General Model of Photon-Pair Detection with an Image Sensor

NASA Astrophysics Data System (ADS)

Defienne, Hugo; Reichert, Matthew; Fleischer, Jason W.

2018-05-01

We develop an analytic model that relates intensity correlation measurements performed by an image sensor to the properties of photon pairs illuminating it. Experiments using an effective single-photon counting camera, a linear electron-multiplying charge-coupled device camera, and a standard CCD camera confirm the model. The results open the field of quantum optical sensing using conventional detectors.

Single-photon-level quantum image memory based on cold atomic ensembles

PubMed Central

Ding, Dong-Sheng; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2013-01-01

A quantum memory is a key component for quantum networks, which will enable the distribution of quantum information. Its successful development requires storage of single-photon light. Encoding photons with spatial shape through higher-dimensional states significantly increases their information-carrying capability and network capacity. However, constructing such quantum memories is challenging. Here we report the first experimental realization of a true single-photon-carrying orbital angular momentum stored via electromagnetically induced transparency in a cold atomic ensemble. Our experiments show that the non-classical pair correlation between trigger photon and retrieved photon is retained, and the spatial structure of input and retrieved photons exhibits strong similarity. More importantly, we demonstrate that single-photon coherence is preserved during storage. The ability to store spatial structure at the single-photon level opens the possibility for high-dimensional quantum memories. PMID:24084711

Quantum chemistry study on the open end of single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Hou, Shimin; Shen, Ziyong; Zhao, Xingyu; Xue, Zengquan

2003-05-01

Geometrical and electronic structures of open-ended single-walled carbon nanotubes (SWCNTs) are calculated using density functional theory (DFT) with hybrid functional (B3LYP) approximation. Due to different distances between carbon atoms along the edge, reconstruction occurs at the open end of the (4,4) armchair SWCNT, i.e., triple bonds are formed in the carbon atom pairs at the mouth; however, for the (6,0) zigzag SWCNT, electrons in dangling bonds still remain at 'no-bonding' states. The ionization potential (IP) of both (4,4) and (6,0) SWCNTs is increased by their negative intrinsic dipole moments, and localized electronic states existed at both of their open ends.

An asymmetric mesoscopic model for single bulges in RNA

NASA Astrophysics Data System (ADS)

de Oliveira Martins, Erik; Weber, Gerald

2017-10-01

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy.

PubMed

Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

2015-10-31

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicted dual binding modes across multiple bacterial species, our approach opens up new possibilities for understanding assembly and catalytic properties of a broad range of multi-enzyme complexes.

Molecular cloning and nucleotide sequence of the alpha and beta subunits of allophycocyanin from the cyanelle genome of Cyanophora paradoxa.

PubMed Central

Bryant, D A; de Lorimier, R; Lambert, D H; Dubbs, J M; Stirewalt, V L; Stevens, S E; Porter, R D; Tam, J; Jay, E

1985-01-01

The genes for the alpha- and beta-subunit apoproteins of allophycocyanin (AP) were isolated from the cyanelle genome of Cyanophora paradoxa and subjected to nucleotide sequence analysis. The AP beta-subunit apoprotein gene was localized to a 7.8-kilobase-pair Pst I restriction fragment from cyanelle DNA by hybridization with a tetradecameric oligonucleotide probe. Sequence analysis using that oligonucleotide and its complement as primers for the dideoxy chain-termination sequencing method confirmed the presence of both AP alpha- and beta-subunit genes on this restriction fragment. Additional oligonucleotide primers were synthesized as sequencing progressed and were used to determine rapidly the nucleotide sequence of a 1336-base-pair region of this cloned fragment. This strategy allowed the sequencing to be completed without a detailed restriction map and without extensive and time-consuming subcloning. The sequenced region contains two open reading frames whose deduced amino acid sequences are 81-85% homologous to cyanobacterial and red algal AP subunits whose amino acid sequences have been determined. The two open reading frames are in the same orientation and are separated by 39 base pairs. AP alpha is 5' to AP beta and both coding sequences are preceded by a polypurine, Shine-Dalgarno-type sequence. Sequences upstream from AP alpha closely resemble the Escherichia coli consensus promoter sequences and also show considerable homology to promoter sequences for several chloroplast-encoded psbA genes. A 56-base-pair palindromic sequence downstream from the AP beta gene could play a role in the termination of transcription or translation. The allophycocyanin apoprotein subunit genes are located on the large single-copy region of the cyanelle genome. PMID:2987916

Melting of genomic DNA: Predictive modeling by nonlinear lattice dynamics

NASA Astrophysics Data System (ADS)

Theodorakopoulos, Nikos

2010-08-01

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the ϕX174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.

Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene.

PubMed Central

Earl, P L; Jones, E V; Moss, B

1986-01-01

A 5400-base-pair segment of the vaccinia virus genome was sequenced and an open reading frame of 938 codons was found precisely where the DNA polymerase had been mapped by transfer of a phosphonoacetate-resistance marker. A single nucleotide substitution changing glycine at position 347 to aspartic acid accounts for the drug resistance of the mutant vaccinia virus. The 5' end of the DNA polymerase mRNA was located 80 base pairs before the methionine codon initiating the open reading frame. Correspondence between the predicted Mr 108,577 polypeptide and the 110,000 purified enzyme indicates that little or no proteolytic processing occurs. Extensive homology, extending over 435 amino acids, was found upon comparing the DNA polymerase of vaccinia virus and DNA polymerase of Epstein-Barr virus. A highly conserved sequence of 14 amino acids in the carboxyl-terminal regions of the above DNA polymerases is also present at a similar location in adenovirus DNA polymerase. This structure, which is predicted to form a turn flanked by beta-pleated sheets, may form part of an essential binding or catalytic site that accounts for its presence in DNA polymerases of poxviruses, herpesviruses, and adenoviruses. Images PMID:3012524

Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations.

PubMed Central

Cotton, R G; Rodrigues, N R; Campbell, R D

1988-01-01

The chemical reactivity of thymine (T), when mismatched with the bases cytosine, guanine, and thymine, and of cytosine (C), when mismatched with thymine, adenine, and cytosine, has been examined. Heteroduplex DNAs containing such mismatched base pairs were first incubated with osmium tetroxide (for T and C mismatches) or hydroxylamine (for C mismatches) and then incubated with piperidine to cleave the DNA at the modified mismatched base. This cleavage was studied with an internally labeled strand containing the mismatched T or C, such that DNA cleavage and thus reactivity could be detected by gel electrophoresis. Cleavage at a total of 13 T and 21 C mismatches isolated (by at least three properly paired bases on both sides) single-base-pair mismatches was identified. All T or C mismatches studied were cleaved. By using end-labeled DNA probes containing T or C single-base-pair mismatches and conditions for limited cleavage, we were able to show that cleavage was at the base predicted by sequence analysis and that mismatches in a length of DNA could be readily detected by such an approach. This procedure may enable detection of all single-base-pair mismatches by use of sense and antisense probes and thus may be used to identify the mutated base and its position in a heteroduplex. Images PMID:3260032

Paired-pulse flash-visual evoked potentials: new methods revive an old test.

PubMed

Cantello, Roberto; Strigaro, Gionata; Prandi, Paolo; Varrasi, Claudia; Mula, Marco; Monaco, Francesco

2011-08-01

We aimed at reviving with modern technology the paired flash-visual evoked potential (F-VEP) testing of the visual system excitability. In the 1960s, methodological problems hindered this test, which was expected to provide important physiologic information. We studied 22 consenting healthy subjects (10 men). We recorded F-VEPs from electrodes over occipital and central brain regions. We delivered single flashes, mixed at random to flash pairs at the interstimulus interval (ISI) of 333, 125, 62.5, 50, 33, and 16.5 ms, (i.e. an internal frequency (IF) of 3, 8, 16, 20, 30, and 60 Hz). Recordings were performed with the subject's eyes closed and opened. The F-VEP was split into a "main complex" and an "afterdischarge", which we analyzed statistically in relation to the eye state (closed or open) and to the changes due to paired stimulation. The eye state affected the single F-VEP size, latency and shape significantly (p<0.05). On paired stimulation, the test (second) F-VEP exhibited significant (p<0.05), ISI-dependent size changes, such as a progressive decrease for ISIs from 62.5 to 16.5 ms (IFs of 16-60 Hz), whose timing/amount varied significantly (p<0.05) according to the eye state and to the F-VEP epoch considered. Suppression of the test F-VEP was never complete, even for the shortest ISI (ISI=16.5 ms, IF=60 Hz). The eye state (closed or open) must be considered meticulously when studying F-VEPs. F-VEP changes on paired stimulation express neural inhibition within the visual system, which can be depicted as ISI-dependent curves. Modern equipment and simplified measures render this an easy test, with statistical validity, providing specific information on the excitability properties of the visual system. Copyright © 2011 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

NASA Technical Reports Server (NTRS)

Vercoutere, Wenonah; DeGuzman, Veronica

2003-01-01

The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

Database of non-canonical base pairs found in known RNA structures

NASA Technical Reports Server (NTRS)

Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

2000-01-01

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

A feasibility of single-incision laparoscopic percutaneous extraperitoneal closure for treatment of incarcerated inguinal hernia in children: our preliminary outcome and review of the literature.

PubMed

Murase, Naruhiko; Uchida, Hiroo; Seki, Takashi; Hiramatsu, Kiyoshi

2016-02-01

The purpose of this study is to examine the feasibility of single-incision laparoscopic percutaneous extraperitoneal closure (LPEC) for incarcerated inguinal hernia (IIH) repair. 6 single-incision LPEC procedures were performed for IIH repair and 60 procedures were performed for reducible inguinal hernia (RIH) in the same period of time in one hospital. The laparoscope and one pair of grasping forceps were placed through the same umbilical incision. In IIH repair, the herniated organ was gently pulled using the grasping forceps with external manual pressure. If it was difficult to reduce the herniated organ with one pair of forceps, another pair of forceps were inserted through a multi-channel port without extending the umbilical incidion. Using the LPEC needle, the hernia orifice was closed extraperitoneally. We performed a retrospective analysis to compare the outcomes of single-incision LPEC for IIH repair or reducible inguinal hernia. All procedures were completed by single-incision without open conversion. A multi-channel port with another pair of forceps was needed in three cases. The operation time and the length of stay were significantly longer with IIH repair than with RIH repair. There were no major complications and there was no evidence of early recurrence in any patient. In conclusion, single-incision LPEC with a multi-channel port is feasible and safe for IIH repair.

Mid-infrared coincidence measurements on twin photons at room temperature

PubMed Central

Mancinelli, M.; Trenti, A.; Piccione, S.; Fontana, G.; Dam, J. S.; Tidemand-Lichtenberg, P.; Pedersen, C.; Pavesi, L.

2017-01-01

Quantum measurements using single-photon detectors are opening interesting new perspectives in diverse fields such as remote sensing, quantum cryptography and quantum computing. A particularly demanding class of applications relies on the simultaneous detection of correlated single photons. In the visible and near infrared wavelength ranges suitable single-photon detectors do exist. However, low detector quantum efficiency or excessive noise has hampered their mid-infrared (MIR) counterpart. Fast and highly efficient single-photon detectors are thus highly sought after for MIR applications. Here we pave the way to quantum measurements in the MIR by the demonstration of a room temperature coincidence measurement with non-degenerate twin photons at about 3.1 μm. The experiment is based on the spectral translation of MIR radiation into the visible region, by means of efficient up-converter modules. The up-converted pairs are then detected with low-noise silicon avalanche photodiodes without the need for cryogenic cooling. PMID:28504244

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy

PubMed Central

Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

2015-01-01

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicteddual binding modes across multiple bacterial species, our approach opens up newpossibilities for understanding assembly and catalytic properties of a broadrange of multi-enzyme complexes. DOI: http://dx.doi.org/10.7554/eLife.10319.001 PMID:26519733

Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

PubMed

Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay

2005-12-01

Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory.

PubMed

Saitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F; Neese, Frank

2017-04-28

The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N 6 ) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.

A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory

NASA Astrophysics Data System (ADS)

Saitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F.; Neese, Frank

2017-04-01

The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N6) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.

Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying.

PubMed

Nonin, S; Leroy, J L; Guéron, M

1995-08-22

We have estimated the dissociation constant of the terminal base pairs of the B-DNA duplexes formed by 5'-d(CGCGATCGCG) and 5'-d(TAGCGCTA) by two methods, one based on the change in imino proton chemical shift with temperature and the other on the apparent pK shift of the imino proton, as monitored by the change in chemical shift of aromatic protons. These methods do not rely on imino proton exchange, whose rate was also measured. (1) The effect of ammonia on the imino proton exchange rate of the terminal pair of the 5'-d(CGCGATCGCG) duplex is 67 times less than on the isolated nucleoside. This provides an upper limit on the exchange rate from the closed pair. In fact, the effect is just as predicted from the dissociation constant, assuming that there is no exchange at all from the closed pair and that, as has been argued previously, external catalysts act on the open state as they do on the isolated nucleoside. The inhibition of catalyzed proton exchange in the closed pair, despite exposure of one face of the pair to solvent, is a new feature of the exchange process. It will allow determination of the dissociation constant of terminal pairs from the exchange rate. (2) Intrinsic catalysis of proton exchange is less efficient for the terminal pair than for an internal one. A possible explanation is that proton transfer across the water bridge responsible for intrinsic catalysis is slower, as expected if the open-state separation of the bases is larger in a terminal pair. This observation may lead to a direct method for the study of fraying. (3) At 0 degrees C, the dissociation constant of the second pair of the 5'-d(CGCGATCGCG) duplex is close to the square of the constant for the terminal pair, as predicted from a simple model of fraying. The enthalpy and entropy of opening of the terminal pairs may be compared with those of nearest neighbor interactions derived from calorimetry [Breslauer, K. J., et al. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750].

Triple helical DNA in a duplex context and base pair opening

PubMed Central

Esguerra, Mauricio; Nilsson, Lennart; Villa, Alessandra

2014-01-01

It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region. PMID:25228466

Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.

PubMed

Nonin, S; Leroy, J L

1996-08-23

At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.

Nucleotide sequence of the gene determining plasmid-mediated citrate utilization.

PubMed Central

Ishiguro, N; Sato, G

1985-01-01

The citrate utilization determinant from transposon Tn3411 has been cloned and sequenced, and its polypeptide products have been characterized in minicell experiments. The nucleotide sequence was determined for a 2,047-base-pair BglII restriction endonuclease fragment that includes the citrate determinant. This region contains an open reading frame that would encode a 431-amino-acid very hydrophobic polypeptide and which is preceded by a reasonable ribosomal binding site. However, the single polypeptide found in minicell experiments had an apparent molecular weight of 35,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Images PMID:2999087

mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets.

PubMed

Dalke, Andrew; Hert, Jérôme; Kramer, Christian

2018-05-29

Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .

Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

The nucleotide sequence of a tRNALys(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNAGly(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long. Images PMID:16593561

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron.

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

The nucleotide sequence of a tRNA(Lys)(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNA(Gly)(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long.

Single-Molecule Patch-Clamp FRET Anisotropy Microscopy Studies of NMDA Receptor Ion Channel Activation and Deactivation under Agonist Ligand Binding in Living Cells.

PubMed

Sasmal, Dibyendu Kumar; Yadav, Rajeev; Lu, H Peter

2016-07-20

N-methyl-d-aspartate (NMDA) receptor ion channel is activated by the binding of two pairs of glycine and glutamate along with the application of action potential. Binding and unbinding of ligands changes its conformation that plays a critical role in the open-close activities of NMDA receptor. Conformation states and their dynamics due to ligand binding are extremely difficult to characterize either by conventional ensemble experiments or single-channel electrophysiology method. Here we report the development of a new correlated technical approach, single-molecule patch-clamp FRET anisotropy imaging and demonstrate by probing the dynamics of NMDA receptor ion channel and kinetics of glycine binding with its ligand binding domain. Experimentally determined kinetics of ligand binding with receptor is further verified by computational modeling. Single-channel patch-clamp and four-channel fluorescence measurement are recorded simultaneously to get correlation among electrical on and off states, optically determined conformational open and closed states by FRET, and binding-unbinding states of the glycine ligand by anisotropy measurement at the ligand binding domain of GluN1 subunit. This method has the ability to detect the intermediate states in addition to electrical on and off states. Based on our experimental results, we have proposed that NMDA receptor gating goes through at least one electrically intermediate off state, a desensitized state, when ligands remain bound at the ligand binding domain with the conformation similar to the fully open state.

Beyond BCS pairing in high-density neutron matter

NASA Astrophysics Data System (ADS)

Rios, A.; Ding, D.; Dussan, H.; Dickhoff, W. H.; Witte, S. J.; Polls, A.

2018-01-01

Pairing gaps in neutron matter need to be computed in a wide range of densities to address open questions in neutron star phenomenology. Traditionally, the Bardeen-Cooper-Schrieffer approach has been used to compute gaps from bare nucleon-nucleon interactions. Here, we incorporate the influence of short- and long-range correlations into pairing properties. Short-range correlations are treated including the appropriate fragmentation of single-particle states, and they suppress the gaps substantially. Long-range correlations dress the pairing interaction via density and spin modes, and provide a relatively small correction. We use three different interactions as a starting point to control for any systematic effects. Results are relevant for neutron-star cooling scenarios, in particular in view of the recent observational data on Cassiopeia A.

Array based Discovery of Aptamer Pairs (Open Access Publisher’s Version)

DTIC Science & Technology

2014-12-11

Array-based Discovery of Aptamer Pairs Minseon Cho,†,‡ Seung Soo Oh,‡ Jeff Nie,§ Ron Stewart,§ Monte J. Radeke,⊥ Michael Eisenstein,†,‡ Peter J...bidentate” target recognition, with affinities greatly exceeding either monovalent component. DNA aptamers are especially well-suited for such...constructs, because they can be linked via standard synthesis techniques without requiring chemical conjugation. Unfortunately, aptamer pairs are difficult

Molecular cloning of an inducible serine esterase gene from human cytotoxic lymphocytes.

PubMed Central

Trapani, J A; Klein, J L; White, P C; Dupont, B

1988-01-01

A cDNA clone encoding a human serine esterase gene was isolated from a library constructed from poly(A)+ RNA of allogeneically stimulated, interleukin 2-expanded peripheral blood mononuclear cells. The clone, designated HSE26.1, represents a full-length copy of a 0.9-kilobase mRNA present in human cytotoxic cells but absent from a wide variety of noncytotoxic cell lines. Clone HSE26.1 contains an 892-base-pair sequence, including a single 741-base-pair open reading frame encoding a putative 247-residue polypeptide. The first 20 amino acids of the polypeptide form a leader sequence. The mature protein is predicted to have an unglycosylated Mr of approximately equal to 26,000 and contains a single potential site for N-linked glycosylation. The nucleotide and predicted amino acid sequences of clone HSE26.1 are homologous with all murine and human serine esterases cloned thus far but are most similar to mouse granzyme B (70% nucleotide and 68% amino acid identity). HSE26.1 protein is expressed weakly in unstimulated peripheral blood mononuclear cells but is strongly induced within 6-hr incubation in medium containing phytohemagglutinin. The data suggest that the protein encoded by HSE26.1 plays a role in cell-mediated cytotoxicity. Images PMID:3261871

Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

PubMed Central

Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

2003-01-01

Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

Space closing versus space opening for bilateral missing upper laterals - aesthetic judgments of laypeople: a web-based survey.

PubMed

Qadri, Salim; Parkin, Nicola A; Benson, Philip E

2016-06-01

To investigate the opinions of laypeople regarding the aesthetic outcome of treating patients with developmental absence of both maxillary lateral incisors using either orthodontic space closure (OSC) or space opening and prosthetic replacement (PR). Cross sectional, web-based survey. A panel of five orthodontists and five restorative dentists examined post-treatment intra-oral images of 21 patients with developmental absence of both upper lateral incisors. A consensus view was obtained about the 10 most attractive images (5 OSC; 5 PR). The 10 selected images were used in a web-based survey involving staff and students at the University of Sheffield. In the first section, the participants were asked to evaluate the attractiveness of the 10 randomly arranged single images using a 5-point Likert scale. In the second section, an image of OSC was paired with an image of PR according to their attractiveness ranking by the clinician panel, and the participants were asked to indicate which of the two images they preferred. The survey received 959 completed responses with 9590 judgements. The images of OSC were perceived to be more attractive (mean rating 3·34 out of 5; SD 0·56) compared with the images of PR (mean rating 3·14 out of 5; SD 0·58) (mean diff 0·21; P < 0·001). Female and staff judges tended to give higher attractiveness ratings. Both females and males preferred the OSC images closing in 3 out of 4 paired images. Space closing was perceived to be more attractive than space opening by lay people. The findings have implications for advising patients about the best aesthetic outcome when both maxillary lateral incisors are missing.

DNA Hairpins Containing the Cytidine Analog Pyrrolo-dC: Structural, Thermodynamic, and Spectroscopic Studies

PubMed Central

Zhang, Xu; Wadkins, Randy M.

2009-01-01

Structures formed by single-strand DNA have become increasingly interesting because of their roles in a number of biological processes, particularly transcription and its regulation. Of particular importance is the fact that antitumor drugs such as Actinomycin D can selectively bind DNA hairpins over fully paired, double-strand DNA. A new fluorescent base analog, pyrrolo-deoxycytidine (PdC), can now be routinely incorporated into single-strand DNA. The fluorescence of PdC is particularly useful for studying the formation of single-strand DNA in regions of double-strand DNA. The fluorescence is quenched when PdC is paired with a complementary guanine residue, and thus is greatly enhanced upon formation of single-strand DNA. Hence, any process that results in melting or opening of DNA strands produces an increase in the fluorescence intensity of this base analog. In this study we measured the structural effects of incorporating PdC into DNA hairpins, and the effect of this incorporation on the binding of the hairpins by a fluorescent analog of the drug Actinomycin D. Two hairpin DNAs were used: one with PdC in the stem (basepaired) and one with PdC in the loop (unpaired). The thermal stability, 7-aminoactinomycin D binding, and three-dimensional structures of PdC incorporated into these DNA hairpins were all quite similar as compared to the hairpins containing an unmodified dC residue. Fluorescence lifetime measurements indicate that two lifetimes are present in PdC, and that the increase in fluorescence of the unpaired PdC residue compared to the basepaired PdC is due to an increase in the contribution of the longer lifetime to the average fluorescence lifetime. Our data indicate that PdC can be used effectively to differentiate paired and unpaired bases in DNA hairpin secondary structures, and should be similarly applicable for related structures such as cruciforms and quadruplexes. Further, our data indicate that PdC can act as a fluorescence resonance energy transfer donor for the fluorescent drug 7-aminoactinomycin D. PMID:19254547

DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies.

PubMed

Zhang, Xu; Wadkins, Randy M

2009-03-04

Structures formed by single-strand DNA have become increasingly interesting because of their roles in a number of biological processes, particularly transcription and its regulation. Of particular importance is the fact that antitumor drugs such as Actinomycin D can selectively bind DNA hairpins over fully paired, double-strand DNA. A new fluorescent base analog, pyrrolo-deoxycytidine (PdC), can now be routinely incorporated into single-strand DNA. The fluorescence of PdC is particularly useful for studying the formation of single-strand DNA in regions of double-strand DNA. The fluorescence is quenched when PdC is paired with a complementary guanine residue, and thus is greatly enhanced upon formation of single-strand DNA. Hence, any process that results in melting or opening of DNA strands produces an increase in the fluorescence intensity of this base analog. In this study we measured the structural effects of incorporating PdC into DNA hairpins, and the effect of this incorporation on the binding of the hairpins by a fluorescent analog of the drug Actinomycin D. Two hairpin DNAs were used: one with PdC in the stem (basepaired) and one with PdC in the loop (unpaired). The thermal stability, 7-aminoactinomycin D binding, and three-dimensional structures of PdC incorporated into these DNA hairpins were all quite similar as compared to the hairpins containing an unmodified dC residue. Fluorescence lifetime measurements indicate that two lifetimes are present in PdC, and that the increase in fluorescence of the unpaired PdC residue compared to the basepaired PdC is due to an increase in the contribution of the longer lifetime to the average fluorescence lifetime. Our data indicate that PdC can be used effectively to differentiate paired and unpaired bases in DNA hairpin secondary structures, and should be similarly applicable for related structures such as cruciforms and quadruplexes. Further, our data indicate that PdC can act as a fluorescence resonance energy transfer donor for the fluorescent drug 7-aminoactinomycin D.

LRET Determination of Molecular Distances during pH Gating of the Mammalian Inward Rectifier Kir1.1b.

PubMed

Nanazashvili, Mikheil; Sánchez-Rodríguez, Jorge E; Fosque, Ben; Bezanilla, Francisco; Sackin, Henry

2018-01-09

Gating of the mammalian inward rectifier Kir1.1 at the helix bundle crossing (HBC) by intracellular pH is believed to be mediated by conformational changes in the C-terminal domain (CTD). However, the exact motion of the CTD during Kir gating remains controversial. Crystal structures and single-molecule fluorescence resonance energy transfer of KirBac channels have implied a rigid body rotation and/or a contraction of the CTD as possible triggers for opening of the HBC gate. In our study, we used lanthanide-based resonance energy transfer on single-Cys dimeric constructs of the mammalian renal inward rectifier, Kir1.1b, incorporated into anionic liposomes plus PIP 2 , to determine unambiguous, state-dependent distances between paired Cys residues on diagonally opposite subunits. Functionality and pH dependence of our proteoliposome channels were verified in separate electrophysiological experiments. The lanthanide-based resonance energy transfer distances measured in closed (pH 6) and open (pH 8) conditions indicated neither expansion nor contraction of the CTD during gating, whereas the HBC gate widened by 8.8 ± 4 Å, from 6.3 ± 2 to 15.1 ± 6 Å, during opening. These results are consistent with a Kir gating model in which rigid body rotation of the large CTD around the permeation axis is correlated with opening of the HBC hydrophobic gate, allowing permeation of a 7 Å hydrated K ion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Universal quantum gates for Single Cooper Pair Box based quantum computing

NASA Technical Reports Server (NTRS)

Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

2000-01-01

We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

Applications of High-Q Microresonators in Cavity Optomechanics and Nonlinear Photonics

NASA Astrophysics Data System (ADS)

Jiang, Wei C.

Optical microresonators confining light to small volumes are indispensable for a great variety of studies and applications. This thesis is devoted to a study of cavity optomechanical and nonlinear optical phenomena in high-Q microresonators with different materials and structures. Based on that, it proposes and demonstrates several novel schemes and device platforms that exhibit great potential for various applications ranging from frequency metrology and quantum photonics, to information processing and sensing. The thesis starts with a demonstration of a high-frequency (above 1 GHz) regenerative optomechanical oscillator based on a 2-mum-radius high-Q silicon microdisk resonator in the silicon-on-insulator platform with an ultra-low threshold pump power at room temperature and atmosphere. It then continues to explore the cavity optomechanics in single-crystal lithium niobate. A compact lithium niobate microdisk optomechanical resonator with high optical and mechanical qualities, large optomechanical coupling, and high mechanical frequency is achieved, enabling the demonstration of regenerative oscillation in the ambience. Meanwhile, I propose and investigate a novel approach for single molecule detection that utilizes the optical spring effect in a high-Q coherent optomechanical oscillator to dramatically enhance the sensing resolution by orders of magnitude compared with conventional resonator-based approaches. In particular, a high-Q silica microsphere is employed to experimentally demonstrate the detection of single Bovine Serum Albumin proteins with a molecular weight of 66 kDalton at a signal-to-noise ratio of 16.8. On the other hand, the thesis focuses on the theoretical and experimental investigation of the generation of high-purity bright photon pairs in a silicon microdisk based on the cavity enhanced four-wave mixing. The device is able to produce multiple photon pairs at different wavelengths in the telecom band with a high spectral brightness of 6.24 x 107 pairs/s/mW 2/GHz and photon-pair correlation with a coincidence-to-accidental ratio of 1386+/-278 while pumped with a continuous-wave laser. Finally, an intriguing approach is proposed for dispersion dynamic tuning and micro-engineering, by taking advantage of the optical forces in nano-optomechanical structures. The proposed approach exhibits great potential for broad applications in dispersion-sensitive processes, which not only offer a new root towards versatile tunable nonlinear photonics, but may also open up a great avenue towards a new regime of nonlinear dynamics coupling between nonlinear optical and optomechanical effects.

Experimental simulation of decoherence in photonics qudits

PubMed Central

Marques, B.; Matoso, A. A.; Pimenta, W. M.; Gutiérrez-Esparza, A. J.; Santos, M. F.; Pádua, S.

2015-01-01

We experimentally perform the simulation of open quantum dynamics in single-qudit systems. Using a spatial light modulator as a dissipative optical device, we implement dissipative-dynamical maps onto qudits encoded in the transverse momentum of spontaneous parametric down-converted photon pairs. We show a well-controlled technique to prepare entangled qudits states as well as to implement dissipative local measurements; the latter realize two specific dynamics: dephasing and amplitude damping. Our work represents a new analogy-dynamical experiment for simulating an open quantum system. PMID:26527330

Self sufficient wireless transmitter powered by foot-pumped urine operating wearable MFC.

PubMed

Taghavi, M; Stinchcombe, A; Greenman, J; Mattoli, V; Beccai, L; Mazzolai, B; Melhuish, C; Ieropoulos, I A

2015-12-10

The first self-sufficient system, powered by a wearable energy generator based on microbial fuel cell (MFC) technology is introduced. MFCs made from compliant material were developed in the frame of a pair of socks, which was fed by urine via a manual gaiting pump. The simple and single loop cardiovascular fish circulatory system was used as the inspiration for the design of the manual pump. A wireless programmable communication module, engineered to operate within the range of the generated electricity, was employed, which opens a new avenue for research in the utilisation of waste products for powering portable as well as wearable electronics.

Recognition Tunneling

PubMed Central

Lindsay, Stuart; He, Jin; Sankey, Otto; Hapala, Prokop; Jelinek, Pavel; Zhang, Peiming; Chang, Shuai; Huang, Shuo

2010-01-01

Single molecules in a tunnel junction can now be interrogated reliably using chemically-functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode (“tethered molecule-pair” configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the “free analyte” configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules. PMID:20522930

Effect of proton transfer on the electronic coupling in DNA

NASA Astrophysics Data System (ADS)

Rak, Janusz; Makowska, Joanna; Voityuk, Alexander A.

2006-06-01

The effects of single and double proton transfer within Watson-Crick base pairs on donor-acceptor electronic couplings, Vda, in DNA are studied on the bases of quantum chemical calculations. Four dimers [AT,AT], [GC,GC], [GC,AT] and [GC,TA)] are considered. Three techniques - the generalized Mulliken-Hush scheme, the fragment charge method and the diabatic states method - are employed to estimate Vda for hole transfer between base pairs. We show that both single- and double proton transfer (PT) reactions may substantially affect the electronic coupling in DNA. The electronic coupling in [AT,AT] is predicted to be most sensitive to PT. Single PT within the first base pair in the dimer leads to increase in the hole transfer efficiency by a factor of 4, while proton transfer within the second pair should substantially, by 2.7 times, decrease the rate of charge transfer. Thus, directional asymmetry of the PT effects on the electronic coupling is predicted. The changes in the Vda matrix elements correlate with the topological properties of orbitals of donor and acceptor and can be qualitatively rationalized in terms of resonance structures of donor and acceptor. Atomic pair contributions to the Vda matrix elements are also analyzed.

Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs.

PubMed

Girelli Zubani, Giulia; Zivojnovic, Marija; De Smet, Annie; Albagli-Curiel, Olivier; Huetz, François; Weill, Jean-Claude; Reynaud, Claude-Agnès; Storck, Sébastien

2017-04-03

During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung -/- Pms2 -/- mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases. © 2017 Girelli Zubani et al.

Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs

PubMed Central

De Smet, Annie; Albagli-Curiel, Olivier; Huetz, François; Weill, Jean-Claude

2017-01-01

During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung−/−Pms2−/− mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases. PMID:28283534

Dissociation of single-strand DNA: single-walled carbon nanotube hybrids by Watson-Crick base-pairing.

PubMed

Jung, Seungwon; Cha, Misun; Park, Jiyong; Jeong, Namjo; Kim, Gunn; Park, Changwon; Ihm, Jisoon; Lee, Junghoon

2010-08-18

It has been known that single-strand DNA wraps around a single-walled carbon nanotube (SWNT) by pi-stacking. In this paper it is demonstrated that such DNA is dissociated from the SWNT by Watson-Crick base-pairing with a complementary sequence. Measurement of field effect transistor characteristics indicates a shift of the electrical properties as a result of this "unwrapping" event. We further confirm the suggested process through Raman spectroscopy and gel electrophoresis. Experimental results are verified in view of atomistic mechanisms with molecular dynamics simulations and binding energy analyses.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

PubMed

Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

2015-02-10

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson–Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine

DOE PAGES

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw; ...

2015-01-29

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

PubMed Central

2016-01-01

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

Tri-state logic circuit

NASA Technical Reports Server (NTRS)

Pryor, Richard Lee (Inventor)

1977-01-01

A line driver including a pair of complementary transistors having their conduction paths serially connected between an operating and a reference potential and their bases connected through a first switch to a signal input terminal. A second switch is connected between the common base connection and the common connection of the conduction paths. With the second switch open and the first closed, an output voltage, responsive to the input signal, corresponding to first or second binary values is obtained. When the second switch is closed and the first opened, the transistor pair is turned off, disconnecting the line driver from its load, thereby providing tri-state logic operation.

Thermal imitators with single directional invisibility

NASA Astrophysics Data System (ADS)

Wang, Ruizhe; Xu, Liujun; Huang, Jiping

2017-12-01

Thermal metamaterials have been intensively studied during the past years to achieve the long-standing dream of invisibility, illusion, and other inconceivable thermal phenomena. However, many thermal metamaterials can only exhibit omnidirectional thermal response, which take on the distinct feature of geometrical isotropy. In this work, we theoretically design and experimentally fabricate a pair of thermal imitators by applying geometrical anisotropy provided by elliptical/ellipsoidal particles and layered structures. This pair of thermal imitators possesses thermal invisibility in one direction, while having thermal opacity in other directions. This work may open a gate in designing direction-dependent thermal metamaterials.

DNA dynamics in aqueous solution: opening the double helix

NASA Technical Reports Server (NTRS)

Pohorille, A.; Ross, W. S.; Tinoco, I. Jr; MacElroy, R. D. (Principal Investigator)

1990-01-01

The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the molecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest reaction in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dynamics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water molecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.

Optical storage networking

NASA Astrophysics Data System (ADS)

Mohr, Ulrich

2001-11-01

For efficient business continuance and backup of mission- critical data an inter-site storage network is required. Where traditional telecommunications costs are prohibitive for all but the largest organizations, there is an opportunity for regional carries to deliver an innovative storage service. This session reveals how a combination of optical networking and protocol-aware SAN gateways can provide an extended storage networking platform with the lowest cost of ownership and the highest possible degree of reliability, security and availability. Companies of every size, with mainframe and open-systems environments, can afford to use this integrated service. Three mayor applications are explained; channel extension, Network Attached Storage (NAS), Storage Area Networks (SAN) and how optical networks address the specific requirements. One advantage of DWDM is the ability for protocols such as ESCON, Fibre Channel, ATM and Gigabit Ethernet, to be transported natively and simultaneously across a single fiber pair, and the ability to multiplex many individual fiber pairs over a single pair, thereby reducing fiber cost and recovering fiber pairs already in use. An optical storage network enables a new class of service providers, Storage Service Providers (SSP) aiming to deliver value to the enterprise by managing storage, backup, replication and restoration as an outsourced service.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Turbulent flow in a partially filled pipe

NASA Astrophysics Data System (ADS)

Ng, Henry; Cregan, Hope; Dodds, Jonathan; Poole, Robert; Dennis, David

2017-11-01

Turbulent flow in a pressure driven pipe running partially full has been investigated using high-speed 2D-3C Stereoscopic Particle Imaging Velocimetry. With the field-of-view spanning the entire pipe cross section we are able to reconstruct the full three dimensional quasi-instantaneous flow field by invoking Taylor's hypothesis. The measurements were carried out over a range of flow depths at a constant Reynolds number based on hydraulic diameter and bulk velocity of Re = 32 , 000 . In agreement with previous studies, the ``velocity dip'' phenomenon, whereby the location of the maximum streamwise velocity occurs below the free surface was observed. A mean flow secondary current is observed near the free surface with each of the counter-rotating rollers filling the half-width of the pipe. Unlike fully turbulent flow in a rectangular open channel or pressurized square duct flow where the secondary flow cells appear in pairs about a corner bisector, the mean secondary motion observed here manifests only as a single pair of vortices mirrored about the pipe vertical centreline.

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

PubMed

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

Using Pair Programming to Teach CAD Based Engineering Graphics

ERIC Educational Resources Information Center

Leland, Robert P.

2010-01-01

Pair programming was introduced into a course in engineering graphics that emphasizes solid modeling using SolidWorks. In pair programming, two students work at a single computer, and periodically trade off roles as driver (hands on the keyboard and mouse) and navigator (discuss strategy and design issues). Pair programming was used in a design…

A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch: General Architecture of the Metalloinsertion Binding Mode†

PubMed Central

Zeglis, Brian M.; Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2009-01-01

Two crystal structures are determined for Δ-Rh(bpy)2(chrysi)3+ (chrysi = 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5′-CGGAAATTACCG-3′ containing two adenosine-adenosine mismatches (italics) through metalloinsertion. Diffraction quality crystals with two different space groups (P3221 and P43212) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2′-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5′-AT-3′ step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Δ-Rh(bpy)2(chrysi)3+ bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single base mismatches. These results underscore the generality of the metalloinsertion as a new mode of non-covalent binding by small molecules with a DNA duplex. PMID:19374348

The Economic Influences of Elementary School Sites on Residential Property Tax Revenue in Selected Urban Neighborhoods.

ERIC Educational Resources Information Center

Grube, Karl William

This study attempted to: (1) develop research criteria and statistically valid analyses; (2) measure the economic influences of well-developed and undeveloped elementary school sites, large open space and small, or limited space school sites, on the market sale prices of comparable single-family residential housing units in matched pairs of urban…

Structural energetics of the adenine tract from an intrinsic transcription terminator.

PubMed

Huang, Yuegao; Weng, Xiaoli; Russu, Irina M

2010-04-02

Intrinsic transcription termination sites generally contain a tract of adenines in the DNA template that yields a tract of uracils at the 3' end of the nascent RNA. To understand how this base sequence contributes to termination of transcription, we have investigated two nucleic acid structures. The first is the RNA-DNA hybrid that contains the uracil tract 5'-rUUUUUAU-3' from the tR2 intrinsic terminator of bacteriophage lambda. The second is the homologous DNA-DNA duplex that contains the adenine tract 5'-dATAAAAA-3'. This duplex is present at the tR2 site when the DNA is not transcribed. The opening and the stability of each rU-dA/dT-dA base pair in the two structures are characterized by imino proton exchange and nuclear magnetic resonance spectroscopy. The results reveal concerted opening of the central rU-dA base pairs in the RNA-DNA hybrid. Furthermore, the stability profile of the adenine tract in the RNA-DNA hybrid is very different from that of the tract in the template DNA-DNA duplex. In the RNA-DNA hybrid, the stabilities of rU-dA base pairs range from 4.3 to 6.5 kcal/mol (at 10 degrees C). The sites of lowest stability are identified at the central positions of the tract. In the template DNA-DNA duplex, the dT-dA base pairs are more stable than the corresponding rU-dA base pairs in the hybrid by 0.9 to 4.6 kcal/mol and, in contrast to the RNA-DNA hybrid, the central base pairs have the highest stability. These results suggest that the central rU-dA/dT-dA base pairs in the adenine tract make the largest energetic contributions to transcription termination by promoting both the dissociation of the RNA transcript and the closing of the transcription bubble. The results also suggest that the high stability of dT-dA base pairs in the DNA provides a signal for the pausing of RNA polymerase at the termination site. Copyright 2010 Elsevier Ltd. All rights reserved.

Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3), and comparison of the closely related E. coli B and K-12 genomes

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

Studier, F.W.; Daegelen, P.; Lenski, R. E.

2009-12-01

Each difference between the genome sequences of Escherichia coli B strains REL606 and BL21(DE3) can be interpreted in light of known laboratory manipulations plus a gene conversion between ribosomal RNA operons. Two treatments with 1-methyl-3-nitro-1-nitrosoguanidine in the REL606 lineage produced at least 93 single-base-pair mutations ({approx} 90% GC-to-AT transitions) and 3 single-base-pair GC deletions. Two UV treatments in the BL21(DE3) lineage produced only 4 single-base-pair mutations but 16 large deletions. P1 transductions from K-12 into the two B lineages produced 317 single-base-pair differences and 9 insertions or deletions, reflecting differences between B DNA in BL21(DE3) and integrated restriction fragments ofmore » K-12 DNA inherited by REL606. Two sites showed selective enrichment of spontaneous mutations. No unselected spontaneous single-base-pair mutations were evident. The genome sequences revealed that a progenitor of REL606 had been misidentified, explaining initially perplexing differences. Limited sequencing of other B strains defined characteristic properties of B and allowed assembly of the inferred genome of the ancestral B of Delbrueck and Luria. Comparison of the B and K-12 genomes shows that more than half of the 3793 proteins of their basic genomes are predicted to be identical, although {approx} 310 appear to be functional in either B or K-12 but not in both. The ancestral basic genome appears to have had {approx} 4039 coding sequences occupying {approx} 4.0 Mbp. Repeated horizontal transfer from diverged Escherichia coli genomes and homologous recombination may explain the observed variable distribution of single-base-pair differences. Fifteen sites are occupied by phage-related elements, but only six by comparable elements at the same site. More than 50 sites are occupied by IS elements in both B and K, 16 in common, and likely founding IS elements are identified. A signature of widespread cryptic phage P4-type mobile elements was identified. Complex deletions (dense clusters of small deletions and substitutions) apparently removed nonessential genes from {approx} 30 sites in the basic genomes.« less

Real-time observation of the initiation of RNA polymerase II transcription.

PubMed

Fazal, Furqan M; Meng, Cong A; Murakami, Kenji; Kornberg, Roger D; Block, Steven M

2015-09-10

Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.

Initial cloning and sequencing of hydHG, an operon homologous to ntrBC and regulating the labile hydrogenase activity in Escherichia coli K-12.

PubMed Central

Stoker, K; Reijnders, W N; Oltmann, L F; Stouthamer, A H

1989-01-01

To isolate genes from Escherichia coli which regulate the labile hydrogenase activity, a plasmid library was used to transform hydL mutants lacking the labile hydrogenase. A single type of gene, designated hydG, was isolated. This gene also partially restored the hydrogenase activity in hydF mutants (which are defective in all hydrogenase isoenzymes), although the low hydrogenase 1 and 2 levels were not induced. Therefore, hydG apparently regulates, specifically, the labile hydrogenase activity. Restoration of this latter activity in hydF mutants was accompanied by a proportional increase of the H2 uptake activity, suggesting a functional relationship. H2:fumarate oxidoreductase activity was not restored in complemented hydL mutants. These latter strains may therefore lack, in addition to the labile hydrogenase, a second component (provisionally designated component R), possibly an electron carrier coupling H2 oxidation to the anerobic respiratory chain. Sequence analysis showed an open reading frame of 1,314 base pairs for hydG. It was preceded by a ribosome-binding site but apparently lacked a promoter. Minicell experiments revealed a single polypeptide of approximately 50 kilodaltons. Comparison of the predicted amino acid sequence with a protein sequence data base revealed strong homology to NtrC from Klebsiella pneumoniae, a DNA-binding transcriptional activator. The 411 base pairs upstream from pHG40 contained a second open reading frame overlapping hydG by four bases. The deduced amino acid sequence showed considerable homology with the C-terminal part of NtrB. This sequence was therefore assumed to be part of a second gene, encoding the NtrB-like component, and was designated hydH. The labile hydrogenase activity in E. coli is apparently regulated by a multicomponent system analogous to the NtrB-NtrC system. This conclusion is in agreement with the results of Birkmann et al. (A. Birkmann, R. G. Sawers, and A. Böck, Mol. Gen. Genet. 210:535-542, 1987), who demonstrated ntrA dependence for the labile hydrogenase activity. Images PMID:2666400

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Sequencing of the amylopullulanase (apu) gene of Thermoanaerobacter ethanolicus 39E, and identification of the active site by site-directed mutagenesis.

PubMed

Mathupala, S P; Lowe, S E; Podkovyrov, S M; Zeikus, J G

1993-08-05

The complete nucleotide sequence of the gene encoding the dual active amylopullulanase of Thermoanaerobacter ethanolicus 39E (formerly Clostridium thermohydrosulfuricum) was determined. The structural gene (apu) contained a single open reading frame 4443 base pairs in length, corresponding to 1481 amino acids, with an estimated molecular weight of 162,780. Analysis of the deduced sequence of apu with sequences of alpha-amylases and alpha-1,6 debranching enzymes enabled the identification of four conserved regions putatively involved in substrate binding and in catalysis. The conserved regions were localized within a 2.9-kilobase pair gene fragment, which encoded a M(r) 100,000 protein that maintained the dual activities and thermostability of the native enzyme. The catalytic residues of amylopullulanase were tentatively identified by using hydrophobic cluster analysis for comparison of amino acid sequences of amylopullulanase and other amylolytic enzymes. Asp597, Glu626, and Asp703 were individually modified to their respective amide form, or the alternate acid form, and in all cases both alpha-amylase and pullulanase activities were lost, suggesting the possible involvement of 3 residues in a catalytic triad, and the presence of a putative single catalytic site within the enzyme. These findings substantiate amylopullulanase as a new type of amylosaccharidase.

A Comparison of the Results of Many-Facet Rasch Analyses Based on Crossed and Judge Pair Designs

ERIC Educational Resources Information Center

Ilhan, Mustafa

2016-01-01

The aim of this study was to compare the results of many-facet Rasch analyses based on crossed and judge pair designs. The study was conducted with 168 eighth grade students and five judges. The study data were collected using an achievement test with open-ended questions and a holistic rubric that was used to rate the responses. In the data…

Accelerating calculations of RNA secondary structure partition functions using GPUs

PubMed Central

2013-01-01

Background RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure determined by the sequence. The conformation of RNA is in part determined by its secondary structure, or the particular set of contacts between pairs of complementary bases. Prediction of the secondary structure of RNA from its sequence is therefore of great interest, but can be computationally expensive. In this work we accelerate computations of base-pair probababilities using parallel graphics processing units (GPUs). Results Calculation of the probabilities of base pairs in RNA secondary structures using nearest-neighbor standard free energy change parameters has been implemented using CUDA to run on hardware with multiprocessor GPUs. A modified set of recursions was introduced, which reduces memory usage by about 25%. GPUs are fastest in single precision, and for some hardware, restricted to single precision. This may introduce significant roundoff error. However, deviations in base-pair probabilities calculated using single precision were found to be negligible compared to those resulting from shifting the nearest-neighbor parameters by a random amount of magnitude similar to their experimental uncertainties. For large sequences running on our particular hardware, the GPU implementation reduces execution time by a factor of close to 60 compared with an optimized serial implementation, and by a factor of 116 compared with the original code. Conclusions Using GPUs can greatly accelerate computation of RNA secondary structure partition functions, allowing calculation of base-pair probabilities for large sequences in a reasonable amount of time, with a negligible compromise in accuracy due to working in single precision. The source code is integrated into the RNAstructure software package and available for download at http://rna.urmc.rochester.edu. PMID:24180434

Detection of no-model input-output pairs in closed-loop systems.

PubMed

Potts, Alain Segundo; Alvarado, Christiam Segundo Morales; Garcia, Claudio

2017-11-01

The detection of no-model input-output (IO) pairs is important because it can speed up the multivariable system identification process, since all the pairs with null transfer functions are previously discarded and it can also improve the identified model quality, thus improving the performance of model based controllers. In the available literature, the methods focus just on the open-loop case, since in this case there is not the effect of the controller forcing the main diagonal in the transfer matrix to one and all the other terms to zero. In this paper, a modification of a previous method able to detect no-model IO pairs in open-loop systems is presented, but adapted to perform this duty in closed-loop systems. Tests are performed by using the traditional methods and the proposed one to show its effectiveness. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Compositions and methods for detecting single nucleotide polymorphisms

DOEpatents

Yeh, Hsin-Chih; Werner, James; Martinez, Jennifer S.

2016-11-22

Described herein are nucleic acid based probes and methods for discriminating and detecting single nucleotide variants in nucleic acid molecules (e.g., DNA). The methods include use of a pair of probes can be used to detect and identify polymorphisms, for example single nucleotide polymorphism in DNA. The pair of probes emit a different fluorescent wavelength of light depending on the association and alignment of the probes when hybridized to a target nucleic acid molecule. Each pair of probes is capable of discriminating at least two different nucleic acid molecules that differ by at least a single nucleotide difference. The methods can probes can be used, for example, for detection of DNA polymorphisms that are indicative of a particular disease or condition.

APOLLO: a quality assessment service for single and multiple protein models.

PubMed

Wang, Zheng; Eickholt, Jesse; Cheng, Jianlin

2011-06-15

We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure. http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise global quality assessment software is also available at the site.

Test of mutually unbiased bases for six-dimensional photonic quantum systems

PubMed Central

D'Ambrosio, Vincenzo; Cardano, Filippo; Karimi, Ebrahim; Nagali, Eleonora; Santamato, Enrico; Marrucci, Lorenzo; Sciarrino, Fabio

2013-01-01

In quantum information, complementarity of quantum mechanical observables plays a key role. The eigenstates of two complementary observables form a pair of mutually unbiased bases (MUBs). More generally, a set of MUBs consists of bases that are all pairwise unbiased. Except for specific dimensions of the Hilbert space, the maximal sets of MUBs are unknown in general. Even for a dimension as low as six, the identification of a maximal set of MUBs remains an open problem, although there is strong numerical evidence that no more than three simultaneous MUBs do exist. Here, by exploiting a newly developed holographic technique, we implement and test different sets of three MUBs for a single photon six-dimensional quantum state (a “qusix”), encoded exploiting polarization and orbital angular momentum of photons. A close agreement is observed between theory and experiments. Our results can find applications in state tomography, quantitative wave-particle duality, quantum key distribution. PMID:24067548

Test of mutually unbiased bases for six-dimensional photonic quantum systems.

PubMed

D'Ambrosio, Vincenzo; Cardano, Filippo; Karimi, Ebrahim; Nagali, Eleonora; Santamato, Enrico; Marrucci, Lorenzo; Sciarrino, Fabio

2013-09-25

In quantum information, complementarity of quantum mechanical observables plays a key role. The eigenstates of two complementary observables form a pair of mutually unbiased bases (MUBs). More generally, a set of MUBs consists of bases that are all pairwise unbiased. Except for specific dimensions of the Hilbert space, the maximal sets of MUBs are unknown in general. Even for a dimension as low as six, the identification of a maximal set of MUBs remains an open problem, although there is strong numerical evidence that no more than three simultaneous MUBs do exist. Here, by exploiting a newly developed holographic technique, we implement and test different sets of three MUBs for a single photon six-dimensional quantum state (a "qusix"), encoded exploiting polarization and orbital angular momentum of photons. A close agreement is observed between theory and experiments. Our results can find applications in state tomography, quantitative wave-particle duality, quantum key distribution.

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Evidence of Knowledge Acquisition in a Cognitive Flexibility-Based Computer Learning Environment

PubMed Central

Heath, Scott; Higgs, John; Ambruso, Daniel R.

2008-01-01

Background A computer-based learning experience was developed using cognitive flexibility theory to overcome the pitfalls often encountered in existing medical education. An earlier study (not published) showed significant pretest-posttest increase in scores, as well as a significant positive correlation between choosing to complete the module individually or in pairs. Method This experience was presented as part of a second-year course in medical school with randomized assignment for students to complete the program as pairs or individuals. Results Sixty-six scores of 101 medical students (31 from students working as singles and 35 from 70 working in pairs) were analyzed. Out of 47 possible points, the mean pretest score was 15.1 (SD = 6.4, range 13.7-15.9). The mean posttest score was 22.9 (SD = 5.2, range 21.1-24.2). Posttest scores were statistically significantly higher than pretest scores (p<.001, Cohen's d = 1.17, average gain 7.8 points). Both pairs and singles showed pre-to-post test score gains, but the score gains of pairs and singles were not significantly different. Conclusion This learning module served as an effective instructional intervention. However, the effect of collaboration, measured by score gains for pairs, was not significantly different from score gains of students completing the assignment individually. PMID:20165544

Theoretical studies on sRNA-mediated regulation in bacteria

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Force regulated dynamics of RPA on a DNA fork

PubMed Central

Kemmerich, Felix E.; Daldrop, Peter; Pinto, Cosimo; Levikova, Maryna; Cejka, Petr; Seidel, Ralf

2016-01-01

Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg2+ concentrations, such that human RPA can melt DNA in absence of force. PMID:27016742

Time series regression-based pairs trading in the Korean equities market

NASA Astrophysics Data System (ADS)

Kim, Saejoon; Heo, Jun

2017-07-01

Pairs trading is an instance of statistical arbitrage that relies on heavy quantitative data analysis to profit by capitalising low-risk trading opportunities provided by anomalies of related assets. A key element in pairs trading is the rule by which open and close trading triggers are defined. This paper investigates the use of time series regression to define the rule which has previously been identified with fixed threshold-based approaches. Empirical results indicate that our approach may yield significantly increased excess returns compared to ones obtained by previous approaches on large capitalisation stocks in the Korean equities market.

Mining Time-Resolved Functional Brain Graphs to an EEG-Based Chronnectomic Brain Aged Index (CBAI).

PubMed

Dimitriadis, Stavros I; Salis, Christos I

2017-01-01

The brain at rest consists of spatially and temporal distributed but functionally connected regions that called intrinsic connectivity networks (ICNs). Resting state electroencephalography (rs-EEG) is a way to characterize brain networks without confounds associated with task EEG such as task difficulty and performance. A novel framework of how to study dynamic functional connectivity under the notion of functional connectivity microstates (FCμstates) and symbolic dynamics is further discussed. Furthermore, we introduced a way to construct a single integrated dynamic functional connectivity graph (IDFCG) that preserves both the strength of the connections between every pair of sensors but also the type of dominant intrinsic coupling modes (DICM). The whole methodology is demonstrated in a significant and unexplored task for EEG which is the definition of an objective Chronnectomic Brain Aged index (CBAI) extracted from resting-state data ( N = 94 subjects) with both eyes-open and eyes-closed conditions. Novel features have been defined based on symbolic dynamics and the notion of DICM and FCμstates. The transition rate of FCμstates, the symbolic dynamics based on the evolution of FCμstates (the Markovian Entropy, the complexity index), the probability distribution of DICM, the novel Flexibility Index that captures the dynamic reconfiguration of DICM per pair of EEG sensors and the relative signal power constitute a valuable pool of features that can build the proposed CBAI. Here we applied a feature selection technique and Extreme Learning Machine (ELM) classifier to discriminate young adults from middle-aged and a Support Vector Regressor to build a linear model of the actual age based on EEG-based spatio-temporal features. The most significant type of features for both prediction of age and discrimination of young vs. adults age groups was the dynamic reconfiguration of dominant coupling modes derived from a subset of EEG sensor pairs. Specifically, our results revealed a very high prediction of age for eyes-open ( R 2 = 0.60; y = 0.79x + 8.03) and lower for eyes-closed ( R 2 = 0.48; y = 0.71x + 10.91) while we succeeded to correctly classify young vs. middle-age group with 97.8% accuracy in eyes-open and 87.2% for eyes-closed. Our results were reproduced also in a second dataset for further external validation of the whole analysis. The proposed methodology proved valuable for the characterization of the intrinsic properties of dynamic functional connectivity through the age untangling developmental differences using EEG resting-state recordings.

Effect of Lower Extremity Stretching Exercises on Balance in Geriatric Population.

PubMed

Reddy, Ravi Shankar; Alahmari, Khalid A

2016-07-01

The purpose of this study was to find "Effect of lower extremity stretching exercises on balance in the geriatric population. 60 subjects (30 male and 30 female) participated in the study. The subjects underwent 10 weeks of lower limb stretching exercise program. Pre and post 10 weeks stretching exercise program, the subjects were assessed for balance, using single limb stance time in seconds and berg balance score. These outcome measures were analyzed. Pre and post lower extremity stretching on balance was analyzed using paired t test. Of 60 subjects 50 subjects completed the stretching exercise program. Paired sample t test analysis showed a significant improvement in single limb stance time (eyes open and eyes closed) (p<0.001) and berg balance score (p<0.001). Lower extremity stretching exercises enhances balance in the geriatric population and thereby reduction in the number of falls.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.

PubMed

Renneberg, Dorte; Dervan, Peter B

2003-05-14

The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.

The formation of catalytically competent enzyme-substrate complex is not a bottleneck in lesion excision by human alkyladenine DNA glycosylase.

PubMed

Kuznetsov, N A; Kiryutin, A S; Kuznetsova, A A; Panov, M S; Barsukova, M O; Yurkovskaya, A V; Fedorova, O S

2017-04-01

Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, T m , and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (T m (F/T) < T m (εA/T) < T m (Hx/T) < T m (A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.

Detail section extending from shore. Note the paired support pilings, ...

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

Detail section extending from shore. Note the paired support pilings, concrete curbs with rectangular openings for drainage, and large-diameter metal pipe suspended under the deck. USS MISSOURI in background - U.S. Naval Base, Pearl Harbor, Gasoline Wharf, Offshore, near the intersection of Hornet Avenue & Curtis Street, Ford Island, Pearl City, Honolulu County, HI

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

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

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka

2015-09-08

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.« less

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

DOE PAGES

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; ...

2015-09-08

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σ A dissociation.« less

van der Waals Interactions on the Mesoscale: Open-Science Implementation, Anisotropy, Retardation, and Solvent Effects.

PubMed

Dryden, Daniel M; Hopkins, Jaime C; Denoyer, Lin K; Poudel, Lokendra; Steinmetz, Nicole F; Ching, Wai-Yim; Podgornik, Rudolf; Parsegian, Adrian; French, Roger H

2015-09-22

The self-assembly of heterogeneous mesoscale systems is mediated by long-range interactions, including van der Waals forces. Diverse mesoscale architectures, built of optically and morphologically anisotropic elements such as DNA, collagen, single-walled carbon nanotubes, and inorganic materials, require a tool to calculate the forces, torques, interaction energies, and Hamaker coefficients that govern assembly in such systems. The mesoscale Lifshitz theory of van der Waals interactions can accurately describe solvent and temperature effects, retardation, and optically and morphologically anisotropic materials for cylindrical and planar interaction geometries. The Gecko Hamaker open-science software implementation of this theory enables new and sophisticated insights into the properties of important organic/inorganic systems: interactions show an extended range of magnitudes and retardation rates, DNA interactions show an imprint of base pair composition, certain SWCNT interactions display retardation-dependent nonmonotonicity, and interactions are mapped across a range of material systems in order to facilitate rational mesoscale design.

Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

NASA Technical Reports Server (NTRS)

Urakawa, Hidetoshi; El Fantroussi, Said; Smidt, Hauke; Smoot, James C.; Tribou, Erik H.; Kelly, John J.; Noble, Peter A.; Stahl, David A.

2003-01-01

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

Breakdown flash at telecom wavelengths in InGaAs avalanche photodiodes

NASA Astrophysics Data System (ADS)

Shi, Yicheng; Lim, Janet Zheng Jie; Poh, Hou Shun; Tan, Peng Kian; Tan, Peiyu Amelia; Ling, Alexander; Kurtsiefer, Christian

2017-11-01

Quantum key distribution (QKD) at telecom wavelengths (1260-1625nm) has the potential for fast deployment due to existing optical fibre infrastructure and mature telecom technologies. At these wavelengths, indium gallium arsenide (InGaAs) avalanche photodiode (APD) based detectors are the preferred choice for photon detection. Similar to their silicon counterparts used at shorter wavelengths, they exhibit fluorescence from recombination of electron-hole pairs generated in the avalanche breakdown process. This fluorescence may open side channels for attacks on QKD systems. Here, we characterize the breakdown fluorescence from two commercial InGaAs single photon counting modules, and find a spectral distribution between 1000nm and 1600nm. We also show that by spectral filtering, this side channel can be efficiently suppressed.

Breakdown flash at telecom wavelengths in InGaAs avalanche photodiodes.

PubMed

Shi, Yicheng; Lim, Janet Zheng Jie; Poh, Hou Shun; Tan, Peng Kian; Tan, Peiyu Amelia; Ling, Alexander; Kurtsiefer, Christian

2017-11-27

Quantum key distribution (QKD) at telecom wavelengths (1260 - 1625 nm) has the potential for fast deployment due to existing optical fibre infrastructure and mature telecom technologies. At these wavelengths, Indium Gallium Arsenide (InGaAs) avalanche photodiode (APD) based detectors are the preferred choice for photon detection. Similar to their Silicon counterparts used at shorter wavelengths, they exhibit fluorescence from recombination of electron-hole pairs generated in the avalanche breakdown process. This fluorescence may open side channels for attacks on QKD systems. Here, we characterize the breakdown fluorescence from two commercial InGaAs single photon counting modules, and find a spectral distribution between 1000 nm and 1600 nm. We also show that by spectral filtering, this side channel can be efficiently suppressed.

Single-Molecule Mechanical (Un)folding of RNA Hairpins: Effects of Single A-U to A∙C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting.

PubMed

Yang, Lixia; Zhong, Zhensheng; Tong, Cailing; Jia, Huan; Liu, Yiran; Chen, Gang

2018-06-08

A wobble A∙C pair can be protonated at near physiological pH to form a more stable wobble A+∙C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A∙C mismatch on the top (near the loop, U22C), middle (U25C) and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A∙C pair substitution, and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (~2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (~1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.

Active Listening in a Bat Cocktail Party: Adaptive Echolocation and Flight Behaviors of Big Brown Bats, Eptesicus fuscus, Foraging in a Cluttered Acoustic Environment.

PubMed

Warnecke, Michaela; Chiu, Chen; Engelberg, Jonathan; Moss, Cynthia F

2015-09-01

In their natural environment, big brown bats forage for small insects in open spaces, as well as in vegetation and in the presence of acoustic clutter. While searching and hunting for prey, bats experience sonar interference, not only from densely cluttered environments, but also from calls of conspecifics foraging in close proximity. Previous work has shown that when two bats compete for a single prey item in a relatively open environment, one of the bats may go silent for extended periods of time, which can serve to minimize sonar interference between conspecifics. Additionally, pairs of big brown bats have been shown to adjust frequency characteristics of their vocalizations to avoid acoustic interference in echo processing. In this study, we extended previous work by examining how the presence of conspecifics and environmental clutter influence the bat's echolocation behavior. By recording multichannel audio and video data of bats engaged in insect capture in open and cluttered spaces, we quantified the bats' vocal and flight behaviors. Big brown bats flew individually and in pairs in an open and cluttered room, and the results of this study shed light on the different strategies that this species employs to negotiate a complex and dynamic environment. © 2015 S. Karger AG, Basel.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

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

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Effect of Loss on Multiplexed Single-Photon Sources (Open Access Publisher’s Version)

DTIC Science & Technology

2015-04-28

lossy components on near- and long-term experimental goals, we simulate themultiplexed sources when used formany- photon state generation under various...efficient integer factorization and digital quantum simulation [7, 8], which relies critically on the development of a high-performance, on-demand photon ...SPDC) or spontaneous four-wave mixing: parametric processes which use a pump laser in a nonlinearmaterial to spontaneously generate photon pairs

High sensitivity Troponin T: an audit of implementation of its protocol in a district general hospital.

PubMed

Kalim, Shahid; Nazir, Shaista; Khan, Zia Ullah

2013-01-01

Protocols based on newer high sensitivity Troponin T (hsTropT) assays can rule in a suspected Acute Myocardial Infarction (AMI) as early as 3 hours. We conducted this study to audit adherence to our Trust's newly introduced AMI diagnostic protocol based on paired hsTropT testing at 0 and 3 hours. We retrospectively reviewed data of all patients who had hsTropT test done between 1st and 7th May 2012. Patient's demographics, utility of single or paired samples, time interval between paired samples, patient's presenting symptoms and ECG findings were noted and their means, medians, Standard deviations and proportions were calculated. A total of 66 patients had hsTropT test done during this period. Mean age was 63.30 +/- 17.46 years and 38 (57.57%) were males. Twenty-four (36.36%) patients had only single, rather than protocol recommended paired hsTropT samples, taken. Among the 42 (63.63%) patients with paired samples, the mean time interval was found to be 4.41 +/- 5.7 hours. Contrary to the recommendations, 15 (22.73%) had a very long whereas 2 (3.03%) had a very short time interval between two samples. A subgroup analysis of patients with single samples, found only 2 (3.03%) patient with ST-segment elevation, appropriate for single testing. Our study confirmed that in a large number of patients the protocol for paired sampling or a recommended time interval of 3 hours between 2 samples was not being followed.

Measurement of Single Channel Currents from Cardiac Gap Junctions

NASA Astrophysics Data System (ADS)

Veenstra, Richard D.; Dehaan, Robert L.

1986-08-01

Cardiac gap junctions consist of arrays of integral membrane proteins joined across the intercellular cleft at points of cell-to-cell contact. These junctional proteins are thought to form pores through which ions can diffuse from cytosol to cytosol. By monitoring whole-cell currents in pairs of embryonic heart cells with two independent patch-clamp circuits, the properties of single gap junction channels have been investigated. These channels had a conductance of about 165 picosiemens and underwent spontaneous openings and closings that were independent of voltage. Channel activity and macroscopic junctional conductance were both decreased by the uncoupling agent 1-octanol.

High-Fidelity Down-Conversion Source for Secure Communications Using On-Demand Single Photons

NASA Technical Reports Server (NTRS)

Roberts, Tony

2015-01-01

AdvR, Inc., has built an efficient, fully integrated, waveguide-based source of spectrally uncorrelated photon pairs that will accelerate research and development (R&D) in the emerging field of quantum information science. Key to the innovation is the use of submicron periodically poled waveguides to produce counter propagating photon pairs, which is enabled by AdvR's patented segmented microelectrode poling technique. This novel device will provide a high brightness source of down-conversion pairs with enhanced spectral properties and low attenuation, and it will operate in the visible to the mid-infrared spectral region. A waveguide-based source of spectrally and spatially pure heralded photons will contribute to a wide range of NASA's advanced technology development efforts, including on-demand single photon sources for high-rate spaced-based secure communications.

Bistable microelectromechanical actuator

DOEpatents

Fleming, James G.

1999-01-01

A bistable microelectromechanical (MEM) actuator is formed on a substrate and includes a stressed membrane of generally rectangular shape that upon release assumes a curvilinear cross-sectional shape due to attachment at a midpoint to a resilient member and at opposing edges to a pair of elongate supports. The stressed membrane can be electrostatically switched between a pair of mechanical states having mirror-image symmetry, with the MEM actuator remaining in a quiescent state after a programming voltage is removed. The bistable MEM actuator according to various embodiments of the present invention can be used to form a nonvolatile memory element, an optical modulator (with a pair of mirrors supported above the membrane and moving in synchronism as the membrane is switched), a switchable mirror (with a single mirror supported above the membrane at the midpoint thereof) and a latching relay (with a pair of contacts that open and close as the membrane is switched). Arrays of bistable MEM actuators can be formed for applications including nonvolatile memories, optical displays and optical computing.

Bistable microelectromechanical actuator

DOEpatents

Fleming, J.G.

1999-02-02

A bistable microelectromechanical (MEM) actuator is formed on a substrate and includes a stressed membrane of generally rectangular shape that upon release assumes a curvilinear cross-sectional shape due to attachment at a midpoint to a resilient member and at opposing edges to a pair of elongate supports. The stressed membrane can be electrostatically switched between a pair of mechanical states having mirror-image symmetry, with the MEM actuator remaining in a quiescent state after a programming voltage is removed. The bistable MEM actuator according to various embodiments of the present invention can be used to form a nonvolatile memory element, an optical modulator (with a pair of mirrors supported above the membrane and moving in synchronism as the membrane is switched), a switchable mirror (with a single mirror supported above the membrane at the midpoint thereof) and a latching relay (with a pair of contacts that open and close as the membrane is switched). Arrays of bistable MEM actuators can be formed for applications including nonvolatile memories, optical displays and optical computing. 49 figs.

Energetics, Ion and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA.

PubMed

Carr, Carolyn E; Khutsishvili, Irine; Marky, Luis A

2018-06-22

Triplex formation occurs via interaction of a third strand with the major groove of double stranded nucleic acid, through Hoogsteen hydrogen bonding. In this work, we use a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to determine complete thermodynamic profiles for the unfolding of poly(rA)•poly(rU) (Duplex) and poly(rA)•2poly(rU) (Triplex). Our thermodynamic results are in good agreement with the much earlier work of Krakauer and Sturtevant using only UV melting techniques. The folding of these two helices yielded an uptake of ions, ΔnNa+ = 0.15 mol Na+/mol base-pair (Duplex) and 0.30 mol Na+/mole base-triplet (Triplex), which are consistent with their polymer behavior and the higher charge density parameter of triple helices. The osmotic stress technique yielded a release of structural water, ΔnW = 2 mol H2O/mol base-pair (Duplex unfolding into single strands) and an uptake of structural water, ΔnW = 2 mol H2O/mole base-pair (Triplex unfolding into Duplex and a single strand). However, an overall release of electrostricted waters is obtained for the unfolding of both complexes from pressure perturbation calorimetric experiments. In total, the ΔV values obtained for the unfolding of Triplex into Duplex and a single strand correspond to an immobilization of two structural waters and a release of three electrostricted waters. The ΔV values obtained for the unfolding of Duplex into two single strands correspond to the release of two structural waters and the immobilization of four electrostricted water molecules.

Time-domain diffuse optics: towards next generation devices

NASA Astrophysics Data System (ADS)

Contini, Davide; Dalla Mora, Alberto; Arridge, Simon; Martelli, Fabrizio; Tosi, Alberto; Boso, Gianluca; Farina, Andrea; Durduran, Turgut; Martinenghi, Edoardo; Torricelli, Alessandro; Pifferi, Antonio

2015-07-01

Diffuse optics is a powerful tool for clinical applications ranging from oncology to neurology, but also for molecular imaging, and quality assessment of food, wood and pharmaceuticals. We show that ideally time-domain diffuse optics can give higher contrast and a higher penetration depth with respect to standard technology. In order to completely exploit the advantages of a time-domain system a distribution of sources and detectors with fast gating capabilities covering all the sample surface is needed. Here, we present the building block to build up such system. This basic component is made of a miniaturised source-detector pair embedded into the probe based on pulsed Vertical-Cavity Surface-Emitting Lasers (VCSEL) as sources and Single-Photon Avalanche Diodes (SPAD) or Silicon Photomultipliers (SiPM) as detectors. The possibility to miniaturized and dramatically increase the number of source detectors pairs open the way to an advancement of diffuse optics in terms of improvement of performances and exploration of new applications. Furthermore, availability of compact devices with reduction in size and cost can boost the application of this technique.

Force-dependent melting of supercoiled DNA at thermophilic temperatures.

PubMed

Galburt, E A; Tomko, E J; Stump, W T; Ruiz Manzano, A

2014-01-01

Local DNA opening plays an important role in DNA metabolism as the double-helix must be melted before the information contained within may be accessed. Cells finely tune the torsional state of their genomes to strike a balance between stability and accessibility. For example, while mesophilic life forms maintain negatively superhelical genomes, thermophilic life forms use unique mechanisms to maintain relaxed or even positively supercoiled genomes. Here, we use a single-molecule magnetic tweezers approach to quantify the force-dependent equilibrium between DNA melting and supercoiling at high temperatures populated by Thermophiles. We show that negatively supercoiled DNA denatures at 0.5 pN lower tension at thermophilic vs. mesophilic temperatures. This work demonstrates the ability to monitor DNA supercoiling at high temperature and opens the possibility to perform magnetic tweezers assays on thermophilic systems. The data allow for an estimation of the relative energies of base-pairing and DNA bending as a function of temperature and support speculation as to different general mechanisms of DNA opening in different environments. Lastly, our results imply that average in vivo DNA tensions range between 0.3 and 1.1 pN. Copyright © 2014 Elsevier B.V. All rights reserved.

Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

PubMed Central

Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

2013-01-01

Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

Galactic Doppelgängers: The Chemical Similarity Among Field Stars and Among Stars with a Common Birth Origin

NASA Astrophysics Data System (ADS)

Ness, M.; Rix, H.-W.; Hogg, David W.; Casey, A. R.; Holtzman, J.; Fouesneau, M.; Zasowski, G.; Geisler, D.; Shetrone, M.; Minniti, D.; Frinchaboy, Peter M.; Roman-Lopes, Alexandre

2018-02-01

We explore to what extent stars within Galactic disk open clusters resemble each other in the high-dimensional space of their photospheric element abundances and contrast this with pairs of field stars. Our analysis is based on abundances for 20 elements, homogeneously derived from APOGEE spectra (with carefully quantified uncertainties of typically 0.03 dex). We consider 90 red giant stars in seven open clusters and find that most stars within a cluster have abundances in most elements that are indistinguishable (in a {χ }2-sense) from those of the other members, as expected for stellar birth siblings. An analogous analysis among pairs of > 1000 field stars shows that highly significant abundance differences in the 20 dimensional space can be established for the vast majority of these pairs, and that the APOGEE-based abundance measurements have high discriminating power. However, pairs of field stars whose abundances are indistinguishable even at 0.03 dex precision exist: ∼0.3% of all field star pairs and ∼1.0% of field star pairs at the same (solar) metallicity [Fe/H] = 0 ± 0.02. Most of these pairs are presumably not birth siblings from the same cluster, but rather doppelgängers. Our analysis implies that “chemical tagging” in the strict sense, identifying birth siblings for typical disk stars through their abundance similarity alone, will not work with such data. However, our approach shows that abundances have extremely valuable information for probabilistic chemo-orbital modeling, and combined with velocities, we have identified new cluster members from the field.

Mutational analysis of the transcriptional activator VirG of Agrobacterium tumefaciens.

PubMed Central

Scheeren-Groot, E P; Rodenburg, K W; den Dulk-Ras, A; Turk, S C; Hooykaas, P J

1994-01-01

To find VirG proteins with altered properties, the virG gene was mutagenized. Random chemical mutagenesis of single-stranded DNA containing the Agrobacterium tumefaciens virG gene led with high frequency to the inactivation of the gene. Sequence analysis showed that 29% of the mutants contained a virG gene with one single-base-pair substitution somewhere in the open reading frame. Thirty-nine different mutations that rendered the VirG protein inactive were mapped. Besides these inactive mutants, two mutants in which the vir genes were active even in the absence of acetosyringone were found on indicator plates. A VirG protein with an N54D substitution turned out to be able to induce a virB-lacZ reporter gene to a high level even in the absence of the inducer acetosyringone. A VirG protein with an I77V substitution exhibited almost no induction in the absence of acetosyringone but showed a maximum induction level already at low concentrations of acetosyringone. Images PMID:7961391

Cloning and characterization of an abalone (Haliotis discus hannai) actin gene

NASA Astrophysics Data System (ADS)

Ma, Hongming; Xu, Wei; Mai, Kangsen; Liufu, Zhiguo; Chen, Hong

2004-10-01

An actin encoding gene was cloned by using RT-PCR, 3‧ RACE and 5‧ RACE from abalone Haliotis discus hannai. The full length of the gene is 1532 base pairs, which contains a long 3‧ untranslated region of 307 base pairs and 79 base pairs of 5‧ untranslated sequence. The open reading frame encodes 376 amino acid residues. Sequence comparison with those of human and other mollusks showed high conservation among species at amino acid level. The identities was 96%, 97% and 96% respectively compared with Aplysia californica, Biomphalaria glabrata and Homo sapience β-actin. It is also indicated that this actin is more similar to the human cytoplasmic actin (β-actin) than to human muscle actin.

Unique Thermal Stability of Unnatural Hydrophobic Ds Bases in Double-Stranded DNAs.

PubMed

Kimoto, Michiko; Hirao, Ichiro

2017-10-20

Genetic alphabet expansion technology, the introduction of unnatural bases or base pairs into replicable DNA, has rapidly advanced as a new synthetic biology area. A hydrophobic unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibited high fidelity as a third base pair in PCR. SELEX methods using the Ds-Px pair enabled high-affinity DNA aptamer generation, and introducing a few Ds bases into DNA aptamers extremely augmented their affinities and selectivities to target proteins. Here, to further scrutinize the functions of this highly hydrophobic Ds base, the thermal stabilities of double-stranded DNAs (dsDNA) containing a noncognate Ds-Ds or G-Ds pair were examined. The thermal stability of the Ds-Ds self-pair was as high as that of the natural G-C pair, and apart from the generally higher stability of the G-C pair than that of the A-T pair, most of the 5'-pyrimidine-Ds-purine-3' sequences, such as CDsA and TDsA, exhibited higher stability than the 5'-purine-Ds-pyrimidine-3' sequences, such as GDsC and ADsC, in dsDNAs. This trait enabled the GC-content-independent control of the thermal stability of the designed dsDNA fragments. The melting temperatures of dsDNA fragments containing the Ds-Ds pair can be predicted from the nearest-neighbor parameters including the Ds base. In addition, the noncognate G-Ds pair can efficiently distinguish its neighboring cognate natural base pairs from noncognate pairs. We demonstrated that real-time PCR using primers containing Ds accurately detected a single-nucleotide mismatch in target DNAs. These unique properties of the Ds base that affect the stabilities of the neighboring base pairs could impart new functions to DNA molecules and technologies.

Base pairing and base mis-pairing in nucleic acids

NASA Technical Reports Server (NTRS)

Wang, A. H. J.; Rich, A.

1986-01-01

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Open Screw Placement in a 1.5 mm LCP Over a Fracture Gap Decreases Fatigue Life

PubMed Central

Alwen, Sarah G. J.; Kapatkin, Amy S.; Garcia, Tanya C.; Milgram, Joshua; Stover, Susan M.

2018-01-01

Objective To investigate the influence of plate and screw hole position on the stability of simulated radial fractures stabilized with a 1.5 mm condylar locking compression plate (LCP). Study Design In vitro mechanical testing of paired cadaveric limbs. Sample Population Paired radii (n = 7) stabilized with a 1.5 mm condylar LCP with an open screw hole positioned either proximal to (PG), or over (OG), a simulated small fracture gap. Methods Constructs were cycled in axial compression at a simulated trot load until failure or a maximum of 200,000 cycles. Specimens that sustained 200,000 cycles without failure were then loaded in axial compression in a single cycle to failure. Construct cyclic axial stiffness and gap strain, fatigue life, and residual strength were evaluated and compared between constructs using analysis of variance. Results Of pairs that had a failure during cyclic loading, OG constructs survived fewer cycles (54,700 ± 60,600) than PG (116,800 ± 49,300). OG constructs had significantly lower initial stiffness throughout cyclic loading and higher gap strain range within the first 1,000 cycles than PG constructs. Residual strength variables were not significantly different between constructs, however yield loads occurred at loads only marginally higher than approximated trot loads. Fatigue life decreased with increasing body weight. Conclusion Fracture fixation stability is compromised by an open screw hole directly over a fracture gap compared to the open screw hole being buttressed by bone in the model studied. The 1.5 mm condylar LCP may be insufficient stabilization in dogs with appropriate radial geometry but high body weights. PMID:29876361

Acid-induced exchange of the imino proton in G.C pairs.

PubMed Central

Nonin, S; Leroy, J L; Gueron, M

1996-01-01

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine. PMID:8604298

Acid-induced exchange of the imino proton in G.C pairs.

PubMed

Nonin, S; Leroy, J L; Gueron, M

1996-02-15

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine.

Quetzal: a transposon of the Tc1 family in the mosquito Anopheles albimanus.

PubMed

Ke, Z; Grossman, G L; Cornel, A J; Collins, F H

1996-10-01

A member of the Tc1 family of transposable elements has been identified in the Central and South American mosquito Anopheles albimanus. The full-length Quetzal element is 1680 base pairs (bp) in length, possesses 236 bp inverted terminal repeats (ITRs), and has a single open reading frame (ORF) with the potential of encoding a 341-amino-acid (aa) protein that is similar to the transposases of other members of the Tc1 family, particularly elements described from three different Drosophila species. The approximately 10-12 copies per genome of Quetzal are found in the euchromatin of all three chromosomes of A. albimanus. One full-length clone, Que27, appears capable of encoding a complete transposase and may represent a functional copy of this element.

Tudor staphylococcal nuclease is a structure-specific ribonuclease that degrades RNA at unstructured regions during microRNA decay.

PubMed

Li, Chia-Lung; Yang, Wei-Zen; Shi, Zhonghao; Yuan, Hanna S

2018-05-01

Tudor staphylococcal nuclease (TSN) is an evolutionarily conserved ribonuclease in eukaryotes that is composed of five staphylococcal nuclease-like domains (SN1-SN5) and a Tudor domain. TSN degrades hyper-edited double-stranded RNA, including primary miRNA precursors containing multiple I•U and U•I pairs, and mature miRNA during miRNA decay. However, how TSN binds and degrades its RNA substrates remains unclear. Here, we show that the C. elegans TSN (cTSN) is a monomeric Ca 2+ -dependent ribonuclease, cleaving RNA chains at the 5'-side of the phosphodiester linkage to produce degraded fragments with 5'-hydroxyl and 3'-phosphate ends. cTSN degrades single-stranded RNA and double-stranded RNA containing mismatched base pairs, but is not restricted to those containing multiple I•U and U•I pairs. cTSN has at least two catalytic active sites located in the SN1 and SN3 domains, since mutations of the putative Ca 2+ -binding residues in these two domains strongly impaired its ribonuclease activity. We further show by small-angle X-ray scattering that rice osTSN has a flexible two-lobed structure with open to closed conformations, indicating that TSN may change its conformation upon RNA binding. We conclude that TSN is a structure-specific ribonuclease targeting not only single-stranded RNA, but also unstructured regions of double-stranded RNA. This study provides the molecular basis for how TSN cooperates with RNA editing to eliminate duplex RNA in cell defense, and how TSN selects and degrades RNA during microRNA decay. © 2018 Li et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Use of visual CO2 feedback as a retrofit solution for improving classroom air quality.

PubMed

Wargocki, P; Da Silva, N A F

2015-02-01

Carbon dioxide (CO2 ) sensors that provide a visual indication were installed in classrooms during normal school operation. During 2-week periods, teachers and students were instructed to open the windows in response to the visual CO2 feedback in 1 week and open them, as they would normally do, without visual feedback, in the other week. In the heating season, two pairs of classrooms were monitored, one pair naturally and the other pair mechanically ventilated. In the cooling season, two pairs of naturally ventilated classrooms were monitored, one pair with split cooling in operation and the other pair with no cooling. Classrooms were matched by grade. Providing visual CO2 feedback reduced CO2 levels, as more windows were opened in this condition. This increased energy use for heating and reduced the cooling requirement in summertime. Split cooling reduced the frequency of window opening only when no visual CO2 feedback was present. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rolling Maneuver Load Alleviation using active controls

NASA Technical Reports Server (NTRS)

Woods-Vedeler, Jessica A.; Pototzky, Anthony S.

1992-01-01

Rolling Maneuver Load Alleviation (RMLA) has been demonstrated on the Active Flexible Wing (AFW) wind tunnel model in the NASA Langley Transonic Dynamics Tunnel. The design objective was to develop a systematic approach for developing active control laws to alleviate wing incremental loads during roll maneuvers. Using linear load models for the AFW wind-tunnel model which were based on experimental measurements, two RMLA control laws were developed based on a single-degree-of-freedom roll model. The RMLA control laws utilized actuation of outboard control surface pairs to counteract incremental loads generated during rolling maneuvers and actuation of the trailing edge inboard control surface pairs to maintain roll performance. To evaluate the RMLA control laws, roll maneuvers were performed in the wind tunnel at dynamic pressures of 150, 200, and 250 psf and Mach numbers of 0.33, .38 and .44, respectively. Loads obtained during these maneuvers were compared to baseline maneuver loads. For both RMLA controllers, the incremental torsion moments were reduced by up to 60 percent at all dynamic pressures and performance times. Results for bending moment load reductions during roll maneuvers varied. In addition, in a multiple function test, RMLA and flutter suppression system control laws were operated simultaneously during roll maneuvers at dynamic pressures 11 percent above the open-loop flutter dynamic pressure.

Force regulated dynamics of RPA on a DNA fork.

PubMed

Kemmerich, Felix E; Daldrop, Peter; Pinto, Cosimo; Levikova, Maryna; Cejka, Petr; Seidel, Ralf

2016-07-08

Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg(2+) concentrations, such that human RPA can melt DNA in absence of force. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mismatch cleavage by single-strand specific nucleases

PubMed Central

Till, Bradley J.; Burtner, Chris; Comai, Luca; Henikoff, Steven

2004-01-01

We have investigated the ability of single-strand specific (sss) nucleases from different sources to cleave single base pair mismatches in heteroduplex DNA templates used for mutation and single-nucleotide polymorphism analysis. The TILLING (Targeting Induced Local Lesions IN Genomes) mismatch cleavage protocol was used with the LI-COR gel detection system to assay cleavage of amplified heteroduplexes derived from a variety of induced mutations and naturally occurring polymorphisms. We found that purified nucleases derived from celery (CEL I), mung bean sprouts and Aspergillus (S1) were able to specifically cleave nearly all single base pair mismatches tested. Optimal nicking of heteroduplexes for mismatch detection was achieved using higher pH, temperature and divalent cation conditions than are routinely used for digestion of single-stranded DNA. Surprisingly, crude plant extracts performed as well as the highly purified preparations for this application. These observations suggest that diverse members of the S1 family of sss nucleases act similarly in cleaving non-specifically at bulges in heteroduplexes, and single-base mismatches are the least accessible because they present the smallest single-stranded region for enzyme binding. We conclude that a variety of sss nucleases and extracts can be effectively used for high-throughput mutation and polymorphism discovery. PMID:15141034

Towards next generation time-domain diffuse optics devices

NASA Astrophysics Data System (ADS)

Dalla Mora, Alberto; Contini, Davide; Arridge, Simon R.; Martelli, Fabrizio; Tosi, Alberto; Boso, Gianluca; Farina, Andrea; Durduran, Turgut; Martinenghi, Edoardo; Torricelli, Alessandro; Pifferi, Antonio

2015-03-01

Diffuse Optics is growing in terms of applications ranging from e.g. oximetry, to mammography, molecular imaging, quality assessment of food and pharmaceuticals, wood optics, physics of random media. Time-domain (TD) approaches, although appealing in terms of quantitation and depth sensibility, are presently limited to large fiber-based systems, with limited number of source-detector pairs. We present a miniaturized TD source-detector probe embedding integrated laser sources and single-photon detectors. Some electronics are still external (e.g. power supply, pulse generators, timing electronics), yet full integration on-board using already proven technologies is feasible. The novel devices were successfully validated on heterogeneous phantoms showing performances comparable to large state-of-the-art TD rack-based systems. With an investigation based on simulations we provide numerical evidence that the possibility to stack many TD compact source-detector pairs in a dense, null source-detector distance arrangement could yield on the brain cortex about 1 decade higher contrast as compared to a continuous wave (CW) approach. Further, a 3-fold increase in the maximum depth (down to 6 cm) is estimated, opening accessibility to new organs such as the lung or the heart. Finally, these new technologies show the way towards compact and wearable TD probes with orders of magnitude reduction in size and cost, for a widespread use of TD devices in real life.

Intrication temporelle et communication quantique

NASA Astrophysics Data System (ADS)

Bussieres, Felix

Quantum communication is the art of transferring a quantum state from one place to another and the study of tasks that can be accomplished with it. This thesis is devoted to the development of tools and tasks for quantum communication in a real-world setting. These were implemented using an underground optical fibre link deployed in an urban environment. The technological and theoretical innovations presented here broaden the range of applications of time-bin entanglement through new methods of manipulating time-bin qubits, a novel model for characterizing sources of photon pairs, new ways of testing non-locality and the design and the first implementation of a new loss-tolerant quantum coin-flipping protocol. Manipulating time-bin qubits. A single photon is an excellent vehicle in which a qubit, the fundamental unit of quantum information, can be encoded. In particular, the time-bin encoding of photonic qubits is well suited for optical fibre transmission. Before this thesis, the applications of quantum communication based on the time-bin encoding were limited due to the lack of methods to implement arbitrary operations and measurements. We have removed this restriction by proposing the first methods to realize arbitrary deterministic operations on time-bin qubits as well as single qubit measurements in an arbitrary basis. We applied these propositions to the specific case of optical measurement-based quantum computing and showed how to implement the feedforward operations, which are essential to this model. This therefore opens new possibilities for creating an optical quantum computer, but also for other quantum communication tasks. Characterizing sources of photon pairs. Experimental quantum communication requires the creation of single photons and entangled photons. These two ingredients can be obtained from a source of photon pairs based on non-linear spontaneous processes. Several tasks in quantum communication require a precise knowledge of the properties of the source being used. We developed and implemented a fast and simple method to characterize a source of photon pairs. This method is well suited for a realistic setting where experimental conditions, such as channel transmittance, may fluctuate, and for which the characterization of the source has to be done in real time. Testing the non-locality of time-bin entanglement. Entanglement is a resource needed for the realization of many important tasks in quantum communication. It also allows two physical systems to be correlated in a way that cannot be explained by classical physics; this manifestation of entanglement is called non-locality. We built a source of time-bin entangled photonic qubits and characterized it with the new methods implementing arbitrary single qubit measurements that we developed. This allowed us to reveal the non-local nature of our source of entanglement in ways that were never implemented before. It also opens the door to study previously untested features of non-locality using this source. Theses experiments were performed in a realistic setting where quantum (non-local) correlations were observed even after transmission of one of the entangled qubits over 12.4 km of an underground optical fibre. Flipping quantum coins. Quantum coin-flipping is a quantum cryptographic primitive proposed in 1984, that is when the very first steps of quantum communication were being taken, where two players alternate in sending classical and quantum information in order to generate a shared random bit. The use of quantum information is such that a potential cheater cannot force the outcome to his choice with certainty. Classically, however, one of the players can always deterministically choose the outcome. Unfortunately, the security of all previous quantum coin-flipping protocols is seriously compromised in the presence of losses on the transmission channel, thereby making this task impractical. We found a solution to this problem and obtained the first loss-tolerant quantum coin-flipping protocol whose security is independent of the amount of the losses. We have also experimentally demonstrated our loss-tolerant protocol using our source of time-bin entanglement combined with our arbitrary single qubit measurement methods. This experiment took place in a realistic setting where qubits travelled over an underground optical fibre link. This new task thus joins quantum key distribution as a practical application of quantum communication. Keywords. quantum communication, photonics, time-bin encoding, source of photon pairs, heralded single photon source, entanglement, non-locality, time-bin entanglement, hybrid entanglement, quantum network, quantum cryptography, quantum coin-flipping, measurement-based quantum computation, telecommunication, optical fibre, nonlinear optics.

Biomechanical comparison of single-row arthroscopic rotator cuff repair technique versus transosseous repair technique.

PubMed

Tocci, Stephen L; Tashjian, Robert Z; Leventhal, Evan; Spenciner, David B; Green, Andrew; Fleming, Braden C

2008-01-01

This study determined the effect of tear size on gap formation of single-row simple-suture arthroscopic rotator cuff repair (ARCR) vs transosseous Mason-Allen suture open RCR (ORCR) in 13 pairs of human cadaveric shoulders. A massive tear was created in 6 pairs and a large tear in 7. Repairs were cyclically tested in low-load and high-load conditions, with no significant difference in gap formation. Under low-load, gapping was greater in massive tears. Under high-load, there was a trend toward increased gap with ARCR for large tears. All repairs of massive tears failed in high-load. Gapping was greater posteriorly in massive tears for both techniques. Gap formation of a modeled RCR depends upon the tear size. ARCR of larger tears may have higher failure rates than ORCR, and the posterior aspect appears to be the site of maximum gapping. Specific attention should be directed toward maximizing initial fixation of larger rotator cuff tears, especially at the posterior aspect.

Optical Voltage Sensing Using DNA Origami

PubMed Central

2018-01-01

We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nanodevices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labeled with a single pair of FRET dyes. The DNA structures were reversibly immobilized on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency. By exchanging the position of a single dye, we could tune the voltage sensitivity of our DNA origami structure, demonstrating the flexibility and versatility of our approach. The experimental studies were complemented by coarse-grained simulations that characterized voltage-dependent elastic deformation of the DNA nanostructures and the associated change in the distance between the FRET pair. Our work opens a novel pathway for determining the mechanical properties of DNA origami structures and highlights potential applications of dynamic DNA nanostructures as voltage sensors. PMID:29430924

Competing bosonic condensates in optical lattice with a mixture of single and pair hoppings

NASA Astrophysics Data System (ADS)

Travin, V. M.; Kopeć, T. K.

2017-01-01

A system of ultra-cold atoms with single boson and pair tunneling of bosonic atoms is considered in an optical lattice at arbitrary temperature. A mean-field theory was applied to the extended Bose-Hubbard Hamiltonian describing the system in order to investigate the competition between superfluid and pair superfluid as a function of the chemical potential and the temperature. To this end we have applied a method based on the Laplace transform method for the efficient calculation of the statistical sum for the quantum Hamiltonian. These results may be of interest for experiments on cold atom systems in optical lattices.

Results on top-quark physics and top-quark-like signatures by CMS

NASA Astrophysics Data System (ADS)

Chabert, Eric; CMS Collaboration

2017-07-01

This report reviews the results obtained by the CMS Collaboration on top quark physics, focusing on the latest ones based on p-p collisions provided by the LHC at \\sqrt{s}=13{{TeV}} during Run II. It covers measurements of single-top, top quark pairs and associated productions as well as measurements of top quark properties. Finally several beyond the standard model searches involving top quark in the final states are presented, such as searches for supersymmetry in the third generation, heavy resonances decaying into a top quark pair, or dark matter produced in association to a single-top or a top quark pair.

Genetically improved BarraCUDA.

PubMed

Langdon, W B; Lam, Brian Yee Hong

2017-01-01

BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using "Genetic Improvement". The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.

FAST TRACK COMMUNICATION: Open string pair creation from worldsheet instantons

NASA Astrophysics Data System (ADS)

Schubert, Christian; Torrielli, Alessandro

2010-10-01

Worldline instantons provide a particularly elegant way to derive Schwinger's well-known formula for the pair creation rate due to a constant electric field in quantum electrodynamics. In this communication, we show how to extend this method to the corresponding problem of open string pair creation.

MO-F-CAMPUS-T-01: Radiosurgery of Multiple Brain Metastases with Single-Isocenter VMAT: Optimizing Treatment Geometry to Reduce Normal Brain Dose

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

Wu, Q; Snyder, K; Liu, C

Purpose: To develop an optimization algorithm to reduce normal brain dose by optimizing couch and collimator angles for single isocenter multiple targets treatment of stereotactic radiosurgery. Methods: Three metastatic brain lesions were retrospectively planned using single-isocenter volumetric modulated arc therapy (VMAT). Three matrices were developed to calculate the projection of each lesion on Beam’s Eye View (BEV) by the rotating couch, collimator and gantry respectively. The island blocking problem was addressed by computing the total area of open space between any two lesions with shared MLC leaf pairs. The couch and collimator angles resulting in the smallest open areas weremore » the optimized angles for each treatment arc. Two treatment plans with and without couch and collimator angle optimization were developed using the same objective functions and to achieve 99% of each target volume receiving full prescription dose of 18Gy. Plan quality was evaluated by calculating each target’s Conformity Index (CI), Gradient Index (GI), and Homogeneity index (HI), and absolute volume of normal brain V8Gy, V10Gy, V12Gy, and V14Gy. Results: Using the new couch/collimator optimization strategy, dose to normal brain tissue was reduced substantially. V8, V10, V12, and V14 decreased by 2.3%, 3.6%, 3.5%, and 6%, respectively. There were no significant differences in the conformity index, gradient index, and homogeneity index between two treatment plans with and without the new optimization algorithm. Conclusion: We have developed a solution to the island blocking problem in delivering radiation to multiple brain metastases with shared isocenter. Significant reduction in dose to normal brain was achieved by using optimal couch and collimator angles that minimize total area of open space between any of the two lesions with shared MLC leaf pairs. This technique has been integrated into Eclipse treatment system using scripting API.« less

Charm (and Beauty) Production at the Tevatron

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

Rademacker, Jonas; /Bristol U.

2007-11-01

The authors present recent results on heavy flavor production at Tevatron Run II for typically {approx} 1 fb{sup -1} of analyzed p{bar p} data at {radical}s = 1.96 TeV. This includes results on single and correlated open charm and bottom cross sections, charm pair production kinematics, J/{psi}, {psi}(2S) and {chi}{sub cJ} cross sections and polarization measurements in J/{psi}, {psi}(2S), {Upsilon}(1S), and {Upsilon}(2S).

Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

NASA Astrophysics Data System (ADS)

Yang, Bo; Rodgers, M. T.

2015-08-01

Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

PubMed Central

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-01-01

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

PubMed

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

PubMed Central

Kondo, Jiro; Westhof, Eric

2011-01-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

NASA Astrophysics Data System (ADS)

Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

2015-06-01

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

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

Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.

2015-06-21

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including thosemore » corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.« less

Switch wear leveling

DOEpatents

Wu, Hunter; Sealy, Kylee; Gilchrist, Aaron

2015-09-01

An apparatus for switch wear leveling includes a switching module that controls switching for two or more pairs of switches in a switching power converter. The switching module controls switches based on a duty cycle control technique and closes and opens each switch in a switching sequence. The pairs of switches connect to a positive and negative terminal of a DC voltage source. For a first switching sequence a first switch of a pair of switches has a higher switching power loss than a second switch of the pair of switches. The apparatus includes a switch rotation module that changes the switching sequence of the two or more pairs of switches from the first switching sequence to a second switching sequence. The second switch of a pair of switches has a higher switching power loss than the first switch of the pair of switches during the second switching sequence.

High-fidelity frequency down-conversion of visible entangled photon pairs with superconducting single-photon detectors

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

Ikuta, Rikizo; Kato, Hiroshi; Kusaka, Yoshiaki

We experimentally demonstrate a high-fidelity visible-to-telecommunicationwavelength conversion of a photon by using a solid-state-based difference frequency generation. In the experiment, one half of a pico-second visible entangled photon pair at 780 nm is converted to a 1522-nm photon. Using superconducting single-photon detectors with low dark count rates and small timing jitters, we observed a fidelity of 0.93±0.04 after the wavelength conversion.

Analyzing the experiences of adolescent control rats: Effects of the absence of physical or social stimulation on anxiety-like behaviour are dependent on the test.

PubMed

Joshi, Namrata; Leslie, Ronald A; Perrot, Tara S

2017-10-01

The present study was designed to systematically assess the control experience routinely used in our laboratory as part of studies on predator odour stress. Specifically, we examined effects of the physical and social components of this control experience on measures of anxiety-like behaviour in adolescent rats. Adolescent animals are at increased susceptibility to environmental perturbations and have been used for such studies much less often. Long-Evans rats of both sexes were subjected to physical stimulation (Exposed or Unexposed) and social stimulation (Single-Housed or Pair-Housed), resulting in four groups. Exposed rats received six 30-min exposures to an enclosed arena containing an unscented piece of cat collar occurring between adolescence and early adulthood, while Unexposed remained in the home cage. Groups of Exposed and Unexposed animals were housed singly (Single-Housed) from early adolescence to early adulthood or Pair-Housed during this time. Experimental procedures began in adolescence and involved repeated assessment of startle amplitude (measure of anxiety-like behaviour) and prepulse inhibition (PPI; a measure of sensorimotor gating) to gauge the short-term impact of social and/or physical stimulation. All animals were re-paired in adulthood prior to a final startle/PPI session to assess if isolation limited to adolescence could impose long-term effects that were not reversible. We also measured anxiety-like behaviour in adulthood using an extended open field test (EOFT; addition of novel objects to the open field on later days), and the elevated plus maze task (EPM), as well as a sucrose preference test (SPT) to measure anhedonia. An absence of social or physical stimulation resulted in increased startle amplitude and some measures of anxiety-like behaviour in the EOFT, but a reduction in such anxiety-like behaviour in the EPM task. These results suggest common neural substrates for the physical and social experiences. Performance in the SPT was unaltered by any experimental treatments. Sensorimotor gating, as measured by PPI, was increased in the absence of physical stimulation with no short-term effect of isolation, or of re-pairing. These results indicate the importance of considering individual components of the rearing environment of rats, while showing the need to use multiple assays of anxiety-like behaviour. Copyright © 2017. Published by Elsevier Inc.

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

PubMed

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

PubMed Central

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C.; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI). PMID:28381997

Measuring kinetics of complex single ion channel data using mean-variance histograms.

PubMed

Patlak, J B

1993-07-01

The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean-variance histogram technique provided a more credible analysis of the open, closed, and subconductance times for the patch. I also show that the method produces accurate results on simulated data in a wide variety of conditions, whereas the half-amplitude method, when applied to complex simulated data shows the same errors as were apparent in the real data. The utility and the limitations of this new method are discussed.

DNA-Mediated Electrochemistry

PubMed Central

Gorodetsky, Alon A.; Buzzeo, Marisa C.

2009-01-01

The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

Green fluorescence protein-based content-mixing assay of SNARE-driven membrane fusion

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

Heo, Paul; Kong, Byoungjae; Jung, Young-Hun

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins mediate intracellular membrane fusion by forming a ternary SNARE complex. A minimalist approach utilizing proteoliposomes with reconstituted SNARE proteins yielded a wealth of information pinpointing the molecular mechanism of SNARE-mediated fusion and its regulation by accessory proteins. Two important attributes of a membrane fusion are lipid-mixing and the formation of an aqueous passage between apposing membranes. These two attributes are typically observed by using various fluorescent dyes. Currently available in vitro assay systems for observing fusion pore opening have several weaknesses such as cargo-bleeding, incomplete removal of unencapsulated dyes, and inadequate information regardingmore » the size of the fusion pore, limiting measurements of the final stage of membrane fusion. In the present study, we used a biotinylated green fluorescence protein and streptavidin conjugated with Dylight 594 (DyStrp) as a Föster resonance energy transfer (FRET) donor and acceptor, respectively. This FRET pair encapsulated in each v-vesicle containing synaptobrevin and t-vesicle containing a binary acceptor complex of syntaxin 1a and synaptosomal-associated protein 25 revealed the opening of a large fusion pore of more than 5 nm, without the unwanted signals from unencapsulated dyes or leakage. This system enabled determination of the stoichiometry of the merging vesicles because the FRET efficiency of the FRET pair depended on the molar ratio between dyes. Here, we report a robust and informative assay for SNARE-mediated fusion pore opening. - Highlights: • SNARE proteins drive membrane fusion and open a pore for cargo release. • Biotinylated GFP and DyStrp was used as the reporter pair of fusion pore opening. • Procedure for efficient SNARE reconstitution and reporter encapsulation was established. • The FRET pair reported opening of a large fusion pore bigger than 5 nm. • The assay was robust and provided information of stoichiometry of vesicle fusion.« less

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

Complete plastid genome sequence of goosegrass (Eleusine indica) and comparison with other Poaceae.

PubMed

Zhang, Hui; Hall, Nathan; McElroy, J Scott; Lowe, Elijah K; Goertzen, Leslie R

2017-02-05

Eleusine indica, also known as goosegrass, is a serious weed in at least 42 countries. In this paper we report the complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. The goosegrass plastome is a circular molecule of 135,151bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively. The plastome of goosegrass has 38.19% GC content and includes 108 unique genes, of which 76 are protein-coding, 28 are transfer RNA, and 4 are ribosomal RNA. The goosegrass plastome sequence was compared to eight other species of Poaceae. Although generally conserved with respect to Poaceae, this genomic resource will be useful for evolutionary studies within this weed species and the genus Eleusine. Copyright © 2016. Published by Elsevier B.V.

Rotating Modulation Imager for the Orphan Source Search Problem

DTIC Science & Technology

2008-01-01

black mask. If the photon hits an open element it is transmitted and the function M(x) = 1. If the photon hits a closed mask element it is not...photon enters the top mask pair in the third slit, but passes through the second slit on the bottom mask. With a single black mask this is physically...modulation efficiency changes as a function of mask thickness for both tungsten and lead masks. The black line shows how the field of view changes with

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

Wang, Weina; Hellinga, Homme W.; Beese, Lorena S.

Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C {center_dot} A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such thatmore » a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.« less

Inherited Creutzfeldt-Jakob disease in a British family associated with a novel 144 base pair insertion of the prion protein gene.

PubMed Central

Nicholl, D; Windl, O; de Silva, R; Sawcer, S; Dempster, M; Ironside, J W; Estibeiro, J P; Yuill, G M; Lathe, R; Will, R G

1995-01-01

A case of familial Creutzfeldt-Jakob disease associated with a 144 base pair insertion in the open reading frame of the prion protein gene is described. Sequencing of the mutated allele showed an arrangement of six octapeptide repeats, distinct from that of a recently described British family with an insertion of similar size. Thirteen years previously the brother of the proband had died from "Huntington's disease", but re-examination of his neuropathology revealed spongiform encephalopathy and anti-prion protein immunocytochemistry gave a positive result. The independent evolution of at least two distinct pathological 144 base pair insertions in Britain is proposed. The importance of maintaining a high index of suspicion of inherited Creutzfeldt-Jakob disease in cases of familial neurodegenerative disease is stressed. Images PMID:7823070

Enantiopure heterobimetallic single-chain magnets from the chiral Ru(III) building block.

PubMed

Ru, Jing; Gao, Feng; Wu, Tao; Yao, Min-Xia; Li, Yi-Zhi; Zuo, Jing-Lin

2014-01-21

A pair of one-dimensional enantiomers based on the versatile chiral dicyanoruthenate(III) building block have been synthesized and they are chiral single-chain magnets with the effective spin-reversal barrier of 28.2 K.

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

Redox Active Colloids as Discrete Energy Storage Carriers.

PubMed

Montoto, Elena C; Nagarjuna, Gavvalapalli; Hui, Jingshu; Burgess, Mark; Sekerak, Nina M; Hernández-Burgos, Kenneth; Wei, Teng-Sing; Kneer, Marissa; Grolman, Joshua; Cheng, Kevin J; Lewis, Jennifer A; Moore, Jeffrey S; Rodríguez-López, Joaquín

2016-10-12

Versatile and readily available battery materials compatible with a range of electrode configurations and cell designs are desirable for renewable energy storage. Here we report a promising class of materials based on redox active colloids (RACs) that are inherently modular in their design and overcome challenges faced by small-molecule organic materials for battery applications, such as crossover and chemical/morphological stability. RACs are cross-linked polymer spheres, synthesized with uniform diameters between 80 and 800 nm, and exhibit reversible redox activity as single particles, as monolayer films, and in the form of flowable dispersions. Viologen-based RACs display reversible cycling, accessing up to 99% of their capacity and 99 ± 1% Coulombic efficiency over 50 cycles by bulk electrolysis owing to efficient, long-distance intraparticle charge transfer. Ferrocene-based RACs paired with viologen-based RACs cycled efficiently in a nonaqueous redox flow battery employing a simple size-selective separator, thus demonstrating a possible application that benefits from their colloidal dimensions. The unprecedented versatility in RAC synthetic and electrochemical design opens new avenues for energy storage.

Clamp-mount device

NASA Technical Reports Server (NTRS)

Clark, K. H. (Inventor)

1983-01-01

A clamp-mount device is disclosed for mounting equipment to an associated I-beam and the like structural member of the type having oppositely extending flanges wherein the device comprises a base and a pair of oppositely facing clamping members carried diagonally on the base clamping flanges therebetween and having flange receiving openings facing one another. Lock means are carried diagonally by the base opposite the clamping members locking the flanges in the clamping members. A resilient hub is carried centrally of the base engaging and biasing a back side of the flanges maintaining tightly clamped and facilitating use on vertical as well as horizontal members. The base turns about the hub to receive the flanges within the clamping members. Equipment may be secured to the base by any suitable means such as bolts in openings. Slidable gate latches secure the hinged locks in an upright locking position. The resilient hub includes a recess opening formed in the base and a rubber-like pad carried in this opening being depressably and rotatably carried therein.

Gluon TMDs in Quarkonium Production

NASA Astrophysics Data System (ADS)

Boer, Daniël

2017-03-01

Quarkonium production offers good possibilities to study gluon TMDs. In this proceedings contribution this topic is explored for the linearly polarized gluons inside unpolarized hadrons and unpolarized gluons inside transversely polarized hadrons. It is argued that χ _{b0/2} and η _b production at LHC are best to study the effects of linearly polarized gluons in hadronic collisions, by means of angular independent ratios of ratios of cross sections. This can be directly compared to cos 2φ asymmetries in heavy quark pair and dijet production in DIS at a future high-energy Electron-Ion Collider (EIC), which probe the same TMDs. In the small- x limit this corresponds to the Weizsäcker-Williams (WW) gluon distributions, which should show a change in behavior for transverse momenta around the saturation scale. Together with investigations of the dipole (DP) gluon distributions, this can provide valuable information about the polarization of the Color Glass Condensate if sufficiently small x-values are reached. Quarkonia can also be useful in the study of single transverse spin asymmetries. For transversely polarized hadrons the gluon distribution can be asymmetric, which is referred to as the Sivers effect. It leads to single spin asymmetries in for instance J{/}ψ (pair) production at AFTER@LHC, which probe the WW or f-type gluon Sivers TMD. It allows for a test of a sign-change relation w.r.t. the gluon Sivers TMD probed at an EIC in open heavy quark pair production. Single spin asymmetries in backward inclusive C-odd quarkonium production, such as J{/}ψ production, may offer probes of the DP or d-type gluon Sivers TMD at small x-values in the polarized proton, which in that limit corresponds to a correlator of a single Wilson loop, describing the spin-dependent odderon.

Single-trial evaluative conditioning can be moderated by instructed forgetting.

PubMed

Gast, Anne; Kattner, Florian

2016-09-01

Evaluative conditioning (EC) is a change in the valence of a conditioned stimulus (CS) due to previous pairing with an affective unconditioned stimulus (US). Several previous studies indicate that EC is related to memory of the CS-US pairs. Previous studies, however, typically cannot distinguish between the influence of CS-US knowledge during measurement and during encoding. In addition, by measuring rather than manipulating memory, they do not test the causal effect of memory on EC. The present study employed a "directed forgetting" procedure to the EC paradigm instructing participants to either forget or remember certain CS-US pairs. We found that EC effects after single learning trials were stronger for to-be-remembered than for to-be-forgotten pairs. Manipulation checks showed that the forgetting manipulation also successfully modulated memory for the target pairs and reduced both retroactive and proactive interference on memory for other pairs. Item-based analyses further demonstrated that the size of EC depended on CS-US memory. The results suggest that EC relies on available memory during measurement of the EC effect.

Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

PubMed

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-09-18

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ultrasonic flow measurements for irrigation process monitoring

NASA Astrophysics Data System (ADS)

Ziani, Elmostafa; Bennouna, Mustapha; Boissier, Raymond

2004-02-01

This paper presents the state of the art of the general principle of liquid flow measurements by ultrasonic method, and problems of flow measurements. We present an ultrasonic flowmeter designed according to smart sensors concept, for the measurement of irrigation water flowing through pipelines or open channels, using the ultrasonic transit time approach. The new flowmeter works on the principle of measuring time delay differences between sound pulses transmitted upstream and downstream in the flowing liquid. The speed of sound in the flowing medium is eliminated as a variable because the flowrate calculations are based on the reciprocals of the transmission times. The transit time difference is digitally measured by means of a suitable, microprocessor controlled logic. This type of ultrasonic flowmeter will be widely used in industry and water management, it is well studied in this work, followed by some experimental results. For pressurized channels, we use one pair of ultrasonic transducer arranged in proper positions and directions of the pipe, in this case, to determine the liquid velocity, a real time on-line analysis taking account the geometries of the hydraulic system, is applied to the obtained ultrasonic data. In the open channels, we use a single or two pairs of ultrasonic emitter-receiver according to the desired performances. Finally, the goals of this work consist in integrating the smart sensor into irrigation systems monitoring in order to evaluate potential advantages and demonstrate their performance, on the other hand, to understand and use ultrasonic approach for determining flow characteristics and improving flow measurements by reducing errors caused by disturbances of the flow profiles.

AfterQC: automatic filtering, trimming, error removing and quality control for fastq data.

PubMed

Chen, Shifu; Huang, Tanxiao; Zhou, Yanqing; Han, Yue; Xu, Mingyan; Gu, Jia

2017-03-14

Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling. For each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer's bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent. Much more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.

Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex.

PubMed

Nonin, S; Jiang, F; Patel, D J

1997-05-02

We report on the dynamics of base-pair opening in the ATP-binding asymmetric internal loop and flanking base-pairs of the AMP-RNA aptamer complex by monitoring the exchange characteristics of the extremely well resolved imino protons in the NMR spectrum of the complex. The kinetics of imino proton exchange as a function of basic pH or added ammonia catalyst are used to measure the apparent base-pair dissociation constants and lifetimes of Watson-Crick and mismatched base-pairs, as well as the solvent accessibility of the unpaired imino protons in the complex. The exchange characteristics of the imino protons identify the existence of four additional hydrogen bonds stabilizing the conformation of the asymmetric ATP-binding internal loop that were not detected by NOEs and coupling constants alone, but are readily accommodated in the previously reported solution structure of the AMP-RNA aptamer complex published from our laboratory. The hydrogen exchange kinetics of the non-Watson-Crick pairs in the asymmetric internal loop of the AMP-RNA aptamer complex have been characterized and yield apparent dissociation constants (alphaKd) that range from 10(-2) to 10(-7). Surprisingly, three of these alphaKd values are amongst the lowest measured for all base-pairs in the AMP-RNA aptamer complex. Comparative studies of hydrogen exchange of the imino protons in the free RNA aptamer and the AMP-RNA aptamer complex establish that complexation stabilizes not only the bases within the ATP-binding asymmetric internal loop, but also the flanking stem base-pairs (two pairs on either side) of the binding site. We also outline some preliminary results related to the exchange properties of a sugar 2'-hydroxyl proton of a guanosine residue involved in a novel hydrogen bond that has been shown to contribute to the immobilization of the bound AMP by the RNA aptamer, and whose resonance is narrow and downfield shifted in the spectrum.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

PubMed

Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

2017-06-17

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.

PubMed

Expósito, Roberto R; Veiga, Jorge; González-Domínguez, Jorge; Touriño, Juan

2017-09-01

This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool. Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es . rreye@udc.es. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

PubMed Central

Tuplin, A.; Evans, D. J.; Buckley, A.; Jones, I. M.; Gould, E. A.; Gritsun, T. S.

2011-01-01

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents. PMID:21622960

Drapery assembly including insulated drapery liner

DOEpatents

Cukierski, Gwendolyn

1983-01-01

A drapery assembly is disclosed for covering a framed wall opening, the assembly including drapery panels hung on a horizontal traverse rod, the rod having a pair of master slides and means for displacing the master slides between open and closed positions. A pair of insulating liner panels are positioned behind the drapery, the remote side edges of the liner panels being connected with the side portions of the opening frame, and the adjacent side edges of the liner panels being connected with a pair of vertically arranged center support members adapted for sliding movement longitudinally of a horizontal track member secured to the upper horizontal portion of the opening frame. Pivotally arranged brackets connect the center support members with the master slides of the traverse rod whereby movement of the master slides to effect opening and closing of the drapery panels effects simultaneous opening and closing of the liner panels.

RNA Structural Analysis by Evolving SHAPE Chemistry

PubMed Central

Spitale, Robert C.; Flynn, Ryan A.; Torre, Eduardo A.; Kool, Eric T.; Chang, Howard Y.

2017-01-01

RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2’-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2’ hydroxyl group flexibility. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (Selective 2’ Hydroxyl Acylation and Primer Extension). Herein we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being used to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merger of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function. PMID:25132067

Synthesis and Properties of Size-expanded DNAs: Toward Designed, Functional Genetic Systems

PubMed Central

Krueger, Andrew T.; Lu, Haige; Lee, Alex H. F.; Kool, Eric T.

2008-01-01

We describe the design, synthesis, and properties of DNA-like molecules in which the base pairs are expanded by benzo homologation. The resulting size-expanded genetic helices are called xDNA (“expanded DNA”) and yDNA (“wide DNA”). The large component bases are fluorescent, and they display high stacking affinity. When singly substituted into natural DNA, they are destabilizing because the benzo-expanded base pair size is too large for the natural helix. However, when all base pairs are expanded, xDNA and yDNA form highly stable, sequence-selective double helices. The size-expanded DNAs are candidates for components of new, functioning genetic systems. In addition, the fluorescence of expanded DNA bases makes them potentially useful in probing nucleic acids. PMID:17309194

The presence of codon-anticodon pairs in the acceptor stem of tRNAs.

PubMed Central

Rodin, S; Rodin, A; Ohno, S

1996-01-01

A total of 1268 available (excluding mitochondrial) tRNA sequences was used to reconstruct the common consensus image of their acceptor domains. Its structure appeared as a 11-bp-long double-stranded palindrome with complementary triplets in the center, each flanked by the 3'-ACCD and NGGU-5' motifs on each strand (D, base determinator). The palindrome readily extends up to the modern tRNA-like cloverleaf passing through an intermediate hairpin having in the center the single-stranded triplet, in supplement to its double-stranded precursor. The latter might represent an original anticodon-codon pair mapped at 1-2-3 positions of the present-day tRNA acceptors. This conclusion is supported by the striking correlation: in pairs of consensus tRNAs with complementary anticodons, their bases at the 2nd position of the acceptor stem were also complementary. Accordingly, inverse complementarity was also evident at the 71st position of the acceptor stem. With a single exception (tRNA(Phe)-tRNA(Glu) pair), the parallelism is especially impressive for the pairs of tRNAs recognized by aminoacyl-tRNA synthetases (aaRS) from the opposite classes. The above complementarity still doubly presented at the key central position of real single-stranded anticodons and their hypothetical double-stranded precursors is consistent with our previous data pointing to the double-strand use of ancient RNAs in the origin of the main actors in translation- tRNAs with complementary anticodons and the two classes of aaRS. Images Fig. 3 Table 2 Fig. 4 PMID:8643439

Effect of Exposure to Lithium-Paired or Amphetamine-Paired Saccharin Solution on Open Arm Avoidance in an Elevated Plus Maze

ERIC Educational Resources Information Center

Rana, Shadna A.; Parker, Linda A.

2006-01-01

Recent evidence suggests that drug-induced conditioned taste avoidance may be mediated by conditioned fear (e.g., Parker, 2003). The experiments reported here evaluated the effect of exposure to a drug-paired flavor on open arm exploration in an elevated plus maze (EPM), a measure of fear. When rats were tested on a familiar (trial 2) EPM, but not…

47 CFR 90.313 - Frequency loading criteria.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., Washington, or more from the location of base stations authorized on that pair without reference to loading... Industrial Radio Services, if the base station facility is to be used by more than a single licensee, the...

Parietal lobe critically supports successful paired immediate and single-item delayed memory for targets.

PubMed

Krumm, Sabine; Kivisaari, Sasa L; Monsch, Andreas U; Reinhardt, Julia; Ulmer, Stephan; Stippich, Christoph; Kressig, Reto W; Taylor, Kirsten I

2017-05-01

The parietal lobe is important for successful recognition memory, but its role is not yet fully understood. We investigated the parietal lobes' contribution to immediate paired-associate memory and delayed item-recognition memory separately for hits (targets) and correct rejections (distractors). We compared the behavioral performance of 56 patients with known parietal and medial temporal lobe dysfunction (i.e. early Alzheimer's Disease) to 56 healthy control participants in an immediate paired and delayed single item object memory task. Additionally, we performed voxel-based morphometry analyses to investigate the functional-neuroanatomic relationships between performance and voxel-based estimates of atrophy in whole-brain analyses. Behaviorally, all participants performed better identifying targets than rejecting distractors. The voxel-based morphometry analyses associated atrophy in the right ventral parietal cortex with fewer correct responses to familiar items (i.e. hits) in the immediate and delayed conditions. Additionally, medial temporal lobe integrity correlated with better performance in rejecting distractors, but not in identifying targets, in the immediate paired-associate task. Our findings suggest that the parietal lobe critically supports successful immediate and delayed target recognition memory, and that the ventral aspect of the parietal cortex and the medial temporal lobe may have complementary preferences for identifying targets and rejecting distractors, respectively, during recognition memory. Copyright © 2017. Published by Elsevier Inc.

Femtosecond Laser--Pumped Source of Entangled Photons for Quantum Cryptography Applications

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

Pan, D.; Donaldson, W.; Sobolewski, R.

2007-07-31

We present an experimental setup for generation of entangled-photon pairs via spontaneous parametric down-conversion, based on the femtosecond-pulsed laser. Our entangled-photon source utilizes a 76-MHz-repetition-rate, 100-fs-pulse-width, mode-locked, ultrafast femtosecond laser, which can produce, on average, more photon pairs than a cw laser of an equal pump power. The resulting entangled pairs are counted by a pair of high-quantum-efficiency, single-photon, silicon avalanche photodiodes. Our apparatus is intended as an efficient source/receiver system for the quantum communications and quantum cryptography applications.

An implicit divalent counterion force field for RNA molecular dynamics

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

Henke, Paul S.; Mak, Chi H., E-mail: cmak@usc.edu; Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grainedmore » models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.« less

Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN

PubMed Central

Burkart-Waco, Diana; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger

2016-01-01

Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included. PMID:27436831

A Brownian motor mechanism of translocation and strand separation by hepatitis C virus helicase.

PubMed

Levin, Mikhail K; Gurjar, Madhura; Patel, Smita S

2005-05-01

Helicases translocate along their nucleic acid substrates using the energy of ATP hydrolysis and by changing conformations of their nucleic acid-binding sites. Our goal is to characterize the conformational changes of hepatitis C virus (HCV) helicase at different stages of ATPase cycle and to determine how they lead to translocation. We have reported that ATP binding reduces HCV helicase affinity for nucleic acid. Now we identify the stage of the ATPase cycle responsible for translocation and unwinding. We show that a rapid directional movement occurs upon helicase binding to DNA in the absence of ATP, resulting in opening of several base pairs. We propose that HCV helicase translocates as a Brownian motor with a simple two-stroke cycle. The directional movement step is fueled by single-stranded DNA binding energy while ATP binding allows for a brief period of random movement that prepares the helicase for the next cycle.

Dilute group III-V nitride intermediate band solar cells with contact blocking layers

DOEpatents

Walukiewicz, Wladyslaw; Yu, Kin Man

2015-02-24

An intermediate band solar cell (IBSC) is provided including a p-n junction based on dilute III-V nitride materials and a pair of contact blocking layers positioned on opposite surfaces of the p-n junction for electrically isolating the intermediate band of the p-n junction by blocking the charge transport in the intermediate band without affecting the electron and hole collection efficiency of the p-n junction, thereby increasing open circuit voltage (V.sub.OC) of the IBSC and increasing the photocurrent by utilizing the intermediate band to absorb photons with energy below the band gap of the absorber layers of the IBSC. Hence, the overall power conversion efficiency of a IBSC will be much higher than an conventional single junction solar cell. The p-n junction absorber layers of the IBSC may further have compositionally graded nitrogen concentrations to provide an electric field for more efficient charge collection.

Dilute Group III-V nitride intermediate band solar cells with contact blocking layers

DOEpatents

Walukiewicz, Wladyslaw [Kensington, CA; Yu, Kin Man [Lafayette, CA

2012-07-31

An intermediate band solar cell (IBSC) is provided including a p-n junction based on dilute III-V nitride materials and a pair of contact blocking layers positioned on opposite surfaces of the p-n junction for electrically isolating the intermediate band of the p-n junction by blocking the charge transport in the intermediate band without affecting the electron and hole collection efficiency of the p-n junction, thereby increasing open circuit voltage (V.sub.OC) of the IBSC and increasing the photocurrent by utilizing the intermediate band to absorb photons with energy below the band gap of the absorber layers of the IBSC. Hence, the overall power conversion efficiency of a IBSC will be much higher than an conventional single junction solar cell. The p-n junction absorber layers of the IBSC may further have compositionally graded nitrogen concentrations to provide an electric field for more efficient charge collection.

Designing heteropolymers to fold into unique structures via water-mediated interactions.

PubMed

Jamadagni, Sumanth N; Bosoy, Christian; Garde, Shekhar

2010-10-28

Hydrophobic homopolymers collapse into globular structures in water driven by hydrophobic interactions. Here we employ extensive molecular dynamics simulations to study the collapse of heteropolymers containing one or two pairs of oppositely charged monomers. We show that charging a pair of monomers can dramatically alter the most stable conformations from compact globular to more open hairpin-like. We systematically explore a subset of the sequence space of one- and two-charge-pair polymers, focusing on the locations of the charge pairs. Conformational stability is governed by a balance of hydrophobic interactions, hydration and interactions of charge groups, water-mediated charged-hydrophobic monomer repulsions, and other factors. As a result, placing charge pairs in the middle, away from the hairpin ends, leads to stable hairpin-like structures. Turning off the monomer-water attractions enhances hydrophobic interactions significantly leading to a collapse into compact globular structures even for two-charge-pair heteropolymers. In contrast, the addition of salt leads to open and extended structures, suggesting that solvation of charged monomer sites by salt ions dominates the salt-induced enhancement of hydrophobic interactions. We also test the ability of a predictive scheme based on the additivity of free energy of contact formation. The success of the scheme for symmetric two-charge-pair sequences and the failure for their flipped versions highlight the complexity of the heteropolymer conformation space and of the design problem. Collectively, our results underscore the ability of tuning water-mediated interactions to design stable nonglobular structures in water and present model heteropolymers for further studies in the extended thermodynamic space and in inhomogeneous environments.

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

NASA Astrophysics Data System (ADS)

Fyta, Maria; Netz, Roland R.

2012-03-01

Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.

Anomeric 2'-Deoxycytidines and Silver Ions: Hybrid Base Pairs with Greatly Enhanced Stability and Efficient DNA Mismatch Detection with α-dC.

PubMed

Guo, Xiurong; Seela, Frank

2017-09-04

α-d-Nucleosides are rare in nature but can develop fascinating properties when incorporated into DNA. This work reports on the first silver-mediated base pair constructed from two anomeric nucleosides: α-dC and β-dC. The hybrid base pair was integrated into the DNA and DNA/RNA double helix. A 12-mer duplex with α-dC and β-dC pair exhibits a higher thermal stability (T m =43 °C) than that incorporating the β-dC-Ag + -β-dC homo pair (T m =34 °C). Furthermore, α-dC shows excellent mismatch discrimination for DNA single nucleotide polymorphism (SNP). All four SNPs were identified on the basis of large T m value differences measured in the presence of silver ions. High resolution melting was not required. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An efficient and near linear scaling pair natural orbital based local coupled cluster method.

PubMed

Riplinger, Christoph; Neese, Frank

2013-01-21

In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009)]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 10(5)-10(6) relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD ("domain based LPNO-CCSD"). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy estimate based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calculations reported here featured >8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.

Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase.

PubMed

Syed, Salman; Pandey, Manjula; Patel, Smita S; Ha, Taekjip

2014-03-27

Bacteriophage T7 gp4 serves as a model protein for replicative helicases that couples deoxythymidine triphosphate (dTTP) hydrolysis to directional movement and DNA strand separation. We employed single-molecule fluorescence resonance energy transfer methods to resolve steps during DNA unwinding by T7 helicase. We confirm that the unwinding rate of T7 helicase decreases with increasing base pair stability. For duplexes containing >35% guanine-cytosine (GC) base pairs, we observed stochastic pauses every 2-3 bp during unwinding. The dwells on each pause were distributed nonexponentially, consistent with two or three rounds of dTTP hydrolysis before each unwinding step. Moreover, we observed backward movements of the enzyme on GC-rich DNAs at low dTTP concentrations. Our data suggest a coupling ratio of 1:1 between base pairs unwound and dTTP hydrolysis, and they further support the concept that nucleic acid motors can have a hierarchy of different-sized steps or can accumulate elastic energy before transitioning to a subsequent phase. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting.

PubMed

Chen, Xiaoyu; Janssen, Josephine M; Liu, Jin; Maggio, Ignazio; 't Jong, Anke E J; Mikkers, Harald M M; Gonçalves, Manuel A F V

2017-09-22

Precise genome editing involves homologous recombination between donor DNA and chromosomal sequences subjected to double-stranded DNA breaks made by programmable nucleases. Ideally, genome editing should be efficient, specific, and accurate. However, besides constituting potential translocation-initiating lesions, double-stranded DNA breaks (targeted or otherwise) are mostly repaired through unpredictable and mutagenic non-homologous recombination processes. Here, we report that the coordinated formation of paired single-stranded DNA breaks, or nicks, at donor plasmids and chromosomal target sites by RNA-guided nucleases based on CRISPR-Cas9 components, triggers seamless homology-directed gene targeting of large genetic payloads in human cells, including pluripotent stem cells. Importantly, in addition to significantly reducing the mutagenicity of the genome modification procedure, this in trans paired nicking strategy achieves multiplexed, single-step, gene targeting, and yields higher frequencies of accurately edited cells when compared to the standard double-stranded DNA break-dependent approach.CRISPR-Cas9-based gene editing involves double-strand breaks at target sequences, which are often repaired by mutagenic non-homologous end-joining. Here the authors use Cas9 nickases to generate coordinated single-strand breaks in donor and target DNA for precise homology-directed gene editing.

A mechanistic investigation of ethylene oxide hydrolysis to ethanediol.

PubMed

Lundin, Angelica; Panas, Itai; Ahlberg, Elisabet

2007-09-20

The B3LYP/6-311+G(d,p) description is employed to study the heterolytic ring opening mechanisms under microsolvation conditions for ethylene oxide in acidic, neutral, and alkaline environments. In acid and alkaline media, a concerted trans S(N)2 reaction is strongly favored as compared to the corresponding cis reaction. The importance of the nucleophile, water in acidic media and hydroxide ion in alkaline media, for lowering the activation enthalpy is emphasized and activation energies of approximately 80 and approximately 60 kJ mol(-1) are obtained under acid and alkaline conditions, respectively. Under neutral conditions, the trans S(N)2 mechanism becomes inaccessible because it invokes the formation of a transient H+ and OH- pair across the 1,2-ethanediol molecule. Rather, epoxide ring opening is achieved by hydrolysis of a single water molecule. The latter mechanism displays significantly greater activation enthalpy (205 kJ mol(-1)) than those in acid and alkaline environments. This is in agreement with experiment. Product distributions of simple olefins in neutral aqueous media, as well as the detrimental impact of acid/base conditions for the selectivity of epoxidation catalysts in aqueous media, are discussed.

Tunable Magnetic Alignment between Trapped Exciton-Polariton Condensates.

PubMed

Ohadi, H; Del Valle-Inclan Redondo, Y; Dreismann, A; Rubo, Y G; Pinsker, F; Tsintzos, S I; Hatzopoulos, Z; Savvidis, P G; Baumberg, J J

2016-03-11

Tunable spin correlations are found to arise between two neighboring trapped exciton-polariton condensates which spin polarize spontaneously. We observe a crossover from an antiferromagnetic to a ferromagnetic pair state by reducing the coupling barrier in real time using control of the imprinted pattern of pump light. Fast optical switching of both condensates is then achieved by resonantly but weakly triggering only a single condensate. These effects can be explained as the competition between spin bifurcations and spin-preserving Josephson coupling between the two condensates, and open the way to polariton Bose-Hubbard ladders.

MRI-based finite element modeling of facial mimics: a case study on the paired zygomaticus major muscles.

PubMed

Fan, Ang-Xiao; Dakpé, Stéphanie; Dao, Tien Tuan; Pouletaut, Philippe; Rachik, Mohamed; Ho Ba Tho, Marie Christine

2017-07-01

Finite element simulation of facial mimics provides objective indicators about soft tissue functions for improving diagnosis, treatment and follow-up of facial disorders. There is a lack of in vivo experimental data for model development and validation. In this study, the contribution of the paired Zygomaticus Major (ZM) muscle contraction on the facial mimics was investigated using in vivo experimental data derived from MRI. Maximal relative differences of 7.7% and 37% were noted between MRI-based measurements and numerical outcomes for ZM and skin deformation behaviors respectively. This study opens a new direction to simulate facial mimics with in vivo data.

A Measurement and Analysis of Buildup Region Dose for Open Field Photon Beams (Cobalt-60 through 24 MV)

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

McCullough, Edwin C.

2015-01-15

The central axis depth dose in the build-up region (surface to d{sub max}) of single open field photon beams (cobalt-60 through 24 MV) has been measured utilizing parallel plate and extrapolation chamber methodology. These data were used to derive, for a prescription dose of 100 cGy, values of surface dose, the maximum value of dose along the central axis (D{sub max}) and the depth (nearest the surface) at which 90% of the prescription dose occurs (d{sub 90}). For both single and parallel opposed pair (POP) open field configurations, data are presented at field sizes of 5 × 5, 15 ×more » 15 and 25 × 25 cm{sup 2} for prescription depths of 10, 15 and 20 cm (midplane for POP). For the treatment machines, field sizes, and prescription depths studied, it is possible to conclude that: for single open field irradiation, surface dose values (as a percentage of the prescription dose) can be either low (<10%) or comparable to the prescription dose itself; for POP open fields, surface dose values are relatively independent of photon energy and midplane depth, and range between 30% and 70% of prescription dose, being principally dependent on field size; the depth of the initial 90 cGy point for a prescription dose of 100 cGy, d{sub 90}, was larger for POP fields. For either single or POP open field treatments, d{sub 90} was always less than 22 mm, while for 6 MV or less, values of d{sub 90} were less than 4 mm; D{sub max} values can be very large (e.g., above 300 cGy) for certain treatment situations and are reduced significantly for POP treatments; for open field POP treatments, the percent reduction in D{sub max} with each increment in beam energy above 10 MV is reduced over that seen at 10 MV or less and, possibly, this further reduction may be clinically insignificant; for open field POP treatments, changes in surface dose, d{sub 90} and D{sub max} with beam energy above 10 MV do not suggest, with regard to these specific build-up curve parameters, any obvious advantage for treatment with beam energies greater than 10 MV for the specific machines and situations studied.« less

Probe insertion apparatus with inflatable seal

NASA Technical Reports Server (NTRS)

Trimarchi, Paul A. (Inventor)

1990-01-01

A sealing apparatus is disclosed for inserting a probe into a pressure vessel having an elongated opening includes a pair of resiliently deformable seals opposingly disposed in sealing engagement with each other. A retainer is connected to the pressure vessel around the elongated opening and holds the pair of seals rigidly to the pressure vessel. A wedge is engageable with the pair of seals and carries the probe, for longitudinally translating the probe in pressure vessel.

A simple and highly selective 2,2-diferrocenylpropane-based multi-channel ion pair receptor for Pb(2+) and HSO4(-).

PubMed

Wan, Qian; Zhuo, Ji-Bin; Wang, Xiao-Xue; Lin, Cai-Xia; Yuan, Yao-Feng

2015-03-28

A structurally simple, 2,2-diferrocenylpropane-based ion pair receptor 1 was synthesized and characterized by (1)H NMR, (13)C NMR, HRMS, elemental analyses, and single-crystal X-ray diffraction. The ion pair receptor 1 showed excellent selectivity and sensitivity towards Pb(2+) with multi-channel responses: a fluorescence enhancement (more than 42-fold), a notable color change from yellow to red, redox anodic shift (ΔE1/2 = 151 mV), while HSO4(-) promoted fluorescence enhancement when Pb(2+) or Zn(2+) was bonded to the cation binding-site. (1)H NMR titration and density functional theory were performed to reveal the sensing mechanism based on photo-induced electron transfer (PET).

Locations of Joint Physical Activity in Parent-Child Pairs Based on Accelerometer and GPS Monitoring

PubMed Central

Dunton, Genevieve Fridlund; Liao, Yue; Almanza, Estela; Jerrett, Micheal; Spruijt-Metz, Donna; Pentz, Mary Ann

2012-01-01

Background Parental factors may play an important role in influencing children’s physical activity levels. Purpose This cross-sectional study sought to describe the locations of joint physical activity among parents and children. Methods Parent-child pairs (N = 291) wore an Actigraph GT2M accelerometer and GlobalSat BT-335 Global Positioning Systems (GPS) device over the same 7-day period. Children were ages 8–14 years. Joint behavior was defined by a linear separation distance of less than 50m between parent and child. Land use classifications were assigned to GPS data points. Results Joint physical activity was spread across residential locations (35%), and commercial venues (24%), and open spaces/parks (20%). Obese children and parents performed less joint physical activity in open spaces/parks than under/normal weight children and parents (p’s < .01). Conclusions Understanding where joint parent-child physical activity naturally occurs may inform location-based interventions to promote these behaviors. PMID:23011914

CAM controlled retractable door latch

NASA Technical Reports Server (NTRS)

Carsley, R. B. (Inventor)

1982-01-01

A latching mechanism in which there is linear movement and rotational movement is described. The umbilical doors of the space shuttle orbiter are required to be open during vehicle launch. After the external tank is released, the doors are closed. Presently, the device for maintaining the doors in an open position is mounted on the external tank and therefore has a single mission life. The latching mechanism of the invention is mounted in the orbiter and therefore is returned and has multimission capability. The latching mechanism is comprised of a pair of concentric nested, cylindrical cams and motors to actuate the cams, and latch pin all contained within a cover mounted on a support bracket carried by the substructure. A shaft having a latch pin is mounted inside the inner cylindrical cam.

A Framework for Final Drive Simultaneous Failure Diagnosis Based on Fuzzy Entropy and Sparse Bayesian Extreme Learning Machine

PubMed Central

Ye, Qing; Pan, Hao; Liu, Changhua

2015-01-01

This research proposes a novel framework of final drive simultaneous failure diagnosis containing feature extraction, training paired diagnostic models, generating decision threshold, and recognizing simultaneous failure modes. In feature extraction module, adopt wavelet package transform and fuzzy entropy to reduce noise interference and extract representative features of failure mode. Use single failure sample to construct probability classifiers based on paired sparse Bayesian extreme learning machine which is trained only by single failure modes and have high generalization and sparsity of sparse Bayesian learning approach. To generate optimal decision threshold which can convert probability output obtained from classifiers into final simultaneous failure modes, this research proposes using samples containing both single and simultaneous failure modes and Grid search method which is superior to traditional techniques in global optimization. Compared with other frequently used diagnostic approaches based on support vector machine and probability neural networks, experiment results based on F 1-measure value verify that the diagnostic accuracy and efficiency of the proposed framework which are crucial for simultaneous failure diagnosis are superior to the existing approach. PMID:25722717

Total teleportation of a single-photon state

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

Humble, Travis S; Bennink, Ryan S; Grice, Warren P

2008-01-01

Recent demonstrations of teleportation have transferred quantum information encoded into either polarization or field-quadrature degrees of freedom (DOFs), but an outstanding question is how to simultaneously teleport quantum information encoded into multiple DOFs. We describe how the transverse-spatial, spectral and polarization states of a single photon can be simultaneously teleported using a pair of multimode, polarization-entangled photons derived from spontaneous parametric down-conversion. Furthermore, when the initial photon pair is maximally entangled in the spatial, spectral, and polarization DOFs then the photon s full quantum state can be reliably teleported using a Bell-state measurement based on sum-frequency generation.

Whole genome amplification of single pollen grains from a sugarcane cultivar and analysis of the genetic relatedness based on SCoT markers

USDA-ARS?s Scientific Manuscript database

Single pollen grains were isolated from an intact anther of a sugarcane cultivar and collected using a pair of special forceps. The single pollen grains were lysed in an alkali/detergent solution respectively. The resulting solution was used as the template for Whole Genome Amplification. Genomic DN...

Measuring kinetics of complex single ion channel data using mean-variance histograms.

PubMed Central

Patlak, J B

1993-01-01

The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean-variance histogram technique provided a more credible analysis of the open, closed, and subconductance times for the patch. I also show that the method produces accurate results on simulated data in a wide variety of conditions, whereas the half-amplitude method, when applied to complex simulated data shows the same errors as were apparent in the real data. The utility and the limitations of this new method are discussed. Images FIGURE 2 FIGURE 4 FIGURE 8 FIGURE 9 PMID:7690261

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

PubMed Central

Keepers, Joe W.; Kollman, Peter A.; Weiner, Paul K.; James, Thomas L.

1982-01-01

Molecular mechanics studies have been carried out on “B-DNA-like” structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)]2 and [d(A)]12·[d(T)]12. Each of the backbone torsion angles (ψ, φ, ω, ω′, φ′) has been “forced” to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 Å in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-Å constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ≈5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH2 hydrogen bond, are qualitatively consistent with the ΔH for a “base pair-open state” suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N—H exchange, but it is localized, and only a small fraction of the N—H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

Concealed d -wave pairs in the s ± condensate of iron-based superconductors

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

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave (s ±) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. In this paper, we propose a new class of s ± statemore » containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave (L=2) motion of the pairs with the internal angular momenta I =2 of the iron orbitals to make a singlet (J =L+I =0), an s ± superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba 1$-$xK XFe 2As 2 as a reconfiguration of the orbital and internal angular momentum into a high spin (J =L+I =4) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. Finally, the formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.« less

Concealed d -wave pairs in the s ± condensate of iron-based superconductors

DOE PAGES

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

2016-05-02

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave (s ±) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. In this paper, we propose a new class of s ± statemore » containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave (L=2) motion of the pairs with the internal angular momenta I =2 of the iron orbitals to make a singlet (J =L+I =0), an s ± superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba 1$-$xK XFe 2As 2 as a reconfiguration of the orbital and internal angular momentum into a high spin (J =L+I =4) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. Finally, the formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.« less

Concealed d-wave pairs in the s± condensate of iron-based superconductors.

PubMed

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

2016-05-17

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave ([Formula: see text]) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. Here, we propose a new class of [Formula: see text] state containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave ([Formula: see text]) motion of the pairs with the internal angular momenta [Formula: see text] of the iron orbitals to make a singlet ([Formula: see text]), an [Formula: see text] superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba1-x KXFe2As2 as a reconfiguration of the orbital and internal angular momentum into a high spin ([Formula: see text]) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. The formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.

High-performance semiconductor quantum-dot single-photon sources

NASA Astrophysics Data System (ADS)

Senellart, Pascale; Solomon, Glenn; White, Andrew

2017-11-01

Single photons are a fundamental element of most quantum optical technologies. The ideal single-photon source is an on-demand, deterministic, single-photon source delivering light pulses in a well-defined polarization and spatiotemporal mode, and containing exactly one photon. In addition, for many applications, there is a quantum advantage if the single photons are indistinguishable in all their degrees of freedom. Single-photon sources based on parametric down-conversion are currently used, and while excellent in many ways, scaling to large quantum optical systems remains challenging. In 2000, semiconductor quantum dots were shown to emit single photons, opening a path towards integrated single-photon sources. Here, we review the progress achieved in the past few years, and discuss remaining challenges. The latest quantum dot-based single-photon sources are edging closer to the ideal single-photon source, and have opened new possibilities for quantum technologies.

Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.

PubMed

Nonin, S; Phan, A T; Leroy, J L

1997-09-15

Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize into an i-motif. The change of folding topology resulting from the substitution of a single nucleoside emphasizes the influence of the loop residues on the i-motif structure formed by two folded strands.

How many tautomerization pathways connect Watson-Crick-like G*·T DNA base mispair and wobble mismatches?

PubMed

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-01-01

In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate - the G·T*(WC) base mispair - and is governed by the planar, highly stable, and zwitterionic [Formula: see text] transition state stabilized by the participation of the unique pattern of the five intermolecular O6(+)H⋯O4(-), O6(+)H⋯N3(-), N1(+)H⋯N3(-), N1(+)H⋯O2(-), and N2(+)H⋯O2(-) H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson-Crick's geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.

pgRNAFinder: a web-based tool to design distance independent paired-gRNA.

PubMed

Xiong, Yuanyan; Xie, Xiaowei; Wang, Yanzhi; Ma, Wenbing; Liang, Puping; Songyang, Zhou; Dai, Zhiming

2017-11-15

The CRISPR/Cas System has been shown to be an efficient and accurate genome-editing technique. There exist a number of tools to design the guide RNA sequences and predict potential off-target sites. However, most of the existing computational tools on gRNA design are restricted to small deletions. To address this issue, we present pgRNAFinder, with an easy-to-use web interface, which enables researchers to design single or distance-free paired-gRNA sequences. The web interface of pgRNAFinder contains both gRNA search and scoring system. After users input query sequences, it searches gRNA by 3' protospacer-adjacent motif (PAM), and possible off-targets, and scores the conservation of the deleted sequences rapidly. Filters can be applied to identify high-quality CRISPR sites. PgRNAFinder offers gRNA design functionality for 8 vertebrate genomes. Furthermore, to keep pgRNAFinder open, extensible to any organism, we provide the source package for local use. The pgRNAFinder is freely available at http://songyanglab.sysu.edu.cn/wangwebs/pgRNAFinder/, and the source code and user manual can be obtained from https://github.com/xiexiaowei/pgRNAFinder. songyang@bcm.edu or daizhim@mail.sysu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Four base recognition by triplex-forming oligonucleotides at physiological pH

PubMed Central

Rusling, David A.; Powers, Vicki E. C.; Ranasinghe, Rohan T.; Wang, Yang; Osborne, Sadie D.; Brown, Tom; Fox, Keith R.

2005-01-01

We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, MeP (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while APP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, MeP and APP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA. PMID:15911633

Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding.

PubMed

Yang, Haozhe; Mei, Hui; Seela, Frank

2015-07-06

Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A positivity result in the theory of Macdonald polynomials

PubMed Central

Garsia, A. M.; Haglund, J.

2001-01-01

We outline here a proof that a certain rational function Cn(q, t), which has come to be known as the “q, t-Catalan,” is in fact a polynomial with positive integer coefficients. This has been an open problem since 1994. Because Cn(q, t) evaluates to the Catalan number at t = q = 1, it has also been an open problem to find a pair of statistics a, b on the collection 𝒟n of Dyck paths Π of length 2n yielding Cn(q, t) = ∑π ta(Π)qb(Π). Our proof is based on a recursion for Cn(q, t) suggested by a pair of statistics recently proposed by J. Haglund. One of the byproducts of our results is a proof of the validity of Haglund's conjecture. PMID:11274351

Page turning system

NASA Technical Reports Server (NTRS)

Kerley, James J. (Inventor); Eklund, Wayne D. (Inventor)

1992-01-01

A device for holding reading materials for use by readers without arm mobility is presented. The device is adapted to hold the reading materials in position for reading with the pages displayed to enable turning by use of a rubber tipped stick that is held in the mouth and has a pair of rectangular frames. The frames are for holding and positioning the reading materials opened in reading posture with the pages displayed at a substantially unobstructed sighting position for reading. The pair of rectangular frames are connected to one another by a hinge so the angle between the frames may be varied thereby varying the inclination of the reading material. A pair of bent spring mounted wires for holding opposing pages of the reading material open for reading without substantial visual interference of the pages is mounted to the base. The wires are also adjustable to the thickness of the reading material and have a variable friction adjustment. This enables the force of the wires against the pages to be varied and permits the reader to manipulate the pages with the stick.

Lead Telluride Quantum Dot Solar Cells Displaying External Quantum Efficiencies Exceeding 120%

PubMed Central

2015-01-01

Multiple exciton generation (MEG) in semiconducting quantum dots is a process that produces multiple charge-carrier pairs from a single excitation. MEG is a possible route to bypass the Shockley-Queisser limit in single-junction solar cells but it remains challenging to harvest charge-carrier pairs generated by MEG in working photovoltaic devices. Initial yields of additional carrier pairs may be reduced due to ultrafast intraband relaxation processes that compete with MEG at early times. Quantum dots of materials that display reduced carrier cooling rates (e.g., PbTe) are therefore promising candidates to increase the impact of MEG in photovoltaic devices. Here we demonstrate PbTe quantum dot-based solar cells, which produce extractable charge carrier pairs with an external quantum efficiency above 120%, and we estimate an internal quantum efficiency exceeding 150%. Resolving the charge carrier kinetics on the ultrafast time scale with pump–probe transient absorption and pump–push–photocurrent measurements, we identify a delayed cooling effect above the threshold energy for MEG. PMID:26488847

Conformational Dynamics inside Amino-Terminal Disease Hotspot of Ryanodine Receptor

PubMed Central

Zhong, Xiaowei; Liu, Ying; Zhu, Li; Meng, Xing; Wang, Ruiwu; Van Petegem, Filip; Wagenknecht, Terence; Wayne Chen, S. R.; Liu, Zheng

2013-01-01

Summary The N-terminal region of both skeletal and cardiac ryanodine receptor is a disease mutation hotspot. Recently, a crystal structure of the RyR1 fragment (residues 1-559) was solved. This N-terminal structure contains three separate domains, A, B, and C, and was docked into a central vestibule in a full-length RyR1 cryo-EM map. Here we reconstructed 3D cryo-EM structures of two GFP-tagged RyR2s with GFP inserted after residue Glu-310 and Ser-437, respectively. The structures of RyR2E310-GFP and RyR2S437-GFP displayed an extra mass on domain B and C, directly validating the predicted docking model. Next, we revealed domain movements in molecular dynamics flexible fitting models in both the closed and open state cryo-EM maps. To further probe the conformational changes, we generated FRET pairs by inserting CFP or YFP in two selected domains, FRET studies of three dual-insertion pairs and three co-expressed single-insertion pairs showed the dynamic structural changes within the N-terminal domains. PMID:24139989

Spectroscopy of Single AlInAs Quantum Dots

NASA Astrophysics Data System (ADS)

Derebezov, I. A.; Gaisler, A. V.; Gaisler, V. A.; Dmitriev, D. V.; Toropov, A. I.; Kozhukhov, A. S.; Shcheglov, D. V.; Latyshev, A. V.; Aseev, A. L.

2018-03-01

A system of quantum dots based on Al x In1- x As/Al y Ga1- y As solid solutions is investigated. The use of Al x In1- x As wide-gap solid solutions as the basis of quantum dots substantially extends the spectral emission range to the short-wavelength region, including the wavelength region near 770 nm, which is of interest for the development of aerospace systems of quantum cryptography. The optical characteristics of Al x In1- x As single quantum dots grown by the Stranski-Krastanov mechanism were studied by cryogenic microphotoluminescence. The statistics of the emission of single quantum dot excitons was studied using a Hanbury Brown-Twiss interferometer. The pair photon correlation function indicates the sub-Poissonian nature of the emission statistics, which directly confirms the possibility of developing single-photon emitters based on Al x In1- x As quantum dots. The fine structure of quantum dot exciton states was investigated at wavelengths near 770 nm. The splitting of the exciton states is found to be similar to the natural width of exciton lines, which is of great interest for the development of entangled photon pair emitters based on Al x In1- x As quantum dots.

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations.

PubMed

Tian, Kai; Chen, Xiaowei; Luan, Binquan; Singh, Prashant; Yang, Zhiyu; Gates, Kent S; Lin, Mengshi; Mustapha, Azlin; Gu, Li-Qun

2018-05-22

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

Four eyes match better than two: Sharing of precise patch-use time among socially foraging domestic chicks.

PubMed

Xin, Qiuhong; Ogura, Yukiko; Matsushima, Toshiya

2017-07-01

To examine how resource competition contributes to patch-use behaviour, we examined domestic chicks foraging in an I-shaped maze equipped with two terminal feeders. In a variable interval schedule, one feeder supplied grains three times more frequently than the other, and the sides were reversed midway through the experiment. The maze was partitioned into two lanes by a transparent wall, so that chicks fictitiously competed without actual interference. Stay time at feeders was compared among three groups. The "single" group contained control chicks; the "pair" group comprised the pairs of chicks tested in the fictitious competition; "mirror" included single chicks accompanied by their respective mirror images. Both "pair" and "mirror" chicks showed facilitated running. In terms of the patch-use ratio, "pair" chicks showed precise matching at approximately 3:1 with significant mutual dependence, whereas "single" and "mirror" chicks showed a comparable under-matching. The facilitated running increased visits to feeders, but failed to predict the patch-use ratio of the subject. At the reversal, quick switching occurred similarly in all groups, but the "pair" chicks revealed a stronger memory-based matching. Perceived competition therefore contributes to precise matching and lasting memory of the better feeder, in a manner dissociated from socially facilitated food search. Copyright © 2017 Elsevier B.V. All rights reserved.

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

PubMed

Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

2017-02-01

Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

Hard choices in assessing survival past dams — a comparison of single- and paired-release strategies

USGS Publications Warehouse

Zydlewski, Joseph D.; Stich, Daniel S.; Sigourney, Douglas B.

2017-01-01

Mark–recapture models are widely used to estimate survival of salmon smolts migrating past dams. Paired releases have been used to improve estimate accuracy by removing components of mortality not attributable to the dam. This method is accompanied by reduced precision because (i) sample size is reduced relative to a single, large release; and (ii) variance calculations inflate error. We modeled an idealized system with a single dam to assess trade-offs between accuracy and precision and compared methods using root mean squared error (RMSE). Simulations were run under predefined conditions (dam mortality, background mortality, detection probability, and sample size) to determine scenarios when the paired release was preferable to a single release. We demonstrate that a paired-release design provides a theoretical advantage over a single-release design only at large sample sizes and high probabilities of detection. At release numbers typical of many survival studies, paired release can result in overestimation of dam survival. Failures to meet model assumptions of a paired release may result in further overestimation of dam-related survival. Under most conditions, a single-release strategy was preferable.

Microfluidic cell trap array for controlled positioning of single cells on adhesive micropatterns.

PubMed

Lin, Laiyi; Chu, Yeh-Shiu; Thiery, Jean Paul; Lim, Chwee Teck; Rodriguez, Isabel

2013-02-21

Adhesive micropattern arrays permit the continuous monitoring and systematic study of the behavior of spatially confined cells of well-defined shape and size in ordered configurations. This technique has contributed to defining mechanisms that control cell polarity and cell functions, including proliferation, apoptosis, differentiation and migration in two-dimensional cell culture systems. These micropattern studies often involve isolating a single cell on one adhesive protein micropattern using random seeding methods. Random seeding has been successful for isolated and, to a lesser degree, paired patterns, where two patterns are placed in close proximity. Using this method, we found that the probability of obtaining one cell per pattern decreases significantly as the number of micropatterns in a cluster increases, from 16% for paired micropatterns to 0.3% for clusters of 6 micropatterns. This work presents a simple yet effective platform based on a microfludic sieve-like trap array to exert precise control over the positioning of single cells on micropatterns. We observed a 4-fold improvement over random seeding in the efficiency of placing a pair of single cells on paired micropattern and a 40-fold improvement for 6-pattern clusters. The controlled nature of this platform can also allow the juxtaposition of two different cell populations through a simple modification in the trap arrangement. With excellent control of the identity, number and position of neighbouring cells, this cell-positioning platform provides a unique opportunity for the extension of two-dimensional micropattern studies beyond paired micropatterns to organizations containing many cells or different cell types.

4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

PubMed Central

2011-01-01

Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible. PMID:21733172

OsDMC1 Is Not Required for Homologous Pairing in Rice Meiosis1[OPEN

PubMed Central

Tang, Ding; Liu, Xiaofei; Du, Guijie; Shen, Yi; Li, Yafei; Cheng, Zhukuan

2016-01-01

Meiotic homologous recombination is pivotal to sexual reproduction. DMC1, a conserved recombinase, is involved in directing single-end invasion between interhomologs during meiotic recombination. In this study, we identified OsDMC1A and OsDMC1B, two closely related proteins in rice (Oryza sativa) with high sequence similarity to DMC1 proteins from other species. Analysis of Osdmc1a and Osdmc1b Tos17 insertion mutants indicated that these genes are functionally redundant. Immunolocalization analysis revealed OsDMC1 foci occurred at leptotene, which disappeared from late pachytene chromosomes in wild-type meiocytes. According to cytological analyses, homologous pairing is accomplished in the Osdmc1a Osdmc1b double mutant, but synapsis is seriously disrupted. The reduced number of bivalents and abnormal OsHEI10 foci in Osdmc1a Osdmc1b establishes an essential role for OsDMC1 in crossover formation. In the absence of OsDMC1, early recombination events probably occur normally, leading to normal localization of γH2AX, PAIR3, OsMRE11, OsCOM1, and OsRAD51C. Moreover, OsDMC1 was not detected in pairing-defective mutants, such as pair2, pair3, Oscom1, and Osrad51c, while it was loaded onto meiotic chromosomes in zep1, Osmer3, Oszip4, and Oshei10. Taken together, these results suggest that during meiosis, OsDMC1 is dispensable for homologous pairing in rice, which is quite different from the DMC1 homologs identified so far in other organisms. PMID:26960731

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.

PubMed

Greenwald, William W; Li, He; Smith, Erin N; Benaglio, Paola; Nariai, Naoki; Frazer, Kelly A

2017-04-07

Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite "pgltools": a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.

Testing the single-state dominance hypothesis

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

Álvarez-Rodríguez, R.; Moreno, O.; Moya de Guerra, E.

2013-12-30

We present a theoretical analysis of the single-state dominance hypothesis for the two-neutrino double-beta decay process. The theoretical framework is a proton-neutron QRPA based on a deformed Hartree-Fock mean field with BCS pairing correlations. We focus on the decays of {sup 100}Mo, {sup 116}Cd and {sup 128}Te. We do not find clear evidences for single-state dominance within the present approach.

Epigenome data release: a participant-centered approach to privacy protection.

PubMed

Dyke, Stephanie O M; Cheung, Warren A; Joly, Yann; Ammerpohl, Ole; Lutsik, Pavlo; Rothstein, Mark A; Caron, Maxime; Busche, Stephan; Bourque, Guillaume; Rönnblom, Lars; Flicek, Paul; Beck, Stephan; Hirst, Martin; Stunnenberg, Henk; Siebert, Reiner; Walter, Jörn; Pastinen, Tomi

2015-07-17

Large-scale epigenome mapping by the NIH Roadmap Epigenomics Project, the ENCODE Consortium and the International Human Epigenome Consortium (IHEC) produces genome-wide DNA methylation data at one base-pair resolution. We examine how such data can be made open-access while balancing appropriate interpretation and genomic privacy. We propose guidelines for data release that both reduce ambiguity in the interpretation of open-access data and limit immediate access to genetic variation data that are made available through controlled access.

Super-Chelators for Advanced Protein Labeling in Living Cells.

PubMed

Gatterdam, Karl; Joest, Eike F; Dietz, Marina S; Heilemann, Mike; Tampé, Robert

2018-05-14

Live-cell labeling, super-resolution microscopy, single-molecule applications, protein localization, or chemically induced assembly are emerging approaches, which require specific and very small interaction pairs. The minimal disturbance of protein function is essential to derive unbiased insights into cellular processes. Herein, we define a new class of hexavalent N-nitrilotriacetic acid (hexaNTA) chelators, displaying the highest affinity and stability of all NTA-based small interaction pairs described so far. Coupled to bright organic fluorophores with fine-tuned photophysical properties, the super-chelator probes were delivered into human cells by chemically gated nanopores. These super-chelators permit kinetic profiling, multiplexed labeling of His 6 - and His 12 -tagged proteins as well as single-molecule-based super-resolution imaging. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A community computational challenge to predict the activity of pairs of compounds.

PubMed

Bansal, Mukesh; Yang, Jichen; Karan, Charles; Menden, Michael P; Costello, James C; Tang, Hao; Xiao, Guanghua; Li, Yajuan; Allen, Jeffrey; Zhong, Rui; Chen, Beibei; Kim, Minsoo; Wang, Tao; Heiser, Laura M; Realubit, Ronald; Mattioli, Michela; Alvarez, Mariano J; Shen, Yao; Gallahan, Daniel; Singer, Dinah; Saez-Rodriguez, Julio; Xie, Yang; Stolovitzky, Gustavo; Califano, Andrea

2014-12-01

Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound pairs, from the most synergistic to the most antagonistic, based on gene-expression profiles of human B cells treated with individual compounds at multiple time points and concentrations. Using scoring metrics based on experimental dose-response curves, we assessed 32 methods (31 community-generated approaches and SynGen), four of which performed significantly better than random guessing. We highlight similarities between the methods. Although the accuracy of predictions was not optimal, we find that computational prediction of compound-pair activity is possible, and that community challenges can be useful to advance the field of in silico compound-synergy prediction.

A rule of seven in Watson-Crick base-pairing of mismatched sequences.

PubMed

Cisse, Ibrahim I; Kim, Hajin; Ha, Taekjip

2012-05-13

Sequence recognition through base-pairing is essential for DNA repair and gene regulation, but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized, despite its potential importance in nucleic acid-based biotechnologies and gene silencing. Here we use single-molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to precisely quantify the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement for seven nucleotides of complementarity to seed gene silencing by small noncoding RNA and may help guide performance improvement in DNA- and RNA-based bio- and nanotechnologies, in which off-target effects can be detrimental.

A single-solenoid pulsed-magnet system for single-crystal scattering studies

NASA Astrophysics Data System (ADS)

Islam, Zahirul; Capatina, Dana; Ruff, Jacob P. C.; Das, Ritesh K.; Trakhtenberg, Emil; Nojiri, Hiroyuki; Narumi, Yasuo; Welp, Ulrich; Canfield, Paul C.

2012-03-01

We present a pulsed-magnet system that enables x-ray single-crystal diffraction in addition to powder and spectroscopic studies with the magnetic field applied on or close to the scattering plane. The apparatus consists of a single large-bore solenoid, cooled by liquid nitrogen. A second independent closed-cycle cryostat is used for cooling samples near liquid helium temperatures. Pulsed magnetic fields close to ˜30 T with a zero-to-peak-field rise time of ˜2.9 ms are generated by discharging a 40 kJ capacitor bank into the magnet coil. The unique characteristic of this instrument is the preservation of maximum scattering angle (˜23.6°) on the entrance and exit sides of the magnet bore by virtue of a novel double-funnel insert. This instrument will facilitate x-ray diffraction and spectroscopic studies that are impractical, if not impossible, to perform using split-pair and narrow-opening solenoid magnets. Furthermore, it offers a practical solution for preserving optical access in future higher-field pulsed magnets.

An Expressive, Lightweight and Secure Construction of Key Policy Attribute-Based Cloud Data Sharing Access Control

NASA Astrophysics Data System (ADS)

Lin, Guofen; Hong, Hanshu; Xia, Yunhao; Sun, Zhixin

2017-10-01

Attribute-based encryption (ABE) is an interesting cryptographic technique for flexible cloud data sharing access control. However, some open challenges hinder its practical application. In previous schemes, all attributes are considered as in the same status while they are not in most of practical scenarios. Meanwhile, the size of access policy increases dramatically with the raise of its expressiveness complexity. In addition, current research hardly notices that mobile front-end devices, such as smartphones, are poor in computational performance while too much bilinear pairing computation is needed for ABE. In this paper, we propose a key-policy weighted attribute-based encryption without bilinear pairing computation (KP-WABE-WB) for secure cloud data sharing access control. A simple weighted mechanism is presented to describe different importance of each attribute. We introduce a novel construction of ABE without executing any bilinear pairing computation. Compared to previous schemes, our scheme has a better performance in expressiveness of access policy and computational efficiency.

Increased occurrence of pesticide residues on crops grown in protected environments compared to crops grown in open field conditions.

PubMed

Allen, Gina; Halsall, Crispin J; Ukpebor, Justina; Paul, Nigel D; Ridall, Gareth; Wargent, Jason J

2015-01-01

Crops grown under plastic-clad structures or in greenhouses may be prone to an increased frequency of pesticide residue detections and higher concentrations of pesticides relative to equivalent crops grown in the open field. To test this we examined pesticide data for crops selected from the quarterly reports (2004-2009) of the UK's Pesticide Residue Committee. Five comparison crop pairs were identified whereby one crop of each pair was assumed to have been grown primarily under some form of physical protection ('protected') and the other grown primarily in open field conditions ('open'). For each pair, the number of detectable pesticide residues and the proportion of crop samples containing pesticides were statistically compared (n=100 s samples for each crop). The mean concentrations of selected photolabile pesticides were also compared. For the crop pairings of cabbage ('open') vs. lettuce ('protected') and 'berries' ('open') vs. strawberries ('protected') there was a significantly higher number of pesticides and proportion of samples with multiple residues for the protected crops. Statistically higher concentrations of pesticides, including cypermethrin, cyprodinil, fenhexamid, boscalid and iprodione were also found in the protected crops compared to the open crops. The evidence here demonstrates that, in general, the protected crops possess a higher number of detectable pesticides compared to analogous crops grown in the open. This may be due to different pesticide-use regimes, but also due to slower rates of pesticide removal in protected systems. The findings of this study raise implications for pesticide management in protected-crop systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

PubMed

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

PubMed Central

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

2014-01-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

Design of two-photon molecular tandem architectures for solar cells by ab initio theory

DOE PAGES

Ornso, Kristian B.; Garcia-Lastra, Juan M.; De La Torre, Gema; ...

2015-03-04

An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range. Three different architectures are considered: the first two involve a complex consisting of two dye molecules with appropriately matched frontier orbitals, connected by a molecular diode. Optimized combinations of dye molecules are determined by taking advantage of our computational database of the structural and energetic properties of several thousand porphyrin dyes. The third design is amore » molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices, such as the synthesis of the tandem molecules and potential loss mechanisms, are addressed.« less

Geodesic regression for image time-series.

PubMed

Niethammer, Marc; Huang, Yang; Vialard, François-Xavier

2011-01-01

Registration of image-time series has so far been accomplished (i) by concatenating registrations between image pairs, (ii) by solving a joint estimation problem resulting in piecewise geodesic paths between image pairs, (iii) by kernel based local averaging or (iv) by augmenting the joint estimation with additional temporal irregularity penalties. Here, we propose a generative model extending least squares linear regression to the space of images by using a second-order dynamic formulation for image registration. Unlike previous approaches, the formulation allows for a compact representation of an approximation to the full spatio-temporal trajectory through its initial values. The method also opens up possibilities to design image-based approximation algorithms. The resulting optimization problem is solved using an adjoint method.

Multi-user distribution of polarization entangled photon pairs

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

Trapateau, J.; Orieux, A.; Diamanti, E.

We experimentally demonstrate multi-user distribution of polarization entanglement using commercial telecom wavelength division demultiplexers. The entangled photon pairs are generated from a broadband source based on spontaneous parametric down conversion in a periodically poled lithium niobate crystal using a double path setup employing a Michelson interferometer and active phase stabilisation. We test and compare demultiplexers based on various technologies and analyze the effect of their characteristics, such as losses and polarization dependence, on the quality of the distributed entanglement for three channel pairs of each demultiplexer. In all cases, we obtain a Bell inequality violation, whose value depends on themore » demultiplexer features. This demonstrates that entanglement can be distributed to at least three user pairs of a network from a single source. Additionally, we verify for the best demultiplexer that the violation is maintained when the pairs are distributed over a total channel attenuation corresponding to 20 km of optical fiber. These techniques are therefore suitable for resource-efficient practical implementations of entanglement-based quantum key distribution and other quantum communication network applications.« less

Derivation of hydrous pyrolysis kinetic parameters from open-system pyrolysis

NASA Astrophysics Data System (ADS)

Tseng, Yu-Hsin; Huang, Wuu-Liang

2010-05-01

Kinetic information is essential to predict the temperature, timing or depth of hydrocarbon generation within a hydrocarbon system. The most common experiments for deriving kinetic parameters are mainly by open-system pyrolysis. However, it has been shown that the conditions of open-system pyrolysis are deviant from nature by its low near-ambient pressure and high temperatures. Also, the extrapolation of heating rates in open-system pyrolysis to geological conditions may be questionable. Recent study of Lewan and Ruble shows hydrous-pyrolysis conditions can simulate the natural conditions better and its applications are supported by two case studies with natural thermal-burial histories. Nevertheless, performing hydrous pyrolysis experiment is really tedious and requires large amount of sample, while open-system pyrolysis is rather convenient and efficient. Therefore, the present study aims at the derivation of convincing distributed hydrous pyrolysis Ea with only routine open-system Rock-Eval data. Our results unveil that there is a good correlation between open-system Rock-Eval parameter Tmax and the activation energy (Ea) derived from hydrous pyrolysis. The hydrous pyrolysis single Ea can be predicted from Tmax based on the correlation, while the frequency factor (A0) is estimated based on the linear relationship between single Ea and log A0. Because the Ea distribution is more rational than single Ea, we modify the predicted single hydrous pyrolysis Ea into distributed Ea by shifting the pattern of Ea distribution from open-system pyrolysis until the weight mean Ea distribution equals to the single hydrous pyrolysis Ea. Moreover, it has been shown that the shape of the Ea distribution is very much alike the shape of Tmax curve. Thus, in case of the absence of open-system Ea distribution, we may use the shape of Tmax curve to get the distributed hydrous pyrolysis Ea. The study offers a new approach as a simple method for obtaining distributed hydrous pyrolysis Ea with only routine open-system Rock-Eval data, which will allow for better estimating hydrocarbon generation.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Genome Editing Tools in Plants

PubMed Central

Mohanta, Tapan Kumar; Bashir, Tufail; Hashem, Abeer; Bae, Hanhong

2017-01-01

Genome editing tools have the potential to change the genomic architecture of a genome at precise locations, with desired accuracy. These tools have been efficiently used for trait discovery and for the generation of plants with high crop yields and resistance to biotic and abiotic stresses. Due to complex genomic architecture, it is challenging to edit all of the genes/genomes using a particular genome editing tool. Therefore, to overcome this challenging task, several genome editing tools have been developed to facilitate efficient genome editing. Some of the major genome editing tools used to edit plant genomes are: Homologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), pentatricopeptide repeat proteins (PPRs), the CRISPR/Cas9 system, RNA interference (RNAi), cisgenesis, and intragenesis. In addition, site-directed sequence editing and oligonucleotide-directed mutagenesis have the potential to edit the genome at the single-nucleotide level. Recently, adenine base editors (ABEs) have been developed to mutate A-T base pairs to G-C base pairs. ABEs use deoxyadeninedeaminase (TadA) with catalytically impaired Cas9 nickase to mutate A-T base pairs to G-C base pairs. PMID:29257124

Fine structures of the ejaculatory sac and sperm pump of the scorpionfly Panorpa liui Hua (Mecoptera: Panorpidae).

PubMed

Shen, Jian; Hua, Baozhen

2013-08-01

Male adults of Panorpidae possess a special sperm pump, through which the males transfer liquid sperm to the females. However, the structures of the sperm pump and the transfer mechanism have not been satisfactorily elucidated hitherto. In this paper the structures of the ejaculatory sac and sperm pump of the scorpionfly Panorpa liui Hua were investigated using light microscopy and scanning electron microscopy. The ejaculatory sac is located between the basal end of the paired vasa deferentia and the aedeagus, comprising a small anterior part and a large posterior part. The anterior part is simple and functions only as a channel for sperm transfer. The epithelial cells of the large posterior part likely have secretory functions. The sperm pump is formed by the posterior region of the ejaculatory sac and derivates of the genital field, which enclose the pumping chamber, a piston and the associated muscles. The orifice of the ejaculatory duct lies ventrad of the piston. The piston of the sperm pump is heavily sclerotized and controlled by two antagonistic muscle pairs. A pair of simple tubular accessory glands opens to the pumping chamber. Two well-developed sex pheromone glands are located on the ventral side of the ejaculatory sac, and are composed of two fan-shaped lamellae. The epithelium of the sex pheromone glands is single-layered, and forms densely filamentous processes. The ejaculation mechanism is briefly discussed based on the morphology of ejaculatory sac and sperm pump. Copyright © 2013 Elsevier Ltd. All rights reserved.

A single base pair in the right terminal domain of tomato planta macho viroid is a virulence determinant factor on tomato.

PubMed

Li, Rugang; Padmanabhan, Chellappan; Ling, Kai-Shu

2017-01-01

Tomato planta macho viroid (TPMVd), including isolates previously designated as Mexican papita viroid (MPVd), causes serious disease on tomatoes in North America. Two predominant variants, sharing 93.8% sequence identity, incited distinct severe (MPVd-S) or mild (MPVd-M) symptoms on tomato. To identify virulence determinant factor, a series of chimeric infectious clones were generated using synthetic DNA approach to progressively replace each structural domain between the two variants. In bioassays on tomato 'Rutgers', three chimeras containing Terminal Left and Pathogenicity (MPVd-H1), Central (MPVd-H2), or Variable (MPVd-H3) of MPVd-S, incited mild to intermediate symptoms. However, a chimera containing Terminal Right (T R ) of MPVd-S (MPVd-H4) incited severe symptoms. Only one base-pair mutation in the T R domain between MPVd-M ( 176 U:A 185 ) and MPVd-S ( 174 G:C 183 ) was identified. A reciprocal mutant (MPVd-H5) rendered the chimeric viroid mild on tomato. This single base-pair in the T R domain was determined as the virulence determinant factor for TPMVd. Published by Elsevier Inc.

Generic Long-Range Interactions Between Passive Bodies in an Active Fluid.

PubMed

Baek, Yongjoo; Solon, Alexandre P; Xu, Xinpeng; Nikola, Nikolai; Kafri, Yariv

2018-02-02

A single nonspherical body placed in an active fluid generates currents via breaking of time-reversal symmetry. We show that, when two or more passive bodies are placed in an active fluid, these currents lead to long-range interactions. Using a multipole expansion, we characterize their leading-order behaviors in terms of single-body properties and show that they decay as a power law with the distance between the bodies, are anisotropic, and do not obey an action-reaction principle. The interactions lead to rich dynamics of the bodies, illustrated by the spontaneous synchronized rotation of pinned nonchiral bodies and the formation of traveling bound pairs. The occurrence of these phenomena depends on tunable properties of the bodies, thus opening new possibilities for self-assembly mediated by active fluids.

Comparative study of the requantization of the time-dependent mean field for the dynamics of nuclear pairing

NASA Astrophysics Data System (ADS)

Ni, Fang; Nakatsukasa, Takashi

2018-04-01

To describe quantal collective phenomena, it is useful to requantize the time-dependent mean-field dynamics. We study the time-dependent Hartree-Fock-Bogoliubov (TDHFB) theory for the two-level pairing Hamiltonian, and compare results of different quantization methods. The one constructing microscopic wave functions, using the TDHFB trajectories fulfilling the Einstein-Brillouin-Keller quantization condition, turns out to be the most accurate. The method is based on the stationary-phase approximation to the path integral. We also examine the performance of the collective model which assumes that the pairing gap parameter is the collective coordinate. The applicability of the collective model is limited for the nuclear pairing with a small number of single-particle levels, because the pairing gap parameter represents only a half of the pairing collective space.

Lid for improved dendritic web growth

DOEpatents

Duncan, Charles S.; Kochka, Edgar L.; Piotrowski, Paul A.; Seidensticker, Raymond G.

1992-03-24

A lid for a susceptor in which a crystalline material is melted by induction heating to form a pool or melt of molten material from which a dendritic web of essentially a single crystal of the material is pulled through an elongated slot in the lid and the lid has a pair of generally round openings adjacent the ends of the slot and a groove extends between each opening and the end of the slot. The grooves extend from the outboard surface of the lid to adjacent the inboard surface providing a strip contiguous with the inboard surface of the lid to produce generally uniform radiational heat loss across the width of the dendritic web adjacent the inboard surface of the lid to reduce thermal stresses in the web and facilitate the growth of wider webs at a greater withdrawal rate.

Comparative analysis of main bio-active components in the herb pair Danshen-Honghua and its single herbs by ultra-high performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry.

PubMed

Qu, Cheng; Pu, Zong-Jin; Zhou, Gui-Sheng; Wang, Jun; Zhu, Zhen-Hua; Yue, Shi-Jun; Li, Jian-Ping; Shang, Li-Li; Tang, Yu-Ping; Shi, Xu-Qin; Liu, Pei; Guo, Jian-Ming; Sun, Jing; Tang, Zhi-Shu; Zhao, Jing; Zhao, Bu-Chang; Duan, Jin-Ao

2017-09-01

A sensitive, reliable, and powerful ultra-high performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry method was developed for simultaneous quantification of the 15 main bio-active components including phenolic acids and flavonoids within 13 min for the first time. The proposed method was first reported and validated by good linearity (r 2  > 0.9975), limit of detection (1.12-7.01 ng/mL), limit of quantification (3.73-23.37 ng/mL), intra- and inter-day precisions (RSD ≤ 1.92%, RSD ≤ 2.45%), stability (RSD ≤ 5.63%), repeatability (RSD ≤ 4.34%), recovery (96.84-102.12%), and matrix effects (0.92-1.02). The established analytical methodology was successfully applied to comparative analysis of main bio-active components in the herb pair Danshen-Honghua and its single herbs. Compared to the single herb, the content of most flavonoid glycosides was remarkably increased in their herb pair, and main phenolic acids were decreased, conversely. The content changes of the main components in the herb pair supported the synergistic effects on promoting blood circulation and removing blood stasis. The results provide a scientific basis and reference for the quality control of Danshen-Honghua herb pair and the drug interactions based on variation of bio-active components in herb pairs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

M&A For Lithography Of Sparse Arrays Of Sub-Micrometer Features

DOEpatents

Brueck, Steven R.J.; Chen, Xiaolan; Zaidi, Saleem; Devine, Daniel J.

1998-06-02

Methods and apparatuses are disclosed for the exposure of sparse hole and/or mesa arrays with line:space ratios of 1:3 or greater and sub-micrometer hole and/or mesa diameters in a layer of photosensitive material atop a layered material. Methods disclosed include: double exposure interferometric lithography pairs in which only those areas near the overlapping maxima of each single-period exposure pair receive a clearing exposure dose; double interferometric lithography exposure pairs with additional processing steps to transfer the array from a first single-period interferometric lithography exposure pair into an intermediate mask layer and a second single-period interferometric lithography exposure to further select a subset of the first array of holes; a double exposure of a single period interferometric lithography exposure pair to define a dense array of sub-micrometer holes and an optical lithography exposure in which only those holes near maxima of both exposures receive a clearing exposure dose; combination of a single-period interferometric exposure pair, processing to transfer resulting dense array of sub-micrometer holes into an intermediate etch mask, and an optical lithography exposure to select a subset of initial array to form a sparse array; combination of an optical exposure, transfer of exposure pattern into an intermediate mask layer, and a single-period interferometric lithography exposure pair; three-beam interferometric exposure pairs to form sparse arrays of sub-micrometer holes; five- and four-beam interferometric exposures to form a sparse array of sub-micrometer holes in a single exposure. Apparatuses disclosed include arrangements for the three-beam, five-beam and four-beam interferometric exposures.

Detecting Single-Nucleotide Substitutions Induced by Genome Editing.

PubMed

Miyaoka, Yuichiro; Chan, Amanda H; Conklin, Bruce R

2016-08-01

The detection of genome editing is critical in evaluating genome-editing tools or conditions, but it is not an easy task to detect genome-editing events-especially single-nucleotide substitutions-without a surrogate marker. Here we introduce a procedure that significantly contributes to the advancement of genome-editing technologies. It uses droplet digital polymerase chain reaction (ddPCR) and allele-specific hydrolysis probes to detect single-nucleotide substitutions generated by genome editing (via homology-directed repair, or HDR). HDR events that introduce substitutions using donor DNA are generally infrequent, even with genome-editing tools, and the outcome is only one base pair difference in 3 billion base pairs of the human genome. This task is particularly difficult in induced pluripotent stem (iPS) cells, in which editing events can be very rare. Therefore, the technological advances described here have implications for therapeutic genome editing and experimental approaches to disease modeling with iPS cells. © 2016 Cold Spring Harbor Laboratory Press.

Multiconfiguration pair-density functional theory for doublet excitation energies and excited state geometries: the excited states of CN.

PubMed

Bao, Jie J; Gagliardi, Laura; Truhlar, Donald G

2017-11-15

Multiconfiguration pair-density functional theory (MC-PDFT) is a post multiconfiguration self-consistent field (MCSCF) method with similar performance to complete active space second-order perturbation theory (CASPT2) but with greater computational efficiency. Cyano radical (CN) is a molecule whose spectrum is well established from experiments and whose excitation energies have been used as a testing ground for theoretical methods to treat excited states of open-shell systems, which are harder and much less studied than excitation energies of closed-shell singlets. In the present work, we studied the adiabatic excitation energies of CN with MC-PDFT. Then we compared this multireference (MR) method to some single-reference (SR) methods, including time-dependent density functional theory (TDDFT) and completely renormalized equation-of-motion coupled-cluster theory with singles, doubles and noniterative triples [CR-EOM-CCSD(T)]; we also compared to some other MR methods, including configuration interaction singles and doubles (MR-CISD) and multistate CASPT2 (MS-CASPT2). Through a comparison between SR and MR methods, we achieved a better appreciation of the need to use MR methods to accurately describe higher excited states, and we found that among the MR methods, MC-PDFT stands out for its accuracy for the first four states out of the five doublet states studied this paper; this shows its efficiency for calculating doublet excited states.

XaNSoNS: GPU-accelerated simulator of diffraction patterns of nanoparticles

NASA Astrophysics Data System (ADS)

Neverov, V. S.

XaNSoNS is an open source software with GPU support, which simulates X-ray and neutron 1D (or 2D) diffraction patterns and pair-distribution functions (PDF) for amorphous or crystalline nanoparticles (up to ∼107 atoms) of heterogeneous structural content. Among the multiple parameters of the structure the user may specify atomic displacements, site occupancies, molecular displacements and molecular rotations. The software uses general equations nonspecific to crystalline structures to calculate the scattering intensity. It supports four major standards of parallel computing: MPI, OpenMP, Nvidia CUDA and OpenCL, enabling it to run on various architectures, from CPU-based HPCs to consumer-level GPUs.

Quasichemical analysis of the cluster-pair approximation for the thermodynamics of proton hydration

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

Pollard, Travis; Beck, Thomas L.; Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221

2014-06-14

A theoretical analysis of the cluster-pair approximation (CPA) is presented based on the quasichemical theory of solutions. The sought single-ion hydration free energy of the proton includes an interfacial potential contribution by definition. It is shown, however, that the CPA involves an extra-thermodynamic assumption that does not guarantee uniform convergence to a bulk free energy value with increasing cluster size. A numerical test of the CPA is performed using the classical polarizable AMOEBA force field and supporting quantum chemical calculations. The enthalpy and free energy differences are computed for the kosmotropic Na{sup +}/F{sup −} ion pair in water clusters ofmore » size n = 5, 25, 105. Additional calculations are performed for the chaotropic Rb{sup +}/I{sup −} ion pair. A small shift in the proton hydration free energy and a larger shift in the hydration enthalpy, relative to the CPA values, are predicted based on the n = 105 simulations. The shifts arise from a combination of sequential hydration and interfacial potential effects. The AMOEBA and quantum chemical results suggest an electrochemical surface potential of water in the range −0.4 to −0.5 V. The physical content of single-ion free energies and implications for ion-water force field development are also discussed.« less

Multi-image CAD employing features derived from ipsilateral mammographic views

NASA Astrophysics Data System (ADS)

Good, Walter F.; Zheng, Bin; Chang, Yuan-Hsiang; Wang, Xiao Hui; Maitz, Glenn S.; Gur, David

1999-05-01

On mammograms, certain kinds of features related to masses (e.g., location, texture, degree of spiculation, and integrated density difference) tend to be relatively invariant, or at last predictable, with respect to breast compression. Thus, ipsilateral pairs of mammograms may contain information not available from analyzing single views separately. To demonstrate the feasibility of incorporating multi-view features into CAD algorithm, `single-image' CAD was applied to each individual image in a set of 60 ipsilateral studies, after which all possible pairs of suspicious regions, consisting of one from each view, were formed. For these 402 pairs we defined and evaluated `multi-view' features such as: (1) relative position of centers of regions; (2) ratio of lengths of region projections parallel to nipple axis lines; (3) ratio of integrated contrast difference; (4) ratio of the sizes of the suspicious regions; and (5) measure of relative complexity of region boundaries. Each pair was identified as either a `true positive/true positive' (T) pair (i.e., two regions which are projections of the same actual mass), or as a falsely associated pair (F). Distributions for each feature were calculated. A Bayesian network was trained and tested to classify pairs of suspicious regions based exclusively on the multi-view features described above. Distributions for all features were significantly difference for T versus F pairs as indicated by likelihood ratios. Performance of the Bayesian network, which was measured by ROC analysis, indicates a significant ability to distinguish between T pairs and F pairs (Az equals 0.82 +/- 0.03), using information that is attributed to the multi-view content. This study is the first demonstration that there is a significant amount of spatial information that can be derived from ipsilateral pairs of mammograms.

Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

PubMed

Hwang, Hanshin; Taylor, John-Stephen

2005-03-29

We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the Klenow fragment, and the lesser role of shape selection in insertion by pol eta due to its more open and less constrained active site.

Ceramic blade attachment system

DOEpatents

Boyd, G.L.

1994-12-13

A turbine blade having a preestablished rate of thermal expansion is attached to a turbine wheel having a preestablished rate of thermal expansion being greater than the preestablished rate of thermal expansion of the turbine blade. The turbine blade has a root portion having a pair of recessed portions thereon. The turbine wheel includes a plurality of openings in which the turbine blade is positioned. Each of the openings have a pair of grooves therein in which are positioned a pair of pins having a generally rectangular cross-section and a reaction surface thereon. A pair of cylindrical rollers interposed respective ones of the pair of reaction surfaces and the pair of recessed portions. The attachment system or turbine assembly provides an economical, reliable and effective attachment of a component having a preestablished rate of thermal expansion to a component having a greater preestablished rate of thermal expansion. 3 figures.

Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline

PubMed Central

Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

2014-01-01

Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual “atlases” that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures. PMID:24567717

Corresponding-states laws for protein solutions.

PubMed

Katsonis, Panagiotis; Brandon, Simon; Vekilov, Peter G

2006-09-07

The solvent around protein molecules in solutions is structured and this structuring introduces a repulsion in the intermolecular interaction potential at intermediate separations. We use Monte Carlo simulations with isotropic, pair-additive systems interacting with such potentials. We test if the liquid-liquid and liquid-solid phase lines in model protein solutions can be predicted from universal curves and a pair of experimentally determined parameters, as done for atomic and colloid materials using several laws of corresponding states. As predictors, we test three properties at the critical point for liquid-liquid separation: temperature, as in the original van der Waals law, the second virial coefficient, and a modified second virial coefficient, all paired with the critical volume fraction. We find that the van der Waals law is best obeyed and appears more general than its original formulation: A single universal curve describes all tested nonconformal isotropic pair-additive systems. Published experimental data for the liquid-liquid equilibrium for several proteins at various conditions follow a single van der Waals curve. For the solid-liquid equilibrium, we find that no single system property serves as its predictor. We go beyond corresponding-states correlations and put forth semiempirical laws, which allow prediction of the critical temperature and volume fraction solely based on the range of attraction of the intermolecular interaction potential.

Recent advances in 193-nm single-layer photoresists based on alternating copolymers of cycloolefins

NASA Astrophysics Data System (ADS)

Houlihan, Francis M.; Wallow, Thomas I.; Timko, Allen G.; Neria, E.; Hutton, Richard S.; Cirelli, Raymond A.; Nalamasu, Omkaram; Reichmanis, Elsa

1997-07-01

We report on our recent investigations on the formulation and processing of 193 nm single layer photoresists based on alternating copolymers of cycloolefins with maleic anhydride. Resists formulated with cycloolefin copolymers are compatible with 0.262 N tetramethylammonium developers, have excellent adhesion, sensitivity, etch resistance and thermal flow properties. The effect of polymer structure and composition, dissolution inhibitor structure and loading as well as the effect of the photoacid generator on the resist dissolution properties was investigated. Based on the results high contrast formulations were evaluated on a GCA XLS (NA equals 0.53, 4X reduction optics) deep-UV stepper to exhibit 0.27 micrometer L/S pair resolution with excellent photosensitivity. Based on the dissolution properties and a spectroscopic examination of the resist, we have designed materials that show less than 0.17 micrometer L/S pair resolution with 193 nm exposures. In this paper, the formulation methodology is detailed and the most recent results upon both with 248 and 193 nm irradiation are described.

Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem.

PubMed Central

Wilson, J H

1979-01-01

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free solution to the winding problem that satisfies all topological constraints. Homologous duplexes associated by their minor-groove surfaces can switch strand pairing to form reciprocal heteroduplexes that coil together into a compact, four-stranded helix throughout the region of pairing. Model building shows that this fused heteroduplex structure is plausible, being composed entirely of right-handed primary helices with Watson-Crick base pairing throughout. Its simplicity of formation, structural symmetry, and high degree of specificity are suggestive of a natural mechanism for alignment by base pairing between intact homologous duplexes. Implications for genetic recombination are discussed. Images PMID:291028

Perinatal nursing education for single-room maternity care: an evaluation of a competency-based model.

PubMed

Janssen, Patricia A; Keen, Lois; Soolsma, Jetty; Seymour, Laurie C; Harris, Susan J; Klein, Michael C; Reime, Birgit

2005-01-01

To evaluate the success of a competency-based nursing orientation programme for a single-room maternity care unit by measuring improvement in self-reported competency after six months. Single-room maternity care has challenged obstetrical nurses to provide comprehensive nursing care during all phases of the in-hospital birth experience. In this model, nurses provide intrapartum, postpartum and newborn care in one room. To date, an evaluation of nursing education for single-room maternity care has not been published. A prospective cohort design comparing self-reported competencies prior to starting work in the single-room maternity care and six months after. Nurses completed a competency-based education programme in which they could select from a menu of learning methods and content areas according to their individual needs. Learning methods included classroom lectures, self-paced learning packages, and preceptorships in the clinical area. Competencies were measured by a standardized perinatal self-efficacy tool and a tool developed by the authors for this study, the Single-Room Maternity Care Competency Tool. A paired analysis was undertaken to take into account the paired (before and after) nature of the design. Scores on the perinatal self-efficacy scale and the single-room maternity care competency tool were improved. These differences were statistically significant. Improvements in perinatal and single-room maternity care-specific competencies suggest that our education programme was successful in preparing nurses for their new role in the single-room maternity care setting. This conclusion is supported by reported increases in nursing and patient satisfaction in the single-room maternity care compared with the traditional labour/delivery and postpartum settings. An education programme tailored to the learning needs of experienced clinical nurses contributes to improvements in nursing competencies and patient care.

Monitoring of surface deformation in open pit mine using DInSAR time-series: a case study in the N5W iron mine (Carajás, Brazil) using TerraSAR-X data

NASA Astrophysics Data System (ADS)

Mura, José C.; Paradella, Waldir R.; Gama, Fabio F.; Santos, Athos R.; Galo, Mauricio; Camargo, Paulo O.; Silva, Arnaldo Q.; Silva, Guilherme G.

2014-10-01

We present an investigation of surface deformation using Differential SAR Interferometry (DInSAR) time-series carried out in an active open pit iron mine, the N5W, located in the Carajás Mineral Province (Brazilian Amazon region), using 33 TerraSAR-X (TSX-1) scenes. This mine has presented a historical of instability and surface monitoring measurements over sectors of the mine (pit walls) have been done based on ground based radar. Two complementary approaches were used: the standard DInSAR configuration, as an early warning of the slope instability conditions, and the DInSAR timeseries analysis. In order to decrease the topographic phase error a high resolution DEM was generated based on a stereo GeoEye-1 pair. Despite the fact that a DinSAR contains atmospheric and topographic phase artifacts and noise, it was possible to detect deformation in some interferometric pairs, covering pit benches, road ramps and waste piles. The timeseries analysis was performed using the 31 interferometric pairs, which were selected based on the highest mean coherence of a stack of 107 interferograms, presenting less phase unwrapping errors. The time-series deformation was retrieved by the Least-Squares (LS) solution using an extension of the Singular Value Decomposition (SVD), with a set of additional weighted constrain on the acceleration deformation. The atmospheric phase artifacts were filtered in the space-time domain and the DEM height errors were estimated based on the normal baseline diversity. The DInSAR time-series investigation showed good results for monitoring surface displacement in the N5W mine located in a tropical rainforest environment, providing very useful information about the ground movement for alarm, planning and risk assessment.

Automatic threshold selection for multi-class open set recognition

NASA Astrophysics Data System (ADS)

Scherreik, Matthew; Rigling, Brian

2017-05-01

Multi-class open set recognition is the problem of supervised classification with additional unknown classes encountered after a model has been trained. An open set classifer often has two core components. The first component is a base classifier which estimates the most likely class of a given example. The second component consists of open set logic which estimates if the example is truly a member of the candidate class. Such a system is operated in a feed-forward fashion. That is, a candidate label is first estimated by the base classifier, and the true membership of the example to the candidate class is estimated afterward. Previous works have developed an iterative threshold selection algorithm for rejecting examples from classes which were not present at training time. In those studies, a Platt-calibrated SVM was used as the base classifier, and the thresholds were applied to class posterior probabilities for rejection. In this work, we investigate the effectiveness of other base classifiers when paired with the threshold selection algorithm and compare their performance with the original SVM solution.

Chromosomal stasis in distinct families of marine Percomorpharia from South Atlantic.

PubMed

Paim, Fabilene Gomes; Almeida, Leandro Aragão da Hora; Affonso, Paulo Roberto Antunes de Mello; Sobrinho-Scudeler, Patrícia Elda; Oliveira, Claudio; Diniz, Débora

2017-01-01

The weakness of physical barriers in the marine environment and the dispersal potential of fish populations have been invoked as explanations of the apparent karyotype stasis of marine Percomorpha, but several taxa remain poorly studied cytogenetically. To increase the chromosomal data in this fish group, we analyzed cytogenetically three widespread Atlantic species from distinct families: Chaetodipterus faber Broussonet, 1782 (Ephippidae), Lutjanus synagris Linnaeus, 1758 (Lutjanidae) and Rypticus randalli Courtenay, 1967 (Serranidae). The three species shared a karyotype composed of 2n=48 acrocentric chromosomes, single nucleolus organizer regions (NORs) and reduced amounts of centromeric heterochromatin. A single NOR-bearing pair was identified in all species by physical mapping of 18S rDNA while non-syntenic 5S rRNA genes were located at centromeric region of a single pair. The similar karyotypic macrostructure observed in unrelated groups of Percomorpharia reinforces the conservative karyoevolution of marine teleosteans. Nonetheless, the species could be differentiated based on the pair bearing ribosomal cistrons, revealing the importance of microstructural analyses in species with symmetric and stable karyotypes.

Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand Exchange Reaction

PubMed Central

Fan, Hsiu-Fang; Cox, Michael M.; Li, Hung-Wen

2011-01-01

RecA recombinases play a central role in homologous recombination. Once assembled on single-stranded (ss) DNA, RecA nucleoprotein filaments mediate the pairing of homologous DNA sequences and strand exchange processes. We have designed two experiments based on tethered particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure the tethered bead Brownian motion indicative of the DNA tether length change resulting from RecA binding and dissociation. Experiments with beads labeled on either the invading strand or the outgoing strand showed that DNA pairing and strand exchange occurs successfully in the presence of either ATP or its non-hydrolyzable analog, ATPγS. The strand exchange rates and efficiencies are similar under both ATP and ATPγS conditions. In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5′-to-3′ fashion, using a synapse segment with a wide and continuous size distribution. PMID:21765895

Anti-wear additive derived from soybean oil and boron utilized in a gear oil formulation

USDA-ARS?s Scientific Manuscript database

The synthesis of lubricant additives based on boron and epoxidized soybean oil are presented. These additives are made from a simple patent pending method involving a ring opening reaction and addition of the borate. A pair of different additives were tested in soybean oil, polyalpha olefin basestoc...

Ultrastructure of the labrum and foregut of Derocheilocaris remanei (Crustacea, Mystacocarida).

PubMed

Herrera-Alvarez, Letizia; Fernández, Isabel; Benito, Jesús; Pardos, Fernando

1996-11-01

The cuticle-lined foregut of Derocheilocaris remanei consists of the mouth with its associated labrum, and an undifferentiated esophagus. It is separated from the midgut by an esophageal valve. The labrum is a conspicuous structure moved by five pairs of muscles (four dorsoventral and one longitudinal). Four pairs of subcuticular glands open to its inner face forming two longitudinal, lateral rows of cuticular pores. Each secretory unit is composed of a glandular component (with one or two secretory cells), a neck cell, and a duct cell. In addition, a single gland cell opens mesially into the buccal cavity. The ventrally located mouth is a complex structure characterized by a filter-like system, a sensory organ, and epithelial cells with highly developed microvilli. The esophagus is a simple tube with a characteristic curvature following the mouth. It has a rounded cross section and a triradiate lumen. A layer of circular musculature surrounds this region. The end of the esophagus protrudes into the midgut lumen forming the so-called esophageal valve. The ultrastructural features of the foregut, with the presence of a mucus-trapping mechanism, a relatively well-developed filter system and associated structures and an esophagus lacking glands confirm the microphagic feeding habits of mystacocarids. © 1996 Wiley-Liss, Inc. Copyright © 1996 Wiley-Liss, Inc.

Unsteady wake of a rotating tire

NASA Astrophysics Data System (ADS)

Lombard, Jean-Eloi; Moxey, Dave; Xu, Hui; Sherwin, Spencer; Sherwin Lab Team

2015-11-01

For open wheel race-cars, such as IndyCar and Formula One, the wheels are responsible for 40% of the total drag. For road cars drag associated to the wheels and under-carriage can represent 60% of total drag at highway cruise speeds. Experimental observations have reported two or three pairs of counter rotating vortices, the relative importance of which still remains an open question, that interact to form a complex wake. Traditional RANS based methods are typically not well equipped to deal with such highly unsteady flows which motivates research into more physical, unsteady models. Leveraging a high-fidelity spectral/hp element based method a Large Eddy Simulation is performed to give further insight into unsteady characteristics of the wake. In particular the unsteady nature of both the jetting and top vortex pair is reported as well as the time and length scales associated with the vortex core trajectories. Correlation with experimentally obtained particle image velocimetry is presented. The authors acknowledge support from the United Kingdom Turbulence Consortium (UKTC) as well as from the Engineering and Physical Sciences Research Council (EPSRC) for access to ARCHER UK National Supercomputing Service.

Intermolecular ‘cross-torque’: the N4-cytosine propargyl residue is rotated to the ‘CH’-edge as a result of Watson–Crick interaction

PubMed Central

Domingo, Olwen; Hellmuth, Isabell; Jäschke, Andres; Kreutz, Christoph; Helm, Mark

2015-01-01

Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson–Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson–Crick face of N4-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N4-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the ‘CH’-edge as a result of base pairing on the Watson–Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson–Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the ‘CH’-edge, consequently preventing Watson–Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N4-substituents to make way for Watson–Crick base pairing, providing no steric hindrance is present on the ‘CH’-edge. PMID:25934805

The importance of different frequency bands in predicting subcutaneous glucose concentration in type 1 diabetic patients.

PubMed

Lu, Yinghui; Gribok, Andrei V; Ward, W Kenneth; Reifman, Jaques

2010-08-01

We investigated the relative importance and predictive power of different frequency bands of subcutaneous glucose signals for the short-term (0-50 min) forecasting of glucose concentrations in type 1 diabetic patients with data-driven autoregressive (AR) models. The study data consisted of minute-by-minute glucose signals collected from nine deidentified patients over a five-day period using continuous glucose monitoring devices. AR models were developed using single and pairwise combinations of frequency bands of the glucose signal and compared with a reference model including all bands. The results suggest that: for open-loop applications, there is no need to explicitly represent exogenous inputs, such as meals and insulin intake, in AR models; models based on a single-frequency band, with periods between 60-120 min and 150-500 min, yield good predictive power (error <3 mg/dL) for prediction horizons of up to 25 min; models based on pairs of bands produce predictions that are indistinguishable from those of the reference model as long as the 60-120 min period band is included; and AR models can be developed on signals of short length (approximately 300 min), i.e., ignoring long circadian rhythms, without any detriment in prediction accuracy. Together, these findings provide insights into efficient development of more effective and parsimonious data-driven models for short-term prediction of glucose concentrations in diabetic patients.

Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.

PubMed

Yakubovskaya, Marianna G; Belyakova, Anna A; Gasanova, Viktoria K; Belitsky, Gennady A; Dolinnaya, Nina G

2010-07-01

Systematic study of chemical reactivity of non-Watson-Crick base pairs depending on their type and microenvironment was performed on a model system that represents two sets of synthetic DNA duplexes with all types of mismatched and unmatched bases flanked by T.A or G.C pairs. Using comparative cleavage pattern analysis, we identified the main and additional target bases and performed quantitative study of the time course and efficacy of DNA modification caused by potassium permanganate or hydroxylamine. Potassium permanganate in combination with tetraethylammonium chloride was shown to induce DNA cleavage at all mismatched or bulged T residues, as well as at thymines of neighboring canonical pairs. Other mispaired (bulged) bases and thymine residues located on the second position from the mismatch site were not the targets for KMnO(4) attack. In contrast, hydroxylamine cleaved only heteroduplexes containing mismatched or unmatched C residues, and did not modify adjacent cytosines. However when G.C pairs flank bulged C residue, neighboring cytosines are also attacked by hydroxylamine due to defect migration. Chemical reactivity of target bases was shown to correlate strongly with the local disturbance of DNA double helix at mismatch or bulge site. With our model system, we were able to prove the absence of false-negative and false-positive results. Portion of heteroduplex reliably revealed in a mixture with corresponding homoduplex consists of 5% for bulge bases and "open" non-canonical pairs, and 10% for wobble base pairs giving minimal violations in DNA structure. This study provides a complete understanding of the principles of mutation detection methodology based on chemical cleavage of mismatches and clarifies the advantages and limitations of this approach in various biological and conformational studies of DNA. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Base opening in RNA and DNA duplexes: implication for RNA stability.

PubMed

Chen, Y Z; Mohan, V; Griffey, R H

2000-05-01

The energetics of a low-energy single base opening in several RNA duplex crystal structures has been calculated and compared to DNA duplexes. Base opening in RNA appears to have an overall preference towards the major groove, similar to results previously reported for B-DNA. Movement of each of the adenine, uracil, and cytosine bases into the minor groove is blocked by a high-energy barrier due to severe close contact with neighboring bases. Guanine bases are able to open towards both grooves because of the unique orientation of the base that avoids steric clash along the opening pathway. RNA bases are found to have a substantially smaller major groove opening extent than that of their B-DNA counterparts. A comparison with base opening behavior of A-DNA duplexes suggests that this difference results from helix constraint associated with A-form backbone conformation. The reduced opening extent correlates with the RNA duplex stability and is consistent with observed slower imino proton exchange rates in RNA duplexes.

Ultrabright, narrow-band photon-pair source for atomic quantum memories

NASA Astrophysics Data System (ADS)

Tsai, Pin-Ju; Chen, Ying-Cheng

2018-06-01

We demonstrate an ultrabright, narrow-band and frequency-tunable photon-pair source based on cavity-enhanced spontaneous parametric down conversion (SPDC) which is compatible with atomic transition of rubidium D 2-line (780 nm) or cesium D 2-line (852 nm). With the pump beam alternating between a high and a low power phase, the output is switching between the optical parametric oscillator (OPO) and photon-pair generation mode. We utilize the OPO output light to lock the cavity length to maintain the double resonances of signal and idler, as well as to lock the signal frequency to cesium atomic transition. With a type-II phase matching and a double-passed pump scheme such that the cluster frequency spacing is larger than the SPDC bandwidth, the photon-pair output is in a nearly single-mode operation as confirmed by a scanning Fabry–Perot interferometer with its output detected by a photomultiplier. The achieved generation and detection rates are 7.24× {10}5 and 6142 s‑1 mW‑1, respectively. The correlation time of the photon pair is 21.6(2.2) ns, corresponding to a bandwidth of 2π × 6.6(6) MHz. The spectral brightness is 1.06× {10}5 s‑1 mW‑1 MHz‑1. This is a relatively high value under a single-mode operation with the cavity-SPDC scheme. The generated single photons can be readily used in experiments related to atomic quantum memories.

The Spectral and Environment Properties of z ∼ 2.0–2.5 Quasar Pairs

NASA Astrophysics Data System (ADS)

Lusso, Elisabeta; Fumagalli, Michele; Rafelski, Marc; Neeleman, Marcel; Prochaska, Jason X.; Hennawi, Joseph F.; O’Meara, John M.; Theuns, Tom

2018-06-01

We present the first results from our survey of intervening and proximate Lyman limit systems (LLSs) at z ∼ 2.0–2.5 using the Wide Field Camera 3 on board the Hubble Space Telescope. The quasars in our sample are projected pairs with proper transverse separations R ⊥ ≤ 150 kpc and line-of-sight velocity separations ≲11,000 km s‑1. We construct a stacked ultraviolet (rest-frame wavelengths 700–2000 Å) spectrum of pairs corrected for the intervening Lyman forest and Lyman continuum absorption. The observed spectral composite presents a moderate flux excess for the most prominent broad emission lines, a ∼30% decrease in flux at λ = 800–900 Å compared to a stack of brighter quasars not in pairs at similar redshifts, and lower values of the mean free path of the H I ionizing radiation for pairs ({λ }mfp}912 = 140.7 ± 20.2 {h}70-1 Mpc) compared to single quasars ({λ }mfp}912 = 213.8 ± 28 {h}70-1 Mpc) at the average redshift z ≃ 2.44. From the modeling of LLS absorption in these pairs, we find a higher (∼20%) incidence of proximate LLSs with log {N}{{H}{{I}}} ≥ 17.2 at δv < 5000 km s‑1 compared to single quasars (∼6%). These two rates are different at the 5σ level. Moreover, we find that optically thick absorbers are equally shared between foreground and background quasars. Based on these pieces of evidence, we conclude that there is a moderate excess of gas-absorbing Lyman continuum photons in our closely projected quasar pairs compared to single quasars. We argue that this gas arises mostly within large-scale structures or partially neutral regions inside the dark matter halos where these close pairs reside.

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

Magie, Robert J.; Morris, Matthew S.; Ledgerwood, Richard D.

In 2008, we sampled migrating juvenile Pacific salmonids Oncorhynchus spp. tagged with passive integrated transponder (PIT) tags using a surface pair trawl in the upper Columbia River estuary (rkm 61-83). The cod-end of the trawl was replaced with a cylindrical PIT-tag detection antenna with an 86-cm-diameter fish-passage opening and two detection coils connected in series. The pair trawl was 105 m long with a 91.5-m opening between the wings and a sample depth of 4.9 m. Also during 2008, we finalized the development of a prototype 'matrix' antenna, which was larger than previous antennas by a considerable magnitude. The matrixmore » antenna consisted of 6 coils: a 3-coil front component and a 3-coil rear component, which were separated by 1.5-m of net mesh. The fish-passage opening was 2.5 m wide by 3.0 m tall and was attached to a standard-size pair trawl net. Intermittent sampling with a single crew began on 7 March and targeted yearling Chinook salmon O. tshawytscha and steelhead O. mykiss. Daily sampling using two crews began on 30 April and continued through 14 June; during this period we detected 2.7% of all juvenile salmonids previously detected at Bonneville Dam--a measure of sample efficiency. Sampling with a single crew continued through 20 August and targeted subyearling Chinook salmon. We detected 7,397 yearling Chinook salmon, 2,735 subyearling Chinook salmon, 291 coho salmon O. kisutch, 5,950 steelhead, and 122 sockeye salmon O. nerka in the upper estuary. We deployed the matrix antenna system and the older, cylindrical antenna system (86-cm-diameter fish-passage opening) simultaneously in mid-May 2008 to test matrix detection efficiency. The cylindrical antenna system had been used successfully in 2007 and early 2008. Because distribution of migrating salmonids in the estuary changes rapidly, we felt that a tandem sampling effort between the two systems was the only way to truly evaluate comparative detection efficiency. We deployed both systems within 1 km of each other during a period of high fish densities on 13, 14, and 15 May. Detections of the matrix system surpassed those of the cylindrical system by 53% in 14 h of simultaneous sampling (total detections 716 and 339, respectively). We believe that the higher detection rate observed with the matrix system was due to fewer smolts escaping the trawl entrance and to more smolts readily passing through the larger fish-passage opening. After tandem sampling, we continued exclusive use of the matrix system for the remainder of the 2008 juvenile migration season. Mean survival rates from Lower Granite to Bonneville Dam for yearling Chinook salmon and steelhead were 42% (SE = 3.7%) and 46% (SE = 1.5%), respectively. Over 358,000 PIT-tagged salmonids were transported, and we detected 4,619 of these fish.« less

Binding of DNA hairpins to an assembler-strand as part of a primordial translation device

NASA Astrophysics Data System (ADS)

Baumann, Ulrich

1987-09-01

A crucial event in the process leading to the origin of life is the emergence of a simple translation device. To approach experimental realization of this device the binding ability of short DNA hairpins to complementary oligonucleotides fixed on a solid support was investigated. The binding is achieved by base pairing between the loop nucleotides of the hairpins containing different numbers of adenosine residues and oligothymidylates covalently linked to cellulose. The loop has to consist of at least five nucleotides to achieve binding. The exact number of established base pairs was determined in two ways. First, the elution temperatures of hairpins and those of oligoadenylates which had the length of the loop were compared. Secondly, the architecture of the loop was analyzed by means of the single-strand-specific nuclease from mung bean acting as structural probe. Onlyn-2 of n loop nucleotides of a hairpin are able to form base pairs. Therefore, a strong evidence for the formation of a triplet of base pairs between primeval tRNA and mRNA sufficient to stabilize the complex enzyme-free is given.

[Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine].

PubMed

Brovarets', O O; Hovorun, D M

2010-01-01

A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*<---->Gua.Cyt<---->Gua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.

Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids

PubMed Central

2015-01-01

Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies. PMID:26505212

Determination of the pairing-strength constants in the isovector plus isoscalar pairing case

NASA Astrophysics Data System (ADS)

Mokhtari, D.; Fellah, M.; Allal, N. H.

2016-05-01

A method for the determination of the pairing-strength constants, in the neutron-proton (n-p) isovector plus isoscalar pairing case, is proposed in the framework of the BCS theory. It is based on the fitting of these constants to reproduce the experimentally known pairing gap parameters as well as the root-mean-squared (r.m.s) charge radii values. The method is applied to some proton-rich even-even nuclei. The single-particle energies used are those of a deformed Woods-Saxon mean field. It is shown that the obtained value of the ratio GnpT=0/G npT=1 is of the same order as the ones, arbitrary chosen, of some previous works. The effect of the inclusion of the isoscalar n-p pairing in the r.m.s matter radii is then numerically studied for the same nuclei.

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

PubMed

Bienko, Magda; Crosetto, Nicola; Teytelman, Leonid; Klemm, Sandy; Itzkovitz, Shalev; van Oudenaarden, Alexander

2013-02-01

We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.

Targeting excited states in all-trans polyenes with electron-pair states.

PubMed

Boguslawski, Katharina

2016-12-21

Wavefunctions restricted to electron pair states are promising models for strongly correlated systems. Specifically, the pair Coupled Cluster Doubles (pCCD) ansatz allows us to accurately describe bond dissociation processes and heavy-element containing compounds with multiple quasi-degenerate single-particle states. Here, we extend the pCCD method to model excited states using the equation of motion (EOM) formalism. As the cluster operator of pCCD is restricted to electron-pair excitations, EOM-pCCD allows us to target excited electron-pair states only. To model singly excited states within EOM-pCCD, we modify the configuration interaction ansatz of EOM-pCCD to contain also single excitations. Our proposed model represents a simple and cost-effective alternative to conventional EOM-CC methods to study singly excited electronic states. The performance of the excited state models is assessed against the lowest-lying excited states of the uranyl cation and the two lowest-lying excited states of all-trans polyenes. Our numerical results suggest that EOM-pCCD including single excitations is a good starting point to target singly excited states.

5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics

NASA Astrophysics Data System (ADS)

Yusufaly, Tahir; Olson, Wilma; Li, Yun

2014-03-01

Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile ``opening'' mode and two shear ``sliding'' and ``tearing'' modes in the orthogonal plane. The stacking interactions of the methyl groups are observed to globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. The results have implications for the epigenetic control of DNA mechanics.

Emergence of structured communities through evolutionary dynamics.

PubMed

Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

2015-10-21

Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Pairing of near-ultraviolet solar cells with electrochromic windows for smart management of the solar spectrum

NASA Astrophysics Data System (ADS)

Davy, Nicholas C.; Sezen-Edmonds, Melda; Gao, Jia; Lin, Xin; Liu, Amy; Yao, Nan; Kahn, Antoine; Loo, Yueh-Lin

2017-08-01

Current smart window technologies offer dynamic control of the optical transmission of the visible and near-infrared portions of the solar spectrum to reduce lighting, heating and cooling needs in buildings and to improve occupant comfort. Solar cells harvesting near-ultraviolet photons could satisfy the unmet need of powering such smart windows over the same spatial footprint without competing for visible or infrared photons, and without the same aesthetic and design constraints. Here, we report organic single-junction solar cells that selectively harvest near-ultraviolet photons, produce open-circuit voltages eclipsing 1.6 V and exhibit scalability in power generation, with active layers (10 cm2) substantially larger than those typical of demonstration organic solar cells (0.04-0.2 cm2). Integration of these solar cells with a low-cost, polymer-based electrochromic window enables intelligent management of the solar spectrum, with near-ultraviolet photons powering the regulation of visible and near-infrared photons for natural lighting and heating purposes.

Simple scheme for encoding and decoding a qubit in unknown state for various topological codes

PubMed Central

Łodyga, Justyna; Mazurek, Paweł; Grudka, Andrzej; Horodecki, Michał

2015-01-01

We present a scheme for encoding and decoding an unknown state for CSS codes, based on syndrome measurements. We illustrate our method by means of Kitaev toric code, defected-lattice code, topological subsystem code and 3D Haah code. The protocol is local whenever in a given code the crossings between the logical operators consist of next neighbour pairs, which holds for the above codes. For subsystem code we also present scheme in a noisy case, where we allow for bit and phase-flip errors on qubits as well as state preparation and syndrome measurement errors. Similar scheme can be built for two other codes. We show that the fidelity of the protected qubit in the noisy scenario in a large code size limit is of , where p is a probability of error on a single qubit per time step. Regarding Haah code we provide noiseless scheme, leaving the noisy case as an open problem. PMID:25754905

Dicephalous v. diprosopus sharks: record of a two-headed embryo of Galeus atlanticus and review of the literature.

PubMed

Sans-Coma, V; Rodríguez, C; López-Unzu, M A; Lorenzale, M; Fernández, B; Vida, L; Durán, A C

2017-01-01

As far as is known, this paper gives the first description of a two-headed shark embryo belonging to an oviparous species, Galeus atlanticus (Carcharhiniformes: Scyliorhinidae). The specimen was detected among 797 embryos intended for cardiovascular studies, which represents a defect incidence of 0·13%. Each head had a mouth, two eyes, a brain, a notochord and five gill openings on each side. The two heads fused behind the gills. On the single body, there were four anticipated dorsal fins, two anterior, right and left and two posterior, right and left. Ventrally, the specimen possessed two pairs of pectoral fins, a pair of pelvic fins and one anal fin. Two adjacent notochords, two neural tubes and two dorsal aortas ran along the body, which bent 180° at its posterior portion. There were two hearts, two oesophaguses, two stomachs, two livers, but a single intestine with a spiral valve. Previous reports of conjoined twins in sharks are scarce and only refer to oviparous and ovoviviparous species. Seven dicephalous sharks reported so far were similar to the specimen described here, namely, with two totally separated heads on one body. Instead, only one case of diprosopus shark has been reported; it had a single body and a single head with partial duplication of the face. Two further cases described in the literature as dicephalous or simply as abnormal sharks should be better regarded as diprosopus, while another three cases, also considered dicephalous, showed a mixture of characteristics of diprosopia and dicephalia. © 2016 The Fisheries Society of the British Isles.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Multiconductor Short/Open Cable Tester

NASA Technical Reports Server (NTRS)

Eichenberg, Dennis

1994-01-01

Frequent or regular testing of multiconductor cables terminated in multipin conductors tedious, if not impossible, task. This inexpensive circuit simplifies open/short testing and is amenable to automation. In operation, pair of connectors selected to match pair of connectors installed on each of cables to be tested. As many connectors accommodated as required, and each can have as many conductors as required. Testing technique implemented with this circuit automated easily with electronic controls and computer interface. Printout provides status of each conductor in cable, indicating which, if any, of conductors has open or short circuit.

Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q.

PubMed

Xie, Wen; Chen, Chunhai; Yang, Zezhong; Guo, Litao; Yang, Xin; Wang, Dan; Chen, Ming; Huang, Jinqun; Wen, Yanan; Zeng, Yang; Liu, Yating; Xia, Jixing; Tian, Lixia; Cui, Hongying; Wu, Qingjun; Wang, Shaoli; Xu, Baoyun; Li, Xianchun; Tan, Xinqiu; Ghanim, Murad; Qiu, Baoli; Pan, Huipeng; Chu, Dong; Delatte, Helene; Maruthi, M N; Ge, Feng; Zhou, Xueping; Wang, Xiaowei; Wan, Fanghao; Du, Yuzhou; Luo, Chen; Yan, Fengming; Preisser, Evan L; Jiao, Xiaoguo; Coates, Brad S; Zhao, Jinyang; Gao, Qiang; Xia, Jinquan; Yin, Ye; Liu, Yong; Brown, Judith K; Zhou, Xuguo Joe; Zhang, Youjun

2017-05-01

The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future 'pan-genomic' comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management. © The Author 2017. Published by Oxford University Press.

Putative Nonribosomal Peptide Synthetase and Cytochrome P450 Genes Responsible for Tentoxin Biosynthesis in Alternaria alternata ZJ33.

PubMed

Li, You-Hai; Han, Wen-Jin; Gui, Xi-Wu; Wei, Tao; Tang, Shuang-Yan; Jin, Jian-Ming

2016-08-02

Tentoxin, a cyclic tetrapeptide produced by several Alternaria species, inhibits the F₁-ATPase activity of chloroplasts, resulting in chlorosis in sensitive plants. In this study, we report two clustered genes, encoding a putative non-ribosome peptide synthetase (NRPS) TES and a cytochrome P450 protein TES1, that are required for tentoxin biosynthesis in Alternaria alternata strain ZJ33, which was isolated from blighted leaves of Eupatorium adenophorum. Using a pair of primers designed according to the consensus sequences of the adenylation domain of NRPSs, two fragments containing putative adenylation domains were amplified from A. alternata ZJ33, and subsequent PCR analyses demonstrated that these fragments belonged to the same NRPS coding sequence. With no introns, TES consists of a single 15,486 base pair open reading frame encoding a predicted 5161 amino acid protein. Meanwhile, the TES1 gene is predicted to contain five introns and encode a 506 amino acid protein. The TES protein is predicted to be comprised of four peptide synthase modules with two additional N-methylation domains, and the number and arrangement of the modules in TES were consistent with the number and arrangement of the amino acid residues of tentoxin, respectively. Notably, both TES and TES1 null mutants generated via homologous recombination failed to produce tentoxin. This study provides the first evidence concerning the biosynthesis of tentoxin in A. alternata.

Airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and multi-pole magnets towards enhanced power density.

PubMed

Leung, Chung Ming; Wang, Ya; Chen, Wusi

2016-11-01

In this letter, the airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and trajectory matching multi-pole magnets was investigated. The magnets were aligned in an alternatively magnetized formation of 6 magnets to explore enhanced power density. In particular, the magnet array was positioned in parallel to the trajectory of the tip coil within its tip deflection span. The finite element simulations of the magnetic flux density and induced voltages at an open circuit condition were studied to find the maximum number of alternatively magnetized magnets that was required for the proposed energy harvester. Experimental results showed that the energy harvester with a pair of 6 alternatively magnetized linear magnet arrays was able to generate an induced voltage (V o ) of 20 V, with an open circuit condition, and 475 mW, under a 30 Ω optimal resistance load operating with the wind speed (U) at 7 m/s and a natural bending frequency of 3.54 Hz. Compared to the traditional electromagnetic energy harvester with a single magnet moving through a coil, the proposed energy harvester, containing multi-pole magnets and parallel array motion, enables the moving coil to accumulate a stronger magnetic flux in each period of the swinging motion. In addition to the comparison made with the airfoil-based piezoelectric energy harvester of the same size, our proposed electromagnetic energy harvester generates 11 times more power output, which is more suitable for high-power-density energy harvesting applications at regions with low environmental frequency.

STS study on single crystal of noncentrosymmetric superconductor PbTaSe2

NASA Astrophysics Data System (ADS)

Ye, Zhiyang; Wu, Rui; Wang, Jihui; Liang, Xuejin; Mao, Hanqing; Zhao, Lingxiao; Chen, Genfu; Pan, Shuheng

2015-03-01

We report our low temperature scanning tunneling spectroscopic study on single crystals of noncentrosymmetric superconductor PbTaSe2. On the background of the normal state tunneling spectrum, a superconducting energy gap opens at a temperature below the bulk Tc = 3.7K. At t = 1.4K, the gap magnitude is estimated to be about 1meV. This energy gap is particle-hole symmetry and is homogeneous in space. Extrapolating the low energy part of the spectrum, we find that the low energy part of the gap spectrum is linear like ``V'' shape. We will present the results of the numerical fit with various gap functions of proposed possible pairing symmetry. We will also present our preliminary results of the magnetic field dependence measurement and discuss the implications of these observations.

Development of a sensor for temperature and water concentration in combustion gases using a single tunable diode laser

NASA Astrophysics Data System (ADS)

Zhou, Xin; Liu, Xiang; Jeffries, Jay B.; Hanson, R. K.

2003-08-01

The water vapour spectrum in the 1-2 µm near-infrared region is systematically analysed to find the best absorption transitions for sensitive measurement of H2O concentration and temperature in combustion environments using a single tunable diode laser with typical distributed feedback single-mode scanning range (1 cm-1). The use of a single laser, even with relatively narrow tuning range, can offer distinct advantages over wavelength-multiplexing techniques. The strategy and spectroscopic criteria for selecting optimum wavelength regions and absorption line combinations are discussed. It should be stressed that no single figure of merit can be derived to simplify the selection process, and the optimum line pair should be chosen case by case. Our investigation reveals that the 1.8 µm spectral region is especially promising, and we have identified 10 of the best water line pairs in this spectral region for temperature measurements in flames. Based on these findings, a pair of H2O transitions near 1.8 µm was targeted for the design and development of an initial single-laser sensor for simultaneously measuring H2O concentration and temperature in atmospheric-pressure flames. As part of the sensor development effort, fundamental spectroscopic parameters including the line strength, line-centre frequency and lower state energies of the probed transitions were measured experimentally to improve the current databases. We conclude with demonstration results in a steady and a forced atmospheric-pressure laboratory combustor.

Milestone Report:3.2.2.26 Appliances, HVAC & Water Heating R&D-Select Sorption Technology

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

Ally, Moonis Raza

The purpose of this report is to select a sorption technology based on recent work completed on characterizing working pairs for both absorption and adsorption technologies based on Global Warming Potential (GWP) of less than 100 (relative to carbon dioxide, 100-year atmospheric life span) and zero Ozone Depletion Potential (ODP). From a total of eighty-three potential working pairs (absorption technology), there were only two candidate working pairs for the absorption technology, and 8 potential working pairs for adsorption technology. After screening these ten potential candidates on the basis of sizes of the desorber, absorber/adsorber, evaporator, condenser, and rectifier (where applicable),more » the ORNL-Georgia Tech study concluded that best working pairs are NH3-H2O for the most compact system in terms of heat transfer equipment surface area, and NH3-LiNO3 and MeOH-[mmin][DMP] where efficiency is most important. Based on a single-stage absorption and adsorption modeling using the Engineering Equation Solver (EES), the performance of both sorption systems was evaluated from known heat transfer correlations, and thermos-physical properties. Based on these results, the technology chosen is absorption technology. The selected technology is absorption for the reasons cited in Section 4.« less

Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.

PubMed

Lu, Fu-Hao; McKenzie, Neil; Kettleborough, George; Heavens, Darren; Clark, Matthew D; Bevan, Michael W

2018-05-01

The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics. Here we use a Fosill 38-kb jumping library to assess medium and longer-range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values. Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.

MCORES: a system for noun phrase coreference resolution for clinical records.

PubMed

Bodnari, Andreea; Szolovits, Peter; Uzuner, Özlem

2012-01-01

Narratives of electronic medical records contain information that can be useful for clinical practice and multi-purpose research. This information needs to be put into a structured form before it can be used by automated systems. Coreference resolution is a step in the transformation of narratives into a structured form. This study presents a medical coreference resolution system (MCORES) for noun phrases in four frequently used clinical semantic categories: persons, problems, treatments, and tests. MCORES treats coreference resolution as a binary classification task. Given a pair of concepts from a semantic category, it determines coreferent pairs and clusters them into chains. MCORES uses an enhanced set of lexical, syntactic, and semantic features. Some MCORES features measure the distance between various representations of the concepts in a pair and can be asymmetric. MCORES was compared with an in-house baseline that uses only single-perspective 'token overlap' and 'number agreement' features. MCORES was shown to outperform the baseline; its enhanced features contribute significantly to performance. In addition to the baseline, MCORES was compared against two available third-party, open-domain systems, RECONCILE(ACL09) and the Beautiful Anaphora Resolution Toolkit (BART). MCORES was shown to outperform both of these systems on clinical records.

Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson–Crick terminal base pairs

PubMed Central

O'Toole, Amanda S.; Miller, Stacy; Haines, Nathan; Zink, M. Coleen; Serra, Martin J.

2006-01-01

Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson–Crick terminal base pairs (GC, AU and UA) with all 16 possible 3′ double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3′ dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner. Results from this study in conjunction with data from a previous study [A. S. O'Toole, S. Miller and M. J. Serra (2005) RNA, 11, 512.] allows for the development of a refined nearest-neighbor model to predict the influence of 3′ double-nucleotide overhangs on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against five oligomers with various core duplex sequences. Phylogenetic analysis of naturally occurring miRNAs was performed to support our results. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent upon the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for 3′ single terminal overhangs adjacent to a UA pair are also presented. PMID:16820533

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

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

NMR studies on the structure and dynamics of lac operator DNA

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

Lee, S.C.

Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with amore » maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent.« less

Two-Drug Antimicrobial Chemotherapy: A Mathematical Model and Experiments with Mycobacterium marinum

PubMed Central

Ankomah, Peter; Levin, Bruce R.

2012-01-01

Multi-drug therapy is the standard-of-care treatment for tuberculosis. Despite this, virtually all studies of the pharmacodynamics (PD) of mycobacterial drugs employed for the design of treatment protocols are restricted to single agents. In this report, mathematical models and in vitro experiments with Mycobacterium marinum and five antimycobacterial drugs are used to quantitatively evaluate the pharmaco-, population and evolutionary dynamics of two-drug antimicrobial chemotherapy regimes. Time kill experiments with single and pairs of antibiotics are used to estimate the parameters and evaluate the fit of Hill-function-based PD models. While Hill functions provide excellent fits for the PD of each single antibiotic studied, rifampin, amikacin, clarithromycin, streptomycin and moxifloxacin, two-drug Hill functions with a unique interaction parameter cannot account for the PD of any of the 10 pairs of these drugs. If we assume two antibiotic-concentration dependent functions for the interaction parameter, one for sub-MIC and one for supra-MIC drug concentrations, the modified biphasic Hill function provides a reasonably good fit for the PD of all 10 pairs of antibiotics studied. Monte Carlo simulations of antibiotic treatment based on the experimentally-determined PD functions are used to evaluate the potential microbiological efficacy (rate of clearance) and evolutionary consequences (likelihood of generating multi-drug resistance) of these different drug combinations as well as their sensitivity to different forms of non-adherence to therapy. These two-drug treatment simulations predict varying outcomes for the different pairs of antibiotics with respect to the aforementioned measures of efficacy. In summary, Hill functions with biphasic drug-drug interaction terms provide accurate analogs for the PD of pairs of antibiotics and M. marinum. The models, experimental protocols and computer simulations used in this study can be applied to evaluate the potential microbiological and evolutionary efficacy of two-drug therapy for any bactericidal antibiotics and bacteria that can be cultured in vitro. PMID:22253599

Glucose transporter distribution in the vessels of the central nervous system of the axolotl Ambystoma mexicanum (Urodela: Ambystomatidae).

PubMed

Lazzari, Maurizio; Bettini, Simone; Ciani, Franco; Franceschini, Valeria

2008-10-01

The GLUT-1 isoform of the glucose transporter is commonly considered a reliable molecular marker of blood-brain barrier endothelia in the neural vasculature organized in a three-dimensional network of single vessels. The central nervous system of the axolotl Ambystoma mexicanum is characterized by a vascular architecture that contains both single and paired vessels. The presence and distribution of the GLUT-1 transporter are studied in this urodele using both immunoperoxidase histochemistry and immunogold technique. Light microscopy reveals immunopositivity in both parenchymal and meningeal vessels. The transverse-sectioned pairs of vessels do not show the same size. Furthermore, in the same pair, the two elements often differ in diameter. The main regions of the central nervous system show a different percentage of the paired structures. Only immunogold cytochemistry reveals different staining intensity in the two adjoined elements of a vascular pair. Colloidal gold particles show an asymmetric distribution in the endothelia of both single and paired vessels. These particles are more numerous on the abluminal surface than on the luminal one. The particle density is calculated in both vascular types. The different values could indicate functional differences between single and paired vessels and between the two adjoined elements of a pair, regarding glucose transport.

Franson Interference Generated by a Two-Level System

NASA Astrophysics Data System (ADS)

Peiris, M.; Konthasinghe, K.; Muller, A.

2017-01-01

We report a Franson interferometry experiment based on correlated photon pairs generated via frequency-filtered scattered light from a near-resonantly driven two-level semiconductor quantum dot. In contrast to spontaneous parametric down-conversion and four-wave mixing, this approach can produce single pairs of correlated photons. We have measured a Franson visibility as high as 66%, which goes beyond the classical limit of 50% and approaches the limit of violation of Bell's inequalities (70.7%).

Triple Helix Formation in a Topologically Controlled DNA Nanosystem.

PubMed

Yamagata, Yutaro; Emura, Tomoko; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki

2016-04-11

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly efficient heralded single-photon source for telecom wavelengths based on a PPLN waveguide.

PubMed

Bock, Matthias; Lenhard, Andreas; Chunnilall, Christopher; Becher, Christoph

2016-10-17

We present the realization of a highly efficient photon pair source based on spontaneous parametric downconversion (SPDC) in a periodically poled lithium niobate (PPLN) ridge waveguide. The source is suitable for long distance quantum communication applications as the photon pairs are located at the centers of the telecommunication O- and C- band at 1312 nm and 1557 nm. The high efficiency is confirmed by a conversion efficiency of 4 × 10^-6 - which is to our knowledge among the highest conversion efficiencies reported so far - and a heralding efficiency of 64.1 ± 2.1%. The heralded single-photon properties are confirmed by the measurement of the photon statistics with a Click/No-Click method as well as the heralded g⁽²⁾-function. A minimum value for g⁽²⁾(0) of 0.001 ± 0.0003 indicating clear antibunching has been observed.

Ionomers for Ion-Conducting Energy Materials

NASA Astrophysics Data System (ADS)

Colby, Ralph

For ionic actuators and battery separators, it is vital to utilize single-ion conducting ionomers that avoid the detrimental polarization of other ions. Single-ion conducting ionomers are synthesized based on DFT calculations, with low glass transition temperatures (facile dynamics) to prepare ion-conducting membranes for battery separators that conduct Li+ or Na+. Characterization by X-ray scattering, dielectric spectroscopy, FTIR, NMR and linear viscoelasticity collectively develop a coherent picture of ionic aggregation and both counterion and polymer dynamics. 7Li NMR diffusion measurements find that diffusion is faster than expected by conductivity using the Nernst-Einstein equation, which means that the majority of Li diffusion occurs by ion pairs moving with the polymer segmental motion. Segmental motion only contributes to ionic conduction in the rare event that one of these ion pairs has an extra Li (a positive triple ion). This leads us to a new metric for ion-conducting soft materials, the product of the cation number density p0 and their diffusion coefficient D; p0D is the diffusive flux of lithium ions. This new metric has a maximum at intermediate ion content that corresponds to the overlap of ion pair polarizability volumes. At higher ion contents, the ion pairs interact strongly and form larger aggregation states that retard segmental motion of both mobile ion pairs and triple ions.

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

PubMed Central

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.

2015-01-01

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s2U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s2U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s2U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s2U:A and s2U:U pairs and their native counterparts. These results indicate that s2U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s2U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s2U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s2U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying. PMID:26240387

A single Watson-Crick G x C base pair in water: aqueous hydrogen bonds in hydrophobic cavities.

PubMed

Sawada, Tomohisa; Fujita, Makoto

2010-05-26

Hydrogen bond (H-bond) formation in water has been a challenging task because water molecules are constant competitors. In biological systems, however, stable H-bonds are formed by shielding the H-bonding sites from the competing water molecules within hydrophobic pockets. Inspired by the nature's elaborated way, we found that even mononucleotides (G and C) can form the minimal G x C Watson-Crick pair in water by simply providing a synthetic cavity that efficiently shields the Watson-Crick H-bonding sites. The minimal Watson-Crick structure in water was elucidated by NMR study and firmly characterized by crystallographic analysis. The crystal structure also displays that, within the cavity, coencapsulated anions and solvents efficiently mediate the minimal G x C Watson-Crick pair formation. Furthermore, the competition experiments with the other nucleobases clearly revealed the evident selectivity for the G x C base pairing in water. These results show the fact that a H-bonded nucleobase pair was effectively induced and stabilized in the local environment of an artificial hydrophobic cavity.

An OpenACC-Based Unified Programming Model for Multi-accelerator Systems

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

Kim, Jungwon; Lee, Seyong; Vetter, Jeffrey S

2015-01-01

This paper proposes a novel SPMD programming model of OpenACC. Our model integrates the different granularities of parallelism from vector-level parallelism to node-level parallelism into a single, unified model based on OpenACC. It allows programmers to write programs for multiple accelerators using a uniform programming model whether they are in shared or distributed memory systems. We implement a prototype of our model and evaluate its performance with a GPU-based supercomputer using three benchmark applications.

Three-color Sagnac source of polarization-entangled photon pairs.

PubMed

Hentschel, Michael; Hübel, Hannes; Poppe, Andreas; Zeilinger, Anton

2009-12-07

We demonstrate a compact and stable source of polarization-entangled pairs of photons, one at 810 nm wavelength for high detection efficiency and the other at 1550 nm for long-distance fiber communication networks. Due to a novel Sagnac-based design of the interferometer no active stabilization is needed. Using only one 30 mm ppKTP bulk crystal the source produces photons with a spectral brightness of 1.13 x 10(6) pairs/s/mW/THz with an entanglement fidelity of 98.2%. Both photons are single-mode fiber coupled and ready to be used in quantum key distribution (QKD) or transmission of photonic quantum states over large distances.

Accurate quantification of magnetic particle properties by intra-pair magnetophoresis for nanobiotechnology

NASA Astrophysics Data System (ADS)

van Reenen, Alexander; Gao, Yang; Bos, Arjen H.; de Jong, Arthur M.; Hulsen, Martien A.; den Toonder, Jaap M. J.; Prins, Menno W. J.

2013-07-01

The application of magnetic particles in biomedical research and in-vitro diagnostics requires accurate characterization of their magnetic properties, with single-particle resolution and good statistics. Here, we report intra-pair magnetophoresis as a method to accurately quantify the field-dependent magnetic moments of magnetic particles and to rapidly generate histograms of the magnetic moments with good statistics. We demonstrate our method with particles of different sizes and from different sources, with a measurement precision of a few percent. We expect that intra-pair magnetophoresis will be a powerful tool for the characterization and improvement of particles for the upcoming field of particle-based nanobiotechnology.

Exploring the Limits of DNA Size: Naphtho-homologated DNA Bases and Pairs

PubMed Central

Lee, Alex H. F.; Kool, Eric T.

2008-01-01

A new design for DNA bases and base pairs is described in which the pyrimidine bases are widened by naphtho-homologation. Two naphtho-homologated deoxyribosides, dyyT (1) and dyyC (2) were synthesized and could be incorporated into oligonucleotides as suitably protected phosphoramidite derivatives. The deoxyribosides were found to be fluorescent, with emission maxima at 446 and 433 nm, respectively. Studies with single substitutions of 1 and 2 in the natural DNA context revealed exceptionally strong base stacking propensity for both. Sequences containing multiple substitutions of 1 and 2 paired opposite adenine and guanine were subsequently mixed and studied by several analytical methods. Data from UV mixing experiments, FRET measurements, fluorescence quenching experiments, and hybridizations on beads suggest that complementary “doublewide DNA” (yyDNA) strands may self-assemble into helical complexes with 1:1 stoichiometry. Data from thermal denaturation plots and CD spectra were less conclusive. Control experiments in one sequence context gave evidence that yyDNA helices, if formed, are preferentially antiparallel and are sequence selective. Hypothesized base pairing schemes are analogous to Watson-Crick pairing, but with glycosidic C1′-C1′ distances widened by over 45%, to ca. 15.2 Å. The possible self-assembly of the double-wide DNA helix establishes a new limit for the size of information-encoding, DNA-like molecules, and the fluorescence of yyDNA bases suggests uses as reporters in monomeric and oligomeric forms. PMID:16834396

SU-F-T-380: Comparing the Effect of Respiration On Dose Distribution Between Conventional Tangent Pair and IMRT Techniques for Adjuvant Radiotherapy in Early Stage Breast Cancer

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

Wu, M; Ramaseshan, R

2016-06-15

Purpose: In this project, we compared the conventional tangent pair technique to IMRT technique by analyzing the dose distribution. We also investigated the effect of respiration on planning target volume (PTV) dose coverage in both techniques. Methods: In order to implement IMRT technique a template based planning protocol, dose constrains and treatment process was developed. Two open fields with optimized field weights were combined with two beamlet optimization fields in IMRT plans. We compared the dose distribution between standard tangential pair and IMRT. The improvement in dose distribution was measured by parameters such as conformity index, homogeneity index and coveragemore » index. Another end point was the IMRT technique will reduce the planning time for staff. The effect of patient’s respiration on dose distribution was also estimated. The four dimensional computed tomography (4DCT) for different phase of breathing cycle was used to evaluate the effect of respiration on IMRT planned dose distribution. Results: We have accumulated 10 patients that acquired 4DCT and planned by both techniques. Based on the preliminary analysis, the dose distribution in IMRT technique was better than conventional tangent pair technique. Furthermore, the effect of respiration in IMRT plan was not significant as evident from the 95% isodose line coverage of PTV drawn on all phases of 4DCT. Conclusion: Based on the 4DCT images, the breathing effect on dose distribution was smaller than what we expected. We suspect that there are two reasons. First, the PTV movement due to respiration was not significant. It might be because we used a tilted breast board to setup patients. Second, the open fields with optimized field weights in IMRT technique might reduce the breathing effect on dose distribution. A further investigation is necessary.« less

NMR studies of DNA oligomers and their interactions with minor groove binding ligands

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

Fagan, Patricia A.

1996-05-01

The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I•C base pairs are functional analogs of A•T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1more » ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.« less

The fine structure of ascospore shape and development in Ceratocystis fimbriata.

PubMed

de Beer, C; van Wyk, P W; Wingfield, M J; Kemp, G H

1995-01-01

Ascospore development in Ceratocystis fimbriata Ell. & Halst. commenced in an eight-nucleate ascus. A single vesicle formed along the periphery of the ascus from fragments of ascospore delimiting membranes, surrounded all eight nuclei and eventually invaginated, first forming pouches with open ends, then finally enclosing each of the eight nuclei in a separate sac, thus delimiting ascospores. Pairing of the ascospores followed and brim formation occurred at the contact area between two ascospores. Osmiophilic bodies contributed to the formation of brim-like appendages by fusing to the ascospore walls. Additional brims were observed at opposite ends of the ascospores giving them a double-brimmed appearance.

Lorentz-violating type-II Dirac fermions in transition metal dichalcogenide PtTe2.

PubMed

Yan, Mingzhe; Huang, Huaqing; Zhang, Kenan; Wang, Eryin; Yao, Wei; Deng, Ke; Wan, Guoliang; Zhang, Hongyun; Arita, Masashi; Yang, Haitao; Sun, Zhe; Yao, Hong; Wu, Yang; Fan, Shoushan; Duan, Wenhui; Zhou, Shuyun

2017-08-15

Topological semimetals have recently attracted extensive research interests as host materials to condensed matter physics counterparts of Dirac and Weyl fermions originally proposed in high energy physics. Although Lorentz invariance is required in high energy physics, it is not necessarily obeyed in condensed matter physics, and thus Lorentz-violating type-II Weyl/Dirac fermions could be realized in topological semimetals. The recent realization of type-II Weyl fermions raises the question whether their spin-degenerate counterpart-type-II Dirac fermions-can be experimentally realized too. Here, we report the experimental evidence of type-II Dirac fermions in bulk stoichiometric PtTe 2 single crystal. Angle-resolved photoemission spectroscopy measurements and first-principles calculations reveal a pair of strongly tilted Dirac cones along the Γ-A direction, confirming PtTe 2 as a type-II Dirac semimetal. Our results provide opportunities for investigating novel quantum phenomena (e.g., anisotropic magneto-transport) and topological phase transition.Whether the spin-degenerate counterpart of Lorentz-violating Weyl fermions, the Dirac fermions, can be realized remains as an open question. Here, Yan et al. report experimental evidence of such type-II Dirac fermions in bulk PtTe 2 single crystal with a pair of strongly tilted Dirac cones.

Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Howard, Cameron M; Horick, Sarah M; Uthe, Peter B; Le, N Minh; Cox, Kari K; Nguyen, Binh; Pacheco, Kimberly A O; Wilson, W David; Lee, Moses

2005-01-19

Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- > -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.

Ligase Detection Reaction Generation of Reverse Molecular Beacons for Near Real-Time Analysis of Bacterial Pathogens Using Single-Pair Fluorescence Resonance Energy Transfer and a Cyclic Olefin Copolymer Microfluidic Chip

PubMed Central

Peng, Zhiyong; Soper, Steven A.; Pingle, Maneesh R.; Barany, Francis; Davis, Lloyd M.

2015-01-01

Detection of pathogenic bacteria and viruses require strategies that can signal the presence of these targets in near real-time due to the potential threats created by rapid dissemination into water and/or food supplies. In this paper, we report an innovative strategy that can rapidly detect bacterial pathogens using reporter sequences found in their genome without requiring polymerase chain reaction (PCR). A pair of strain-specific primers was designed based on the 16S rRNA gene and were end-labeled with a donor (Cy5) or acceptor (Cy5.5) dye. In the presence of the target bacterium, the primers were joined using a ligase detection reaction (LDR) only when the primers were completely complementary to the target sequence to form a reverse molecular beacon (rMB), thus bringing Cy5 (donor) and Cy5.5 (acceptor) into close proximity to allow fluorescence resonance energy transfer (FRET) to occur. These rMBs were subsequently analyzed using single-molecule detection of the FRET pairs (single-pair FRET; spFRET). The LDR was performed using a continuous flow thermal cycling process configured in a cyclic olefin copolymer (COC) microfluidic device using either 2 or 20 thermal cycles. Single-molecule photon bursts from the resulting rMBs were detected on-chip and registered using a simple laser-induced fluorescence (LIF) instrument. The spFRET signatures from the target pathogens were reported in as little as 2.6 min using spFRET. PMID:21047095

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Assessment of compatibility among Armillaria cepistipes, A. sinapina, and North American biological species X and XI, using culture morphology and molecular biology

Treesearch

Mark T. Banik; Harold H. Burdsall

1998-01-01

Ten single-spore isolates each of Armillaria sinapina, A. cepistipes, and North American biological species (NABS)X and XI were paired in all combinations. A second set of ten single-spore isolates of each species was likewise paired. Each pairing was duplicated for a total of 3280 pairs. Using the standard morphological criteria (e.g., fluffy, crustose) to assess the...

Characterization of the IMF By-dependent field-aligned currents in the cleft region based on DE 2 observations

NASA Technical Reports Server (NTRS)

Taguchi, S.; Sugiura, M.; Winningham, J. D.; Slavin, J. A.

1993-01-01

The magnetic field and plasma data from 47 passes of DE-2 are used to study the IMF By-dependent distribution of field-aligned currents in the cleft region. It is proposed that the low-latitude cleft current (LCC) region is not an extension of the region 1 or region 2 current system and that a pair of LCCs and high-latitude cleft currents (HCCs) constitutes the cleft field-aligned current regime. The proposed pair of cleft field-aligned currents is explained with a qualitative model in which this pair of currents is generated on open field lines that have just been reconnected on the dayside magnetopause. The electric fields are transmitted along the field lines to the ionosphere, creating a poleward electric field and a pair of field-aligned currents when By is positive; the pair of field-aligned currents consists of a downward current at lower latitudes and an upward current at higher latitudes. In the By negative case, the model explains the reversal of the field-aligned current direction in the LCC and HCC regions.

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.

PubMed

Leonard, D A; Rajaram, N; Kerppola, T K

1997-05-13

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos-Jun-AP-1 complex may contribute to its functional versatility at different promoters.

Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2;#8242;-deoxyadenosine:dT Base Pairing in DNA

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

Kowal, Ewa A.; Ganguly, Manjori; Pallan, Pradeep S.

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2'-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson-Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C-H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 {angstrom} resolution in the presence of Mg{sup 2+}. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry andmore » the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.« less

Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2′-deoxyadenosine:dT Base Pairing in DNA

PubMed Central

2011-01-01

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2′-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson–Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C–H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 Å resolution in the presence of Mg2+. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA. PMID:22059929

Pair correlations in low-lying T =0 states of odd-odd nuclei with six nucleons

NASA Astrophysics Data System (ADS)

Fu, G. J.; Zhao, Y. M.; Arima, A.

2018-02-01

In this paper, we study pair correlations in low-lying T =0 states for two typical cases of odd-odd N =Z nuclei. The first case is six nucleons in a single j =9 /2 shell, for which we study the S -broken-pair approximation, the isoscalar spin-1 pair condensation, and the isoscalar spin-aligned pair condensation, with schematic interactions. In the second case, we study pair approximations and correlation energies for 22Na, 34Cl, 46V, 62Ga, and 94Ag in multi-j shells with effective interactions. A few T =0 states are found to be well represented by isoscalar nucleon pairs. The isoscalar spin-aligned pairs play an important role for the yrast T =0 states with I ˜2 j and I ˜Imax in 22Na, 46V, and 94Ag. The overlap between the isoscalar J =1 pair wave function and the shell-model wave function is around 0.5 for the I =1 ,3 states of 34Cl and the I =1 state of 94Ag. The I =9 state of 62Ga is very well described by the isoscalar J =3 pair condensation. The broken-pair approximation (which is similar to the 2-quasiparticle excitation of the isovector pair condensation) is appropriate for quite few states, such as the I =1 -3 states of 34Cl and the I =5 state of 62Ga. The correlation energies are presented in this paper. It is noted that the picture based on nucleon-pair wave functions is not always in agreement with the picture based on correlation energies.

Modeling and experimental validation of angular radiance and distance-dependent radiance in a turbid medium

NASA Astrophysics Data System (ADS)

Liu, Lingling; Li, Chenxi; Zhao, Huijuan; Yi, Xi; Gao, Feng; Meng, Wei; Lu, Yiming

2014-03-01

Radiance is sensitive to the variations of tissue optical parameters, such as absorption coefficient μa, scattering coefficient μs, and anisotropy factor g. Therefore, similar to fluence, radiance can be used for tissue characterization. Compared with fluence, radiance has the advantage of offering the direction information of light intensity. Taking such advantage, the optical parameters can be determined by rotating the detector through 360 deg with only a single optode pair. Instead of the translation mode used in the fluence-based technologies, the Rotation mode has less invasiveness in the clinical diagnosis. This paper explores a new method to obtain the optical properties by measuring the distribution of light intensity in liquid phantom with only a single optode pair and the detector rotation through 360 deg. The angular radiance and distance-dependent radiance are verified by comparing experimental measurement data with Monte Carlo (MC) simulation for the short source-detector separations and diffusion approximation for the large source-detector separations. Detecting angular radiance with only a single optode pair under a certain source-detection separation will present a way for prostate diagnose and light dose calculation during the photon dynamic therapy (PDT).

Characterization of a 29.4-kilodalton structural protein of Giardia lamblia and localization to the ventral disk [corrected

PubMed Central

Aggarwal, A; Adam, R D; Nash, T E

1989-01-01

The amino acid sequence of a 29.4-kilodalton [corrected] structural protein located in the ventral disk and axostyle of Giardia lamblia was determined. Clone lambda M16 from a mung bean expression library in lambda gt11 expressed a fusion protein recognized by three different isolate-specific antisera and sera from G. lamblia-infected gerbils. One of the three EcoRI fragments (M16; 1.26 kilobases) encoded the recognized protein. Sequence analysis revealed a single open reading frame of 813 base pairs. Two areas showed conservation of the positions of some amino acids. The abundance of arginine, glutamic acid, and threonine was increased. Two potential alpha-helical regions were deduced in the regions of repeats. Antisera to the M16 fusion protein reacted specifically with internal components of the ventral disk and axostyle, as well as Giardia fractions enriched for ventral disk structural proteins. An identical protein was recognized in different isolates by anti-M16, and a single identical band was recognized in Southern blots using the M16 1.26-kilobase fragment as a probe. Therefore, the 29.4-kilodaltion [corrected] protein appears to be highly conserved compared with variant surface proteins. Images PMID:2925253

Electro-optic modulation for high-speed characterization of entangled photon pairs

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

Lukens, Joseph M.; Odele, Ogaga D.; Leaird, Daniel E.

In this study, we demonstrate a new biphoton manipulation and characterization technique based on electro-optic intensity modulation and time shifting. By applying fast modulation signals with a sharply peaked cross-correlation to each photon from an entangled pair, it is possible to measure temporal correlations with significantly higher precision than that attainable using standard single-photon detection. Low-duty-cycle pulses and maximal-length sequences are considered as modulation functions, reducing the time spread in our correlation measurement by a factor of five compared to our detector jitter. With state-of-the-art electro-optic components, we expect the potential to surpass the speed of any single-photon detectors currentlymore » available.« less

Electro-optic modulation for high-speed characterization of entangled photon pairs

DOE PAGES

Lukens, Joseph M.; Odele, Ogaga D.; Leaird, Daniel E.; ...

2015-11-10

In this study, we demonstrate a new biphoton manipulation and characterization technique based on electro-optic intensity modulation and time shifting. By applying fast modulation signals with a sharply peaked cross-correlation to each photon from an entangled pair, it is possible to measure temporal correlations with significantly higher precision than that attainable using standard single-photon detection. Low-duty-cycle pulses and maximal-length sequences are considered as modulation functions, reducing the time spread in our correlation measurement by a factor of five compared to our detector jitter. With state-of-the-art electro-optic components, we expect the potential to surpass the speed of any single-photon detectors currentlymore » available.« less

Phase-space analysis of the Schwinger effect in inhomogeneous electromagnetic fields

NASA Astrophysics Data System (ADS)

Kohlfürst, Christian

2018-05-01

Schwinger pair production in spatially and temporally inhomogeneous electric and magnetic fields is studied. The focus is on the particle phase-space distribution within a high-intensity few-cycle pulse. Accurate numerical solutions of a quantum kinetic theory (DHW formalism) are presented in momentum space and, with the aid of coarse-graining techniques, in a mixed spatial-momentum representation. Additionally, signatures of the carrier-envelope phase as well as spin-field interactions are discussed on the basis of a trajectory-based model taking into account instantaneous pair production and relativistic single-particle dynamics. Although our simple semi-classical single-particle model cannot describe every aspect of the particle production process (quantum interferences), essential features such as spin-field interactions are captured.

A process-based approach to characterizing the effect of acute alprazolam challenge on visual paired associate learning and memory in healthy older adults.

PubMed

Pietrzak, Robert H; Scott, James Cobb; Harel, Brian T; Lim, Yen Ying; Snyder, Peter J; Maruff, Paul

2012-11-01

Alprazolam is a benzodiazepine that, when administered acutely, results in impairments in several aspects of cognition, including attention, learning, and memory. However, the profile (i.e., component processes) that underlie alprazolam-related decrements in visual paired associate learning has not been fully explored. In this double-blind, placebo-controlled, randomized cross-over study of healthy older adults, we used a novel, "process-based" computerized measure of visual paired associate learning to examine the effect of a single, acute 1-mg dose of alprazolam on component processes of visual paired associate learning and memory. Acute alprazolam challenge was associated with a large magnitude reduction in visual paired associate learning and memory performance (d = 1.05). Process-based analyses revealed significant increases in distractor, exploratory, between-search, and within-search error types. Analyses of percentages of each error type suggested that, relative to placebo, alprazolam challenge resulted in a decrease in the percentage of exploratory errors and an increase in the percentage of distractor errors, both of which reflect memory processes. Results of this study suggest that acute alprazolam challenge decreases visual paired associate learning and memory performance by reducing the strength of the association between pattern and location, which may reflect a general breakdown in memory consolidation, with less evidence of reductions in executive processes (e.g., working memory) that facilitate visual paired associate learning and memory. Copyright © 2012 John Wiley & Sons, Ltd.

Age-related Associative Memory Deficits in Value-based Remembering: The Contribution of Agenda-based Regulation and Strategy Use

PubMed Central

Ariel, Robert; Price, Jodi; Hertzog, Christopher

2015-01-01

Value-based remembering in free recall tasks may be spared from the typical age-related cognitive decline observed for episodic memory. However, it is unclear whether value-based remembering for associative information is also spared from age-related cognitive decline. The current experiments evaluated the contribution of agenda-based based regulation and strategy use during study to age differences and similarities in value-based remembering of associative information. Participants studied word pairs (Experiments 1-2) or single words (Experiment 2) slated with different point values by moving a mouse controlled cursor to different spatial locations to reveal either items for study or the point value associated with remembering each item. Some participants also provided strategy reports for each item. Younger and older adults allocated greater time to studying high than low valued information, reported using normatively effective encoding strategies to learn high-valued pairs, and avoided study of low-valued pairs. As a consequence, both age groups selectively remembered more high than low-valued items. Despite nearly identical regulatory behavior, an associative memory deficit for older adults was present for high valued pairs. Age differences in value-based remembering did not occur when the materials were word lists. Fluid intelligence also moderated the effectiveness of older adults’ strategy use for high valued pairs (Experiment 2). These results suggest that age differences in associative value-based remembering may be due to some older adults’ gleaning less benefit from using normatively effective encoding strategies rather than age differences in metacognitive self-regulation per se. PMID:26523692

Using Single Colors and Color Pairs to Communicate Basic Tastes.

PubMed

Woods, Andy T; Spence, Charles

2016-01-01

Recently, it has been demonstrated that people associate each of the basic tastes (e.g., sweet, sour, bitter, and salty) with specific colors (e.g., red, green, black, and white). In the present study, we investigated whether pairs of colors (both associated with a particular taste or taste word) would give rise to stronger associations relative to pairs of colors that were associated with different tastes. We replicate the findings of previous studies highlighting the existence of a robust crossmodal correspondence between individual colors and basic tastes. However, while there was evidence that pairs of colors could indeed communicate taste information more consistently than single colors, our participants took more than twice as long to match the color pairs with tastes than the single colors. Possible reasons for these results are discussed.

Lewis Acid Pairs for the Activation of Biomass-derived Oxygenates in Aqueous Media

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

Roman, Yuriy

2015-09-14

The objective of this project is to understand the mechanistic aspects behind the cooperative activation of oxygenates by catalytic pairs in aqueous media. Specifically, we will investigate how the reactivity of a solid Lewis acid can be modulated by pairing the active site with other catalytic sites at the molecular level, with the ultimate goal of enhancing activation of targeted functional groups. Although unusual catalytic properties have been attributed to the cooperative effects promoted by such catalytic pairs, virtually no studies exist detailing the use heterogeneous water-tolerant Lewis pairs. A main goal of this work is to devise rational pathwaysmore » for the synthesis of porous heterogeneous catalysts featuring isolated Lewis pairs that are active in the transformation of biomass-derived oxygenates in the presence of bulk water. Achieving this technical goal will require closely linking advanced synthesis techniques; detailed kinetic and mechanistic investigations; strict thermodynamic arguments; and comprehensive characterization studies of both materials and reaction intermediates. For the last performance period (2014-2015), two technical aims were pursued: 1) C-C coupling using Lewis acid and base pairs in Lewis acidic zeolites. Tin-, zirconium-, and hafnium containing zeolites (e.g., Sn-, Zr-, and Hf-Beta) are versatile solid Lewis acids that selectively activate carbonyl functional groups. In this aim, we demonstrate that these zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions. 2) One-pot synthesis of MWW zeolite nanosheets for activation of bulky substrates. Through post-synthetic modifications, layered zeolite precursors can be transformed into 2-dimensional (2D), zeolites with open architectures. These novel hierarchical microporous/mesoporous materials with exposed active sites can facilitate the conversion of bulky substrates while maintaining higher stability than amorphous mesoporous materials. However, post-synthetic exfoliation techniques are energy intensive, multi-step and require highly alkaline conditions that result in low silica yields and a partially amorphous product. In this aim, we demonstrate an effective one-pot synthesis method to generate exfoliated single-unit-cell thick MWW nanosheets. The new material, named MIT-1, is synthesized using a rationally-designed OSDA and results in a material with high crystallinity, surface area, and acidity that does not require post-synthetic treatments other than calcination. A parametric study of Al, Na, and water content reveals that MIT-1 crystallizes over a wide synthetic window. Characterization data show that MIT-1 has high mesoporosity with an external surface area exceeding 500 m2g-1 and a high external acid site density of 21 x 10-5 mol g-1. Catalytic tests demonstrate that MIT-1 has three-fold higher catalytic activity for the Friedel-Crafts alkylation of benzene with benzyl alcohol as compared to that of other 3D MWW topology zeolites.« less

PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.

PubMed

Yang, Guangyuan; Jiang, Wei; Yang, Qiang; Yu, Weichuan

2015-05-01

The importance of testing associations allowing for interactions has been demonstrated by Marchini et al. (2005). A fast method detecting associations allowing for interactions has been proposed by Wan et al. (2010a). The method is based on likelihood ratio test with the assumption that the statistic follows the χ(2) distribution. Many single nucleotide polymorphism (SNP) pairs with significant associations allowing for interactions have been detected using their method. However, the assumption of χ(2) test requires the expected values in each cell of the contingency table to be at least five. This assumption is violated in some identified SNP pairs. In this case, likelihood ratio test may not be applicable any more. Permutation test is an ideal approach to checking the P-values calculated in likelihood ratio test because of its non-parametric nature. The P-values of SNP pairs having significant associations with disease are always extremely small. Thus, we need a huge number of permutations to achieve correspondingly high resolution for the P-values. In order to investigate whether the P-values from likelihood ratio tests are reliable, a fast permutation tool to accomplish large number of permutations is desirable. We developed a permutation tool named PBOOST. It is based on GPU with highly reliable P-value estimation. By using simulation data, we found that the P-values from likelihood ratio tests will have relative error of >100% when 50% cells in the contingency table have expected count less than five or when there is zero expected count in any of the contingency table cells. In terms of speed, PBOOST completed 10(7) permutations for a single SNP pair from the Wellcome Trust Case Control Consortium (WTCCC) genome data (Wellcome Trust Case Control Consortium, 2007) within 1 min on a single Nvidia Tesla M2090 device, while it took 60 min in a single CPU Intel Xeon E5-2650 to finish the same task. More importantly, when simultaneously testing 256 SNP pairs for 10(7) permutations, our tool took only 5 min, while the CPU program took 10 h. By permuting on a GPU cluster consisting of 40 nodes, we completed 10(12) permutations for all 280 SNP pairs reported with P-values smaller than 1.6 × 10⁻¹² in the WTCCC datasets in 1 week. The source code and sample data are available at http://bioinformatics.ust.hk/PBOOST.zip. gyang@ust.hk; eeyu@ust.hk Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Microscopic description of pair transfer between two superfluid Fermi systems: Combining phase-space averaging and combinatorial techniques

NASA Astrophysics Data System (ADS)

Regnier, David; Lacroix, Denis; Scamps, Guillaume; Hashimoto, Yukio

2018-03-01

In a mean-field description of superfluidity, particle number and gauge angle are treated as quasiclassical conjugated variables. This level of description was recently used to describe nuclear reactions around the Coulomb barrier. Important effects of the relative gauge angle between two identical superfluid nuclei (symmetric collisions) on transfer probabilities and fusion barrier have been uncovered. A theory making contact with experiments should at least average over different initial relative gauge-angles. In the present work, we propose a new approach to obtain the multiple pair transfer probabilities between superfluid systems. This method, called phase-space combinatorial (PSC) technique, relies both on phase-space averaging and combinatorial arguments to infer the full pair transfer probability distribution at the cost of multiple mean-field calculations only. After benchmarking this approach in a schematic model, we apply it to the collision 20O+20O at various energies below the Coulomb barrier. The predictions for one pair transfer are similar to results obtained with an approximated projection method, whereas significant differences are found for two pairs transfer. Finally, we investigated the applicability of the PSC method to the contact between nonidentical superfluid systems. A generalization of the method is proposed and applied to the schematic model showing that the pair transfer probabilities are reasonably reproduced. The applicability of the PSC method to asymmetric nuclear collisions is investigated for the 14O+20O collision and it turns out that unrealistically small single- and multiple pair transfer probabilities are obtained. This is explained by the fact that relative gauge angle play in this case a minor role in the particle transfer process compared to other mechanisms, such as equilibration of the charge/mass ratio. We conclude that the best ground for probing gauge-angle effects in nuclear reaction and/or for applying the proposed PSC approach on pair transfer is the collisions of identical open-shell spherical nuclei.

Three-photon N00N states generated by photon subtraction from double photon pairs.

PubMed

Kim, Heonoh; Park, Hee Su; Choi, Sang-Kyung

2009-10-26

We describe an experimental demonstration of a novel three-photon N00N state generation scheme using a single source of photons based on spontaneous parametric down-conversion (SPDC). The three-photon entangled state is generated when a photon is subtracted from a double pair of photons and detected by a heralding counter. Interference fringes measured with an emulated three-photon detector reveal the three-photon de Broglie wavelength and exhibit visibility > 70% without background subtraction.

Dynamics of Cancer Cell near Collagen Fiber Chain

NASA Astrophysics Data System (ADS)

Kim, Jihan; Sun, Bo

Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. When cell migrates through connective extracellular matrix (ECM), it applies cellular traction force to ECM and senses the rigidity of their local environment. We used human breast cancer cell (MDA-MB-231) which is highly invasive and applies strong traction force to ECM. As cancer cell applies traction force to type I collage-based ECM, it deforms collagen fibers near the surface. Patterns of deforming collagen fibers are significantly different with pairs of cancer cells compared to a single cancer cell. While a pair of cancer cells within 60 um creates aligned collagen fiber chains between them permanently, a single cancer cell does not form any fiber chains. In this experiment we measured a cellular response and an interaction between a pair of cells through the chain. Finally, we analyzed correlation of directions between cancer cell migration and the collagen chain alignment.

Joint spectral characterization of photon-pair sources

NASA Astrophysics Data System (ADS)

Zielnicki, Kevin; Garay-Palmett, Karina; Cruz-Delgado, Daniel; Cruz-Ramirez, Hector; O'Boyle, Michael F.; Fang, Bin; Lorenz, Virginia O.; U'Ren, Alfred B.; Kwiat, Paul G.

2018-06-01

The ability to determine the joint spectral properties of photon pairs produced by the processes of spontaneous parametric downconversion (SPDC) and spontaneous four-wave mixing (SFWM) is crucial for guaranteeing the usability of heralded single photons and polarization-entangled pairs for multi-photon protocols. In this paper, we compare six different techniques that yield either a characterization of the joint spectral intensity or of the closely related purity of heralded single photons. These six techniques include: (i) scanning monochromator measurements, (ii) a variant of Fourier transform spectroscopy designed to extract the desired information exploiting a resource-optimized technique, (iii) dispersive fibre spectroscopy, (iv) stimulated-emission-based measurement, (v) measurement of the second-order correlation function ? for one of the two photons, and (vi) two-source Hong-Ou-Mandel interferometry. We discuss the relative performance of these techniques for the specific cases of a SPDC source designed to be factorable and SFWM sources of varying purity, and compare the techniques' relative advantages and disadvantages.

Search for top squark pair production in pp collisions at s=13$$ \\sqrt{s}=13 $$ TeV using single lepton events

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

Sirunyan, A. M.; Tumasyan, A.; Adam, W.

A search for top squark pair production in pp collisions at sqrt(s) = 13 TeV is performed using events with a single isolated electron or muon, jets, and a large transverse momentum imbalance. The results are based on data collected in 2016 with the CMS detector at the LHC, corresponding to an integrated luminosity of 35.9 inverse femtobarns. No significant excess of events is observed above the expectation from standard model processes. Exclusion limits are set in the context of supersymmetric models of pair production of top squarks that decay either to a top quark and a neutralino or tomore » a bottom quark and a chargino. Depending on the details of the model, we exclude top squarks with masses as high as 1120 GeV. Detailed information is also provided to facilitate theoretical interpretations in other scenarios of physics beyond the standard model.« less

A minimal model for kinetochore-microtubule dynamics

NASA Astrophysics Data System (ADS)

Liu, Andrea

2014-03-01

During mitosis, chromosome pairs align at the center of a bipolar microtubule (MT) spindle and oscillate as MTs attaching them to the cell poles polymerize and depolymerize. The cell fixes misaligned pairs by a tension-sensing mechanism. Pairs later separate as shrinking MTs pull each chromosome toward its respective cell pole. We present a minimal model for these processes based on properties of MT kinetics. We apply the measured tension-dependence of single MT kinetics to a stochastic many MT model, which we solve numerically and with master equations. We find that the force-velocity curve for the single chromosome system is bistable and hysteretic. Above some threshold load, tension fluctuations induce MTs to spontaneously switch from a pulling state into a growing, pushing state. To recover pulling from the pushing state, the load must be reduced far below the threshold. This leads to oscillations in the two-chromosome system. Our minimal model quantitatively captures several aspects of kinetochore dynamics observed experimentally. This work was supported by NSF-DMR-1104637.

Search for top squark pair production in pp collisions at s=13$$ \\sqrt{s}=13 $$ TeV using single lepton events

DOE PAGES

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; ...

2017-10-03

A search for top squark pair production in pp collisions at sqrt(s) = 13 TeV is performed using events with a single isolated electron or muon, jets, and a large transverse momentum imbalance. The results are based on data collected in 2016 with the CMS detector at the LHC, corresponding to an integrated luminosity of 35.9 inverse femtobarns. No significant excess of events is observed above the expectation from standard model processes. Exclusion limits are set in the context of supersymmetric models of pair production of top squarks that decay either to a top quark and a neutralino or tomore » a bottom quark and a chargino. Depending on the details of the model, we exclude top squarks with masses as high as 1120 GeV. Detailed information is also provided to facilitate theoretical interpretations in other scenarios of physics beyond the standard model.« less

Search for top squark pair production in pp collisions at √{s}=13 TeV using single lepton events

NASA Astrophysics Data System (ADS)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Ambrogi, F.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Grossmann, J.; Hrubec, J.; Jeitler, M.; König, A.; Krammer, N.; Krätschmer, I.; Liko, D.; Madlener, T.; Mikulec, I.; Pree, E.; Rabady, D.; Rad, N.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Spanring, M.; Spitzbart, D.; Strauss, J.; Waltenberger, W.; Wittmann, J.; Wulz, C.-E.; Zarucki, M.; Chekhovsky, V.; Mossolov, V.; Suarez Gonzalez, J.; De Wolf, E. A.; Di Croce, D.; Janssen, X.; Lauwers, J.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; De Bruyn, I.; De Clercq, J.; Deroover, K.; Flouris, G.; Lontkovskyi, D.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Skovpen, K.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Gul, M.; Khvastunov, I.; Poyraz, D.; Roskas, C.; Salva, S.; Tytgat, M.; Verbeke, W.; Zaganidis, N.; Bakhshiansohi, H.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Jafari, A.; Komm, M.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Piotrzkowski, K.; Quertenmont, L.; Vidal Marono, M.; Wertz, S.; Beliy, N.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Martins Junior, M. Correa; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Melo De Almeida, M.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Torres Da Silva De Araujo, F.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Misheva, M.; Rodozov, M.; Shopova, M.; Stoykova, S.; Sultanov, G.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Gao, X.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Jiang, C. H.; Leggat, D.; Liao, H.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Yazgan, E.; Zhang, H.; Zhao, J.; Ban, Y.; Chen, G.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Courbon, B.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Mesic, B.; Starodumov, A.; Susa, T.; Ather, M. W.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Finger, M.; Finger, M.; Carrera Jarrin, E.; Assran, Y.; Mahmoud, M. A.; Mahrous, A.; Dewanjee, R. K.; Kadastik, M.; Perrini, L.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Faure, J. L.; Ferri, F.; Ganjour, S.; Ghosh, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Kucher, I.; Locci, E.; Machet, M.; Malcles, J.; Negro, G.; Rander, J.; Rosowsky, A.; Sahin, M. Ö.; Titov, M.; Abdulsalam, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Charlot, C.; Granier de Cassagnac, R.; Jo, M.; Lisniak, S.; Lobanov, A.; Martin Blanco, J.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Stahl Leiton, A. G.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Jansová, M.; Le Bihan, A.-C.; Tonon, N.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Bernet, C.; Boudoul, G.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fay, J.; Finco, L.; Gascon, S.; Gouzevitch, M.; Grenier, G.; Ille, B.; Lagarde, F.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Popov, A.; Sordini, V.; Vander Donckt, M.; Viret, S.; Toriashvili, T.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Feld, L.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Preuten, M.; Schomakers, C.; Schulz, J.; Verlage, T.; Albert, A.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hamer, M.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Knutzen, S.; Merschmeyer, M.; Meyer, A.; Millet, P.; Mukherjee, S.; Olschewski, M.; Padeken, K.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Teyssier, D.; Thüer, S.; Flügge, G.; Kargoll, B.; Kress, T.; Künsken, A.; Lingemann, J.; Müller, T.; Nehrkorn, A.; Nowack, A.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Arndt, T.; Asawatangtrakuldee, C.; Beernaert, K.; Behnke, O.; Behrens, U.; Bermúdez Martínez, A.; Bin Anuar, A. A.; Borras, K.; Botta, V.; Campbell, A.; Connor, P.; Contreras-Campana, C.; Costanza, F.; Diez Pardos, C.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Eren, E.; Gallo, E.; Garay Garcia, J.; Geiser, A.; Gizhko, A.; Grados Luyando, J. M.; Grohsjean, A.; Gunnellini, P.; Harb, A.; Hauk, J.; Hempel, M.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Keaveney, J.; Kleinwort, C.; Korol, I.; Krücker, D.; Lange, W.; Lelek, A.; Lenz, T.; Leonard, J.; Lipka, K.; Lohmann, W.; Mankel, R.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Ntomari, E.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Roland, B.; Savitskyi, M.; Saxena, P.; Shevchenko, R.; Spannagel, S.; Stefaniuk, N.; Van Onsem, G. P.; Walsh, R.; Wen, Y.; Wichmann, K.; Wissing, C.; Zenaiev, O.; Bein, S.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Dreyer, T.; Garutti, E.; Gonzalez, D.; Haller, J.; Hinzmann, A.; Hoffmann, M.; Karavdina, A.; Klanner, R.; Kogler, R.; Kovalchuk, N.; Kurz, S.; Lapsien, T.; Marchesini, I.; Marconi, D.; Meyer, M.; Niedziela, M.; Nowatschin, D.; Pantaleo, F.; Peiffer, T.; Perieanu, A.; Scharf, C.; Schleper, P.; Schmidt, A.; Schumann, S.; Schwandt, J.; Sonneveld, J.; Stadie, H.; Steinbrück, G.; Stober, F. M.; Stöver, M.; Tholen, H.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Vormwald, B.; Akbiyik, M.; Barth, C.; Baur, S.; Butz, E.; Caspart, R.; Chwalek, T.; Colombo, F.; De Boer, W.; Dierlamm, A.; Freund, B.; Friese, R.; Giffels, M.; Gilbert, A.; Haitz, D.; Hartmann, F.; Heindl, S. M.; Husemann, U.; Kassel, F.; Kudella, S.; Mildner, H.; Mozer, M. U.; Müller, Th.; Plagge, M.; Quast, G.; Rabbertz, K.; Schröder, M.; Shvetsov, I.; Sieber, G.; Simonis, H. J.; Ulrich, R.; Wayand, S.; Weber, M.; Weiler, T.; Williamson, S.; Wöhrmann, C.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Topsis-Giotis, I.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Evangelou, I.; Foudas, C.; Kokkas, P.; Mallios, S.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Strologas, J.; Triantis, F. A.; Csanad, M.; Filipovic, N.; Pasztor, G.; Bencze, G.; Hajdu, C.; Horvath, D.; Hunyadi, Á.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Makovec, A.; Molnar, J.; Szillasi, Z.; Bartók, M.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Choudhury, S.; Komaragiri, J. R.; Bahinipati, S.; Bhowmik, S.; Mal, P.; Mandal, K.; Nayak, A.; Sahoo, D. K.; Sahoo, N.; Swain, S. K.; Bansal, S.; Beri, S. B.; Bhatnagar, V.; Bhawandeep, U.; Chawla, R.; Dhingra, N.; Kalsi, A. K.; Kaur, A.; Kaur, M.; Kumar, R.; Kumari, P.; Mehta, A.; Singh, J. B.; Walia, G.; Kumar, Ashok; Shah, Aashaq; Bhardwaj, A.; Chauhan, S.; Choudhary, B. C.; Garg, R. B.; Keshri, S.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, R.; Sharma, V.; Bhardwaj, R.; Bhattacharya, R.; Bhattacharya, S.; Dey, S.; Dutt, S.; Dutta, S.; Ghosh, S.; Majumdar, N.; Modak, A.; Mondal, K.; Mukhopadhyay, S.; Nandan, S.; Purohit, A.; Roy, A.; Roy, D.; Roy Chowdhury, S.; Sarkar, S.; Sharan, M.; Thakur, S.; Behera, P. K.; Chudasama, R.; Dutta, D.; Jha, V.; Kumar, V.; Mohanty, A. K.; Netrakanti, P. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Dugad, S.; Mahakud, B.; Mitra, S.; Mohanty, G. B.; Parida, B.; Sur, N.; Sutar, B.; Banerjee, S.; Bhattacharya, S.; Chatterjee, S.; Das, P.; Guchait, M.; Jain, Sa.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Sarkar, T.; Wickramage, N.; Chauhan, S.; Dube, S.; Hegde, V.; Kapoor, A.; Kothekar, K.; Pandey, S.; Rane, A.; Sharma, S.; Chenarani, S.; Eskandari Tadavani, E.; Etesami, S. M.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Errico, F.; Fiore, L.; Iaselli, G.; Lezki, S.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Chhibra, S. S.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Albergo, S.; Costa, S.; Di Mattia, A.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Chatterjee, K.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Lenzi, P.; Meschini, M.; Paoletti, S.; Russo, L.; Sguazzoni, G.; Strom, D.; Viliani, L.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Primavera, F.; Calvelli, V.; Ferro, F.; Robutti, E.; Tosi, S.; Brianza, L.; Brivio, F.; Ciriolo, V.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Ghezzi, A.; Govoni, P.; Malberti, M.; Malvezzi, S.; Manzoni, R. A.; Menasce, D.; Moroni, L.; Paganoni, M.; Pauwels, K.; Pedrini, D.; Pigazzini, S.; Ragazzi, S.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Esposito, M.; Fabozzi, F.; Fienga, F.; Iorio, A. O. M.; Khan, W. A.; Lanza, G.; Lista, L.; Meola, S.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Badoer, S.; Bellato, M.; Benato, L.; Benettoni, M.; Bisello, D.; Boletti, A.; Carlin, R.; Carvalho Antunes De Oliveira, A.; Dall'Osso, M.; De Castro Manzano, P.; Dorigo, T.; Dosselli, U.; Gasparini, F.; Gasparini, U.; Gozzelino, A.; Lacaprara, S.; Meneguzzo, A. T.; Pozzobon, N.; Ronchese, P.; Rossin, R.; Simonetto, F.; Torassa, E.; Zanetti, M.; Zotto, P.; Zumerle, G.; Braghieri, A.; Fallavollita, F.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Ressegotti, M.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Biasini, M.; Bilei, G. M.; Cecchi, C.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Leonardi, R.; Manoni, E.; Mantovani, G.; Mariani, V.; Menichelli, M.; Rossi, A.; Santocchia, A.; Spiga, D.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Borrello, L.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Fedi, G.; Giannini, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Manca, E.; Mandorli, G.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; Del Re, D.; Diemoz, M.; Gelli, S.; Longo, E.; Margaroli, F.; Marzocchi, B.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Cenna, F.; Costa, M.; Covarelli, R.; Degano, A.; Demaria, N.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Monteno, M.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Ruspa, M.; Sacchi, R.; Shchelina, K.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, J.; Lee, S.; Lee, S. 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J.; Kellams, N.; Lannon, K.; Loukas, N.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Wayne, M.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Ji, W.; Liu, B.; Luo, W.; Puigh, D.; Winer, B. L.; Wulsin, H. W.; Benaglia, A.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Higginbotham, S.; Lange, D.; Luo, J.; Marlow, D.; Mei, K.; Ojalvo, I.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Tully, C.; Malik, S.; Norberg, S.; Barker, A.; Barnes, V. E.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Khatiwada, A.; Miller, D. H.; Neumeister, N.; Peng, C. C.; Schulte, J. F.; Sun, J.; Wang, F.; Xie, W.; Cheng, T.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Ciesielski, R.; Goulianos, K.; Mesropian, C.; Agapitos, A.; Chou, J. P.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Montalvo, R.; Nash, K.; Osherson, M.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Delannoy, A. G.; Foerster, M.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Castaneda Hernandez, A.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Damgov, J.; De Guio, F.; Dudero, P. R.; Faulkner, J.; Gurpinar, E.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Hirosky, R.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Sun, X.; Wang, Y.; Wolfe, E.; Xia, F.; Harr, R.; Karchin, P. E.; Sturdy, J.; Zaleski, S.; Brodski, M.; Buchanan, J.; Caillol, C.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Hussain, U.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Pierro, G. A.; Polese, G.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.

2017-10-01

A search for top squark pair production in pp collisions at √{s}=13 TeV is performed using events with a single isolated electron or muon, jets, and a large transverse momentum imbalance. The results are based on data collected in 2016 with the CMS detector at the LHC, corresponding to an integrated luminosity of 35.9 fb-1. No significant excess of events is observed above the expectation from standard model processes. Exclusion limits are set in the context of supersymmetric models of pair production of top squarks that decay either to a top quark and a neutralino or to a bottom quark and a chargino. Depending on the details of the model, we exclude top squarks with masses as high as 1120 GeV. Detailed information is also provided to facilitate theoretical interpretations in other scenarios of physics beyond the standard model. [Figure not available: see fulltext.

Physics of base-pairing dynamics in DNA

NASA Astrophysics Data System (ADS)

Manghi, Manoel; Destainville, Nicolas

2016-05-01

As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

Pairing tendencies in a two-orbital Hubbard model in one dimension

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

Patel, Niravkumar D.; Nocera, Adriana; Alvarez, Gonzalo

The recent discovery of superconductivity under high pressure in the ladder compound BaFe2S3 has opened a new field of research in iron-based superconductors with focus on quasi-one-dimensional geometries. In this publication, using the density matrix renormalization group technique, we study a two-orbital Hubbard model defined in one-dimensional chains. Our main result is the presence of hole binding tendencies at intermediate Hubbard U repulsion and robust Hund coupling JH / U = 0.25. Binding does not occur either in weak coupling or at very strong coupling. The pair-pair correlations that are dominant near half-filling, or of similar strength as the chargemore » and spin correlation channels, involve hole-pair operators that are spin singlets, use nearest-neighbor sites, and employ different orbitals for each hole. As a result, the Hund coupling strength, presence of robust magnetic moments, and antiferromagnetic correlations among them are important for the binding tendencies found here.« less

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

PubMed Central

Toh, Desiree-Faye Kaixin; Devi, Gitali; Patil, Kiran M.; Qu, Qiuyu; Maraswami, Manikantha; Xiao, Yunyun; Loh, Teck Peng; Zhao, Yanli; Chen, Gang

2016-01-01

RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair. Remarkably, the relatively short PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. The attached guanidine group stabilizes the base triple through hydrogen bonding with the G base in a C-G pair. Selective binding towards an RNA duplex over a single-stranded RNA can be rationalized by the fact that alkylation of the amine of a 5-methyl C base blocks the Watson–Crick edge. PNAs incorporating multiple guanidine-modified cytosine residues are able to enter HeLa cells without any transfection agent. PMID:27596599

Pen confinement of yearling ewes with cows or heifers for 14 days to produce bonded sheep.

PubMed

Fredrickson, E L.; Anderson, D M.; Estell, R E.; Havstad, K M.; Shupe, W L.; Remmenga, M D.

2001-06-01

Mixed species stocking is commonly a more ecologically sound and efficient use of forage resources than single species stocking, especially in pastures having complex assemblages of forage species. However, in many environments livestock predation on especially smaller ruminants adds an extra challenge to mixed species stocking. When mixed sheep and cattle remain consistently as a cohesive group (flerd), predation risks are lessened, while fencing and herding costs are reduced. To establish a cohesive group (bond), a 30-day bonding period in which young sheep and cattle pairs are penned together is currently recommended. The purpose of this research was to test if a bond could be produced in <30 days (14 days) using pen confinement; thus reducing feed, labor, and overhead costs. Additionally, we tested whether cow age affects cohesiveness of bonded pairs immediately following 14 days of pen confinement. Sixteen mature cows (7-8 years of age) and sixteen 9-month-old heifers were randomly paired with one of 32 yearling ewe lambs. Eight cow/ewe (PC) and eight heifer/ewe (PH) pairs were maintained individually in 2mx6m pens for 14 days. The other eight-cow/ewe (NC) and heifer/ewe (NH) pairs were separated by species with each species maintained on separate pastures for the 14-day period. After 14 days, pairs were released in observation paddocks and separation distance between treatment pairs was measured during a 30-min open field test. Other behaviors were also noted and recorded during the field test. Separation distance did not differ (P=0.973) between the PC and PH treatments; however, separation distance for NC versus NH (P<0.004), NC versus PC (P<0.001), and NH versus PH (P<0.002) all differed. Mean separation distance (meters) and standard errors were 40+/-3.9, 3+/-0.3, 76+/-5.3, and 4+/-1.4 for NH, PH, NC, and PC treatments, respectively. Overall, the animals that were penned spent more time grazing and less time walking than animals not previously penned for 14 days. Penned animals also vocalized less than non-penned animals during the open field test. The bond sheep formed to the bovines was not affected by cow age. These data suggest that inter-specific bond formation using pen confinement can be accomplished within 14 days, representing a 53% savings in time and associated costs when compared to pen confinement lasting 30 days.

Basic study of entire whole-body PET scanners based on the OpenPET geometry

NASA Astrophysics Data System (ADS)

Yoshida, Eiji; Yamaya, Taiga; Nishikido, Fumihiko; Inadama, Naoko; Murayama, Hideo

2010-09-01

A conventional PET scanner has a 15-25 cm axial field-of-view (FOV) and images a whole body using about six bed positions. An OpenPET geometry can extend the axial FOV with a limited number of detectors. The entire whole-body PET scanner must be able to process a large amount of data effectively. In this work, we study feasibility of the fully 3D entire whole-body PET scanner using the GATE simulation. The OpenPET has 12 block detector rings with the ring diameter of 840 mm and each block detector ring consists of 48 depth-of-interaction (DOI) detectors. The OpenPET has the axial length of 895.95 mm with five parts of 58.95 mm open gaps. The OpenPET has higher single data loss than a conventional PET scanner at grouping circuits. NECR of the OpenPET decreases by single data loss. But single data loss is mitigated by separating the axially arranged detector into two parts. Also, multiple coincidences are found to be important for the entire whole-body PET scanner. The entire whole-body PET scanner with the OpenPET geometry promises to provide a large axial FOV with the open space and to have sufficient performance values. But single data loss at the grouping circuits and multiple coincidences are limited to the peak noise equivalent count rate (NECR) for the entire whole-body PET scanner.

Effects of the deletion of early region 4 (E4) open reading frame 1 (orf1), orf1-2, orf1-3 and orf1-4 on virus-host cell interaction, transgene expression, and immunogenicity of replicating adenovirus HIV vaccine vectors.

PubMed

Thomas, Michael A; Song, Rui; Demberg, Thorsten; Vargas-Inchaustegui, Diego A; Venzon, David; Robert-Guroff, Marjorie

2013-01-01

The global health burden engendered by human immunodeficiency virus (HIV)-induced acquired immunodeficiency syndrome (AIDS) is a sobering reminder of the pressing need for a preventative vaccine. In non-human primate models replicating adenovirus (Ad)-HIV/SIV recombinant vaccine vectors have been shown to stimulate potent immune responses culminating in protection against challenge exposures. Nonetheless, an increase in the transgene carrying capacity of these Ad vectors, currently limited to approximately 3000 base pairs, would greatly enhance their utility. Using a replicating, E3-deleted Ad type 5 host range mutant (Ad5 hr) encoding full-length single-chain HIVBaLgp120 linked to the D1 and D2 domains of rhesus macaque CD4 (rhFLSC) we systematically deleted the genes encoding early region 4 open reading frame 1 (E4orf1) through E4orf4. All the Ad-rhFLSC vectors produced similar levels of viral progeny. Cell cycle analysis of infected human and monkey cells revealed no differences in virus-host interaction. The parental and E4-deleted viruses expressed comparable levels of the transgene with kinetics similar to Ad late proteins. Similar levels of cellular immune responses and transgene-specific antibodies were elicited in vaccinated mice. However, differences in recognition of Ad proteins and induced antibody subtypes were observed, suggesting that the E4 gene products might modulate antibody responses by as yet unknown mechanisms. In short, we have improved the transgene carrying capacity by one thousand base pairs while preserving the replicability, levels of transgene expression, and immunogenicity critical to these vaccine vectors. This additional space allows for flexibility in vaccine design that could not be obtained with the current vector and as such should facilitate the goal of improving vaccine efficacy. To the best of our knowledge, this is the first report describing the effects of these E4 deletions on transgene expression and immunogenicity in a replicating Ad vector.

Effects of the Deletion of Early Region 4 (E4) Open Reading Frame 1 (orf1), orf1-2, orf1-3 and orf1-4 on Virus-Host Cell Interaction, Transgene Expression, and Immunogenicity of Replicating Adenovirus HIV Vaccine Vectors

PubMed Central

Thomas, Michael A.; Song, Rui; Demberg, Thorsten; Vargas-Inchaustegui, Diego A.; Venzon, David; Robert-Guroff, Marjorie

2013-01-01

The global health burden engendered by human immunodeficiency virus (HIV)-induced acquired immunodeficiency syndrome (AIDS) is a sobering reminder of the pressing need for a preventative vaccine. In non-human primate models replicating adenovirus (Ad)-HIV/SIV recombinant vaccine vectors have been shown to stimulate potent immune responses culminating in protection against challenge exposures. Nonetheless, an increase in the transgene carrying capacity of these Ad vectors, currently limited to approximately 3000 base pairs, would greatly enhance their utility. Using a replicating, E3-deleted Ad type 5 host range mutant (Ad5 hr) encoding full-length single-chain HIVBaLgp120 linked to the D1 and D2 domains of rhesus macaque CD4 (rhFLSC) we systematically deleted the genes encoding early region 4 open reading frame 1 (E4orf1) through E4orf4. All the Ad-rhFLSC vectors produced similar levels of viral progeny. Cell cycle analysis of infected human and monkey cells revealed no differences in virus-host interaction. The parental and E4-deleted viruses expressed comparable levels of the transgene with kinetics similar to Ad late proteins. Similar levels of cellular immune responses and transgene-specific antibodies were elicited in vaccinated mice. However, differences in recognition of Ad proteins and induced antibody subtypes were observed, suggesting that the E4 gene products might modulate antibody responses by as yet unknown mechanisms. In short, we have improved the transgene carrying capacity by one thousand base pairs while preserving the replicability, levels of transgene expression, and immunogenicity critical to these vaccine vectors. This additional space allows for flexibility in vaccine design that could not be obtained with the current vector and as such should facilitate the goal of improving vaccine efficacy. To the best of our knowledge, this is the first report describing the effects of these E4 deletions on transgene expression and immunogenicity in a replicating Ad vector. PMID:24143187

Klein tunneling phenomenon with pair creation process

NASA Astrophysics Data System (ADS)

Wu, G. Z.; Zhou, C. T.; Fu, L. B.

2018-01-01

In this paper, we study the Klein tunneling phenomenon with electron-positron pair creation process. Pairs can be created from the vacuum by a supercritical single-well potential (for electrons). In the time region, the time-dependent growth pattern of the created pairs can be characterized by four distinct regimes which can be considered as four different statuses of the single well. We find that if positrons penetrate the single well by Klein tunneling in different statuses, the total number of the tunneling positrons will be different. If Klein tunneling begins at the initial stage of the first status i.e. when the sing well is empty, the tunneling process and the total number of tunneling positrons are similar to the traditional Klein tunneling case without considering the pair creation process. As the tunneling begins later, the total tunneling positron number increases. The number will finally settle to an asymptotic value when the tunneling begins later than the settling-down time t s of the single well which has been defined in this paper.

Using Single Colors and Color Pairs to Communicate Basic Tastes II: Foreground-Background Color Combinations.

PubMed

Woods, Andy T; Marmolejo-Ramos, Fernando; Velasco, Carlos; Spence, Charles

2016-01-01

People associate basic tastes (e.g., sweet, sour, bitter, and salty) with specific colors (e.g., pink or red, green or yellow, black or purple, and white or blue). In the present study, we investigated whether a color bordered by another color (either the same or different) would give rise to stronger taste associations relative to a single patch of color. We replicate previous findings, highlighting the existence of a robust crossmodal correspondence between individual colors and basic tastes. On occasion, color pairs were found to communicate taste expectations more consistently than were single color patches. Furthermore, and in contrast to a recent study in which the color pairs were shown side-by-side, participants took no longer to match the color pairs with tastes than the single colors (they had taken twice as long to respond to the color pairs in the previous study). Possible reasons for these results are discussed, and potential applications for the results, and for the testing methodology developed, are outlined.

Using Single Colors and Color Pairs to Communicate Basic Tastes II: Foreground–Background Color Combinations

PubMed Central

Marmolejo-Ramos, Fernando; Velasco, Carlos; Spence, Charles

2016-01-01

People associate basic tastes (e.g., sweet, sour, bitter, and salty) with specific colors (e.g., pink or red, green or yellow, black or purple, and white or blue). In the present study, we investigated whether a color bordered by another color (either the same or different) would give rise to stronger taste associations relative to a single patch of color. We replicate previous findings, highlighting the existence of a robust crossmodal correspondence between individual colors and basic tastes. On occasion, color pairs were found to communicate taste expectations more consistently than were single color patches. Furthermore, and in contrast to a recent study in which the color pairs were shown side-by-side, participants took no longer to match the color pairs with tastes than the single colors (they had taken twice as long to respond to the color pairs in the previous study). Possible reasons for these results are discussed, and potential applications for the results, and for the testing methodology developed, are outlined. PMID:27708752

Charge recombination in organic photovoltaic devices with high open-circuit voltages.

PubMed

Westenhoff, Sebastian; Howard, Ian A; Hodgkiss, Justin M; Kirov, Kiril R; Bronstein, Hugo A; Williams, Charlotte K; Greenham, Neil C; Friend, Richard H

2008-10-15

A detailed charge recombination mechanism is presented for organic photovoltaic devices with a high open-circuit voltage. In a binary blend comprised of polyfluorene copolymers, the performance-limiting process is found to be the efficient recombination of tightly bound charge pairs into neutral triplet excitons. We arrive at this conclusion using optical transient absorption (TA) spectroscopy with visible and IR probes and over seven decades of time resolution. By resolving the polarization of the TA signal, we track the movement of polaronic states generated at the heterojunction not only in time but also in space. It is found that the photogenerated charge pairs are remarkably immobile at the heterojunction during their lifetime. The charge pairs are shown to be subject to efficient intersystem crossing and terminally recombine into F8BT triplet excitons within approximately 40 ns. Long-range charge separation competes rather unfavorably with intersystem crossing--75% of all charge pairs decay into triplet excitons. Triplet exciton states are thermodynamically accessible in polymer solar cells with high open circuit voltage, and we therefore suggest this loss mechanism to be general. We discuss guidelines for the design of the next generation of organic photovoltaic materials where separating the metastable interfacial charge pairs within approximately 40 ns is paramount.

Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing.

PubMed

Nakano, Shu-ichi; Sugimoto, Naoki

2014-08-05

The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G • C > D • T ≈ I • C > A • T > G • T > I • T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

Substituent effects on rates and torquoselectivities of electrocyclic ring-openings of N-substituted 2-azetines.

PubMed

Lopez, Steven A; Houk, K N

2014-07-03

Transition structures for the conrotatory electrocyclic ring-opening reactions of N-substituted 2-azetines were computed with the density functional M06-2X/6-31+G(d,p). A wide range of substituents from π acceptors (e.g., CHO, CN) to π donors (NMe2, OMe) was explored. Acceptor substituents delocalize the nitrogen lone pair and stabilize the reactant state of 2-azetines, while donors destabilize the 2-azetine reactant state. The conrotatory ring-opening is torquoselective, and the transition state for the outward rotation of the N-substituent and inward rotation of the nitrogen lone pair is preferred. This transition structure is stabilized by an interaction between the nitrogen lone pair and the vacant π* orbital. The activation free energies are linearly related to the reaction free energies and the Taft σR(0) parameter.

Ordering states with various coherence measures

NASA Astrophysics Data System (ADS)

Yang, Long-Mei; Chen, Bin; Fei, Shao-Ming; Wang, Zhi-Xi

2018-04-01

Quantum coherence is one of the most significant theories in quantum physics. Ordering states with various coherence measures is an intriguing task in quantification theory of coherence. In this paper, we study this problem by use of four important coherence measures—the l_1 norm of coherence, the relative entropy of coherence, the geometric measure of coherence and the modified trace distance measure of coherence. We show that each pair of these measures give a different ordering of qudit states when d≥3. However, for single-qubit states, the l_1 norm of coherence and the geometric coherence provide the same ordering. We also show that the relative entropy of coherence and the geometric coherence give a different ordering for single-qubit states. Then we partially answer the open question proposed in Liu et al. (Quantum Inf Process 15:4189, 2016) whether all the coherence measures give a different ordering of states.

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo.

PubMed

Schnier, P D; Klassen, J S; Strittmatter, E F; Williams, E R

1998-09-23

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7)*T(7) (3-), A(7)*A(7) (3-), T(7)*T(7) (3-), and A(7)*C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7)*T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7)*A(7) (3-) and T(7)*T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7)*A(7) (3-) and A(7)*C(7) (3-) but not for A(7)*T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7)*T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.

THE VALIDITY OF USING ROC SOFTWARE FOR ANALYSING VISUAL GRADING CHARACTERISTICS DATA: AN INVESTIGATION BASED ON THE NOVEL SOFTWARE VGC ANALYZER.

PubMed

Hansson, Jonny; Månsson, Lars Gunnar; Båth, Magnus

2016-06-01

The purpose of the present work was to investigate the validity of using single-reader-adapted receiver operating characteristics (ROC) software for analysis of visual grading characteristics (VGC) data. VGC data from four published VGC studies on optimisation of X-ray examinations, previously analysed using ROCFIT, were reanalysed using a recently developed software dedicated to VGC analysis (VGC Analyzer), and the outcomes [the mean and 95 % confidence interval (CI) of the area under the VGC curve (AUCVGC) and the p-value] were compared. The studies included both paired and non-paired data and were reanalysed both for the fixed-reader and the random-reader situations. The results showed good agreement between the softwares for the mean AUCVGC For non-paired data, wider CIs were obtained with VGC Analyzer than previously reported, whereas for paired data, the previously reported CIs were similar or even broader. Similar observations were made for the p-values. The results indicate that the use of single-reader-adapted ROC software such as ROCFIT for analysing non-paired VGC data may lead to an increased risk of committing Type I errors, especially in the random-reader situation. On the other hand, the use of ROC software for analysis of paired VGC data may lead to an increased risk of committing Type II errors, especially in the fixed-reader situation. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Pairing from strong repulsion in triangular lattice Hubbard model

NASA Astrophysics Data System (ADS)

Zhang, Shang-Shun; Zhu, Wei; Batista, Cristian D.

2018-04-01

We propose a pairing mechanism between holes in the dilute limit of doped frustrated Mott insulators. Hole pairing arises from a hole-hole-magnon three-body bound state. This pairing mechanism has its roots on single-hole kinetic energy frustration, which favors antiferromagnetic (AFM) correlations around the hole. We demonstrate that the AFM polaron (hole-magnon bound state) produced by a single hole propagating on a field-induced polarized background is strong enough to bind a second hole. The effective interaction between these three-body bound states is repulsive, implying that this pairing mechanism is relevant for superconductivity.

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

PubMed Central

Glocke, Isabelle; Meyer, Matthias

2017-01-01

The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with single-strand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. The combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments. Our work may thus open the door for genetic analyses on even older material. PMID:28408382

Self-assembling, cystine-derived, fused nanotubes based on spirane architecture: design, synthesis, and crystal structure of cystinospiranes.

PubMed

Ranganathan, D; Samant, M P; Karle, I L

2001-06-20

A novel family of cystine-based spirobicyclic peptides (cystinospiranes) has been synthesized by a single-step procedure involving condensation of pentaerythritol-derived tetrachloride with either the simple L-cystine dimethyl ester or its C,C'-extended bispeptides leading to a variety of 19-membered spirobicyclic peptides or its N,N'-extended bispeptides affording the ring-expanded 25-membered cystinospiranes. The design is flexible with respect to the ring size that can be adjusted depending upon the length of the N,N'-extended cystine bispeptide, and the choice of an amino acid, as illustrated here with the preparation of a large number of cystinospiranes containing a wide variety of amino acids. X-ray crystal structure of the parent spirane (5a) revealed nanotube formation by vertical stacking of relatively flat spirobicyclic molecules through contiguous NH- - -O==C hydrogen bonding. The fused pair of parallel nanotubes is open-ended, hollow, and extends to infinity. Crystallographic parameters are the following: C(33)H(52)N(4)O(16)S(4), space group C2, a = 42.181(3) A, b = 5.1165(7) A, c = 11.8687(9) A, beta = 106.23(1) degrees.

pyBSM: A Python package for modeling imaging systems

NASA Astrophysics Data System (ADS)

LeMaster, Daniel A.; Eismann, Michael T.

2017-05-01

There are components that are common to all electro-optical and infrared imaging system performance models. The purpose of the Python Based Sensor Model (pyBSM) is to provide open source access to these functions for other researchers to build upon. Specifically, pyBSM implements much of the capability found in the ERIM Image Based Sensor Model (IBSM) V2.0 along with some improvements. The paper also includes two use-case examples. First, performance of an airborne imaging system is modeled using the General Image Quality Equation (GIQE). The results are then decomposed into factors affecting noise and resolution. Second, pyBSM is paired with openCV to evaluate performance of an algorithm used to detect objects in an image.

Finite element analysis of the axial stiffness of a ball screw

NASA Astrophysics Data System (ADS)

Zhou, L.-X.; Li, P.-Y.

2018-06-01

The ball screw was developed for high speed and high precision operation; therefore, increasingly greater demands have been placed on the stiffness of the ball screw. Firstly, ANSYS software was used to compare the axial stiffness of a single-nut and single-arc ball screw and a single-nut and double-arc ball screw when the spiral angle is not considered. On this basis, the model of a single-nut ball screw was established taking into consideration the spiral lead angle, and then the variations in displacement and stiffness when the ball screw pair was subjected to an axial force were determined. The axial contact stiffness of the double-nut ball screw pair, subject to a pre-tightening force, was analyzed, according to the above-mentioned steps. The simulation results demonstrated that under the same working conditions, the stiffness of the double-arc ball screw was larger by between 5∼100 N/um than that of the single-arc ball screw. The spiral lead angle increased the axial stiffness of the ball screw pair, and the axial stiffness of the double-nut ball screw pair subject to a pre-tightening force was larger by between 790∼1360 N/um than that of the axial stiffness of the single-nut ball screw pair.

Photon pair source via two coupling single quantum emitters

NASA Astrophysics Data System (ADS)

Peng, Yong-Gang; Zheng, Yu-Jun

2015-10-01

We study the two coupling two-level single molecules driven by an external field as a photon pair source. The probability of emitting two photons, P2, is employed to describe the photon pair source quality in a short time, and the correlation coefficient RAB is employed to describe the photon pair source quality in a long time limit. The results demonstrate that the coupling single quantum emitters can be considered as a stable photon pair source. Project supported by the National Natural Science Foundation of China (Grand Nos. 91021009, 21073110, and 11374191), the Natural Science Foundation of Shandong Province, China (Grant No. ZR2013AQ020), the Postdoctoral Science Foundation of China (Grant No. 2013M531584), the Doctoral Program of Higher Education of China (Grant Nos. 20130131110005 and 20130131120006), and the Taishan Scholarship Project of Shandong Province, China.

Using Single Colors and Color Pairs to Communicate Basic Tastes

PubMed Central

Spence, Charles

2016-01-01

Recently, it has been demonstrated that people associate each of the basic tastes (e.g., sweet, sour, bitter, and salty) with specific colors (e.g., red, green, black, and white). In the present study, we investigated whether pairs of colors (both associated with a particular taste or taste word) would give rise to stronger associations relative to pairs of colors that were associated with different tastes. We replicate the findings of previous studies highlighting the existence of a robust crossmodal correspondence between individual colors and basic tastes. However, while there was evidence that pairs of colors could indeed communicate taste information more consistently than single colors, our participants took more than twice as long to match the color pairs with tastes than the single colors. Possible reasons for these results are discussed. PMID:27698979

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.

PubMed

Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy

NASA Astrophysics Data System (ADS)

Barabas, Federico M.; Masullo, Luciano A.; Stefani, Fernando D.

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

An ex vivo mechanical evaluation of single versus double semitubular plate fixation of a transverse distal-third scapular osteotomy in the dog.

PubMed

Mair, Jacqueline J; Belkoff, Stephen M; Boudrieau, Randy J

2003-01-01

To compare single versus double semitubular plate fixation for scapular body fractures. Ex vivo mechanical study. Eighteen paired cadaveric canine scapulae. Transverse scapular body osteotomies were created in the distal third of 18 pairs of scapulae. One scapula of each pair was repaired with a single plate, whereas the contralateral scapula was repaired with 2 plates. Initial strength and stiffness of the constructs were measured in 10 pairs of scapulae. Eight pairs of scapulae underwent cyclic loading and then were subjected to failure testing. Double-plate fixation was significantly stronger (3,899 +/- 632 N) but not stiffer (614 +/- 130 N/mm) than the single-plate fixation (3,238 +/- 935 N and 537 +/- 202 N/mm, respectively). Cyclic loading variables were not significantly different between the 2 methods of fixation. After cyclic loading, double-plate fixation was significantly stronger (2,916 +/- 618 N) than single-plate fixation (2,347 +/- 495 N). There was no significant difference (P =.11) in stiffness between double- versus single-plate fixations: 734 +/- 247 N/mm and 595 +/- 139 N/mm, respectively. Double-plate fixation was generally stronger and stiffer than single-plate fixation. Because all constructs failed at loads that greatly exceeded those estimated to occur clinically, any difference between the 2 methods of fixation probably is not clinically relevant. Single-plate fixation may be of sufficient strength for fixation of scapular body fractures. Copyright 2003 by The American College of Veterinary Surgeons

Schizophrenia: A genome scan targets chromosomes 3p and 8p as potential sites of susceptibility genes

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

Pulver, A.E.; Lasseter, V.K.; Kasch, L.

Using a systematically ascertained sample of 57 families, each having 2 or more members with a consensus diagnosis of schizophrenia (DSM-III-R criteria), we have carried out linkage studies of 520 loci, covering approximately 70% of the genome for susceptibility loci for schizophrenia. A two-stage strategy based on lod score thresholds from simulation studies of our sample identified regions for further exploration. In each region, a dense map of highly informative dinucleotide repeat polymorphisms (heterozygosity greater than .70) was analyzed using dominant, recessive, and {open_quotes}affected only{close_quotes} models and nonparametric sib pair identity-by-descent methods. For one region, 8p22-p21, affected sib-pair analyses gavemore » a P value = .0001, corresponding to a lod score approximately equal to 3.00. For 8p22-p21, the maximum two-point lod score occurred using the {open_quotes}affected only{close_quotes} recessive model (Z{sub max} = 2.35; {theta}{sub M} = {theta}{sub F}); allowing for a constant sex difference in recombination fractions found in reference pedigrees, Z{sub max} = 2.78 ({theta}{sub M}/{theta}{sub F} = 3). For a second region, 3p26-p24, the maximum two-point lod score was 2.34 ({open_quotes}affected only{close_quotes} dominant model), and the affected sib-pair P value was .01. These two regions are worthy of further exploration as potential sites of susceptibility genes for schizophrenia. 59 refs., 2 figs., 4 tabs.« less

Separated-pair independent particle model and the generalized Brillouin theorem: ab initio calculations on the dissociation of polyatomic molecules

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

Sundberg, Kenneth Randall

1976-01-01

A method is developed to optimize the separated-pair independent particle (SPIP) wave function; it is a special case of the separated-pair theory obtained by using two-term natural expansions of the geminals. The orbitals are optimized by a theory based on the generalized Brillouin theorem and iterative configuration interaction (CI) calculations in the space of the SPIP function and its single excitations. The geminal expansion coefficients are optimized by serial 2 x 2 CI calculations. Formulas are derived for the matrix elements. An algorithm to implement the method is presented, and the work needed to evaluate the molecular integrals is discussed.

Personality Homophily and Geographic Distance in Facebook.

PubMed

Noë, Nyala; Whitaker, Roger M; Allen, Stuart M

2018-05-24

Personality homophily remains an understudied aspect of social networks, with the traditional focus concerning sociodemographic variables as the basis for assortativity, rather than psychological dispositions. We consider the effect of personality homophily on one of the biggest constraints to human social networks: geographic distance. We use the Big five model of personality to make predictions for each of the five facets: Openness to experience, Conscientiousness, Extraversion, Agreeableness, and Neuroticism. Using a network of 313,669 Facebook users, we investigate the difference in geographic distance between homophilous pairs, in which both users scored similarly on a particular facet, and mixed pairs. In accordance with our hypotheses, we find that pairs of open and conscientious users are geographically further apart than mixed pairs. Pairs of extraverts, on the other hand, tend to be geographically closer together. We find mixed results for the Neuroticism facet, and no significant effects for the Agreeableness facet. The results are discussed in the context of personality homophily and the impact of geographic distance on social connections.

Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths

PubMed Central

Gül, O. Tolga; Pugliese, Kaitlin M.; Choi, Yongki; Sims, Patrick C.; Pan, Deng; Rajapakse, Arith J.; Weiss, Gregory A.; Collins, Philip G.

2016-01-01

As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures. PMID:27348011

Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths.

PubMed

Gül, O Tolga; Pugliese, Kaitlin M; Choi, Yongki; Sims, Patrick C; Pan, Deng; Rajapakse, Arith J; Weiss, Gregory A; Collins, Philip G

2016-06-24

As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein's activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF's base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.

A sensitivity analysis for missing outcomes due to truncation by death under the matched-pairs design.

PubMed

Imai, Kosuke; Jiang, Zhichao

2018-04-29

The matched-pairs design enables researchers to efficiently infer causal effects from randomized experiments. In this paper, we exploit the key feature of the matched-pairs design and develop a sensitivity analysis for missing outcomes due to truncation by death, in which the outcomes of interest (e.g., quality of life measures) are not even well defined for some units (e.g., deceased patients). Our key idea is that if 2 nearly identical observations are paired prior to the randomization of the treatment, the missingness of one unit's outcome is informative about the potential missingness of the other unit's outcome under an alternative treatment condition. We consider the average treatment effect among always-observed pairs (ATOP) whose units exhibit no missing outcome regardless of their treatment status. The naive estimator based on available pairs is unbiased for the ATOP if 2 units of the same pair are identical in terms of their missingness patterns. The proposed sensitivity analysis characterizes how the bounds of the ATOP widen as the degree of the within-pair similarity decreases. We further extend the methodology to the matched-pairs design in observational studies. Our simulation studies show that informative bounds can be obtained under some scenarios when the proportion of missing data is not too large. The proposed methodology is also applied to the randomized evaluation of the Mexican universal health insurance program. An open-source software package is available for implementing the proposed research. Copyright © 2018 John Wiley & Sons, Ltd.

OpenSimulator Interoperability with DRDC Simulation Tools: Compatibility Study

DTIC Science & Technology

2014-09-01

into two components: (1) backend data services consisting of user accounts, login service, assets, and inventory; and (2) the simulator server which...components are combined into a single OpenSimulator process. In grid mode, the two components are separated, placing the backend services into a ROBUST... mobile devices. Potential points of compatibility between Unity and OpenSimulator include: a Unity-based desktop computer OpenSimulator viewer; a

Effective fragment potential study of the interaction of DNA bases.

PubMed

Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V

2011-10-20

Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.

Water Detection Based on Color Variation

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.

2012-01-01

This software has been designed to detect water bodies that are out in the open on cross-country terrain at close range (out to 30 meters), using imagery acquired from a stereo pair of color cameras mounted on a terrestrial, unmanned ground vehicle (UGV). This detector exploits the fact that the color variation across water bodies is generally larger and more uniform than that of other naturally occurring types of terrain, such as soil and vegetation. Non-traversable water bodies, such as large puddles, ponds, and lakes, are detected based on color variation, image intensity variance, image intensity gradient, size, and shape. At ranges beyond 20 meters, water bodies out in the open can be indirectly detected by detecting reflections of the sky below the horizon in color imagery. But at closer range, the color coming out of a water body dominates sky reflections, and the water cue from sky reflections is of marginal use. Since there may be times during UGV autonomous navigation when a water body does not come into a perception system s field of view until it is at close range, the ability to detect water bodies at close range is critical. Factors that influence the perceived color of a water body at close range are the amount and type of sediment in the water, the water s depth, and the angle of incidence to the water body. Developing a single model of the mixture ratio of light reflected off the water surface (to the camera) to light coming out of the water body (to the camera) for all water bodies would be fairly difficult. Instead, this software detects close water bodies based on local terrain features and the natural, uniform change in color that occurs across the surface from the leading edge to the trailing edge.

Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

NASA Technical Reports Server (NTRS)

Urakawa, Hidetoshi; Noble, Peter A.; El Fantroussi, Said; Kelly, John J.; Stahl, David A.

2002-01-01

The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Satellite-based quantum communication terminal employing state-of-the-art technology

NASA Astrophysics Data System (ADS)

Pfennigbauer, Martin; Aspelmeyer, Markus; Leeb, Walter R.; Baister, Guy; Dreischer, Thomas; Jennewein, Thomas; Neckamm, Gregor; Perdigues, Josep M.; Weinfurter, Harald; Zeilinger, Anton

2005-09-01

Feature Issue on Optical Wireless Communications (OWC) We investigate the design and the accommodation of a quantum communication transceiver in an existing classical optical communication terminal on board a satellite. Operation from a low earth orbit (LEO) platform (e.g., the International Space Station) would allow transmission of single photons and pairs of entangled photons to ground stations and hence permit quantum communication applications such as quantum cryptography on a global scale. Integration of a source generating entangled photon pairs and single-photon detection into existing optical terminal designs is feasible. Even more, major subunits of the classical terminals such as those for pointing, acquisition, and tracking as well as those providing the required electronic, thermal, and structural backbone can be adapted so as to meet the quantum communication terminal needs.

Enhanced Security and Pairing-free Handover Authentication Scheme for Mobile Wireless Networks

NASA Astrophysics Data System (ADS)

Chen, Rui; Shu, Guangqiang; Chen, Peng; Zhang, Lijun

2017-10-01

With the widely deployment of mobile wireless networks, we aim to propose a secure and seamless handover authentication scheme that allows users to roam freely in wireless networks without worrying about security and privacy issues. Given the open characteristic of wireless networks, safety and efficiency should be considered seriously. Several previous protocols are designed based on a bilinear pairing mapping, which is time-consuming and inefficient work, as well as unsuitable for practical situations. To address these issues, we designed a new pairing-free handover authentication scheme for mobile wireless networks. This scheme is an effective improvement of the protocol by Xu et al., which is suffer from the mobile node impersonation attack. Security analysis and simulation experiment indicate that the proposed protocol has many excellent security properties when compared with other recent similar handover schemes, such as mutual authentication and resistance to known network threats, as well as requiring lower computation and communication cost.

Einstein-Podolsky-Rosen paradox in single pairs of images.

PubMed

Lantz, Eric; Denis, Séverine; Moreau, Paul-Antoine; Devaux, Fabrice

2015-10-05

Spatially entangled twin photons provide a test of the Einstein-Podolsky-Rosen (EPR) paradox in its original form of position (image plane) versus impulsion (Fourier plane). We show that recording a single pair of images in each plane is sufficient to safely demonstrate an EPR paradox. On each pair of images, we have retrieved the fluctuations by subtracting the fitted deterministic intensity shape and then have obtained an intercorrelation peak with a sufficient signal to noise ratio to safely distinguish this peak from random fluctuations. A 95% confidence interval has been determined, confirming a high degree of paradox whatever the considered single pairs. Last, we have verified that the value of the variance of the difference between twin images is always below the quantum (poissonian) limit, in order to ensure the particle character of the demonstration. Our demonstration shows that a single image pattern can reveal the quantum and non-local behavior of light.

Projector-Camera Systems for Immersive Training

DTIC Science & Technology

2006-01-01

average to a sequence of 100 captured distortion corrected images. The OpenCV library [ OpenCV ] was used for camera calibration. To correct for...rendering application [Treskunov, Pair, and Swartout, 2004]. It was transposed to take into account different matrix conventions between OpenCV and...Screen Imperfections. Proc. Workshop on Projector-Camera Systems (PROCAMS), Nice, France, IEEE. OpenCV : Open Source Computer Vision. [Available

Variability of hydrologic regimes and morphology in constructed open-ditch channels

USGS Publications Warehouse

Strock, J.S.; Magner, J.A.; Richardson, W.B.; Sadowsky, M.J.; Sands, G.R.; Venterea, R.T.; ,

2004-01-01

Open-ditch ecosystems are potential transporters of considerable loads of nutrients, sediment, pathogens and pesticides from direct inflow from agricultural land to small streams and larger rivers. Our objective was to compare hydrology and channel morphology between two experimental open-ditch channels. An open-ditch research facility incorporating a paired design was constructed during 2002 near Lamberton, MN. A200-m reach of existing drainage channel was converted into a system of four parallel channels. The facility was equipped with water level control devices and instrumentation for flow monitoring and water sample collection on upstream and downstream ends of the system. Hydrographs from simulated flow during year one indicated that paired open-ditch channels responded similarly to changes in inflow. Variability in hydrologic response between open-ditches was attributed to differences in open-ditch channel bottom elevation and vegetation density. No chemical, biological, or atmospheric measurements were made during 2003. Potential future benefits of this research include improved biological diversity and integrity of open-ditch ecosystems, reduce flood peaks and increased flow during critical low-flow periods, improved and more efficient nitrogen retention within the open-ditch ecosystem, and decreased maintenance cost associated with reduced frequency of open-ditch maintenance.

Experiment and modeling of paired effect on evacuation from a three-dimensional space

NASA Astrophysics Data System (ADS)

Jun, Hu; Huijun, Sun; Juan, Wei; Xiaodan, Chen; Lei, You; Musong, Gu

2014-10-01

A novel three-dimensional cellular automata evacuation model was proposed based on stairs factor for paired effect and variety velocities in pedestrian evacuation. In the model pedestrians' moving probability of target position at the next moment was defined based on distance profit and repulsive force profit, and evacuation strategy was elaborated in detail through analyzing variety velocities and repulsive phenomenon in moving process. At last, experiments with the simulation platform were conducted to study the relationships of evacuation time, average velocity and pedestrian velocity. The results showed that when the ratio of single pedestrian was higher in the system, the shortest route strategy was good for improving evacuation efficiency; in turn, if ratio of paired pedestrians was higher, it is good for improving evacuation efficiency to adopt strategy that avoided conflicts, and priority should be given to scattered evacuation.

A Novel Optimal Joint Resource Allocation Method in Cooperative Multicarrier Networks: Theory and Practice

PubMed Central

Gao, Yuan; Zhou, Weigui; Ao, Hong; Chu, Jian; Zhou, Quan; Zhou, Bo; Wang, Kang; Li, Yi; Xue, Peng

2016-01-01

With the increasing demands for better transmission speed and robust quality of service (QoS), the capacity constrained backhaul gradually becomes a bottleneck in cooperative wireless networks, e.g., in the Internet of Things (IoT) scenario in joint processing mode of LTE-Advanced Pro. This paper focuses on resource allocation within capacity constrained backhaul in uplink cooperative wireless networks, where two base stations (BSs) equipped with single antennae serve multiple single-antennae users via multi-carrier transmission mode. In this work, we propose a novel cooperative transmission scheme based on compress-and-forward with user pairing to solve the joint mixed integer programming problem. To maximize the system capacity under the limited backhaul, we formulate the joint optimization problem of user sorting, subcarrier mapping and backhaul resource sharing among different pairs (subcarriers for users). A novel robust and efficient centralized algorithm based on alternating optimization strategy and perfect mapping is proposed. Simulations show that our novel method can improve the system capacity significantly under the constraint of the backhaul resource compared with the blind alternatives. PMID:27077865

Putative Nonribosomal Peptide Synthetase and Cytochrome P450 Genes Responsible for Tentoxin Biosynthesis in Alternaria alternata ZJ33

PubMed Central

Li, You-Hai; Han, Wen-Jin; Gui, Xi-Wu; Wei, Tao; Tang, Shuang-Yan; Jin, Jian-Ming

2016-01-01

Tentoxin, a cyclic tetrapeptide produced by several Alternaria species, inhibits the F1-ATPase activity of chloroplasts, resulting in chlorosis in sensitive plants. In this study, we report two clustered genes, encoding a putative non-ribosome peptide synthetase (NRPS) TES and a cytochrome P450 protein TES1, that are required for tentoxin biosynthesis in Alternaria alternata strain ZJ33, which was isolated from blighted leaves of Eupatorium adenophorum. Using a pair of primers designed according to the consensus sequences of the adenylation domain of NRPSs, two fragments containing putative adenylation domains were amplified from A. alternata ZJ33, and subsequent PCR analyses demonstrated that these fragments belonged to the same NRPS coding sequence. With no introns, TES consists of a single 15,486 base pair open reading frame encoding a predicted 5161 amino acid protein. Meanwhile, the TES1 gene is predicted to contain five introns and encode a 506 amino acid protein. The TES protein is predicted to be comprised of four peptide synthase modules with two additional N-methylation domains, and the number and arrangement of the modules in TES were consistent with the number and arrangement of the amino acid residues of tentoxin, respectively. Notably, both TES and TES1 null mutants generated via homologous recombination failed to produce tentoxin. This study provides the first evidence concerning the biosynthesis of tentoxin in A. alternata. PMID:27490569

A Frameshift Mutation in the Cubilin Gene (CUBN) in Border Collies with Imerslund-Gräsbeck Syndrome (Selective Cobalamin Malabsorption)

PubMed Central

Owczarek-Lipska, Marta; Jagannathan, Vidhya; Drögemüller, Cord; Lutz, Sabina; Glanemann, Barbara

2013-01-01

Imerslund-Gräsbeck syndrome (IGS) or selective cobalamin malabsorption has been described in humans and dogs. IGS occurs in Border Collies and is inherited as a monogenic autosomal recessive trait in this breed. Using 7 IGS cases and 7 non-affected controls we mapped the causative mutation by genome-wide association and homozygosity mapping to a 3.53 Mb interval on chromosome 2. We re-sequenced the genome of one affected dog at ∼10× coverage and detected 17 non-synonymous variants in the critical interval. Two of these non-synonymous variants were in the cubilin gene (CUBN), which is known to play an essential role in cobalamin uptake from the ileum. We tested these two CUBN variants for association with IGS in larger cohorts of dogs and found that only one of them was perfectly associated with the phenotype. This variant, a single base pair deletion (c.8392delC), is predicted to cause a frameshift and premature stop codon in the CUBN gene. The resulting mutant open reading frame is 821 codons shorter than the wildtype open reading frame (p.Q2798Rfs*3). Interestingly, we observed an additional nonsense mutation in the MRC1 gene encoding the mannose receptor, C type 1, which was in perfect linkage disequilibrium with the CUBN frameshift mutation. Based on our genetic data and the known role of CUBN for cobalamin uptake we conclude that the identified CUBN frameshift mutation is most likely causative for IGS in Border Collies. PMID:23613799

Ab initio molecular orbital and density functional studies on the ring-opening reaction of oxetene.

PubMed

Jayaprakash, S; Jeevanandam, Jebakumar; Subramani, K

2014-11-01

Electrocyclic ring opening (ERO) reaction of 2H-Oxete (oxetene) has been carried out computationally in the gas phase and ring opening barrier has been computed. When comparing the ERO reaction of oxetene with the parent hydrocarbon (cyclobutene), the ring opening of cyclobutene is found to exhibit pericyclic behavior while oxetene shows mild pseudopericyclic nature. Computation of the nucleus-independent chemical shift (NICS) of oxetene adds evidence for pseudopericyclic behavior of oxetene. By locking of lone pair of electrons by hydrogen bonding, it is seen that the pseudopericyclic nature of the ring opening of oxetene is converted into a pericyclic one. CASSCF(5,6)/6-311+G** computation was carried out to understand the extent of involvement of lone pair of electrons during the course of the reaction. CR-CCSD(T)/6-311+G** computation was performed to assess the energies of the reactant, transition state and the product more accurately.

Porrocaecum parvum n. sp. and P. reticulatum (Linstow, 1899) (Nematoda: Ascaridoidea) from birds in China.

PubMed

Li, Liang; Guo, Yan-Ning; Zhang, Lu-Ping

2015-10-01

Porrocaecum parvum n. sp. is described from the grey-faced buzzard Butastur indicus (Gmelin) (Accipitriformes: Accipitridae) in China. The new species differs from its congeners in having well-developed cervical alae, small interlabia and very short intestinal caecum (0.34 mm long, representing 11.9% of oesophageal length) and in the number and arrangement of the caudal papillae (29 pairs in total, arranged as follows: 21 pairs precloacal, single double pair paracloacal and seven pairs postcloacal) and in the morphology of the male tail. In addition, Porrocaecum reticulatum (Linstow, 1899), collected from the purple heron Ardea purpurea L., the grey heron A. cinerea L. and the little egret Egretta garzetta (L.) (Pelecaniformes: Ardeidae) in China, was also studied using light and, for the first time, scanning electron microscopy. Previously unreported and erroneous morphological features of taxonomic significance are revealed, including the presence of narrow cervical alae, single pair of small, submedial pores and single, short medial ditch on each lip, interlabia with very pointed anterior prolongation, single medio-ventral precloacal papilla on anterior cloacal lip and double paracloacal papillae slightly posterior to cloaca.

High-resolution Spectroscopic Observations of Single Red Giants in Three Open Clusters: NGC 2360, NGC 3680, and NGC 5822

NASA Astrophysics Data System (ADS)

Peña Suárez, V. J.; Sales Silva, J. V.; Katime Santrich, O. J.; Drake, N. A.; Pereira, C. B.

2018-02-01

Single stars in open clusters with known distances are important targets in constraining the nucleosynthesis process since their ages and luminosities are also known. In this work, we analyze a sample of 29 single red giants of the open clusters NGC 2360, NGC 3680, and NGC 5822 using high-resolution spectroscopy. We obtained atmospheric parameters, abundances of the elements C, N, O, Na, Mg, Al, Ca, Si, Ti, Ni, Cr, Y, Zr, La, Ce, and Nd, as well as radial and rotational velocities. We employed the local thermodynamic equilibrium atmospheric models of Kurucz and the spectral analysis code MOOG. Rotational velocities and light-element abundances were derived using spectral synthesis. Based on our analysis of the single red giants in these three open clusters, we could compare, for the first time, their abundance pattern with that of the binary stars of the same clusters previously studied. Our results show that the abundances of both single and binary stars of the open clusters NGC 2360, NGC 3680, and NGC 5822 do not have significant differences. For the elements created by the s-process, we observed that the open clusters NGC 2360, NGC 3680, and NGC 5822 also follow the trend already raised in the literature that young clusters have higher s-process element abundances than older clusters. Finally, we observed that the three clusters of our sample exhibit a trend in the [Y/Mg]-age relation, which may indicate the ability of the [Y/Mg] ratio to be used as a clock for the giants. Based on the observations made with the 2.2 m telescope at the European Southern Observatory (La Silla, Chile) under an agreement with Observatório Nacional and under an agreement between Observatório Nacional and Max-Planck Institute für Astronomie.

Recognition of T·G mismatched base pairs in DNA by stacked imidazole-containing polyamides: surface plasmon resonance and circular dichroism studies

PubMed Central

Lacy, Eilyn R.; Cox, Kari K.; Wilson, W. David; Lee, Moses

2002-01-01

An imidazole-containing polyamide trimer, f-ImImIm, where f is a formamido group, was recently found using NMR methods to recognize T·G mismatched base pairs. In order to characterize in detail the T·G recognition affinity and specificity of imidazole-containing polyamides, f-ImIm, f-ImImIm and f-PyImIm were synthesized. The kinetics and thermodynamics for the polyamides binding to Watson–Crick and mismatched (containing one or two T·G, A·G or G·G mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm binds significantly more strongly to the T·G mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson–Crick base pairs. Compared with the Watson–Crick CCGG sequence, f-ImImIm associates more slowly with DNAs containing T·G mismatches in place of one or two C·G base pairs and, more importantly, the dissociation rate from the T·G oligonucleotides is very slow (small kd). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for T·G mismatches and show that the affinity and specificity increase arise from much lower kd values with the T·G mismatched duplexes. CD titration studies of f-ImImIm complexes with T·G mismatched sequences produce strong induced bands at ∼330 nm with clear isodichroic points, in support of a single minor groove complex. CD DNA bands suggest that the complexes remain in the B conformation. PMID:11937638

Sequetyping: Serotyping Streptococcus pneumoniae by a Single PCR Sequencing Strategy

PubMed Central

Leung, Marcus H.; Bryson, Kevin; Freystatter, Kathrin; Pichon, Bruno; Edwards, Giles; Gillespie, Stephen H.

2012-01-01

The introduction of pneumococcal conjugate vaccines necessitates continued monitoring of circulating strains to assess vaccine efficacy and replacement serotypes. Conventional serological methods are costly, labor-intensive, and prone to misidentification, while current DNA-based methods have limited serotype coverage requiring multiple PCR primers. In this study, a computer algorithm was developed to interrogate the capsulation locus (cps) of vaccine serotypes to locate primer pairs in conserved regions that border variable regions and could differentiate between serotypes. In silico analysis of cps from 92 serotypes indicated that a primer pair spanning the regulatory gene cpsB could putatively amplify 84 serotypes and differentiate 46. This primer set was specific to Streptococcus pneumoniae, with no amplification observed for other species, including S. mitis, S. oralis, and S. pseudopneumoniae. One hundred thirty-eight pneumococcal strains covering 48 serotypes were tested. Of 23 vaccine serotypes included in the study, most (19/22, 86%) were identified correctly at least to the serogroup level, including all of the 13-valent conjugate vaccine and other replacement serotypes. Reproducibility was demonstrated by the correct sequetyping of different strains of a serotype. This novel sequence-based method employing a single PCR primer pair is cost-effective and simple. Furthermore, it has the potential to identify new serotypes that may evolve in the future. PMID:22553238

Shape evolution of 72,74Kr with temperature in covariant density functional theory

NASA Astrophysics Data System (ADS)

Zhang, Wei; Niu, Yi-Fei

2017-09-01

The rich phenomena of deformations in neutron-deficient krypton isotopes, such as shape evolution with neutron number and shape coexistence, have attracted the interest of nuclear physicists for decades. It is interesting to study such shape phenomena using a novel way, e.g. by thermally exciting the nucleus. In this work, we develop the finite temperature covariant density functional theory for axially deformed nuclei with the treatment of pairing correlations by the BCS approach, and apply this approach for the study of shape evolution in 72,74Kr with increasing temperature. For 72Kr, with temperature increasing, the nucleus firstly experiences a relatively quick weakening in oblate deformation at temperature T ˜0.9 MeV, and then changes from oblate to spherical at T ˜2.1 MeV. For 74Kr, its global minimum is at quadrupole deformation β 2 ˜ -0.14 and abruptly changes to spherical at T˜ 1.7 MeV. The proton pairing transition occurs at critical temperature 0.6 MeV following the rule T c=0.6Δ p(0), where Δ p(0) is the proton pairing gap at zero temperature. The signatures of the above pairing transition and shape changes can be found in the specific heat curve. The single-particle level evolutions with temperature are presented. Supported by National Natural Science Foundation of China (11105042, 11305161, 11505157), Open Fund of Key Laboratory of Time and Frequency Primary Standards, CAS, and Support from Henan Administration of Foreign Experts Affairs

Tomato apical stunt viroid - Data Sheet

USDA-ARS?s Scientific Manuscript database

Tomato apical stunt viroid (TASVd), a member of the family Pospiviroidae, genus Pospiviroid, is a small, covalently closed, circular single-stranded, highly base-paired RNA molecule that ranges in size from 362 to 364 nucleotides. Viroids do not encode peptides or proteins, and use host proteins for...

The cDNA sequence of mouse Pgp-1 and homology to human CD44 cell surface antigen and proteoglycan core/link proteins.

PubMed

Wolffe, E J; Gause, W C; Pelfrey, C M; Holland, S M; Steinberg, A D; August, J T

1990-01-05

We describe the isolation and sequencing of a cDNA encoding mouse Pgp-1. An oligonucleotide probe corresponding to the NH2-terminal sequence of the purified protein was synthesized by the polymerase chain reaction and used to screen a mouse macrophage lambda gt11 library. A cDNA clone with an insert of 1.2 kilobases was selected and sequenced. In Northern blot analysis, only cells expressing Pgp-1 contained mRNA species that hybridized with this Pgp-1 cDNA. The nucleotide sequence of the cDNA has a single open reading frame that yields a protein-coding sequence of 1076 base pairs followed by a 132-base pair 3'-untranslated sequence that includes a putative polyadenylation signal but no poly(A) tail. The translated sequence comprises a 13-amino acid signal peptide followed by a polypeptide core of 345 residues corresponding to an Mr of 37,800. Portions of the deduced amino acid sequence were identical to those obtained by amino acid sequence analysis from the purified glycoprotein, confirming that the cDNA encodes Pgp-1. The predicted structure of Pgp-1 includes an NH2-terminal extracellular domain (residues 14-265), a transmembrane domain (residues 266-286), and a cytoplasmic tail (residues 287-358). Portions of the mouse Pgp-1 sequence are highly similar to that of the human CD44 cell surface glycoprotein implicated in cell adhesion. The protein also shows sequence similarity to the proteoglycan tandem repeat sequences found in cartilage link protein and cartilage proteoglycan core protein which are thought to be involved in binding to hyaluronic acid.

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution.

PubMed

Koh, Hye Ran; Roy, Rahul; Sorokina, Maria; Tang, Guo-Qing; Nandakumar, Divya; Patel, Smita S; Ha, Taekjip

2018-05-17

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products. Copyright © 2018 Elsevier Inc. All rights reserved.

A DNA methylation map of human cancer at single base-pair resolution.

PubMed

Vidal, E; Sayols, S; Moran, S; Guillaumet-Adkins, A; Schroeder, M P; Royo, R; Orozco, M; Gut, M; Gut, I; Lopez-Bigas, N; Heyn, H; Esteller, M

2017-10-05

Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling is incomplete across human cancer types. This prompted us to perform genome-wide DNA methylation profiling of 22 samples derived from normal tissues and associated neoplasms, including primary tumors and cancer cell lines. Unlike their invariant normal counterparts, cancer samples exhibited highly variable CpG methylation levels in a large proportion of the genome, involving progressive changes during tumor evolution. The whole-genome sequencing results from selected samples were replicated in a large cohort of 1112 primary tumors of various cancer types using genome-scale DNA methylation analysis. Specifically, we determined DNA hypermethylation of promoters and enhancers regulating tumor-suppressor genes, with potential cancer-driving effects. DNA hypermethylation events showed evidence of positive selection, mutual exclusivity and tissue specificity, suggesting their active participation in neoplastic transformation. Our data highlight the extensive changes in DNA methylation that occur in cancer onset, progression and dissemination.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

Ozone column density determination from direct irradiance measurements in the ultraviolet performed by a four-channel precision filter radiometer.

PubMed

Ingold, T; Mätzler, C; Wehrli, C; Heimo, A; Kämpfer, N; Philipona, R

2001-04-20

Ultraviolet light was measured at four channels (305, 311, 318, and 332 nm) with a precision filter radiometer (UV-PFR) at Arosa, Switzerland (46.78 degrees , 9.68 degrees , 1850 m above sea level), within the instrument trial phase of a cooperative venture of the Swiss Meteorological Institute (MeteoSwiss) and the Physikalisch-Meteorologisches Observatorium Davos/World Radiation Center. We retrieved ozone-column density data from these direct relative irradiance measurements by adapting the Dobson standard method for all possible single-difference wavelength pairs and one double-difference pair (305/311 and 305/318) under conditions of cloud-free sky and of thin clouds (cloud optical depth <2.5 at 500 nm). All UV-PFR retrievals exhibited excellent agreement with those of collocated Dobson and Brewer spectrophotometers for data obtained during two months in 1999. Combining the results of the error analysis and the findings of the validation, we propose to retrieve ozone-column density by using the 305/311 single difference pair and the double-difference pair. Furthermore, combining both retrievals by building the ratio of ozone-column density yields information that is relevant to data quality control. Estimates of the 305/311 pair agree with measurements by the Dobson and Brewer instruments within 1% for both the mean and the standard deviation of the differences. For the double pair these values are in a range up to 1.6%. However, this pair is less sensitive to model errors. The retrieval performance is also consistent with satellite-based data from the Earth Probe Total Ozone Mapping Spectrometer (EP-TOMS) and the Global Ozone Monitoring Experiment instrument (GOME).

Ozone Column Density Determination From Direct Irradiance Measurements in the Ultraviolet Performed by a Four-Channel Precision Filter Radiometer

NASA Astrophysics Data System (ADS)

Ingold, Thomas; Mätzler, Christian; Wehrli, Christoph; Heimo, Alain; Kämpfer, Niklaus; Philipona, Rolf

2001-04-01

Ultraviolet light was measured at four channels (305, 311, 318, and 332 nm) with a precision filter radiometer (UV-PFR) at Arosa, Switzerland (46.78 , 9.68 , 1850 m above sea level), within the instrument trial phase of a cooperative venture of the Swiss Meteorological Institute (MeteoSwiss) and the Physikalisch-Meteorologisches Observatorium Davos /World Radiation Center. We retrieved ozone-column density data from these direct relative irradiance measurements by adapting the Dobson standard method for all possible single-difference wavelength pairs and one double-difference pair (305 /311 and 305 /318) under conditions of cloud-free sky and of thin clouds (cloud optical depth <2.5 at 500 nm). All UV-PFR retrievals exhibited excellent agreement with those of collocated Dobson and Brewer spectrophotometers for data obtained during two months in 1999. Combining the results of the error analysis and the findings of the validation, we propose to retrieve ozone-column density by using the 305 /311 single difference pair and the double-difference pair. Furthermore, combining both retrievals by building the ratio of ozone-column density yields information that is relevant to data quality control. Estimates of the 305 /311 pair agree with measurements by the Dobson and Brewer instruments within 1% for both the mean and the standard deviation of the differences. For the double pair these values are in a range up to 1.6%. However, this pair is less sensitive to model errors. The retrieval performance is also consistent with satellite-based data from the Earth Probe Total Ozone Mapping Spectrometer (EP-TOMS) and the Global Ozone Monitoring Experiment instrument (GOME).

CALUTRON ION SOURCE

DOEpatents

Lofgren, E.J.

1959-02-17

An improvement is described in ion source mechanisms whereby the source structure is better adapted to withstanid the ravages of heat, erosion, and deterioration concomitant with operation of an ion source of the calutron type. A pair of molybdenum plates define the exit opening of the arc chamber and are in thermal contact with the walls of the chamber. These plates are maintained at a reduced temperature by a pair of copper blocks in thermal conducting contact therewith to form subsequent diverging margins for the exit opening.

Selectively Sized Graphene-Based Nanopores for in Situ Single Molecule Sensing

PubMed Central

2015-01-01

The use of nanopore biosensors is set to be extremely important in developing precise single molecule detectors and providing highly sensitive advanced analysis of biological molecules. The precise tailoring of nanopore size is a significant step toward achieving this, as it would allow for a nanopore to be tuned to a corresponding analyte. The work presented here details a methodology for selectively opening nanopores in real-time. The tunable nanopores on a quartz nanopipette platform are fabricated using the electroetching of a graphene-based membrane constructed from individual graphene nanoflakes (ø ∼30 nm). The device design allows for in situ opening of the graphene membrane, from fully closed to fully opened (ø ∼25 nm), a feature that has yet to be reported in the literature. The translocation of DNA is studied as the pore size is varied, allowing for subfeatures of DNA to be detected with slower DNA translocations at smaller pore sizes, and the ability to observe trends as the pore is opened. This approach opens the door to creating a device that can be target to detect specific analytes. PMID:26204996

Targeting the Mevalonate Pathway to Reduce Mortality from Ovarian Cancer

DTIC Science & Technology

2017-12-01

at cis-regulatory elements such as enhancers to facilitate gene transcription. CRISPR /Cas9- mediated ablation of a putative Meis1 enhancer carrying...Tables S4 and S5. 10 Cancer Cell 30, 1–16, July 11, 2016the CRISPR /Cas9-based genomic editing technology. Cas9 and a pair of single guide RNAs (sgRNA... CRISPR /Cas9-mediated deletio sgMeis1, a pair of sgRNAs that target the DMR boundaries. (N) Sequencing of the genomic PCR products from F2/R2 primers shows

Electron Heating and Quasiparticle Tunnelling in Superconducting Charge Qubits

NASA Technical Reports Server (NTRS)

Shaw, M. D.; Bueno, J.; Delsing, P.; Echternach, P. M.

2008-01-01

We have directly measured non-equilibrium quasiparticle tunnelling in the time domain as a function of temperature and RF carrier power for a pair of charge qubits based on the single Cooper-pair box, where the readout is performed with a multiplexed quantum capacitance technique. We have extracted an effective electron temperature for each applied RF power, using the data taken at the lowest power as a reference curve. This data has been fit to a standard T? electron heating model, with a reasonable correspondence with established material parameters.

Ant Lion Optimization algorithm for kidney exchanges.

PubMed

Hamouda, Eslam; El-Metwally, Sara; Tarek, Mayada

2018-01-01

The kidney exchange programs bring new insights in the field of organ transplantation. They make the previously not allowed surgery of incompatible patient-donor pairs easier to be performed on a large scale. Mathematically, the kidney exchange is an optimization problem for the number of possible exchanges among the incompatible pairs in a given pool. Also, the optimization modeling should consider the expected quality-adjusted life of transplant candidates and the shortage of computational and operational hospital resources. In this article, we introduce a bio-inspired stochastic-based Ant Lion Optimization, ALO, algorithm to the kidney exchange space to maximize the number of feasible cycles and chains among the pool pairs. Ant Lion Optimizer-based program achieves comparable kidney exchange results to the deterministic-based approaches like integer programming. Also, ALO outperforms other stochastic-based methods such as Genetic Algorithm in terms of the efficient usage of computational resources and the quantity of resulting exchanges. Ant Lion Optimization algorithm can be adopted easily for on-line exchanges and the integration of weights for hard-to-match patients, which will improve the future decisions of kidney exchange programs. A reference implementation for ALO algorithm for kidney exchanges is written in MATLAB and is GPL licensed. It is available as free open-source software from: https://github.com/SaraEl-Metwally/ALO_algorithm_for_Kidney_Exchanges.

Single-particle spectral density of the unitary Fermi gas: Novel approach based on the operator product expansion, sum rules and the maximum entropy method

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

Gubler, Philipp, E-mail: pgubler@riken.jp; RIKEN Nishina Center, Wako, Saitama 351-0198; Yamamoto, Naoki

2015-05-15

Making use of the operator product expansion, we derive a general class of sum rules for the imaginary part of the single-particle self-energy of the unitary Fermi gas. The sum rules are analyzed numerically with the help of the maximum entropy method, which allows us to extract the single-particle spectral density as a function of both energy and momentum. These spectral densities contain basic information on the properties of the unitary Fermi gas, such as the dispersion relation and the superfluid pairing gap, for which we obtain reasonable agreement with the available results based on quantum Monte-Carlo simulations.

High-power, cladding-pumped all-fiber laser with selective transverse mode generation property.

PubMed

Li, Lei; Wang, Meng; Liu, Tong; Leng, Jinyong; Zhou, Pu; Chen, Jinbao

2017-06-10

We demonstrate, to the best of our knowledge, the first cladding-pumped all-fiber oscillator configuration with selective transverse mode generation based on a mode-selective fiber Bragg grating pair. Operating in the second-order (LP 11 ) mode, maximum output power of 4.2 W is obtained with slope efficiency of about 38%. This is the highest reported output power of single higher-order transverse mode generation in an all-fiber configuration. The intensity distribution profile and spectral evolution have also been investigated in this paper. Our work suggests the potential of realizing higher power with selective transverse mode operation based on a mode-selective fiber Bragg grating pair.

All-optical diffractive/transmissive switch based on coupled cycloidal diffractive waveplates.

PubMed

Serak, Svetlana V; Hakobyan, Rafael S; Nersisyan, Sarik R; Tabiryan, Nelson V; White, Timothy J; Bunning, Timothy J; Steeves, Diane M; Kimball, Brian R

2012-02-27

Pairs of cycloidal diffractive waveplates can be used to doubly diffract or collinearly propagate laser radiation of the appropriate wavelength. The use of a dynamic phase retarder placed in between the pair can be utilized to switch between the two optical states. We present results from the implementation of an azo-based retarder whose optical properties can be modulated using light itself. We show fast and efficient switching between the two states for both CW and single nanosecond laser pulses of green radiation. Contrasts greater than 100:1 were achieved. The temporal response as a function of light intensity is presented and the optical switching is shown to be polarization independent.

A versatile electrostatic trap with open optical access

NASA Astrophysics Data System (ADS)

Li, Sheng-Qiang; Yin, Jian-Ping

2018-04-01

A versatile electrostatic trap with open optical access for cold polar molecules in weak-field-seeking state is proposed in this paper. The trap is composed of a pair of disk electrodes and a hexapole. With the help of a finite element software, the spatial distribution of the electrostatic field is calculated. The results indicate that a three-dimensional closed electrostatic trap is formed. Taking ND3 molecules as an example, the dynamic process of loading and trapping is simulated. The results show that when the velocity of the molecular beam is 10 m/s and the loading time is 0.9964 ms, the maximum loading efficiency reaches 94.25% and the temperature of the trapped molecules reaches about 30.3 mK. A single well can be split into two wells, which is of significant importance to the precision measurement and interference of matter waves. This scheme, in addition, can be further miniaturized to construct one-dimensional, two-dimensional, and three-dimensional spatial electrostatic lattices.

High-Efficiency Plug-and-Play Source of Heralded Single Photons

NASA Astrophysics Data System (ADS)

Montaut, Nicola; Sansoni, Linda; Meyer-Scott, Evan; Ricken, Raimund; Quiring, Viktor; Herrmann, Harald; Silberhorn, Christine

2017-08-01

Reliable generation of single photons is of key importance for fundamental physical experiments and to demonstrate quantum protocols. Waveguide-based photon-pair sources have shown great promise in this regard due to their large spectral tunability, high generation rates, and long temporal coherence of the photon wave packet. However, integrating such sources with fiber-optic networks often results in a strong degradation of performance. We answer this challenge by presenting an alignment-free source of photon pairs in the telecommunications band that maintains heralding efficiency >50 % even after fiber pigtailing, photon separation, and pump suppression. The source combines this outstanding performance in heralding efficiency with a compact, stable, and easy-to-use "plug-and-play" package: one simply connects a laser to the input and detectors to the output, and the source is ready to use. This high performance can be achieved even outside the lab without the need for alignment which makes the source extremely useful for any experiment or demonstration needing heralded single photons.

Prototype pre-clinical PET scanner with depth-of-interaction measurements using single-layer crystal array and single-ended readout

NASA Astrophysics Data System (ADS)

Lee, Min Sun; Kim, Kyeong Yun; Ko, Guen Bae; Lee, Jae Sung

2017-05-01

In this study, we developed a proof-of-concept prototype PET system using a pair of depth-of-interaction (DOI) PET detectors based on the proposed DOI-encoding method and digital silicon photomultiplier (dSiPM). Our novel cost-effective DOI measurement method is based on a triangular-shaped reflector that requires only a single-layer pixelated crystal and single-ended signal readout. The DOI detector consisted of an 18  ×  18 array of unpolished LYSO crystal (1.47  ×  1.47  ×  15 mm3) wrapped with triangular-shaped reflectors. The DOI information was encoded by depth-dependent light distribution tailored by the reflector geometry and DOI correction was performed using four-step depth calibration data and maximum-likelihood (ML) estimation. The detector pair and the object were placed on two motorized rotation stages to demonstrate 12-block ring PET geometry with 11.15 cm diameter. Spatial resolution was measured and phantom and animal imaging studies were performed to investigate imaging performance. All images were reconstructed with and without the DOI correction to examine the impact of our DOI measurement. The pair of dSiPM-based DOI PET detectors showed good physical performances respectively: 2.82 and 3.09 peak-to-valley ratios, 14.30% and 18.95% energy resolution, and 4.28 and 4.24 mm DOI resolution averaged over all crystals and all depths. A sub-millimeter spatial resolution was achieved at the center of the field of view (FOV). After applying ML-based DOI correction, maximum 36.92% improvement was achieved in the radial spatial resolution and a uniform resolution was observed within 5 cm of transverse PET FOV. We successfully acquired phantom and animal images with improved spatial resolution and contrast by using the DOI measurement. The proposed DOI-encoding method was successfully demonstrated in the system level and exhibited good performance, showing its feasibility for animal PET applications with high spatial resolution and sensitivity.

A novel nitrilase from Rhodobacter sphaeroides LHS-305: cloning, heterologous expression and biochemical characterization.

PubMed

Wang, Hualei; Li, Guinan; Li, Mingyang; Wei, Dongzhi; Wang, Xuedong

2014-01-01

In this study, a novel nitrilase gene from Rhodobacter sphaeroides was cloned and overexpressed in Escherichia coli. The open reading frame of the nitrilase gene includes 969 base pairs, which encodes a putative polypeptide of 322 amino acid residues. The molecular weight of the purified native nitrilase was about 560 kDa determined by size exclusion chromatography. This nitrilase showed one single band on SDS-PAGE with a molecular weight of 40 kDa. This suggested that the native nitrilase consisted of 14 subunits with identical size. The optimal pH and temperature of the purified enzyme were 7.0 and 40 °C, respectively. The kinetic parameters V max and K m toward 3-cyanopyridine were 77.5 μmol min(-1) mg(-1) and 73.1 mmol/l, respectively. The enzyme can easily convert aliphatic nitrile and aromatic nitriles to their corresponding acids. Furthermore, this enzyme demonstrated regioselectivity in hydrolysis of aliphatic dinitriles. This specific characteristic makes this nitrilase have a great potential for commercial production of various cyanocarboxylic acids by hydrolyzing readily available dinitriles.

Free Open Access Medical Education (FOAM) Resources in a Team-Based Learning Educational Series.

PubMed

Fallon, Timothy; Strout, Tania D

2018-01-01

Although Free Open Access Medical Education (FOAM) has become popular within emergency medicine, concerns exist regarding its role in resident education. We sought to develop an educational intervention whereby residents could review FOAM resources while maintaining faculty oversight. We created a novel curriculum pairing FOAM from the Academic Life in Emergence Medicine (ALiEM) Approved Instructional Resources (Air) series with a team-based learning (TBL) format. Residents have an opportunity to engage with FOAM in a structured setting with faculty input on possible practice changes. This series has been well-received by residents and appears to have increased engagement with core content material. Qualitative feedback from residents on this series has been positive and we believe this is the first described use of TBL in emergency medicine.

Large-scale parentage inference with SNPs: an efficient algorithm for statistical confidence of parent pair allocations.

PubMed

Anderson, Eric C

2012-11-08

Advances in genotyping that allow tens of thousands of individuals to be genotyped at a moderate number of single nucleotide polymorphisms (SNPs) permit parentage inference to be pursued on a very large scale. The intergenerational tagging this capacity allows is revolutionizing the management of cultured organisms (cows, salmon, etc.) and is poised to do the same for scientific studies of natural populations. Currently, however, there are no likelihood-based methods of parentage inference which are implemented in a manner that allows them to quickly handle a very large number of potential parents or parent pairs. Here we introduce an efficient likelihood-based method applicable to the specialized case of cultured organisms in which both parents can be reliably sampled. We develop a Markov chain representation for the cumulative number of Mendelian incompatibilities between an offspring and its putative parents and we exploit it to develop a fast algorithm for simulation-based estimates of statistical confidence in SNP-based assignments of offspring to pairs of parents. The method is implemented in the freely available software SNPPIT. We describe the method in detail, then assess its performance in a large simulation study using known allele frequencies at 96 SNPs from ten hatchery salmon populations. The simulations verify that the method is fast and accurate and that 96 well-chosen SNPs can provide sufficient power to identify the correct pair of parents from amongst millions of candidate pairs.

Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

NASA Astrophysics Data System (ADS)

Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

2015-09-01

A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.

SINGLE-BASE-PAIR MISMATCH DISCRIMINATION USING OLIGONUCLEOTIDE DNA MICROARRAYS AND MELTING PROFILES. (R829458C004)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Complete particle-pair annihilation as a dynamical signature of the spectral singularity

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

Li, G.R.; Zhang, X.Z.; Song, Z., E-mail: nkquantum@gmail.com

2014-10-15

Motivated by the physical relevance of a spectral singularity of interacting many-particle system, we explore the dynamics of two bosons as well as fermions in one-dimensional system with imaginary delta interaction strength. Based on the exact solution, it shows that the two-particle collision leads to amplitude-reduction of the wave function. For fermion pair, the amplitude-reduction depends on the spin configuration of two particles. In both cases, the residual amplitude can vanish when the relative group velocity of two single-particle Gaussian wave packets with equal width reaches the magnitude of the interaction strength, exhibiting complete particle-pair annihilation at the spectral singularity.more » - Highlights: • We investigate the physical relevance of a spectral singularity. • The two-particle collision leads to amplitude-reduction of the wave function. • There is a singularity spectrum which leads to complete particle-pair annihilation. • Complete particle-pair annihilation can only occur for two distinguishable bosons and singlet fermions. • Pair annihilation provides a detection method of the spectral singularity in the experiment.« less

Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species

PubMed Central

Khan, Abdul Latif; Khan, Muhammad Aaqil; Shahzad, Raheem; Lubna; Kang, Sang Mo; Al-Harrasi, Ahmed; Al-Rawahi, Ahmed; Lee, In-Jung

2018-01-01

Pinaceae, the largest family of conifers, has a diversified organization of chloroplast (cp) genomes with two typical highly reduced inverted repeats (IRs). In the current study, we determined the complete sequence of the cp genome of an economically and ecologically important conifer tree, the loblolly pine (Pinus taeda L.), using Illumina paired-end sequencing and compared the sequence with those of other pine species. The results revealed a genome size of 121,531 base pairs (bp) containing a pair of 830-bp IR regions, distinguished by a small single copy (42,258 bp) and large single copy (77,614 bp) region. The chloroplast genome of P. taeda encodes 120 genes, comprising 81 protein-coding genes, four ribosomal RNA genes, and 35 tRNA genes, with 151 randomly distributed microsatellites. Approximately 6 palindromic, 34 forward, and 22 tandem repeats were found in the P. taeda cp genome. Whole cp genome comparison with those of other Pinus species exhibited an overall high degree of sequence similarity, with some divergence in intergenic spacers. Higher and lower numbers of indels and single-nucleotide polymorphism substitutions were observed relative to P. contorta and P. monophylla, respectively. Phylogenomic analyses based on the complete genome sequence revealed that 60 shared genes generated trees with the same topologies, and P. taeda was closely related to P. contorta in the subgenus Pinus. Thus, the complete P. taeda genome provided valuable resources for population and evolutionary studies of gymnosperms and can be used to identify related species. PMID:29596414

16 CFR 303.29 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2012 CFR

2012-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other textile fiber products are marketed or handled in pairs or ensembles of the same fiber content...

16 CFR 300.12 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2014 CFR

2014-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other wool products are marketed or handled in pairs or ensembles of the same fiber content, only one...

16 CFR 303.29 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2010 CFR

2010-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other textile fiber products are marketed or handled in pairs or ensembles of the same fiber content...

16 CFR 300.12 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2013 CFR

2013-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other wool products are marketed or handled in pairs or ensembles of the same fiber content, only one...

16 CFR 303.29 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2013 CFR

2013-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other textile fiber products are marketed or handled in pairs or ensembles of the same fiber content...

16 CFR 300.12 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2012 CFR

2012-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other wool products are marketed or handled in pairs or ensembles of the same fiber content, only one...

16 CFR 300.12 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2011 CFR

2011-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other wool products are marketed or handled in pairs or ensembles of the same fiber content, only one...

16 CFR 303.29 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2014 CFR

2014-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other textile fiber products are marketed or handled in pairs or ensembles of the same fiber content...

16 CFR 300.12 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2010 CFR

2010-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other wool products are marketed or handled in pairs or ensembles of the same fiber content, only one...

16 CFR 303.29 - Labeling of pairs or products containing two or more units.

Code of Federal Regulations, 2011 CFR

2011-01-01

... handled as a single product or ensemble and are sold and delivered to the ultimate consumer as a single product or ensemble, the required information may be set out on a single label in such a manner as to... other textile fiber products are marketed or handled in pairs or ensembles of the same fiber content...

ac Josephson effect and resonant Cooper pair tunneling emission of a single Cooper pair transistor.

PubMed

Billangeon, P-M; Pierre, F; Bouchiat, H; Deblock, R

2007-05-25

We measure the high-frequency emission of a single Cooper pair transistor (SCPT) in the regime where transport is only due to tunneling of Cooper pairs. This is achieved by coupling on chip the SCPT to a superconductor-insulator-superconductor junction and by measuring the photon assisted tunneling current of quasiparticles across the junction. This technique allows a direct detection of the ac Josephson effect of the SCPT and provides evidence of Landau-Zener transitions for proper gate voltage. The emission in the regime of resonant Cooper pair tunneling is also investigated. It is interpreted in terms of transitions between charge states coupled by the Josephson effect.

Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing.

PubMed

Cartwright, Joseph F; Anderson, Karin; Longworth, Joseph; Lobb, Philip; James, David C

2018-06-01

High-fidelity replication of biologic-encoding recombinant DNA sequences by engineered mammalian cell cultures is an essential pre-requisite for the development of stable cell lines for the production of biotherapeutics. However, immortalized mammalian cells characteristically exhibit an increased point mutation frequency compared to mammalian cells in vivo, both across their genomes and at specific loci (hotspots). Thus unforeseen mutations in recombinant DNA sequences can arise and be maintained within producer cell populations. These may affect both the stability of recombinant gene expression and give rise to protein sequence variants with variable bioactivity and immunogenicity. Rigorous quantitative assessment of recombinant DNA integrity should therefore form part of the cell line development process and be an essential quality assurance metric for instances where synthetic/multi-component assemblies are utilized to engineer mammalian cells, such as the assessment of recombinant DNA fidelity or the mutability of single-site integration target loci. Based on Pacific Biosciences (Menlo Park, CA) single molecule real-time (SMRT™) circular consensus sequencing (CCS) technology we developed a rDNA sequence analysis tool to process the multi-parallel sequencing of ∼40,000 single recombinant DNA molecules. After statistical filtering of raw sequencing data, we show that this analytical method is capable of detecting single point mutations in rDNA to a minimum single mutation frequency of 0.0042% (<1/24,000 bases). Using a stable CHO transfectant pool harboring a randomly integrated 5 kB plasmid construct encoding GFP we found that 28% of recombinant plasmid copies contained at least one low frequency (<0.3%) point mutation. These mutations were predominantly found in GC base pairs (85%) and that there was no positional bias in mutation across the plasmid sequence. There was no discernable difference between the mutation frequencies of coding and non-coding DNA. The putative ratio of non-synonymous and synonymous changes within the open reading frames (ORFs) in the plasmid sequence indicates that natural selection does not impact upon the prevalence of these mutations. Here we have demonstrated the abundance of mutations that fall outside of the reported range of detection of next generation sequencing (NGS) and second generation sequencing (SGS) platforms, providing a methodology capable of being utilized in cell line development platforms to identify the fidelity of recombinant genes throughout the production process. © 2018 Wiley Periodicals, Inc.

Crystal and Solution Structures of a Prokaryotic M16B Peptidase: an Open and Shut Case

PubMed Central

Aleshin, Alexander E.; Gramatikova, Svetlana; Hura, Gregory L.; Bobkov, Andrey; Strongin, Alex Y.; Stec, Boguslaw; Tainer, John A.; Liddington, Robert C.; Smith, Jeffrey W.

2013-01-01

SUMMARY The M16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a ‘‘clam-shell’’ surrounding the active site. The M16A and M16C subfamilies form one class (‘‘peptidasomes’’): they degrade 30–70 residue peptides, and adopt both open and closed conformations. The eukaryotic M16B subfamily forms a second class (‘‘processing proteases’’): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. Here, we report the solution and crystal structures of a prokaryotic M16B peptidase, and demonstrate that it has features of both classes: thus, it forms stable ‘‘open’’ homodimers in solution that resemble the processing proteases; but the clam-shell closes upon binding substrate, a feature of the M16A/C peptidasomes. Moreover, clam-shell closure is required for proteolytic activity. We predict that other prokaryotic M16B family members will form dimeric peptidasomes, and propose a model for the evolution of the M16 family. PMID:19913481

Unique Dynamic Properties of DNA Duplexes Containing Interstrand Crosslinks†

PubMed Central

Friedman, Joshua I.; Jiang, Yu Lin; Miller, Paul S.; Stivers, James T.

2010-01-01

Bifunctional DNA alkylating agents form a diverse assortment of covalent DNA interstrand crosslinked (ICL) structures that are potent cytotoxins. Since it is implausible that cells could possess distinct DNA repair systems for each individual ICL, it is believed that common structural and dynamic features of ICL damage are recognized, rather than specific structural characteristics of each cross-linking agent. Investigation of the structural and dynamic properties of ICLs that might be important for recognition has been complicated by heterogeneous incorporation of these lesions into DNA. To address this problem we have synthesized and characterized several homogenous ICL-DNAs containing site–specific staggered N4-cytosine-ethyl-N4-cytosine crosslinks. Staggered crosslinks were introduced in two ways: in a manner that preserves the overall structure of B-form duplex DNA, and in a manner that highly distorts the DNA structure, with the goal of understanding how structural and dynamic properties of diverse ICL duplexes might flag these sites for repair. Measurements of base pair opening dynamics in the B-form ICL duplex by 1H NMR linewidth or imino proton solvent exchange showed that the guanine base opposite to the crosslinked cytosine opened at least an order of magnitude more slowly than when in a control matched normal duplex. To a lesser degree, the B-form ICL also induced a decrease in base pair opening dynamics that extended from the site of the crosslink to adjacent base pairs. In contrast, the non-B-form ICL showed extensive conformational dynamics at the site of the cross link, which extended over the entire DNA sequence. Since DNA duplexes containing the B-form and non-B-form ICL crosslinks have both been shown to be incised when incubated in mammalian whole cell extracts, while a matched normal duplex is not, we conclude that intrinsic DNA dynamics is not a requirement for specific damage incision of these ICLs. Instead, we propose a general model where destabilized ICL-duplexes serve to energetically facilitate binding of DNA repair factors that must induce bubbles or other distortions in the duplex. However, the essential requirement for incision is an immobile Y-junction where the repair factors are stably bound at the site of the ICL, and the two DNA strands are unpaired. PMID:21174443

Entanglement-based Free Space Quantum Cryptography in Daylight

NASA Astrophysics Data System (ADS)

Gerhardt, Ilja; Peloso, Matthew P.; Ho, Caleb; Lamas-Linares, Antia; Kurtsiefer, Christian

2009-05-01

In quantum key distribution (QKD) two families of protocols are established: One, based on preparing and sending approximations of single photons, the other based on measurements on entangled photon pairs, which allow to establish a secret key using less assumptions on the size of a Hilbert space. The larger optical bandwidth of photon pairs in comparison with light used for the first family makes establishing a free space link challenging. We present a complete entanglement based QKD system following the BBM92 protocol, which generates a secure key continuously 24 hours a day between distant parties. Spectral, spatial and temporal filtering schemes were introduced to a previous setup, suppressing more than 30,B of background. We are able to establish the link during daytime, and have developed an algorithm to start and maintain time synchronization with simple crystal oscillators.

Economic method for helical gear flank surface characterisation

NASA Astrophysics Data System (ADS)

Koulin, G.; Reavie, T.; Frazer, R. C.; Shaw, B. A.

2018-03-01

Typically the quality of a gear pair is assessed based on simplified geometric tolerances which do not always correlate with functional performance. In order to identify and quantify functional performance based parameters, further development of the gear measurement approach is required. Methodology for interpolation of the full active helical gear flank surface, from sparse line measurements, is presented. The method seeks to identify the minimum number of line measurements required to sufficiently characterise an active gear flank. In the form ground gear example presented, a single helix and three profile line measurements was considered to be acceptable. The resulting surfaces can be used to simulate the meshing engagement of a gear pair and therefore provide insight into functional performance based parameters. Therefore the assessment of the quality can be based on the predicted performance in the context of an application.

Generation of a pair of independently binding DNA aptamers in a single round of selection using proximity ligation.

PubMed

Chumphukam, O; Le, T T; Piletsky, S; Cass, A E G

2015-05-28

The ability to rapidly generate a pair of aptamers that bind independently to a protein target would greatly extend their use as reagents for two site ('sandwich') assays. We describe here a method to achieve this through proximity ligation. Using lysozyme as a target we demonstrate that under optimal conditions such a pair of aptamers, with nanomolar affinities, can be generated in a single round.

Aging and IQ effects on associative recognition and priming in item recognition

PubMed Central

McKoon, Gail; Ratcliff, Roger

2012-01-01

Two ways to examine memory for associative relationships between pairs of words were tested: an explicit method, associative recognition, and an implicit method, priming in item recognition. In an experiment with both kinds of tests, participants were asked to learn pairs of words. For the explicit test, participants were asked to decide whether two words of a test pair had been studied in the same or different pairs. For the implicit test, participants were asked to decide whether single words had or had not been among the studied pairs. Some test words were immediately preceded in the test list by the other word of the same pair and some by a word from a different pair. Diffusion model (Ratcliff, 1978; Ratcliff & McKoon, 2008) analyses were carried out for both tasks for college-age participants, 60–74 year olds, and 75–90 year olds, and for higher- and lower-IQ participants, in order to compare the two measures of associative strength. Results showed parallel behavior of drift rates for associative recognition and priming across ages and across IQ, indicating that they are based, at least to some degree, on the same information in memory. PMID:24976676

THE EVOLUTION OF PRIMORDIAL BINARY OPEN STAR CLUSTERS: MERGERS, SHREDDED SECONDARIES, AND SEPARATED TWINS

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

De la Fuente Marcos, R.; De la Fuente Marcos, C., E-mail: raul@galaxy.suffolk.e

2010-08-10

The properties of the candidate binary star cluster population in the Magellanic Clouds and Milky Way are similar. The fraction of candidate binaries is {approx}10% and the pair separation histogram exhibits a bimodal distribution commonly attributed to their transient nature. However, if primordial pairs cannot survive for long as recognizable bound systems, how are they ending up? Here, we use simulations to confirm that merging, extreme tidal distortion, and ionization are possible depending on the initial orbital elements and mass ratio of the cluster pair. Merging is observed for initially close pairs but also for wider systems in nearly parabolicmore » orbits. Its characteristic timescale depends on the initial orbital semi-major axis, eccentricity, and cluster pair mass ratio, becoming shorter for closer, more eccentric equal mass pairs. Shredding of the less massive cluster and subsequent separation is observed in all pairs with appreciably different masses. Wide pairs evolve into separated twins characterized by the presence of tidal bridges and separations of 200-500 pc after one Galactic orbit. Most observed binary candidates appear to be following this evolutionary path which translates into the dominant peak (25-30 pc) in the observed pair separation distribution. The secondary peak at smaller separations (10-15 pc) can be explained as due to close pairs in almost circular orbits and/or undergoing merging. Merged clusters exhibit both peculiar radial density and velocity dispersion profiles shaped by synchronization and gravogyro instabilities. Simulations and observations show that long-term binary open cluster stability is unlikely.« less

Recursive model for the fragmentation of polarized quarks

NASA Astrophysics Data System (ADS)

Kerbizi, A.; Artru, X.; Belghobsi, Z.; Bradamante, F.; Martin, A.

2018-04-01

We present a model for Monte Carlo simulation of the fragmentation of a polarized quark. The model is based on string dynamics and the 3P0 mechanism of quark pair creation at string breaking. The fragmentation is treated as a recursive process, where the splitting function of the subprocess q →h +q' depends on the spin density matrix of the quark q . The 3P0 mechanism is parametrized by a complex mass parameter μ , the imaginary part of which is responsible for single spin asymmetries. The model has been implemented in a Monte Carlo program to simulate jets made of pseudoscalar mesons. Results for single hadron and hadron pair transverse-spin asymmetries are found to be in agreement with experimental data from SIDIS and e+e- annihilation. The model predictions on the jet-handedness are also discussed.

Operation of the PAVE PAWS Radar System at Beale Air Force Base, California. Part 2. Public Comment & AF Response.

DTIC Science & Technology

1980-07-01

trip next month to Europe , and when I come back. It’s for this reason that I was not able to have it all typed and prepared, and the Air Force was...millimeter of culture medium. A mutational event such as a change in a single base pair in the bacterial DNA, which is impossible to detect by standard...100) bacteria, a rare single mutation event with a probability of say I in 100,000,000, the probability of 10-8, will thus be amplified by a factor of

Excimers from stable and persistent supramolecular radical-pairs in red/NIR-emitting organic nanoparticles and polymeric films.

PubMed

Blasi, Davide; Nikolaidou, Domna M; Terenziani, Francesca; Ratera, Imma; Veciana, Jaume

2017-03-29

In this work, the luminescence properties of new materials based on open-shell molecular systems are studied. In particular, we prepared polymeric films and organic nanoparticles (ONPs) doped with triphenylmethyl radical molecules. ONPs exhibit a uniform size distribution, spherical morphology and high colloidal stability. The emission spectrum of low-doped ONP suspensions and low-doped films is very similar to the emission spectrum of TTM in solution, while the luminescence lifetime and the luminescence quantum yield (LQY) are highly increased. Increasing the radical doping leads to a progressive decrease of the LQY and the appearance of a new broad excimeric band at longer wavelengths, both for ONPs and films. Thus, not only the luminescence properties were improved, but also the formation of excimers from stable and persistent supramolecular radical-pairs was observed for the first time. The good stability and luminescence properties with emission in the red-NIR region (650-800 nm), together with the open-shell nature of the emitter, make these free-radical excimer-forming materials promising candidates for optoelectronic and bioimaging applications.

Comparative Transcriptomic Analyses of Three Species of Placobdella (Rhynchobdellida: Glossiphoniidae) Confirms a Single Origin of Blood Feeding in Leeches.

PubMed

Siddall, Mark E; Brugler, Mercer R; Kvist, Sebastian

2016-02-01

One of the recalcitrant questions regarding the evolutionary history of clitellate annelids involves the feeding preference of the common ancestor of extant rhynchobdellid (proboscis bearing) and arhynchobdellid (jaw bearing) leeches. Whereas early evidence, based on morphological data, pointed towards independent acquisitions of blood feeding in the 2 orders, molecular-based phylogenetic data suggest that the ancestor of modern leeches was a sanguivore. Here, we use a comparative transcriptomic approach in order to increase our understanding of the diversity of anticoagulation factors for 3 species of the genus Placobdella, for which comparative data have been lacking, and inspect these in light of archetypal anticoagulant data for both arhynchobdellid and other rhynchobdellid species. Notwithstanding the varying levels of host specificity displayed by the 3 different species of Placobdella, transcriptomic profiles with respect to anticoagulation factors were largely similar -this despite the fact that Placobdella kwetlumye only retains a single pair of salivary glands, as opposed to the 2 pairs more common in the genus. Results show that 9 different anticoagulant proteins and an additional 5 putative antihemostasis proteins are expressed in salivary secretions of the 3 species. In particular, an ortholog of the archetypal, single-copy, anticoagulant hirudin (not previously available as comparative data for rhynchobdellids) is present in at least 2 of 3 species examined, corroborating the notion of a single origin of blood feeding in the ancestral leech.

Disordered Kitaev chains with long-range pairing.

PubMed

Cai, Xiaoming

2017-03-22

We study the competition of disorder and superconductivity for a generalized Kitaev model in incommensurate potentials. The generalized Kitaev model describes one dimensional spinless fermions with long-range p-wave superconducting pairing, which decays with distance l as a power law  ∼[Formula: see text]. We focus on the transition from the topological superconducting phase to the topologically trivial Anderson localized phase, and effects of the exponent α on this phase transition. In the topological superconducting phase, for a system under open boundary condition the amplitude of zero-mode Majorana fermion has a hybrid exponential-algebraic decay as the distance increases from the edge. In the Anderson localized phase, some single-particle states remain critical for very strong disorders and the number of critical states increases as α decreases. In addition, except for critical disorders, the correlation function always has an exponential decay at the short range and an algebraic decay at the long range. Phase transition points are also numerically determined and the topological phase transition happens earlier at a smaller disorder strength for a system with smaller α.

A ‘Simple Anterior Fish Excluder’ (SAFE) for Mitigating Penaeid-Trawl Bycatch

PubMed Central

McHugh, Matthew J.; Broadhurst, Matt K.; Sterling, David J.; Millar, Russell B.

2015-01-01

Various plastic strips and sheets (termed ‘simple anterior fish excluders’−SAFEs) were positioned across the openings of penaeid trawls in attempts at reducing the unwanted bycatches of small teleosts. Initially, three SAFEs (a single wire without, and with small and large plastic panels) were compared against a control (no SAFE) on paired beam trawls. All SAFEs maintained targeted Metapenaeus macleayi catches, while the largest plastic SAFE significantly reduced total bycatch by 51% and the numbers of Pomatomus saltatrix, Mugil cephalus and Herklotsichthys castelnaui by up to 58%. A redesigned SAFE (‘continuous plastic’) was subsequently tested (against a control) on paired otter trawls, significantly reducing total bycatch by 28% and P. saltatrix and H. castelnaui by up to 42%. The continuous-plastic SAFE also significantly reduced M. macleayi catches by ~7%, but this was explained by ~5% less wing-end spread, and could be simply negated through otter-board refinement. Further work is required to refine the tested SAFEs, and to quantify species-specific escape mechanisms. Nevertheless, the SAFE concept might represent an effective approach for improving penaeid-trawl selectivity. PMID:25837892

Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain

PubMed Central

Koch, Miriam; Willi, Jessica; Pradère, Ugo; Hall, Jonathan

2017-01-01

Abstract The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson–Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. PMID:28369621

Design of two-photon molecular tandem architectures for solar cells by ab initio theory† †Electronic supplementary information (ESI) available: Visualizations of molecular orbitals, one-particle mechanisms and a table with Kohn–Sham eigenvalues. See DOI: 10.1039/c4sc03835e

PubMed Central

Garcia-Lastra, Juan M.; De La Torre, Gema; Himpsel, F. J.; Rubio, Angel

2015-01-01

An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range. Three different architectures are considered: the first two involve a complex consisting of two dye molecules with appropriately matched frontier orbitals, connected by a molecular diode. Optimized combinations of dye molecules are determined by taking advantage of our computational database of the structural and energetic properties of several thousand porphyrin dyes. The third design is a molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices, such as the synthesis of the tandem molecules and potential loss mechanisms, are addressed. PMID:29142685

The pair-production channel in atomic processes

NASA Astrophysics Data System (ADS)

Belkacem, Ali; Sørensen, Allan H.

2006-06-01

Assisted by the creation of electron-positron pairs, new channels for ionization, excitation, and charge transfer open in atomic collisions when the energy is raised to relativistic values. At extreme energies these pair-production channels usually dominate the "traditional" contributions to cross sections that involve only "positive-energy" electrons. An extensive body of theoretical and experimental work has been performed over the last two decades to investigate charge-changing processes catalyzed by pair production in relativistic heavy ion collisions. We review some of these studies.

A Toda lattice model of DNA

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

Christiansen, P.L.; Scott, A.C.; Muto, V.

In recent years the possibility that anharmonic excitations could play a role in the dynamics of SNA has been considered by several authors. It has been suggested that solitons may be generated thermally at biological temperatures. The denaturation of the DNA double helix has been investigated by statistical mechanics methods and by dynamical simulations. Here the potential for the hydrogen bond in each base pair is approximated by a Morse potential. In the present paper we describe the Toda lattice model of DNA. Temperature enters via the initial conditions and through a perturbation of the dynamical equations. The model ismore » refined by introduction of transversal motion of the Toda lattice and by transversal coupling of two lattices in the hydrogen bonds present in the base pairs. Using Lennard-Jones potentials to model these bonds we are able to obtain results concerning the open states of DNA at biological temperatures. 39 refs., 7 figs.« less

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.

PubMed

Pandey, Ram Vinay; Pulverer, Walter; Kallmeyer, Rainer; Beikircher, Gabriel; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both methods have advantages and limitations. Thus, an integrated approach would be extremely useful to quantify the DNA methylation status successfully with great sensitivity and specificity. Designing specific and optimized primers for target regions is the most critical and challenging step in obtaining the adequate DNA methylation results using PCR-based methods. Currently, no integrated, optimized, and high-throughput methylation-specific primer design software methods are available for both BS- and MSRE-based methods. Therefore an integrated, powerful, and easy-to-use methylation-specific primer design pipeline with great accuracy and success rate will be very useful. We have developed a new web-based pipeline, called MSP-HTPrimer, to design primers pairs for MSP, BSP, pyrosequencing, COBRA, and MSRE assays on both genomic strands. First, our pipeline converts all target sequences into bisulfite-treated templates for both forward and reverse strand and designs all possible primer pairs, followed by filtering for single nucleotide polymorphisms (SNPs) and known repeat regions. Next, each primer pairs are annotated with the upstream and downstream RefSeq genes, CpG island, and cut sites (for COBRA and MSRE). Finally, MSP-HTPrimer selects specific primers from both strands based on custom and user-defined hierarchical selection criteria. MSP-HTPrimer produces a primer pair summary output table in TXT and HTML format for display and UCSC custom tracks for resulting primer pairs in GTF format. MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size of target sequences and designs MSP, BSP, pyrosequencing, COBRA, and MSRE assays. It is the only pipeline, which automatically designs primers on both genomic strands to increase the success rate. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 66 BSP primer pairs, 63 were successfully validated without any further optimization step and using the same qPCR conditions. The MSP-HTPrimer pipeline is freely available from http://sourceforge.net/p/msp-htprimer.

Prevention of longitudinal crack propagation around a femoral prosthesis: a study of cerclage wire fixation.

PubMed

Difazio, F A; Incavo, S J; Howe, J D

1993-09-01

This study examined the effect of single versus triple-wrap cerclage fixation techniques in preventing propagation of a longitudinal fracture around a cementless femoral prosthesis. A proximal filling femoral component was implanted in 14 matched pairs of fresh-frozen bovine femora, following placement of a 45-mm longitudinal crack in the anteromedial cortical wall of the proximal femur. In one group of seven pairs, a single cerclage wire was applied to one specimen of each pair. A triple-wrap of a single cerclage wire was similarly placed in one specimen of each of the other seven pairs. All specimens were axially loaded on a materials testing system machine and the force required to propagate the fracture of the proximal femur was recorded. A triple-wrap cerclage technique required a significant increase in the force to propagate a proximal femur fracture around a non-cemented prosthesis when compared to a single cerclage wire. Copyright © 1993. Published by Elsevier Ltd.

Direct observation of single flexible polymers using single stranded DNA†

PubMed Central

Brockman, Christopher; Kim, Sun Ju

2012-01-01

Over the last 15 years, double stranded DNA (dsDNA) has been used as a model polymeric system for nearly all single polymer dynamics studies. However, dsDNA is a semiflexible polymer with markedly different molecular properties compared to flexible chains, including synthetic organic polymers. In this work, we report a new system for single polymer studies of flexible chains based on single stranded DNA (ssDNA). We developed a method to synthesize ssDNA for fluorescence microscopy based on rolling circle replication, which generates long strands (>65 kb) of ssDNA containing “designer” sequences, thereby preventing intramolecular base pair interactions. Polymers are synthesized to contain amine-modified bases randomly distributed along the backbone, which enables uniform labelling of polymer chains with a fluorescent dye to facilitate fluorescence microscopy and imaging. Using this approach, we synthesized ssDNA chains with long contour lengths (>30 μm) and relatively low dye loading ratios (~1 dye per 100 bases). In addition, we used epifluorescence microscopy to image single ssDNA polymer molecules stretching in flow in a microfluidic device. Overall, we anticipate that ssDNA will serve as a useful model system to probe the dynamics of polymeric materials at the molecular level. PMID:22956981

Double Negative Materials (DNM), Phenomena and Applications

DTIC Science & Technology

2009-07-01

Nanoparticles Formed by Pairs Of Concentric Double-Negative (DNG), Single-Negative ( SNG ) and/or Double-Positive (DPS) Metamaterial Layers.” J. Appl...material RRL Rapid Research Letters SHG second-harmonic generation SNG single-negative SSR split-ring resonator A-1 Appendix A. October 2008...Pairs of Concentric Double-Negative (DNG), Single-Negative ( SNG ), and/or Double-Positive (DPS) Metamaterial Layers.” J. Appl. Phys. 97, no. 9 (May

Dynamic use of wetlands by black ducks and mallards: evidence against competitive exclusion

USGS Publications Warehouse

McAuley, D.G.; Clugston, D.A.; Longcore, J.R.

2004-01-01

The decline of the American black duck (Anas rubripes) has been attributed to competition from mallards (A. platyrhynchos) that led to exclusive use of fertile wetlands by mallards. Data from annual breeding waterfowl surveys provide instantaneous, single observations of breeding pairs, which are used to estimate breeding population size and evaluate the condition of habitat. Data from these surveys have been used to document habitat use by black ducks and mallards. We used quiet-observation surveys from elevated platforms to study sympatric black ducks and mallards in northern Maine during the breeding season. Our objectives were to document occupancy of wetlands by breeding black ducks and mallards throughout the day during prenesting and early nesting periods to determine whether 1) wetlands were occupied by only a single species, 2) pairs of the same species occupied wetlands throughout the period, and 3) single observations of short duration adequately determine numbers and species using a wetland. We observed ducks at 5-minute intervals from elevated platforms on wetland margins to determine numbers and species of indicated pairs using each wetland over time. We visited 80% of the wetlands >2 times, with mean total time per wetland averaging 267 minutes. For each wetland we determined the most frequently observed grouping of black ducks and mallards from all combinations recorded during all intervals (e.g., 1 black duck [BO] pair during 9 intervals; 2 mallard [MA] pairs and 1 BO pair during 22 intervals; 0 pairs during 3 intervals). A single pair, a lone male, or no ducks were recorded during 34% of the 5-minute intervals. For wetlands with >2 hours of observations (n=65), all but 2 were used by >2 different combinations of ducks. On most wetlands, the most frequent grouping was observed during 2 hours were used by both species, random visits detected both species on only 27 wetlands. Our data do not support assertions that the mallard has caused the decline of black ducks through interspecific competition for habitat, or that wetlands are occupied continuously by single pairs that aggressively exclude conspecifics. Our data indicated that single, short-duration visits with disturbance to wetlands are unreliable and inappropriate to document seasonal use of wetlands by breeding black ducks and mallards.

Methods of developing core collections based on the predicted genotypic value of rice ( Oryza sativa L.).

PubMed

Li, C T; Shi, C H; Wu, J G; Xu, H M; Zhang, H Z; Ren, Y L

2004-04-01

The selection of an appropriate sampling strategy and a clustering method is important in the construction of core collections based on predicted genotypic values in order to retain the greatest degree of genetic diversity of the initial collection. In this study, methods of developing rice core collections were evaluated based on the predicted genotypic values for 992 rice varieties with 13 quantitative traits. The genotypic values of the traits were predicted by the adjusted unbiased prediction (AUP) method. Based on the predicted genotypic values, Mahalanobis distances were calculated and employed to measure the genetic similarities among the rice varieties. Six hierarchical clustering methods, including the single linkage, median linkage, centroid, unweighted pair-group average, weighted pair-group average and flexible-beta methods, were combined with random, preferred and deviation sampling to develop 18 core collections of rice germplasm. The results show that the deviation sampling strategy in combination with the unweighted pair-group average method of hierarchical clustering retains the greatest degree of genetic diversities of the initial collection. The core collections sampled using predicted genotypic values had more genetic diversity than those based on phenotypic values.

An Assessment of Some Design Constraints on Heat Production of a 3D Conceptual EGS Model Using an Open-Source Geothermal Reservoir Simulation Code

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

Yidong Xia; Mitch Plummer; Robert Podgorney

2016-02-01

Performance of heat production process over a 30-year period is assessed in a conceptual EGS model with a geothermal gradient of 65K per km depth in the reservoir. Water is circulated through a pair of parallel wells connected by a set of single large wing fractures. The results indicate that the desirable output electric power rate and lifespan could be obtained under suitable material properties and system parameters. A sensitivity analysis on some design constraints and operation parameters indicates that 1) the fracture horizontal spacing has profound effect on the long-term performance of heat production, 2) the downward deviation anglemore » for the parallel doublet wells may help overcome the difficulty of vertical drilling to reach a favorable production temperature, and 3) the thermal energy production rate and lifespan has close dependence on water mass flow rate. The results also indicate that the heat production can be improved when the horizontal fracture spacing, well deviation angle, and production flow rate are under reasonable conditions. To conduct the reservoir modeling and simulations, an open-source, finite element based, fully implicit, fully coupled hydrothermal code, namely FALCON, has been developed and used in this work. Compared with most other existing codes that are either closed-source or commercially available in this area, this new open-source code has demonstrated a code development strategy that aims to provide an unparalleled easiness for user-customization and multi-physics coupling. Test results have shown that the FALCON code is able to complete the long-term tests efficiently and accurately, thanks to the state-of-the-art nonlinear and linear solver algorithms implemented in the code.« less

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.

PubMed

Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis

2015-01-01

Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug discovery projects. Graphical abstractAtom pair fingerprints based on through-space distances (3DAPfp) provide better shape encoding than atom pair fingerprints based on topological distances (APfp) as measured by the recovery of ROCS shape analogs by fp similarity.

Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe 2 S 3 : Combined ab initio and density matrix renormalization group study

DOE PAGES

Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; ...

2016-08-10

The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe 2S 3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015)] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe 2S 3. Themore » model is studied with the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only oneWannier orbital receiving the hole carriers while the other remains half-filled. Lastly, these results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.« less

The structure of the L3 loop from the hepatitis delta virus ribozyme: a syn cytidine.

PubMed Central

Lynch, S R; Tinoco, I

1998-01-01

The structure of the L3 central hairpin loop isolated from the antigenomic sequence of the hepatitis delta virus ribozyme with the P2 and P3 stems from the ribozyme stacked on top of the loop has been determined by NMR spectroscopy. The 26 nt stem-loop structure contains nine base pairs and a 7 nt loop (5'-UCCUCGC-3'). This hairpin loop is critical for efficient catalysis in the intact ribozyme. The structure was determined using homonuclear and heteronuclear NMR techniques on non-labeled and15N-labeled RNA oligonucleotides. The overall root mean square deviation for the structure was 1.15 A (+/- 0.28 A) for the loop and the closing C.G base pair and 0.90 A (+/- 0.18 A) for the loop and the closing C.G base pair but without the lone purine in the loop, which is not well defined in the structure. The structure indicates a U.C base pair between the nucleotides on the 5'- and 3'-ends of the loop. This base pair is formed with a single hydrogen bond involving the cytosine exocyclic amino proton and the carbonyl O4 of the uracil. The most unexpected finding in the loop is a syn cytidine. While not unprecedented, syn pyrimidines are highly unusual. This one can be confidently established by intranucleotide distances between the ribose and the base determined by NMR spectroscopy. A similar study of the structure of this loop showed a somewhat different three-dimensional structure. A discussion of differences in the two structures, as well as possible sites of interaction with the cleavage site, will be presented. PMID:9461457

A Comparison of Two Online Learning Systems

ERIC Educational Resources Information Center

Nichols, Mark

2016-01-01

Open Polytechnic is a single-mode provider of distance education with a rich history of print-based provision. Strategically, the institution is rapidly adopting an online-only approach, with some exceptions for programmes that require student contact. A recent and internal review of Moodle, the Open Polytechnic's learning management system (LMS)…

Pair-Wise, Deformable Mirror, Image Plane-Based Diversity Electric Field Estimation for High Contrast Coronagraphy

NASA Technical Reports Server (NTRS)

Give'on, Amir; Kern, Brian D.; Shaklan, Stuart

2011-01-01

In this paper we describe the complex electric field reconstruction from image plane intensity measurements for high contrast coronagraphic imaging. A deformable mirror (DM) surface is modied with pairs of complementary shapes to create diversity in the image plane of the science camera where the intensity of the light is measured. Along with the Electric Field Conjugation correction algorithm, this estimation method has been used in various high contrast imaging testbeds to achieve the best contrasts to date both in narrow and in broad band light. We present the basic methodology of estimation in easy to follow list of steps, present results from HCIT and raise several open quations we are confronted with using this method.

In silico cloning and B/T cell epitope prediction of triosephosphate isomerase from Echinococcus granulosus.

PubMed

Wang, Fen; Ye, Bin

2016-10-01

Cystic echinococcosis is a worldwide zoonosis caused by Echinococcus granulosus. Because the methods of diagnosis and treatment for cystic echinococcosis were limited, it is still necessary to screen target proteins for the development of new anti-hydatidosis vaccine. In this study, the triosephosphate isomerase gene of E. granulosus was in silico cloned. The B cell and T cell epitopes were predicted by bioinformatics methods. The cDNA sequence of EgTIM was composition of 1094 base pairs, with an open reading frame of 753 base pairs. The deduced amino acid sequences were composed of 250 amino acids. Five cross-reactive epitopes, locating on 21aa-35aa, 43aa-57aa, 94aa-107aa, 115-129aa, and 164aa-183aa, could be expected to serve as candidate epitopes in the development of vaccine against E. granulosus. These results could provide bases for gene cloning, recombinant expression, and the designation of anti-hydatidosis vaccine.

Reciprocal uniparental disomy in yeast.

PubMed

Andersen, Sabrina L; Petes, Thomas D

2012-06-19

In the diploid cells of most organisms, including humans, each chromosome is usually distinguishable from its partner homolog by multiple single-nucleotide polymorphisms. One common type of genetic alteration observed in tumor cells is uniparental disomy (UPD), in which a pair of homologous chromosomes are derived from a single parent, resulting in loss of heterozygosity for all single-nucleotide polymorphisms while maintaining diploidy. Somatic UPD events are usually explained as reflecting two consecutive nondisjunction events. Here we report a previously undescribed mode of chromosome segregation in Saccharomyces cerevisiae in which one cell division produces daughter cells with reciprocal UPD for the same pair of chromosomes without an aneuploid intermediate. One pair of sister chromatids is segregated into one daughter cell and the other pair is segregated into the other daughter cell, mimicking a meiotic chromosome segregation pattern. We term this process "reciprocal uniparental disomy."

Constrained-pairing mean-field theory. IV. Inclusion of corresponding pair constraints and connection to unrestricted Hartree-Fock theory.

PubMed

Tsuchimochi, Takashi; Henderson, Thomas M; Scuseria, Gustavo E; Savin, Andreas

2010-10-07

Our previously developed constrained-pairing mean-field theory (CPMFT) is shown to map onto an unrestricted Hartree-Fock (UHF) type method if one imposes a corresponding pair constraint to the correlation problem that forces occupation numbers to occur in pairs adding to one. In this new version, CPMFT has all the advantages of standard independent particle models (orbitals and orbital energies, to mention a few), yet unlike UHF, it can dissociate polyatomic molecules to the correct ground-state restricted open-shell Hartree-Fock atoms or fragments.

Concentric agonist-antagonist robots for minimally invasive surgeries

NASA Astrophysics Data System (ADS)

Oliver-Butler, Kaitlin; Epps, Zane H.; Rucker, Daniel Caleb

2017-03-01

We present a novel continuum robot design concept, Concentric Agonist-Antagonist Robots (CAAR), that uses push-pull, agonist-antagonist action of a pair of concentric tubes. The CAAR tubes are designed to have noncentral, offset neutral axes, and they are fixed together at their distal ends. Axial base translations then induce bending in the device. A CAAR segment can be created by selectively cutting asymmetric notches into the profile of two stock tubes, which relocates the neutral bending plane away from the center of the inner lumen. Like conventional concentric-tube robots (CTRs) based on counter-rotating precurved tubes, a CAAR can be made at very small scales and contain a large, open lumen. In contrast with CTRs, the CAAR concept has no elastic stability issues, offers a larger range of motion, and has lower overall stiffness. Furthermore, by varying the position of the neutral axes along the length of each tube, arbitrary, variable curvature actuation modes can be achieved. Precurving the tubes can additionally increase the workspace of a single segment. A single two-tube assembly can be used to create 3 degree-of-freedom (DOF) robot segments, and multiple segments can be deployed concentrically. Both additive manufacturing and traditional machining of stock tubes can create and customize the geometry and performance of the CAAR. In this paper, we explore the CAAR concept, provide kinematic and static models, and experimentally evaluate the model with a both a straight and a precurved CAAR. We conclude with a discussion of the significance and our plans for future work.

Quantum teleportation of multiple degrees of freedom of a single photon

NASA Astrophysics Data System (ADS)

Wang, Xi-Lin; Cai, Xin-Dong; Su, Zu-En; Chen, Ming-Cheng; Wu, Dian; Li, Li; Liu, Nai-Le; Lu, Chao-Yang; Pan, Jian-Wei

2015-02-01

Quantum teleportation provides a `disembodied' way to transfer quantum states from one object to another at a distant location, assisted by previously shared entangled states and a classical communication channel. As well as being of fundamental interest, teleportation has been recognized as an important element in long-distance quantum communication, distributed quantum networks and measurement-based quantum computation. There have been numerous demonstrations of teleportation in different physical systems such as photons, atoms, ions, electrons and superconducting circuits. All the previous experiments were limited to the teleportation of one degree of freedom only. However, a single quantum particle can naturally possess various degrees of freedom--internal and external--and with coherent coupling among them. A fundamental open challenge is to teleport multiple degrees of freedom simultaneously, which is necessary to describe a quantum particle fully and, therefore, to teleport it intact. Here we demonstrate quantum teleportation of the composite quantum states of a single photon encoded in both spin and orbital angular momentum. We use photon pairs entangled in both degrees of freedom (that is, hyper-entangled) as the quantum channel for teleportation, and develop a method to project and discriminate hyper-entangled Bell states by exploiting probabilistic quantum non-demolition measurement, which can be extended to more degrees of freedom. We verify the teleportation for both spin-orbit product states and hybrid entangled states, and achieve a teleportation fidelity ranging from 0.57 to 0.68, above the classical limit. Our work is a step towards the teleportation of more complex quantum systems, and demonstrates an increase in our technical control of scalable quantum technologies.

Quantum teleportation of multiple degrees of freedom of a single photon.

PubMed

Wang, Xi-Lin; Cai, Xin-Dong; Su, Zu-En; Chen, Ming-Cheng; Wu, Dian; Li, Li; Liu, Nai-Le; Lu, Chao-Yang; Pan, Jian-Wei

2015-02-26

Quantum teleportation provides a 'disembodied' way to transfer quantum states from one object to another at a distant location, assisted by previously shared entangled states and a classical communication channel. As well as being of fundamental interest, teleportation has been recognized as an important element in long-distance quantum communication, distributed quantum networks and measurement-based quantum computation. There have been numerous demonstrations of teleportation in different physical systems such as photons, atoms, ions, electrons and superconducting circuits. All the previous experiments were limited to the teleportation of one degree of freedom only. However, a single quantum particle can naturally possess various degrees of freedom--internal and external--and with coherent coupling among them. A fundamental open challenge is to teleport multiple degrees of freedom simultaneously, which is necessary to describe a quantum particle fully and, therefore, to teleport it intact. Here we demonstrate quantum teleportation of the composite quantum states of a single photon encoded in both spin and orbital angular momentum. We use photon pairs entangled in both degrees of freedom (that is, hyper-entangled) as the quantum channel for teleportation, and develop a method to project and discriminate hyper-entangled Bell states by exploiting probabilistic quantum non-demolition measurement, which can be extended to more degrees of freedom. We verify the teleportation for both spin-orbit product states and hybrid entangled states, and achieve a teleportation fidelity ranging from 0.57 to 0.68, above the classical limit. Our work is a step towards the teleportation of more complex quantum systems, and demonstrates an increase in our technical control of scalable quantum technologies.

Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson–Crick Base Pairing in Vacuo

PubMed Central

Schnier, Paul D.; Klassen, John S.; Strittmatter, Eric F.; Williams*, Evan R.

2005-01-01

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)23−, (CCGG)23−, (AATTAAT)23−, (CCGGCCG)23−, A7·T73−, A7·A73−, T7·T73−, and A7·C73− were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 1013 to 1019 s−1. Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a – base) and w ions. Four pieces of evidence are presented which indicate that Watson–Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A7·T73−, to the single strands is significantly higher than that for the related noncomplementary A7·A73− and T7·T73− dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A7·A73− and A7·C73− but not for A7·T73− consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (−ΔHd) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A7·T73− duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent. PMID:16498487

Principal component analysis-based imaging angle determination for 3D motion monitoring using single-slice on-board imaging.

PubMed

Chen, Ting; Zhang, Miao; Jabbour, Salma; Wang, Hesheng; Barbee, David; Das, Indra J; Yue, Ning

2018-04-10

Through-plane motion introduces uncertainty in three-dimensional (3D) motion monitoring when using single-slice on-board imaging (OBI) modalities such as cine MRI. We propose a principal component analysis (PCA)-based framework to determine the optimal imaging plane to minimize the through-plane motion for single-slice imaging-based motion monitoring. Four-dimensional computed tomography (4DCT) images of eight thoracic cancer patients were retrospectively analyzed. The target volumes were manually delineated at different respiratory phases of 4DCT. We performed automated image registration to establish the 4D respiratory target motion trajectories for all patients. PCA was conducted using the motion information to define the three principal components of the respiratory motion trajectories. Two imaging planes were determined perpendicular to the second and third principal component, respectively, to avoid imaging with the primary principal component of the through-plane motion. Single-slice images were reconstructed from 4DCT in the PCA-derived orthogonal imaging planes and were compared against the traditional AP/Lateral image pairs on through-plane motion, residual error in motion monitoring, absolute motion amplitude error and the similarity between target segmentations at different phases. We evaluated the significance of the proposed motion monitoring improvement using paired t test analysis. The PCA-determined imaging planes had overall less through-plane motion compared against the AP/Lateral image pairs. For all patients, the average through-plane motion was 3.6 mm (range: 1.6-5.6 mm) for the AP view and 1.7 mm (range: 0.6-2.7 mm) for the Lateral view. With PCA optimization, the average through-plane motion was 2.5 mm (range: 1.3-3.9 mm) and 0.6 mm (range: 0.2-1.5 mm) for the two imaging planes, respectively. The absolute residual error of the reconstructed max-exhale-to-inhale motion averaged 0.7 mm (range: 0.4-1.3 mm, 95% CI: 0.4-1.1 mm) using optimized imaging planes, averaged 0.5 mm (range: 0.3-1.0 mm, 95% CI: 0.2-0.8 mm) using an imaging plane perpendicular to the minimal motion component only and averaged 1.3 mm (range: 0.4-2.8 mm, 95% CI: 0.4-2.3 mm) in AP/Lateral orthogonal image pairs. The root-mean-square error of reconstructed displacement was 0.8 mm for optimized imaging planes, 0.6 mm for imaging plane perpendicular to the minimal motion component only, and 1.6 mm for AP/Lateral orthogonal image pairs. When using the optimized imaging planes for motion monitoring, there was no significant absolute amplitude error of the reconstructed motion (P = 0.0988), while AP/Lateral images had significant error (P = 0.0097) with a paired t test. The average surface distance (ASD) between overlaid two-dimensional (2D) tumor segmentation at end-of-inhale and end-of-exhale for all eight patients was 0.6 ± 0.2 mm in optimized imaging planes and 1.4 ± 0.8 mm in AP/Lateral images. The Dice similarity coefficient (DSC) between overlaid 2D tumor segmentation at end-of-inhale and end-of-exhale for all eight patients was 0.96 ± 0.03 in optimized imaging planes and 0.89 ± 0.05 in AP/Lateral images. Both ASD (P = 0.034) and DSC (P = 0.022) were significantly improved in the optimized imaging planes. Motion monitoring using imaging planes determined by the proposed PCA-based framework had significantly improved performance. Single-slice image-based motion tracking can be used for clinical implementations such as MR image-guided radiation therapy (MR-IGRT). © 2018 American Association of Physicists in Medicine.

Generation, storage, and retrieval of nonclassical states of light using atomic ensembles

NASA Astrophysics Data System (ADS)

Eisaman, Matthew D.

This thesis presents the experimental demonstration of several novel methods for generating, storing, and retrieving nonclassical states of light using atomic ensembles, and describes applications of these methods to frequency-tunable single-photon generation, single-photon memory, quantum networks, and long-distance quantum communication. We first demonstrate emission of quantum-mechanically correlated pulses of light with a time delay between the pulses that is coherently controlled by utilizing 87Rb atoms. The experiment is based on Raman scattering, which produces correlated pairs of excited atoms and photons, followed by coherent conversion of the atomic states into a different photon field after a controllable delay. We then describe experiments demonstrating a novel approach for conditionally generating nonclassical pulses of light with controllable photon numbers, propagation direction, timing, and pulse shapes. We observe nonclassical correlations in relative photon number between correlated pairs of photons, and create few-photon light pulses with sub-Poissonian photon-number statistics via conditional detection on one field of the pair. Spatio-temporal control over the pulses is obtained by exploiting long-lived coherent memory for photon states and electromagnetically induced transparency (EIT) in an optically dense atomic medium. Finally, we demonstrate the use of EIT for the controllable generation, transmission, and storage of single photons with tunable frequency, timing, and bandwidth. To this end, we study the interaction of single photons produced in a "source" ensemble of 87Rb atoms at room temperature with another "target" ensemble. This allows us to simultaneously probe the spectral and quantum statistical properties of narrow-bandwidth single-photon pulses, revealing that their quantum nature is preserved under EIT propagation and storage. We measure the time delay associated with the reduced group velocity of the single-photon pulses and report observations of their storage and retrieval. Together these experiments utilize atomic ensembles to realize a narrow-bandwidth single-photon source, single-photon memory that preserves the quantum nature of the single photons, and a primitive quantum network comprised of two atomic-ensemble quantum memories connected by a single photon in an optical fiber. Each of these experimental demonstrations represents an essential element for the realization of long-distance quantum communication.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.

PubMed

Poehlman, William L; Rynge, Mats; Branton, Chris; Balamurugan, D; Feltus, Frank A

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid

PubMed Central

Poehlman, William L.; Rynge, Mats; Branton, Chris; Balamurugan, D.; Feltus, Frank A.

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments. PMID:27499617

Motions, efforts and actuations in constrained dynamic systems: a multi-link open-chain example

NASA Astrophysics Data System (ADS)

Duke Perreira, N.

1999-08-01

The effort-motion method, which describes the dynamics of open- and closed-chain topologies of rigid bodies interconnected with revolute and prismatic pairs, is interpreted geometrically. Systems are identified for which the simultaneous control of forces and velocities is desirable, and a representative open-chain system is selected for use in the ensuing analysis. Gauge invariant transformations are used to recast the commonly used kinetic and kinematic equations into a dimensional gauge invariant form. Constraint elimination techniques based on singular value decompositions then recast the invariant equations into orthogonal and reciprocal sets of motion and effort equations written in state variable form. The ideal actuation is found that simultaneously achieves the obtainable portions of the desired constraining efforts and motions. The performance is then evaluated of using the actuation closest to the ideal actuation.

High-throughput deterministic single-cell encapsulation and droplet pairing, fusion, and shrinkage in a single microfluidic device.

PubMed

Schoeman, Rogier M; Kemna, Evelien W M; Wolbers, Floor; van den Berg, Albert

2014-02-01

In this article, we present a microfluidic device capable of successive high-yield single-cell encapsulation in droplets, with additional droplet pairing, fusion, and shrinkage. Deterministic single-cell encapsulation is realized using Dean-coupled inertial ordering of cells in a Yin-Yang-shaped curved microchannel using a double T-junction, with a frequency over 2000 Hz, followed by controlled droplet pairing with a 100% success rate. Subsequently, droplet fusion is realized using electrical actuation resulting in electro-coalescence of two droplets, each containing a single HL60 cell, with 95% efficiency. Finally, volume reduction of the fused droplet up to 75% is achieved by a triple pitchfork structure. This droplet volume reduction is necessary to obtain close cell-cell membrane contact necessary for final cell electrofusion, leading to hybridoma formation, which is the ultimate aim of this research. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The origin of the mass of the Nambu-Goldstone bosons

NASA Astrophysics Data System (ADS)

Arraut, Ivan

2018-03-01

We explain the origin of the mass for the Nambu-Goldstone bosons when there is a chemical potential in the action which explicitly breaks the symmetry. The method is based on the number of independent histories for the interaction of the pair of Nambu-Goldstone bosons with the degenerate vacuum (triangle relations). The analysis suggests that under some circumstances, pairs of massive Nambu-Goldstone bosons can become a single degree of freedom with an effective mass defined by the superposition of the individual masses of each boson. Possible mass oscillations for the Nambu-Goldstone bosons are discussed.

Can monaural temporal masking explain the ongoing precedence effect?

PubMed

Freyman, Richard L; Morse-Fortier, Charlotte; Griffin, Amanda M; Zurek, Patrick M

2018-02-01

The precedence effect for transient sounds has been proposed to be based primarily on monaural processes, manifested by asymmetric temporal masking. This study explored the potential for monaural explanations with longer ("ongoing") sounds exhibiting the precedence effect. Transient stimuli were single lead-lag noise burst pairs; ongoing stimuli were trains of 63 burst pairs. Unlike with transients, monaural masking data for ongoing sounds showed no advantage for the lead, and are inconsistent with asymmetric audibility as an explanation for ongoing precedence. This result, along with supplementary measurements of interaural time discrimination, suggests different explanations for transient and ongoing precedence.

Epigenetic Therapy of Hematopoietic Malignancies: Novel Approaches for Tissue-Specific and Global Inhibition of EZH2 Enzymatic Activities

DTIC Science & Technology

2017-10-01

at cis-regulatory elements such as enhancers to facilitate gene transcription. CRISPR /Cas9- mediated ablation of a putative Meis1 enhancer carrying...Tables S4 and S5. 10 Cancer Cell 30, 1–16, July 11, 2016the CRISPR /Cas9-based genomic editing technology. Cas9 and a pair of single guide RNAs (sgRNA... CRISPR /Cas9-mediated deletio sgMeis1, a pair of sgRNAs that target the DMR boundaries. (N) Sequencing of the genomic PCR products from F2/R2 primers shows

21. INTERIOR OF UTILITY ROOM SHOWING OPEN REAR DOOR AT ...

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

21. INTERIOR OF UTILITY ROOM SHOWING OPEN REAR DOOR AT PHOTO CENTER, PAIRED NARROW 1-LIGHT OVER 1-LIGHT, DOUBLE-HUNG, WOOD-FRAMED WINDOWS AT PHOTO LEFT. OPEN DOOR AT PHOTO RIGHT LEADS TO BATHROOM. VIEW TO SOUTHWEST. - Bishop Creek Hydroelectric System, Plant 4, Worker Cottage, Bishop Creek, Bishop, Inyo County, CA

3' Untranslated regions mediate transcriptional interference between convergent genes both locally and ectopically in Saccharomyces cerevisiae.

PubMed

Wang, Luwen; Jiang, Ning; Wang, Lin; Fang, Ou; Leach, Lindsey J; Hu, Xiaohua; Luo, Zewei

2014-01-01

Paired sense and antisense (S/AS) genes located in cis represent a structural feature common to the genomes of both prokaryotes and eukaryotes, and produce partially complementary transcripts. We used published genome and transcriptome sequence data and found that over 20% of genes (645 pairs) in the budding yeast Saccharomyces cerevisiae genome are arranged in convergent pairs with overlapping 3'-UTRs. Using published microarray transcriptome data from the standard laboratory strain of S. cerevisiae, our analysis revealed that expression levels of convergent pairs are significantly negatively correlated across a broad range of environments. This implies an important role for convergent genes in the regulation of gene expression, which may compensate for the absence of RNA-dependent mechanisms such as micro RNAs in budding yeast. We selected four representative convergent gene pairs and used expression assays in wild type yeast and its genetically modified strains to explore the underlying patterns of gene expression. Results showed that convergent genes are reciprocally regulated in yeast populations and in single cells, whereby an increase in expression of one gene produces a decrease in the expression of the other, and vice-versa. Time course analysis of the cell cycle illustrated the functional significance of this relationship for the three pairs with relevant functional roles. Furthermore, a series of genetic modifications revealed that the 3'-UTR sequence plays an essential causal role in mediating transcriptional interference, which requires neither the sequence of the open reading frame nor the translation of fully functional proteins. More importantly, transcriptional interference persisted even when one of the convergent genes was expressed ectopically (in trans) and therefore does not depend on the cis arrangement of convergent genes; we conclude that the mechanism of transcriptional interference cannot be explained by the transcriptional collision model, which postulates a clash between simultaneous transcriptional processes occurring on opposite DNA strands.

3′ Untranslated Regions Mediate Transcriptional Interference between Convergent Genes Both Locally and Ectopically in Saccharomyces cerevisiae

PubMed Central

Wang, Luwen; Jiang, Ning; Wang, Lin; Fang, Ou; Leach, Lindsey J.; Hu, Xiaohua; Luo, Zewei

2014-01-01

Paired sense and antisense (S/AS) genes located in cis represent a structural feature common to the genomes of both prokaryotes and eukaryotes, and produce partially complementary transcripts. We used published genome and transcriptome sequence data and found that over 20% of genes (645 pairs) in the budding yeast Saccharomyces cerevisiae genome are arranged in convergent pairs with overlapping 3′-UTRs. Using published microarray transcriptome data from the standard laboratory strain of S. cerevisiae, our analysis revealed that expression levels of convergent pairs are significantly negatively correlated across a broad range of environments. This implies an important role for convergent genes in the regulation of gene expression, which may compensate for the absence of RNA-dependent mechanisms such as micro RNAs in budding yeast. We selected four representative convergent gene pairs and used expression assays in wild type yeast and its genetically modified strains to explore the underlying patterns of gene expression. Results showed that convergent genes are reciprocally regulated in yeast populations and in single cells, whereby an increase in expression of one gene produces a decrease in the expression of the other, and vice-versa. Time course analysis of the cell cycle illustrated the functional significance of this relationship for the three pairs with relevant functional roles. Furthermore, a series of genetic modifications revealed that the 3′-UTR sequence plays an essential causal role in mediating transcriptional interference, which requires neither the sequence of the open reading frame nor the translation of fully functional proteins. More importantly, transcriptional interference persisted even when one of the convergent genes was expressed ectopically (in trans) and therefore does not depend on the cis arrangement of convergent genes; we conclude that the mechanism of transcriptional interference cannot be explained by the transcriptional collision model, which postulates a clash between simultaneous transcriptional processes occurring on opposite DNA strands. PMID:24465217

Measures and Relative Motions of Some Mostly F. G. W. Struve Doubles

NASA Astrophysics Data System (ADS)

Wiley, E. O.

2012-04-01

Measures of 59 pairs of double stars with long observational histories using "lucky imaging" techniques are reported. Relative motions of 59 pairs are investigated using histories of observation, scatter plots of relative motion, ordinary least-squares (OLS) and total proper motion analyses performed in "R," an open source programming language. A scatter plot of the coefficient of determinations derived from the OLS y|epoch and OLS x|epoch clearly separates common proper motion pairs from optical pairs and what are termed "long-period binary candidates." Differences in proper motion separate optical pairs from long-term binary candidates. An Appendix is provided that details how to use known rectilinear pairs as calibration pairs for the program REDUC.

A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.

PubMed

Isalan, M; Klug, A; Choo, Y

2001-07-01

DNA-binding domains with predetermined sequence specificity are engineered by selection of zinc finger modules using phage display, allowing the construction of customized transcription factors. Despite remarkable progress in this field, the available protein-engineering methods are deficient in many respects, thus hampering the applicability of the technique. Here we present a rapid and convenient method that can be used to design zinc finger proteins against a variety of DNA-binding sites. This is based on a pair of pre-made zinc finger phage-display libraries, which are used in parallel to select two DNA-binding domains each of which recognizes given 5 base pair sequences, and whose products are recombined to produce a single protein that recognizes a composite (9 base pair) site of predefined sequence. Engineering using this system can be completed in less than two weeks and yields proteins that bind sequence-specifically to DNA with Kd values in the nanomolar range. To illustrate the technique, we have selected seven different proteins to bind various regions of the human immunodeficiency virus 1 (HIV-1) promoter.

The effect of RNA stiffness on the self-assembly of virus particles

NASA Astrophysics Data System (ADS)

Li, Siyu; Erdemci-Tandogan, Gonca; van der Schoot, Paul; Zandi, Roya

2018-01-01

Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.

VarioML framework for comprehensive variation data representation and exchange.

PubMed

Byrne, Myles; Fokkema, Ivo Fac; Lancaster, Owen; Adamusiak, Tomasz; Ahonen-Bishopp, Anni; Atlan, David; Béroud, Christophe; Cornell, Michael; Dalgleish, Raymond; Devereau, Andrew; Patrinos, George P; Swertz, Morris A; Taschner, Peter Em; Thorisson, Gudmundur A; Vihinen, Mauno; Brookes, Anthony J; Muilu, Juha

2012-10-03

Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

VarioML framework for comprehensive variation data representation and exchange

PubMed Central

2012-01-01

Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity. PMID:23031277

Letter order is not coded by open bigrams

PubMed Central

Kinoshita, Sachiko; Norris, Dennis

2013-01-01

Open bigram (OB) models (e.g., SERIOL: Whitney, 2001, 2008; Binary OB, Grainger & van Heuven, 2003; Overlap OB, Grainger et al., 2006; Local combination detector model, Dehaene et al., 2005) posit that letter order in a word is coded by a set of ordered letter pairs. We report three experiments using bigram primes in the same-different match task, investigating the effects of order reversal and the number of letters intervening between the letters in the target. Reversed bigrams (e.g., fo-OF, ob-ABOLISH) produced robust priming, in direct contradiction to the assumption that letter order is coded by the presence of ordered letter pairs. Also in contradiction to the core assumption of current open bigram models, non-contiguous bigrams spanning three letters in the target (e.g., bs-ABOLISH) showed robust priming effects, equivalent in size to contiguous bigrams (e.g., bo-ABOLISH). These results question the role of open bigrams in coding letter order. PMID:23914048

Perceiving and Acting on Complex Affordances: How Children and Adults Bicycle Across Two Lanes of Opposing Traffic

PubMed Central

Grechkin, Timofey Y.; Chihak, Benjamin J.; Cremer, James F.; Kearney, Joseph K.; Plumert, Jodie M.

2014-01-01

This investigation examined how children and adults negotiate a challenging perceptual-motor problem with significant real-world implications – bicycling across two lanes of opposing traffic. Twelve- and 14-year-olds and adults rode a bicycling simulator through an immersive virtual environment. Participants crossed intersections with continuous cross traffic coming from opposing directions. Opportunities for crossing were divided into aligned (far gap opens with or before near gap) and rolling (far gap opens after near gap) gap pairs. Children and adults preferred rolling to aligned gap pairs, though this preference was stronger for adults than for children. Crossing aligned versus rolling gap pairs produced substantial differences in direction of travel, speed of crossing, and timing of entry into the near and far lanes. For both aligned and rolling gap pairs, children demonstrated less skill than adults in coordinating self and object movement. These findings have implications for understanding perception-action-cognition links and for understanding risk factors underlying car-bicycle collisions. PMID:22924952

Morphologies and ages of star cluster pairs and multiplets in the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

de Oliveira, M. R.; Dutra, C. M.; Bica, E.; Dottori, H.

2000-10-01

An isophotal atlas of 75 star cluster pairs and multiplets in the Small Magellanic Cloud is presented, comprising 176 objects. They are concentrated in the SMC main body. The isophotal contours were made from Digitized Sky Survey* images and showed relevant structural features possibly related to interactions in about 25% of the sample. Previous N-body simulations indicate that such shapes could be due to tidal tails, bridges or common envelopes. The diameter ratio between the members of a pair is preferentially in the range 1 - 2, with a peak at 1. The projected separation is in the range ~ 3 - 22 pc with a pronounced peak at ~ 13 pc. For 91 objects it was possible to derive ages from Colour-Magnitude Diagrams using the OGLE-II photometric survey. The cluster multiplets in general occur in OB stellar associations and/or HII region complexes. This indicates a common origin and suggests that multiplets coalesce into pairs or single clusters in a short time scale. Pairs in the SMC appear to be mostly coeval and consequently captures are a rare phenomenon. We find evidence that star cluster pairs and multiplets may have had an important role in the dynamical history of clusters presently seen as large single objects. The images in this study are based on photographic data obtained using the UK Schmidt Telescope, which was operated by the Royal Observatory Edinburgh, with funding from the UK Science and Engineering Research Council, until 1988 June, and thereafter by the Anglo-Australian Observatory. Original plate material is copyright by the Royal Observatory Edinburgh and the Anglo-Australian Observatory. The plates were processed into the present compressed digital form with their permission. The Digitized Sky Survey was produced at the Space Telescope Science Institute under US Government grant NAG W-2166.

Pairing call-response surveys and distance sampling for a mammalian carnivore

USGS Publications Warehouse

Hansen, Sara J. K.; Frair, Jacqueline L.; Underwood, Harold B.; Gibbs, James P.

2015-01-01

Density estimates accounting for differential animal detectability are difficult to acquire for wide-ranging and elusive species such as mammalian carnivores. Pairing distance sampling with call-response surveys may provide an efficient means of tracking changes in populations of coyotes (Canis latrans), a species of particular interest in the eastern United States. Blind field trials in rural New York State indicated 119-m linear error for triangulated coyote calls, and a 1.8-km distance threshold for call detectability, which was sufficient to estimate a detection function with precision using distance sampling. We conducted statewide road-based surveys with sampling locations spaced ≥6 km apart from June to August 2010. Each detected call (be it a single or group) counted as a single object, representing 1 territorial pair, because of uncertainty in the number of vocalizing animals. From 524 survey points and 75 detections, we estimated the probability of detecting a calling coyote to be 0.17 ± 0.02 SE, yielding a detection-corrected index of 0.75 pairs/10 km2 (95% CI: 0.52–1.1, 18.5% CV) for a minimum of 8,133 pairs across rural New York State. Importantly, we consider this an index rather than true estimate of abundance given the unknown probability of coyote availability for detection during our surveys. Even so, pairing distance sampling with call-response surveys provided a novel, efficient, and noninvasive means of monitoring populations of wide-ranging and elusive, albeit reliably vocal, mammalian carnivores. Our approach offers an effective new means of tracking species like coyotes, one that is readily extendable to other species and geographic extents, provided key assumptions of distance sampling are met.

A "spare" compensates for the risk of destruction of the elongated penis of earwigs (Insecta: Dermaptera)

NASA Astrophysics Data System (ADS)

Kamimura, Yoshitaka; Matsuo, Yoh

2001-11-01

Male animals in several groups have multiple intromittent organs that outnumber the corresponding female gonopore. In Dermaptera (earwigs), males of the family Anisolabididae have paired, elongated male intromittent organs (virgae), while females have a single sperm-storage organ (spermatheca). Several authors have assumed that one of the paired virgae is non-functional, because it points in the "wrong" direction. We investigated the mating success of handicapped males of Euborellia plebeja in which one of their paired virgae was removed experimentally. These handicapped males succeeded in inseminating a mate. Males with genital damage are found in the field, suggesting that the "spare" functions under natural conditions. Based on phylogenetic information on earwigs, we discuss possible evolutionary scenarios for this genital peculiarity.

Simulation of defects in fusion plasma first wall materials

NASA Astrophysics Data System (ADS)

T, Troev; N, Nankov; T, Yoshiie

2014-06-01

Numerical calculations of radiation damages in beryllium, alpha-iron and tungsten irradiated by fusion neutrons were performed using molecular dynamics (MD) simulations. The displacement cascades efficiency has been calculated using the Norgett-Robinson-Torrens (NRT) formula, the universal pair-potential of Ziegler-Biersack-Littmark (ZBL) and the EAM inter-atomic potential. The pair potential overestimates the defects production by a factor of 2. The ZBL pair potential results and the EAM are comparable at higher primary knock-on atom (PKA) energies (E > 100 keV). We found that the most common types of defects are single vacancies, di-vacancies, interstitials and small number of interstitial clusters. On the bases of calculated results, the behavior of vacancies, empty nano-voids and nano-voids with hydrogen and helium were discussed.

The energetics of tightly bent DNA: a composite elastica model including local melting

NASA Astrophysics Data System (ADS)

Evans, Arthur; Levine, Alex

2012-02-01

Melting transitions are well-known to be affected by the application of mechanical stress. Motivated by the experiments of Zocchi and collaborators (Qu and Zocchi 2011, EPL 94 18003), we explore the effect of the application of mechanical stress on DNA melting in a particular composite of a stiff double stranded piece of DNA (dsDNA), shorter than its own persistence length, whose ends are linked by a flexible single stranded piece of DNA (ssDNA). The flexible ssDNA acts as a Gaussian polymer coil bending the stiff dsDNA through an elastic force that is controllable by the length of the ssDNA chain. In this talk we present theoretical predictions for two experimentally accessible features: the degree of local dsDNA melting and the local elastic energy of the dsDNA/ssDNA construct both as a function of the length of the attached ssDNA. We also address the effect of introducing a nick (broken covalent bond) in the dsDNA backbone on these results and discuss the implications of such data on the relative importance of backbone elasticity versus base stacking and base pairing interactions in determining the elasticity of dsDNA. This work also addresses open questions in the nonlinear elasticity of DNA in tightly bent curves.

Asymmetric adiabatic couplers for fully-integrated broadband quantum-polarization state preparation.

PubMed

Chung, Hung-Pin; Huang, Kuang-Hsu; Wang, Kai; Yang, Sung-Lin; Yang, Shih-Yuan; Sung, Chun-I; Solntsev, Alexander S; Sukhorukov, Andrey A; Neshev, Dragomir N; Chen, Yen-Hung

2017-12-04

Spontaneous parametric down-conversion (SPDC) is a widely used method to generate entangled photons, enabling a range of applications from secure communication to tests of quantum physics. Integrating SPDC on a chip provides interferometric stability, allows to reduce a physical footprint, and opens a pathway to true scalability. However, dealing with different photon polarizations and wavelengths on a chip presents a number of challenging problems. In this work, we demonstrate an on-chip polarization beam-splitter based on z-cut titanium-diffused lithium niobate asymmetric adiabatic couplers (AAC) designed for integration with a type-II SPDC source. Our experimental measurements reveal unique polarization beam-splitting regime with the ability to tune the splitting ratios based on wavelength. In particular, we measured a splitting ratio of 17 dB over broadband regions (>60 nm) for both H- and V-polarized lights and a specific 50%/50% splitting ratio for a cross-polarized photon pair from the AAC. The results show that such a system can be used for preparing different quantum polarization-path states that are controllable by changing the phase-matching conditions in the SPDC over a broad band. Furthermore, we propose a fully integrated electro-optically tunable type-II SPDC polarization-path-entangled state preparation circuit on a single lithium niobate photonic chip.

Baryon Spectroscopy at ELSA and at MAMI - selected results

NASA Astrophysics Data System (ADS)

Krusche, B.

2014-05-01

Spectroscopy of baryons and their excited states plays a key role for our understanding of the strong interaction in the non-perturbative regime. Both, in theory and in experiment, large progress has been made during the last few years. The rapid developments in lattice gauge calculations and the application of the Dyson-Schwinger equation to QCD have opened new perspectives for the interpretation of the excitation spectrum of the nucleon. In parallel, large efforts have been undertaken world-wide, and are still running, to investigate excited nucleon states experimentally, in particular with photon-induced production of mesons. In the present contribution we discuss such experimental programs conducted at the tagged photon beams of the electron accelerators ELSA in Bonn and MAMI in Mainz. These programs are diverse. They include the measurement of cross sections, single- and double polarization observables for single meson production and production of meson pairs off free protons as well as of quasi-free nucleons bound in the deuteron (and sometimes other light nuclei).