can be achieved with small molecules and biologics.
Market access through bound tariffs
DEFF Research Database (Denmark)
Sala, Davide; Yalcin, Erdal; Schröder, Philipp
2010-01-01
on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and longterm...
Market Access through Bound Tariffs
DEFF Research Database (Denmark)
Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal
on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long...
Quivers of Bound Path Algebras and Bound Path Coalgebras
Directory of Open Access Journals (Sweden)
Dr. Intan Muchtadi
2010-09-01
Full Text Available bras and coalgebras can be represented as quiver (directed graph, and from quiver we can construct algebras and coalgebras called path algebras and path coalgebras. In this paper we show that the quiver of a bound path coalgebra (resp. algebra is the dual quiver of its bound path algebra (resp. coalgebra.
Lower complexity bounds for lifted inference
DEFF Research Database (Denmark)
Jaeger, Manfred
2015-01-01
instances of the model. Numerous approaches for such “lifted inference” techniques have been proposed. While it has been demonstrated that these techniques will lead to significantly more efficient inference on some specific models, there are only very recent and still quite restricted results that show...... the feasibility of lifted inference on certain syntactically defined classes of models. Lower complexity bounds that imply some limitations for the feasibility of lifted inference on more expressive model classes were established earlier in Jaeger (2000; Jaeger, M. 2000. On the complexity of inference about...... that under the assumption that NETIME≠ETIME, there is no polynomial lifted inference algorithm for knowledge bases of weighted, quantifier-, and function-free formulas. Further strengthening earlier results, this is also shown to hold for approximate inference and for knowledge bases not containing...
Structure of a rare non-standard sequence k-turn bound by L7Ae protein
Huang, Lin; Lilley, David M.J.
2014-01-01
Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates. PMID:24482444
Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction
Directory of Open Access Journals (Sweden)
Sarai Akinori
2011-02-01
Full Text Available Abstract Background Protein-RNA interactions play important role in many biological processes such as gene regulation, replication, protein synthesis and virus assembly. Although many structures of various types of protein-RNA complexes have been determined, the mechanism of protein-RNA recognition remains elusive. We have earlier shown that the simplest electrostatic properties viz. charge, dipole and quadrupole moments, calculated from backbone atomic coordinates of proteins are biased relative to other proteins, and these quantities can be used to identify DNA-binding proteins. Closely related, RNA-binding proteins are investigated in this study. In particular, discrimination between various types of RNA-binding proteins, evolutionary conservation of these bulk electrostatic features and effect of conformational changes by complex formation are investigated. Basic binding mechanism of a putative RNA-binding protein (HI1333 from Haemophilus influenza is suggested as a potential application of this study. Results We found that similar to DNA-binding proteins (DBPs, RNA-binding proteins (RBPs also show significantly higher values of electric moments. However, higher moments in RBPs are found to strongly depend on their functional class: proteins binding to ribosomal RNA (rRNA constitute the only class with all three of the properties (charge, dipole and quadrupole moments being higher than control proteins. Neural networks were trained using leave-one-out cross-validation to predict RBPs from control data as well as pair-wise classification capacity between proteins binding to various RNA types. RBPs and control proteins reached up to 78% accuracy measured by the area under the ROC curve. Proteins binding to rRNA are found to be best distinguished (AUC = 79%. Changes in dipole and quadrupole moments between unbound and bound structures were small and these properties are found to be robust under complex formation. Conclusions Bulk electric
Analysis of RNA metabolism in fission yeast
DEFF Research Database (Denmark)
Wise, Jo Ann; Nielsen, Olaf
2017-01-01
Here we focus on the biogenesis and function of messenger RNA (mRNA) in fission yeast cells. Following a general introduction that also briefly touches on other classes of RNA, we provide an overview of methods used to analyze mRNAs throughout their life cycles....
Bounds for Asian basket options
Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle
2008-09-01
In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.
Product differentiation under bounded rationality
Vermeulen, B.; Poutré, La J.A.; Kok, de A.G.; Pyka, A.; Handa, H.; Ishibuchi, H.; Ong, Y.-S.; Tan, K.-C.
2015-01-01
We study product differentiation equilibria and dynamics on the Salop circle under bounded rationality. Due to bounded rationality, firms tend to agglomerate in pairs. Upon adding a second tier of component suppliers, downstream assemblers may escape pairwise horizontal agglomeration. Moreover, we
Metabolism of organically bound tritium
International Nuclear Information System (INIS)
Travis, C.C.
1984-01-01
The classic methodology for estimating dose to man from environmental tritium ignores the fact that organically bound tritium in foodstuffs may be directly assimilated in the bound compartment of tissues without previous oxidation. We propose a four-compartment model consisting of a free body water compartment, two organic compartments, and a small, rapidly metabolizing compartment. The utility of this model lies in the ability to input organically bound tritium in foodstuffs directly into the organic compartments of the model. We found that organically bound tritium in foodstuffs can increase cumulative total body dose by a factor of 1.7 to 4.5 times the free body water dose alone, depending on the bound-to-loose ratio of tritium in the diet. Model predictions are compared with empirical measurements of tritium in human urine and tissue samples, and appear to be in close agreement. 10 references, 4 figures, 3 tables
RNase-assisted RNA chromatography
Michlewski, Gracjan; Cáceres, Javier F.
2010-01-01
RNA chromatography combined with mass spectrometry represents a widely used experimental approach to identify RNA-binding proteins that recognize specific RNA targets. An important drawback of most of these protocols is the high background due to direct or indirect nonspecific binding of cellular proteins to the beads. In many cases this can hamper the detection of individual proteins due to their low levels and/or comigration with contaminating proteins. Increasing the salt concentration during washing steps can reduce background, but at the cost of using less physiological salt concentrations and the likely loss of important RNA-binding proteins that are less stringently bound to a given RNA, as well as the disassembly of protein or ribonucleoprotein complexes. Here, we describe an improved RNA chromatography method that relies on the use of a cocktail of RNases in the elution step. This results in the release of proteins specifically associated with the RNA ligand and almost complete elimination of background noise, allowing a more sensitive and thorough detection of RNA-binding proteins recognizing a specific RNA transcript. PMID:20571124
Kodiak: An Implementation Framework for Branch and Bound Algorithms
Smith, Andrew P.; Munoz, Cesar A.; Narkawicz, Anthony J.; Markevicius, Mantas
2015-01-01
Recursive branch and bound algorithms are often used to refine and isolate solutions to several classes of global optimization problems. A rigorous computation framework for the solution of systems of equations and inequalities involving nonlinear real arithmetic over hyper-rectangular variable and parameter domains is presented. It is derived from a generic branch and bound algorithm that has been formally verified, and utilizes self-validating enclosure methods, namely interval arithmetic and, for polynomials and rational functions, Bernstein expansion. Since bounds computed by these enclosure methods are sound, this approach may be used reliably in software verification tools. Advantage is taken of the partial derivatives of the constraint functions involved in the system, firstly to reduce the branching factor by the use of bisection heuristics and secondly to permit the computation of bifurcation sets for systems of ordinary differential equations. The associated software development, Kodiak, is presented, along with examples of three different branch and bound problem types it implements.
Efficiency bounds for nonequilibrium heat engines
International Nuclear Information System (INIS)
Mehta, Pankaj; Polkovnikov, Anatoli
2013-01-01
We analyze the efficiency of thermal engines (either quantum or classical) working with a single heat reservoir like an atmosphere. The engine first gets an energy intake, which can be done in an arbitrary nonequilibrium way e.g. combustion of fuel. Then the engine performs the work and returns to the initial state. We distinguish two general classes of engines where the working body first equilibrates within itself and then performs the work (ergodic engine) or when it performs the work before equilibrating (non-ergodic engine). We show that in both cases the second law of thermodynamics limits their efficiency. For ergodic engines we find a rigorous upper bound for the efficiency, which is strictly smaller than the equivalent Carnot efficiency. I.e. the Carnot efficiency can be never achieved in single reservoir heat engines. For non-ergodic engines the efficiency can be higher and can exceed the equilibrium Carnot bound. By extending the fundamental thermodynamic relation to nonequilibrium processes, we find a rigorous thermodynamic bound for the efficiency of both ergodic and non-ergodic engines and show that it is given by the relative entropy of the nonequilibrium and initial equilibrium distributions. These results suggest a new general strategy for designing more efficient engines. We illustrate our ideas by using simple examples. -- Highlights: ► Derived efficiency bounds for heat engines working with a single reservoir. ► Analyzed both ergodic and non-ergodic engines. ► Showed that non-ergodic engines can be more efficient. ► Extended fundamental thermodynamic relation to arbitrary nonequilibrium processes
Model checking of time Petri nets using the state class timed automaton
DEFF Research Database (Denmark)
Lime, Didier; Roux, Olivier H.
2006-01-01
In this paper, we propose a method for building the state class graph of a bounded time Petri net (TPN) as a timed automaton (TA), which we call the state class timed automaton. We consider bounded TPN, whose underlying net is not necessarily bounded. We prove that our translation preserves the b...
Curvature bound from gravitational catalysis
Gies, Holger; Martini, Riccardo
2018-04-01
We determine bounds on the curvature of local patches of spacetime from the requirement of intact long-range chiral symmetry. The bounds arise from a scale-dependent analysis of gravitational catalysis and its influence on the effective potential for the chiral order parameter, as induced by fermionic fluctuations on a curved spacetime with local hyperbolic properties. The bound is expressed in terms of the local curvature scalar measured in units of a gauge-invariant coarse-graining scale. We argue that any effective field theory of quantum gravity obeying this curvature bound is safe from chiral symmetry breaking through gravitational catalysis and thus compatible with the simultaneous existence of chiral fermions in the low-energy spectrum. With increasing number of dimensions, the curvature bound in terms of the hyperbolic scale parameter becomes stronger. Applying the curvature bound to the asymptotic safety scenario for quantum gravity in four spacetime dimensions translates into bounds on the matter content of particle physics models.
Combining Alphas via Bounded Regression
Directory of Open Access Journals (Sweden)
Zura Kakushadze
2015-11-01
Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.
Improved Range Searching Lower Bounds
DEFF Research Database (Denmark)
Larsen, Kasper Green; Nguyen, Huy L.
2012-01-01
by constructing a hard input set and query set, and then invoking Chazelle and Rosenberg's [CGTA'96] general theorem on the complexity of navigation in the pointer machine. For the group model, we show that input sets and query sets that are hard for range reporting in the pointer machine (i.e. by Chazelle...... and Rosenberg's theorem), are also hard for dynamic range searching in the group model. This theorem allows us to reuse decades of research on range reporting lower bounds to immediately obtain a range of new group model lower bounds. Amongst others, this includes an improved lower bound for the fundamental...
Schulz, Marc Daniel; Dusuel, Sébastien; Vidal, Julien
2016-11-01
We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.
On functions of bounded semivariation
Czech Academy of Sciences Publication Activity Database
Monteiro, Giselle Antunes
2015-01-01
Roč. 40, č. 2 (2015), s. 233-276 ISSN 0147-1937 Institutional support: RVO:67985840 Keywords : semivariation * functions of bounded variation * regulated functions Subject RIV: BA - General Mathematics http://projecteuclid.org/euclid.rae/1491271216
DEFF Research Database (Denmark)
Rijkhoff, Jan
2007-01-01
in grammatical descriptions of some 50 languages, which together constitute a representative sample of the world’s languages (Hengeveld et al. 2004: 529). It appears that there are both quantitative and qualitative differences between word class systems of individual languages. Whereas some languages employ...... a parts-of-speech system that includes the categories Verb, Noun, Adjective and Adverb, other languages may use only a subset of these four lexical categories. Furthermore, quite a few languages have a major word class whose members cannot be classified in terms of the categories Verb – Noun – Adjective...... – Adverb, because they have properties that are strongly associated with at least two of these four traditional word classes (e.g. Adjective and Adverb). Finally, this article discusses some of the ways in which word class distinctions interact with other grammatical domains, such as syntax and morphology....
Uniform sparse bounds for discrete quadratic phase Hilbert transforms
Kesler, Robert; Arias, Darío Mena
2017-09-01
For each α \\in T consider the discrete quadratic phase Hilbert transform acting on finitely supported functions f : Z → C according to H^{α }f(n):= \\sum _{m ≠ 0} e^{iα m^2} f(n - m)/m. We prove that, uniformly in α \\in T , there is a sparse bound for the bilinear form for every pair of finitely supported functions f,g : Z→ C . The sparse bound implies several mapping properties such as weighted inequalities in an intersection of Muckenhoupt and reverse Hölder classes.
Identifying microRNA/mRNA dysregulations in ovarian cancer.
Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan
2012-03-27
MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify
'Critical' behaviour of weakly bound systems
International Nuclear Information System (INIS)
Lassaut, M.; Lombard, R.J.; Bulboaca, I.
1995-11-01
The class of 3-dimensional finite range or similar potentials λW(r) is discussed, depending on a strength constant λ. The behaviour of the eigenvalue E as function of λ-λ c is studied, where λ c is the critical value at the transition from 0 → 1 bound state. For the l=0 case, E α (λ-λ c ) 2 was found, whereas the relationship is linear for l≥1. Treating l as a continuous parameter in the radial Schroedinger equation, the evolution of the power-law between l=0 and l=1 is given. Besides spherically symmetric scalar potentials, the case of a repulsive scalar potential combined with a spin-orbit component of the Thomas form is also discussed. (author)
Class size versus class composition
DEFF Research Database (Denmark)
Jones, Sam
Raising schooling quality in low-income countries is a pressing challenge. Substantial research has considered the impact of cutting class sizes on skills acquisition. Considerably less attention has been given to the extent to which peer effects, which refer to class composition, also may affect...... bias from omitted variables, the preferred IV results indicate considerable negative effects due to larger class sizes and larger numbers of overage-for-grade peers. The latter, driven by the highly prevalent practices of grade repetition and academic redshirting, should be considered an important...
Generalized bounds for convex multistage stochastic programs
Künzi, H; Fandel, G; Trockel, W; Basile, A; Drexl, A; Dawid, H; Inderfurth, K; Kürsten, W; Schittko, U
2005-01-01
This work was completed during my tenure as a scientific assistant and d- toral student at the Institute for Operations Research at the University of St. Gallen. During that time, I was involved in several industry projects in the field of power management, on the occasion of which I was repeatedly c- fronted with complex decision problems under uncertainty. Although usually hard to solve, I quickly learned to appreciate the benefit of stochastic progr- ming models and developed a strong interest in their theoretical properties. Motivated both by practical questions and theoretical concerns, I became p- ticularly interested in the art of finding tight bounds on the optimal value of a given model. The present work attempts to make a contribution to this important branch of stochastic optimization theory. In particular, it aims at extending some classical bounding methods to broader problem classes of practical relevance. This book was accepted as a doctoral thesis by the University of St. Gallen in June 2004.1...
Simulation bounds for system availability
International Nuclear Information System (INIS)
Tietjen, G.L.; Waller, R.A.
1976-01-01
System availability is a dominant factor in the practicality of nuclear power electrical generating plants. A proposed model for obtaining either lower bounds or interval estimates on availability uses observed data on ''n'' failure-to-repair cycles of the system to estimate the parameters in the time-to-failure and time-to-repair models. These estimates are then used in simulating failure/repair cycles of the system. The availability estimate is obtained for each of 5000 samples of ''n'' failure/repair cycles to form a distribution of estimates. Specific percentile points of those simulated distributions are selected as lower simulation bounds or simulation interval bounds for the system availability. The method is illustrated with operational data from two nuclear plants for which an exponential time-to-failure and a lognormal time-to-repair are assumed
Directory of Open Access Journals (Sweden)
Isabel Garrido
2016-04-01
Full Text Available The class of metric spaces (X,d known as small-determined spaces, introduced by Garrido and Jaramillo, are properly defined by means of some type of real-valued Lipschitz functions on X. On the other hand, B-simple metric spaces introduced by Hejcman are defined in terms of some kind of bornologies of bounded subsets of X. In this note we present a common framework where both classes of metric spaces can be studied which allows us to see not only the relationships between them but also to obtain new internal characterizations of these metric properties.
Relativistic bound state wave functions
International Nuclear Information System (INIS)
Micu, L.
2005-01-01
A particular method of writing the bound state wave functions in relativistic form is applied to the solutions of the Dirac equation with confining potentials in order to obtain a relativistic description of a quark antiquark bound system representing a given meson. Concerning the role of the effective constituent in the present approach we first observe that without this additional constituent we couldn't expand the bound state wave function in terms of products of free states. Indeed, we notice that if the wave function depends on the relative coordinates only, all the expansion coefficients would be infinite. Secondly we remark that the effective constituent enabled us to give a Lorentz covariant meaning to the potential energy of the bound system which is now seen as the 4th component of a 4-momentum. On the other side, by relating the effective constituent to the quantum fluctuations of the background field which generate the binding, we provided a justification for the existence of some spatial degrees of freedom accompanying the interaction potential. These ones, which are quite unusual in quantum mechanics, in our model are the natural consequence of the the independence of the quarks and can be seen as the effect of the imperfect cancellation of the vector momenta during the quantum fluctuations. Related with all these we remark that the adequate representation for the relativistic description of a bound system is the momentum representation, because of the transparent and easy way of writing the conservation laws and the transformation properties of the wave functions. The only condition to be fulfilled is to find a suitable way to take into account the potential energy of the bound system. A particular feature of the present approach is that the confining forces are due to a kind of glue where both quarks are embedded. This recalls other bound state models where the wave function is factorized in terms of constituent wave functions and the confinement is
International Nuclear Information System (INIS)
Zouzou, S.
1986-01-01
In the framework of simple non-relativistic potential models, we examine the system consisting of two quarks and two antiquarks with equal or unequal masses. We search for possible bound states below the threshold for the spontaneous dissociation into two mesons. We solve the four body problem by empirical or systematic variational methods and we include the virtual meson-meson components of the wave function. With standard two-body potentials, there is no proliferation of multiquarks. With unequal quark masses, we obtain however exotic (anti Qanti Qqq) bound states with a baryonic antidiquark-quark-quark structure very analogous to the heavy flavoured (Q'qq) baryons. (orig.)
Bound entanglement and local realism
International Nuclear Information System (INIS)
Kaszlikowski, Dagomir; Zukowski, Marek; Gnacinski, Piotr
2002-01-01
We show using a numerical approach, which gives necessary and sufficient conditions for the existence of local realism, that the bound entangled state presented in Bennett et al. [Phys. Rev. Lett. 82, 5385 (1999)] admits a local and realistic description. We also find the lowest possible amount of some appropriate entangled state that must be ad-mixed to the bound entangled state so that the resulting density operator has no local and realistic description and as such can be useful in quantum communication and quantum computation
Young people, drinking and social class
DEFF Research Database (Denmark)
Kolind, Torsten
2011-01-01
Analytical concepts such as 'bounded consumption' or 'controlled loss of control' have been applied to characterise contemporary youth intoxication. This article argues that this kind of cultural diagnosis benefits from being related to a focus on differences in social class. It is shown that in ......Analytical concepts such as 'bounded consumption' or 'controlled loss of control' have been applied to characterise contemporary youth intoxication. This article argues that this kind of cultural diagnosis benefits from being related to a focus on differences in social class. It is shown...... people to construct social class-related identities: mainstream youngsters continually confirm their taken-for-granted normality, and mainstream breakers resist the mainstream hegemonic (school) culture which usually defies them. In conclusion, bounded consumption, corresponding with contemporary ideals...
DEFF Research Database (Denmark)
Aktor, Mikael
2018-01-01
. Although this social structure was ideal in nature and not equally confirmed in other genres of ancient and medieval literature, it has nevertheless had an immense impact on Indian society. The chapter presents an overview of the system with its three privileged classes, the Brahmins, the Kṣatriyas......The notions of class (varṇa) and caste (jāti) run through the dharmaśāstra literature (i.e. Hindu Law Books) on all levels. They regulate marriage, economic transactions, work, punishment, penance, entitlement to rituals, identity markers like the sacred thread, and social interaction in general...
Semiclassical bounds in magnetic bottles
Czech Academy of Sciences Publication Activity Database
Barseghyan, Diana; Exner, Pavel; Kovařík, H.; Weidl, T.
2016-01-01
Roč. 28, č. 1 (2016), s. 1650002 ISSN 0129-055X R&D Projects: GA ČR(CZ) GA14-06818S Institutional support: RVO:61389005 Keywords : magnetic Laplacian * discrete spectrum * eigenvalue bounds Subject RIV: BE - Theoretical Physics Impact factor: 1.426, year: 2016
Positivity bounds for Sivers functions
International Nuclear Information System (INIS)
Kang Zhongbo; Soffer, Jacques
2011-01-01
We generalize a positivity constraint derived initially for parity-conserving processes to the parity-violating ones, and use it to derive non-trivial bounds on several Sivers functions, entering in the theoretical description of single spin asymmetry for various processes.
Bound states of 'dressed' particles
International Nuclear Information System (INIS)
Shirokov, M.I.
1994-01-01
A new approach to the problem of bound states in relativistic quantum field theories is suggested. It uses the creation - destruction operators of 'dresses' particles which have been granted by Faddeev's (1963) 'dressing' formalism. Peculiarities of the proposed approach as compared to the known ones are discussed. 8 refs. (author)
Quantum lower bound for sorting
Shi, Yaoyun
2000-01-01
We prove that \\Omega(n log(n)) comparisons are necessary for any quantum algorithm that sorts n numbers with high success probability and uses only comparisons. If no error is allowed, at least 0.110nlog_2(n) - 0.067n + O(1) comparisons must be made. The previous known lower bound is \\Omega(n).
Simple bounds for counting processes with monotone rate of occurrence of failures
International Nuclear Information System (INIS)
Kaminskiy, Mark P.
2007-01-01
The article discusses some aspects of analogy between certain classes of distributions used as models for time to failure of nonrepairable objects, and the counting processes used as models for failure process for repairable objects. The notion of quantiles for the counting processes with strictly increasing cumulative intensity function is introduced. The classes of counting processes with increasing (decreasing) rate of occurrence of failures are considered. For these classes, the useful nonparametric bounds for cumulative intensity function based on one known quantile are obtained. These bounds, which can be used for repairable objects, are similar to the bounds introduced by Barlow and Marshall [Barlow, R. Marshall, A. Bounds for distributions with monotone hazard rate, I and II. Ann Math Stat 1964; 35: 1234-74] for IFRA (DFRA) time to failure distributions applicable to nonrepairable objects
Binding energies of two deltas bound states
International Nuclear Information System (INIS)
Sato, Hiroshi; Saito, Koichi.
1982-06-01
Bound states of the two-deltas system are investigated by employing the realistic one boson exchange potential. It is found that there exist many bound states in each isospin channel and also found that the tensor interaction plays important role in producing these bound states. Relationship between these bound states and dibaryon resonances is discussed. (J.P.N.)
... management options. Breastfeeding basics. Caring for baby at home. Birthing classes are not just for new parents, though. ... midwife. Postpartum care. Caring for your baby at home, including baby first aid. Lamaze One of the most popular birthing techniques in the U.S., Lamaze has been around ...
Modelling Toehold-Mediated RNA Strand Displacement
Šulc, Petr; Ouldridge, Thomas E.; Romano, Flavio; Doye, Jonathan P.K.; Louis, Ard A.
2015-01-01
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperat...
Evading Lyth bound in models of quintessential inflation
International Nuclear Information System (INIS)
Hossain, Md. Wali; Myrzakulov, R.; Sami, M.; Saridakis, Emmanuel N.
2014-01-01
Quintessential inflation refers to an attempt to unify inflation and late-time cosmic acceleration using a single scalar field. In this letter we consider two different classes of quintessential inflation, one of which is based upon a Lagrangian with non-canonical kinetic term k 2 (ϕ)∂ μ ϕ∂ μ ϕ and a steep exponential potential while the second class uses the concept of steep brane world inflation. We show that in both cases the Lyth bound can be evaded, despite the large tensor-to-scalar ratio of perturbations. The post-inflationary dynamics is consistent with nucleosynthesis constraint in these cases
Preparation of Total RNA from Fission Yeast.
Bähler, Jürg; Wise, Jo Ann
2017-04-03
Treatment with hot phenol breaks open fission yeast cells and begins to strip away bound proteins from RNA. Deproteinization is completed by multiple extractions with chloroform/isoamyl alcohol and separation of the aqueous and organic phases using MaXtract gel, an inert material that acts as a physical barrier between the phases. The final step is concentration of the RNA by ethanol precipitation. The protocol can be used to prepare RNA from several cultures grown in parallel, but it is important not to process too many samples at once because delays can be detrimental to RNA quality. A reasonable number of samples to process at once would be three to four for microarray or RNA sequencing analyses and six for preliminary investigations of mutants implicated in RNA metabolism. © 2017 Cold Spring Harbor Laboratory Press.
Dp spaces on bounded symmetric domains of Cn
International Nuclear Information System (INIS)
Shi Jihuai.
1989-06-01
In this paper, the space D p (Ω) of functions holomorphic on bounded symmetric domain of C m is defined. We prove that H p (Ω) is contained in D p (Ω) if 0 p (Ω) is contained in H p (Ω) if p ≥2, and both inclusions are proper. Further we find that some theorems on H p (Ω) can be extended to the wider class D p (Ω) for 0 < p ≤ 2. (author). 12 refs
QCD bound states at finite temperature and baryon number
International Nuclear Information System (INIS)
Kalinovsky, Yu.L.; Muenchow, L.
1991-04-01
Quark-antiquark bound states are described within the Bethe-Salpeter equation for a class of quark models with instantaneous 4-quark interaction at finite temperature. Thereby decompositions of the Bethe-Salpeter vertex and wave functions according to their Lorentz structures and the particles content are used. As an application of general scheme, we determine the mass spectrum of low-lying mesons for a special Nambu-Jona-Lasinio model inspired by QCD for hadrons. (orig.)
Trial and Error: A new Approach to Space-Bounded Learning
DEFF Research Database (Denmark)
Ameur, F.; Fischer, Paul; Hoeffgen, H.-U.
1996-01-01
A pac-learning algorithm is d-space bounded, if it stores at most d examples from the sample at any time. We characterize the d-space learnable concept classes. For this purpose we introduce the compression parameter of a concept class 𝒞 and design our trial and error learning algorithm. We ...
Rigorous lower bound on the dynamic critical exponent of some multilevel Swendsen-Wang algorithms
International Nuclear Information System (INIS)
Li, X.; Sokal, A.D.
1991-01-01
We prove the rigorous lower bound z exp ≥α/ν for the dynamic critical exponent of a broad class of multilevel (or ''multigrid'') variants of the Swendsen-Wang algorithm. This proves that such algorithms do suffer from critical slowing down. We conjecture that such algorithms in fact lie in the same dynamic universality class as the stanard Swendsen-Wang algorithm
A symmetric Roos bound for linear codes
Duursma, I.M.; Pellikaan, G.R.
2006-01-01
The van Lint–Wilson AB-method yields a short proof of the Roos bound for the minimum distance of a cyclic code. We use the AB-method to obtain a different bound for the weights of a linear code. In contrast to the Roos bound, the role of the codes A and B in our bound is symmetric. We use the bound
DEFF Research Database (Denmark)
Ejsing-Duun, Stine; Hansbøl, Mikala
Denne rapport rummer evaluering og dokumentation af Coding Class projektet1. Coding Class projektet blev igangsat i skoleåret 2016/2017 af IT-Branchen i samarbejde med en række medlemsvirksomheder, Københavns kommune, Vejle Kommune, Styrelsen for IT- og Læring (STIL) og den frivillige forening...... Coding Pirates2. Rapporten er forfattet af Docent i digitale læringsressourcer og forskningskoordinator for forsknings- og udviklingsmiljøet Digitalisering i Skolen (DiS), Mikala Hansbøl, fra Institut for Skole og Læring ved Professionshøjskolen Metropol; og Lektor i læringsteknologi, interaktionsdesign......, design tænkning og design-pædagogik, Stine Ejsing-Duun fra Forskningslab: It og Læringsdesign (ILD-LAB) ved Institut for kommunikation og psykologi, Aalborg Universitet i København. Vi har fulgt og gennemført evaluering og dokumentation af Coding Class projektet i perioden november 2016 til maj 2017...
Computer simulation of bounded plasmas
International Nuclear Information System (INIS)
Lawson, W.S.
1987-01-01
The problems of simulating a one-dimensional bounded plasma system using particles in a gridded space are systematically explored and solutions to them are given. Such problems include the injection of particles at the boundaries, the solution of Poisson's equation, and the inclusion of an external circuit between the confining boundaries. A recently discovered artificial cooling effect is explained as being a side-effect of quiet injection, and its potential for causing serious but subtle errors in bounded simulation is noted. The methods described in the first part of the thesis are then applied to the simulation of an extension of the Pierce diode problem, specifically a Pierce diode modified by an external circuit between the electrodes. The results of these simulations agree to high accuracy with theory when a theory exists, and also show some interesting chaotic behavior in certain parameter regimes. The chaotic behavior is described in detail
Bounded Rationality in Transposition Processes
DEFF Research Database (Denmark)
Vollaard, Hans; Martinsen, Dorte Sindbjerg
2014-01-01
Studies explaining the timeliness and correctness of the transposition of EU directives into national legislation have provided rather inconclusive findings. They do not offer a clear-cut prediction concerning the transposition of the patients’ rights directive, which is one of the first that con......Studies explaining the timeliness and correctness of the transposition of EU directives into national legislation have provided rather inconclusive findings. They do not offer a clear-cut prediction concerning the transposition of the patients’ rights directive, which is one of the first...... that concerns the organisation and financing of national healthcare systems. This article applies the perspective of bounded rationality to explain (irregularities in) the timely and correct transposition of EU directives. The cognitive and organisational constraints long posited by the bounded rationality...
2013-03-26
...; Comment Request; Upward Bound and Upward Bound Math Science Annual Performance Report AGENCY: The Office... considered public records. Title of Collection: Upward Bound and Upward Bound Math Science Annual Performance...) and Upward Bound Math and Science (UBMS) Programs. The Department is requesting a new APR because of...
Spectrum of gluino bound states
International Nuclear Information System (INIS)
Chanowitz, M.; Sharpe, S.; California Univ., Berkeley
1983-01-01
Using the bag model to first order in αsub(s) we find that if light gluinos exist they will appear as constituents of electrically charged bound states which are stable against strong interaction decay. We review the present experimental constraints and conclude that light, long-lived charged hadrons containing gluinos might exist with lifetimes between 2x10 - 8 and 10 - 14 s. (orig.)
DEFF Research Database (Denmark)
Kjaer, L. K.; Cejvanovic, V.; Henriken, T.
2015-01-01
.9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...
International Nuclear Information System (INIS)
Denman, R.; Krzyzosiak, W.; Nurse, K.; Ofengand, J.
1987-01-01
The gene coding for E. coli 16S rRNA was placed in pUC19 under the control of the strong class III T7 promoter, phi 10, by ligation of the 1490 bp BclI/BstEII fragment of the rrnB operon with appropriate synthetic oligodeoxynucleotides. Such constructs allowed efficient in vitro synthesis of full-length transcripts (up to 900 mol RNA/mol template) free of modified bases. The synthetic RNA could be assembled into 30S subunits upon addition of E. coli 30S ribosomal proteins. The particles co-sedimented with authentic 30S particles and were electron microscopically indistinguishable from them. Upon addition of 50S subunits, codon-dependent P-site binding of tRNA and codon-dependent polypeptide synthesis were >80% of 30S reconstituted from natural 16S RNA and >50% of isolated 30S. UV-induced crosslinking of P-site bound AcVal-tRNA to residue C 1400 was preserved. Changing C 1400 to A had little effect on reconstitution, P-site binding, or polypeptide synthesis. However, the substitution of C 1499 by G markedly inhibited assembly. The effect on P-site binding and polypeptide synthesis is under study. These results show (1) none of the modified bases of 16S RNA are essential for protein synthesis, (2) substitution of A for C 1400 has little functional effect, and (3) position 1400 may be important for ribosome assembly
Cyclotron transitions of bound ions
Bezchastnov, Victor G.; Pavlov, George G.
2017-06-01
A charged particle in a magnetic field possesses discrete energy levels associated with particle rotation around the field lines. The radiative transitions between these levels are the well-known cyclotron transitions. We show that a bound complex of particles with a nonzero net charge displays analogous transitions between the states of confined motion of the entire complex in the field. The latter bound-ion cyclotron transitions are affected by a coupling between the collective and internal motions of the complex and, as a result, differ from the transitions of a "reference" bare ion with the same mass and charge. We analyze the cyclotron transitions for complex ions by including the coupling within a rigorous quantum approach. Particular attention is paid to comparison of the transition energies and oscillator strengths to those of the bare ion. Selection rules based on integrals of collective motion are derived for the bound-ion cyclotron transitions analytically, and the perturbation and coupled-channel approaches are developed to study the transitions quantitatively. Representative examples are considered and discussed for positive and negative atomic and cluster ions.
Exact quasinormal modes for a special class of black holes
International Nuclear Information System (INIS)
Oliva, Julio; Troncoso, Ricardo
2010-01-01
Analytic exact expressions for the quasinormal modes of scalar and electromagnetic perturbations around a special class of black holes are found in d≥3 dimensions. It is shown that the size of the black hole provides a lower bound for the angular momentum of the perturbation. Quasinormal modes appear when this bound is fulfilled; otherwise the excitations become purely damped.
Labeling schemes for bounded degree graphs
DEFF Research Database (Denmark)
Adjiashvili, David; Rotbart, Noy Galil
2014-01-01
We investigate adjacency labeling schemes for graphs of bounded degree Δ = O(1). In particular, we present an optimal (up to an additive constant) log n + O(1) adjacency labeling scheme for bounded degree trees. The latter scheme is derived from a labeling scheme for bounded degree outerplanar...... graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...
Characterizing the transcriptome upon depletion of RNA processing factors
DEFF Research Database (Denmark)
Herudek, Jan
, it is not clear how they target and discriminate their RNA substrates. Moreover, many novel RNA species are poorly characterized and their function is not understood. Over the last decade, protein function has been studied using RNA interference. However, this approach does not allow investigation of instant......The human genome is pervasively transcribed and produces an enormous amount of non-coding RNA (ncRNA). Compared to protein-coding transcripts, many classes of ncRNAs are very unstable and rapidly degraded by the RNA decay machinery. The RNA exosome complex is a main RNA ‘degrader’ in the human...... nucleus and is responsible for the proper processing and decay of a wide range of RNA molecules. Notably, the RNA exosome complex associates with a plethora of co-factors and activators that assist in the recognition of specific RNA substrates. Although many exosome partners have been characterized...
Voronoi Diagrams Without Bounding Boxes
Sang, E. T. K.
2015-10-01
We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010) and Nerbonne et al (2011).
Sensitivity analysis using probability bounding
International Nuclear Information System (INIS)
Ferson, Scott; Troy Tucker, W.
2006-01-01
Probability bounds analysis (PBA) provides analysts a convenient means to characterize the neighborhood of possible results that would be obtained from plausible alternative inputs in probabilistic calculations. We show the relationship between PBA and the methods of interval analysis and probabilistic uncertainty analysis from which it is jointly derived, and indicate how the method can be used to assess the quality of probabilistic models such as those developed in Monte Carlo simulations for risk analyses. We also illustrate how a sensitivity analysis can be conducted within a PBA by pinching inputs to precise distributions or real values
Bounded Densities and Their Derivatives
DEFF Research Database (Denmark)
Kozine, Igor; Krymsky, V.
2009-01-01
This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...... quantities of interest. To be able to utilise the evidence about the derivative it is suggested to adapt the ‘conventional’ problem statement to variational calculus and the way to do so is demonstrated. A number of examples are given throughout the paper....
Removal of bound metal fasteners
Kramer, R. F.
1981-04-01
This project explored the removal of bound metal fasteners through the use of ultrasonically assisted wrenches. Two wrenches were designed, fabricated and tested. Previous studies had indicated an increase in thread tension for a given torque application under the influence of ultrasonics. Based on this, the loosening of seized and corroded fasteners with the aid of ultrasonics was explored. Experimental data confirmed our prior analysis of the torque-tension relationship under the influence of ultrasonics; however, our progress did not satisfy the requirements necessary to loosen seized studs in a shipyard environment.
Space mappings with bounded distortion
Reshetnyak, Yu G
1989-01-01
This book is intended for researchers and students concerned with questions in analysis and function theory. The author provides an exposition of the main results obtained in recent years by Soviet and other mathematicians in the theory of mappings with bounded distortion, an active direction in contemporary mathematics. The mathematical tools presented can be applied to a broad spectrum of problems that go beyond the context of the main topic of investigation. For a number of questions in the theory of partial differential equations and the theory of functions with generalized derivatives, this is the first time they have appeared in an internationally distributed monograph.
Lin, Mingqun; Liu, Hongyan; Xiong, Qingming; Niu, Hua; Cheng, Zhihui; Yamamoto, Akitsugu; Rikihisa, Yasuko
2016-11-01
Ehrlichia chaffeensis is an obligatory intracellular bacterium that causes a potentially fatal emerging zoonosis, human monocytic ehrlichiosis. E. chaffeensis has a limited capacity for biosynthesis and metabolism and thus depends mostly on host-synthesized nutrients for growth. Although the host cell cytoplasm is rich with these nutrients, as E. chaffeensis is confined within the early endosome-like membrane-bound compartment, only host nutrients that enter the compartment can be used by this bacterium. How this occurs is unknown. We found that ehrlichial replication depended on autophagy induction involving class III phosphatidylinositol 3-kinase (PtdIns3K) activity, BECN1 (Beclin 1), and ATG5 (autophagy-related 5). Ehrlichia acquired host cell preincorporated amino acids in a class III PtdIns3K-dependent manner and ehrlichial growth was enhanced by treatment with rapamycin, an autophagy inducer. Moreover, ATG5 and RAB5A/B/C were routed to ehrlichial inclusions. RAB5A/B/C siRNA knockdown, or overexpression of a RAB5-specific GTPase-activating protein or dominant-negative RAB5A inhibited ehrlichial infection, indicating the critical role of GTP-bound RAB5 during infection. Both native and ectopically expressed ehrlichial type IV secretion effector protein, Etf-1, bound RAB5 and the autophagy-initiating class III PtdIns3K complex, PIK3C3/VPS34, and BECN1, and homed to ehrlichial inclusions. Ectopically expressed Etf-1 activated class III PtdIns3K as in E. chaffeensis infection and induced autophagosome formation, cleared an aggregation-prone mutant huntingtin protein in a class III PtdIns3K-dependent manner, and enhanced ehrlichial proliferation. These data support the notion that E. chaffeensis secretes Etf-1 to induce autophagy to repurpose the host cytoplasm and capture nutrients for its growth through RAB5 and class III PtdIns3K, while avoiding autolysosomal killing.
A new Class of Extremal Composites
DEFF Research Database (Denmark)
Sigmund, Ole
2000-01-01
microstructure belonging to the new class of composites has maximum bulk modulus and lower shear modulus than any previously known composite. Inspiration for the new composite class comes from a numerical topology design procedure which solves the inverse homogenization problem of distributing two isotropic......The paper presents a new class of two-phase isotropic composites with extremal bulk modulus. The new class consists of micro geometrics for which exact solutions can be proven and their bulk moduli are shown to coincide with the Hashin-Shtrikman bounds. The results hold for two and three dimensions...... and for both well- and non-well-ordered isotropic constituent phases. The new class of composites constitutes an alternative to the three previously known extremal composite classes: finite rank laminates, composite sphere assemblages and Vigdergauz microstructures. An isotropic honeycomb-like hexagonal...
Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins
Directory of Open Access Journals (Sweden)
Gayani N. P. Dedduwa-Mudalige
2015-09-01
Full Text Available Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.
NCI RNA Biology 2017 symposium recap | Center for Cancer Research
The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher Auditorium. Learn more...
NCI RNA Biology 2017 symposium recap | Center for Cancer Research
The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher
Determining Normal-Distribution Tolerance Bounds Graphically
Mezzacappa, M. A.
1983-01-01
Graphical method requires calculations and table lookup. Distribution established from only three points: mean upper and lower confidence bounds and lower confidence bound of standard deviation. Method requires only few calculations with simple equations. Graphical procedure establishes best-fit line for measured data and bounds for selected confidence level and any distribution percentile.
On semidefinite programming bounds for graph bandwidth
de Klerk, E.; Nagy, M.; Sotirov, R.
2013-01-01
In this paper, we propose two new lower bounds on graph bandwidth and cyclic bandwidth based on semidefinite programming (SDP) relaxations of the quadratic assignment problem. We compare the new bounds with two other SDP bounds reported in [A. Blum, G. Konjevod, R. Ravi, and S. Vempala,
The replisome uses mRNA as a primer after colliding with RNA polymerase.
Pomerantz, Richard T; O'Donnell, Mike
2008-12-11
Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.
Exploring RNA structure by integrative molecular modelling
DEFF Research Database (Denmark)
Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice
2010-01-01
RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...
Quantum bounds on Bell inequalities
Pál, Károly F.; Vértesi, Tamás
2009-02-01
We have determined the maximum quantum violation of 241 tight bipartite Bell inequalities with up to five two-outcome measurement settings per party by constructing the appropriate measurement operators in up to six-dimensional complex and eight-dimensional real-component Hilbert spaces using numerical optimization. Out of these inequalities 129 have been introduced here. In 43 cases higher-dimensional component spaces gave larger violation than qubits, and in three occasions the maximum was achieved with six-dimensional spaces. We have also calculated upper bounds on these Bell inequalities using a method proposed recently. For all but 20 inequalities the best solution found matched the upper bound. Surprisingly, the simplest inequality of the set examined, with only three measurement settings per party, was not among them, despite the high dimensionality of the Hilbert space considered. We also computed detection threshold efficiencies for the maximally entangled qubit pair. These could be lowered in several instances if degenerate measurements were also allowed.
Minimax bounds for active learning
Castro, R.M.; Nowak, R.; Bshouty, N.H.; Gentile, C.
2007-01-01
This paper aims to shed light on achievable limits in active learning. Using minimax analysis techniques, we study the achievable rates of classification error convergence for broad classes of distributions characterized by decision boundary regularity and noise conditions. The results clearly
Photochemistry of triarylmethane dyes bound to proteins
Indig, Guilherme L.
1996-04-01
Triarylmethanes represent a class of cationic dyes whose potential as photosensitizers for use in photodynamic therapy of neoplastic diseases has never been comprehensively evaluated. Here, the laser-induced photodecomposition of three triarylmethane dyes, crystal violet, ethyl violet, and malachite green, non-covalently bound to bovine serum albumin (a model biological target) was investigated. Upon laser excitation at 532 nm, the bleaching of the corresponding dye-protein molecular complexes follows spectroscopic patterns that suggest the formation of reduced forms of the dyes as major reaction photoproducts. That implies that an electron or hydrogen atom transfer from the protein to the dye's moiety within the guest-host complex is the first step of the photobleaching process. Since the availability of dissolved molecular oxygen was not identified as a limiting factor for the phototransformations to occur, these dyes can be seen as potential phototherapeutic agents for use in hypoxic areas of tumors. These triarylmethane dyes strongly absorb at relatively long wavelengths (absorption maximum around 600 nm; (epsilon) max approximately equals 105 M-1 cm-1), and only minor changes in their absorption characteristics are observed upon binding to the protein. However the binding event leads to a remarkable increase in their fluorescence quantum yield and photoreactivity.
Phosphatidic acid produced by phospholipase D promotes RNA replication of a plant RNA virus.
Directory of Open Access Journals (Sweden)
Kiwamu Hyodo
2015-05-01
Full Text Available Eukaryotic positive-strand RNA [(+RNA] viruses are intracellular obligate parasites replicate using the membrane-bound replicase complexes that contain multiple viral and host components. To replicate, (+RNA viruses exploit host resources and modify host metabolism and membrane organization. Phospholipase D (PLD is a phosphatidylcholine- and phosphatidylethanolamine-hydrolyzing enzyme that catalyzes the production of phosphatidic acid (PA, a lipid second messenger that modulates diverse intracellular signaling in various organisms. PA is normally present in small amounts (less than 1% of total phospholipids, but rapidly and transiently accumulates in lipid bilayers in response to different environmental cues such as biotic and abiotic stresses in plants. However, the precise functions of PLD and PA remain unknown. Here, we report the roles of PLD and PA in genomic RNA replication of a plant (+RNA virus, Red clover necrotic mosaic virus (RCNMV. We found that RCNMV RNA replication complexes formed in Nicotiana benthamiana contained PLDα and PLDβ. Gene-silencing and pharmacological inhibition approaches showed that PLDs and PLDs-derived PA are required for viral RNA replication. Consistent with this, exogenous application of PA enhanced viral RNA replication in plant cells and plant-derived cell-free extracts. We also found that a viral auxiliary replication protein bound to PA in vitro, and that the amount of PA increased in RCNMV-infected plant leaves. Together, our findings suggest that RCNMV hijacks host PA-producing enzymes to replicate.
Effect of Telecollaboration on Translation of Culture-Bound Texts
Directory of Open Access Journals (Sweden)
Vahid Rafieyan
2016-07-01
Full Text Available One of the most problematic perspectives of translation phenomenon is the cultural gap between the source language and the target language (Yang, 2010. This gap can be ideally filled through telecollaboration which provides internationally dispersed language learners in parallel language classes with cost-effective access to, and engagement with, peers who are expert speakers of the language under study (Belz, 2005. To investigate the effect of telecollaboration on the quality of translation of culture-bound texts, the current study was conducted on 64 Iranian undergraduate students of English translation at a university in Iran. Instruments used in the study consisted of three texts containing news excerpts from Voice of America (VOA. The study consisted of three phases: 1 assessing quality of translation of culture-bound texts, 2 random assignment of participants to two groups: one merely receiving cultural instruction while the other being linked to native English speakers through LinkedIn alongside receiving cultural instruction, and 3 assessing quality of translation of culture-bound texts immediately and two months following treatment. The results of mixed between-within subjects analysis of variance revealed the significant positive effect of telecollaboration on developing quality of translation of culture-bound texts and sustaining the attained knowledge. The pedagogical implications of the findings suggested incorporation of cultural components of source language society into translation courses and providing opportunities for translation students to be exposed to authentic and intensive source language culture through telecollaboration.
Maximum and minimum entropy states yielding local continuity bounds
Hanson, Eric P.; Datta, Nilanjana
2018-04-01
Given an arbitrary quantum state (σ), we obtain an explicit construction of a state ρɛ * ( σ ) [respectively, ρ * , ɛ ( σ ) ] which has the maximum (respectively, minimum) entropy among all states which lie in a specified neighborhood (ɛ-ball) of σ. Computing the entropy of these states leads to a local strengthening of the continuity bound of the von Neumann entropy, i.e., the Audenaert-Fannes inequality. Our bound is local in the sense that it depends on the spectrum of σ. The states ρɛ * ( σ ) and ρ * , ɛ (σ) depend only on the geometry of the ɛ-ball and are in fact optimizers for a larger class of entropies. These include the Rényi entropy and the minimum- and maximum-entropies, providing explicit formulas for certain smoothed quantities. This allows us to obtain local continuity bounds for these quantities as well. In obtaining this bound, we first derive a more general result which may be of independent interest, namely, a necessary and sufficient condition under which a state maximizes a concave and Gâteaux-differentiable function in an ɛ-ball around a given state σ. Examples of such a function include the von Neumann entropy and the conditional entropy of bipartite states. Our proofs employ tools from the theory of convex optimization under non-differentiable constraints, in particular Fermat's rule, and majorization theory.
Global stabilization of linear continuous time-varying systems with bounded controls
International Nuclear Information System (INIS)
Phat, V.N.
2004-08-01
This paper deals with the problem of global stabilization of a class of linear continuous time-varying systems with bounded controls. Based on the controllability of the nominal system, a sufficient condition for the global stabilizability is proposed without solving any Riccati differential equation. Moreover, we give sufficient conditions for the robust stabilizability of perturbation/uncertain linear time-varying systems with bounded controls. (author)
Small Molecule Modifiers of the microRNA and RNA Interference Pathway
Deiters, Alexander
2009-01-01
Recently, the RNA interference (RNAi) pathway has become the target of small molecule inhibitors and activators. RNAi has been well established as a research tool in the sequence-specific silencing of genes in eukaryotic cells and organisms by using exogenous, small, double-stranded RNA molecules of approximately 20 nucleotides. Moreover, a recently discovered post-transcriptional gene regulatory mechanism employs microRNAs (miRNAs), a class of endogenously expressed small RNA molecules, whic...
Evidence for a bound on the lifetime of de Sitter space
International Nuclear Information System (INIS)
Freivogel, Ben; Lippert, Matthew
2008-01-01
Recent work has suggested a surprising new upper bound on the lifetime of de Sitter vacua in string theory. The bound is parametrically longer than the Hubble time but parametrically shorter than the recurrence time. We investigate whether the bound is satisfied in a particular class of de Sitter solutions, the KKLT vacua. Despite the freedom to make the supersymmetry breaking scale exponentially small, which naively would lead to extremely stable vacua, we find that the lifetime is always less than about exp(10 22 ) Hubble times, in agreement with the proposed bound. This result, however, is contingent on several estimates and assumptions; in particular, we rely on a conjectural upper bound on the Euler number of the Calabi-Yau fourfolds used in KKLT compactifications.
Capacity Bounds for Parallel Optical Wireless Channels
Chaaban, Anas; Rezki, Zouheir; Alouini, Mohamed-Slim
2016-01-01
A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.
Chen, Tao; Cui, Peng; Xiong, Liming
2015-01-01
MicroRNAs are a class of small regulatory RNAs that are generated from primary miRNA (pri-miRNA) transcripts with a stem-loop structure. Accuracy of the processing of pri-miRNA into mature miRNA in plants can be enhanced by SERRATE (SE
DEFF Research Database (Denmark)
Ernst, Erik
Typically, objects are monolithic entities with a fixed interface. To increase the flexibility in this area, this paper presents first-class object sets as a language construct. An object set offers an interface which is a disjoint union of the interfaces of its member objects. It may also be used...... for a special kind of method invocation involving multiple objects in a dynamic lookup process. With support for feature access and late-bound method calls object sets are similar to ordinary objects, only more flexible. The approach is made precise by means of a small calculus, and the soundness of its type...
Spinless Salpeter equation: Laguerre bounds on energy levels
International Nuclear Information System (INIS)
Lucha, W.; Schoeberl, F.F.
1996-08-01
The spinless Salpeter equation may be considered either as a standard approximation to the Bethe-Salpeter formalism, designed for the description of bound states within a relativistic quantum field theory, or as the most simple, to a certain extent relativistic generalization of the customary non relativistic Schroedinger formalism. Because of the presence of the rather difficult-to-handle square-root operator of the relativistic kinetic energy in the corresponding Hamiltonian, very frequently the corresponding (discrete) spectrum of energy eigenvalues cannot be determined analytically. Therefore, we show how to calculate, by some clever choice of basis vectors in the Hilbert space of solutions, for the rather large class of power-law potentials, at least (sometimes excellent) upper bounds on these energy eigenvalues, for the lowest-lying levels this even analytically. (author)
The bounds of feasible space on constrained nonconvex quadratic programming
Zhu, Jinghao
2008-03-01
This paper presents a method to estimate the bounds of the radius of the feasible space for a class of constrained nonconvex quadratic programmingsE Results show that one may compute a bound of the radius of the feasible space by a linear programming which is known to be a P-problem [N. Karmarkar, A new polynomial-time algorithm for linear programming, Combinatorica 4 (1984) 373-395]. It is proposed that one applies this method for using the canonical dual transformation [D.Y. Gao, Canonical duality theory and solutions to constrained nonconvex quadratic programming, J. Global Optimization 29 (2004) 377-399] for solving a standard quadratic programming problem.
Pricing summer day options by good-deal bounds
International Nuclear Information System (INIS)
Kanamura, Takashi; Ohashi, Kazuhiko
2009-01-01
Despite the worldwide popularity of CDD- and HDD-type weather derivatives based on temperature, a different class of weather derivatives, so-called summer day options, is more popular in Japan; the payoffs are determined by the number of summer days (i.e., the days whose average temperature is above 25 C) during the contract period. In this paper, we price such summer day options by the good-deal bounds of Cochrane and Saa-Requejo [Cochrane, J.H., and J. Saa-Requejo, 2000, Beyond Arbitrage: Good-Deal Asset Price Bounds in Incomplete Markets, Journal of Political Economy 108, 79-119.], using temperature data for Tokyo. (author)
VORONOI DIAGRAMS WITHOUT BOUNDING BOXES
Directory of Open Access Journals (Sweden)
E. T. K. Sang
2015-10-01
Full Text Available We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010 and Nerbonne et al (2011.
Spectral computations for bounded operators
Ahues, Mario; Limaye, Balmohan
2001-01-01
Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...
Accidental bound states in the continuum in an open Sinai billiard
Energy Technology Data Exchange (ETDEWEB)
Pilipchuk, A.S. [Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk (Russian Federation); Siberian Federal University, 660080 Krasnoyarsk (Russian Federation); Sadreev, A.F., E-mail: almas@tnp.krasn.ru [Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk (Russian Federation)
2017-02-19
The fundamental mechanism of the bound states in the continuum is the full destructive interference of two resonances when two eigenlevels of the closed system are crossing. There is, however, a wide class of quantum chaotic systems which display only avoided crossings of eigenlevels. As an example of such a system we consider the Sinai billiard coupled with two semi-infinite waveguides. We show that notwithstanding the absence of degeneracy bound states in the continuum occur due to accidental decoupling of the eigenstates of the billiard from the waveguides. - Highlights: • Bound states in the continuum in open chaotic billiards occur to accidental vanishing of coupling of eigenstate of billiard with waveguides.
Parallel Branch-and-Bound Methods for the Job Shop Scheduling
DEFF Research Database (Denmark)
Clausen, Jens; Perregaard, Michael
1998-01-01
Job-shop scheduling (JSS) problems are among the more difficult to solve in the class of NP-complete problems. The only successful approach has been branch-and-bound based algorithms, but such algorithms depend heavily on good bound functions. Much work has been done to identify such functions...... for the JSS problem, but with limited success. Even with recent methods, it is still not possible to solve problems substantially larger than 10 machines and 10 jobs. In the current study, we focus on parallel methods for solving JSS problems. We implement two different parallel branch-and-bound algorithms...
Coexistence of a bound state and scattering at the same energy value: a quantum paradox
International Nuclear Information System (INIS)
Chabanov, V.M.; Zakhar'ev, B.N.
1998-01-01
The example of a multi-channel system which possesses both bound (not quasi-bound !) and scattering states at the same energy value E is demonstrated. A special interaction has ability to confine waves near the origin and simultaneously admit scattering (even with transparency) at the fixed spectral point. These interaction matrices and wave functions can be continued to the whole axis. As another multi-channel peculiarity having no one-channel analogues was found a class of absolutely transparent interaction matrices without bound states
Operationalizing Max Weber's probability concept of class situation: the concept of social class.
Smith, Ken
2007-03-01
In this essay I take seriously Max Weber's astonishingly neglected claim that class situation may be defined, not in categorial terms, but probabilistically. I then apply this idea to another equally neglected claim made by Weber that the boundaries of social classes may be determined by the degree of social mobility within such classes. Taking these two ideas together I develop the idea of a non-categorial boundary 'surface' between classes and of a social class 'corridor' made up of all those people who are still to be found within the boundaries of the social class into which they were born. I call social mobility within a social class 'intra-class social mobility' and social mobility between classes 'inter-class social mobility'. I also claim that this distinction resolves the dispute between those sociologists who claim that late industrial societies are still highly class bound and those who think that this is no longer the case. Both schools are right I think, but one is referring to a high degree of intra-class social mobility and the other to an equally high degree of inter-class mobility. Finally I claim that this essay provides sociology with only one example among many other possible applications of how probability theory might usefully be used to overcome boundary problems generally in sociology.
Analysis of RNA binding by the dengue virus NS5 RNA capping enzyme.
Directory of Open Access Journals (Sweden)
Brittney R Henderson
Full Text Available Flaviviruses are small, capped positive sense RNA viruses that replicate in the cytoplasm of infected cells. Dengue virus and other related flaviviruses have evolved RNA capping enzymes to form the viral RNA cap structure that protects the viral genome and directs efficient viral polyprotein translation. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. The mechanism for flavivirus guanylyltransferase activity is currently unknown, and how the capping enzyme binds its diphosphorylated RNA substrate is important for deciphering how the flavivirus guanylyltransferase functions. In this report we examine how flavivirus NS5 N-terminal capping enzymes bind to the 5' end of the viral RNA using a fluorescence polarization-based RNA binding assay. We observed that the K(D for RNA binding is approximately 200 nM Dengue, Yellow Fever, and West Nile virus capping enzymes. Removal of one or both of the 5' phosphates reduces binding affinity, indicating that the terminal phosphates contribute significantly to binding. RNA binding affinity is negatively affected by the presence of GTP or ATP and positively affected by S-adensyl methoninine (SAM. Structural superpositioning of the dengue virus capping enzyme with the Vaccinia virus VP39 protein bound to RNA suggests how the flavivirus capping enzyme may bind RNA, and mutagenesis analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. Several mutants show differential binding to 5' di-, mono-, and un-phosphorylated RNAs. The mode of RNA binding appears similar to that found with other methyltransferase enzymes, and a discussion of diphosphorylated RNA binding is presented.
Factors influencing gene silencing of granule-bound starch synthase in potato
Heilersig, H.J.B.
2005-01-01
In the past, antisense RNA technology was used to modify the composition of potato tuber starch. Potato starch comprises amylose and amylopectin, polymers of glucose. Amylose production in potato is completely dependent on the presence of granule-bound starch synthase I (GBSSI). Inhibition of GBSSI
Species-independent MicroRNA Gene Discovery
Kamanu, Timothy K.
2012-12-01
MicroRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other incurable diseases such as autism and Alzheimer’s. Functional miRNAs are excised from hairpin-like sequences that are known as miRNA genes. There are about 21,000 known miRNA genes, most of which have been determined using experimental methods. miRNA genes are classified into different groups (miRNA families). This study reports about 19,000 unknown miRNA genes in nine species whereby approximately 15,300 predictions were computationally validated to contain at least one experimentally verified functional miRNA product. The predictions are based on a novel computational strategy which relies on miRNA family groupings and exploits the physics and geometry of miRNA genes to unveil the hidden palindromic signals and symmetries in miRNA gene sequences. Unlike conventional computational miRNA gene discovery methods, the algorithm developed here is species-independent: it allows prediction at higher accuracy and resolution from arbitrary RNA/DNA sequences in any species and thus enables examination of repeat-prone genomic regions which are thought to be non-informative or ’junk’ sequences. The information non-redundancy of uni-directional RNA sequences compared to information redundancy of bi-directional DNA is demonstrated, a fact that is overlooked by most pattern discovery algorithms. A novel method for computing upstream and downstream miRNA gene boundaries based on mathematical/statistical functions is suggested, as well as cutoffs for annotation of miRNA genes in different miRNA families. Another tool is proposed to allow hypotheses generation and visualization of data matrices, intra- and inter-species chromosomal distribution of miRNA genes or miRNA families. Our results indicate that: miRNA and miRNA
New class of uncertainty relations for partially coherent light
Bastiaans, M.J.
1984-01-01
A class of uncertainty relations for partially coherent light is derived; the uncertainty relations in this class express the fact that the product of the effective widths of the space-domain intensity and the spatial-frequency-domain intensity of the light has a lower bound and that this lower
Near Optimal Decentralized H-infinity Control: Bounded vs. Unbounded Controller Order
DEFF Research Database (Denmark)
Stoustrup, Jakob; Niemann, H.H.
1997-01-01
It is shown that for a class of decentralized control problems there does not exist a sequence of controllers of bounded order which obtains near optimal control. Neither does there exist an infinite dimensional optimal controller. Using the insight of the line of proof of these results, a heuris......It is shown that for a class of decentralized control problems there does not exist a sequence of controllers of bounded order which obtains near optimal control. Neither does there exist an infinite dimensional optimal controller. Using the insight of the line of proof of these results...
Instanton bound states in ABJM theory
Energy Technology Data Exchange (ETDEWEB)
Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics
2013-06-15
The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.
Bounded elements in Locally C*-algebras
International Nuclear Information System (INIS)
El Harti, Rachid
2001-09-01
In order to get more useful information about Locally C*-algebras, we introduce in this paper the notion of bounded elements. First, we study the connection between bounded elements and spectrally bounded elements. Some structural results of Locally C*-algebras are established in Theorems 1 , 2 and 3. As an immediate consequence of Theorem 3, we give a characterization of the connected component of the identity in the group of unitary elements for a Locally C*-algebra. (author)
Fuzzy upper bounds and their applications
Energy Technology Data Exchange (ETDEWEB)
Soleimani-damaneh, M. [Department of Mathematics, Faculty of Mathematical Science and Computer Engineering, Teacher Training University, 599 Taleghani Avenue, Tehran 15618 (Iran, Islamic Republic of)], E-mail: soleimani_d@yahoo.com
2008-04-15
This paper considers the concept of fuzzy upper bounds and provides some relevant applications. Considering a fuzzy DEA model, the existence of a fuzzy upper bound for the objective function of the model is shown and an effective approach to solve that model is introduced. Some dual interpretations are provided, which are useful for practical purposes. Applications of the concept of fuzzy upper bounds in two physical problems are pointed out.
Shielding the messenger (RNA): microRNA-based anticancer therapies
Sotillo, Elena; Thomas-Tikhonenko, Andrei
2011-01-01
It has been a decade since scientists realized that microRNAs (miRNAs) are not an oddity invented by worms to regulate gene expression at post-transcriptional levels. Rather, many of these 21–22-nucleotide-short RNAs exist in invertebrates and vertebrates alike and some of them are in fact highly conserved. miRNAs are now recognized as an important class of non-coding small RNAs that inhibit gene expression by targeting mRNA stability and translation. In the last ten years, our knowledge of the miRNAs world was expanding at vertiginous speed, propelled by the development of computational engines for miRNA identification and target prediction, biochemical tools and techniques to modulate miRNA activity, and last but not least, the emergence of miRNA-centric animal models. One important conclusion that has emerged from this effort is that many microRNAs and their cognate targets are strongly implicated in cancer, either as oncogenes or tumor and metastasis suppressors. In this review we will discuss the diverse role that miRNAs play in cancer initiation and progression and also the tools with which miRNA expression could be corrected in vivo. While the idea of targeting microRNAs towards therapeutic ends is getting considerable traction, basic, translational, and clinical research done in the next few years will tell whether this promise is well-founded. PMID:21514318
Bounded cohomology of discrete groups
Frigerio, Roberto
2017-01-01
The author manages a near perfect equilibrium between necessary technicalities (always well motivated) and geometric intuition, leading the readers from the first simple definition to the most striking applications of the theory in 13 very pleasant chapters. This book can serve as an ideal textbook for a graduate topics course on the subject and become the much-needed standard reference on Gromov's beautiful theory. -Michelle Bucher The theory of bounded cohomology, introduced by Gromov in the late 1980s, has had powerful applications in geometric group theory and the geometry and topology of manifolds, and has been the topic of active research continuing to this day. This monograph provides a unified, self-contained introduction to the theory and its applications, making it accessible to a student who has completed a first course in algebraic topology and manifold theory. The book can be used as a source for research projects for master's students, as a thorough introduction to the field for graduate student...
Some Improved Nonperturbative Bounds for Fermionic Expansions
Energy Technology Data Exchange (ETDEWEB)
Lohmann, Martin, E-mail: marlohmann@gmail.com [Universita di Roma Tre, Dipartimento di Matematica (Italy)
2016-06-15
We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.
DEFF Research Database (Denmark)
Ernst, Erik; Ostermann, Klaus; Cook, William Randall
2006-01-01
Virtual classes are class-valued attributes of objects. Like virtual methods, virtual classes are defined in an object's class and may be redefined within subclasses. They resemble inner classes, which are also defined within a class, but virtual classes are accessed through object instances...... model for virtual classes has been a long-standing open question. This paper presents a virtual class calculus, vc, that captures the essence of virtual classes in these full-fledged programming languages. The key contributions of the paper are a formalization of the dynamic and static semantics of vc...
Kumaraswamy autoregressive moving average models for double bounded environmental data
Bayer, Fábio Mariano; Bayer, Débora Missio; Pumi, Guilherme
2017-12-01
In this paper we introduce the Kumaraswamy autoregressive moving average models (KARMA), which is a dynamic class of models for time series taking values in the double bounded interval (a,b) following the Kumaraswamy distribution. The Kumaraswamy family of distribution is widely applied in many areas, especially hydrology and related fields. Classical examples are time series representing rates and proportions observed over time. In the proposed KARMA model, the median is modeled by a dynamic structure containing autoregressive and moving average terms, time-varying regressors, unknown parameters and a link function. We introduce the new class of models and discuss conditional maximum likelihood estimation, hypothesis testing inference, diagnostic analysis and forecasting. In particular, we provide closed-form expressions for the conditional score vector and conditional Fisher information matrix. An application to environmental real data is presented and discussed.
Bound states for non-symmetric evolution Schroedinger potentials
Energy Technology Data Exchange (ETDEWEB)
Corona, Gulmaro Corona [Area de Analisis Matematico y sus Aplicaciones, Universidad Autonoma Metropolitana-Azcapotalco, Atzcapotzalco, DF (Mexico)). E-mail: ccg@correo.azc.uam.mx
2001-09-14
We consider the spectral problem associated with the evolution Schroedinger equation, (D{sup 2}+ k{sup 2}){phi}=u{phi}, where u is a matrix-square-valued function, with entries in the Schwartz class defined on the real line. The solution {phi}, called the wavefunction, consists of a function of one real variable, matrix-square-valued with entries in the Schwartz class. This problem has been dealt for symmetric potentials u. We found for the present case that the bound states are localized similarly to the scalar and symmetric cases, but by the zeroes of an analytic matrix-valued function. If we add an extra condition to the potential u, we can determine these states by an analytic scalar function. We do this by generalizing the scalar and symmetric cases but without using the fact that the Wronskian of a pair of wavefunction is constant. (author)
Centrosymmetric Graphs And A Lower Bound For Graph Energy Of Fullerenes
Directory of Open Access Journals (Sweden)
Katona Gyula Y.
2014-11-01
Full Text Available The energy of a molecular graph G is defined as the summation of the absolute values of the eigenvalues of adjacency matrix of a graph G. In this paper, an infinite class of fullerene graphs with 10n vertices, n ≥ 2, is considered. By proving centrosymmetricity of the adjacency matrix of these fullerene graphs, a lower bound for its energy is given. Our method is general and can be extended to other class of fullerene graphs.
Energy Technology Data Exchange (ETDEWEB)
Teplova, Marianna; Farazi, Thalia A.; Tuschl, Thomas; Patel, Dinshaw J.
2015-09-08
RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations
Variational lower bound on the scattering length
International Nuclear Information System (INIS)
Rosenberg, L.; Spruch, L.
1975-01-01
The scattering length A characterizes the zero-energy scattering of one system by another. It was shown some time ago that a variational upper bound on A could be obtained using methods, of the Rayleigh-Ritz type, which are commonly employed to obtain upper bounds on energy eigenvalues. Here we formulate a method for obtaining a variational lower bound on A. Once again the essential idea is to express the scattering length as a variational estimate plus an error term and then to reduce the problem of bounding the error term to one involving bounds on energy eigenvalues. In particular, the variational lower bound on A is rigorously established provided a certin modified Hamiltonian can be shown to have no discrete states lying below the level of the continuum threshold. It is unfortunately true that necessary conditions for the existence of bound states are not available for multiparticle systems in general. However, in the case of positron-atom scattering the adiabatic approximation can be introduced as an (essentially) solvable comparison problem to rigorously establish the nonexistence of bound states of the modified Hamiltonian. It has recently been shown how the validity of the variational upper bound on A can be maintained when the target ground-state wave function is imprecisely known. Similar methods can be used to maintain the variational lower bound on A. Since the bound is variational, the error in the calculated scattering length will be of second order in the error in the wave function. The use of the adiabatic approximation in the present context places no limitation in principle on the accuracy achievable
Bounded-oscillation Pushdown Automata
Directory of Open Access Journals (Sweden)
Pierre Ganty
2016-09-01
Full Text Available We present an underapproximation for context-free languages by filtering out runs of the underlying pushdown automaton depending on how the stack height evolves over time. In particular, we assign to each run a number quantifying the oscillating behavior of the stack along the run. We study languages accepted by pushdown automata restricted to k-oscillating runs. We relate oscillation on pushdown automata with a counterpart restriction on context-free grammars. We also provide a way to filter all but the k-oscillating runs from a given PDA by annotating stack symbols with information about the oscillation. Finally, we study closure properties of the defined class of languages and the complexity of the k-emptiness problem asking, given a pushdown automaton P and k >= 0, whether P has a k-oscillating run. We show that, when k is not part of the input, the k-emptiness problem is NLOGSPACE-complete.
Extracellular RNA Communication (ExRNA)
Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...
International Nuclear Information System (INIS)
Stevens, A.
1982-01-01
Investigations in this laboratory center on basic enzymatic reactions of RNA. Still undefined are reactions involved in the conversion of precursors of mRA (pre-mRNA) to mRNA in eukaryotes. The pre-mRNA is called heterogeneous nuclear RNA and is 2 to 6 times larger than mRNA. The conversion, called splicing, involves a removal of internal sequences called introns by endoribonuclease action followed by a rejoining of the 3'- and 5'-end fragments, called exons, by ligating activity. It has not been possible yet to study the enzymes involved in vitro. Also undefined are reactions involved in the turnover or discarding of certain of the pre-mRNA molecules. Yeast is a simple eukaryote and may be expected to have the same, but perhaps simpler, processing reactions as the higher eukaryotes. Two enzymes involved in the processing of pre-mRNA and mRNA in yeast are under investigation. Both enzymes have been partially purified from ribonucleoprotein particles of yeast. The first is a unique decapping enzyme which cleaves [ 3 H]m 7 Gppp [ 14 C]RNA-poly (A) of yeast, yielding [ 3 H]m 7 GDP and is suggested by the finding that the diphosphate product, m 7 GpppA(G), and UDP-glucose are not hydrolyzed. The second enzyme is an endoribonuclease which converts both the [ 3 H] and [ 14 C] labels of [ 3 H]m 7 Gppp[ 14 C]RNA-poly(A) from an oligo(dT)-cellulose bound form to an unbound, acid-insoluble form. Results show that the stimulation involves an interaction of the labeled RNA with the small nuclear RNA. The inhibition of the enzyme by ethidium bromide and its stimulation by small nuclear RNA suggest that it may be a processing ribonuclease, requiring specific double-stranded features in its substrate. The characterization of the unique decapping enzyme and endoribonuclease may help to understand reactions involved in the processing of pre-mRNA and mRNA in eukaryotes
Stacked spheres and lower bound theorem
Indian Academy of Sciences (India)
BASUDEB DATTA
2011-11-20
Nov 20, 2011 ... Preliminaries. Lower bound theorem. On going work. Definitions. An n-simplex is a convex hull of n + 1 affinely independent points. (called vertices) in some Euclidean space R. N . Stacked spheres and lower bound theorem. Basudeb Datta. Indian Institute of Science. 2 / 27 ...
A strongly quasiconvex PAC-Bayesian bound
DEFF Research Database (Denmark)
Thiemann, Niklas; Igel, Christian; Wintenberger, Olivier
2017-01-01
We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured by the Ku...
On the range of completely bounded maps
Directory of Open Access Journals (Sweden)
Richard I. Loebl
1978-01-01
Full Text Available It is shown that if every bounded linear map from a C*-algebra α to a von Neumann algebra β is completely bounded, then either α is finite-dimensional or β⫅⊗Mn, where is a commutative von Neumann algebra and Mn is the algebra of n×n complex matrices.
Bounds in the location-allocation problem
DEFF Research Database (Denmark)
Juel, Henrik
1981-01-01
Develops a family of stronger lower bounds on the objective function value of the location-allocation problem. Solution methods proposed to solve problems in location-allocation; Efforts to develop a more efficient bound solution procedure; Determination of the locations of the sources....
Experimental evidence for bounds on quantum correlations.
Bovino, F A; Castagnoli, G; Degiovanni, I P; Castelletto, S
2004-02-13
We implemented the experiment proposed by Cabello in the preceding Letter to test the bounds of quantum correlation. As expected from the theory we found that, for certain choices of local observables, Tsirelson's bound of the Clauser-Horne-Shimony-Holt inequality (2 x square root of 2) is not reached by any quantum states.
Exponential Lower Bounds For Policy Iteration
Fearnley, John
2010-01-01
We study policy iteration for infinite-horizon Markov decision processes. It has recently been shown policy iteration style algorithms have exponential lower bounds in a two player game setting. We extend these lower bounds to Markov decision processes with the total reward and average-reward optimality criteria.
Conductivity bound from dirty black holes
Energy Technology Data Exchange (ETDEWEB)
Bitaghsir Fadafan, Kazem, E-mail: bitaghsir@shahroodut.ac.ir
2016-11-10
We propose a lower bound of the dc electrical conductivity in strongly disordered, strongly interacting quantum field theories using holography. We study linear response of black holes with broken translational symmetry in Einstein–Maxwell-dilaton theories of gravity. Using the generalized Stokes equations at the horizon, we derive the lower bound of the electrical conductivity for the dual two dimensional disordered field theory.
No-arbitrage bounds for financial scenarios
DEFF Research Database (Denmark)
Geyer, Alois; Hanke, Michael; Weissensteiner, Alex
2014-01-01
We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...
SHARP ENTRYWISE PERTURBATION BOUNDS FOR MARKOV CHAINS.
Thiede, Erik; VAN Koten, Brian; Weare, Jonathan
For many Markov chains of practical interest, the invariant distribution is extremely sensitive to perturbations of some entries of the transition matrix, but insensitive to others; we give an example of such a chain, motivated by a problem in computational statistical physics. We have derived perturbation bounds on the relative error of the invariant distribution that reveal these variations in sensitivity. Our bounds are sharp, we do not impose any structural assumptions on the transition matrix or on the perturbation, and computing the bounds has the same complexity as computing the invariant distribution or computing other bounds in the literature. Moreover, our bounds have a simple interpretation in terms of hitting times, which can be used to draw intuitive but rigorous conclusions about the sensitivity of a chain to various types of perturbations.
New bounds on isotropic Lorentz violation
International Nuclear Information System (INIS)
Carone, Christopher D.; Sher, Marc; Vanderhaeghen, Marc
2006-01-01
Violations of Lorentz invariance that appear via operators of dimension four or less are completely parametrized in the Standard Model Extension (SME). In the pure photonic sector of the SME, there are 19 dimensionless, Lorentz-violating parameters. Eighteen of these have experimental upper bounds ranging between 10 -11 and 10 -32 ; the remaining parameter, k-tilde tr , is isotropic and has a much weaker bound of order 10 -4 . In this Brief Report, we point out that k-tilde tr gives a significant contribution to the anomalous magnetic moment of the electron and find a new upper bound of order 10 -8 . With reasonable assumptions, we further show that this bound may be improved to 10 -14 by considering the renormalization of other Lorentz-violating parameters that are more tightly constrained. Using similar renormalization arguments, we also estimate bounds on Lorentz-violating parameters in the pure gluonic sector of QCD
Covariant entropy bound and loop quantum cosmology
International Nuclear Information System (INIS)
Ashtekar, Abhay; Wilson-Ewing, Edward
2008-01-01
We examine Bousso's covariant entropy bound conjecture in the context of radiation filled, spatially flat, Friedmann-Robertson-Walker models. The bound is violated near the big bang. However, the hope has been that quantum gravity effects would intervene and protect it. Loop quantum cosmology provides a near ideal setting for investigating this issue. For, on the one hand, quantum geometry effects resolve the singularity and, on the other hand, the wave function is sharply peaked at a quantum corrected but smooth geometry, which can supply the structure needed to test the bound. We find that the bound is respected. We suggest that the bound need not be an essential ingredient for a quantum gravity theory but may emerge from it under suitable circumstances.
Resource-constrained project scheduling: computing lower bounds by solving minimum cut problems
Möhring, R.H.; Nesetril, J.; Schulz, A.S.; Stork, F.; Uetz, Marc Jochen
1999-01-01
We present a novel approach to compute Lagrangian lower bounds on the objective function value of a wide class of resource-constrained project scheduling problems. The basis is a polynomial-time algorithm to solve the following scheduling problem: Given a set of activities with start-time dependent
RNA as a small molecule druggable target.
Rizvi, Noreen F; Smith, Graham F
2017-12-01
Small molecule drugs have readily been developed against many proteins in the human proteome, but RNA has remained an elusive target for drug discovery. Increasingly, we see that RNA, and to a lesser extent DNA elements, show a persistent tertiary structure responsible for many diverse and complex cellular functions. In this digest, we have summarized recent advances in screening approaches for RNA targets and outlined the discovery of novel, drug-like small molecules against RNA targets from various classes and therapeutic areas. The link of structure, function, and small-molecule Druggability validates now for the first time that RNA can be the targets of therapeutic agents. Copyright © 2017 Elsevier Ltd. All rights reserved.
MicroRNA Implication in Cancer
Directory of Open Access Journals (Sweden)
Iker BADIOLA
2010-03-01
Full Text Available MicroRNAs (miRNA are a new class of posttranscriptional regulators. These small non-coding RNAs regulate the expression of target mRNA transcripts and are linked to several human disease such as Alzheimer, cancer or heart disease. But it has been the cancer disease which has experimented the major number of studies of miRNA linked to the disease progression. In the last years it has been reported the deregulation pattern of the miRNAs in malignant cells which have disrupted the control of the proliferation, differentiation or apoptosis. The evidence of the presence of specific miRNA deregulated in concrete cancer types has become the miRNAs like possible biomarkers and therapeutic targets. The specific miRNA patterns deregulated in concrete cancer cell types open new opportunities to the diagnosis and therapy.
Identifying and characterizing Hfq-RNA interactions.
Faner, M A; Feig, A L
2013-09-15
To regulate stress responses and virulence, bacteria use small regulatory RNAs (sRNAs). These RNAs can up or down regulate target mRNAs through base pairing by influencing ribosomal access and RNA decay. A large class of these sRNAs, called trans-encoded sRNAs, requires the RNA binding protein Hfq to facilitate base pairing between the regulatory RNA and its target mRNA. The resulting network of regulation is best characterized in Escherichia coli and Salmonella typhimurium, but the importance of Hfq dependent sRNA regulation is recognized in a diverse population of bacteria. In this review we present the approaches and methods used to discover Hfq binding RNAs, characterize their interactions and elucidate their functions. Copyright © 2013 Elsevier Inc. All rights reserved.
Xia, Hongjie; Wang, Peipei; Wang, Guang-Chuan; Yang, Jie; Sun, Xianlin; Wu, Wenzhe; Qiu, Yang; Shu, Ting; Zhao, Xiaolu; Yin, Lei; Qin, Cheng-Feng; Hu, Yuanyang; Zhou, Xi
2015-01-01
RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our
Optimality Bounds for a Variational Relaxation of the Image Partitioning Problem
Lellmann, Jan
2012-11-09
We consider a variational convex relaxation of a class of optimal partitioning and multiclass labeling problems, which has recently proven quite successful and can be seen as a continuous analogue of Linear Programming (LP) relaxation methods for finite-dimensional problems. While for the latter several optimality bounds are known, to our knowledge no such bounds exist in the infinite-dimensional setting. We provide such a bound by analyzing a probabilistic rounding method, showing that it is possible to obtain an integral solution of the original partitioning problem from a solution of the relaxed problem with an a priori upper bound on the objective. The approach has a natural interpretation as an approximate, multiclass variant of the celebrated coarea formula. © 2012 Springer Science+Business Media New York.
Lower Bounds for Sorted Geometric Queries in the I/O Model
DEFF Research Database (Denmark)
Afshani, Peyman; Zeh, Norbert
2012-01-01
. This is highly relevant in an I/O context because storing a massive data set in a superlinear-space data structure is often infeasible. We also prove that answering queries using I/Os requires space, where N is the input size, B is the block size, and M is the size of the main memory. This bound is unlikely...... to be optimal and in fact we can show that, for a particular class of “persistence-based” data structures, the space lower bound can be improved to Ω(N2 / MO(1)). Both these lower bounds are a first step towards understanding the complexity of sorted geometric query problems. All our lower bounds assume...
International Nuclear Information System (INIS)
Amin, Anthony; Zaccardi, Joe; Mullen, Stanley; Olland, Stephane; Orlowski, Mark; Feld, Boris; Labonte, Patrick; Mak, Paul
2003-01-01
A class of disulfide constrained peptides containing a core motif FPWG was identified from a screen of phage displayed library using the HCV RNA-dependent RNA polymerase (NS5B) as a bait. Surface plasmon resonance studies showed that three highly purified synthetic constrained peptides bound to immobilized NS5B with estimated K d values ranging from 30 to 60 μM. In addition, these peptides inhibited the NS5B activity in vitro with IC 50 ranging from 6 to 48 μM, whereas in contrast they had no inhibitory effect on the enzymatic activities of calf thymus polymerase α, human polymerase β, RSV polymerase, and HIV reverse transcriptase in vitro. Two peptides demonstrated conformation-dependent inhibition since their synthetic linear versions were not inhibitory in the NS5B assay. A constrained peptide with the minimum core motif FPWG retained selective inhibition of NS5B activity with an IC 50 of 50 μM. Alanine scan analyses of a representative constrained peptide, FPWGNTW, indicated that residues F1 and W7 were critical for the inhibitory effect of this peptide, although residues P2 and N5 had some measurable inhibitory effect as well. Further analyses of the mechanism of inhibition indicated that these peptides inhibited the formation of preelongation complexes required for the elongation reaction. However, once the preelongation complex was formed, its activity was refractory to peptide inhibition. Furthermore, the constrained peptide FPWGNTW inhibited de novo initiated RNA synthesis by NS5B from a poly(rC) template. These data indicate that the peptides confer selective inhibition of NS5B activity by binding to the enzyme and perturbing an early step preceding the processive elongation step of RNA synthesis
U.S. Department of Health & Human Services — The RxClass Browser is a web application for exploring and navigating through the class hierarchies to find the RxNorm drug members associated with each class....
Micro RNA in Exosomes from HIV-Infected Macrophages
Directory of Open Access Journals (Sweden)
William W. Roth
2015-12-01
Full Text Available Exosomes are small membrane-bound vesicles secreted by cells that function to shuttle RNA and proteins between cells. To examine the role of exosomal micro RNA (miRNA during the early stage of HIV-1 infection we characterized miRNA in exosomes from HIV-infected macrophages, compared with exosomes from non-infected macrophages. Primary human monocytes from uninfected donors were differentiated to macrophages (MDM which were either mock-infected or infected with the macrophage-tropic HIV-1 BaL strain. Exosomes were recovered from culture media and separated from virus particles by centrifugation on iodixanol density gradients. The low molecular weight RNA fraction was prepared from purified exosomes. After pre-amplification, RNA was hybridized to microarrays containing probes for 1200 miRNA species of known and unknown function. We observed 48 miRNA species in both infected and uninfected MDM exosomes. Additionally, 38 miRNAs were present in infected-cell exosomes but not uninfected-cell exosomes. Of these, 13 miRNAs were upregulated in exosomes from HIV-infected cells, including 4 miRNA species that were increased by more than 10-fold. Though numerous miRNA species have been identified in HIV-infected cells, relatively little is known about miRNA content in exosomes from these cells. In the future, we plan to investigate whether the upregulated miRNA species we identified are increased in exosomes from HIV-1-positive patients.
Competing to destroy: a fight between two RNA-degradation systems
DEFF Research Database (Denmark)
Thon, Genevieve
2008-01-01
The Argonaute-1 (Ago1) protein bound to small interfering RNAs (siRNAs) directs heterochromatin formation in fission yeast. A high-throughput sequencing approach reveals that the composition of the Ago1-bound siRNA population is sensitive to the noncanonical poly(A) polymerase Cid14, indicating t...... that the RNA-interference and Cid14-TRAMP RNA-degradation pathways compete for substrates in fission yeast.......The Argonaute-1 (Ago1) protein bound to small interfering RNAs (siRNAs) directs heterochromatin formation in fission yeast. A high-throughput sequencing approach reveals that the composition of the Ago1-bound siRNA population is sensitive to the noncanonical poly(A) polymerase Cid14, indicating...
The Complexity of Identifying Large Equivalence Classes
DEFF Research Database (Denmark)
Skyum, Sven; Frandsen, Gudmund Skovbjerg; Miltersen, Peter Bro
1999-01-01
We prove that at least 3k−4/k(2k−3)(n/2) – O(k)equivalence tests and no more than 2/k (n/2) + O(n) equivalence tests are needed in the worst case to identify the equivalence classes with at least k members in set of n elements. The upper bound is an improvement by a factor 2 compared to known res...
Synchronizing a class of uncertain chaotic systems
International Nuclear Information System (INIS)
Chen Maoyin; Zhou Donghua; Shang Yun
2005-01-01
This Letter deals with the synchronization of a class of uncertain chaotic systems in the drive-response framework. A robust adaptive observer based response system is designed to synchronize a given chaotic system with unknown parameters and external disturbances. Lyapunov stability ensures the global synchronization between the drive and response systems even if Lipschitz constants on function matrices and bounds on uncertainties are unknown. Numerical simulation of Genesio-Tesi system verifies the effectiveness of this scheme
Inverse folding of RNA pseudoknot structures
Directory of Open Access Journals (Sweden)
Li Linda YM
2010-06-01
Full Text Available Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.
Class of regular bouncing cosmologies
Vasilić, Milovan
2017-06-01
In this paper, I construct a class of everywhere regular geometric sigma models that possess bouncing solutions. Precisely, I show that every bouncing metric can be made a solution of such a model. My previous attempt to do so by employing one scalar field has failed due to the appearance of harmful singularities near the bounce. In this work, I use four scalar fields to construct a class of geometric sigma models which are free of singularities. The models within the class are parametrized by their background geometries. I prove that, whatever background is chosen, the dynamics of its small perturbations is classically stable on the whole time axis. Contrary to what one expects from the structure of the initial Lagrangian, the physics of background fluctuations is found to carry two tensor, two vector, and two scalar degrees of freedom. The graviton mass, which naturally appears in these models, is shown to be several orders of magnitude smaller than its experimental bound. I provide three simple examples to demonstrate how this is done in practice. In particular, I show that graviton mass can be made arbitrarily small.
Iwata, Yuji
2013-08-05
Efficient and precise microRNA (miRNA) biogenesis in Arabidopsis is mediated by the RNaseIII-family enzyme DICER-LIKE 1 (DCL1), double-stranded RNA-binding protein HYPONASTIC LEAVES 1 and the zinc-finger (ZnF) domain-containing protein SERRATE (SE). In the present study, we examined primary miRNA precursor (pri-miRNA) processing by highly purified recombinant DCL1 and SE proteins and found that SE is integral to pri-miRNA processing by DCL1. SE stimulates DCL1 cleavage of the pri-miRNA in an ionic strength-dependent manner. SE uses its N-terminal domain to bind to RNA and requires both N-terminal and ZnF domains to bind to DCL1. However, when DCL1 is bound to RNA, the interaction with the ZnF domain of SE becomes indispensible and stimulates the activity of DCL1 without requiring SE binding to RNA. Our results suggest that the interactions among SE, DCL1 and RNA are a potential point for regulating pri-miRNA processing. 2013 The Author(s) 2013.
Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI.
Directory of Open Access Journals (Sweden)
Mohan Zhao
Full Text Available RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet-dependent methyltransferases (MTases that are responsible for the 2'-O-methylation and N4-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m4Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently found to contribute to the virulence of Staphylococcus aureus in host animals. Here we report the 2.20-Å crystal structure of homodimeric RsmI from Escherichia coli in complex with the cofactor AdoMet. RsmI consists of an N-terminal putative RNA-binding domain (NTD and a C-terminal catalytic domain (CTD with a Rossmann-like fold, and belongs to the class III MTase family. AdoMet is specifically bound into a negatively charged deep pocket formed by both domains by making extensive contacts. Structure-based mutagenesis and isothermal titration calorimetry (ITC assays revealed Asp100 and Ala124 are vital for AdoMet-binding. Although the overall fold of RsmI shows remarkable similarities to the characterized MTases involved in vitamin B12 biosynthesis, it exhibits a distinct charge distribution especially around the AdoMet-binding pocket because of different substrate specificity. The docking model of RsmI-AdoMet-RNA ternary complex suggested a possible base-flipping mechanism of the substrate RNA that has been observed in several known RNA MTases. Our structural and biochemical studies provide novel insights into the catalytic mechanism of C1402 methylation in 16S rRNA.
Continuous bounded cohomology of locally compact groups
2001-01-01
Recent research has repeatedly led to connections between important rigidity questions and bounded cohomology. However, the latter has remained by and large intractable. This monograph introduces the functorial study of the continuous bounded cohomology for topological groups, with coefficients in Banach modules. The powerful techniques of this more general theory have successfully solved a number of the original problems in bounded cohomology. As applications, one obtains, in particular, rigidity results for actions on the circle, for representations on complex hyperbolic spaces and on Teichmüller spaces. A special effort has been made to provide detailed proofs or references in quite some generality.
Positivity bounds on double parton distributions
International Nuclear Information System (INIS)
Diehl, Markus; Kasemets, Tomas
2013-03-01
Double hard scattering in proton-proton collisions is described in terms of double parton distributions. We derive bounds on these distributions that follow from their interpretation as probability densities, taking into account all possible spin correlations between two partons in an unpolarized proton. These bounds constrain the size of the polarized distributions and can for instance be used to set upper limits on the effects of spin correlations in double hard scattering. We show that the bounds are stable under leading-order DGLAP evolution to higher scales.
Remarks on Bousso's covariant entropy bound
Mayo, A E
2002-01-01
Bousso's covariant entropy bound is put to the test in the context of a non-singular cosmological solution of general relativity found by Bekenstein. Although the model complies with every assumption made in Bousso's original conjecture, the entropy bound is violated due to the occurrence of negative energy density associated with the interaction of some the matter components in the model. We demonstrate how this property allows for the test model to 'elude' a proof of Bousso's conjecture which was given recently by Flanagan, Marolf and Wald. This corroborates the view that the covariant entropy bound should be applied only to stable systems for which every matter component carries positive energy density.
The bound state problem and quark confinement
International Nuclear Information System (INIS)
Chaichian, M.; Demichev, A.P.; Nelipa, N.F.
1980-01-01
A quantum field-theoretic model in which quark is confined is considered. System of equations for the Green functions of colour singlet and octet bound states is obtained. The method is based on the nonperturbative Schwinger-Dyson equations with the use of Slavnov-Taylor identities. It is shown that in the framework of the model if there exist singlet, then also exist octet bound states of the quark-antiquark system. Thus in general, confinement of free quarks does not mean absence of their coloured bound states. (author)
Quasi-bound states in continuum
International Nuclear Information System (INIS)
Nakamura, Hiroaki; Hatano, Naomichi; Garmon, Sterling; Petrosky, Tomio
2007-08-01
We report the prediction of quasi-bound states (resonant states with very long lifetimes) that occur in the eigenvalue continuum of propagating states for a wide region of parameter space. These quasi-bound states are generated in a quantum wire with two channels and an adatom, when the energy bands of the two channels overlap. A would-be bound state that lays just below the upper energy band is slightly destabilized by the lower energy band and thereby becomes a resonant state with a very long lifetime (a second QBIC lays above the lower energy band). (author)
Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins
Chatterjee, Raghunath; Zhao, Jianfei; He, Ximiao; Shlyakhtenko, Andrey; Mann, Ishminder; Waterfall, Joshua J.; Meltzer, Paul; Sathyanarayana, B. K.; FitzGerald, Peter C.; Vinson, Charles
2012-01-01
Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X4-N1-30-X4) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (C/GCCGGAAGCGGAA) and the ETS⇔CRE motif (C/GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif. PMID:23050235
tRNA--the golden standard in molecular biology.
Barciszewska, Mirosława Z; Perrigue, Patrick M; Barciszewski, Jan
2016-01-01
Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.
RNA Structural Alignments, Part I
DEFF Research Database (Denmark)
Havgaard, Jakob Hull; Gorodkin, Jan
2014-01-01
Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....
Tight Bounds for Distributed Functional Monitoring
DEFF Research Database (Denmark)
Woodruff, David P.; Zhang, Qin
2011-01-01
$, our bound resolves their main open question. Our lower bounds are based on new direct sum theorems for approximate majority, and yield significant improvements to problems in the data stream model, improving the bound for estimating $F_p, p > 2,$ in $t$ passes from $\\tilde{\\Omega}(n^{1-2/p}/(\\eps^{2/p......} t))$ to $\\tilde{\\Omega}(n^{1-2/p}/(\\eps^{4/p} t))$, giving the first bound for estimating $F_0$ in $t$ passes of $\\Omega(1/(\\eps^2 t))$ bits of space that does not use the gap-hamming problem, and showing a distribution for the gap-hamming problem with high external information cost or super...
Redshift-space limits of bound structures
Duenner, Rolando; Reisenegger, Andreas; Meza, Andres; Araya, Pablo A.; Quintana, Hernan
2007-01-01
An exponentially expanding Universe, possibly governed by a cosmological constant, forces gravitationally bound structures to become more and more isolated, eventually becoming causally disconnected from each other and forming so-called 'island universes'. This new scenario reformulates the question
Error Bounds: Necessary and Sufficient Conditions
Czech Academy of Sciences Publication Activity Database
Outrata, Jiří; Kruger, A.Y.; Fabian, Marián; Henrion, R.
2010-01-01
Roč. 18, č. 2 (2010), s. 121-149 ISSN 1877-0533 R&D Projects: GA AV ČR IAA100750802 Institutional research plan: CEZ:AV0Z10750506; CEZ:AV0Z10190503 Keywords : Error bounds * Calmness * Subdifferential * Slope Subject RIV: BA - General Mathematics Impact factor: 0.333, year: 2010 http://library.utia.cas.cz/separaty/2010/MTR/outrata-error bounds necessary and sufficient conditions.pdf
Malabsorption of protein bound vitamin B12.
Dawson, D W; Sawers, A H; Sharma, R K
1984-01-01
Patients with subnormal serum vitamin B12 concentrations were tested for absorption of protein bound vitamin B12 and compared with controls. Absorption of the protein bound vitamin appeared to decrease with increasing age in healthy subjects. Differences between the result of this test and the result of the Schilling test in patients who had undergone gastric surgery were confirmed; such differences were also seen in some patients who had iron deficiency anaemia, an excessive alcohol intake, ...
New Spectral Features from Bound Dark Matter
DEFF Research Database (Denmark)
Catena, Riccardo; Kouvaris, Chris
2016-01-01
We demonstrate that dark matter particles gravitationally bound to the Earth can induce a characteristic nuclear recoil signal at low energies in direct detection experiments. The new spectral feature we predict can provide the ultimate smoking gun for dark matter discovery for experiments...... with positive signal but unclear background. The new feature is universal, in that the ratio of bound over halo dark matter event rates at detectors is independent of the dark matter-nucleon cross section....
Matrin 3 binds and stabilizes mRNA.
Directory of Open Access Journals (Sweden)
Maayan Salton
Full Text Available Matrin 3 (MATR3 is a highly conserved, inner nuclear matrix protein with two zinc finger domains and two RNA recognition motifs (RRM, whose function is largely unknown. Recently we found MATR3 to be phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Here, we show that MATR3 interacts in an RNA-dependent manner with several proteins with established roles in RNA processing, and maintains its interaction with RNA via its RRM2 domain. Deep sequencing of the bound RNA (RIP-seq identified several small noncoding RNA species. Using microarray analysis to explore MATR3's role in transcription, we identified 77 transcripts whose amounts depended on the presence of MATR3. We validated this finding with nine transcripts which were also bound to the MATR3 complex. Finally, we demonstrated the importance of MATR3 for maintaining the stability of several of these mRNA species and conclude that it has a role in mRNA stabilization. The data suggest that the cellular level of MATR3, known to be highly regulated, modulates the stability of a group of gene transcripts.
Generalized surface tension bounds in vacuum decay
Masoumi, Ali; Paban, Sonia; Weinberg, Erick J.
2018-02-01
Coleman and De Luccia (CDL) showed that gravitational effects can prevent the decay by bubble nucleation of a Minkowski or AdS false vacuum. In their thin-wall approximation this happens whenever the surface tension in the bubble wall exceeds an upper bound proportional to the difference of the square roots of the true and false vacuum energy densities. Recently it was shown that there is another type of thin-wall regime that differs from that of CDL in that the radius of curvature grows substantially as one moves through the wall. Not only does the CDL derivation of the bound fail in this case, but also its very formulation becomes ambiguous because the surface tension is not well defined. We propose a definition of the surface tension and show that it obeys a bound similar in form to that of the CDL case. We then show that both thin-wall bounds are special cases of a more general bound that is satisfied for all bounce solutions with Minkowski or AdS false vacua. We discuss the limit where the parameters of the theory attain critical values and the bound is saturated. The bounce solution then disappears and a static planar domain wall solution appears in its stead. The scalar field potential then is of the form expected in supergravity, but this is only guaranteed along the trajectory in field space traced out by the bounce.
Protein-driven inference of miRNA-disease associations
DEFF Research Database (Denmark)
Mørk, Søren; Pletscher-Frankild, Sune; Palleja, Albert
2014-01-01
MicroRNAs (miRNAs) are a highly abundant class of non-coding RNA genes involved in cellular regulation and thus also diseases. Despite miRNAs being important disease factors, miRNA-disease associations remain low in number and of variable reliability. Furthermore, existing databases and prediction...
Moravcikova, J.; Matusikova, I.; Libantova, J.; Bauer, M.; Mlynarova, L.
2004-01-01
The genes encoding for a cucumber class III chitinase and Nicotiana plumbaginifolia class I glucanase were co-introduced into Slovak potato (Solanum tuberosum L.) breeding line 116/86 using Agrobacterium tumefaciens. For both transgenes the number of integrated copies and level of RNA expression
NLRC5: a key regulator of MHC class I-dependent immune responses.
Kobayashi, Koichi S; van den Elsen, Peter J
2012-12-01
The expression of MHC class I molecules is crucial for the initiation and regulation of adaptive immune responses against pathogens. NOD-, LRR- and CARD-containing 5 (NLRC5) was recently identified as a specific transactivator of MHC class I genes (CITA). NLRC5 and the master regulator for MHC class II genes, class II transactivator (CIITA), interact with similar MHC promoter-bound factors. Here, we provide a broad overview of the molecular mechanisms behind MHC class I transcription and the role of the class I transactivator NLRC5 in MHC class I-dependent immune responses.
Symanzik approach in modeling of bound states of Dirac particle in singular background
Directory of Open Access Journals (Sweden)
Pismak Yu. M.
2017-01-01
Full Text Available In the model of interaction of spinor field with homogeneous isotropic material plane constructed in framework of Symanzik approach, the bound states are studied. For localized near plane Dirac particle the expression for current, charge and density are presented. For bound state with massless dispersion law the current, charge and density are calculated for simplified model with 2 parameter exactly.The model can find application to a wide class of phenomena arising by the interaction of fields of quantum electrodynamics with two-dimensional materials.
Unitarity Bounds and RG Flows in Time Dependent Quantum Field Theory
Energy Technology Data Exchange (ETDEWEB)
Dong, Xi; Horn, Bart; Silverstein, Eva; Torroba, Gonzalo; /Stanford U., ITP /Stanford U., Phys. Dept. /SLAC
2012-04-05
We generalize unitarity bounds on operator dimensions in conformal field theory to field theories with spacetime dependent couplings. Below the energy scale of spacetime variation of the couplings, their evolution can strongly affect the physics, effectively shifting the infrared operator scaling and unitarity bounds determined from correlation functions in the theory. We analyze this explicitly for large-N double-trace flows, and connect these to UV complete field theories. One motivating class of examples comes from our previous work on FRW holography, where this effect explains the range of flavors allowed in the dual, time dependent, field theory.
The existence and the stability of solutions for equilibrium problems with lower and upper bounds
Directory of Open Access Journals (Sweden)
Congjun Zhang
2012-12-01
Full Text Available In this paper, we study a class of equilibrium problems with lower and upper bounds. We obtain some existence results of solutions for equilibrium problems with lower and upper bounds by employing some classical fixed-point theorems. We investigate the stability of the solution sets for the problems, and establish sufficient conditions for the upper semicontinuity, lower semicontinuity and continuity of the solution set mapping $S:Lambda_1imesLambda_2o2^{X}$ in a Hausdorff topological vector space, in the case where a set $K$ and a mapping $f$ are perturbed respectively by parameters $lambda$ and $mu.$
Directory of Open Access Journals (Sweden)
Komang Ayu Tri Widhiyanti
2013-11-01
Full Text Available This study was conducted to know the improvement the explosive power of leg muscle. It was done through 5 set 12 repetitions during 6 weeks in the field of SMP Negeri 3 Sukawati started from 4 p.m. until 6 p.m. There were 3 groups applied in this study such as group 1 (control group that was instructed to kick a ball, group 2 (plyometric training of alternate leg bound, and group 3 (plyometric training of double leg bound. The sample was 14 male students who were in the seventh grade class of SMP Negeri 3 Sukawati in the academic year 2012/2013. The data was gained by doing the movement of alternate leg bound and double leg bound that each movement was done three times before and after the training. The hypothesis was examined by using independent t-test with the result 0.05 (p<0.05. Based on the different result of analysis test in each group, the gain score of the group 2 with the group 1 about 0,51 that shows the significant differences p = 0,00, the gain score of the group 2 with the group 3 about 0,31 that shows the significant differences p = 0,00, the gain score of the group 3 with the group 1 about 0,20 that shows the significant differences p = 0,00. Thus, alternate leg bound plyometric training is more effective than double leg bound. It is expected that the coach and the gym teacher to apply alternate leg bound plyometric training as an alternative to improve the explosive power of leg muscle.
Structural imprints in vivo decode RNA regulatory mechanisms.
Spitale, Robert C; Flynn, Ryan A; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y; Batista, Pedro J; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y
2015-03-26
Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
Upper bounds on superpartner masses from upper bounds on the Higgs boson mass.
Cabrera, M E; Casas, J A; Delgado, A
2012-01-13
The LHC is putting bounds on the Higgs boson mass. In this Letter we use those bounds to constrain the minimal supersymmetric standard model (MSSM) parameter space using the fact that, in supersymmetry, the Higgs mass is a function of the masses of sparticles, and therefore an upper bound on the Higgs mass translates into an upper bound for the masses for superpartners. We show that, although current bounds do not constrain the MSSM parameter space from above, once the Higgs mass bound improves big regions of this parameter space will be excluded, putting upper bounds on supersymmetry (SUSY) masses. On the other hand, for the case of split-SUSY we show that, for moderate or large tanβ, the present bounds on the Higgs mass imply that the common mass for scalars cannot be greater than 10(11) GeV. We show how these bounds will evolve as LHC continues to improve the limits on the Higgs mass.
Dynamic nuclear polarization of nucleic acid with endogenously bound manganese
International Nuclear Information System (INIS)
Wenk, Patricia; Kaushik, Monu; Richter, Diane; Vogel, Marc; Suess, Beatrix; Corzilius, Björn
2015-01-01
We report the direct dynamic nuclear polarization (DNP) of 13 C nuclei of a uniformly [ 13 C, 15 N]-labeled, paramagnetic full-length hammerhead ribozyme (HHRz) complex with Mn 2+ where the enhanced polarization is fully provided by the endogenously bound metal ion and no exogenous polarizing agent is added. A 13 C enhancement factor of ε = 8 was observed by intra-complex DNP at 9.4 T. In contrast, “conventional” indirect and direct DNP experiments were performed using AMUPol as polarizing agent where we obtained a 1 H enhancement factor of ε ≈ 250. Comparison with the diamagnetic (Mg 2+ ) HHRz complex shows that the presence of Mn 2+ only marginally influences the (DNP-enhanced) NMR properties of the RNA. Furthermore two-dimensional correlation spectra ( 15 N– 13 C and 13 C– 13 C) reveal structural inhomogeneity in the frozen, amorphous state indicating the coexistence of several conformational states. These demonstrations of intra-complex DNP using an endogenous metal ion as well as DNP-enhanced MAS NMR of RNA in general yield important information for the development of new methods in structural biology
Dynamic nuclear polarization of nucleic acid with endogenously bound manganese
Energy Technology Data Exchange (ETDEWEB)
Wenk, Patricia [University of Tübingen, Werner Siemens Imaging Center and Department of Preclinical Imaging and Radiopharmacy (Germany); Kaushik, Monu; Richter, Diane [Goethe University, Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ) (Germany); Vogel, Marc; Suess, Beatrix [Technical University Darmstadt, Department of Biology (Germany); Corzilius, Björn, E-mail: corzilius@em.uni-frankfurt.de [Goethe University, Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)
2015-09-15
We report the direct dynamic nuclear polarization (DNP) of {sup 13}C nuclei of a uniformly [{sup 13}C,{sup 15}N]-labeled, paramagnetic full-length hammerhead ribozyme (HHRz) complex with Mn{sup 2+} where the enhanced polarization is fully provided by the endogenously bound metal ion and no exogenous polarizing agent is added. A {sup 13}C enhancement factor of ε = 8 was observed by intra-complex DNP at 9.4 T. In contrast, “conventional” indirect and direct DNP experiments were performed using AMUPol as polarizing agent where we obtained a {sup 1}H enhancement factor of ε ≈ 250. Comparison with the diamagnetic (Mg{sup 2+}) HHRz complex shows that the presence of Mn{sup 2+} only marginally influences the (DNP-enhanced) NMR properties of the RNA. Furthermore two-dimensional correlation spectra ({sup 15}N–{sup 13}C and {sup 13}C–{sup 13}C) reveal structural inhomogeneity in the frozen, amorphous state indicating the coexistence of several conformational states. These demonstrations of intra-complex DNP using an endogenous metal ion as well as DNP-enhanced MAS NMR of RNA in general yield important information for the development of new methods in structural biology.
Bounds on poloidal kinetic energy in plane layer convection
Tilgner, A.
2017-12-01
A numerical method is presented that conveniently computes upper bounds on heat transport and poloidal energy in plane layer convection for infinite and finite Prandtl numbers. The bounds obtained for the heat transport coincide with earlier results. These bounds imply upper bounds for the poloidal energy, which follow directly from the definitions of dissipation and energy. The same constraints used for computing upper bounds on the heat transport lead to improved bounds for the poloidal energy.
A class of convergent neural network dynamics
Fiedler, Bernold; Gedeon, Tomáš
1998-01-01
We consider a class of systems of differential equations in Rn which exhibits convergent dynamics. We find a Lyapunov function and show that every bounded trajectory converges to the set of equilibria. Our result generalizes the results of Cohen and Grossberg (1983) for convergent neural networks. It replaces the symmetry assumption on the matrix of weights by the assumption on the structure of the connections in the neural network. We prove the convergence result also for a large class of Lotka-Volterra systems. These are naturally defined on the closed positive orthant. We show that there are no heteroclinic cycles on the boundary of the positive orthant for the systems in this class.
Achieving the physical limits of the bounded-storage model
International Nuclear Information System (INIS)
Mandayam, Prabha; Wehner, Stephanie
2011-01-01
Secure two-party cryptography is possible if the adversary's quantum storage device suffers imperfections. For example, security can be achieved if the adversary can store strictly less then half of the qubits transmitted during the protocol. This special case is known as the bounded-storage model, and it has long been an open question whether security can still be achieved if the adversary's storage were any larger. Here, we answer this question positively and demonstrate a two-party protocol which is secure as long as the adversary cannot store even a small fraction of the transmitted pulses. We also show that security can be extended to a larger class of noisy quantum memories.
Integral bounds for N-body total cross sections
International Nuclear Information System (INIS)
Osborn, T.A.; Bolle, D.
1979-01-01
We study the behavior of the total cross sections in the three- and N-body scattering problem. Working within the framework of the time-dependent two-Hilbert space scattering theory, we give a simple derivation of integral bounds for the total cross section for all processes initiated by the collision of two clusters. By combining the optical theorem with a trace identity derived by Jauch, Sinha, and Misra, we find, roughly speaking, that if the local pairwise interaction falls off faster than r -3 , then sigma/sub tot/(E) must decrease faster than E/sup -1/2/ at high energy. This conclusion is unchanged if one introduces a class of well-behaved three-body interactions
A cosmological lower bound on the neutron electric dipole moment
International Nuclear Information System (INIS)
Ellis, J.; Nanopoulos, D.V.; Rudaz, S.; Gaillard, M.K.
1980-10-01
We argue that in a wide class of grand unified theories diagrams similar to those generating baryon number in the early universe also contribute to renormalization of the CP-violating theta parameter of QCD and hence to the neutron electric dipole moment dsub(n). We then use the apparent baryon-to-photon ratio (nsub(B)/nsub(γ))>=1.3 x 10 -10 to deduce an order-of-magnitude lower bound on the neutron electric dipole moment: dsub(n) > approximately 3 x 10 -28 e-cm. Conversely the present experimental upper limit on dsub(n) implies (nsub(B)/nsub(γ) -7 . We find as a corollary that there is not much scope for entropy generation after the creation of the baryon-antibaryon asymmetry in the very early universe
Thermalization Time Bounds for Pauli Stabilizer Hamiltonians
Temme, Kristan
2017-03-01
We prove a general lower bound to the spectral gap of the Davies generator for Hamiltonians that can be written as the sum of commuting Pauli operators. These Hamiltonians, defined on the Hilbert space of N-qubits, serve as one of the most frequently considered candidates for a self-correcting quantum memory. A spectral gap bound on the Davies generator establishes an upper limit on the life time of such a quantum memory and can be used to estimate the time until the system relaxes to thermal equilibrium when brought into contact with a thermal heat bath. The bound can be shown to behave as {λ ≥ O(N^{-1} exp(-2β overline{ɛ}))}, where {overline{ɛ}} is a generalization of the well known energy barrier for logical operators. Particularly in the low temperature regime we expect this bound to provide the correct asymptotic scaling of the gap with the system size up to a factor of N -1. Furthermore, we discuss conditions and provide scenarios where this factor can be removed and a constant lower bound can be proven.
Universal bounds in even-spin CFTs
Energy Technology Data Exchange (ETDEWEB)
Qualls, Joshua D. [Department of Physics, National Taiwan University,Taipei, Taiwan (China)
2015-12-01
We prove using invariance under the modular S− and ST−transformations that every unitary two-dimensional conformal field theory (CFT) having only even-spin primary operators (with no extended chiral algebra and with right- and left-central charges c,c̃>1) contains a primary operator with dimension Δ{sub 1} satisfying 0<Δ{sub 1}<((c+c̃)/24)+0.09280…. After deriving both analytical and numerical bounds, we discuss how to extend our methods to bound higher conformal dimensions before deriving lower and upper bounds on the number of primary operators in a given energy range. Using the AdS{sub 3}/CFT{sub 2} dictionary, the bound on Δ{sub 1} proves the lightest massive excitation in appropriate theories of 3D matter and gravity with cosmological constant Λ<0 can be no heavier than 1/8G{sub N}+O(√(−Λ)); the bounds on the number of operators are related via AdS/CFT to the entropy of states in the dual gravitational theory. In the flat-space approximation, the limiting mass is exactly that of the lightest BTZ black hole.
Direct Adaptive Control of a Class of Nonlinear Discrete-Time Systems
DEFF Research Database (Denmark)
Bendtsen, Jan Dimon
2004-01-01
In this paper we deal with direct adaptive control of a specific class of discrete-time SISO systems, where the nonlinearities are convex and an upper bound is known. We use a control law based on a linear combination of a set of globally uniformly bounded basis functions with compact support, wh...
Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection.
Directory of Open Access Journals (Sweden)
Evgeny A Glazov
Full Text Available MicroRNA (miRNA and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.
Upper Bounds on Performance Measures of Heterogeneous // Queues
Directory of Open Access Journals (Sweden)
F. S. Q. Alves
2011-01-01
Full Text Available In many real-life queueing systems, the servers are often heterogeneous, namely they work at different rates. This paper provides a simple method to compute tight upper bounds on two important performance measures of single-class heterogeneous multi-server Markovian queueing systems, namely the average number in queue and the average waiting time in queue. This method is based on an expansion of the state space that is followed by an approximate reduction of the state space, only considering the most probable states. In most cases tested, we were able to approximate the actual behavior of the system with smaller errors than those obtained from traditional homogeneous multiserver Markovian queues, as shown by GPSS simulations. In addition, we have correlated the quality of the approximation with the degree of heterogeneity of the system, which was evaluated using its Gini index. Finally, we have shown that the bounds are robust and still useful, even considering quite different allocation strategies. A large number of simulation results show the accuracy of the proposed method that is better than that of classical homogeneous multiserver Markovian formulae in many situations.
Responses of mRNA expression of PepT1 in small intestine to ...
African Journals Online (AJOL)
To study the effect of circulation small peptides concentration on mRNA expression in small intestine, graded amount of soybean small peptides (SSP) were infused into lactating goats through duodenal fistulas. Peptide-bound amino acid (PBAA) concentration in arterial plasma and the mRNA expression of PepT1 was ...
Measuring RNA-Ligand Interactions with Microscale Thermophoresis.
Moon, Michelle H; Hilimire, Thomas A; Sanders, Allix M; Schneekloth, John S
2018-01-31
In recent years, there has been dramatic growth in the study of RNA. RNA has gone from being known as an intermediate in the central dogma of molecular biology to a molecule with a large diversity of structure and function that is involved in all aspects of biology. As new functions are rapidly discovered, it has become clear that there is a need for RNA-targeting small molecule probes to investigate RNA biology and clarify the potential for therapeutics based on RNA-small molecule interactions. While a host of techniques exist to measure RNA-small molecule interactions, many of these have drawbacks that make them intractable for routine use and are often not broadly applicable. A newer technology called microscale thermophoresis (MST), which measures the directed migration of a molecule and/or molecule-ligand complex along a temperature gradient, can be used to measure binding affinities using very small amounts of sample. The high sensitivity of this technique enables measurement of affinity constants in the nanomolar and micromolar range. Here, we demonstrate how MST can be used to study a range of biologically relevant RNA interactions, including peptide-RNA interactions, RNA-small molecule interactions, and displacement of an RNA-bound peptide by a small molecule.
Protein solubility and folding enhancement by interaction with RNA.
Directory of Open Access Journals (Sweden)
Seong Il Choi
Full Text Available While basic mechanisms of several major molecular chaperones are well understood, this machinery has been known to be involved in folding of only limited number of proteins inside the cells. Here, we report a chaperone type of protein folding facilitated by interaction with RNA. When an RNA-binding module is placed at the N-terminus of aggregation-prone target proteins, this module, upon binding with RNA, further promotes the solubility of passenger proteins, potentially leading to enhancement of proper protein folding. Studies on in vitro refolding in the presence of RNA, coexpression of RNA molecules in vivo and the mutants with impaired RNA binding ability suggests that RNA can exert chaperoning effect on their bound proteins. The results suggest that RNA binding could affect the overall kinetic network of protein folding pathway in favor of productive folding over off-pathway aggregation. In addition, the RNA binding-mediated solubility enhancement is extremely robust for increasing soluble yield of passenger proteins and could be usefully implemented for high-throughput protein expression for functional and structural genomic research initiatives. The RNA-mediated chaperone type presented here would give new insights into de novo folding in vivo.
Novel Approach to Analyzing MFE of Noncoding RNA Sequences.
George, Tina P; Thomas, Tessamma
2016-01-01
Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers.
Yukawa Bound States and Their LHC Phenomenology
Directory of Open Access Journals (Sweden)
Enkhbat Tsedenbaljir
2013-01-01
Full Text Available We present the current status on the possible bound states of extra generation quarks. These include phenomenology and search strategy at the LHC. If chiral fourth-generation quarks do exist their strong Yukawa couplings, implied by current experimental lower bound on their masses, may lead to formation of bound states. Due to nearly degenerate 4G masses suggested by Precision Electroweak Test one can employ “heavy isospin” symmetry to classify possible spectrum. Among these states, the color-octet isosinglet vector ω 8 is the easiest to be produced at the LHC. The discovery potential and corresponding decay channels are covered in this paper. With possible light Higgs at ~125 GeV two-Higgs doublet version is briefly discussed.
Braneworld black holes and entropy bounds
Directory of Open Access Journals (Sweden)
Y. Heydarzade
2018-01-01
Full Text Available The Bousso's D-bound entropy for the various possible black hole solutions on a 4-dimensional brane is checked. It is found that the D-bound entropy here is apparently different from that of obtained for the 4-dimensional black hole solutions. This difference is interpreted as the extra loss of information, associated to the extra dimension, when an extra-dimensional black hole is moved outward the observer's cosmological horizon. Also, it is discussed that N-bound entropy is hold for the possible solutions here. Finally, by adopting the recent Bohr-like approach to black hole quantum physics for the excited black holes, the obtained results are written also in terms of the black hole excited states.
Energy conditions bounds and supernovae data
International Nuclear Information System (INIS)
Lima, M.P.; Vitenti, S.D.P.; Reboucas, M.J.
2008-01-01
The energy conditions play an important role in the description of some important properties of the Universe, including the current accelerating expansion phase and the possible recent phase of super-acceleration. In a recent work we have provided a detailed study of the energy conditions for the recent past by deriving bounds from energy conditions and by making the confrontation of the bounds with supernovae data. Here, we extend and update these results in two different ways. First, by carrying out a new statistical analysis for q(z) estimates needed for the confrontation between the bounds and supernovae data. Second, by providing a new picture of the energy conditions fulfillment and violation in the light of the recently compiled Union set of 307 type Ia supernovae and by using two different statistical approaches
Bound water in Kevlar 49 fibers
International Nuclear Information System (INIS)
Garza, R.G.; Pruneda, C.O.; Morgan, R.J.
1981-01-01
From elemental analyses, thermogravimetric-mass spectroscopy studies and re-evaluation of previous water diffusion studies in Kevlar 49 fibers it is concluded that these fibers can contain two types of sorbed moisture. The fibers can absorb up to approx. 6 wt % loosely bound water with an activation energy for outgassing by desorption of 6 kcal/mole. This loosely bound water is a direct result of the presence of Na 2 SO 4 impurities and the perturbations they induce on the packing of the rod-like poly (p-phenylene terephthalamide) macromolecules. Kevlar 49 fibers also inherently contain up to 30 wt % additional water which is tightly bound within the crystal lattice. This water exhibits an activation energy for outgassing by diffusion of approx. 40 kcal/mole and is only evolved from the fiber in significant quantities at t > 350 0 C over a period of hours
Cosmological implications of Dark Matter bound states
Energy Technology Data Exchange (ETDEWEB)
Mitridate, Andrea [Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa (Italy); Redi, Michele; Smirnov, Juri [INFN, Sezione di Firenze, and Dipartimento di Fisica e Astronomia, Università di Firenze, Via G. Sansone 1, 50019 Sesto Fiorentino (Italy); Strumia, Alessandro, E-mail: andrea.mitridate@gmail.com, E-mail: michele.redi@fi.infn.it, E-mail: juri.smirnov@mpi-hd.mpg.de, E-mail: alessandro.strumia@cern.ch [Dipartimento di Fisica dell' Università di Pisa and INFN, Pisa (Italy)
2017-05-01
We present generic formulæ for computing how Sommerfeld corrections together with bound-state formation affects the thermal abundance of Dark Matter with non-abelian gauge interactions. We consider DM as a fermion 3plet (wino) or 5plet under SU(2) {sub L} . In the latter case bound states raise to 11.5 TeV the DM mass required to reproduce the cosmological DM abundance and give indirect detection signals such as (for this mass) a dominant γ-line around 70 GeV. Furthermore, we consider DM co-annihilating with a colored particle, such as a squark or a gluino, finding that bound state effects are especially relevant in the latter case.
Analysis of the RNA species isolated from defective particles of vesicular stomatitis virus.
Adler, R; Banerjee, A K
1976-10-01
Serial high multiplicity passage of a cloned stock of vesicular stomatitis virus was found to generate defective interfering particles containing three size classes of RNA, with sedimentaiton coefficients of 31 S, 23 S and 19 S. The 31 S and 23 S RNA species were found to be complementary to both the 12 to 18 S and 31 S size classes of VSV mRNAs. The 19 S class of RNA was found to be partially base-paired. All three RNA species were found to contain ppAp at their 5' termini.
de Klerk, Etienne; Laurent, Monique
We consider the problem of minimizing a continuous function f over a compact set K. We compare the hierarchy of upper bounds proposed by Lasserre in [SIAM J. Optim. 21(3) (2011), pp. 864-885] to bounds that may be obtained from simulated annealing. We show that, when f is a polynomial and K a convex
Creed, Peter A.; Patton, Wendy; Hood, Michelle
2010-01-01
We surveyed 506 Australian high school students on career development (exploration, planning, job-knowledge, decision-making, indecision), personal functioning (well-being, self-esteem, life satisfaction, school satisfaction) and control variables (parent education, school achievement), and tested differences among work-bound, college-bound and…
U.S. Environmental Protection Agency — A "Class 1" area is a geographic area recognized by the EPA as being of the highest environmental quality and requiring maximum protection. Class I areas are areas...
Town of Cary, North Carolina — This data is specific to Parks and Recreation classes, workshops, and activities within the course catalog. It contains an entry for upcoming classes.*This data set...
[Membrane-bound cytokine and feedforward regulation].
Wu, Ke-Fu; Zheng, Guo-Guang; Ma, Xiao-Tong; Song, Yu-Hua
2013-10-01
Feedback and feedforward widely exist in life system, both of them are the basic processes of control system. While the concept of feedback has been widely used in life science, feedforward regulation was systematically studied in neurophysiology, awaiting further evidence and mechanism in molecular biology and cell biology. The authors put forward a hypothesis about the feedforward regulation of membrane bound macrophage colony stimulation factor (mM-CSF) on the basis of their previous work. This hypothesis might provide a new direction for the study on the biological effects of mM-CSF on leukemia and solid tumors, and contribute to the study on other membrane bound cytokines.
The covariant entropy bound in gravitational collapse
International Nuclear Information System (INIS)
Gao, Sijie; Lemos, Jose P. S.
2004-01-01
We study the covariant entropy bound in the context of gravitational collapse. First, we discuss critically the heuristic arguments advanced by Bousso. Then we solve the problem through an exact model: a Tolman-Bondi dust shell collapsing into a Schwarzschild black hole. After the collapse, a new black hole with a larger mass is formed. The horizon, L, of the old black hole then terminates at the singularity. We show that the entropy crossing L does not exceed a quarter of the area of the old horizon. Therefore, the covariant entropy bound is satisfied in this process. (author)
Bound states in curved quantum waveguides
International Nuclear Information System (INIS)
Exner, P.; Seba, P.
1987-01-01
We study free quantum particle living on a curved planar strip Ω of a fixed width d with Dirichlet boundary conditions. It can serve as a model for electrons in thin films on a cylindrical-type substrate, or in a curved quantum wire. Assuming that the boundary of Ω is infinitely smooth and its curvature decays fast enough at infinity, we prove that a bound state with energy below the first transversal mode exists for all sufficiently small d. A lower bound on the critical width is obtained using the Birman-Schwinger technique. (orig.)
Lower Bounds for External Memory Dictionaries
DEFF Research Database (Denmark)
Brodal, Gerth Stølting; Fagerberg, Rolf
2003-01-01
We study trade-offs between the update time and the query time for comparison based external memory dictionaries. The main contributions of this paper are two lower bound trade offs between the I/O complexity of member queries and insertions: If N < M insertions perform at most δ · N/B I/Os, then......We study trade-offs between the update time and the query time for comparison based external memory dictionaries. The main contributions of this paper are two lower bound trade offs between the I/O complexity of member queries and insertions: If N
Finding Maximal Pairs with Bounded Gap
DEFF Research Database (Denmark)
Brodal, Gerth Stølting; Lyngsø, Rune B.; Pedersen, Christian N. S.
1999-01-01
. In this paper we present methods for finding all maximal pairs under various constraints on the gap. In a string of length n we can find all maximal pairs with gap in an upper and lower bounded interval in time O(n log n+z) where z is the number of reported pairs. If the upper bound is removed the time reduces...... to O(n+z). Since a tandem repeat is a pair where the gap is zero, our methods can be seen as a generalization of finding tandem repeats. The running time of our methods equals the running time of well known methods for finding tandem repeats....
Bound constrained quadratic programming via piecewise
DEFF Research Database (Denmark)
Madsen, Kaj; Nielsen, Hans Bruun; Pinar, M. C.
1999-01-01
of a symmetric, positive definite matrix, and is solved by Newton iteration with line search. The paper describes the algorithm and its implementation including estimation of lambda/sub 1/ , how to get a good starting point for the iteration, and up- and downdating of Cholesky factorization. Results of extensive......We consider the strictly convex quadratic programming problem with bounded variables. A dual problem is derived using Lagrange duality. The dual problem is the minimization of an unconstrained, piecewise quadratic function. It involves a lower bound of lambda/sub 1/ , the smallest eigenvalue...
Quantum Kolmogorov complexity and bounded quantum memory
International Nuclear Information System (INIS)
Miyadera, Takayuki
2011-01-01
The effect of bounded quantum memory in a primitive information protocol has been examined using the quantum Kolmogorov complexity as a measure of information. We employed a toy two-party protocol in which Bob, by using a bounded quantum memory and an unbounded classical memory, estimates a message that was encoded in qubits by Alice in one of the bases X or Z. Our theorem gave a nontrivial effect of the memory boundedness. In addition, a generalization of the uncertainty principle in the presence of quantum memory has been obtained.
Methods for Determination of 2′-O-Me in RNA
DEFF Research Database (Denmark)
Birkedal, Ulf; Krogh, Nicolai; Andersen, Kasper Langebjerg
2016-01-01
mechanism of ribose methylation is found in rRNA of Archaea and Eukarya where a methyltransferase (fibrillarin) use sRNA (Archaea) or box C/D snoRNA (Eukarya) as guide RNAs to specify the site of modification. The general function of these modifications is to promote ribosome biogenesis, in particular...... for mapping modifications and quantitating the fraction of RNA molecules modified in a population until recently remained poorly developed. Here, we review the methods that have been used to study 2′-O-Me in RNA starting with the original approach employing in vivo isotope labeling followed by paper......Ribose methylation is one of the most abundant RNA modifications and is found in all kingdoms of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. The most abundant...
DEFF Research Database (Denmark)
Nielsen, Henrik
2011-01-01
Working with RNA is not a special discipline in molecular biology. However, RNA is chemically and structurally different from DNA and a few simple work rules have to be implemented to maintain the integrity of the RNA. Alkaline pH, high temperatures, and heavy metal ions should be avoided when po...
Class Notes for "Class-Y-News."
Stuart, Judy L.
1991-01-01
A self-contained class of students with mild to moderate disabilities published a monthly newsletter which was distributed to students' families. Students became involved in writing, typing, drawing, folding, basic editing, and disseminating. (JDD)
Classed identities in adolescence
Jay, Sarah
2015-01-01
peer-reviewed The central argument of this thesis is that social class remains a persistent system of inequality in education, health, life chances and opportunities. Therefore class matters. But why is it that so little attention has been paid to class in the psychological literature? Three papers are presented here which draw together theoretical advances in psychological understandings of group processes and sociological understandings of the complexity of class. As western labour marke...
Neeleman, L; Olsthoorn, R C; Linthorst, H J; Bol, J F
2001-12-04
On entering a host cell, positive-strand RNA virus genomes have to serve as messenger for the translation of viral proteins. Efficient translation of cellular messengers requires interactions between initiation factors bound to the 5'-cap structure and the poly(A) binding protein bound to the 3'-poly(A) tail. Initiation of infection with the tripartite RNA genomes of alfalfa mosaic virus (AMV) and viruses from the genus Ilarvirus requires binding of a few molecules of coat protein (CP) to the 3' end of the nonpolyadenylated viral RNAs. Moreover, infection with the genomic RNAs can be initiated by addition of the subgenomic messenger for CP, RNA 4. We report here that extension of the AMV RNAs with a poly(A) tail of 40 to 80 A-residues permitted initiation of infection independently of CP or RNA 4 in the inoculum. Specifically, polyadenylation of RNA 1 relieved an apparent bottleneck in the translation of the viral RNAs. Translation of RNA 4 in plant protoplasts was autocatalytically stimulated by its encoded CP. Mutations that interfered with CP binding to the 3' end of viral RNAs reduced translation of RNA 4 to undetectable levels. Possibly, CP of AMV and ilarviruses stimulates translation of viral RNAs by acting as a functional analogue of poly(A) binding protein or other cellular proteins.
The Piwi pathway: from piRNA methylation to histone methylation
Luteijn, M.J.
2013-01-01
Piwi-interacting RNAs (piRNAs) are germ line-specific small RNA molecules that have a function in genome defense and germ cell development. They associate with a specific class of Argonaute proteins, named Piwi, and function through an RNA interference-like mechanism. These small RNA molecules play
Burroughs, A Maxwell; Ando, Yoshinari; de Hoon, Michiel J L; Tomaru, Yasuhiro; Nishibu, Takahiro; Ukekawa, Ryo; Funakoshi, Taku; Kurokawa, Tsutomu; Suzuki, Harukazu; Hayashizaki, Yoshihide; Daub, Carsten O
2010-10-01
Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after knockdown of nucleotidyltransferase enzymes. The PAPD4 nucleotidyltransferase adenylates a wide range of miRNA loci, but adenylation does not appear to affect miRNA stability on a genome-wide scale. Adenine addition appears to reduce effectiveness of miRNA targeting of mRNA transcripts while deep-sequencing of RNA bound to immunoprecipitated Argonaute (AGO) subfamily proteins EIF2C1-EIF2C3 revealed substantial reduction of adenine addition in miRNA associated with EIF2C2 and EIF2C3. Our findings show 3' addition events are widespread and conserved across animals, PAPD4 is a primary miRNA adenylating enzyme, and suggest a role for 3' adenine addition in modulating miRNA effectiveness, possibly through interfering with incorporation into the RNA-induced silencing complex (RISC), a regulatory role that would complement the role of miRNA uridylation in blocking DICER1 uptake.
Burroughs, A. Maxwell; Ando, Yoshinari; de Hoon, Michiel J.L.; Tomaru, Yasuhiro; Nishibu, Takahiro; Ukekawa, Ryo; Funakoshi, Taku; Kurokawa, Tsutomu; Suzuki, Harukazu; Hayashizaki, Yoshihide; Daub, Carsten O.
2010-01-01
Animal microRNA sequences are subject to 3′ nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3′ adenylation function, we deep-sequenced RNA after knockdown of nucleotidyltransferase enzymes. The PAPD4 nucleotidyltransferase adenylates a wide range of miRNA loci, but adenylation does not appear to affect miRNA stability on a genome-wide scale. Adenine addition appears to reduce effectiveness of miRNA targeting of mRNA transcripts while deep-sequencing of RNA bound to immunoprecipitated Argonaute (AGO) subfamily proteins EIF2C1–EIF2C3 revealed substantial reduction of adenine addition in miRNA associated with EIF2C2 and EIF2C3. Our findings show 3′ addition events are widespread and conserved across animals, PAPD4 is a primary miRNA adenylating enzyme, and suggest a role for 3′ adenine addition in modulating miRNA effectiveness, possibly through interfering with incorporation into the RNA-induced silencing complex (RISC), a regulatory role that would complement the role of miRNA uridylation in blocking DICER1 uptake. PMID:20719920
Bounds on the entanglement entropy of droplet states in the XXZ spin chain
Beaud, V.; Warzel, S.
2018-01-01
We consider a class of one-dimensional quantum spin systems on the finite lattice Λ ⊂Z , related to the XXZ spin chain in its Ising phase. It includes in particular the so-called droplet Hamiltonian. The entanglement entropy of energetically low-lying states over a bipartition Λ = B ∪ Bc is investigated and proven to satisfy a logarithmic bound in terms of min{n, |B|, |Bc|}, where n denotes the maximal number of down spins in the considered state. Upon addition of any (positive) random potential, the bound becomes uniformly constant on average, thereby establishing an area law. The proof is based on spectral methods: a deterministic bound on the local (many-body integrated) density of states is derived from an energetically motivated Combes-Thomas estimate.
New approximation to the bound states of Schroedinger operators with coulomb interaction
International Nuclear Information System (INIS)
Nunez, M.A.; Izquierdo B., G.
1994-01-01
In this work, the authors present a mathematical formulation of the physical fact that the bound states of a quantum system confined into a box Ω (with impenetrable walls) are similar to those of the unconfined system, if the box Ω is sufficiently large, and it is shown how the bound states of atomic and molecular Hamiltonians can be approximated by those of the system confined for a box Ω large enough (Dirichlet eigenproblem in Ω). Thus, a method for computing bound states is obtained which has the advantage of reducing the problem to the case of compact operators. This implies that a broad class of numerical and analytic techniques used for solving the Dirichlet problem, may be applied in full strength to obtain accurate computations of energy levels, wave functions, and other physical properties of interest
On some classes of unbounded commutants of unbounded operator families
International Nuclear Information System (INIS)
Shabani, J.
1985-08-01
We consider some classes of unbounded commutants and bicommutants and we investigate their behaviour with respect to the quasi weak* topology which seems to play here the role of the weak topology for bounded operators. In particular we give some sufficient conditions in order that the bicommutants be the quasi weak* closure of the original set of operators. (author)
The synthesis of polyadenylated messenger RNA in herpes simplex type I virus infected BHK cells.
Harris, T J; Wildy, P
1975-09-01
The pattern of polyadenylated messenger RNA (mRNA) synthesis in BHK cell monolayers, infected under defined conditions with herpes simplex type I virus has been investigated by polyacrylamide gel electrophoresis or pulse-labelled RNA isolated by oligo dT-cellulose chromatography. Two classes of mRNA molecules were synthesized in infected cells; these were not detected in uninfected cells. The rate of synthesis of the larger, 18 to 30S RNA class reached a maximum soon after injection and then declined, whereas the rate of synthesis of the 7 to 11 S RNA class did not reach a maximum until much later and did not decline. In the presence of cytosine arabinoside, the rate of mRNA synthesis in infected cells was reduced but the electrophoretic pattern remained the same.
Using small RNA (sRNA) deep sequencing to understand global virus distribution in plants
Small RNAs (sRNAs), a class of regulatory RNAs, have been used to serve as the specificity determinants of suppressing gene expression in plants and animals. Next generation sequencing (NGS) uncovered the sRNA landscape in most organisms including their associated microbes. In the current study, w...
DEFF Research Database (Denmark)
Olivarius, Signe
of the transcriptome, 5’ end capture of RNA is combined with next-generation sequencing for high-throughput quantitative assessment of transcription start sites by two different methods. The methods presented here allow for functional investigation of coding as well as noncoding RNA and contribute to future...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA...
Mechanism of action of mRNA-based vaccines.
Iavarone, Carlo; O'hagan, Derek T; Yu, Dong; Delahaye, Nicolas F; Ulmer, Jeffrey B
2017-09-01
The present review summarizes the growing body of work defining the mechanisms of action of this exciting new vaccine technology that should allow rational approaches in the design of next generation mRNA vaccines. Areas covered: Bio-distribution of mRNA, localization of antigen production, role of the innate immunity, priming of the adaptive immune response, route of administration and effects of mRNA delivery systems. Expert commentary: In the last few years, the development of RNA vaccines had a fast growth, the rising number of proof will enable rational approaches to improving the effectiveness and safety of this modern class of medicine.
Models of bounded rationality under certainty
Rasouli, S.; Timmermans, H.J.P.; Rasouli, S.; Timmermans, H.J.P.
2015-01-01
Purpose This chapter reviews models of decision-making and choice under conditions of certainty. It allows readers to position the contribution of the other chapters in this book in the historical development of the topic area. Theory Bounded rationality is defined in terms of a strategy to simplify
Sobolev spaces on bounded symmetric domains
Czech Academy of Sciences Publication Activity Database
Engliš, Miroslav
Roč. 60, č. 12 ( 2015 ), s. 1712-1726 ISSN 1747-6933 Institutional support: RVO:67985840 Keywords : bounded symmetric domain * Sobolev space * Bergman space Subject RIV: BA - General Mathematics Impact factor: 0.466, year: 2015 http://www.tandfonline.com/doi/abs/10.1080/17476933. 2015 .1043910
Properties of Excitons Bound to Ionized Donors
DEFF Research Database (Denmark)
Skettrup, Torben; Suffczynski, M.; Gorzkowski, W.
1971-01-01
Binding energies, interparticle distances, oscillator strengths, and exchange corrections are calculated for the three-particle complex corresponding to an exciton bound to an ionized donor. The results are given as functions of the mass ratio of the electron and hole. Binding of the complex is o...
Bogomol'nyi bounds for cosmic strings
International Nuclear Information System (INIS)
Comtet, A.; Gibbons, G.W.; Cambridge Univ.
1987-09-01
We establish Bogomol'nyi inequalities for the deficit angle of some cylindrically symmetric asymptotically local flat (CALF) spacetimes containing cosmic strings. These results prove the stability against arbitrary cylindrical deformations of those configurations which saturate the bound. Such configurations satisfy first order equations which can, in some cases, be solved exactly
Bounding the bias of contrastive divergence learning
DEFF Research Database (Denmark)
Fischer, Anja; Igel, Christian
2011-01-01
Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k...
Bound States in the Mirror TBA
Arutyunov, G.E.; Frolov, S.; van Tongeren, S.J.
2012-01-01
The spectrum of the light-cone AdS_5 \\times S^5 superstring contains states composed of particles with complex momenta including in particular those which turn into bound states in the decompactification limit. We propose the mirror TBA description for these states. We focus on a three-particle
Harmonic maps of the bounded symmetric domains
International Nuclear Information System (INIS)
Xin, Y.L.
1994-06-01
A shrinking property of harmonic maps into R IV (2) is proved which is used to classify complete spacelike surfaces of the parallel mean curvature in R 4 2 with a reasonable condition on the Gauss image. Liouville-type theorems of harmonic maps from the higher dimensional bounded symmetric domains are also established. (author). 25 refs
Scattering theory methods for bound state problems
International Nuclear Information System (INIS)
Raphael, R.B.; Tobocman, W.
1978-01-01
For the analysis of the properties of a bound state system one may use in place of the Schroedinger equation the Lippmann-Schwinger (LS) equation for the wave function or the LS equation for the reactance operator. Use of the LS equation for the reactance operator constrains the solution to have correct asymptotic behaviour, so this approach would appear to be desirable when the bound state wave function is to be used to calculate particle transfer form factors. The Schroedinger equation based N-level analysis of the s-wave bound states of a square well is compared to the ones based on the LS equation. It is found that the LS equation methods work better than the Schroedinger equation method. The method that uses the LS equation for the wave function gives the best results for the wave functions while the method that uses the LS equation for the reactance operator gives the best results for the binding energies. The accuracy of the reactance operator based method is remarkably insensitive to changes in the oscillator constant used for the harmonic oscillator function basis set. It is also remarkably insensitive to the number of nodes in the bound state wave function. (Auth.)
Lower bounds on scintillation detector timing performance
International Nuclear Information System (INIS)
Clinthorne, N.H.; Rogers, W.L.; Hero, A.O. III.; Petrick, N.A.
1990-01-01
Fundamental method-independent limits on the timing performance of scintillation detectors are useful for identifying regimes in which either present timing methods are nearly optimal or where a considerable performance gain might be realized using better pulse processing techniques. Several types of lower bounds on mean-squared timing error (MSE) performance have been developed and applied to scintillation detectors. The simple Cramer-Rao (CR) bound can be useful in determining the limiting MSE for scintillators having a relatively high rate of photon problction such as BaF 2 and NaI(Tl); however, it tends to overestimate the achievalbe performance for scintillators with lower rates such as BGO. For this reason, alternative bounds have been developed using rate-distortion theory or by assuming that the conversion of energy to scintillation light must pass through excited states which have exponential lifetime densities. The bounds are functions of the mean scintillation pulse shape, the scintillation intensity, and photodetector characteristics; they are simple to evaluate and can be used to conveniently assess the limiting timing performance of scintillation detectors. (orig.)
Efficiency gains, bounds, and risk in finance
Sarisoy, Cisil
2015-01-01
This thesis consists of three chapters. The first chapter analyzes efficiency gains in the estimation of expected returns based on asset pricing models and examines the economic implications of such gains in portfolio allocation exercises. The second chapter provides nonparametric efficiency bounds
Book Selection, Collection Development, and Bounded Rationality.
Schwartz, Charles A.
1989-01-01
Reviews previously proposed schemes of classical rationality in book selection, describes new approaches to rational choice behavior, and presents a model of book selection based on bounded rationality in a garbage can decision process. The role of tacit knowledge and symbolic content in the selection process are also discussed. (102 references)…
Monotonicity and bounds on Bessel functions
Directory of Open Access Journals (Sweden)
Larry Landau
2000-07-01
Full Text Available survey my recent results on monotonicity with respect to order of general Bessel functions, which follow from a new identity and lead to best possible uniform bounds. Application may be made to the "spreading of the wave packet" for a free quantum particle on a lattice and to estimates for perturbative expansions.
Collisional properties of weakly bound heteronuclear dimers
Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.
2008-01-01
We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating
Bounded Rationality of Generalized Abstract Fuzzy Economies
Directory of Open Access Journals (Sweden)
Lei Wang
2014-01-01
Full Text Available By using a nonlinear scalarization technique, the bounded rationality model M for generalized abstract fuzzy economies in finite continuous spaces is established. Furthermore, by using the model M, some new theorems for structural stability and robustness to (λ,ϵ-equilibria of generalized abstract fuzzy economies are proved.
Bounded Rationality in Individual Decision Making
Camerer, Colin F.
1998-01-01
The main objectives of this paper are: (i) To give a pithy, opinionated summary of what has been learned about bounded rationality in individual decision making from experiments in economics and psychology (drawing on my 1995 Handbook of Experimental Economics chapter); and (ii) mention some promising new directions for research which would be included if that chapter were written today.
Loosely coupled class families
DEFF Research Database (Denmark)
Ernst, Erik
2001-01-01
are expressed using virtual classes seem to be very tightly coupled internally. While clients have achieved the freedom to dynamically use one or the other family, it seems that any given family contains a xed set of classes and we will need to create an entire family of its own just in order to replace one...... of the members with another class. This paper shows how to express class families in such a manner that the classes in these families can be used in many dierent combinations, still enabling family polymorphism and ensuring type safety....
International Nuclear Information System (INIS)
Zarling, D.A.; Calhoun, C.J.; Hardin, C.C.; Zarling, A.H.
1987-01-01
Specific immunochemical probes for Z-RNA were generated and characterized to search for possible Z-RNA-like double helices in cells. Z-RNA was detected in the cytoplasm of fixed protozoan cells by immunofluorescence microscopy using these anti-Z-RNA IgCs. In contrast, autoimmune or experimentally elicited anti-DNA antibodies, specifically reactive with B-DNA or Z-DNA, stained the nuclei. Pre-or nonimmune IgGs did not bind to the cells. RNase A or T1 digestion eliminated anti-Z-RNA IgG binding to cytoplasmic determinants; however, DNase I or mung bean nuclease had no effect. Doxorubicin and ethidium bromide prevented anti-Z-RNA antibody binding; however, actinomycin D, which does not bind double-stranded RNA, did not. Anti-Z-RNA immunofluorescence was specifically blocked in competition assays by synthetic Z-RNA but not Z-DNA, A-RNA, or single-stranded RNAs. Thus, some cytoplasmic sequences in fixed cells exist in the left-handed Z-RNA conformation
Sharp Bounds for Symmetric and Asymmetric Diophantine Approximation
Institute of Scientific and Technical Information of China (English)
Cornelis KRAAIKAMP; Ionica SMEETS
2011-01-01
In 2004,Tong found bounds for the approximation quality of a regular continued fraction convergent to a rational number,expressed in bounds for both the previous and next approximation.The authors sharpen his results with a geometric method and give both sharp upper and lower bounds.The asymptotic frequencies that these bounds occur are also calculated.
Bounds for the b-Chromatic Number of Subgraphs and Edge-Deleted Subgraphs
Directory of Open Access Journals (Sweden)
Francis P.
2016-11-01
Full Text Available A b-coloring of a graph G with k colors is a proper coloring of G using k colors in which each color class contains a color dominating vertex, that is, a vertex which has a neighbor in each of the other color classes. The largest positive integer k for which G has a b-coloring using k colors is the b-chromatic number b(G of G. In this paper, we obtain bounds for the b- chromatic number of induced subgraphs in terms of the b-chromatic number of the original graph. This turns out to be a generalization of the result due to R. Balakrishnan et al. [Bounds for the b-chromatic number of G−v, Discrete Appl. Math. 161 (2013 1173-1179]. Also we show that for any connected graph G and any e ∈ E(G, b(G - e ≤ b(G + -2. Further, we determine all graphs which attain the upper bound. Finally, we conclude by finding bound for the b-chromatic number of any subgraph.
Bounds on fluid permeability for viscous flow through porous media
International Nuclear Information System (INIS)
Berryman, J.G.
1985-01-01
General properties of variational bounds on Darcy's constant for slow viscous flow through porous media are studied. The bounds are also evaluated numerically for the penetrable sphere model. The bound of Doi depending on two-point correlations and the analytical bound of Weissberg and Prager give comparable results in the low density limit but the analytical bound is superior for higher densities. Prager's bound depending on three-point correlation functions is worse than the analytical bound at low densities but better (although comparable to it) at high densities. A procedure for methodically improving Prager's three point bound is presented. By introducing a Gaussian trial function, the three-point bound is improved by an order of magnitude for moderate values of porosity. The new bounds are comparable in magnitude to the Kozeny--Carman empirical relation for porous materials
Point-like bounding chains in open Gromov-Witten theory
Solomon, Jake P.; Tukachinsky, Sara B.
2016-01-01
We use $A_\\infty$ algebras to define open Gromov-Witten invariants with both boundary and interior constraints, associated to a Lagrangian submanifold $L\\subset X$ of arbitrary odd dimension. The boundary constraints are bounding chains, which are shown to behave like points. The interior constraints are arbitrary even degree classes in the cohomology of $X$ relative to $L.$ We show the invariants satisfy analogs of the axioms of closed Gromov-Witten theory. Our definition of invariants depen...
Bounds of Double Integral Dynamic Inequalities in Two Independent Variables on Time Scales
Directory of Open Access Journals (Sweden)
S. H. Saker
2011-01-01
Full Text Available Our aim in this paper is to establish some explicit bounds of the unknown function in a certain class of nonlinear dynamic inequalities in two independent variables on time scales which are unbounded above. These on the one hand generalize and on the other hand furnish a handy tool for the study of qualitative as well as quantitative properties of solutions of partial dynamic equations on time scales. Some examples are considered to demonstrate the applications of the results.
New insights into siRNA amplification and RNAi.
Zhang, Chi; Ruvkun, Gary
2012-08-01
In the nematode Caenorhabditis elegans (C. elegans), gene inactivation by RNA interference can achieve remarkable potency due to the amplification of initial silencing triggers by RNA-dependent RNA polymerases (RdRPs). RdRPs catalyze the biogenesis of an abundant species of secondary small interfering RNAs (siRNAs) using the target mRNA as template. The interaction between primary siRNAs derived from the exogenous double-stranded RNA (dsRNA) trigger and the target mRNA is required for the recruitment of RdRPs. Other genetic requirements for RdRP activities have not been characterized. Recent studies have identified the RDE-10/RDE-11 complex which interacts with the primary siRNA bound target mRNA and acts upstream of the RdRPs. rde-10 and rde-11 mutants show an RNAi defective phenotype because the biogenesis of secondary siRNAs is completely abolished. In addition, the RDE-10/RDE-11 complex plays a similar role in the endogenous RNAi pathway for the biogenesis of a subset of siRNAs targeting recently acquired, duplicated genes.
Probing binding hot spots at protein-RNA recognition sites.
Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad
2016-01-29
We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Upper bounds for reversible circuits based on Young subgroups
DEFF Research Database (Denmark)
Abdessaied, Nabila; Soeken, Mathias; Thomsen, Michael Kirkedal
2014-01-01
We present tighter upper bounds on the number of Toffoli gates needed in reversible circuits. Both multiple controlled Toffoli gates and mixed polarity Toffoli gates have been considered for this purpose. The calculation of the bounds is based on a synthesis approach based on Young subgroups...... that results in circuits using a more generalized gate library. Starting from an upper bound for this library we derive new bounds which improve the existing bound by around 77%....
TFIIIC bound DNA elements in nuclear organization and insulation.
Kirkland, Jacob G; Raab, Jesse R; Kamakaka, Rohinton T
2013-01-01
tRNA genes (tDNAs) have been known to have barrier insulator function in budding yeast, Saccharomyces cerevisiae, for over a decade. tDNAs also play a role in genome organization by clustering at sites in the nucleus and both of these functions are dependent on the transcription factor TFIIIC. More recently TFIIIC bound sites devoid of pol III, termed Extra-TFIIIC sites (ETC) have been identified in budding yeast and these sites also function as insulators and affect genome organization. Subsequent studies in Schizosaccharomyces pombe showed that TFIIIC bound sites were insulators and also functioned as Chromosome Organization Clamps (COC); tethering the sites to the nuclear periphery. Very recently studies have moved to mammalian systems where pol III genes and their associated factors have been investigated in both mouse and human cells. Short interspersed nuclear elements (SINEs) that bind TFIIIC, function as insulator elements and tDNAs can also function as both enhancer - blocking and barrier insulators in these organisms. It was also recently shown that tDNAs cluster with other tDNAs and with ETCs but not with pol II transcribed genes. Intriguingly, TFIIIC is often found near pol II transcription start sites and it remains unclear what the consequences of TFIIIC based genomic organization are and what influence pol III factors have on pol II transcribed genes and vice versa. In this review we provide a comprehensive overview of the known data on pol III factors in insulation and genome organization and identify the many open questions that require further investigation. This article is part of a Special Issue entitled: Transcription by Odd Pols. Copyright © 2012 Elsevier B.V. All rights reserved.
Setting Optimal Bounds on Risk in Asset Allocation - a Convex Program
Directory of Open Access Journals (Sweden)
James E. Falk
2002-10-01
Full Text Available The 'Portfolio Selection Problem' is traditionally viewed as selecting a mix of investment opportunities that maximizes the expected return subject to a bound on risk. However, in reality, portfolios are made up of a few 'asset classes' that consist of similar opportunities. The asset classes are managed by individual `sub-managers', under guidelines set by an overall portfolio manager. Once a benchmark (the `strategic' allocation has been set, an overall manager may choose to allow the sub-managers some latitude in which opportunities make up the classes. He may choose some overall bound on risk (as measured by the variance and wish to set bounds that constrain the submanagers. Mathematically we show that the problem is equivalent to finding a hyper-rectangle of maximal volume within an ellipsoid. It is a convex program, albeit with potentially a large number of constraints. We suggest a cutting plane algorithm to solve the problem and include computational results on a set of randomly generated problems as well as a real-world problem taken from the literature.
Yan, Yumeng; Wen, Zeyu; Zhang, Di; Huang, Sheng-You
2018-05-18
RNA-RNA interactions play fundamental roles in gene and cell regulation. Therefore, accurate prediction of RNA-RNA interactions is critical to determine their complex structures and understand the molecular mechanism of the interactions. Here, we have developed a physics-based double-iterative strategy to determine the effective potentials for RNA-RNA interactions based on a training set of 97 diverse RNA-RNA complexes. The double-iterative strategy circumvented the reference state problem in knowledge-based scoring functions by updating the potentials through iteration and also overcame the decoy-dependent limitation in previous iterative methods by constructing the decoys iteratively. The derived scoring function, which is referred to as DITScoreRR, was evaluated on an RNA-RNA docking benchmark of 60 test cases and compared with three other scoring functions. It was shown that for bound docking, our scoring function DITScoreRR obtained the excellent success rates of 90% and 98.3% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 63.3% and 71.7% for van der Waals interactions, 45.0% and 65.0% for ITScorePP, and 11.7% and 26.7% for ZDOCK 2.1, respectively. For unbound docking, DITScoreRR achieved the good success rates of 53.3% and 71.7% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 13.3% and 28.3% for van der Waals interactions, 11.7% and 26.7% for our ITScorePP, and 3.3% and 6.7% for ZDOCK 2.1, respectively. DITScoreRR also performed significantly better in ranking decoys and obtained significantly higher score-RMSD correlations than the other three scoring functions. DITScoreRR will be of great value for the prediction and design of RNA structures and RNA-RNA complexes.
Targeted siRNA Delivery and mRNA Knockdown Mediated by Bispecific Digoxigenin-binding Antibodies
Directory of Open Access Journals (Sweden)
Britta Schneider
2012-01-01
Full Text Available Bispecific antibodies (bsAbs that bind to cell surface antigens and to digoxigenin (Dig were used for targeted small interfering RNA (siRNA delivery. They are derivatives of immunoglobulins G (IgGs that bind tumor antigens, such as Her2, IGF1-R, CD22, and LeY, with stabilized Dig-binding variable domains fused to the C-terminal ends of the heavy chains. siRNA that was digoxigeninylated at its 3′end was bound in a 2:1 ratio to the bsAbs. These bsAb–siRNA complexes delivered siRNAs specifically to cells that express the corresponding antigen as demonstrated by flow cytometry and confocal microscopy. The complexes internalized into endosomes and Dig-siRNAs separated from bsAbs, but Dig-siRNA was not released into the cytoplasm; bsAb-targeting alone was thus not sufficient for effective mRNA knockdown. This limitation was overcome by formulating the Dig-siRNA into nanoparticles consisting of dynamic polyconjugates (DPCs or into lipid-based nanoparticles (LNPs. The resulting complexes enabled bsAb-targeted siRNA-specific messenger RNA (mRNA knockdown with IC50 siRNA values in the low nanomolar range for a variety of bsAbs, siRNAs, and target cells. Furthermore, pilot studies in mice bearing tumor xenografts indicated mRNA knockdown in endothelial cells following systemic co-administration of bsAbs and siRNA formulated in LNPs that were targeted to the tumor vasculature.
A wheelchair-bound child integration in the class supported by dance workshops
Tegelj, Anja
2016-01-01
Expressed through the rhythm a dance is a body talk, a beauty of the art, even a sport where two or more bodies are synchronously intertwined. Dance liberates body and soul, it connects and brings happiness. Since 1996 Slovenia encourages physically disabled children to enroll in regular learning programs in primary schools. While it sets significant challenges to the educators it contributes greatly to a better acceptance of differences between children. For successful integration of ...
International Nuclear Information System (INIS)
Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi
2010-01-01
The RNA-binding protein Hfq from B. subtilis was crystallized using the hanging-drop vapour-diffusion method in two crystal forms that belonged to space groups I422 and F222; diffraction data were collected to 2.2 Å resolution from both forms. The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq–RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq–RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 Å, while the type 2 Hfq–RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 Å. Diffraction data were collected to a resolution of 2.20 Å from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis
Modelling toehold-mediated RNA strand displacement.
Šulc, Petr; Ouldridge, Thomas E; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A
2015-03-10
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
DEFF Research Database (Denmark)
Harrits, Gitte Sommer
2013-01-01
Even though contemporary discussions of class have moved forward towards recognizing a multidimensional concept of class, empirical analyses tend to focus on cultural practices in a rather narrow sense, that is, as practices of cultural consumption or practices of education. As a result......, discussions within political sociology have not yet utilized the merits of a multidimensional conception of class. In light of this, the article suggests a comprehensive Bourdieusian framework for class analysis, integrating culture as both a structural phenomenon co-constitutive of class and as symbolic...... practice. Further, the article explores this theoretical framework in a multiple correspondence analysis of a Danish survey, demonstrating how class and political practices are indeed homologous. However, the analysis also points at several elements of field autonomy, and the concluding discussion...
Bhanot, Gyan [Princeton, NJ; Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton On Hudson, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Takken, Todd E [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY
2009-09-08
Class network routing is implemented in a network such as a computer network comprising a plurality of parallel compute processors at nodes thereof. Class network routing allows a compute processor to broadcast a message to a range (one or more) of other compute processors in the computer network, such as processors in a column or a row. Normally this type of operation requires a separate message to be sent to each processor. With class network routing pursuant to the invention, a single message is sufficient, which generally reduces the total number of messages in the network as well as the latency to do a broadcast. Class network routing is also applied to dense matrix inversion algorithms on distributed memory parallel supercomputers with hardware class function (multicast) capability. This is achieved by exploiting the fact that the communication patterns of dense matrix inversion can be served by hardware class functions, which results in faster execution times.
Miyamoto, Yuri
2017-12-01
A large body of research in Western cultures has demonstrated the psychological and health effects of social class. This review outlines a cultural psychological approach to social stratification by comparing psychological and health manifestations of social class across Western and East Asian cultures. These comparisons suggest that cultural meaning systems shape how people make meaning and respond to material/structural conditions associated with social class, thereby leading to culturally divergent manifestations of social class. Specifically, unlike their counterparts in Western cultures, individuals of high social class in East Asian cultures tend to show high conformity and other-orientated psychological attributes. In addition, cultures differ in how social class impacts health (i.e. on which bases, through which pathways, and to what extent). Copyright © 2017 Elsevier Ltd. All rights reserved.
Semantic Analysis of Virtual Classes and Nested Classes
DEFF Research Database (Denmark)
Madsen, Ole Lehrmann
1999-01-01
Virtual classes and nested classes are distinguishing features of BETA. Nested classes originated from Simula, but until recently they have not been part of main stream object- oriented languages. C++ has a restricted form of nested classes and they were included in Java 1.1. Virtual classes...... classes and parameterized classes have been made. Although virtual classes and nested classes have been used in BETA for more than a decade, their implementation has not been published. The purpose of this paper is to contribute to the understanding of virtual classes and nested classes by presenting...
DEFF Research Database (Denmark)
Faber, Stine Thidemann; Prieur, Annick
This paper asks how class can have importance in one of the worlds’ most equal societies: Denmark. The answer is that class here appears in disguised forms. The field under study is a city, Aalborg, in the midst of transition from a stronghold of industrialism to a post industrial economy. The pa....... The paper also raises questions about how sociological discourses may contribute to the veiling of class....
Optima and bounds for irreversible thermodynamic processes
International Nuclear Information System (INIS)
Hoffmann, K.H.
1990-01-01
In this paper bounds and optima for irreversible thermodynamic processes and their application in different fields are discussed. The tools of finite time thermodynamics are presented and especially optimal control theory is introduced. These methods are applied to heat engines, including models of the Diesel engine and a light-driven engine. Further bounds for irreversible processes are introduced, discussing work deficiency and its relation to thermodynamic length. Moreover the problem of dissipation in systems composed of several subsystems is studied. Finally, the methods of finite time thermodynamics are applied to thermodynamic processes described on a more microscopic level. The process used as an example is simulated annealing. It is shown how optimal control theory is applied to find the optimal cooling schedule for this important stochastic optimization method
Bounded excursion stable gravastars and black holes
Energy Technology Data Exchange (ETDEWEB)
Rocha, P [Instituto de Fisica, Universidade Federal Fluminense, Avenida Litoranea, s/n, Boa Viagem 24210-340, Niteroi, RJ (Brazil); Miguelote, A Y; Chan, R [Coordenacao de Astronomia e Astrofisica, Observatorio Nacional, Rua General Jose Cristino, 77, Sao Cristovao 20921-400, Rio de Janeiro, RJ (Brazil); Da Silva, M F; Wang, Anzhong [Departamento de Fisica Teorica, Instituto de Fisica, Universidade do Estado do Rio de Janeiro, Rua Sao Francisco Xavier 524, Maracana 20550-900, Rio de Janeiro-RJ (Brazil); Santos, N O, E-mail: pedrosennarocha@gmail.com, E-mail: yasuda@on.br, E-mail: chan@on.br, E-mail: mfasnic@gmail.com, E-mail: N.O.Santos@qmul.ac.uk, E-mail: anzhong_wang@baylor.edu [LERMA/CNRS-FRE 2460, Universite Pierre et Marie Curie, ERGA, Boite 142, 4 Place Jussieu, 75005 Paris Cedex 05 (France)
2008-06-15
Dynamical models of prototype gravastars were constructed in order to study their stability. The models are the Visser-Wiltshire three-layer gravastars, in which an infinitely thin spherical shell of stiff fluid divides the whole spacetime into two regions, where the internal region is de Sitter, and the external one is Schwarzschild. It is found that in some cases the models represent the 'bounded excursion' stable gravastars, where the thin shell is oscillating between two finite radii, while in other cases they collapse until the formation of black holes occurs. In the phase space, the region for the 'bounded excursion' gravastars is very small in comparison to that of black holes, but not empty. Therefore, although the possibility of the existence of gravastars cannot be excluded from such dynamical models, our results indicate that, even if gravastars do indeed exist, that does not exclude the possibility of the existence of black holes.
Optimal Bounds in Parametric LTL Games
Directory of Open Access Journals (Sweden)
Martin Zimmermann
2011-06-01
Full Text Available We consider graph games of infinite duration with winning conditions in parameterized linear temporal logic, where the temporal operators are equipped with variables for time bounds. In model checking such specifications were introduced as "PLTL" by Alur et al. and (in a different version called "PROMPT-LTL" by Kupferman et al.. We present an algorithm to determine optimal variable valuations that allow a player to win a game. Furthermore, we show how to determine whether a player wins a game with respect to some, infinitely many, or all valuations. All our algorithms run in doubly-exponential time; so, adding bounded temporal operators does not increase the complexity compared to solving plain LTL games.
Asymptotic Sharpness of Bounds on Hypertrees
Directory of Open Access Journals (Sweden)
Lin Yi
2017-08-01
Full Text Available The hypertree can be defined in many different ways. Katona and Szabó introduced a new, natural definition of hypertrees in uniform hypergraphs and investigated bounds on the number of edges of the hypertrees. They showed that a k-uniform hypertree on n vertices has at most (nk−1$\\left( {\\matrix{n \\cr {k - 1} } } \\right$ edges and they conjectured that the upper bound is asymptotically sharp. Recently, Szabó verified that the conjecture holds by recursively constructing an infinite sequence of k-uniform hypertrees and making complicated analyses for it. In this note we give a short proof of the conjecture by directly constructing a sequence of k-uniform k-hypertrees.
A holographic bound for D3-brane
Energy Technology Data Exchange (ETDEWEB)
Momeni, Davood; Myrzakul, Aizhan; Myrzakulov, Ratbay [Eurasian National University, Eurasian International Center for Theoretical Physics, Astana (Kazakhstan); Eurasian National University, Department of General Theoretical Physics, Astana (Kazakhstan); Faizal, Mir [University of British Columbia-Okanagan, Irving K. Barber School of Arts and Sciences, Kelowna, BC (Canada); University of Lethbridge, Department of Physics and Astronomy, Lethbridge, AB (Canada); Bahamonde, Sebastian [University College London, Department of Mathematics, London (United Kingdom)
2017-06-15
In this paper, we will regularize the holographic entanglement entropy, holographic complexity and fidelity susceptibility for a configuration of D3-branes. We will also study the regularization of the holographic complexity from the action for a configuration of D3-branes. It will be demonstrated that for a spherical shell of D3-branes the regularized holographic complexity is always greater than or equal to the regularized fidelity susceptibility. Furthermore, we will also demonstrate that the regularized holographic complexity is related to the regularized holographic entanglement entropy for this system. Thus, we will obtain a holographic bound involving regularized holographic complexity, regularized holographic entanglement entropy and regularized fidelity susceptibility of a configuration of D3-brane. We will also discuss a bound for regularized holographic complexity from action, for a D3-brane configuration. (orig.)
Bound states in weakly disordered spin ladders
Energy Technology Data Exchange (ETDEWEB)
Arlego, M. [Departamento de Fisica, Universidad Nacional de La Plata, CC 67 (1900) La Plata (Argentina)]. E-mail: arlego@venus.fisica.unlp.edu.ar; Brenig, W. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Cabra, D.C. [Laboratoire de Physique Theorique, Universite Louis Pasteur Strasbourg (France); Heidrich-Meisner, F. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Honecker, A. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Rossini, G. [Departamento de Fisica, Universidad Nacional de La Plata, CC 67 (1900) La Plata (Argentina)
2005-04-30
We study the appearance of bound states in the spin gap of spin-12 ladders induced by weak bond disorder. Starting from the strong-coupling limit, i.e., the limit of weakly coupled dimers, we perform a projection on the single-triplet subspace and derive the position of bound states for the single impurity problem of one modified coupling as well as for small impurity clusters. The case of a finite concentration of impurities is treated with the coherent-potential approximation (CPA) in the strong-coupling limit and compared with numerical results. Further, we analyze the details in the structure of the density of states and relate their origin to the influence of impurity clusters.
Entanglement detection with bounded reference frames
International Nuclear Information System (INIS)
Costa, Fabio; Brukner, Caslav; Harrigan, Nicholas; Rudolph, Terry
2009-01-01
Quantum experiments usually assume the existence of perfect, classical reference frames (RFs), which allow for the specification of measurement settings (e.g. orientation of the Stern-Gerlach magnet in spin measurements) with arbitrary precision. If the RFs are 'bounded' (i.e. quantum systems themselves, having a finite number of degrees of freedom), only limited precision can be attained. Using spin coherent states as bounded RFs, we have found the minimum size needed for them to violate local realism for entangled spin systems. For composite systems of spin 1/2 particles, RFs of very small size are sufficient for the violation; however, to see this violation for macroscopic entangled spins, the size of the RF must be at least quadratically larger than that of the spins. The unavailability of such RFs gives a possible explanation for the non-observance of violation of local realism in everyday experience.
A proof of the conformal collider bounds
Energy Technology Data Exchange (ETDEWEB)
Hofman, Diego M. [Institute for Theoretical Physics, University of Amsterdam, Science Park 904, Postbus 94485, 1090 GL, Amsterdam (Netherlands); Li, Daliang [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Meltzer, David [Department of Physics, Yale University, New Haven, CT 06511 (United States); Poland, David [Department of Physics, Yale University, New Haven, CT 06511 (United States); School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540 (United States); Rejon-Barrera, Fernando [Institute for Theoretical Physics, University of Amsterdam, Science Park 904, Postbus 94485, 1090 GL, Amsterdam (Netherlands)
2016-06-20
In this paper, we prove that the “conformal collider bounds” originally proposed in http://dx.doi.org/10.1088/1126-6708/2008/05/012 hold for any unitary parity-preserving conformal field theory (CFT) with a unique stress tensor in dimensions d≥3. In particular this implies that the ratio of central charges for a unitary 4d CFT lies in the interval (31/18)≥(a/c)≥(1/3). For superconformal theories this is further reduced to (3/2)≥(a/c)≥(1/2). The proof relies only on CFT first principles — in particular, bootstrap methods — and thus constitutes the first complete field theory proof of these bounds. We further elaborate on similar bounds for non-conserved currents and relate them to results obtained recently from deep inelastic scattering.
Bounded-Degree Approximations of Stochastic Networks
Energy Technology Data Exchange (ETDEWEB)
Quinn, Christopher J.; Pinar, Ali; Kiyavash, Negar
2017-06-01
We propose algorithms to approximate directed information graphs. Directed information graphs are probabilistic graphical models that depict causal dependencies between stochastic processes in a network. The proposed algorithms identify optimal and near-optimal approximations in terms of Kullback-Leibler divergence. The user-chosen sparsity trades off the quality of the approximation against visual conciseness and computational tractability. One class of approximations contains graphs with speci ed in-degrees. Another class additionally requires that the graph is connected. For both classes, we propose algorithms to identify the optimal approximations and also near-optimal approximations, using a novel relaxation of submodularity. We also propose algorithms to identify the r-best approximations among these classes, enabling robust decision making.
Recent advances in bound state quantum electrodynamics
International Nuclear Information System (INIS)
Brodsky, S.J.; Lepage, G.P.
1977-06-01
Recent developments are reviewed in four areas of computational quantum electrodynamics: a new relativistic two-body formalism equal in rigor to the Bethe-Salpeter formalism but with strong calculational advantages is discussed; recent work on the computation of the decay rate of bound systems (positronium in particular) is presented; limits on possible composite structure of leptons are discussed; a new multidimensional integration program ('VEGAS') suitable for higher order calculations is presented
Bounding probabilistic safety assessment probabilities by reality
International Nuclear Information System (INIS)
Fragola, J.R.; Shooman, M.L.
1991-01-01
The investigation of the failure in systems where failure is a rare event makes the continual comparisons between the developed probabilities and empirical evidence difficult. The comparison of the predictions of rare event risk assessments with historical reality is essential to prevent probabilistic safety assessment (PSA) predictions from drifting into fantasy. One approach to performing such comparisons is to search out and assign probabilities to natural events which, while extremely rare, have a basis in the history of natural phenomena or human activities. For example the Segovian aqueduct and some of the Roman fortresses in Spain have existed for several millennia and in many cases show no physical signs of earthquake damage. This evidence could be used to bound the probability of earthquakes above a certain magnitude to less than 10 -3 per year. On the other hand, there is evidence that some repetitive actions can be performed with extremely low historical probabilities when operators are properly trained and motivated, and sufficient warning indicators are provided. The point is not that low probability estimates are impossible, but continual reassessment of the analysis assumptions, and a bounding of the analysis predictions by historical reality. This paper reviews the probabilistic predictions of PSA in this light, attempts to develop, in a general way, the limits which can be historically established and the consequent bounds that these limits place upon the predictions, and illustrates the methodology used in computing such limits. Further, the paper discusses the use of empirical evidence and the requirement for disciplined systematic approaches within the bounds of reality and the associated impact on PSA probabilistic estimates
Closed form bound-state perturbation theory
Directory of Open Access Journals (Sweden)
Ollie J. Rose
1980-01-01
Full Text Available The perturbed Schrödinger eigenvalue problem for bound states is cast into integral form using Green's Functions. A systematic algorithm is developed and applied to the resulting equation giving rise to approximate solutions expressed as functions of the given perturbation parameter. As a by-product, convergence radii for the traditional Rayleigh-Schrödinger and Brillouin-Wigner perturbation theories emerge in a natural way.
Exact BPS bound for noncommutative baby Skyrmions
International Nuclear Information System (INIS)
Domrin, Andrei; Lechtenfeld, Olaf; Linares, Román; Maceda, Marco
2013-01-01
The noncommutative baby Skyrme model is a Moyal deformation of the two-dimensional sigma model plus a Skyrme term, with a group-valued or Grassmannian target. Exact abelian solitonic solutions have been identified analytically in this model, with a singular commutative limit. Inside any given Grassmannian, we establish a BPS bound for the energy functional, which is saturated by these baby Skyrmions. This asserts their stability for unit charge, as we also test in second-order perturbation theory
The organically bound tritium: an analyst vision
International Nuclear Information System (INIS)
Ansoborlo, E.; Baglan, N.
2009-01-01
The authors report the work of a work group on tritium analysis. They recall the different physical forms of tritium: gas (HT, hydrogen-tritium), water vapour (HTO or tritiated water) or methane (CH3T), but also in organic compounds (OBT, organically bound tritium) which are either exchangeable or non-exchangeable. They evoke measurement techniques and methods, notably to determine the tritium volume activity. They discuss the possibilities to analyse and distinguish exchangeable and non-exchangeable OBTs
New approach to calculate bound state eigenvalues
International Nuclear Information System (INIS)
Gerck, E.; Gallas, J.A.C.
1983-01-01
A method of solving the radial Schrodinger equation for bound states is discussed. The method is based on a new piecewise representation of the second derivative operator on a set of functions that obey the boundary conditions. This representation is trivially diagonalised and leads to closed form expressions of the type E sub(n)=E(ab+b+c/n+...) for the eigenvalues. Examples are given for the power-law and logarithmic potentials. (Author) [pt
A sorting network in bounded arithmetic
Czech Academy of Sciences Publication Activity Database
Jeřábek, Emil
2011-01-01
Roč. 162, č. 4 (2011), s. 341-355 ISSN 0168-0072 R&D Projects: GA AV ČR IAA1019401; GA MŠk(CZ) 1M0545 Institutional research plan: CEZ:AV0Z10190503 Keywords : bounded arithmetic * sorting network * proof complexity * monotone sequent calculus Subject RIV: BA - General Mathematics Impact factor: 0.450, year: 2011 http://www.sciencedirect.com/science/article/pii/S0168007210001272
Heterogeneity, Bounded Rationality and Market Dysfunctionality
Xue-Zhong He; Lei Shi
2008-01-01
As the main building blocks of the modern finance theory, homogeneity and rational expectation have faced difficulty in explaining many market anomalies, stylized factors, and market inefficiency in empirical studies. As a result, heterogeneity and bounded rationality have been used as an alterative paradigm of asset price dynamics and this paradigm has been widely recognized recently in both academic and financial market practitioners. Within the framework of Chiarella, Dieci and He (2006a, ...
Kinetic simulation on collisional bounded plasma
International Nuclear Information System (INIS)
Zhu, S.P.; Sato, Tetsuya; Tomita, Yukihiro; Hatori, Tadatsugu
1998-01-01
A self-consistent kinetic simulation model on collisional bounded plasma is presented. The electric field is given by solving Poisson equation and collisions among particles (including charged particles and neutral particles) are included. The excitation and ionization of neutral particle, and recombination are also contained in the present model. The formation of potential structure near a boundary for a discharge system was used as an application of this model. (author)
RNA decay by messenger RNA interferases
DEFF Research Database (Denmark)
Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo
2008-01-01
Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mR...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs.......Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...
Analysis of the organically bound tritium
International Nuclear Information System (INIS)
Baglan, N.; Alanic, G.
2011-01-01
In environmental samples, tritium is very often combined with the fraction of bulk water accumulated in the sample but also in the form of organically bound tritium. When the tritium is organically bound, 2 forms can coexist: the exchangeable fraction and the non-exchangeable fraction. The analysis of the different forms of tritium present in the sample is necessary to assess the sanitary hazards due to tritium. The total tritium is obtained from the analysis of the water released when the fresh sample is burnt while the organically bound tritium is obtained from the analysis of the water released when the dry extract of the sample is burnt. The measurement of the exchangeable fraction and the non-exchangeable fraction requires an additional stage of labile exchange. The exchangeable fraction is determined from the analysis of the water released during the labile exchange and the non-exchangeable fraction is determined from the water released during the combustion of the dry extract of the labile exchange
Search for quasi bound η mesons
International Nuclear Information System (INIS)
Machner, H
2015-01-01
The search for a quasi bound η meson in atomic nuclei is reviewed. This tentative state is studied theoretically as well as experimentally. The theory starts from elastic η nucleon scattering which is derived from production data within some models. From this interaction the η nucleus interaction is derived. Model calculations predict binding energies and widths of the quasi bound state. Another method is to derive the η nucleus interaction from excitation functions of η production experiments. The s wave interaction is extracted from such data via final state interaction (FSI) theorem. We give the derivation of s wave amplitudes in partial wave expansion and in helicity amplitudes and their relation to observables. Different experiments extracting the FSI are discussed as are production experiments. So far only three experiments give evidence for the existence of the quasi bound state: a pion double charge exchange experiment, an effective mass measurement, and a transfer reaction at recoil free kinematics with observation of the decay of the state. (topical review)
Lower bounds for the minimum distance of algebraic geometry codes
DEFF Research Database (Denmark)
Beelen, Peter
, such as the Goppa bound, the Feng-Rao bound and the Kirfel-Pellikaan bound. I will finish my talk by giving several examples. Especially for two-point codes, the generalized order bound is fairly easy to compute. As an illustration, I will indicate how a lower bound can be obtained for the minimum distance of some...... description of these codes in terms of order domains has been found. In my talk I will indicate how one can use the ideas behind the order bound to obtain a lower bound for the minimum distance of any AG-code. After this I will compare this generalized order bound with other known lower bounds...
Antisense RNA mediated inhibition of granule - bound starch synthase gene expression in potato
Kuipers, A.
1994-01-01
Potato starch and its derivatives are widely used in several fields of application. The manufacturing of most products requires the modification of native starch with respect to, for example, viscosity and physical stability. In addition to the currently used physical, chemical and
Nuclear RNA sequencing of the mouse erythroid cell transcriptome.
Directory of Open Access Journals (Sweden)
Jennifer A Mitchell
Full Text Available In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.
Global RNA association with the transcriptionally active chromosome of chloroplasts.
Lehniger, Marie-Kristin; Finster, Sabrina; Melonek, Joanna; Oetke, Svenja; Krupinska, Karin; Schmitz-Linneweber, Christian
2017-10-01
Processed chloroplast RNAs are co-enriched with preparations of the chloroplast transcriptionally active chromosome. Chloroplast genomes are organized as a polyploid DNA-protein structure called the nucleoid. Transcriptionally active chloroplast DNA together with tightly bound protein factors can be purified by gel filtration as a functional entity called the transcriptionally active chromosome (TAC). Previous proteomics analyses of nucleoids and of TACs demonstrated a considerable overlap in protein composition including RNA binding proteins. Therefore the RNA content of TAC preparations from Nicotiana tabacum was determined using whole genome tiling arrays. A large number of chloroplast RNAs was found to be associated with the TAC. The pattern of RNAs attached to the TAC consists of RNAs produced by different chloroplast RNA polymerases and differs from the pattern of RNA found in input controls. An analysis of RNA splicing and RNA editing of selected RNA species demonstrated that TAC-associated RNAs are processed to a similar extent as the RNA in input controls. Thus, TAC fractions contain a specific subset of the processed chloroplast transcriptome.
Tablante, Courtney B.; Fiske, Susan T.
2015-01-01
Discussing socioeconomic status in college classes can be challenging. Both teachers and students feel uncomfortable, yet social class matters more than ever. This is especially true, given increased income inequality in the United States and indications that higher education does not reduce this inequality as much as many people hope. Resources…
Generalized Fourier transforms classes
DEFF Research Database (Denmark)
Berntsen, Svend; Møller, Steen
2002-01-01
The Fourier class of integral transforms with kernels $B(\\omega r)$ has by definition inverse transforms with kernel $B(-\\omega r)$. The space of such transforms is explicitly constructed. A slightly more general class of generalized Fourier transforms are introduced. From the general theory...
Taylor, Lewis A., III
2012-01-01
An accessible business school population of undergraduate students was investigated in three independent, but related studies to determine effects on grades due to cutting class and failing to take advantage of optional reviews and study quizzes. It was hypothesized that cutting classes harms exam scores, attending preexam reviews helps exam…
Topology of RNA-RNA interaction structures
DEFF Research Database (Denmark)
Andersen, Jørgen Ellegaard; Huang, Fenix Wenda; Penner, Robert
2012-01-01
Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exist...
Dauns, John
2006-01-01
Because traditional ring theory places restrictive hypotheses on all submodules of a module, its results apply only to small classes of already well understood examples. Often, modules with infinite Goldie dimension have finite-type dimension, making them amenable to use with type dimension, but not Goldie dimension. By working with natural classes and type submodules (TS), Classes of Modules develops the foundations and tools for the next generation of ring and module theory. It shows how to achieve positive results by placing restrictive hypotheses on a small subset of the complement submodules, Furthermore, it explains the existence of various direct sum decompositions merely as special cases of type direct sum decompositions. Carefully developing the foundations of the subject, the authors begin by providing background on the terminology and introducing the different module classes. The modules classes consist of torsion, torsion-free, s[M], natural, and prenatural. They expand the discussion by exploring...
Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages.
Yang, Xianbin
2017-09-18
The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.
Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi
2010-05-01
The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq-RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq-RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 A, while the type 2 Hfq-RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 A. Diffraction data were collected to a resolution of 2.20 A from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis.
Molecular architecture of protein-RNA recognition sites.
Barik, Amita; C, Nithin; Pilla, Smita P; Bahadur, Ranjit Prasad
2015-01-01
The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.
Development of a new method to identify aminoacylated RNA
Directory of Open Access Journals (Sweden)
Wang Ji
2014-02-01
Full Text Available A RT-PCR method is developed to isolate RNA aminoacylated on their 3’ end from large pools of RNA. The method is being applied in two separate projects. We are interested in isolating a new class of ribozymes that could successively catalyze the two chemical reactions leading to their own 3’ aminoacylation (ATP activation of an amino acid followed by 3' esterification of the RNA. The catalysis of each of the two reactions has independently been demonstrated for some RNA isolated with the SELEX methodology [1-2]. However, the coupling of both reactions on a same molecule has not been achieved yet. The identification of these still hypothetical ribozymes may help understand how the former translation system started in the absence of the aminoacyltRNA Synthetase, which catalyzes the above two reactions on tRNA in modern cells. In another project, we would like to identify the whole repertoire of aminoacylated RNA (the “aminoacylome” in cells. There are strong indications that other RNA besides tRNA and tmRNA may be aminoacylated for biological purposes [3-4].
The origin and effect of small RNA signaling in plants
Directory of Open Access Journals (Sweden)
Jean-Sébastien eParent
2012-08-01
Full Text Available Given their sessile condition, land plants need to integrate environmental cues rapidly and send signal throughout the organism to modify their metabolism accordingly. Small RNA (sRNA molecules are among the messengers that plant cells use to carry such signals. These molecules originate from fold-back stem-loops transcribed from endogenous loci or from perfect double-stranded RNA produced through the action of RNA-dependent RNA polymerases. Once produced, sRNAs associate with Argonaute and other proteins to form the RNA-induced silencing complex (RISC that executes silencing of complementary RNA molecules. Depending on the nature of the RNA target and the Argonaute protein involved, RISC triggers either DNA methylation and chromatin modification (leading to transcriptional gene silencing, TGS or RNA cleavage or translational inhibition (leading to post-transcriptional gene silencing, PTGS. In some cases, sRNAs move to neighboring cells and/or to the vascular tissues for long-distance trafficking. Many genes are involved in the biogenesis of sRNAs and recent studies have shown that both their origin and their protein partners have great influence on their activity and range. Here we summarize the work done to uncover the mode of action of the different classes of small RNA with special emphasis on their movement and how plants can take advantage of their mobility. We also review the various genetic requirements needed for production, movement and perception of the silencing signal.
Optimal Control for a Class of Chaotic Systems
Directory of Open Access Journals (Sweden)
Jianxiong Zhang
2012-01-01
Full Text Available This paper proposes the optimal control methods for a class of chaotic systems via state feedback. By converting the chaotic systems to the form of uncertain piecewise linear systems, we can obtain the optimal controller minimizing the upper bound on cost function by virtue of the robust optimal control method of piecewise linear systems, which is cast as an optimization problem under constraints of bilinear matrix inequalities (BMIs. In addition, the lower bound on cost function can be achieved by solving a semidefinite programming (SDP. Finally, numerical examples are given to illustrate the results.
RNA Localization in Astrocytes
DEFF Research Database (Denmark)
Thomsen, Rune
2012-01-01
, regulation of the blood brain barrier and glial scar tissue formation. Despite the involvement in various CNS functions only a limited number of studies have addressed mRNA localization in astrocytes. This PhD project was initially focused on developing and implementing methods that could be used to asses mRNA......Messenger RNA (mRNA) localization is a mechanism by which polarized cells can regulate protein synthesis to specific subcellular compartments in a spatial and temporal manner, and plays a pivotal role in multiple physiological processes from embryonic development to cell differentiation...... localization in astrocyte protrusions, and following look into the subcellular localization pattern of specific mRNA species of both primary astrocytes isolated from cortical hemispheres of newborn mice, and the mouse astrocyte cell line, C8S. The Boyden chamber cell fractionation assay was optimized, in a way...
Wegner-type Bounds for a Two-particle Lattice Model with a Generic 'Rough' Quasi-periodic Potential
International Nuclear Information System (INIS)
Gaume, Martin
2010-01-01
In this paper, we consider a class of two-particle tight-binding Hamiltonians, describing pairs of interacting quantum particles on the lattice Z d , d ≥ 1, subject to a common external potential V(x) which we assume quasi-periodic and depending on auxiliary parameters. Such parametric families of ergodic deterministic potentials ('grands ensembles') have been introduced earlier in Chulaevsky (2007), in the framework of single-particle lattice systems, where it was proved that a non-uniform analog of the Wegner bound holds true for a class of quasi-periodic grands ensembles. Using the approach proposed in Chulaevsky and Suhov (Commun Math Phys 283(2):479-489, 2008), we establish volume-dependent Wegner-type bounds for a class of quasi-periodic two-particle lattice systems with a non-random short-range interaction.
OPRA capacity bounds for selection diversity over generalized fading channels
Hanif, Muhammad Fainan; Yang, Hongchuan; Alouini, Mohamed-Slim
2014-01-01
, lower and upper bounds on OPRA capacity for selection diversity scheme are presented. These bounds hold for variety of fading channels including log-normal and generalized Gamma distributed models and have very simple analytic expressions for easy
Unexpected strong attraction in the presence of continuum bound state
International Nuclear Information System (INIS)
Delfino, A.; Frederico, T.
1992-06-01
The result of few-particle ground-state calculation employing a two-particle non-local potential supporting a continuum bound state in addition to a negative-energy bound state has occasionally revealed unexpected large attraction in producing a very strongly bound ground state. In the presence of the continuum bound state the difference of phase shift between zero and infinite energies has an extra jump of φ as in the presence of an additional bound state. The wave function of the continuum bound state is identical with that of a strongly bound negative-energy state, which leads us to postulate a pseudo bound state in the two-particle system in order to explain the unexpected attraction. The role of the Pauli forbidden states is expected to be similar to these pseudo states. (author)
Bounded Perturbation Regularization for Linear Least Squares Estimation
Ballal, Tarig; Suliman, Mohamed Abdalla Elhag; Al-Naffouri, Tareq Y.
2017-01-01
This paper addresses the problem of selecting the regularization parameter for linear least-squares estimation. We propose a new technique called bounded perturbation regularization (BPR). In the proposed BPR method, a perturbation with a bounded
Bound values for Hall conductivity of heterogeneous medium under ...
Indian Academy of Sciences (India)
- ditions in inhomogeneous medium has been studied. It is shown that bound values for. Hall conductivity differ from bound values for metallic conductivity. This is due to the unusual character of current percolation under quantum Hall effect ...
International Nuclear Information System (INIS)
Simonetti, Angelita; Marzi, Stefano; Fabbretti, Attilio; Hazemann, Isabelle; Jenner, Lasse; Urzhumtsev, Alexandre; Gualerzi, Claudio O.; Klaholz, Bruno P.
2013-01-01
The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue
Energy Technology Data Exchange (ETDEWEB)
Simonetti, Angelita [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Marzi, Stefano [Architecture et Réactivité de l’ARN, UPR 9002 CNRS, IBMC (Institute of Molecular and Cellular Biology), 15 Rue R. Descartes, 67084 Strasbourg, France, Université de Strasbourg, 67000 Strasbourg (France); Fabbretti, Attilio [University of Camerino, 62032 Camerino (Monaco) (Italy); Hazemann, Isabelle; Jenner, Lasse [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale -INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Urzhumtsev, Alexandre [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Université de Lorraine, 54506 Vandoeuvre-lès-Nancy (France); Gualerzi, Claudio O. [University of Camerino, 62032 Camerino (Monaco) (Italy); Klaholz, Bruno P., E-mail: klaholz@igbmc.fr [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France)
2013-06-01
The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.
Inhibition of poliovirus RNA synthesis by brefeldin A.
Maynell, L A; Kirkegaard, K; Klymkowsky, M W
1992-01-01
Brefeldin A (BFA), a fungal metabolite that blocks transport of newly synthesized proteins from the endoplasmic reticulum, was found to inhibit poliovirus replication 10(5)- to 10(6)-fold. BFA does not inhibit entry of poliovirus into the cell or translation of viral RNA. Poliovirus RNA synthesis, however, is completely inhibited by BFA. A specific class of membranous vesicles, with which the poliovirus replication complex is physically associated, is known to proliferate in poliovirus-infect...
International Nuclear Information System (INIS)
Oset, E.; Cabrera, D.; Li, Q.B.; Magas, V.K.; Vicente Vacas, M.J.
2005-01-01
We study the binding energy and the width of the Θ + in nuclei, associated to the KN and KπN components. The first one leads to negligible contributions while the second one leads to a sizeable attraction, enough to bind the Θ + in nuclei. Pauli blocking and binding effects on the KN decay reduce considerably the Θ + decay width in nuclei and medium effects associated to the KπN component also lead to a very small width, as a consequence of which one finds separation between the bound levels considerably larger than the width of the states
Fermionic bound states in distinct kinklike backgrounds
Energy Technology Data Exchange (ETDEWEB)
Bazeia, D. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, Paraiba (Brazil); Mohammadi, A. [Universidade Federal de Campina Grande, Departamento de Fisica, Caixa Postal 10071, Campina Grande, Paraiba (Brazil)
2017-04-15
This work deals with fermions in the background of distinct localized structures in the two-dimensional spacetime. Although the structures have a similar topological character, which is responsible for the appearance of fractionally charged excitations, we want to investigate how the geometric deformations that appear in the localized structures contribute to the change in the physical properties of the fermionic bound states. We investigate the two-kink and compact kinklike backgrounds, and we consider two distinct boson-fermion interactions, one motivated by supersymmetry and the other described by the standard Yukawa coupling. (orig.)
Quarks as quasiparticles of bound states
International Nuclear Information System (INIS)
Tyapkin, A.A.
1977-01-01
Interpretation of quarks as strongly bound subsystems of the baryon structure, being in various states with integer the quantum numbers Q and B, is considered. Three original quark states, distinguished by Q, B, and J, are unambiguously determined from the condition that the quarks have the corresponding fractional quantum numbers while the integer quantum numbers for the whole system are known. With this in view the new quantum number ''colour'' is interpreted as a quantity, specifying the appearance of the subsystems in various eigen-states. Basing on the generalized Sakata model, the self-consistency of change of the colour states in the three-quark system is explained
Magnetic moment of a bound electron
Czarnecki, Andrzej; Mondejar, Jorge; Piclum, Jan H
2010-01-01
Theoretical predictions underlying determinations of the fine structure constant alpha and the electron-to-proton mass ratio m_e/m_p are reviewed, with the emphasis on the bound electron magnetic anomaly g-2. The theory of the interaction of hydrogen-like ions with a magnetic field is discussed. The status of efforts aimed at the determination of O(alpha (Z alpha)^5) and O(alpha^2 (Z alpha)^5) corrections to the g factor is presented. The reevaluation of analogous corrections to the Lamb shift and the hyperfine splitting is summarized.
Andreev bound states. Some quasiclassical reflections
International Nuclear Information System (INIS)
Lin, Y.; Leggett, A. J.
2014-01-01
We discuss a very simple and essentially exactly solvable model problem which illustrates some nice features of Andreev bound states, namely, the trapping of a single Bogoliubov quasiparticle in a neutral s-wave BCS superfluid by a wide and shallow Zeeman trap. In the quasiclassical limit, the ground state is a doublet with a splitting which is proportional to the exponentially small amplitude for “normal” reflection by the edges of the trap. We comment briefly on a prima facie paradox concerning the continuity equation and conjecture a resolution to it
Andreev bound states. Some quasiclassical reflections
Energy Technology Data Exchange (ETDEWEB)
Lin, Y., E-mail: yiriolin@illinois.edu; Leggett, A. J. [University of Illinois at Urhana-Champaign, Dept. of Physics (United States)
2014-12-15
We discuss a very simple and essentially exactly solvable model problem which illustrates some nice features of Andreev bound states, namely, the trapping of a single Bogoliubov quasiparticle in a neutral s-wave BCS superfluid by a wide and shallow Zeeman trap. In the quasiclassical limit, the ground state is a doublet with a splitting which is proportional to the exponentially small amplitude for “normal” reflection by the edges of the trap. We comment briefly on a prima facie paradox concerning the continuity equation and conjecture a resolution to it.
Uniformly bounded representations of the Lorentz groups
International Nuclear Information System (INIS)
Brega, A.O.
1982-01-01
For the Lorentz group G = SO/sub e/(n + 1, 1)(ngreater than or equal to 2) the author constructs a family of uniformly bounded representations by means of analytically continuing a certain normalization of the unitary principal series. The method the author uses relies on an analysis of various operators under a Mellin transform and extends earlier work of E.N. Wilson. In a series of papers Kunze and Stein initiated the theory of uniformly bounded representations of semisimple Lie groups; the starting point is the unitary principal series T(sigma,s) obtained in a certain subgroup M of G and a purely imaginary number s. From there Kunze and Stein constructed families of representations R(sigma,s) depending analytically on a parameter s in a domain D of C containing the imaginary axis which are unitarily equilvalent to T(sigma,s) for s contained in the set of imaginary numbers and whose operator norms are uniformly bounded for each s in D. In the case of the Lorentz groups SO/sub e/(n + 1, 1)(ngreater than or equal to2) and the trivial representation 1 of M, E.N. Wilson obtained such a family R(1,s) for the domain D = [s contained in the set of C: absolute value Re(s) Vertical Bar2]. For this domain D and for any representation sigma of M the author provides a family R(sigma,s) of uniformly bounded representations analytically continuing T(sigma,s), thereby generalizing Wilson's work. The author has also investigated certain symmetry properties of the representations R(sigma,s) under the action of the Weyl group. The trivial representation is Weyl group invariant and the family R(1,s) obtained by Wilson satisfies R(1,s) = R(1,-s) reflecting this. Obtained was the analogous result R(sigma,s) = R(sigma,-s) for some well known representations sigma that are Weyl group invariant. This involves the explicit computation of certain constants arising in the Fourier transforms of intertwining operators
BOUND PERIODICAL HOLDINGS BATTELLE - NORTHWEST LIBRARY
Energy Technology Data Exchange (ETDEWEB)
None
1967-05-01
This report lists the bound periodicals in the Technical Library at the Pacific Northwest Laboratory, operated by Battelle Memorial Institute. It was prepared from a computer program and is arranged in two parts. Part one is an alphabetical list of journals by title; part two is an arrangement of the journals by subject. The list headings are self-explanatory, with the exception of the title code, which is necessary in the machine processing. The listing is complete through June, 1966 and updates an earlier publication issued in March, 1965.
Total-variation regularization with bound constraints
International Nuclear Information System (INIS)
Chartrand, Rick; Wohlberg, Brendt
2009-01-01
We present a new algorithm for bound-constrained total-variation (TV) regularization that in comparison with its predecessors is simple, fast, and flexible. We use a splitting approach to decouple TV minimization from enforcing the constraints. Consequently, existing TV solvers can be employed with minimal alteration. This also makes the approach straightforward to generalize to any situation where TV can be applied. We consider deblurring of images with Gaussian or salt-and-pepper noise, as well as Abel inversion of radiographs with Poisson noise. We incorporate previous iterative reweighting algorithms to solve the TV portion.
Bound Alternative Direction Optimization for Image Deblurring
Directory of Open Access Journals (Sweden)
Xiangrong Zeng
2014-01-01
the ℓp regularizer by a novel majorizer and then, based on a variable splitting, to reformulate the bound unconstrained problem into a constrained one, which is then addressed via an augmented Lagrangian method. The proposed algorithm actually combines the reweighted ℓ1 minimization method and the alternating direction method of multiples (ADMM such that it succeeds in extending the application of ADMM to ℓp minimization problems. The conducted experimental studies demonstrate the superiority of the proposed algorithm for the synthesis ℓp minimization over the state-of-the-art algorithms for the synthesis ℓ1 minimization on image deblurring.
Accelerated probabilistic inference of RNA structure evolution
Directory of Open Access Journals (Sweden)
Holmes Ian
2005-03-01
Full Text Available Abstract Background Pairwise stochastic context-free grammars (Pair SCFGs are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License.
Lower bound on inconclusive probability of unambiguous discrimination
International Nuclear Information System (INIS)
Feng Yuan; Zhang Shengyu; Duan Runyao; Ying Mingsheng
2002-01-01
We derive a lower bound on the inconclusive probability of unambiguous discrimination among n linearly independent quantum states by using the constraint of no signaling. It improves the bound presented in the paper of Zhang, Feng, Sun, and Ying [Phys. Rev. A 64, 062103 (2001)], and when the optimal discrimination can be reached, these two bounds coincide with each other. An alternative method of constructing an appropriate measurement to prove the lower bound is also presented
2013-01-01
Background The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change of the transcriptional activity of the genome. This complex network of genes is orchestrated by proteins as well as regulatory RNA elements. Here we present an RNA-Seq based study considering selected phases of an industry-oriented fermentation of Bacillus licheniformis. Results A detailed analysis of 20 strand-specific RNA-Seq datasets revealed a multitude of transcriptionally active genomic regions. 3314 RNA features encoded by such active loci have been identified and sorted into ten functional classes. The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs. An unexpectedly high number of 855 RNA features are encoded antisense to annotated protein and RNA genes, in addition to 461 independently transcribed small RNAs. These antisense transcripts contain molecules with a remarkable size range variation from 38 to 6348 base pairs in length. The genome of the type strain B. licheniformis DSM13 was completely reannotated using data obtained from RNA-Seq analyses and from public databases. Conclusion The hereby generated data-sets represent a solid amount of knowledge on the dynamic transcriptional activities during the investigated fermentation stages. The identified regulatory elements enable research on the understanding and the optimization of crucial metabolic activities during a productive fermentation of Bacillus licheniformis strains. PMID:24079885
Wiegand, Sandra; Dietrich, Sascha; Hertel, Robert; Bongaerts, Johannes; Evers, Stefan; Volland, Sonja; Daniel, Rolf; Liesegang, Heiko
2013-10-01
The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change of the transcriptional activity of the genome. This complex network of genes is orchestrated by proteins as well as regulatory RNA elements. Here we present an RNA-Seq based study considering selected phases of an industry-oriented fermentation of Bacillus licheniformis. A detailed analysis of 20 strand-specific RNA-Seq datasets revealed a multitude of transcriptionally active genomic regions. 3314 RNA features encoded by such active loci have been identified and sorted into ten functional classes. The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs. An unexpectedly high number of 855 RNA features are encoded antisense to annotated protein and RNA genes, in addition to 461 independently transcribed small RNAs. These antisense transcripts contain molecules with a remarkable size range variation from 38 to 6348 base pairs in length. The genome of the type strain B. licheniformis DSM13 was completely reannotated using data obtained from RNA-Seq analyses and from public databases. The hereby generated data-sets represent a solid amount of knowledge on the dynamic transcriptional activities during the investigated fermentation stages. The identified regulatory elements enable research on the understanding and the optimization of crucial metabolic activities during a productive fermentation of Bacillus licheniformis strains.
Jenkins, Jermaine L; Krucinska, Jolanta; McCarty, Reid M; Bandarian, Vahe; Wedekind, Joseph E
2011-07-15
Riboswitches are RNA regulatory elements that govern gene expression by recognition of small molecule ligands via a high affinity aptamer domain. Molecular recognition can lead to active or attenuated gene expression states by controlling accessibility to mRNA signals necessary for transcription or translation. Key areas of inquiry focus on how an aptamer attains specificity for its effector, the extent to which the aptamer folds prior to encountering its ligand, and how ligand binding alters expression signal accessibility. Here we present crystal structures of the preQ(1) riboswitch from Thermoanaerobacter tengcongensis in the preQ(1)-bound and free states. Although the mode of preQ(1) recognition is similar to that observed for preQ(0), surface plasmon resonance revealed an apparent K(D) of 2.1 ± 0.3 nm for preQ(1) but a value of 35.1 ± 6.1 nm for preQ(0). This difference can be accounted for by interactions between the preQ(1) methylamine and base G5 of the aptamer. To explore conformational states in the absence of metabolite, the free-state aptamer structure was determined. A14 from the ceiling of the ligand pocket shifts into the preQ(1)-binding site, resulting in "closed" access to the metabolite while simultaneously increasing exposure of the ribosome-binding site. Solution scattering data suggest that the free-state aptamer is compact, but the "closed" free-state crystal structure is inadequate to describe the solution scattering data. These observations are distinct from transcriptional preQ(1) riboswitches of the same class that exhibit strictly ligand-dependent folding. Implications for gene regulation are discussed.
Thermodynamic Upper Bound on Broadband Light Coupling with Photonic Structures
Yu, Zongfu; Raman, Aaswath; Fan, Shanhui
2012-01-01
to an upper bound dictated by the second law of thermodynamics. Such bound limits how efficient light can be coupled to any photonic structure. As one example of application, we use this upper bound to derive the limit of light absorption in broadband solar
Bounds on the capacity of constrained two-dimensional codes
DEFF Research Database (Denmark)
Forchhammer, Søren; Justesen, Jørn
2000-01-01
Bounds on the capacity of constrained two-dimensional (2-D) codes are presented. The bounds of Calkin and Wilf apply to first-order symmetric constraints. The bounds are generalized in a weaker form to higher order and nonsymmetric constraints. Results are given for constraints specified by run-l...
Bounded Rationality, Retaliation, and the Spread of Urban Violence
Jacobs, Bruce A.; Wright, Richard
2010-01-01
Drawing from in-depth interviews with 52 active street criminals, this article examines the grounded theoretic implications of bounded rationality for retaliatory street violence. The bounds on rationality that this article explores are anger, uncertainty, and time pressure. These bounds create imperfections in the retaliatory decision-making…
Bauer, William J.; Heath, Jason; Jenkins, Jermaine L.; Kielkopf, Clara L.
2012-01-01
T-cell intracellular antigen-1 (TIA-1) regulates developmental and stress-responsive pathways through distinct activities at the levels of alternative pre-mRNA splicing and mRNA translation. The TIA-1 polypeptide contains three RNA recognition motifs (RRMs). The central RRM2 and C-terminal RRM3 associate with cellular mRNAs. The N-terminal RRM1 enhances interactions of a C-terminal Q-rich domain of TIA-1 with the U1-C splicing factor, despite linear separation of the domains in the TIA-1 sequence. Given the expanded functional repertoire of the RRM family, it was unknown whether TIA-1 RRM1 contributes to RNA binding as well as documented protein interactions. To address this question, we used isothermal titration calorimetry and small-angle X-ray scattering (SAXS) to dissect the roles of the TIA-1 RRMs in RNA recognition. Notably, the fas RNA exhibited two binding sites with indistinguishable affinities for TIA-1. Analyses of TIA-1 variants established that RRM1 was dispensable for binding AU-rich fas sites, yet all three RRMs were required to bind a polyU RNA with high affinity. SAXS analyses demonstrated a `V' shape for a TIA-1 construct comprising the three RRMs, and revealed that its dimensions became more compact in the RNA-bound state. The sequence-selective involvement of TIA-1 RRM1 in RNA recognition suggests a possible role for RNA sequences in regulating the distinct functions of TIA-1. Further implications for U1-C recruitment by the adjacent TIA-1 binding sites of the fas pre-mRNA and the bent TIA-1 shape, which organizes the N- and C-termini on the same side of the protein, are discussed. PMID:22154808
International Nuclear Information System (INIS)
Wei Nanxia; Xue Jukui
2006-01-01
Taking into account the boundary, particle collisions, and dust charging effects, dust-acoustic waves in a uniform cylindrically bounded dusty plasma is investigated analytically, and the dispersion relation for the dust-acoustic wave is obtained. The effects of boundary, dust charge variation, particle collision, and dust size on the dust-acoustic wave are discussed in detail. Due to the bounded cylindrical boundary effects, the radial wave number is discrete, i.e., the spectrum is discrete. It is shown that the discrete spectrum, the adiabatic dust charge variation, dust grain size, and the particle collision have significant effects on the dust-acoustic wave
Social Class Dialogues and the Fostering of Class Consciousness
Madden, Meredith
2015-01-01
How do critical pedagogies promote undergraduate students' awareness of social class, social class identity, and social class inequalities in education? How do undergraduate students experience class consciousness-raising in the intergroup dialogue classroom? This qualitative study explores undergraduate students' class consciousness-raising in an…
Analytic quantum bounds on Bell inequalities
International Nuclear Information System (INIS)
Filipp, S.; Svozil, K.
2005-01-01
Full text: Can realism be combined with the quantum world? An important tool to investigate in this question are Bell's inequalities and violations thereof - they represent a cornerstone of our present understanding of quantum mechanics and therefore the description of nature. Here we present a simple algebraic method to calculate violations for any measurement arrangements that are maximal in the sense that quantum mechanics does not allow a stronger violation. Having two or more polarization analyzers available and a source producing photon-pairs in arbitrary polarization states Bell-type inequalities tell us which probabilities for measuring the polarization in particular directions are viable in a deterministic theory. Quantum mechanics does not obey these rules, but yields a violation of these inequalities. The questions is to what extent the inequalities are violated. Making use of a min-max principle analytical expressions can be found for the 'fine structure' of the maximal violations of arbitrary Bell-like inequalities, i. e. the upper bound reachable by any state when the analyzers measure in given directions. Knowing these bounds is useful for experimental tests of the validity of quantum mechanics and can serve as a prerequisite to answer the even more pressing question, why no stronger violation has been observed until now. (author)
Electromagnetic structure of a bound nucleon
International Nuclear Information System (INIS)
Nogami, Y.
1977-01-01
The effect of binding on the electromagnetic (e.m.) structure of a nucleon in a nucleus is examined by means of a model consisting of a single nucleon which is bound in a harmonic oscillator potential and also coupled to the pion field through the Chew-Low interaction. The 'two-pion contribution' to the e.m. structure is considered. This is the part which is probably most susceptible to the binding effect. By the binding effect it is meant the one which arises because the nucleon wave functions, in the intermediate state as well as in the initial and final states, are distorted by the potential in which the nucleon is bound. This may be compared to a similar correction to the impulse approximation for pion-nucleus scattering. Unlike the latter which is likely to be quite appreciable, the binding correction to the e.m. structure of the nucleon is found to be negligibly small. The so-called quenching effect due to the Pauli principle when there are other nucleons is also discussed [pt
Dynamic bounds coupled with Monte Carlo simulations
Energy Technology Data Exchange (ETDEWEB)
Rajabalinejad, M., E-mail: M.Rajabalinejad@tudelft.n [Faculty of Civil Engineering, Delft University of Technology, Delft (Netherlands); Meester, L.E. [Delft Institute of Applied Mathematics, Delft University of Technology, Delft (Netherlands); Gelder, P.H.A.J.M. van; Vrijling, J.K. [Faculty of Civil Engineering, Delft University of Technology, Delft (Netherlands)
2011-02-15
For the reliability analysis of engineering structures a variety of methods is known, of which Monte Carlo (MC) simulation is widely considered to be among the most robust and most generally applicable. To reduce simulation cost of the MC method, variance reduction methods are applied. This paper describes a method to reduce the simulation cost even further, while retaining the accuracy of Monte Carlo, by taking into account widely present monotonicity. For models exhibiting monotonic (decreasing or increasing) behavior, dynamic bounds (DB) are defined, which in a coupled Monte Carlo simulation are updated dynamically, resulting in a failure probability estimate, as well as a strict (non-probabilistic) upper and lower bounds. Accurate results are obtained at a much lower cost than an equivalent ordinary Monte Carlo simulation. In a two-dimensional and a four-dimensional numerical example, the cost reduction factors are 130 and 9, respectively, where the relative error is smaller than 5%. At higher accuracy levels, this factor increases, though this effect is expected to be smaller with increasing dimension. To show the application of DB method to real world problems, it is applied to a complex finite element model of a flood wall in New Orleans.
More loosely bound hadron molecules at CDF?
Bignamini, C; Piccinini, F; Polosa, A D; Riquer, V; Sabelli, C
2010-01-01
In a recent paper we have proposed a method to estimate the prompt production cross section of X(3872) at the Tevatron assuming that this particle is a loosely bound molecule of a D and a D*bar meson. Under this hypothesis we find that it is impossible to explain the high prompt production cross section found by CDF at sigma(X(3872)) \\sim 30-70 nb as our theoretical prediction is about 300 times smaller than the measured one. Following our work, Artoisenet and Braaten, have suggested that final state interactions in the DD*bar system might be so strong to push the result we obtained for the cross section up to the experimental value. Relying on their conclusions we show that the production of another very narrow loosely bound molecule, the X_s=D_s D_s*bar, could be similarly enhanced. X_s should then be detectable at CDF with a mass of 4080 MeV and a prompt production cross section of sigma(X_s) \\sim 1-3 nb.
Phenomenological bounds in inclusive neutrino interactions
International Nuclear Information System (INIS)
Aubrecht, G.J. II; Takasugi, E.; Tanaka, K.
1975-01-01
Using expressions for the ν and anti ν charged and neutral current cross sections and the electroproduction structure function integral and positivity requirements of the sea contribution, bounds are obtained on sigma/sup anti nu N//sigma/sup anti nu N/, and sigma/sup anti nu N//sub nc//sigma/sup nu N//sub nc/ in the standard model. A bound on sigma/sup anti nu N//sigma/sup nu N/ obtained with a V + A term anti p'γ/sub mu/(1-γ 5 )n is used to rule out such a term in the current. A plot of sigma/sup nu N//sub nc/ + sigma/sup anti nu N//sub nc/ versus sigma/sup nu N//sub nc/ - sigma/sup anti nu N//sub nc/ is introduced to analyze the neutral current data. A new relation connecting moments of y and y distributions at a particular point y/sub n/ for ν and anti ν interactions is found. The results do not depend on the neutral current data
Search for a bound K− pp system
Directory of Open Access Journals (Sweden)
Camerini P.
2010-04-01
Full Text Available Data from the K− absorption reaction on 6,7Li, 9Be, 13C and 16O have recently been collected by FINUDA at the DAΦNE φ-factory (Laboratori Nazionali di Frascati-INFN, following an earlier lower statitics run on 12C and some other targets. FINUDA is a high acceptance magnetic spectrometer which performed a wide range of studies by detecting the charged particles and neutrons exiting the targets after the absorption event. In this paper it is discussed about the study of the A(K− , Λp reaction in the context of the search for deeply bound $ar{K}$ - nuclear states. The observation of a bump in the Λp invariant mass distribution is discussed in terms of a possible signature of a deeply bound K− pp kaonic cluster as well as of more conventional physics. An overview of the experimental situation in this ﬁeld will be given.
Bounds on area and charge for marginally trapped surfaces with a cosmological constant
International Nuclear Information System (INIS)
Simon, Walter
2012-01-01
We sharpen the known inequalities AΛ ≤ 4π(1 - g) (Hayward et al 1994 Phys. Rev. D 49 5080, Woolgar 1999 Class. Quantum Grav. 16 3005) and A ≤ 4πQ 2 (Dain et al 2012 Class. Quantum Grav. 29 035013) between the area A and the electric charge Q of a stable marginally outer-trapped surface (MOTS) of genus g in the presence of a cosmological constant Λ. In particular, instead of requiring stability we include the principal eigenvalue λ of the stability operator. For Λ* Λ+λ > 0, we obtain a lower and an upper bound for Λ*A in terms of Λ*Q 2 , as well as the upper bound Q≤1/(2√(Λ * )) for the charge, which reduces to Q≤1/(2√(Λ)) in the stable case λ ≥ 0. For Λ* < 0, there only remains a lower bound on A. In the spherically symmetric, static, stable case, one of our area inequalities is saturated iff the surface gravity vanishes. We also discuss implications of our inequalities for 'jumps' and mergers of charged MOTS. (fast track communication)
Nezir, Veysel; Mustafa, Nizami
2017-04-01
In 2008, P.K. Lin provided the first example of a nonreflexive space that can be renormed to have fixed point property for nonexpansive mappings. This space was the Banach space of absolutely summable sequences l1 and researchers aim to generalize this to c0, Banach space of null sequences. Before P.K. Lin's intriguing result, in 1979, Goebel and Kuczumow showed that there is a large class of non-weak* compact closed, bounded, convex subsets of l1 with fixed point property for nonexpansive mappings. Then, P.K. Lin inspired by Goebel and Kuczumow's ideas to give his result. Similarly to P.K. Lin's study, Hernández-Linares worked on L1 and in his Ph.D. thesis, supervisored under Maria Japón, showed that L1 can be renormed to have fixed point property for affine nonexpansive mappings. Then, related questions for c0 have been considered by researchers. Recently, Nezir constructed several equivalent norms on c0 and showed that there are non-weakly compact closed, bounded, convex subsets of c0 with fixed point property for affine nonexpansive mappings. In this study, we construct a family of equivalent norms containing those developed by Nezir as well and show that there exists a large class of non-weakly compact closed, bounded, convex subsets of c0 with fixed point property for affine nonexpansive mappings.
International Nuclear Information System (INIS)
Rosevear, P.R.; Powers, V.M.; Dowhan, D.; Mildvan, A.S.; Kenyon, G.L.
1987-01-01
Nuclear Overhauser effects were used to determine interproton distances on MgATP bound to rabbit muscle creatine kinase. The internuclear distances were used in a distance geometry program that objectively determines both the conformation of the bound MgATP and its uniqueness. Two classes of structures were found that satisfied the measured interproton distances. Both classes had the same anti glycosidic torsional angle (X = 78 +/- 10 0 ) but differed in their ribose ring puckers (O1'-endo or C4'-exo). The uniqueness of the glycosidic torsional angle is consistent with the preference of creatine kinase for adenine nucleotides. One of these conformations of MgATP bound to creatine kinase is indistinguishable from the conformation found for Co(NH 3 ) 4 ATP bound to the catalytic subunit of protein kinase, which also has a high specificity for adenine nucleotides. Distance geometry calculations also suggest that upper limit distances, when low enough (≤ 3.4 A), can be used instead of measured distances to define, within experimental error, the glycosidic torsional angle of bound nucleotides. However, this approach does not permit an evaluation of the ribose ring pucker
Constructing decidable hybrid systems with velocity bounds
Belta, C.; Habets, L.C.G.J.M.
2004-01-01
In this paper, the question of bi-similarity between hybrid systems and their discrete quotients is studied from a new point of view. We consider two classes of hybrid systems: piecewise affine hybrid systems on simplices and piecewise multi-affine systems on multi-dimensional rectangles. Given a
Resource-Bounded Information Acquisition and Learning
2012-05-01
Different combinations of voting and confidence evaluation schemes...H. Wang, ... Facial Expression Decomposition..., ICCV, 2003. (E)..., H. Wang, ... Tensor Approximation..., SIGGRAPH. 2005. (F)..., H. Wang, ... High...two of the possible schemes for combining the evidence in the output space. In the first scheme, we take a majority 67 vote , i.e., the class with the
Xiao, Shou-Jun
2017-01-01
RNA nanoparticles are designed and self-assembled according to noncanonical interactions of naturally conserved RNA motifs and/or canonical Watson-Crick base-pairing interactions, which have potential applications in gene therapy and nanomedicine. These artificially engineered nanoparticles are mainly synthesized from in vitro transcribed RNAs, purified by denaturing and native polyacrylamide gel electrophoresis (PAGE), and characterized with native PAGE, AFM, and TEM technologies. The protocols of in vitro transcription, denaturing and native PAGE, and RNA nanoparticle self-assembly are described in detail.
Directory of Open Access Journals (Sweden)
Sergievskiy Maxim
2018-01-01
Full Text Available Most of object-oriented development technologies rely on the use of the universal modeling language UML; class diagrams play a very important role in the design process play, used to build a software system model. Modern CASE tools, which are the basic tools for object-oriented development, can’t be used to optimize UML diagrams. In this manuscript we will explain how, based on the use of design patterns and anti-patterns, class diagrams could be verified and optimized. Certain transformations can be carried out automatically; in other cases, potential inefficiencies will be indicated and recommendations given. This study also discusses additional CASE tools for validating and optimizing of UML class diagrams. For this purpose, a plugin has been developed that analyzes an XMI file containing a description of class diagrams.
... Introduction Types of Heart Failure Classes of Heart Failure Heart Failure in Children Advanced Heart Failure • Causes and ... and Advanced HF • Tools and Resources • Personal Stories Heart Failure Questions to Ask Your Doctor Use these questions ...
Generalized Fourier transforms classes
DEFF Research Database (Denmark)
Berntsen, Svend; Møller, Steen
2002-01-01
The Fourier class of integral transforms with kernels $B(\\omega r)$ has by definition inverse transforms with kernel $B(-\\omega r)$. The space of such transforms is explicitly constructed. A slightly more general class of generalized Fourier transforms are introduced. From the general theory foll...... follows that integral transform with kernels which are products of a Bessel and a Hankel function or which is of a certain general hypergeometric type have inverse transforms of the same structure....
Fitness Club
2015-01-01
Four classes of one hour each are held on Tuesdays. RDV barracks parking at Entrance A, 10 minutes before class time. Spring Course 2015: 05.05/12.05/19.05/26.05 Prices 40 CHF per session + 10 CHF club membership 5 CHF/hour pole rental Check out our schedule and enroll at: https://espace.cern.ch/club-fitness/Lists/Nordic%20Walking/NewForm.aspx? Hope to see you among us! fitness.club@cern.ch
The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
Directory of Open Access Journals (Sweden)
Giulio Caravagna
Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.
The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto
2013-01-01
After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.
Short versus long range interactions and the size of two-body weakly bound objects
International Nuclear Information System (INIS)
Lombard, R.J.; Volpe, C.
2003-01-01
Very weakly bound systems may manifest intriguing ''universal'' properties, independent of the specific interaction which keeps the system bound. An interesting example is given by relations between the size of the system and the separation energy, or scaling laws. So far, scaling laws have been investigated for short-range and long-range (repulsive) potentials. We report here on scaling laws for weakly bound two-body systems valid for a larger class of potentials, i.e. short-range potentials having a repulsive core and long-range attractive potentials. We emphasize analogies and differences between the short- and the long-range case. In particular, we show that the emergence of halos is a threshold phenomenon which can arise when the system is bound not only by short-range interactions but also by long-range ones, and this for any value of the orbital angular momentum l. These results enlarge the image of halo systems we are accustomed to. (orig.)
Bounding the HL-index of a graph: a majorization approach.
Clemente, Gian Paolo; Cornaro, Alessandra
2016-01-01
In mathematical chemistry, the median eigenvalues of the adjacency matrix of a molecular graph are strictly related to orbital energies and molecular orbitals. In this regard, the difference between the occupied orbital of highest energy (HOMO) and the unoccupied orbital of lowest energy (LUMO) has been investigated (see Fowler and Pisansky in Acta Chim. Slov. 57:513-517, 2010). Motivated by the HOMO-LUMO separation problem, Jaklič et al. in (Ars Math. Contemp. 5:99-115, 2012) proposed the notion of HL -index that measures how large in absolute value are the median eigenvalues of the adjacency matrix. Several bounds for this index have been provided in the literature. The aim of the paper is to derive alternative inequalities to bound the HL -index. By applying majorization techniques and making use of some known relations, we derive new and sharper upper bounds for this index. Analytical and numerical results show the performance of these bounds on different classes of graphs.
Rigorous Statistical Bounds in Uncertainty Quantification for One-Layer Turbulent Geophysical Flows
Qi, Di; Majda, Andrew J.
2018-04-01
Statistical bounds controlling the total fluctuations in mean and variance about a basic steady-state solution are developed for the truncated barotropic flow over topography. Statistical ensemble prediction is an important topic in weather and climate research. Here, the evolution of an ensemble of trajectories is considered using statistical instability analysis and is compared and contrasted with the classical deterministic instability for the growth of perturbations in one pointwise trajectory. The maximum growth of the total statistics in fluctuations is derived relying on the statistical conservation principle of the pseudo-energy. The saturation bound of the statistical mean fluctuation and variance in the unstable regimes with non-positive-definite pseudo-energy is achieved by linking with a class of stable reference states and minimizing the stable statistical energy. Two cases with dependence on initial statistical uncertainty and on external forcing and dissipation are compared and unified under a consistent statistical stability framework. The flow structures and statistical stability bounds are illustrated and verified by numerical simulations among a wide range of dynamical regimes, where subtle transient statistical instability exists in general with positive short-time exponential growth in the covariance even when the pseudo-energy is positive-definite. Among the various scenarios in this paper, there exist strong forward and backward energy exchanges between different scales which are estimated by the rigorous statistical bounds.
Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav
2002-12-01
The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.
Plant RNA binding proteins for control of RNA virus infection
Directory of Open Access Journals (Sweden)
Sung Un eHuh
2013-12-01
Full Text Available Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific binding. Host plants intensively use RNA binding proteins for defense against viral infections in nature. In this mini review, we will summarize the function of some host RNA binding proteins which act in a sequence-specific binding manner to the infecting virus RNA. It is important to understand how plants effectively suppresses RNA virus infections via RNA binding proteins, and this defense system can be potentially developed as a synthetic virus defense strategy for use in crop engineering.
Degenerate quantum codes and the quantum Hamming bound
International Nuclear Information System (INIS)
Sarvepalli, Pradeep; Klappenecker, Andreas
2010-01-01
The parameters of a nondegenerate quantum code must obey the Hamming bound. An important open problem in quantum coding theory is whether the parameters of a degenerate quantum code can violate this bound for nondegenerate quantum codes. In this article we show that Calderbank-Shor-Steane (CSS) codes, over a prime power alphabet q≥5, cannot beat the quantum Hamming bound. We prove a quantum version of the Griesmer bound for the CSS codes, which allows us to strengthen the Rains' bound that an [[n,k,d
Shapes of interacting RNA complexes
DEFF Research Database (Denmark)
Fu, Benjamin Mingming; Reidys, Christian
2014-01-01
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....
National Research Council Canada - National Science Library
2002-01-01
.... Remote Network Access (RNA) includes or is associated with all communication devices/software, firewalls, intrusion detection systems and virus protection applications to ensure security of the OIG, DoD, Network from remote...
Indian Academy of Sciences (India)
In this approach we want to develop structural analogue of the leader that might have higher affinity towards the Phosphoprotein, but would impair the dimerization process and viral leader RNA binding.
A tale of two sequences: microRNA-target chimeric reads.
Broughton, James P; Pasquinelli, Amy E
2016-04-04
In animals, a functional interaction between a microRNA (miRNA) and its target RNA requires only partial base pairing. The limited number of base pair interactions required for miRNA targeting provides miRNAs with broad regulatory potential and also makes target prediction challenging. Computational approaches to target prediction have focused on identifying miRNA target sites based on known sequence features that are important for canonical targeting and may miss non-canonical targets. Current state-of-the-art experimental approaches, such as CLIP-seq (cross-linking immunoprecipitation with sequencing), PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), and iCLIP (individual-nucleotide resolution CLIP), require inference of which miRNA is bound at each site. Recently, the development of methods to ligate miRNAs to their target RNAs during the preparation of sequencing libraries has provided a new tool for the identification of miRNA target sites. The chimeric, or hybrid, miRNA-target reads that are produced by these methods unambiguously identify the miRNA bound at a specific target site. The information provided by these chimeric reads has revealed extensive non-canonical interactions between miRNAs and their target mRNAs, and identified many novel interactions between miRNAs and noncoding RNAs.
Tight bounds on computing error-correcting codes by bounded-depth circuits with arbitrary gates
Czech Academy of Sciences Publication Activity Database
Gál, A.; Hansen, A. K.; Koucký, Michal; Pudlák, Pavel; Viola, E.
2013-01-01
Roč. 59, č. 10 (2013), s. 6611-6627 ISSN 0018-9448 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : bounded-depth circuits * error-correcting codes * hashing Subject RIV: BA - General Mathematics Impact factor: 2.650, year: 2013 http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6578188
Tight bounds on computing error-correcting codes by bounded-depth circuits with arbitrary gates
Czech Academy of Sciences Publication Activity Database
Gál, A.; Hansen, A. K.; Koucký, Michal; Pudlák, Pavel; Viola, E.
2013-01-01
Roč. 59, č. 10 (2013), s. 6611-6627 ISSN 0018-9448 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : bounded-depth circuits * error -correcting codes * hashing Subject RIV: BA - General Mathematics Impact factor: 2.650, year: 2013 http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6578188
Structure and dynamics of weakly bound complexes
International Nuclear Information System (INIS)
Skouteris, D.
1998-01-01
The present thesis deals with the spectroscopic and theoretical investigation of weakly bound complexes involving a methane molecule. Studies of these Van der Waals complexes can give valuable information on the relevant intermolecular dynamics and promote the understanding of the interactions between molecules (which can ultimately lead to chemical reactions). Especially interesting are complexes involving molecules of high symmetry (e.g. tetrahedral, such as methane) because of the unusual effects arising from it (selection rules, nuclear Spin statistical weights etc.). The infrared spectrum of the Van der Waals complex between a CH 4 and a N 2 O molecule has been recorded and most of it has been assigned in the region of the N - O stretch (approximately 2225.0 cm -1 ). Despite the fact that this is really a weakly bound complex, it is nevertheless rigid enough so that the standard model for asymmetric top spectra can be applied to it with the usual quantum numbers. From the value of the inertial defect, it turns out that the methane unit is locked in a rigid configuration within the complex rather than freely rotating. The intermolecular distance as well as the tilting angle of the N 2 O linear unit are determined from the rotational constants. The complex itself turns out to have a T - shaped configuration. The infrared spectrum of the Ar - CH 4 complex at the ν 4 (bending) band of methane is also assigned. This is different from the previous one in that the methane unit rotates almost freely Within the complex. As a result, the quantum numbers used to classify rovibrational energy levels include these of the free unit. The concept of 'overall symmetry' is made use of to rationalise selection rules in various sub-bands of the spectrum. Moreover, new terms in the potential anisotropy Hamiltonian are calculated through the use of the overall symmetry concept. These are termed 'mixed anisotropy' terms since they involve both rotational and vibrational degrees of
Götze, Michael; Dufourt, Jérémy; Ihling, Christian; Rammelt, Christiane; Pierson, Stephanie; Sambrani, Nagraj; Temme, Claudia; Sinz, Andrea; Simonelig, Martine; Wahle, Elmar
2017-10-01
Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, we identified Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. We suggest that "coating" of the RNA by a Me31B•Tral complex may be at the core of repression. © 2017 Götze et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Unique small RNA signatures uncovered in the tammar wallaby genome
Directory of Open Access Journals (Sweden)
Lindsay James
2012-10-01
Full Text Available Abstract Background Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs. Results Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi RNAs, piwi interacting (pi RNAs, and the centromere repeat associated short interacting (crasi RNAs in the tammar. We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. A survey of the tammar gonadal piRNAs shows that these small RNAs are enriched in retroelements and carry members from both marsupial and tammar-specific repeat classes. Lastly, this study includes the first in-depth analyses of the newly
International Nuclear Information System (INIS)
Donner, E.B.; Low, J.M.; Lux, C.R.
1992-01-01
DOE Order 6430.1A, General Design Criteria (GDC), requires that DOE facilities be evaluated with respect to ''safety class items.'' Although the GDC defines safety class items, it does not provide a methodology for selecting safety class items. The methodology described in this paper was developed to assure that Safety Class Items at the Savannah River Site (SRS) are selected in a consistent and technically defensible manner. Safety class items are those in the highest of four categories determined to be of special importance to nuclear safety and, merit appropriately higher-quality design, fabrication, and industrial test standards and codes. The identification of safety class items is approached using a cascading strategy that begins at the 'safety function' level (i.e., a cooling function, ventilation function, etc.) and proceeds down to the system, component, or structure level. Thus, the items that are required to support a safety function are SCls. The basic steps in this procedure apply to the determination of SCls for both new project activities, and for operating facilities. The GDC lists six characteristics of SCls to be considered as a starting point for safety item classification. They are as follows: 1. Those items whose failure would produce exposure consequences that would exceed the guidelines in Section 1300-1.4, ''Guidance on Limiting Exposure of the Public,'' at the site boundary or nearest point of public access 2. Those items required to maintain operating parameters within the safety limits specified in the Operational Safety Requirements during normal operations and anticipated operational occurrences. 3. Those items required for nuclear criticality safety. 4. Those items required to monitor the release of radioactive material to the environment during and after a Design Basis Accident. Those items required to achieve, and maintain the facility in a safe shutdown condition 6. Those items that control Safety Class Item listed above
Directory of Open Access Journals (Sweden)
Hernan Garcia-Ruiz
2018-03-01
Full Text Available Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.
Directory of Open Access Journals (Sweden)
Daisy W. Leung
2015-04-01
Full Text Available During viral RNA synthesis, Ebola virus (EBOV nucleoprotein (NP alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48 that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
Leung, Daisy W; Borek, Dominika; Luthra, Priya; Binning, Jennifer M; Anantpadma, Manu; Liu, Gai; Harvey, Ian B; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; Shabman, Reed S; Chiu, Wah; Davey, Robert A; Otwinowski, Zbyszek; Basler, Christopher F; Amarasinghe, Gaya K
2015-04-21
During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
On the solvability of the compressible Navier–Stokes system in bounded domains
International Nuclear Information System (INIS)
Danchin, Raphaël
2010-01-01
This paper is dedicated to the well-posedness issue for the barotropic Navier–Stokes system with homogeneous Dirichlet boundary conditions in bounded domains of R N . We aim at considering data in as large a class as possible. Our main result is that if the initial density is bounded away from zero and belongs to some W 1,r with r > N, if the initial velocity is in the Besov space B 2-(2/p) r,p (and satisfies a suitable boundary condition), and if the body force is in L p loc (R + ;L r ) for some p > 1 then the system has a unique local solution. Our regularity assumptions are consistent with a dimensional analysis which shows that critical data would correspond to r = N and p = 1, and improve an old result by Solonnikov (1980 J. Sov. Math. 14 1120–32)
Characterization of the bound volatile extract from baby kiwi (Actinidia arguta).
Garcia, Coralia V; Quek, Siew-Young; Stevenson, Ralph J; Winz, Robert A
2011-08-10
The glycosidically bound volatile fraction of baby kiwi ( Actinidia arguta ) was studied. Glycosidic precursors were isolated from juice by adsorption onto an Amberlite XAD-2 column. After enzymatic hydrolysis with Rapidase AR2000, the released aglycones were analyzed by GC-MS. Alcohols, terpenoids, and benzenoids were the most abundant compound classes. Aromatic compounds and norisoprenoids showed the highest concentrations. Major compounds were 2,5-dimethyl-4-hydroxy-3(2H)-furanone (Furaneol), benzyl alcohol, 3-hydroxy-β-damascone, hexanal, and (Z)-3-hexen-1-ol. Precursors of aroma compounds including benzoic acid, cinnamic acid, and coniferyl alcohol were also found. Eugenol, raspberry ketone, and 4-vinylguaiacol were identified for the first time in the fruit of an Actinidia species. The high concentration of 2,5-dimethyl-4-hydroxy-3(2H)-furanone in bound form (95.36 μg/kg) is particularly interesting and justifies further investigation.
Quantum metrology in open systems: dissipative Cramér-Rao bound.
Alipour, S; Mehboudi, M; Rezakhani, A T
2014-03-28
Estimation of parameters is a pivotal task throughout science and technology. The quantum Cramér-Rao bound provides a fundamental limit of precision allowed to be achieved under quantum theory. For closed quantum systems, it has been shown how the estimation precision depends on the underlying dynamics. Here, we propose a general formulation for metrology scenarios in open quantum systems, aiming to relate the precision more directly to properties of the underlying dynamics. This feature may be employed to enhance an estimation precision, e.g., by quantum control techniques. Specifically, we derive a Cramér-Rao bound for a fairly large class of open system dynamics, which is governed by a (time-dependent) dynamical semigroup map. We illustrate the utility of this scenario through three examples.
On the unlikeliness of multi-field inflation: bounded random potentials and our vacuum
International Nuclear Information System (INIS)
Battefeld, Diana; Battefeld, Thorsten; Schulz, Sebastian
2012-01-01
Based on random matrix theory, we compute the likelihood of saddles and minima in a class of random potentials that are softly bounded from above and below, as required for the validity of low energy effective theories. Imposing this bound leads to a random mass matrix with non-zero mean of its entries. If the dimensionality of field-space is large, inflation is rare, taking place near a saddle point (if at all), since saddles are more likely than minima or maxima for common values of the potential. Due to the boundedness of the potential, the latter become more ubiquitous for rare low/large values respectively. Based on the observation of a positive cosmological constant, we conclude that the dimensionality of field-space after (and most likely during) inflation has to be low if no anthropic arguments are invoked, since the alternative, encountering a metastable deSitter vacuum by chance, is extremely unlikely
Tight upper bound for the maximal quantum value of the Svetlichny operators
Li, Ming; Shen, Shuqian; Jing, Naihuan; Fei, Shao-Ming; Li-Jost, Xianqing
2017-10-01
It is a challenging task to detect genuine multipartite nonlocality (GMNL). In this paper, the problem is considered via computing the maximal quantum value of Svetlichny operators for three-qubit systems and a tight upper bound is obtained. The constraints on the quantum states for the tightness of the bound are also presented. The approach enables us to give the necessary and sufficient conditions of violating the Svetlichny inequality (SI) for several quantum states, including the white and color noised Greenberger-Horne-Zeilinger (GHZ) states. The relation between the genuine multipartite entanglement concurrence and the maximal quantum value of the Svetlichny operators for mixed GHZ class states is also discussed. As the SI is useful for the investigation of GMNL, our results give an effective and operational method to detect the GMNL for three-qubit mixed states.
Hadamard States for the Klein-Gordon Equation on Lorentzian Manifolds of Bounded Geometry
Gérard, Christian; Oulghazi, Omar; Wrochna, Michał
2017-06-01
We consider the Klein-Gordon equation on a class of Lorentzian manifolds with Cauchy surface of bounded geometry, which is shown to include examples such as exterior Kerr, Kerr-de Sitter spacetime and the maximal globally hyperbolic extension of the Kerr outer region. In this setup, we give an approximate diagonalization and a microlocal decomposition of the Cauchy evolution using a time-dependent version of the pseudodifferential calculus on Riemannian manifolds of bounded geometry. We apply this result to construct all pure regular Hadamard states (and associated Feynman inverses), where regular refers to the state's two-point function having Cauchy data given by pseudodifferential operators. This allows us to conclude that there is a one-parameter family of elliptic pseudodifferential operators that encodes both the choice of (pure, regular) Hadamard state and the underlying spacetime metric.
Helioscope bounds on hidden sector photons
International Nuclear Information System (INIS)
Redondo, J.
2008-01-01
The flux of hypothetical ''hidden photons'' from the Sun is computed under the assumption that they interact with normal matter only through kinetic mixing with the ordinary standard model photon. Requiring that the exotic luminosity is smaller than the standard photon luminosity provides limits for the mixing parameter down to χ -14 , depending on the hidden photon mass. Furthermore, it is pointed point out that helioscopes looking for solar axions are also sensitive to hidden photons. The recent results of the CAST collaboration are used to further constrain the mixing parameter χ at low masses (m γ' <1 eV) where the luminosity bound is weaker. In this regime the solar hidden photon ux has a sizable contribution of longitudinally polarized hidden photons of low energy which are invisible for current helioscopes. (orig.)
Frenetic Bounds on the Entropy Production
Maes, Christian
2017-10-01
We give a systematic derivation of positive lower bounds for the expected entropy production (EP) rate in classical statistical mechanical systems obeying a dynamical large deviation principle. The logic is the same for the return to thermodynamic equilibrium as it is for steady nonequilibria working under the condition of local detailed balance. We recover there recently studied "uncertainty" relations for the EP, appearing in studies about the effectiveness of mesoscopic machines. In general our refinement of the positivity of the expected EP rate is obtained in terms of a positive and even function of the expected current(s) which measures the dynamical activity in the system, a time-symmetric estimate of the changes in the system's configuration. Also underdamped diffusions can be included in the analysis.
Bounded rational choice behaviour: applications in transport
DEFF Research Database (Denmark)
Jensen, Anders Fjendbo
2016-01-01
Even though the theory of rational behaviour has been challenged for almost 100 years, the dominant approach within the field of transport has been based upon the assumptions of neoclassical economics that we live in a world of rational decision makers who always have perfect knowledge and aim...... rational choice behaviour focuses on how the latter approach can be seriously taken into account within transport applications. As the editors discuss in the introduction, a true optimal choice can only be made if an individual has full and perfect information of all relevant attributes in his/her choice...... set. An individual is said to demonstrate bounded rational behaviour if he/she does not systematically consider all attributes deemed relevant for the decision problem at hand, does not consider all choice options and/or does not choose the best choice alternative. Such simplified representation...
Diffraction scattering of strongly bound system
International Nuclear Information System (INIS)
Kuzmichev, V.E.
1982-04-01
The scattering of a hadron on a strongly bound system of two hadrons (dihadron) is considered in the high-energy limit for the relative hadron-dihadron motion. The dihadron scatterer motion and the internal interaction are included in our consideration. It is shown that only small values of the internal transfer momentum of dihadron particles bring the principal contribution to the three-particle propagator in eikonal approximation. On the basis of the exact analytical solution of the integral equation for the total Green function the scattering amplitude is derived. It is shown that the scattering amplitude contains only single, double, and triple scattering terms. The three new terms to the Glauber formula for the total cross section are obtained. These terms decrease both the true total hadron-hadron cross section and the screening correction. (orig.)
Transient response in granular bounded heap flows
Xiao, Hongyi; Ottino, Julio M.; Lueptow, Richard M.; Umbanhowar, Paul B.
2017-11-01
Heap formation, a canonical granular flow, is common in industry and is also found in nature. Here, we study the transition between steady flow states in quasi-2D bounded heaps by suddenly changing the feed rate from one fixed value to another. During the transition, in both experiments and discrete element method simulations, an additional wedge of flowing particles propagates over the rising free surface. The downstream edge of the wedge - the wedge front - moves downstream with velocity inversely proportional to the square root of time. An additional longer duration transient process continues after the wedge front reaches the downstream wall. The transient flux profile during the entire transition is well modeled by a diffusion-like equation derived from local mass balance and a local linear relation between the flux and the surface slope. Scalings for the transient kinematics during the flow transitions are developed based on the flux profiles. Funded by NSF Grant CBET-1511450.
Similarity problems and completely bounded maps
Pisier, Gilles
2001-01-01
These notes revolve around three similarity problems, appearing in three different contexts, but all dealing with the space B(H) of all bounded operators on a complex Hilbert space H. The first one deals with group representations, the second one with C* -algebras and the third one with the disc algebra. We describe them in detail in the introduction which follows. This volume is devoted to the background necessary to understand these three problems, to the solutions that are known in some special cases and to numerous related concepts, results, counterexamples or extensions which their investigation has generated. While the three problems seem different, it is possible to place them in a common framework using the key concept of "complete boundedness", which we present in detail. Using this notion, the three problems can all be formulated as asking whether "boundedness" implies "complete boundedness" for linear maps satisfying certain additional algebraic identities. Two chapters have been added on the HALMO...
Entanglement negativity bounds for fermionic Gaussian states
Eisert, Jens; Eisler, Viktor; Zimborás, Zoltán
2018-04-01
The entanglement negativity is a versatile measure of entanglement that has numerous applications in quantum information and in condensed matter theory. It can not only efficiently be computed in the Hilbert space dimension, but for noninteracting bosonic systems, one can compute the negativity efficiently in the number of modes. However, such an efficient computation does not carry over to the fermionic realm, the ultimate reason for this being that the partial transpose of a fermionic Gaussian state is no longer Gaussian. To provide a remedy for this state of affairs, in this work, we introduce efficiently computable and rigorous upper and lower bounds to the negativity, making use of techniques of semidefinite programming, building upon the Lagrangian formulation of fermionic linear optics, and exploiting suitable products of Gaussian operators. We discuss examples in quantum many-body theory and hint at applications in the study of topological properties at finite temperature.
Dilation volumes of sets of bounded perimeter
DEFF Research Database (Denmark)
Kiderlen, Markus; Rataj, Jan
, this derivative coincides up to sign with the directional derivative of the covariogram of A in direction u. By known results for the covariogram, this derivative can therefore be expressed by the cosine transform of the surface area measure of A. We extend this result to sets Q that are at most countable and use...... it to determine the derivative of the contact distribution function of a stationary random closed set at zero. A variant for uncountable Q is given, too. The proofs are based on approximation of the characteristic function of A by smooth functions of bounded variation and showing corresponding formulas for them....
Hyperquarks and bosonic preon bound states
International Nuclear Information System (INIS)
Schmid, Michael L.; Buchmann, Alfons J.
2009-01-01
In a model in which leptons, quarks, and the recently introduced hyperquarks are built up from two fundamental spin-(1/2) preons, the standard model weak gauge bosons emerge as preon bound states. In addition, the model predicts a host of new composite gauge bosons, in particular, those responsible for hyperquark and proton decay. Their presence entails a left-right symmetric extension of the standard model weak interactions and a scheme for a partial and grand unification of nongravitational interactions based on, respectively, the effective gauge groups SU(6) P and SU(9) G . This leads to a prediction of the Weinberg angle at low energies in good agreement with experiment. Furthermore, using evolution equations for the effective coupling strengths, we calculate the partial and grand unification scales, the hyperquark mass scale, as well as the mass and decay rate of the lightest hyperhadron.
Factorization Procedure for Harmonically Bound Brownian Particle
International Nuclear Information System (INIS)
Omolo, JK.
2006-01-01
The method of factorization to solve the problem of the one-dimensional harmonically bound Brownian particle was applied. Assuming the the rapidily fluctuating random force is Gaussian and has an infinitely short correlation time, explicit expressions for the position-position,velocity-velocity, and the position-velocity correlation functions, which are also use to write down appropriate distribution functions were used. The correlation and distribution functions for the complex quantity (amplititude) which provides the expressions for the position and velocity of the particle are calculated. Finally, Fokker-Planck equations for the joint probability distribution functions for the amplititude and it's complex conjugate as well as for the position and velocity of the particle are obtained. (author)
Surface-bound states in nanodiamonds
Han, Peng; Antonov, Denis; Wrachtrup, Jörg; Bester, Gabriel
2017-05-01
We show via ab initio calculations and an electrostatic model that the notoriously low, but positive, electron affinity of bulk diamond becomes negative for hydrogen passivated nanodiamonds and argue that this peculiar situation (type-II offset with a vacuum level at nearly midgap) and the three further conditions: (i) a surface dipole with positive charge on the outside layer, (ii) a spherical symmetry, and (iii) a dielectric mismatch at the surface, results in the emergence of a peculiar type of surface state localized just outside the nanodiamond. These states are referred to as "surface-bound states" and have consequently a strong environmental sensitivity. These type of states should exist in any nanostructure with negative electron affinity. We further quantify the band offsets of different type of nanostructures as well as the exciton binding energy and contrast the results with results for "conventional" silicon quantum dots.
Volume Stability of Bitumen Bound Building Blocks
Directory of Open Access Journals (Sweden)
Thanaya I.N.A.
2010-01-01
Full Text Available This paper covers results of laboratory investigations on the volume stability of masonry units incorporating waste materials bound with bitumen (Bitublocks, due to moisture adsorption, thermal exposure and vacuum saturation. The materials used were steel slag, crushed glass, coal fly ash, and 50 pen bitumen. The samples were produced in hot mix method, compacted, then exposed to moist and temperature. It was found that moisture adsorption from the environment caused the Bitublock to expand. The samples with less intense curing regime experienced lower expansion and became stable faster, and vice versa. Under thermal condition (at 70°C, the samples with less intense curing regime underwent higher expansion, and vice versa. They were also highly reversible. Their volume stability was found unique under water exposure. The expansion on first vacuum saturation cycle was irreversible, then largely reversible on the following cycles.