Retinal biometrics based on Iterative Closest Point algorithm.

PubMed

Hatanaka, Yuji; Tajima, Mikiya; Kawasaki, Ryo; Saito, Koko; Ogohara, Kazunori; Muramatsu, Chisako; Sunayama, Wataru; Fujita, Hiroshi

2017-07-01

The pattern of blood vessels in the eye is unique to each person because it rarely changes over time. Therefore, it is well known that retinal blood vessels are useful for biometrics. This paper describes a biometrics method using the Jaccard similarity coefficient (JSC) based on blood vessel regions in retinal image pairs. The retinal image pairs were rough matched by the center of their optic discs. Moreover, the image pairs were aligned using the Iterative Closest Point algorithm based on detailed blood vessel skeletons. For registration, perspective transform was applied to the retinal images. Finally, the pairs were classified as either correct or incorrect using the JSC of the blood vessel region in the image pairs. The proposed method was applied to temporal retinal images, which were obtained in 2009 (695 images) and 2013 (87 images). The 87 images acquired in 2013 were all from persons already examined in 2009. The accuracy of the proposed method reached 100%.

Quantifying the impacts of vegetation changes on catchment storage-discharge dynamics using paired-catchment data

NASA Astrophysics Data System (ADS)

Cheng, Lei; Zhang, Lu; Chiew, Francis H. S.; Canadell, Josep G.; Zhao, Fangfang; Wang, Ying-Ping; Hu, Xianqun; Lin, Kairong

2017-07-01

It is widely recognized that vegetation changes can significantly affect the local water availability. Methods have been developed to predict the effects of vegetation change on water yield or total streamflow. However, it is still a challenge to predict changes in base flow following vegetation change due to limited understanding of catchment storage-discharge dynamics. In this study, the power law relationship for describing catchment storage-discharge dynamics is reformulated to quantify the changes in storage-discharge relationship resulting from vegetation changes using streamflow data from six paired-catchment experiments, of which two are deforestation catchments and four are afforestation catchments. Streamflow observations from the paired-catchment experiments clearly demonstrate that vegetation changes have led to significant changes in catchment storage-discharge relationships, accounting for about 83-128% of the changes in groundwater discharge in the treated catchments. Deforestation has led to increases in groundwater discharge (or base flow) but afforestation has resulted in decreases in groundwater discharge. Further analysis shows that the contribution of changes in groundwater discharge to the total changes in streamflow varies greatly among experimental catchments ranging from 12% to 80% with a mean of 38 ± 22% (μ ± σ). This study proposed a new method to quantify the effects of vegetation changes on groundwater discharge from catchment storage and will improve our predictability about the impacts of vegetation changes on catchment water yields.

Radical-pair based avian magnetoreception

NASA Astrophysics Data System (ADS)

Procopio, Maria; Ritz, Thorsten

2014-03-01

Behavioural experiments suggest that migratory birds possess a magnetic compass sensor able to detect the direction of the geomagnetic. One hypothesis for the basis of this remarkable sensory ability is that the coherent quantum spin dynamics of photoinduced radical pair reactions transduces directional magnetic information from the geomagnetic field into changes of reaction yields, possibly involving the photoreceptor cryptochrome in the birds retina. The suggested radical-pair based avian magnetoreception has attracted attention in the field of quantum biology as an example of a biological sensor which might exploit quantum coherences for its biological function. Investigations on such a spin-based sensor have focussed on uncovering the design features for the design of a biomimetic magnetic field sensor. We study the effects of slow fluctuations in the nuclear spin environment on the directional signal. We quantitatively evaluate the robustness of signals under fluctuations on a timescale longer than the lifetime of a radical pair, utilizing two models of radical pairs. Our results suggest design principles for building a radical-pair based compass sensor that is both robust and highly directional sensitive.

Geometrical correlations in the nucleosomal DNA conformation and the role of the covalent bonds rigidity

PubMed Central

Ghorbani, Maryam; Mohammad-Rafiee, Farshid

2011-01-01

We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle. In this model, the changes in the energy of the covalent bonds that connect the base pairs of each strand of the DNA double helix, as well as the lateral displacements and the rotation of adjacent base pairs are considered. We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results. This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results. PMID:20972223

Evaluating changes in matrix based, recovery-adjusted concentrations in paired data for pesticides in groundwater

USGS Publications Warehouse

Zimmerman, Tammy M.; Breen, Kevin J.

2012-01-01

Pesticide concentration data for waters from selected carbonate-rock aquifers in agricultural areas of Pennsylvania were collected in 1993–2009 for occurrence and distribution assessments. A set of 30 wells was visited once in 1993–1995 and again in 2008–2009 to assess concentration changes. The data include censored matched pairs (nondetections of a compound in one or both samples of a pair). A potentially improved approach for assessing concentration changes is presented where (i) concentrations are adjusted with models of matrix-spike recovery and (ii) area-wide temporal change is tested by use of the paired Prentice-Wilcoxon (PPW) statistical test. The PPW results for atrazine, simazine, metolachlor, prometon, and an atrazine degradate, deethylatrazine (DEA), are compared using recovery-adjusted and unadjusted concentrations. Results for adjusted compared with unadjusted concentrations in 2008–2009 compared with 1993–1995 were similar for atrazine and simazine (significant decrease; 95% confidence level) and metolachlor (no change) but differed for DEA (adjusted, decrease; unadjusted, increase) and prometon (adjusted, decrease; unadjusted, no change). The PPW results were different on recovery-adjusted compared with unadjusted concentrations. Not accounting for variability in recovery can mask a true change, misidentify a change when no true change exists, or assign a direction opposite of the true change in concentration that resulted from matrix influences on extraction and laboratory method performance. However, matrix-based models of recovery derived from a laboratory performance dataset from multiple studies for national assessment, as used herein, rather than time- and study-specific recoveries may introduce uncertainty in recovery adjustments for individual samples that should be considered in assessing change.

Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

PubMed Central

2015-01-01

Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

Measuring interfraction and intrafraction lung function changes during radiation therapy using four-dimensional cone beam CT ventilation imaging

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

Kipritidis, John, E-mail: john.kipritidis@sydney.edu.au; Keall, Paul J.; Hugo, Geoffrey

Purpose: Adaptive ventilation guided radiation therapy could minimize the irradiation of healthy lung based on repeat lung ventilation imaging (VI) during treatment. However the efficacy of adaptive ventilation guidance requires that interfraction (e.g., week-to-week), ventilation changes are not washed out by intrafraction (e.g., pre- and postfraction) changes, for example, due to patient breathing variability. The authors hypothesize that patients undergoing lung cancer radiation therapy exhibit larger interfraction ventilation changes compared to intrafraction function changes. To test this, the authors perform the first comparison of interfraction and intrafraction lung VI pairs using four-dimensional cone beam CT ventilation imaging (4D-CBCT VI), amore » novel technique for functional lung imaging. Methods: The authors analyzed a total of 215 4D-CBCT scans acquired for 19 locally advanced non-small cell lung cancer (LA-NSCLC) patients over 4–6 weeks of radiation therapy. This set of 215 scans was sorted into 56 interfraction pairs (including first day scans and each of treatment weeks 2, 4, and 6) and 78 intrafraction pairs (including pre/postfraction scans on the same-day), with some scans appearing in both sets. VIs were obtained from the Jacobian determinant of the transform between the 4D-CBCT end-exhale and end-inhale images after deformable image registration. All VIs were deformably registered to their corresponding planning CT and normalized to account for differences in breathing effort, thus facilitating image comparison in terms of (i) voxelwise Spearman correlations, (ii) mean image differences, and (iii) gamma pass rates for all interfraction and intrafraction VI pairs. For the side of the lung ipsilateral to the tumor, we applied two-sided t-tests to determine whether interfraction VI pairs were more different than intrafraction VI pairs. Results: The (mean ± standard deviation) Spearman correlation for interfraction VI pairs was r{sup -}{sub Inter}=0.52±0.25, which was significantly lower than for intrafraction pairs (r{sup -}{sub Intra}=0.67±0.20, p = 0.0002). Conversely, mean absolute ventilation differences were larger for interfraction pairs than for intrafraction pairs, with |ΔV{sup -}{sub Inter}|=0.42±0.65 and |ΔV{sup -}{sub Intra}|=0.32±0.53, respectively (p < 10{sup −15}). Applying a gamma analysis with ventilation/distance tolerance of 25%/10 mm, we observed mean pass rate of (69% ± 20%) for interfraction VIs, which was significantly lower compared to intrafraction pairs (80% ± 15%, with p ∼ 0.0003). Compared to the first day scans, all patients experienced at least one subsequent change in median ipsilateral ventilation ≥10%. Patients experienced both positive and negative ventilation changes throughout treatment, with the maximum change occurring at different weeks for different patients. Conclusions: The authors’ data support the hypothesis that interfraction ventilation changes are larger than intrafraction ventilation changes for LA-NSCLC patients over a course of conventional lung cancer radiation therapy. Longitudinal ventilation changes are observed to be highly patient-dependent, supporting a possible role for adaptive ventilation guidance based on repeat 4D-CBCT VIs. We anticipate that future improvement of 4D-CBCT image reconstruction algorithms will improve the capability of 4D-CBCT VI to resolve interfraction ventilation changes.« less

Measuring interfraction and intrafraction lung function changes during radiation therapy using four-dimensional cone beam CT ventilation imaging.

PubMed

Kipritidis, John; Hugo, Geoffrey; Weiss, Elisabeth; Williamson, Jeffrey; Keall, Paul J

2015-03-01

Adaptive ventilation guided radiation therapy could minimize the irradiation of healthy lung based on repeat lung ventilation imaging (VI) during treatment. However the efficacy of adaptive ventilation guidance requires that interfraction (e.g., week-to-week), ventilation changes are not washed out by intrafraction (e.g., pre- and postfraction) changes, for example, due to patient breathing variability. The authors hypothesize that patients undergoing lung cancer radiation therapy exhibit larger interfraction ventilation changes compared to intrafraction function changes. To test this, the authors perform the first comparison of interfraction and intrafraction lung VI pairs using four-dimensional cone beam CT ventilation imaging (4D-CBCT VI), a novel technique for functional lung imaging. The authors analyzed a total of 215 4D-CBCT scans acquired for 19 locally advanced non-small cell lung cancer (LA-NSCLC) patients over 4-6 weeks of radiation therapy. This set of 215 scans was sorted into 56 interfraction pairs (including first day scans and each of treatment weeks 2, 4, and 6) and 78 intrafraction pairs (including pre/postfraction scans on the same-day), with some scans appearing in both sets. VIs were obtained from the Jacobian determinant of the transform between the 4D-CBCT end-exhale and end-inhale images after deformable image registration. All VIs were deformably registered to their corresponding planning CT and normalized to account for differences in breathing effort, thus facilitating image comparison in terms of (i) voxelwise Spearman correlations, (ii) mean image differences, and (iii) gamma pass rates for all interfraction and intrafraction VI pairs. For the side of the lung ipsilateral to the tumor, we applied two-sided t-tests to determine whether interfraction VI pairs were more different than intrafraction VI pairs. The (mean ± standard deviation) Spearman correlation for interfraction VI pairs was r̄(Inter)=0.52±0.25, which was significantly lower than for intrafraction pairs (r̄(Intra)=0.67±0.20, p = 0.0002). Conversely, mean absolute ventilation differences were larger for interfraction pairs than for intrafraction pairs, with |ΔV̄(Inter)|=0.42±0.65 and |ΔV̄(Intra)|=0.32±0.53, respectively (p < 10(-15)). Applying a gamma analysis with ventilation/distance tolerance of 25%/10 mm, we observed mean pass rate of (69% ± 20%) for interfraction VIs, which was significantly lower compared to intrafraction pairs (80% ± 15%, with p ∼ 0.0003). Compared to the first day scans, all patients experienced at least one subsequent change in median ipsilateral ventilation ≥10%. Patients experienced both positive and negative ventilation changes throughout treatment, with the maximum change occurring at different weeks for different patients. The authors' data support the hypothesis that interfraction ventilation changes are larger than intrafraction ventilation changes for LA-NSCLC patients over a course of conventional lung cancer radiation therapy. Longitudinal ventilation changes are observed to be highly patient-dependent, supporting a possible role for adaptive ventilation guidance based on repeat 4D-CBCT VIs. We anticipate that future improvement of 4D-CBCT image reconstruction algorithms will improve the capability of 4D-CBCT VI to resolve interfraction ventilation changes.

Demonstration of spectral correlation control in a source of polarization-entangled photon pairs at telecom wavelength.

PubMed

Lutz, Thomas; Kolenderski, Piotr; Jennewein, Thomas

2014-03-15

Spectrally correlated photon pairs can be used to improve the performance of long-range fiber-based quantum communication protocols. We present a source based on spontaneous parametric downconversion, which allows one to control spectral correlations within the entangled photon pair without spectral filtering by changing the pump-pulse duration or the characteristics of the coupled spatial modes. The spectral correlations and polarization entanglement are characterized. We find that the generated photon pairs can feature both positive spectral correlations, decorrelation, or negative correlations at the same time as polarization entanglement with a high fidelity of 0.97 (no background subtraction) with the expected Bell state.

Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

PubMed

Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

2009-03-18

It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.

PubMed

Grove, A; Figueiredo, M L; Galeone, A; Mayol, L; Geiduschek, E P

1997-05-16

The DNA-bending protein TF1 is the Bacillus subtilis bacteriophage SPO1-encoded homolog of the bacterial HU proteins and the Escherichia coli integration host factor. We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility. Here, we show that two hmU-A base pair steps coinciding with two previously proposed sites of DNA distortion are critical for complex formation. The affinity of TF1 is reduced 10-fold when both of these hmU-A base pair steps are replaced with A-hmU, G-C, or C-G steps; only modest changes in affinity result when substitutions are made at other base pairs of the TF1 binding site. Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA. T-DNA constructs with 3-base bulges spaced apart by 9 base pairs of duplex also generate nM affinity of TF1. We suggest that twin hmU-A base pair steps located at the proposed sites of distortion are key to target site selection by TF1 and that recognition is based largely, if not entirely, on sequence-dependent DNA flexibility.

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

DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds

PubMed Central

Potapova, Olga; Chan, Chikio; DeLucia, Angela M.; Helquist, Sandra A.; Kool, Eric T.; Grindley, Nigel D. F.; Joyce, Catherine M.

2008-01-01

We report the first pre-steady-state kinetic studies of DNA replication in the absence of hydrogen bonds. We have used nonpolar nucleotide analogues that mimic the shape of a Watson-Crick base pair in order to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA Polymerase I from Escherichia coli. With a thymine isostere lacking hydrogen bonding ability in the nascent pair, the efficiency (kpol/Kd) of the polymerase reaction is decreased by 30-fold, affecting ground state (Kd) and transition state (kpol) approximately equally. When both thymine and adenine analogues in the nascent pair lack hydrogen bonding ability, the efficiency of the polymerase reaction is decreased by about 1000-fold, with most the decrease attributable to the transition state. Reactions using nonpolar analogues at the primer terminal base pair demonstrated the requirement for a hydrogen bond between the polymerase and the minor groove of the primer-terminal base. The R668A mutation of Klenow fragment abolished this requirement, identifying R668 as the probable hydrogen bond donor. Detailed examination of the kinetic data suggested that Klenow fragment has an extremely low tolerance of even minor deviations of the analogue base pairs from ideal Watson-Crick geometry. Consistent with this idea, some analogue pairings were better tolerated by Klenow fragment mutants having more spacious active sites. By contrast, the Y-family polymerase Dbh was much less sensitive to changes in base pair dimensions, and more dependent on hydrogen bonding between base-paired partners. PMID:16411765

Carbon Nanotube-based Sensor and Method for Continually Sensing Changes in a Structure

NASA Technical Reports Server (NTRS)

Jordan, Jeffry D. (Inventor); Watkins, Anthony Neal (Inventor); Oglesby, Donald M. (Inventor); Ingram, JoAnne L. (Inventor)

2007-01-01

A sensor has a plurality of carbon nanotube (CNT)-based conductors operatively positioned on a substrate. The conductors are arranged side-by-side, such as in a substantially parallel relationship to one another. At least one pair of spaced-apart electrodes is coupled to opposing ends of the conductors. A portion of each of the conductors spanning between each pair of electrodes comprises a plurality of carbon nanotubes arranged end-to-end and substantially aligned along an axis. Because a direct correlation exists between resistance of a carbon nanotube and carbon nanotube strain, changes experienced by the portion of the structure to which the sensor is coupled induce a change in electrical properties of the conductors.

Duration comparison: relative stimulus differences stimulus age, and stimulus predictiveness.

PubMed Central

Stubbs, D A; Dreyfus, L R; Fetterman, J G; Boynton, D M; Locklin, N; Smith, L D

1994-01-01

Under a psychophysical trials procedure, pigeons were presented with a red light of one duration followed by a green light of a second duration. Eight geometrically spaced base durations were paired with one of four shorter and four longer durations as the alternate member of a duration pair, with different pairs randomly intermixed. One choice was reinforced if red had lasted longer than green, and a second choice was reinforced if green had lasted longer. Performance was compared when all the base durations and their pair members were included (entire-range condition) or when only the four longest base durations and their comparison durations (restricted-range condition) were used. Discrimination sensitivity decreased for longer duration pairs under both conditions, supporting a memory-based account. Sensitivity was lower under the restricted-range condition. Under both conditions, a bias to report "green as longer" increased as the second green duration increased. Bias changed as a matching function of the green-duration predictiveness of the correct choice. The results are related to a quantitative model of timing and remembering proposed by Staddon. PMID:8064211

Quantum cryptography using entangled photons in energy-time bell states

PubMed

Tittel; Brendel; Zbinden; Gisin

2000-05-15

We present a setup for quantum cryptography based on photon pairs in energy-time Bell states and show its feasibility in a laboratory experiment. Our scheme combines the advantages of using photon pairs instead of faint laser pulses and the possibility to preserve energy-time entanglement over long distances. Moreover, using four-dimensional energy-time states, no fast random change of bases is required in our setup: Nature itself decides whether to measure in the energy or in the time base, thus rendering eavesdropper attacks based on "photon number splitting" less efficient.

Age-Related Brain Activation Changes during Rule Repetition in Word-Matching.

PubMed

Methqal, Ikram; Pinsard, Basile; Amiri, Mahnoush; Wilson, Maximiliano A; Monchi, Oury; Provost, Jean-Sebastien; Joanette, Yves

2017-01-01

Objective: The purpose of this study was to explore the age-related brain activation changes during a word-matching semantic-category-based task, which required either repeating or changing a semantic rule to be applied. In order to do so, a word-semantic rule-based task was adapted from the Wisconsin Sorting Card Test, involving the repeated feedback-driven selection of given pairs of words based on semantic category-based criteria. Method: Forty healthy adults (20 younger and 20 older) performed a word-matching task while undergoing a fMRI scan in which they were required to pair a target word with another word from a group of three words. The required pairing is based on three word-pair semantic rules which correspond to different levels of semantic control demands: functional relatedness, moderately typical-relatedness (which were considered as low control demands), and atypical-relatedness (high control demands). The sorting period consisted of a continuous execution of the same sorting rule and an inferred trial-by-trial feedback was given. Results: Behavioral performance revealed increases in response times and decreases of correct responses according to the level of semantic control demands (functional vs. typical vs. atypical) for both age groups (younger and older) reflecting graded differences in the repetition of the application of a given semantic rule. Neuroimaging findings of significant brain activation showed two main results: (1) Greater task-related activation changes for the repetition of the application of atypical rules relative to typical and functional rules, and (2) Changes (older > younger) in the inferior prefrontal regions for functional rules and more extensive and bilateral activations for typical and atypical rules. Regarding the inter-semantic rules comparison, only task-related activation differences were observed for functional > typical (e.g., inferior parietal and temporal regions bilaterally) and atypical > typical (e.g., prefrontal, inferior parietal, posterior temporal, and subcortical regions). Conclusion: These results suggest that healthy cognitive aging relies on the adaptive changes of inferior prefrontal resources involved in the repetitive execution of semantic rules, thus reflecting graded differences in support of task demands.

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.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.

PubMed

Gertz, E Michael; Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

PubMed Central

Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A.

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees. PMID:27362268

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).

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

Identification in a pseudoknot of a U.G motif essential for the regulation of the expression of ribosomal protein S15.

PubMed

Bénard, L; Mathy, N; Grunberg-Manago, M; Ehresmann, B; Ehresmann, C; Portier, C

1998-03-03

The ribosomal protein S15 from Escherichia coli binds to a pseudoknot in its own messenger. This interaction is an essential step in the mechanism of S15 translational autoregulation. In a previous study, a recognition determinant for S15 autoregulation, involving a U.G wobble pair, was located in the center of stem I of the pseudoknot. In this study, an extensive mutagenesis analysis has been conducted in and around this U.G pair by comparing the effects of these mutations on the expression level of S15. The results show that the U.G wobble pair cannot be substituted by A.G, C.A, A.C, G.U, or C.G without loss of the autocontrol. In addition, the base pair C.G, adjacent to the 5' side of U, cannot be flipped or changed to another complementary base pair without also inducing derepression of translation. A unique motif, made of only two adjacent base pairs, U.G/C.G, is essential for S15 autoregulation and is presumably involved in direct recognition by the S15 protein.

Identification in a pseudoknot of a U⋅G motif essential for the regulation of the expression of ribosomal protein S15

PubMed Central

Bénard, Lionel; Mathy, Nathalie; Grunberg-Manago, Marianne; Ehresmann, Bernard; Ehresmann, Chantal; Portier, Claude

1998-01-01

The ribosomal protein S15 from Escherichia coli binds to a pseudoknot in its own messenger. This interaction is an essential step in the mechanism of S15 translational autoregulation. In a previous study, a recognition determinant for S15 autoregulation, involving a U⋅G wobble pair, was located in the center of stem I of the pseudoknot. In this study, an extensive mutagenesis analysis has been conducted in and around this U⋅G pair by comparing the effects of these mutations on the expression level of S15. The results show that the U⋅G wobble pair cannot be substituted by A⋅G, C⋅A, A⋅C, G⋅U, or C⋅G without loss of the autocontrol. In addition, the base pair C⋅G, adjacent to the 5′ side of U, cannot be flipped or changed to another complementary base pair without also inducing derepression of translation. A unique motif, made of only two adjacent base pairs, U⋅G/C⋅G, is essential for S15 autoregulation and is presumably involved in direct recognition by the S15 protein. PMID:9482926

Design of multi-wavelength tunable filter based on Lithium Niobate

NASA Astrophysics Data System (ADS)

Zhang, Ailing; Yao, Yuan; Zhang, Yue; Song, Hongyun

2018-05-01

A multi-wavelength tunable filter is designed. It consists of multiple waveguides among multiple waveguide gratings. A pair of electrodes were placed on both sides of each waveguide. The tunable filter uses the electro-optic effect of Lithium Niobate to tune the phase caused by each waveguide. Consequently, the wavelength and wavelength spacing of the filter are tuned by changing external voltages added on the electrode pairs. The tunable property of the filter is analyzed by phase matching condition and transfer-matrix method. Numerical results show that not only multiple wavelengths with narrow bandwidth are tuned with nearly equal spacing by synchronously changing the voltages added on all electrode pairs, but also the number of wavelengths is determined by the number of phase shifts caused by electrode pairs. Furthermore, due to the electro-optic effect of Lithium Niobate, the tuning speed of the filter can reach the order of ns.

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.

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

Temporal Wind Pairs for Space Launch Vehicle Capability Assessment and Risk Mitigation

NASA Technical Reports Server (NTRS)

Decker, Ryan K.; Barbre, Robert E., Jr.

2015-01-01

Space launch vehicles incorporate upper-level wind assessments to determine wind effects on the vehicle and for a commit to launch decision. These assessments make use of wind profiles measured hours prior to launch and may not represent the actual wind the vehicle will fly through. Uncertainty in the winds over the time period between the assessment and launch introduces uncertainty in assessment of vehicle controllability and structural integrity that must be accounted for to ensure launch safety. Temporal wind pairs are used in engineering development of allowances to mitigate uncertainty. Five sets of temporal wind pairs at various times (0.75, 1.5, 2, 3 and 4-hrs) at the United States Air Force Eastern Range and Western Range, as well as the National Aeronautics and Space Administration's Wallops Flight Facility are developed for use in upper-level wind assessments on vehicle performance. Historical databases are compiled from balloon-based and vertically pointing Doppler radar wind profiler systems. Various automated and manual quality control procedures are used to remove unacceptable profiles. Statistical analyses on the resultant wind pairs from each site are performed to determine if the observed extreme wind changes in the sample pairs are representative of extreme temporal wind change. Wind change samples in the Eastern Range and Western Range databases characterize extreme wind change. However, the small sample sizes in the Wallops Flight Facility databases yield low confidence that the sample population characterizes extreme wind change that could occur.

Temporal Wind Pairs for Space Launch Vehicle Capability Assessment and Risk Mitigation

NASA Technical Reports Server (NTRS)

Decker, Ryan K.; Barbre, Robert E., Jr.

2014-01-01

Space launch vehicles incorporate upper-level wind assessments to determine wind effects on the vehicle and for a commit to launch decision. These assessments make use of wind profiles measured hours prior to launch and may not represent the actual wind the vehicle will fly through. Uncertainty in the winds over the time period between the assessment and launch introduces uncertainty in assessment of vehicle controllability and structural integrity that must be accounted for to ensure launch safety. Temporal wind pairs are used in engineering development of allowances to mitigate uncertainty. Five sets of temporal wind pairs at various times (0.75, 1.5, 2, 3 and 4-hrs) at the United States Air Force Eastern Range and Western Range, as well as the National Aeronautics and Space Administration's Wallops Flight Facility are developed for use in upper-level wind assessments on vehicle performance. Historical databases are compiled from balloon-based and vertically pointing Doppler radar wind profiler systems. Various automated and manual quality control procedures are used to remove unacceptable profiles. Statistical analyses on the resultant wind pairs from each site are performed to determine if the observed extreme wind changes in the sample pairs are representative of extreme temporal wind change. Wind change samples in the Eastern Range and Western Range databases characterize extreme wind change. However, the small sample sizes in the Wallops Flight Facility databases yield low confidence that the sample population characterizes extreme wind change that could occur.

Building Development Monitoring in Multitemporal Remotely Sensed Image Pairs with Stochastic Birth-Death Dynamics.

PubMed

Benedek, C; Descombes, X; Zerubia, J

2012-01-01

In this paper, we introduce a new probabilistic method which integrates building extraction with change detection in remotely sensed image pairs. A global optimization process attempts to find the optimal configuration of buildings, considering the observed data, prior knowledge, and interactions between the neighboring building parts. We present methodological contributions in three key issues: 1) We implement a novel object-change modeling approach based on Multitemporal Marked Point Processes, which simultaneously exploits low-level change information between the time layers and object-level building description to recognize and separate changed and unaltered buildings. 2) To answer the challenges of data heterogeneity in aerial and satellite image repositories, we construct a flexible hierarchical framework which can create various building appearance models from different elementary feature-based modules. 3) To simultaneously ensure the convergence, optimality, and computation complexity constraints raised by the increased data quantity, we adopt the quick Multiple Birth and Death optimization technique for change detection purposes, and propose a novel nonuniform stochastic object birth process which generates relevant objects with higher probability based on low-level image features.

Identifying miRNA-mediated signaling subpathways by integrating paired miRNA/mRNA expression data with pathway topology.

PubMed

Vrahatis, Aristidis G; Dimitrakopoulos, Georgios N; Tsakalidis, Athanasios K; Bezerianos, Anastasios

2015-01-01

In the road for network medicine the newly emerged systems-level subpathway-based analysis methods offer new disease genes, drug targets and network-based biomarkers. In parallel, paired miRNA/mRNA expression data enable simultaneously monitoring of the micronome effect upon the signaling pathways. Towards this orientation, we present a methodological pipeline for the identification of differentially expressed subpathways along with their miRNA regulators by using KEGG signaling pathway maps, miRNA-target interactions and expression profiles from paired miRNA/mRNA experiments. Our pipeline offered new biological insights on a real application of paired miRNA/mRNA expression profiles with respect to the dynamic changes from colostrum to mature milk whey; several literature supported genes and miRNAs were recontextualized through miRNA-mediated differentially expressed subpathways.

How Mg2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study.

PubMed

Shanker, Sudhanshu; Bandyopadhyay, Pradipta

2017-08-01

The non-Watson-Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg 2+ ions through water-mediated interaction. It is important to know the synergic role of Mg 2+ and the water network surrounding Mg 2+ in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg 2+ is pulled from RNA, which causes disturbance of the water network. It was found that Mg 2+ remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg 2+ interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg 2+ and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we propose that hexahydrated Mg 2+ is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the [Formula: see text]. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1×1 Nucleotide UU Internal Loop Conformations⊥

PubMed Central

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D.

2011-01-01

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5′CUG/3′GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures are disclosed of a model DM1 triplet repeating construct, 5′r(UUGGGC(CUG)3GUCC)2, refined to 2.20 Å and 1.52 Å resolution. Here, differences in orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that non-canonical 1×1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′UU forms one hydrogen-bonded pairs with a 5′UU of a neighboring helix in the unit cell to form a pseudo-infinite helix. The central 1×1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1×1 nucleotide UU internal loops each form a one hydrogen-bonded pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonical paired bases show no change in base pairing, in CUGb the terminal 1×1 nucleotide UU internal loops form now two hydrogen-bonded pairs. Thus, the shift in major groove induced by the 5′UU dangling end alters non-canonical base patterns. Collectively, these structures indicate that 1×1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands. PMID:21988728

Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

PubMed

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W; Disney, Matthew D

2011-11-15

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

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

Kumar, Amit; Park, HaJeung; Fang, Pengfei

2012-03-27

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations.more » In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.« less

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism.

PubMed

Reymer, Anna; Zakrzewska, Krystyna; Lavery, Richard

2018-02-28

Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure.

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

PubMed Central

Reymer, Anna; Zakrzewska, Krystyna; Lavery, Richard

2018-01-01

Abstract Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure. PMID:29267977

Effect of Destined High-Pressure Torsion on the Structure and Mechanical Properties of Rare Earth-Based Metallic Glasses

NASA Astrophysics Data System (ADS)

Zhao, W.; Cheng, H.; Jiang, X.; Wu, M. L.; Li, G.

2018-03-01

Changes in the atomic structure and mechanical properties of rare earth-based metallic glasses caused by destined high-pressure torsion (HPT) were studied by X-ray diffraction synchrotron radiation and nanoindentation. Results showed that destined HPT improved nanohardness and wear resistance, which indicated the significant contributions of this technique. The diffraction patterns showed that the contents of pairs between solvent and solute atoms with a large negative mixing enthalpy increased, whereas those of pairs between solvent atoms and between solute atoms decreased after destined HPT. Thus, the process was improved by increasing the proportion of high-intensity pairs between solvent and solute atoms.

Using electron irradiation to probe iron-based superconductors

NASA Astrophysics Data System (ADS)

Cho, Kyuil; Kończykowski, M.; Teknowijoyo, S.; Tanatar, M. A.; Prozorov, R.

2018-06-01

High-energy electron irradiation at low temperatures is an efficient and controlled way to create vacancy–interstitial Frenkel pairs in a crystal lattice, thereby inducing nonmagnetic point-like scattering centers. In combination with London penetration depth and resistivity measurements, the electron irradiation was used as a phase-sensitive probe to study the superconducting order parameter in iron-based superconductors (FeSCs), lending strong support to sign-changing s ± pairing. Here, we review the key results of the effect of electron irradiation in FeSCs.

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.

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.

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

Gao, X.; Patel, D.J.

The authors report on two-dimensional proton NMR studies of echinomycin complexes with the self-complementary d(A1-C2-G3-Tr) and d(T1-C2-G3-A4) duplexes in aqueous solution. The exchangeable and nonexchangeable antibiotic and nucleic acid protons in the 1 echinomycin per tetranucleotide duplex complexes have been assigned from analyses of scalar coupling and distance connectivities in two-dimensional data sets records in H/sub 2/O and D/sub 2/O solution. An analysis of the intermolecular NOE patterns for both complexes combined with large upfield imino proton and large downfield phosphorus complexation chemical shift changes demonstrates that the two quinoxaline chromophores of echinomycin bisintercalate into the minor groove surrounding themore » dC-dG step of each tetranucleotide duplex. Further, the quinoxaline rings selectively stack between A1 and C2 bases in the d(ACGT) complex and between T1 and C2 bases in the d(TCGA) complex. The intermolecular NOE patterns and the base and sugar proton chemical shifts for residues C2 and G3 are virtually identical for the d(ACGT) and d(TCGA) complexes. A large set of intermolecular contacts established from nuclear Overhauser effects (NOEs) between antibiotic and nucleic acid protons in the echinomycin-tetranucleotide complexes in solution are consistent with corresponding contacts reported for echinomycin-oligonucleotide complexes in the crystalline state. The authors demonstrate that the G x G base pairs adopt Watson-Crick pairing in both d(ACGT) and d(TCGA) complexes in solution. By contrast, the A1 x T4 base pairs adopt Hoogsteen pairing for the echinomycin-d(A1-C2-G3-Tr) complex while the T1 x A4 base pairs adopt Watson-Crick pairing for the echinomycin-d(T1-C2-G3-A4) complex in aqueous solution. These results emphasize the role of sequence in discriminating between Watson-Crick and Hoogsteen pairs at base pairs flanking the echinomycin bisintercalation site in solution.« less

Orbital-selective pairing and superconductivity in iron selenides

NASA Astrophysics Data System (ADS)

Nica, Emilian M.; Yu, Rong; Si, Qimiao

2017-12-01

An important challenge in condensed matter physics is understanding iron-based superconductors. Among these systems, the iron selenides hold the record for highest superconducting transition temperature and pose especially striking puzzles regarding the nature of superconductivity. The pairing state of the alkaline iron selenides appears to be of d-wave type based on the observation of a resonance mode in neutron scattering, while it seems to be of s-wave type from the nodeless gaps observed everywhere on the Fermi surface. Here we propose an orbital-selective pairing state, dubbed sτ3, as a natural explanation of these disparate properties. The pairing function, containing a matrix τ3 in the basis of 3d-electron orbitals, does not commute with the kinetic part of the Hamiltonian. This dictates the existence of both intraband and interband pairing terms in the band basis. A spin resonance arises from a d-wave-type sign change in the intraband pairing component, whereas the quasiparticle excitation is fully gapped on the FS due to an s-wave-like form factor associated with the addition in quadrature of the intraband and interband pairing terms. We demonstrate that this pairing state is energetically favored when the electron correlation effects are orbitally selective. More generally, our results illustrate how the multiband nature of correlated electrons affords unusual types of superconducting states, thereby shedding new light not only on the iron-based materials but also on a broad range of other unconventional superconductors such as heavy fermion and organic systems.

PAIRS, The GIS-Based Incident Response System for Pennsylvania, and NASA

NASA Technical Reports Server (NTRS)

Conrad, Eric; Arbegast, Daniel; Maynard, Nancy; Vicente, Gilberto

2003-01-01

Over the past several years the Pennsylvania Departments of Environmental Protection (DEP), Health (DOH), and Agriculture (PDA) built the GIs-based Pennsylvania West Nile Surveillance System. That system has become a model for collecting data that has a field component, laboratory component, reporting and mapping component, and a public information component. Given the success of the West Nile Virus System and the events of September 11, 2001, DEP then embarked on the development of the Pennsylvania Incident Response System, or PAIRS. PAIRS is an effective GIs-based approach to providing a system for response to incidents of any kind, including terrorism because it is building upon the existing experience, infrastructure and databases that were successfully developed to respond to the West Nile Virus by DEP, DOH, and PDA. The proposed system can be described as one that supports data acquisition, laboratory forensics, decision making/response, and communications. Decision makers will have tools to view and analyze data from various sources and, at the same time, to communicate with the large numbers of people responding to the same incident. Recent collaborations with NASA partners are creating mechanisms for the PAIRS system to incorporate space-based and other remote sensing geophysical parameters relevant to public health assessment and management, such as surface temperatures, precipitation, land cover/land use change, and humidity. This presentation will describe the PAIRS system and outline the Pennsylvania-NASA collaboration for integration of space-based data into the PAIRS system.

Changes in latent fingerprint examiners' markup between analysis and comparison.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2015-02-01

After the initial analysis of a latent print, an examiner will sometimes revise the assessment during comparison with an exemplar. Changes between analysis and comparison may indicate that the initial analysis of the latent was inadequate, or that confirmation bias may have affected the comparison. 170 volunteer latent print examiners, each randomly assigned 22 pairs of prints from a pool of 320 total pairs, provided detailed markup documenting their interpretations of the prints and the bases for their comparison conclusions. We describe changes in value assessments and markup of features and clarity. When examiners individualized, they almost always added or deleted minutiae (90.3% of individualizations); every examiner revised at least some markups. For inconclusive and exclusion determinations, changes were less common, and features were added more frequently when the image pair was mated (same source). Even when individualizations were based on eight or fewer corresponding minutiae, in most cases some of those minutiae had been added during comparison. One erroneous individualization was observed: the markup changes were notably extreme, and almost all of the corresponding minutiae had been added during comparison. Latents assessed to be of value for exclusion only (VEO) during analysis were often individualized when compared to a mated exemplar (26%); in our previous work, where examiners were not required to provide markup of features, VEO individualizations were much less common (1.8%). Published by Elsevier Ireland Ltd.

Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.

PubMed

Xia, Shuangluo; Konigsberg, William H

2014-04-01

Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn(2+) indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affected by its microenvironment, we determined 10 structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states. © 2014 The Protein Society.

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules

PubMed Central

Nakano, Shu-ichi; Uotani, Yuuki; Sato, Yuichi; Oka, Hirohito; Fujii, Masayuki; Sugimoto, Naoki

2013-01-01

DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2′-deoxyadenosine and 2′-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2′-deoxycytidine lesions form the base pair with guanine while the 2′-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides. PMID:23873956

Base pairing between the 3' exon and an internal guide sequence increases 3' splice site specificity in the Tetrahymena self-splicing rRNA intron.

PubMed Central

Suh, E R; Waring, R B

1990-01-01

It has been proposed that recognition of the 3' splice site in many group I introns involves base pairing between the start of the 3' exon and a region of the intron known as the internal guide sequence (R. W. Davies, R. B. Waring, J. Ray, T. A. Brown, and C. Scazzocchio, Nature [London] 300:719-724, 1982). We have examined this hypothesis, using the self-splicing rRNA intron from Tetrahymena thermophila. Mutations in the 3' exon that weaken this proposed pairing increased use of a downstream cryptic 3' splice site. Compensatory mutations in the guide sequence that restore this pairing resulted in even stronger selection of the normal 3' splice site. These changes in 3' splice site usage were more pronounced in the background of a mutation (414A) which resulted in an adenine instead of a guanine being the last base of the intron. These results show that the proposed pairing (P10) plays an important role in ensuring that cryptic 3' splice sites are selected against. Surprisingly, the 414A mutation alone did not result in activation of the cryptic 3' splice site. Images PMID:2342465

From Local to Global: A Birds-Eye View of Changing Landscapes

ERIC Educational Resources Information Center

Wilson, Courtney R.; Murphy, James; Trautmann, Nancy M.; Makinster, James G.

2009-01-01

As part of a curriculum development project entitled Crossing Boundaries, these authors designed an inquiry-based activity that introduces students to landscape change and potential impacts on associated biological communities. Using pairs of current and historical satellite images, students explore landscape change in a variety of U.S. and…

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

PubMed

Csaszar, K; Spacková, N; Stefl, R; Sponer, J; Leontis, N B

2001-11-09

Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at specific sites. The most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. To increase sampling of rare events, the native simulation was continued at 400 K. A partial, irreversible unfolding of the molecule was initiated by slippage of C8(N3+) relative to G12 and continued by sudden concerted changes in hydrogen-bonding involving A23, A24, and A25. These events were followed by a gradual loss of stacking interactions in loop 2. Of the Watson-Crick base-pairs, only the 5'-terminal pair of stem 1 dissociated at 400 K, while the trans sugar-edge/sugar-edge A20.G4 interaction remained surprisingly stable. Four additional room-temperature simulations were carried out to obtain insights into the structural and dynamic effects of selected mutations. In two of these, C8 was left unprotonated. Considerable local rearrangements occurred that were not observed in the crystal structure, thus confirming N3-protonation of C8 in the native molecule. We also investigated the effect of mutating C8(N3+) to U8, to correlate with experimental and phylogenetic studies, and of changing the G4 x C17 base-pair to A4 x U17 to weaken the trans sugar-edge interaction between positions 4 and 20 and to test models of unfolding. The simulations indicate that the C8 x G12 x C26 base-triple at the junction is the most labile region of the frame-shifting pseudoknot. They provide insights into the roles of the other non-Watson-Crick base-pairs in the early stages of unfolding of the pseudoknot, which must occur to allow readthrough of the message by the ribosome. The simulations revealed several critical, highly ordered hydration sites with close to 100 % occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50 % were also observed. Copyright 2001 Academic Press.

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.

Frontal Cortex Activation Causes Rapid Plasticity of Auditory Cortical Processing

PubMed Central

Winkowski, Daniel E.; Bandyopadhyay, Sharba; Shamma, Shihab A.

2013-01-01

Neurons in the primary auditory cortex (A1) can show rapid changes in receptive fields when animals are engaged in sound detection and discrimination tasks. The source of a signal to A1 that triggers these changes is suspected to be in frontal cortical areas. How or whether activity in frontal areas can influence activity and sensory processing in A1 and the detailed changes occurring in A1 on the level of single neurons and in neuronal populations remain uncertain. Using electrophysiological techniques in mice, we found that pairing orbitofrontal cortex (OFC) stimulation with sound stimuli caused rapid changes in the sound-driven activity within A1 that are largely mediated by noncholinergic mechanisms. By integrating in vivo two-photon Ca2+ imaging of A1 with OFC stimulation, we found that pairing OFC activity with sounds caused dynamic and selective changes in sensory responses of neural populations in A1. Further, analysis of changes in signal and noise correlation after OFC pairing revealed improvement in neural population-based discrimination performance within A1. This improvement was frequency specific and dependent on correlation changes. These OFC-induced influences on auditory responses resemble behavior-induced influences on auditory responses and demonstrate that OFC activity could underlie the coordination of rapid, dynamic changes in A1 to dynamic sensory environments. PMID:24227723

Utilizing Molecular Dynamics ' Multipotent Methodologies to Measure Microscopic Motions of DNA Molecules: A Magniloquent Manuscript On DNA's Means and Mannerisms

NASA Astrophysics Data System (ADS)

Kingsland, Addie

DNA is an amazing molecule which is the basic template for all genetics. It is the primary molecule for storing biological information, and has many applications in nanotechnology. Double-stranded DNA may contain mismatched base pairs beyond the Watson-Crick pairs guanine-cytosine and adenine-thymine. To date, no one has found a physical property of base pair mismatches which describes the behavior of naturally occurring mismatch repair enzymes. Many materials properties of DNA are also unknown, for instance, when pulling DNA in different configurations, different energy differences are observed with no obvious reason why. DNA mismatches also affect their local environment, for instance changing the quantum yield of nearby azobenzene moieties. We utilize molecular dynamics computer simulations to study the structure and dynamics for both matched and mismatched base pairs, within both biological and materials contexts, and in both equilibrium and biased dynamics. We show that mismatched pairs shift further in the plane normal to the DNA strand and are more likely to exhibit non-canonical structures, including the e-motif. Base pair mismatches alter their local environment, affecting the trans- to cis- photoisomerization quantum yield of azobenzene, as well as increasing the likelihood of observing the e-motif. We also show that by using simulated data, we can give new insights on theoretical models to calculate the energetics of pulling DNA strands apart. These results, all relatively inexpensive on modern computer hardware, can help guide the design of DNA-based nanotechnologies, as well as give new insights into the functioning of mismatch repair systems in cancer prevention.

Evolutionary prisoner's dilemma games coevolving on adaptive networks.

PubMed

Lee, Hsuan-Wei; Malik, Nishant; Mucha, Peter J

2018-02-01

We study a model for switching strategies in the Prisoner's Dilemma game on adaptive networks of player pairings that coevolve as players attempt to maximize their return. We use a node-based strategy model wherein each player follows one strategy at a time (cooperate or defect) across all of its neighbors, changing that strategy and possibly changing partners in response to local changes in the network of player pairing and in the strategies used by connected partners. We compare and contrast numerical simulations with existing pair approximation differential equations for describing this system, as well as more accurate equations developed here using the framework of approximate master equations. We explore the parameter space of the model, demonstrating the relatively high accuracy of the approximate master equations for describing the system observations made from simulations. We study two variations of this partner-switching model to investigate the system evolution, predict stationary states, and compare the total utilities and other qualitative differences between these two model variants.

A structural MRI study in monozygotic twins concordant or discordant for attention/hyperactivity problems: Evidence for genetic and environmental heterogeneity in the developing brain

PubMed Central

van ’t Ent, D.; Lehn, H.; Derks, E.M.; Hudziak, J.J.; Van Strien, N.M.; Veltman, D.J.; De Geus, E.J.C.; Todd, R.D.; Boomsma, D.I.

2007-01-01

Several structural brain abnormalities have been reported in patients with Attention Deficit Hyperactivity Disorder (ADHD). However, the aetiology of these brain changes is still unclear. To investigate genetic and environmental influences on ADHD related neurobiological changes we performed Voxel Based Morphometry on MRI scans from monozygotic (MZ) twins selected from a large longitudinal population database to be highly concordant or highly discordant for ratings on the Child Behavior Checklist Attention Problem scale (CBCL-AP). Children scoring low on the CBCL-AP are at low risk for ADHD, whereas children scoring high on this scale are at high risk for ADHD. Brain differences between concordant high risk twin pairs and concordant low risk twin pairs likely reflect the genetic risk for ADHD; brain differences between the low risk and high risk twins from discordant MZ twin pairs reflect the environmental risk for ADHD. A major difference between comparisons of high and low risk twins from concordant pairs and high/low twins from discordant pairs was found for the prefrontal lobes. The concordant high risk pairs showed volume loss in orbitofrontal subdivisions. High risk members from the discordant twin pairs exhibited volume reduction in the right inferior dorsolateral prefontal cortex. In addition, the posterior corpus callosum was compromised in concordant high risk pairs, only. Our findings indicate that inattention and hyperactivity symptoms are associated with anatomical abnormalities of a distributed action-attentional network. Different brain areas of this network appear to be affected in inattention/hyperactivity caused by genetic (i.e., high concordant MZ pairs) versus environmental (i.e., high-low discordant MZ pairs) risk factors. These results provide clues that further our understanding of brain alterations in ADHD. PMID:17346990

Improved forest change detection with terrain illumination corrected landsat images

USDA-ARS?s Scientific Manuscript database

An illumination correction algorithm has been developed to improve the accuracy of forest change detection from Landsat reflectance data. This algorithm is based on an empirical rotation model and was tested on the Landsat imagery pair over Cherokee National Forest, Tennessee, Uinta-Wasatch-Cache N...

Magnetoreception in birds: different physical processes for two types of directional responses

PubMed Central

Wiltschko, Roswitha; Stapput, Katrin; Ritz, Thorsten; Thalau, Peter; Wiltschko, Wolfgang

2007-01-01

Migratory orientation in birds involves an inclination compass based on radical-pair processes. Under certain light regimes, however, “fixed-direction” responses are observed that do not undergo the seasonal change between spring and autumn typical for migratory orientation. To identify the underlying transduction mechanisms, we analyzed a fixed-direction response under a combination of 502 nm turquoise and 590 nm yellow light, with migratory orientation under 565 nm green light serving as the control. High-frequency fields, diagnostic for a radical-pair mechanism, disrupted migratory orientation without affecting fixed-direction responses. Local anaesthesia of the upper beak where magnetite is found in birds, in contrast, disrupted the fixed-direction response without affecting migratory orientation. The two types of responses are thus based on different physical principles, with the compass response based on a radical pair mechanism and the fixed-direction responses probably originating in magnetite-based receptors in the upper beak. Directional input from these receptors seems to affect the behavior only when the regular inclination compass does not work properly. Evolutionary considerations suggest that magnetite-based receptors may represent an ancient mechanism that, in birds, has been replaced by the modern inclination compass based on radical-pair processes now used for directional orientation. PMID:19404459

Carbon nanotube-based sensor and method for detection of crack growth in a structure

NASA Technical Reports Server (NTRS)

Smits, Jan M. (Inventor); Moore, Thomas C. (Inventor); Kite, Marlen T. (Inventor); Wincheski, Russell A. (Inventor); Ingram, JoAnne L. (Inventor); Watkins, Anthony N. (Inventor); Williams, Phillip A. (Inventor)

2007-01-01

A sensor has a plurality of carbon nanotube (CNT)-based conductors operatively positioned on a substrate. The conductors are arranged side-by-side, such as in a substantially parallel relationship to one another. At least one pair of spaced-apart electrodes is coupled to opposing ends of the conductors. A portion of each of the conductors spanning between each pair of electrodes comprises a plurality of carbon nanotubes arranged end-to-end and substantially aligned along an axis. Because a direct correlation exists between the resistance of a carbon nanotube and its strain, changes experienced by the portion of the structure to which the sensor is coupled induce a corresponding change in the electrical properties of the conductors, thereby enabling detection of crack growth in the structure.

The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

PubMed Central

Beisel, Chase L.; Storz, Gisela

2011-01-01

SUMMARY Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression. PMID:21292161

Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry.

PubMed

Huan, Tao; Li, Liang

2015-07-21

Generating precise and accurate quantitative information on metabolomic changes in comparative samples is important for metabolomics research where technical variations in the metabolomic data should be minimized in order to reveal biological changes. We report a method and software program, IsoMS-Quant, for extracting quantitative information from a metabolomic data set generated by chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). Unlike previous work of relying on mass spectral peak ratio of the highest intensity peak pair to measure relative quantity difference of a differentially labeled metabolite, this new program reconstructs the chromatographic peaks of the light- and heavy-labeled metabolite pair and then calculates the ratio of their peak areas to represent the relative concentration difference in two comparative samples. Using chromatographic peaks to perform relative quantification is shown to be more precise and accurate. IsoMS-Quant is integrated with IsoMS for picking peak pairs and Zero-fill for retrieving missing peak pairs in the initial peak pairs table generated by IsoMS to form a complete tool for processing CIL LC-MS data. This program can be freely downloaded from the www.MyCompoundID.org web site for noncommercial use.

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.

Proactive effects of memory in young and older adults: The role of change recollection

PubMed Central

Wahlheim, Christopher N.

2015-01-01

Age-related deficits in episodic memory are sometimes attributed to older adults being more susceptible to proactive interference. These deficits have been explained by impaired abilities to inhibit competing information and to recollect target information. In the present article, I propose that a change recollection deficit also contributes to age differences in proactive interference. Change recollection occurs when individuals can remember how information changed across episodes, and this counteracts proactive interference by preserving the temporal order of information. Three experiments were conducted to determine whether older adults are less likely to counteract proactive interference by recollecting change. Paired-associate learning paradigms with two lists of word pairs included pairs that repeated across lists, pairs that only appeared in List 2 (control items), and pairs with cues that repeated and responses that changed across lists. Young and older adults’ abilities to detect changed pairs in List 2 and to later recollect those changes at test were measured, along with cued recall of the List 2 responses and confidence in recall performance. Change recollection produced proactive facilitation in the recall of changed pairs, whereas the failure to recollect change resulted in proactive interference. Confidence judgments were sensitive to these effects. The critical finding was that older adults recollected change less than did young adults, and this partially explained older adults’ greater susceptibility to proactive interference. These findings have theoretical implications, showing that a change recollection deficit contributes to age-related deficits in episodic memory. PMID:24710672

Proactive effects of memory in young and older adults: the role of change recollection.

PubMed

Wahlheim, Christopher N

2014-08-01

Age-related deficits in episodic memory are sometimes attributed to older adults being more susceptible to proactive interference. These deficits have been explained by impaired abilities to inhibit competing information and to recollect target information. In the present article, I propose that a change recollection deficit also contributes to age differences in proactive interference. Change recollection occurs when individuals can remember how information changed across episodes, and this counteracts proactive interference by preserving the temporal order of information. Three experiments were conducted to determine whether older adults are less likely to counteract proactive interference by recollecting change. Paired-associate learning paradigms with two lists of word pairs included pairs that repeated across lists, pairs that only appeared in List 2 (control items), and pairs with cues that repeated and responses that changed across lists. Young and older adults' abilities to detect changed pairs in List 2 and to later recollect those changes at test were measured, along with cued recall of the List 2 responses and confidence in recall performance. Change recollection produced proactive facilitation in the recall of changed pairs, whereas the failure to recollect change resulted in proactive interference. Confidence judgments were sensitive to these effects. The critical finding was that older adults recollected change less than did young adults, and this partially explained older adults' greater susceptibility to proactive interference. These findings have theoretical implications, showing that a change recollection deficit contributes to age-related deficits in episodic memory.

A general framework for the solvatochromism of pyridinium phenolate betaine dyes

NASA Astrophysics Data System (ADS)

Rezende, Marcos Caroli; Aracena, Andrés

2013-02-01

A general framework for the solvatochromic behavior of pyridinium phenolate betaine dyes is presented, based on the variations with the medium of the electrophilic Fukui functions of their electron-pair donor and acceptor moieties. The model explains the ‘anomalous' solvatochromic behavior of large betaines, which change their behavior from negative to inverted, when electron-pair donor and acceptor groups are separated by a conjugated chain of variable size.

An Evaluation of Stereoscopic Digital Mammography for Earlier Detection of Breast Cancer and Reduced Rate of Recall

DTIC Science & Technology

2004-08-01

on a pair of high -resolution, LCD medical monitors. The change to the new workstation has required us to rewrite the software... In the original CRT-based system, the two 7 images forming a stereo pair were displayed alternately on the same CRT face, at a high frame rate (120 Hz...then, separately, receive the stereo screening exam on the research GE digital mammography unit.

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd.

PubMed

Duguid, J; Bloomfield, V A; Benevides, J; Thomas, G J

1993-11-01

Interactions of divalent metal cations (Mg2+, Ca2+, Ba2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) with DNA have been investigated by laser Raman spectroscopy. Both genomic calf-thymus DNA (> 23 kilobase pairs) and mononucleosomal fragments (160 base pairs) were employed as targets of metal interaction in solutions containing 5 weight-% DNA and metal:phosphate molar ratios of 0.6:1. Raman difference spectra reveal that transition metal cations (Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) induce the greatest structural changes in B-DNA. The Raman (vibrational) band differences are extensive and indicate partial disordering of the B-form backbone, reduction in base stacking, reduction in base pairing, and specific metal interaction with acceptor sites on the purine (N7) and pyrimidine (N3) rings. Many of the observed spectral changes parallel those accompanying thermal denaturation of B-DNA and suggest that the metals link the bases of denatured DNA. While exocyclic carbonyls of dT, dG, and dC may stabilize metal ligation, correlation plots show that perturbations of the carbonyls are mainly a consequence of metal-induced denaturation of the double helix. Transition metal interactions with the DNA phosphates are weak in comparison to interactions with the bases, except in the case of Cu2+, which strongly perturbs both base and phosphate group vibrations. On the other hand, the Raman signature of B-DNA is largely unperturbed by Mg2+, Ca2+, Sr2+, and Ba2+, suggesting much weaker interactions of the alkaline earth metals with both base and phosphate sites. A notable exception is a moderate perturbation by alkaline earths of purine N7 sites in 160-base pair DNA, with Ca2+ causing the greatest effect. Correlation plots demonstrate a strong interrelationship between perturbations of Raman bands assigned to ring vibrations of the bases and those of bands assigned to exocyclic carbonyls and backbone phosphodiester groups. However, strong correlations do not occur between the Raman phosphodioxy band (centered near 1092 cm-1) and other Raman bands, suggesting that the former is not highly sensitive to the structural changes induced by divalent metal cations. The structural perturbations induced by divalent cations are much greater for > 23-kilobase pair DNA than for 160-base pair DNA, as evidenced by both the Raman difference spectra and the tendency toward the formation of insoluble aggregates. In the presence of transition metals, aggregation of high-molecular-weight DNA is evident at temperatures as low as 11 degrees C. A relationship between DNA melting and aggregation is proposed in which initial metal binding at major groove sites locally destabilizes the B-DNA double helix, causing displacement of the bases away from one another and exposing additional metal binding sites. Metal cation linkage of two displaced bases would allow separate DNA strands to crosslink. Aggregation is proposed to result from the formation of an extended network of these crosslinks.

Transition from Sign-Reversed to Sign-Preserved Cooper-Pairing Symmetry in Sulfur-Doped Iron Selenide Superconductors.

PubMed

Wang, Qisi; Park, J T; Feng, Yu; Shen, Yao; Hao, Yiqing; Pan, Bingying; Lynn, J W; Ivanov, A; Chi, Songxue; Matsuda, M; Cao, Huibo; Birgeneau, R J; Efremov, D V; Zhao, Jun

2016-05-13

An essential step toward elucidating the mechanism of superconductivity is to determine the sign or phase of the superconducting order parameter, as it is closely related to the pairing interaction. In conventional superconductors, the electron-phonon interaction induces attraction between electrons near the Fermi energy and results in a sign-preserved s-wave pairing. For high-temperature superconductors, including cuprates and iron-based superconductors, prevalent weak coupling theories suggest that the electron pairing is mediated by spin fluctuations which lead to repulsive interactions, and therefore that a sign-reversed pairing with an s_{±} or d-wave symmetry is favored. Here, by using magnetic neutron scattering, a phase sensitive probe of the superconducting gap, we report the observation of a transition from the sign-reversed to sign-preserved Cooper-pairing symmetry with insignificant changes in T_{c} in the S-doped iron selenide superconductors K_{x}Fe_{2-y}(Se_{1-z}S_{z})_{2}. We show that a rather sharp magnetic resonant mode well below the superconducting gap (2Δ) in the undoped sample (z=0) is replaced by a broad hump structure above 2Δ under 50% S doping. These results cannot be readily explained by simple spin fluctuation-exchange pairing theories and, therefore, multiple pairing channels are required to describe superconductivity in this system. Our findings may also yield a simple explanation for the sometimes contradictory data on the sign of the superconducting order parameter in iron-based materials.

Cross-activation and Detraining Effects of Tongue Exercise in Aged Rats

PubMed Central

Schaser, Allison J.; Ciucci, Michelle R.; Connor, Nadine P.

2015-01-01

Voice and swallowing deficits can occur with aging. Tongue exercise paired with a swallow may be used to treat swallowing disorders, but may also benefit vocal function due to cross-system activation effects. It is unknown how exercise-based neuroplasticity contributes to behavior and maintenance following treatment. Eighty rats were used to examine behavioral parameters and changes in neurotrophins after tongue exercise paired with a swallow. Tongue forces and ultrasonic vocalizations were recorded before and after training/detraining in young and old rats. Tissue was analyzed for neurotrophin content. Results showed tongue exercise paired with a swallow was associated with increased tongue forces at all ages. Gains diminished after detraining in old rats. Age-related changes in vocalizations, neurotrophin 4 (NT4), and brain derived neurotrophic factor (BDNF) were found. Minimal cross-system activation effects were observed. Neuroplastic benefits were demonstrated with exercise in old rats through behavioral improvements and up-regulation of BDNF in the hypoglossal nucleus. Tongue exercise paired with a swallow should be developed, studied, and optimized in human clinical research to treat swallowing and voice disorders in elderly people. PMID:26477376

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

PubMed

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

MOCC: A Fast and Robust Correlation-Based Method for Interest Point Matching under Large Scale Changes

NASA Astrophysics Data System (ADS)

Zhao, Feng; Huang, Qingming; Wang, Hao; Gao, Wen

2010-12-01

Similarity measures based on correlation have been used extensively for matching tasks. However, traditional correlation-based image matching methods are sensitive to rotation and scale changes. This paper presents a fast correlation-based method for matching two images with large rotation and significant scale changes. Multiscale oriented corner correlation (MOCC) is used to evaluate the degree of similarity between the feature points. The method is rotation invariant and capable of matching image pairs with scale changes up to a factor of 7. Moreover, MOCC is much faster in comparison with the state-of-the-art matching methods. Experimental results on real images show the robustness and effectiveness of the proposed method.

Image Mosaic Method Based on SIFT Features of Line Segment

PubMed Central

Zhu, Jun; Ren, Mingwu

2014-01-01

This paper proposes a novel image mosaic method based on SIFT (Scale Invariant Feature Transform) feature of line segment, aiming to resolve incident scaling, rotation, changes in lighting condition, and so on between two images in the panoramic image mosaic process. This method firstly uses Harris corner detection operator to detect key points. Secondly, it constructs directed line segments, describes them with SIFT feature, and matches those directed segments to acquire rough point matching. Finally, Ransac method is used to eliminate wrong pairs in order to accomplish image mosaic. The results from experiment based on four pairs of images show that our method has strong robustness for resolution, lighting, rotation, and scaling. PMID:24511326

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

Otto, C., Thomas, G.A.; Peticolas, W.L.; Rippe, K.

Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due tomore » changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.« less

In-stem labelling allows visualization of DNA strand displacements by distinct fluorescent colour change.

PubMed

Barrois, Sebastian; Wagenknecht, Hans-Achim

2013-05-21

The combination of thiazole orange (TO) and thiazole red (TR) as an internal pair of fluorescent DNA base surrogates ("DNA traffic lights") allows us to follow at least two consecutive DNA strand displacements in real time through a distinct fluorescence colour change from green to red and vice versa.

Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots†

PubMed Central

2009-01-01

RNA pseudoknots have important functions, and thermodynamic stability is a key to predicting pseudoknots in RNA sequences and to understanding their functions. Traditional methods, such as UV melting and differential scanning calorimetry, for measuring RNA thermodynamics are restricted to temperature ranges around the melting temperature for a pseudoknot. Here, we report RNA pseudoknot free energy changes at 37 °C measured by fluorescence competition assays. Sequence-dependent studies for the loop 1−stem 2 region reveal (1) the individual nearest-neighbor hydrogen bonding (INN-HB) model provides a reasonable estimate for the free energy change when a Watson−Crick base pair in stem 2 is changed, (2) the loop entropy can be estimated by a statistical polymer model, although some penalty for certain loop sequences is necessary, and (3) tertiary interactions can significantly stabilize pseudoknots and extending the length of stem 2 may alter tertiary interactions such that the INN-HB model does not predict the net effect of adding a base pair. The results can inform writing of algorithms for predicting and/or designing RNA secondary structures. PMID:19921809

Circular dichroism and DNA secondary structure.

PubMed Central

Baase, W A; Johnson, W C

1979-01-01

The change in average rotation of the DNA helix has been determined for the transfer from 0.05 M NaCl to 3.0 M CsCl, 6.2 M LiCl and 5.4 M NH4Cl. This work, combined with data at lower salt from other laboratories, allows us to relate the intensity of the CD of DNA at 275 nm directly to the change in the number of base pairs per turn. The change in secondary structure for the transfer of DNA from 0.05 M NaCl (where it is presumably in the B-form) to high salt (where the characteristic CD has been interpreted as corresponding to C-form geometry) is found to be -0.22 (+/- 0.02) base pairs per turn. In the case of mononucleosomes, where the CD indicates the "C-form", the change in secondary structure (including temperature effects) would add -0.31 (+/- 0.03) turns about the histone core to the -1.25 turns estimated from work on SV40 chromatin. Accurate winding angles and molar extinction coefficients were determined for ethidium. PMID:424316

Changing to AIS 2005 and agreement of injury severity scores in a trauma registry with scores based on manual chart review.

PubMed

Stewart, Kenneth E; Cowan, Linda D; Thompson, David M

2011-09-01

The Abbreviated Injury Scale (AIS) recently underwent a major revision from AIS 98 to AIS 05. AIS injury codes form the basis of widely used injury severity scores such as the injury severity score (ISS). ISS thresholds are often used in trauma case definitions and ISS is widely used in injury research to adjust for injury severity. This study evaluated changes from AIS 98 to AIS 05, the changes' effect on ISS distributions, and presents an application of the results. Injury descriptions from medical records of 137 randomly selected patients in the Oklahoma Trauma Registry (OTR) were obtained. A single trained coder used AIS 98 and AIS 05 to code each injury. ISS values were calculated and grouped into 4 categories: 1-8, 9-14, 16-24, >24. Paired ISS was compared using Kappa statistics and tests of symmetry. We identified common injury diagnoses for which AIS severity changed between versions. Estimates of the proportion of patients changing ISS groups were applied to the entire OTR to assess the impact on reporting and on a model for reimbursement. OTR AIS 98 and manual AIS 98-based ISS values had a weighted Kappa of 0.71. OTR AIS 98 and manual AIS 05-based ISS values had a Kappa of 0.58. Manual AIS 98 and manual AIS 05 ISS had the highest Kappa of 0.81, however, though the scores differed by only 1 ISS category, there were 30 discordant pairs. The distribution of these discordant pairs was not symmetrical (Bowker's S=30; df=6; p<0.0001) with AIS 05-based ISS values consistently shifted to a lower ISS category. Reductions in AIS severity and ISS values using AIS 05 were common for extremity fractures and thorax injuries. The results suggest fewer patients would be reported to the OTR or be eligible for reimbursement. Changing from AIS 98 to AIS 05 injury coding resulted in systematic changes in AIS codes and ISS. Specific injuries and body regions were differentially affected. Trauma registries and injury researchers that use AIS based injury coding can use this information to evaluate the potential impact of changes in AIS 2005. Copyright © 2010 Elsevier Ltd. All rights reserved.

Changing partners: moving from non-homologous to homologous centromere pairing in meiosis

PubMed Central

Stewart, Mara N.; Dawson, Dean S.

2010-01-01

Reports of centromere pairing in early meiotic cells have appeared sporadically over the past thirty years. Recent experiments demonstrate that early centromere pairing occurs between non-homologous centromeres. As meiosis proceeds, centromeres change partners, becoming arranged in homologous pairs. Investigations of these later centromere pairs indicate that paired homologous centromeres are actively associated rather than positioned passively, side-by-side. Meiotic centromere pairing has been observed in organisms as diverse as mice, wheat and yeast, indicating that non-homologous centromere pairing in early meiosis and active homologous centromere pairing in later meiosis might be themes in meiotic chromosome behavior. Moreover, such pairing could have previously unrecognized roles in mediating chromosome organization or architecture that impact meiotic segregation fidelity. PMID:18804891

EXPERIMENTAL ACIDIFICATION CAUSES SOIL BASE-CATION DEPLETION AT THE BEAR BROOK WATERSHED IN MAINE

EPA Science Inventory

There is concern that changes in atmospheric deposition, climate, or land use have altered the biogeochemistry of forests causing soil base-cation depletion, particularly Ca. The Bear Brook Watershed in Maine (BBWM) is a paired watershed experiment with one watershed subjected to...

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.

Integrated model of multiple kernel learning and differential evolution for EUR/USD trading.

PubMed

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits.

Pattern-histogram-based temporal change detection using personal chest radiographs

NASA Astrophysics Data System (ADS)

Ugurlu, Yucel; Obi, Takashi; Hasegawa, Akira; Yamaguchi, Masahiro; Ohyama, Nagaaki

1999-05-01

An accurate and reliable detection of temporal changes from a pair of images has considerable interest in the medical science. Traditional registration and subtraction techniques can be applied to extract temporal differences when,the object is rigid or corresponding points are obvious. However, in radiological imaging, loss of the depth information, the elasticity of object, the absence of clearly defined landmarks and three-dimensional positioning differences constraint the performance of conventional registration techniques. In this paper, we propose a new method in order to detect interval changes accurately without using an image registration technique. The method is based on construction of so-called pattern histogram and comparison procedure. The pattern histogram is a graphic representation of the frequency counts of all allowable patterns in the multi-dimensional pattern vector space. K-means algorithm is employed to partition pattern vector space successively. Any differences in the pattern histograms imply that different patterns are involved in the scenes. In our experiment, a pair of chest radiographs of pneumoconiosis is employed and the changing histogram bins are visualized on both of the images. We found that the method can be used as an alternative way of temporal change detection, particularly when the precise image registration is not available.

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

PubMed

Sakuraba, Shun; Asai, Kiyoshi; Kameda, Tomoshi

2015-11-05

The dimerization free energies of RNA-RNA duplexes are fundamental values that represent the structural stability of RNA complexes. We report a comparative analysis of RNA-RNA duplex dimerization free-energy changes upon mutations, estimated from a molecular dynamics simulation and experiments. A linear regression for nine pairs of double-stranded RNA sequences, six base pairs each, yielded a mean absolute deviation of 0.55 kcal/mol and an R(2) value of 0.97, indicating quantitative agreement between simulations and experimental data. The observed accuracy indicates that the molecular dynamics simulation with the current molecular force field is capable of estimating the thermodynamic properties of RNA molecules.

Large‐scale analysis reveals populational contributions of cortical spike rate and synchrony to behavioural functions

PubMed Central

Saiki, Akiko; Fujiwara‐Tsukamoto, Yoko; Sakai, Yutaka; Isomura, Yoshikazu

2016-01-01

Key points There have been few systematic population‐wide analyses of relationships between spike synchrony within a period of several milliseconds and behavioural functions.In this study, we obtained a large amount of spike data from > 23,000 neuron pairs by multiple single‐unit recording from deep layer neurons in motor cortical areas in rats performing a forelimb movement task.The temporal changes of spike synchrony in the whole neuron pairs were statistically independent of behavioural changes during the task performance, although some neuron pairs exhibited correlated changes in spike synchrony.Mutual information analyses revealed that spike synchrony made a smaller contribution than spike rate to behavioural functions.The strength of spike synchrony between two neurons was statistically independent of the spike rate‐based preferences of the pair for behavioural functions. Abstract Spike synchrony within a period of several milliseconds in presynaptic neurons enables effective integration of functional information in the postsynaptic neuron. However, few studies have systematically analysed the population‐wide relationships between spike synchrony and behavioural functions. Here we obtained a sufficiently large amount of spike data among regular‐spiking (putatively excitatory) and fast‐spiking (putatively inhibitory) neuron subtypes (> 23,000 pairs) by multiple single‐unit recording from deep layers in motor cortical areas (caudal forelimb area, rostral forelimb area) in rats performing a forelimb movement task. After holding a lever, rats pulled the lever either in response to a cue tone (external‐trigger trials) or spontaneously without any cue (internal‐trigger trials). Many neurons exhibited functional spike activity in association with forelimb movements, and the preference of regular‐spiking neurons in the rostral forelimb area was more biased toward externally triggered movement than that in the caudal forelimb area. We found that a population of neuron pairs with spike synchrony does exist, and that some neuron pairs exhibit a dependence on movement phase during task performance. However, the population‐wide analysis revealed that spike synchrony was statistically independent of the movement phase and the spike rate‐based preferences of the pair for behavioural functions, whereas spike rates were clearly dependent on the movement phase. In fact, mutual information analyses revealed that the contribution of spike synchrony to the behavioural functions was small relative to the contribution of spike rate. Our large‐scale analysis revealed that cortical spike rate, rather than spike synchrony, contributes to population coding for movement. PMID:27488936

Large-scale analysis reveals populational contributions of cortical spike rate and synchrony to behavioural functions.

PubMed

Kimura, Rie; Saiki, Akiko; Fujiwara-Tsukamoto, Yoko; Sakai, Yutaka; Isomura, Yoshikazu

2017-01-01

There have been few systematic population-wide analyses of relationships between spike synchrony within a period of several milliseconds and behavioural functions. In this study, we obtained a large amount of spike data from > 23,000 neuron pairs by multiple single-unit recording from deep layer neurons in motor cortical areas in rats performing a forelimb movement task. The temporal changes of spike synchrony in the whole neuron pairs were statistically independent of behavioural changes during the task performance, although some neuron pairs exhibited correlated changes in spike synchrony. Mutual information analyses revealed that spike synchrony made a smaller contribution than spike rate to behavioural functions. The strength of spike synchrony between two neurons was statistically independent of the spike rate-based preferences of the pair for behavioural functions. Spike synchrony within a period of several milliseconds in presynaptic neurons enables effective integration of functional information in the postsynaptic neuron. However, few studies have systematically analysed the population-wide relationships between spike synchrony and behavioural functions. Here we obtained a sufficiently large amount of spike data among regular-spiking (putatively excitatory) and fast-spiking (putatively inhibitory) neuron subtypes (> 23,000 pairs) by multiple single-unit recording from deep layers in motor cortical areas (caudal forelimb area, rostral forelimb area) in rats performing a forelimb movement task. After holding a lever, rats pulled the lever either in response to a cue tone (external-trigger trials) or spontaneously without any cue (internal-trigger trials). Many neurons exhibited functional spike activity in association with forelimb movements, and the preference of regular-spiking neurons in the rostral forelimb area was more biased toward externally triggered movement than that in the caudal forelimb area. We found that a population of neuron pairs with spike synchrony does exist, and that some neuron pairs exhibit a dependence on movement phase during task performance. However, the population-wide analysis revealed that spike synchrony was statistically independent of the movement phase and the spike rate-based preferences of the pair for behavioural functions, whereas spike rates were clearly dependent on the movement phase. In fact, mutual information analyses revealed that the contribution of spike synchrony to the behavioural functions was small relative to the contribution of spike rate. Our large-scale analysis revealed that cortical spike rate, rather than spike synchrony, contributes to population coding for movement. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.

PubMed

Millen, Andrea L; Churchill, Cassandra D M; Manderville, Richard A; Wetmore, Stacey D

2010-10-14

Bulky DNA addition products (adducts) formed through attack at the C8 site of guanine can adopt the syn orientation about the glycosidic bond due to changes in conformational stability or hydrogen-bonding preferences directly arising from the bulky group. Indeed, the bulky substituent may improve the stability of (non-native) Hoogsteen pairs. Therefore, such adducts often result in mutations upon DNA replication. This work examines the hydrogen-bonded pairs between the Watson-Crick and Hoogsteen faces of the ortho or para C8-phenoxyl-2'-deoxyguanosine adduct and each natural (undamaged) nucleobase with the goal to clarify the conformational preference of this type of damage, as well as provide insight into the likelihood of subsequent mutation events. B3LYP/6-311+G(2df,p)//B3LYP/6-31G(d) hydrogen-bond strengths were determined using both nucleobase and nucleoside models for adduct pairs, as well as the corresponding complexes involving natural 2'-deoxyguanosine. In addition to the magnitude of the binding strengths, the R(C1'···C1') distances and ∠(N9C1'C1') angles, as well as the degree of propeller-twist and buckle distortions, were carefully compared to the values observed in natural DNA strands. Due to structural changes in the adduct monomer upon inclusion of the sugar moiety, the monomer deformation energy significantly affects the relative hydrogen-bond strengths calculated with the nucleobase and nucleoside models. Therefore, we recommend the use of at least a nucleoside model to accurately evaluate hydrogen-bond strengths of base pairs involving flexible, bulky nucleobase adducts. Our results also emphasize the importance of considering both the magnitude of the hydrogen-bond strength and the structure of the base pair when predicting the preferential binding patterns of nucleobases. Using our best models, we conclude that the Watson-Crick face of the ortho phenoxyl adduct forms significantly more stable complexes than the Hoogsteen face, which implies that the anti orientation of the damaged base will be favored by hydrogen bonding in DNA helices. Additionally, regardless of the hydrogen-bonding face involved, cytosine forms the most stable base pair with the ortho adduct, which implies that misincorporation due to this type of damage is unlikely. Similarly, cytosine is the preferred binding partner for the Watson-Crick face of the para adduct. However, Hoogsteen interactions with the para adduct are stronger than those with natural 2'-deoxyguanosine or the ortho adduct, and this form of damage binds with nearly equal stability to both cytosine and guanine in the Hoogsteen orientation. Therefore, the para adduct may adopt multiple orientations in DNA helices and potentially cause mutations by forming pairs with different natural bases. Models of oligonucleotide duplexes must be used in future work to further evaluate other factors (stacking, major groove contacts) that may influence the conformation and binding preference of these adducts in DNA helices.

An Adaptation of Family-Based Behavioral Pediatric Obesity Treatment for a Primary Care Setting: Group Health Family Wellness Program Pilot

PubMed Central

Riggs, Karin R; Lozano, Paula; Mohelnitzky, Amy; Rudnick, Sarah; Richards, Julie

2014-01-01

Objective: To assess the feasibility and acceptability of family-based group pediatric obesity treatment in a primary care setting, to obtain an estimate of its effectiveness, and to describe participating parents’ experiences of social support for healthy lifestyle changes. Methods: We adapted an evidence-based intervention to a group format and completed six 12- to 16-week groups over 3 years. We assessed program attendance and completion, changes in child and parent body mass index (BMI; calculated as weight in kilograms divided by height in meters squared), and changes in child quality of life in a single-arm before-and-after trial. Qualitative interviews explored social support for implementing healthy lifestyle changes. Results: Thirty-eight parent-child pairs enrolled (28% of the 134 pairs invited). Of those, 24 (63%) completed the program and another 6 (16%) attended at least 4 sessions but did not complete the program. Children who completed the program achieved a mean change in BMI Z-scores (Z-BMI) of −0.1 (0.1) (p < 0.001) and significant improvement in parent-reported child quality of life (mean change = 8.5; p = 0.002). Mean BMI of parents changed by −0.9 (p = 0.003). Parents reported receiving a wide range of social support for healthy lifestyle changes and placed importance on the absence or presence of support. Conclusions: A pilot group program for family-based treatment of pediatric obesity is feasible and acceptable in a primary care setting. Change in child and parent BMI outcomes and child quality of life among completers were promising despite the pilot’s low intensity. Parent experiences with lack of social support suggest possible ways to improve retention and adherence. PMID:24937148

Report on Pairing-based Cryptography.

PubMed

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

Report on Pairing-based Cryptography

PubMed Central

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

Effect of structural mount dynamics on a pair of operating Stirling Convertors

NASA Astrophysics Data System (ADS)

Goodnight, Thomas W.; Suárez, Vicente J.; Hughes, William O.; Samorezov, Sergey

2002-01-01

The U.S. Department of Energy (DOE), in conjunction with NASA John H. Glenn Research Center and Stirling Technology Company, are currently developing a Stirling convertor for a Stirling Radioisotope Generator (SRG). NASA Headquarters and DOE have identified the SRG for potential use as an advanced spacecraft power system for future NASA deep-space and Mars surface missions. Low-level dynamic base-shake tests were conducted on a dynamic simulation of the structural mount for a pair of Operating Stirling Convertors. These tests were conducted at NASA Glenn Research Center's Structural Dynamics Laboratory as part of the development of this technology. The purpose of these tests was to identify the changes in transmissibility and the effect on structural dynamic response on a pair of operating Stirling Technology Demonstration Convertors (TDCs). This paper addresses the base-shake test, setup, procedure and results conducted on the Stirling TDC mount simulator in April 2001. .

Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

PubMed Central

Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

2015-01-01

Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection.

PubMed

Yoon, Dukyong; Kim, Hyosil; Suh-Kim, Haeyoung; Park, Rae Woong; Lee, KiYoung

2011-01-01

Microarray analyses based on differentially expressed genes (DEGs) have been widely used to distinguish samples across different cellular conditions. However, studies based on DEGs have not been able to clearly determine significant differences between samples of pathophysiologically similar HIV-1 stages, e.g., between acute and chronic progressive (or AIDS) or between uninfected and clinically latent stages. We here suggest a novel approach to allow such discrimination based on stage-specific genetic features of HIV-1 infection. Our approach is based on co-expression changes of genes known to interact. The method can identify a genetic signature for a single sample as contrasted with existing protein-protein-based analyses with correlational designs. Our approach distinguishes each sample using differentially co-expressed interacting protein pairs (DEPs) based on co-expression scores of individual interacting pairs within a sample. The co-expression score has positive value if two genes in a sample are simultaneously up-regulated or down-regulated. And the score has higher absolute value if expression-changing ratios are similar between the two genes. We compared characteristics of DEPs with that of DEGs by evaluating their usefulness in separation of HIV-1 stage. And we identified DEP-based network-modules and their gene-ontology enrichment to find out the HIV-1 stage-specific gene signature. Based on the DEP approach, we observed clear separation among samples from distinct HIV-1 stages using clustering and principal component analyses. Moreover, the discrimination power of DEPs on the samples (70-100% accuracy) was much higher than that of DEGs (35-45%) using several well-known classifiers. DEP-based network analysis also revealed the HIV-1 stage-specific network modules; the main biological processes were related to "translation," "RNA splicing," "mRNA, RNA, and nucleic acid transport," and "DNA metabolism." Through the HIV-1 stage-related modules, changing stage-specific patterns of protein interactions could be observed. DEP-based method discriminated the HIV-1 infection stages clearly, and revealed a HIV-1 stage-specific gene signature. The proposed DEP-based method might complement existing DEG-based approaches in various microarray expression analyses.

Long-Term In Vivo Electromechanical Reshaping for Auricular Reconstruction in the New Zealand White Rabbit Model

PubMed Central

Badran, Karam W.; Manuel, Cyrus T.; Loy, Anthony Chin; Conderman, Christian; Yau, Yuk Yee; Lin, Jennifer; Tjoa, Tjoson; Su, Erica; Protsenko, Dmitriy; Wong, Brian J. F.

2016-01-01

Objectives/Hypothesis To demonstrate the dosimetry effect of electromechanical reshaping (EMR) on cartilage shape change, structural integrity, cellular viability, and remodeling of grafts in an in vivo long-term animal model. Study Design Animal study. Methods A subperichondrial cartilaginous defect was created within the base of the pinna of 31 New Zealand white rabbits. Autologous costal cartilage grafts were electromechanically reshaped to resemble the rabbit auricular base framework and mechanically secured into the pinna base defect. Forty-nine costal cartilage specimens (four control and 45 experimental) successfully underwent EMR using a paired set of voltage-time combinations and survived for 6 or 12 weeks. Shape change was measured, and specimens were analyzed using digital imaging, tissue histology, and confocal microscopy with LIVE-DEAD viability assays. Results Shape change was proportional to charge transfer in all experimental specimens (P <.01) and increased with voltage. All experimental specimens contoured to the auricular base. Focal cartilage degeneration and fibrosis was observed where needle electrodes were inserted, ranging from 2.2 to 3.9 mm. The response to injury increased with increasing charge transfer and survival duration. Conclusions EMR results in appropriate shape change in cartilage grafts with chondrocyte injury highly localized. These studies suggest that elements of auricular reconstruction may be feasible using EMR. Extended survival periods and further optimization of voltage-time pairs are necessary to evaluate the long-term effects and shape-change potential of EMR. PMID:25779479

Spatial, Temporal and Spectral Satellite Image Fusion via Sparse Representation

NASA Astrophysics Data System (ADS)

Song, Huihui

Remote sensing provides good measurements for monitoring and further analyzing the climate change, dynamics of ecosystem, and human activities in global or regional scales. Over the past two decades, the number of launched satellite sensors has been increasing with the development of aerospace technologies and the growing requirements on remote sensing data in a vast amount of application fields. However, a key technological challenge confronting these sensors is that they tradeoff between spatial resolution and other properties, including temporal resolution, spectral resolution, swath width, etc., due to the limitations of hardware technology and budget constraints. To increase the spatial resolution of data with other good properties, one possible cost-effective solution is to explore data integration methods that can fuse multi-resolution data from multiple sensors, thereby enhancing the application capabilities of available remote sensing data. In this thesis, we propose to fuse the spatial resolution with temporal resolution and spectral resolution, respectively, based on sparse representation theory. Taking the study case of Landsat ETM+ (with spatial resolution of 30m and temporal resolution of 16 days) and MODIS (with spatial resolution of 250m ~ 1km and daily temporal resolution) reflectance, we propose two spatial-temporal fusion methods to combine the fine spatial information of Landsat image and the daily temporal resolution of MODIS image. Motivated by that the images from these two sensors are comparable on corresponding bands, we propose to link their spatial information on available Landsat- MODIS image pair (captured on prior date) and then predict the Landsat image from the MODIS counterpart on prediction date. To well-learn the spatial details from the prior images, we use a redundant dictionary to extract the basic representation atoms for both Landsat and MODIS images based on sparse representation. Under the scenario of two prior Landsat-MODIS image pairs, we build the corresponding relationship between the difference images of MODIS and ETM+ by training a low- and high-resolution dictionary pair from the given prior image pairs. In the second scenario, i.e., only one Landsat- MODIS image pair being available, we directly correlate MODIS and ETM+ data through an image degradation model. Then, the fusion stage is achieved by super-resolving the MODIS image combining the high-pass modulation in a two-layer fusion framework. Remarkably, the proposed spatial-temporal fusion methods form a unified framework for blending remote sensing images with phenology change or land-cover-type change. Based on the proposed spatial-temporal fusion models, we propose to monitor the land use/land cover changes in Shenzhen, China. As a fast-growing city, Shenzhen faces the problem of detecting the rapid changes for both rational city planning and sustainable development. However, the cloudy and rainy weather in region Shenzhen located makes the capturing circle of high-quality satellite images longer than their normal revisit periods. Spatial-temporal fusion methods are capable to tackle this problem by improving the spatial resolution of images with coarse spatial resolution but frequent temporal coverage, thereby making the detection of rapid changes possible. On two Landsat-MODIS datasets with annual and monthly changes, respectively, we apply the proposed spatial-temporal fusion methods to the task of multiple change detection. Afterward, we propose a novel spatial and spectral fusion method for satellite multispectral and hyperspectral (or high-spectral) images based on dictionary-pair learning and sparse non-negative matrix factorization. By combining the spectral information from hyperspectral image, which is characterized by low spatial resolution but high spectral resolution and abbreviated as LSHS, and the spatial information from multispectral image, which is featured by high spatial resolution but low spectral resolution and abbreviated as HSLS, this method aims to generate the fused data with both high spatial and high spectral resolutions. Motivated by the observation that each hyperspectral pixel can be represented by a linear combination of a few endmembers, this method first extracts the spectral bases of LSHS and HSLS images by making full use of the rich spectral information in LSHS data. The spectral bases of these two categories data then formulate a dictionary-pair due to their correspondence in representing each pixel spectra of LSHS data and HSLS data, respectively. Subsequently, the LSHS image is spatially unmixed by representing the HSLS image with respect to the corresponding learned dictionary to derive its representation coefficients. Combining the spectral bases of LSHS data and the representation coefficients of HSLS data, we finally derive the fused data characterized by the spectral resolution of LSHS data and the spatial resolution of HSLS data.

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.

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

PubMed Central

2016-01-01

ABSTRACT Gene regulation by base pairing between small noncoding RNAs (sRNAs) and their mRNA targets is an important mechanism that allows bacteria to maintain homeostasis and respond to dynamic environments. In Gram-negative bacteria, sRNA pairing and regulation are mediated by several RNA-binding proteins, including the sRNA chaperone Hfq and polynucleotide phosphorylase (PNPase). PNPase and its homolog RNase PH together represent the two 3′ to 5′ phosphorolytic exoribonucleases found in Escherichia coli; however, the role of RNase PH in sRNA regulation has not yet been explored and reported. Here, we have examined in detail how PNPase and RNase PH interact to support sRNA stability, activity, and base pairing in exponential and stationary growth conditions. Our results indicate that these proteins facilitate the stability and regulatory function of the sRNAs RyhB, CyaR, and MicA during exponential growth. PNPase further appears to contribute to pairing between RyhB and its mRNA targets. During stationary growth, each sRNA responded differently to the absence or presence of PNPase and RNase PH. Finally, our results suggest that PNPase and RNase PH stabilize only Hfq-bound sRNAs. Taken together, these results confirm and extend previous findings that PNPase participates in sRNA regulation and reveal that RNase PH serves a similar, albeit more limited, role as well. These proteins may, therefore, act to protect sRNAs from spurious degradation while also facilitating regulatory pairing with their targets. IMPORTANCE In many bacteria, Hfq-dependent base-pairing sRNAs facilitate rapid changes in gene expression that are critical for maintaining homeostasis and responding to stress and environmental changes. While a role for Hfq in this process was identified more than 2 decades ago, the identity and function of the other proteins required for Hfq-dependent regulation by sRNAs have not been resolved. Here, we demonstrate that PNPase and RNase PH, the two phosphorolytic RNases in E. coli, stabilize sRNAs against premature degradation and, in the case of PNPase, also accelerate regulation by sRNA-mRNA pairings for certain sRNAs. These findings are the first to demonstrate that RNase PH influences and supports sRNA regulation and suggest shared and distinct roles for these phosphorolytic RNases in this process. PMID:27698082

Theoretical Probing of Weak Anion-Cation Interactions in Certain Pyridinium-Based Ionic Liquid Ion Pairs and the Application of Molecular Electrostatic Potential in Their Ionic Crystal Density Determination: A Comparative Study Using Density Functional Approach.

PubMed

Joseph, Aswathy; Thomas, Vibin Ipe; Żyła, Gaweł; Padmanabhan, A S; Mathew, Suresh

2018-01-11

A comprehensive study on the structure, nature of interaction, and properties of six ionic pairs of 1-butylpyridinium and 1-butyl-4-methylpyridinium cations in combination with tetrafluoroborate (BF 4 - ), chloride (Cl - ), and bromide (Br - ) anions have been carried out using density functional theory (DFT). The anion-cation interaction energy (ΔE int ), thermochemistry values, theoretical band gap, molecular orbital energy order, DFT-based chemical activity descriptors [chemical potential (μ), chemical hardness (η), and electrophilicity index (ω)], and distribution of density of states (DOS) of these ion pairs were investigated. The ascendancy of the -CH 3 substituent at the fourth position of the 1-butylpyridinium cation ring on the values of ΔE int , theoretical band gap and chemical activity descriptors was evaluated. The ΔE int values were negative for all six ion pairs and were highest for Cl - containing ion pairs. The theoretical band gap value after -CH 3 substitution increased from 3.78 to 3.96 eV (for Cl - ) and from 2.74 to 2.88 eV (for Br - ) and decreased from 4.9 to 4.89 eV (for BF 4 - ). Ion pairs of BF 4 - were more susceptible to charge transfer processes as inferred from their significantly high η values and comparatively small difference in ω value after -CH 3 substitution. The change in η and μ values due to the -CH 3 substituent is negligibly small in all cases except for the ion pairs of Cl - . Critical-point (CP) analyses were carried out to investigate the AIM topological parameters at the interionic bond critical points (BCPs). The RDG isosurface analysis indicated that the anion-cation interaction was dominated by strong H cat ···X ani and C cat ···X ani interactions in ion pairs of Cl - and Br - whereas a weak van der Waal's effect dominated in ion pairs of BF 4 - . The molecular electrostatic potential (MESP)-based parameter ΔΔV min measuring the anion-cation interaction strength showed a good linear correlation with ΔE int for all 1-butylpyridinium ion pairs (R 2 = 0.9918). The ionic crystal density values calculated by using DFT-based MESP showed only slight variations from experimentally reported values.

Nucleic acid duplexes incorporating a dissociable covalent base pair

NASA Technical Reports Server (NTRS)

Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

Testing can counteract proactive interference by integrating competing information.

PubMed

Wahlheim, Christopher N

2015-01-01

Testing initially learned information before presenting new information has been shown to counteract the deleterious effects of proactive interference by segregating competing sources of information. The present experiments were conducted to demonstrate that testing can also have its effects in part by integrating competing information. Variations of classic A-B, A-D paired-associate learning paradigms were employed that included two lists of word pairs and a cued-recall test. Repeated pairs appeared in both lists (A-B, A-B), control pairs appeared in List 2 only (A-B, C-D), and changed pairs appeared with the same cue in both lists but with different responses (A-B, A-D). The critical manipulation was whether pairs were tested or restudied in an interpolated phase that occurred between Lists 1 and 2. On a final cued-recall test, participants recalled List 2 responses and then indicated when they recollected that responses had earlier changed between lists. The change recollection measure indexed the extent to which competing responses were integrated during List 2. Change was recollected more often for tested than for restudied pairs. Proactive facilitation was obtained in cued recall when change was recollected, whereas proactive interference was obtained when change was not recollected. These results provide evidence that testing counteracted proactive interference in part by making List 1 responses more accessible during List 2, thus promoting integration and increasing later recollection of change. These results have theoretical implications because they show that testing can counteract proactive interference by integrating or segregating competing information.

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

PubMed

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair

NASA Astrophysics Data System (ADS)

Wang, Yujie; Wang, Zhen; Wang, Yanli; Liu, Taigang; Zhang, Wenbing

2018-01-01

The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

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

Nucleic acid duplexes incorporating a dissociable covalent base pair

PubMed Central

Gao, Kui; Orgel, Leslie E.

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

PubMed Central

Yesudhas, Dhanusha; Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Durai, Prasannavenkatesh; Shah, Masaud; Choi, Sangdun

2016-01-01

The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox20bp) or 3 base pairs (Oct4/Sox23bp) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox20bp and Oct4/Sox23bp complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming. PMID:26790000

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

PubMed Central

Shen, Manli; Bellaousov, Stanislav; Hiller, Michael; de La Grange, Pierre; Creamer, Trevor P.; Malina, Orit; Sperling, Ruth; Mathews, David H.; Stoilov, Peter; Stamm, Stefan

2013-01-01

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2′-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5′-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch. PMID:23393189

Integrated Model of Multiple Kernel Learning and Differential Evolution for EUR/USD Trading

PubMed Central

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits. PMID:25097891

SAR image change detection using watershed and spectral clustering

NASA Astrophysics Data System (ADS)

Niu, Ruican; Jiao, L. C.; Wang, Guiting; Feng, Jie

2011-12-01

A new method of change detection in SAR images based on spectral clustering is presented in this paper. Spectral clustering is employed to extract change information from a pair images acquired on the same geographical area at different time. Watershed transform is applied to initially segment the big image into non-overlapped local regions, leading to reduce the complexity. Experiments results and system analysis confirm the effectiveness of the proposed algorithm.

Mass spectrometry based on a coupled Cooper-pair box and nanomechanical resonator system

NASA Astrophysics Data System (ADS)

Jiang, Cheng; Chen, Bin; Li, Jin-Jin; Zhu, Ka-Di

2011-10-01

Nanomechanical resonators (NRs) with very high frequency have a great potential for mass sensing with unprecedented sensitivity. In this study, we propose a scheme for mass sensing based on the NR capacitively coupled to a Cooper-pair box (CPB) driven by two microwave currents. The accreted mass landing on the resonator can be measured conveniently by tracking the resonance frequency shifts because of mass changes in the signal absorption spectrum. We demonstrate that frequency shifts induced by adsorption of ten 1587 bp DNA molecules can be well resolved in the absorption spectrum. Integration with the CPB enables capacitive readout of the mechanical resonance directly on the chip.

Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples

PubMed Central

Cheng, Jun; He, Jun; Liu, Huaping; Cai, Hao; Hong, Guini; Zhang, Jiahui; Li, Na; Ao, Lu; Guo, Zheng

2017-01-01

Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA. PMID:28036264

Titi Monkeys as a Novel Non-Human Primate Model for the Neurobiology of Pair Bonding


PubMed Central

Bales, Karen L.; Arias del Razo, Rocío; Conklin, Quinn A.; Hartman, Sarah; Mayer, Heather S.; Rogers, Forrest D.; Simmons, Trenton C.; Smith, Leigh K.; Williams, Alexia; Williams, Donald R.; Witczak, Lynea R.; Wright, Emily C.

2017-01-01

It is now widely recognized that social bonds are critical to human health and well-being. One of the most important social bonds is the attachment relationship between two adults, known as the pair bond. The pair bond involves many characteristics that are inextricably linked to quality of health, including providing a secure psychological base and acting as a social buffer against stress. The majority of our knowledge about the neurobiology of pair bonding comes from studies of a socially monogamous rodent, the prairie vole (Microtus ochrogaster), and from human imaging studies, which inherently lack control. Here, we first review what is known of the neurobiology of pair bonding from humans and prairie voles. We then present a summary of the studies we have conducted in titi monkeys (Callicebus cupreus)—a species of socially monogamous New World primates. Finally, we construct a neural model based on the location of neuropeptide receptors in the titi monkey brain, as well as the location of neural changes in our imaging studies, with some basic assumptions based on the prairie vole model. In this model, we emphasize the role of visual mating stimuli as well as contributions of the dopaminergic reward system and a strong role for the lateral septum. This model represents an important step in understanding the neurobiology of social bonds in non-human primates, which will in turn facilitate a better understanding of these mechanisms in humans. PMID:28955178

Double acting stirling engine phase control

DOEpatents

Berchowitz, David M.

1983-01-01

A mechanical device for effecting a phase change between the expansion and compression volumes of a double-acting Stirling engine uses helical elements which produce opposite rotation of a pair of crankpins when a control rod is moved, so the phase between two pairs of pistons is changed by +.psi. and the phase between the other two pairs of pistons is changed by -.psi.. The phase can change beyond .psi.=90.degree. at which regenerative braking and then reversal of engine rotation occurs.

MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT

PubMed Central

Zhang, Guo-Qiang; Zhu, Wei; Sun, Mengmeng; Tao, Shiqiang; Bodenreider, Olivier; Cui, Licong

2015-01-01

Non-lattice fragments are often indicative of structural anomalies in ontological systems and, as such, represent possible areas of focus for subsequent quality assurance work. However, extracting the non-lattice fragments in large ontological systems is computationally expensive if not prohibitive, using a traditional sequential approach. In this paper we present a general MapReduce pipeline, called MaPLE (MapReduce Pipeline for Lattice-based Evaluation), for extracting non-lattice fragments in large partially ordered sets and demonstrate its applicability in ontology quality assurance. Using MaPLE in a 30-node Hadoop local cloud, we systematically extracted non-lattice fragments in 8 SNOMED CT versions from 2009 to 2014 (each containing over 300k concepts), with an average total computing time of less than 3 hours per version. With dramatically reduced time, MaPLE makes it feasible not only to perform exhaustive structural analysis of large ontological hierarchies, but also to systematically track structural changes between versions. Our change analysis showed that the average change rates on the non-lattice pairs are up to 38.6 times higher than the change rates of the background structure (concept nodes). This demonstrates that fragments around non-lattice pairs exhibit significantly higher rates of change in the process of ontological evolution. PMID:25705725

MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT.

PubMed

Zhang, Guo-Qiang; Zhu, Wei; Sun, Mengmeng; Tao, Shiqiang; Bodenreider, Olivier; Cui, Licong

2014-10-01

Non-lattice fragments are often indicative of structural anomalies in ontological systems and, as such, represent possible areas of focus for subsequent quality assurance work. However, extracting the non-lattice fragments in large ontological systems is computationally expensive if not prohibitive, using a traditional sequential approach. In this paper we present a general MapReduce pipeline, called MaPLE (MapReduce Pipeline for Lattice-based Evaluation), for extracting non-lattice fragments in large partially ordered sets and demonstrate its applicability in ontology quality assurance. Using MaPLE in a 30-node Hadoop local cloud, we systematically extracted non-lattice fragments in 8 SNOMED CT versions from 2009 to 2014 (each containing over 300k concepts), with an average total computing time of less than 3 hours per version. With dramatically reduced time, MaPLE makes it feasible not only to perform exhaustive structural analysis of large ontological hierarchies, but also to systematically track structural changes between versions. Our change analysis showed that the average change rates on the non-lattice pairs are up to 38.6 times higher than the change rates of the background structure (concept nodes). This demonstrates that fragments around non-lattice pairs exhibit significantly higher rates of change in the process of ontological evolution.

Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA.

PubMed

Hughes, J M

1996-06-21

The U3 nucleolar RNA has a remarkably wide phyletic distribution extending from the Eukarya to the Archaea. It functions in maturation of the small subunit (SSU) rRNA through a mechanism which is as yet unknown but which involves base-pairing with pre-rRNA. The most conserved part of U3 is within 30 nucleotides of the 5' end, but as yet no function for this domain has been proposed. Elements within this domain are complementary to highly conserved sequences in the SSU rRNA which, in the mature form, fold into a universally conserved pseudoknot. The nature of the complementarity suggests a novel mechanism for U3 function whereby U3 facilitates correct folding of the pseudoknot. Wide phylogenetic comparison provides compelling evidence in support of the interaction in that significant complementary changes have taken place, particularly in the archaeon Sulfolobus, which maintain the base-pairing. Base-substitution mutations in yeast U3 designed to disrupt the base-pairing indicate that the interaction is probably essential. These include cold-sensitivity mutations which exhibit phenotypes similar to U3-depletion, but without impairment of the AO processing step, which occurs within the 5' ETS. These phenotypes are consistent with the destabilization of SSU precursors and partial impairment of the processing steps A1, at the 5' ETS/18 S boundary, and A2, within the ITS1.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.

PubMed

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

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.

Active Space Dependence in Multiconfiguration Pair-Density Functional Theory.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-02-13

In multiconfiguration pair-density functional theory (MC-PDFT), multiconfiguration self-consistent-field calculations and on-top density functionals are combined to describe both static and dynamic correlation. Here, we investigate how the MC-PDFT total energy and its components depend on the active space choice in the case of the H 2 and N 2 molecules. The active space dependence of the on-top pair density, the total density, the ratio of on-top pair density to half the square of the electron density, and the satisfaction of the virial theorem are also explored. We find that the density and on-top pair density do not change significantly with changes in the active space. However, the on-top ratio does change significantly with respect to active space change, and this affects the on-top energy. This study provides a foundation for designing on-top density functionals and automatizing the active space choice in MC-PDFT.

Persistence or Change in Leisure-Time Physical Activity Habits and Waist Gain During Early Adulthood: A Twin-Study

PubMed Central

Rottensteiner, Mirva; Pietiläinen, Kirsi H.; Kaprio, Jaakko; Kujala, Urho M.

2014-01-01

Objective To determine the relationship between persistence or change in leisure-time physical activity habits and waist gain among young adults. Design and Methods Population-based cohort study among 3383 Finnish twin individuals (1578 men) from five birth cohorts (1975–1979), who answered questionnaires at mean ages of 24.4 y (SD 0.9) and 33.9 y (SD 1.2), with reported self-measured waist circumference. Persistence or change in leisure-time physical activity habits was defined based on thirds of activity metabolic equivalent h/day during follow-up (mean 9.5 y; SD 0.7). Results Decreased activity was linked to greater waist gain compared to increased activity (3.6 cm, P<0.001 for men; 3.1 cm, P<0.001 for women). Among same-sex activity discordant twin pairs, twins who decreased activity gained an average 2.8 cm (95%CI 0.4 to 5.1, P=0.009) more waist than their co-twins who increased activity (n=85 pairs); among MZ twin pairs (n=43), the difference was 4.2 cm (95%CI 1.2 to 7.2, P=0.008). Conclusions Among young adults, an increase in leisure-time physical activity or staying active during a decade of follow-up was associated with less waist gain, but any decrease in activity level, regardless baseline activity, led to waist gain that was similar to that associated with being persistently inactive. PMID:24839266

Testing can counteract proactive interference by integrating competing information

PubMed Central

Wahlheim, Christopher N.

2015-01-01

Testing initially learned information before presenting new information has been shown to counteract the deleterious effects of proactive interference by segregating competing sources of information. The present experiments were conducted to demonstrate that testing can also have its effects in part by integrating competing information. Variations of classic A–B, A–D paired-associate learning paradigms were employed that included two lists of word pairs and a cued-recall test. Repeated pairs appeared in both lists (A–B, A–B), control pairs appeared in List 2 only (A–B, C–D), and changed pairs appeared with the same cue in both lists but with different responses (A–B, A–D). The critical manipulation was whether pairs were tested or restudied in an interpolated phase that occurred between Lists 1 and 2. On a final cued-recall test, participants recalled List 2 responses and then indicated when they recollected that responses had earlier changed between lists. The change recollection measure indexed the extent to which competing responses were integrated during List 2. Change was recollected more often for tested than for restudied pairs. Proactive facilitation was obtained in cued recall when change was recollected, whereas proactive interference was obtained when change was not recollected. These results provide evidence that testing counteracted proactive interference in part by making List 1 responses more accessible during List 2, thus promoting integration and increasing later recollection of change. These results have theoretical implications because they show that testing can counteract proactive interference by integrating or segregating competing information. PMID:25120241

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.

Helix-coil transition of a four-way DNA junction observed by multiple fluorescence parameters.

PubMed

Vámosi, György; Clegg, Robert M

2008-10-16

The thermal denaturation of immobile four-way DNA ("Holliday-") junctions with 17 base pair arms was studied via fluorescence spectroscopic measurements. Two arms of the molecule were labeled at the 5'-end with fluorescein and tetramethylrhodamine, respectively. Melting was monitored by the fluorescence intensity of the dyes, the fluorescence anisotropy of tetramethylrhodamine, and Forster resonance energy transfer (FRET) between fluorescein and rhodamine. To fit the thermal denaturation curves of the four-way junctions, two basic thermodynamic models were tested: (1) all-or-none transitions assuming a molecularity of one, two, or four and (2) a statistical "zipper" model. The all-or-none models correspond to reaction mechanisms assuming that the cooperative melting unit (that is, the structure changing from complete helix to complete coil) consists of (1) one arm, (2) two neighboring arms (which have one continuous strand common to the two arms), or (3) all four arms. In each case, the melting of the cooperative unit takes place in a single step. The tetramolecular reaction model (four-arm melting) yielded unrealistically low van't Hoff enthalpy and entropy values, whereas the monomolecular model (one-arm melting) resulted in a poor fit to the experimental data. The all-or-none bimolecular (two neighboring arm model) fit gave intermediate standard enthalpy change (Delta H) values between those expected for the melting of a duplex with a total length between the helix lengths of one and two arms (17 and 34 base pairs). Simulations according to the zipper model fit the experimental curves best when the length of the simulated duplex was assumed to be 34 base pairs, the length of a single strand. This suggests that the most important parameter determining the melting behavior of the molecule is the end-to-end distance of the strands (34 bases) rather than the length of the individual arms (17 base pairs) and that the equilibrium concentration of partially denatured intermediate states has to be taken into account. These findings are in good agreement with results obtained for three-way DNA junctions ( Stuhmeier, F. ; Lilley, D. M. ; Clegg, R. M. Biochemistry 1997, 36, 13539 ). An interesting result is that the extent-of-melting curves derived from the fluorescence intensity and anisotropy nearly agree, whereas the curve derived from the FRET data shows a change prior to the melting. This may be an indication of a conformational change leaving the double-stranded structure intact but changing the end-to-end distance of the different arms in a way consistent with the transition to the extended square configuration ( Clegg, R. M. ; Murchie, A. I. ; Lilley, D. M. Biophys. J. 1994, 66, 99 ) of this branched molecule.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides

PubMed Central

Buchmueller, Karen L.; Staples, Andrew M.; Uthe, Peter B.; Howard, Cameron M.; Pacheco, Kimberly A. O.; Cox, Kari K.; Henry, James A.; Bailey, Suzanna L.; Horick, Sarah M.; Nguyen, Binh; Wilson, W. David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, –ImPy– and –PyPy–. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and ΔTM experiments. The f/Py pairing, when placed next to the –ImPy– or –PyPy– central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With –ImPy– central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson–Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the –PyPy– central pairings. PMID:15703305

Distortions induced in double-stranded oligonucleotides by the binding of cis- or trans-diammine-dichloroplatinum(II) to the d(GTG) sequence.

PubMed Central

Anin, M F; Leng, M

1990-01-01

Conformational changes induced in double-stranded oligonucleotides by the binding of trans- or cis-diamminedichloro platinum(II) to the d(GTG) sequence have been characterized by means of melting temperatures, electrophoretic migrations in non-denaturing polyacrylamide gels, reactivities with the artificial nuclease Phenanthroline-copper and with chemical probes. The cis-platinum adduct behaves more as a centre of directed bend than as a hinge joint, the induced bend angle being of the order of 25-30 degrees. The double helix is locally denatured over 2 base pairs (corresponding to the platinated 5'G residue and the central T residue) and is distorted over 4-5 base pairs. The trans-platinum adduct behaves also more as a centre of directed bend than as a hinge joint, the induced bend angle being of the order of 60 degrees. The double helix is locally denatured over 4 base pairs (corresponding to the immediately 5'T residue adjacent to the adduct and to the three base residues of the adduct). Both the cis- and trans-platinum adducts decrease the thermal stability of the double helix. Images PMID:2388824

Training mentors of clinical and translational research scholars: a randomized controlled trial.

PubMed

Pfund, Christine; House, Stephanie C; Asquith, Pamela; Fleming, Michael F; Buhr, Kevin A; Burnham, Ellen L; Eichenberger Gilmore, Julie M; Huskins, W Charles; McGee, Richard; Schurr, Kathryn; Shapiro, Eugene D; Spencer, Kimberly C; Sorkness, Christine A

2014-05-01

To determine whether a structured mentoring curriculum improves research mentoring skills. The authors conducted a randomized controlled trial (RCT) at 16 academic health centers (June 2010 to July 2011). Faculty mentors of trainees who were conducting clinical/translational research ≥50% of the time were eligible. The intervention was an eight-hour, case-based curriculum focused on six mentoring competencies. The primary outcome was the change in mentors' self-reported pretest to posttest composite scores on the Mentoring Competency Assessment (MCA). Secondary outcomes included changes in the following: mentors' awareness as measured by their self-reported retrospective change in MCA scores, mentees' ratings of their mentors' competency as measured by MCA scores, and mentoring behaviors as reported by mentors and their mentees. A total of 283 mentor-mentee pairs were enrolled: 144 mentors were randomized to the intervention; 139 to the control condition. Self-reported pre-/posttest change in MCA composite scores was higher for mentors in the intervention group compared with controls (P < .001). Retrospective changes in MCA composite scores between the two groups were even greater, and extended to all six subscale scores (P < .001). More intervention-group mentors reported changes in their mentoring practices than control mentors (P < .001). Mentees working with intervention-group mentors reported larger changes in retrospective MCA pre-/posttest scores (P = .003) and more changes in their mentors' behavior (P = .002) than those paired with control mentors. This RCT demonstrates that a competency-based research mentor training program can improve mentors' skills.

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.

Theoretical determination of one-electron redox potentials for DNA bases, base pairs, and stacks.

PubMed

Paukku, Y; Hill, G

2011-05-12

Electron affinities, ionization potentials, and redox potentials for DNA bases, base pairs, and N-methylated derivatives are computed at the DFT/M06-2X/6-31++G(d,p) level of theory. Redox properties of a guanine-guanine stack model are explored as well. Reduction and oxidation potentials are in good agreement with the experimental ones. Electron affinities of base pairs were found to be negative. Methylation of canonical bases affects the ionization potentials the most. Base pair formation and base stacking lower ionization potentials by 0.3 eV. Pairing of guanine with the 5-methylcytosine does not seem to influence the redox properties of this base pair much.

Inhibiting Polysulfide Shuttle in Lithium-Sulfur Batteries through Low-Ion-Pairing Salts and a Triflamide Solvent.

PubMed

Shyamsunder, Abhinandan; Beichel, Witali; Klose, Petra; Pang, Quan; Scherer, Harald; Hoffmann, Anke; Murphy, Graham K; Krossing, Ingo; Nazar, Linda F

2017-05-22

The step-change in gravimetric energy density needed for electrochemical energy storage devices to power unmanned autonomous vehicles, electric vehicles, and enable low-cost clean grid storage is unlikely to be provided by conventional lithium ion batteries. Lithium-sulfur batteries comprising lightweight elements provide a promising alternative, but the associated polysulfide shuttle in typical ether-based electrolytes generates loss in capacity and low coulombic efficiency. The first new electrolyte based on a unique combination of a relatively hydrophobic sulfonamide solvent and a low ion-pairing salt, which inhibits the polysulfide shuttle, is presented. This system behaves as a sparingly solvating electrolyte at slightly elevated temperatures, where it sustains reversible capacities as high as 1200-1500 mAh g -1 over a wide range of current density (2C-C/5, respectively) when paired with a lithium metal anode, with a coulombic efficiency of >99.7 % in the absence of LiNO 3 additive. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Why the tautomerization of the G·C Watson-Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis.

PubMed

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

2014-01-01

The ground-state tautomerization of the G·C Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4), corresponding to a hydrophobic interface of protein-nucleic acid interactions, using DFT and MP2 levels of quantum-mechanical (QM) theory and quantum theory "Atoms in molecules" (QTAIM). Based on the sweeps of the electron-topological, geometric, polar, and energetic parameters, which describe the course of the G·C ↔ G*·C* tautomerization (mutagenic tautomers of the G and C bases are marked with an asterisk) through the DPT along the intrinsic reaction coordinate (IRC), it was proved that it is, strictly speaking, a concerted asynchronous process both at the DFT and MP2 levels of theory, in which protons move with a small time gap in vacuum, while this time delay noticeably increases in the continuum with ϵ = 4. It was demonstrated using the conductor-like polarizable continuum model (CPCM) that the continuum with ϵ = 4 does not qualitatively affect the course of the tautomerization reaction. The DPT in the G·C Watson-Crick base pair occurs without any intermediates both in vacuum and in the continuum with ϵ = 4 at the DFT/MP2 levels of theory. The nine key points along the IRC of the G·C base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These key points have been used to define the reactant, transition state, and product regions of the DPT reaction in the G·C base pair. Analysis of the energetic characteristics of the H-bonds allows us to arrive at a definite conclusion that the middle N1H⋯N3/N3H⋯N1 and the lower N2H⋯O2/N2H⋯O2 parallel H-bonds in the G·C/G*·C* base pairs, respectively, are anticooperative, that is, the strengthening of the middle H-bond is accompanied by the weakening of the lower H-bond. At that point, the upper N4H⋯O6 and O6H⋯N4 H-bonds in the G·C and G*·C* base pairs, respectively, remain constant at the changes of the middle and the lower H-bonds at the beginning and at the ending of the G·C ↔ G*·C* tautomerization. Aiming to answer the question posed in the title of the article, we established that the G*·C* Löwdin's base pair satisfies all the requirements necessary to cause point mutations in DNA except its lifetime, which is much less than the period of time required for the replication machinery to forcibly dissociate a base pair into the monomers (several ns) during DNA replication. So, from the physicochemical point of view, the G*·C* Löwdin's base pair cannot be considered as a source of point mutations arising during DNA replication.

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.

The coevolution of long-term pair bonds and cooperation.

PubMed

Song, Z; Feldman, M W

2013-05-01

The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair-matching distribution of the population, and the latter often emerges as a collective outcome of individual pair-bonding traits, which are also under selection. Here, we develop an analytical model and individual-based simulations to study the coevolution of long-term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long-term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long-term pair bonds lead to assortative interactions through pair-matching dynamics, they may promote the prevalence of cooperation. In addition to the pay-off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair-bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Sign reversal of the order parameter in (Li1-xFex)OHFe1-yZnySe

NASA Astrophysics Data System (ADS)

Du, Zengyi; Yang, Xiong; Altenfeld, Dustin; Gu, Qiangqiang; Yang, Huan; Eremin, Ilya; Hirschfeld, Peter J.; Mazin, Igor I.; Lin, Hai; Zhu, Xiyu; Wen, Hai-Hu

2018-02-01

Iron pnictides are the only known family of unconventional high-temperature superconductors besides cuprates. Until recently, it was widely accepted that superconductivity is driven by spin fluctuations and intimately related to the fermiology, specifically, hole and electron pockets separated by the same wavevector that characterizes the dominant spin fluctuations, and supporting order parameters (OP) of opposite signs. This picture was questioned after the discovery of intercalated or monolayer form of FeSe-based systems without hole pockets, which seemingly undermines the basis for spin-fluctuation theory and the idea of a sign-changing OP. Using the recently proposed phase-sensitive quasiparticle interference technique, here we show that in LiOH-intercalated FeSe compound the OP does change sign, albeit within the electronic pockets. This result unifies the pairing mechanism of iron-based superconductors with or without the hole Fermi pockets and supports the conclusion that spin fluctuations play the key role in electron pairing.

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.

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

Pogosov, Walter V.; Institute for Theoretical and Applied Electrodynamics, Russian Academy of Sciences, Izhorskaya 13, 125412 Moscow; Combescot, Monique

While the one-Cooper-pair problem is now a textbook exercise, the energy of two pairs of electrons with opposite spins and zero total momentum has not been derived yet, the exact handling of Pauli blocking between bound pairs being not that easy for N=2 already. The two-Cooper-pair problem however is quite enlightening to understand the very peculiar role played by the Pauli exclusion principle in superconductivity. Pauli blocking is known to drive the change from 1 to N pairs but no precise description of this continuous change has been given so far. Using Richardson's procedure, we here prove that Pauli blockingmore » increases the free part of the two-pair ground-state energy but decreases the binding part when compared to two isolated pairs--the excitation gap to break a pair however increasing from one to two pairs. When extrapolated to the dense BCS regime, the decrease in the pair binding while the gap increases strongly indicates that at odd with common belief, the average pair binding energy cannot be on the order of the gap.« less

Changes in intrapopulation resource use patterns of an endangered raptor in response to a disease-mediated crash in prey abundance.

PubMed

Moleón, Marcos; Sebastián-González, Esther; Sánchez-Zapata, José A; Real, Joan; Pires, Mathias M; Gil-Sánchez, José M; Bautista, Jesús; Palma, Luís; Bayle, Patrick; Guimarães, Paulo R; Beja, Pedro

2012-11-01

1. A long-standing question in ecology is how natural populations respond to a changing environment. Emergent optimal foraging theory-based models for individual variation go beyond the population level and predict how its individuals would respond to disturbances that produce changes in resource availability. 2. Evaluating variations in resource use patterns at the intrapopulation level in wild populations under changing environmental conditions would allow to further advance in the research on foraging ecology and evolution by gaining a better idea of the underlying mechanisms explaining trophic diversity. 3. In this study, we use a large spatio-temporal scale data set (western continental Europe, 1968-2006) on the diet of Bonelli's Eagle Aquila fasciata breeding pairs to analyse the predator trophic responses at the intrapopulation level to a prey population crash. In particular, we borrow metrics from studies on network structure and intrapopulation variation to understand how an emerging infectious disease [the rabbit haemorrhagic disease (RHD)] that caused the density of the eagle's primary prey (rabbit Oryctolagus cuniculus) to dramatically drop across Europe impacted on resource use patterns of this endangered raptor. 4. Following the major RHD outbreak, substantial changes in Bonelli's Eagle's diet diversity and organisation patterns at the intrapopulation level took place. Dietary variation among breeding pairs was larger after than before the outbreak. Before RHD, there were no clusters of pairs with similar diets, but significant clustering emerged after RHD. Moreover, diets at the pair level presented a nested pattern before RHD, but not after. 5. Here, we reveal how intrapopulation patterns of resource use can quantitatively and qualitatively vary, given drastic changes in resource availability. 6. For the first time, we show that a pathogen of a prey species can indirectly impact the intrapopulation patterns of resource use of an endangered predator. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells.

PubMed Central

Homann, M; Tabler, M; Tzortzakaki, S; Sczakiel, G

1994-01-01

When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure. In the case of an inhibitory 429 nucleotides long trans-ribozyme (2as-Rz12) which was directed against the 5'-leader/gag region of the human immunodeficiency virus type 1 (HIV-1), helix II was not pre-formed in the single-stranded molecule. Thus, major structural changes are necessary before cleavage can occur. To study whether pre-formation of helix II in the non-paired 2as-Rz12 RNA could influence the observed cleavage rate in vitro and its inhibitory activity on HIV-1 replication, we extended the 4 base pair helix II of 2as-Rz12 to 6, 10, 21, and 22 base pairs respectively. Limited RNase cleavage reactions performed in vitro at 37 degrees C and at physiological ion strength indicated that a helix II of the hammerhead domain was pre-formed when its length was at least six base pairs. This modification neither affected the association rate with target RNA nor the cleavage rate in vitro. In contrast to this, extension of helix II led to a significantly decreased inhibition of HIV-1 replication in human cells. Together with the finding of others that shortening of helix II to less than two base pairs reduces the catalytic activity in vitro, this observation indicates that the length of helix II in the naturally occurring RNAs with a hammerhead domain is already close or identical to the optimal length for catalytic activity in vitro and in vivo. Images PMID:7524030

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

NASA Astrophysics Data System (ADS)

(O' Lee, Dominic J.

2018-02-01

At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex.

PubMed Central

Zhang, X; Gottlieb, P A

1995-01-01

Guanine residues in the lac operator were replaced by 2-aminopurine or purine analogues, pairing the modified nucleotides with C. The observed equilibrium dissociation constants for lac repressor binding to substituted operators were measured in 10 mM Tris, 150 mM KCl, 0.1 mM EDTA, 0.1 mM DTE, pH 7.6 at 25 degrees C. These measurements revealed five positions that destabilized the complex when substituted with either analogue. Two positions, which are related by a 2-fold symmetry, are in the major groove of the operator thought to directly interact with the protein. Three sites were in the central region of the operator. A purine analogue at a sixth site perturbed the local DNA structure and destabilized the complex. Alkylation interference experiments of the 2-aminopurine substituted operators demonstrated that, of the five affected, two substitutions displayed altered phosphate interference patterns at the phosphate adjacent to the substituted base. For these operators, complex formation was measured in different concentrations of KCl to assess the contribution of counterion release to the bimolecular process. The results indicated that both complexes were similar to wild-type, although minor changes were observed. The Kobs of the complex was then measured when 2-aminopurine or purine analogues were paired with uracil nucleotide, a base pair that serves to stabilize the DNA. The introduction of the new base pairs revealed two effects on the bimolecular interaction. For those operator sites that are thought to perturb the interaction directly, the affinity of the complex was weakened to levels observed for the singly-substituted operators. In contrast, the nucleotides of 2-aminopurine paired with uracil positioned in the central region of the operator served to enhance the stability of the complex. The purine-uracil base pair substitution on the other hand had a significant destabilizing effect on the interaction. We propose that the central base pairs modulate binding of the complex by altering the intrinsic properties of the DNA. Two specific attributes are required to achieve the lowest free energy of interaction. The DNA must have two interstrand hydrogen bonds to stabilize the duplex and it must have properties associated with directional bending or unwinding. This analysis does not rule out contributions by direct interactions between the protein and the central region of the operator but underscores how indirect effects play a major role in complex formation in this system. Images PMID:7784203

Time-Resolved Magnetic Field Effects Distinguish Loose Ion Pairs from Exciplexes

PubMed Central

2013-01-01

We describe the experimental investigation of time-resolved magnetic field effects in exciplex-forming organic donor–acceptor systems. In these systems, the photoexcited acceptor state is predominantly deactivated by bimolecular electron transfer reactions (yielding radical ion pairs) or by direct exciplex formation. The delayed fluorescence emitted by the exciplex is magnetosensitive if the reaction pathway involves loose radical ion pair states. This magnetic field effect results from the coherent interconversion between the electronic singlet and triplet radical ion pair states as described by the radical pair mechanism. By monitoring the changes in the exciplex luminescence intensity when applying external magnetic fields, details of the reaction mechanism can be elucidated. In this work we present results obtained with the fluorophore-quencher pair 9,10-dimethylanthracene/N,N-dimethylaniline (DMA) in solvents of systematically varied permittivity. A simple theoretical model is introduced that allows discriminating the initial state of quenching, viz., the loose ion pair and the exciplex, based on the time-resolved magnetic field effect. The approach is validated by applying it to the isotopologous fluorophore-quencher pairs pyrene/DMA and pyrene-d10/DMA. We detect that both the exciplex and the radical ion pair are formed during the initial quenching stage. Upon increasing the solvent polarity, the relative importance of the distant electron transfer quenching increases. However, even in comparably polar media, the exciplex pathway remains remarkably significant. We discuss our results in relation to recent findings on the involvement of exciplexes in photoinduced electron transfer reactions. PMID:24041160

Two-Month-Old Infants' Sensitivity to Changes in Arbitrary Syllable-Object Pairings: The Role of Temporal Synchrony

ERIC Educational Resources Information Center

Gogate, Lakshmi J.; Prince, Christopher G.; Matatyaho, Dalit J.

2009-01-01

To explore early lexical development, the authors examined infants' sensitivity to changes in spoken syllables and objects given different temporal relations between syllable-object pairings. In Experiment 1, they habituated 2-month-olds to 1 syllable, /tah/ or /gah/, paired with an object in "synchronous" (utterances coincident with object…

Hydatid cyst of the liver-criteria for the selection of appropriate treatment.

PubMed

Menezes da Silva, A

2003-02-01

The appropriate treatment of hydatid cysts of the liver is determined by several factors, namely the patient, the cyst, the therapeutic resources and the physician. Characteristics of cysts, can be described by ultrasonography (US). Based on US images, we can classify hydatid cysts, according the evolutionary phase of the larval parasite and to choose the most appropriate therapeutic approach. US is also important to evaluate the efficacy of the treatment. Concerning the therapeutic methods, surgery had long been the only treatment available for the hydatid cyst of the liver. Beginning the 1970s benzimidazoles, Mebendazole and Albendazole, have been used for the treatment of the hydatid disease and in the early 1980s, with the development of diagnostic US, the deliberate puncture of abdominal cysts, particularly those in the liver, was evaluated this lead to puncture/aspiration, followed by injection of a scolicide which became a therapeutic method known as puncture, aspiration, injection and re-aspiration (PAIR). So, according to the cyst's characteristics based on US evaluation we can establish a therapeutic strategy: cysts type 1 and 3 may be treated by chemotherapy. Alternative treatment should be PAIR but only if the cysts cannot be treated with benzimidazoles. If there are contraindications for PAIR and chemotherapy the treatment should be surgical. Type 2 hydatid cysts can be treated by PAIR following initial treatment with benzimidazoles. If PAIR is not feasible or there is no evidence of degenerative changes after chemotherapy, surgery is indicated. Type 4 cysts are usually inactive and, in these cases, treatment is not indicated. If there is evidence that the cysts contents are still viable PAIR may be indicate. If PAIR is not possible, surgery is the method of choice. Cysts type 5 do not require treatment.

THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhao, Dongbo; Dong, Hao; Jiang, Ling; Huang, Lin; Liu, Yunfei; Li, Shuhua

2018-07-01

The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most Nsbnd H and Csbnd H bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.

Sequence-dependent DNA deformability studied using molecular dynamics simulations.

PubMed

Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

2007-01-01

Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

Monitoring Integrated Activity of Individual Neurons Using FRET-Based Voltage-Sensitive Dyes.

PubMed

Briggman, Kevin L; Kristan, William B; González, Jesús E; Kleinfeld, David; Tsien, Roger Y

2015-01-01

Pairs of membrane-associated molecules exhibiting fluorescence resonance energy transfer (FRET) provide a sensitive technique to measure changes in a cell's membrane potential. One of the FRET pair binds to one surface of the membrane and the other is a mobile ion that dissolves in the lipid bilayer. The voltage-related signal can be measured as a change in the fluorescence of either the donor or acceptor molecules, but measuring their ratio provides the largest and most noise-free signal. This technology has been used in a variety of ways; three are documented in this chapter: (1) high throughput drug screening, (2) monitoring the activity of many neurons simultaneously during a behavior, and (3) finding synaptic targets of a stimulated neuron. In addition, we provide protocols for using the dyes on both cultured neurons and leech ganglia. We also give an updated description of the mathematical basis for measuring the coherence between electrical and optical signals. Future improvements of this technique include faster and more sensitive dyes that bleach more slowly, and the expression of one of the FRET pair genetically.

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.

Anomalous scaling of Δ C versus T c in the Fe-based superconductors: the $${S}_{\\pm }$$-wave pairing state model

DOE PAGES

Bang, Yunkyu; Stewart, G. R.

2016-02-01

The strong power law behavior of the specific heat jumpmore » $${\\rm{\\Delta }}C\\;$$ versus T c $$({\\rm{\\Delta }}C/{T}_{{\\rm{c}}}\\sim {T}_{{\\rm{c}}}^{\\alpha },\\alpha \\approx 2)$$, first observed by Bud'ko et al (2009 Phys. Rev. B 79 220516), has been confirmed with several families of the Fe-based superconducting compounds with various dopings. We tested a minimal two band BCS model to understand this anomalous behavior and showed that this non-BCS relation between $${\\rm{\\Delta }}C\\;$$ versus T c is a generic property of the multiband superconducting state paired by a dominant interband interaction ($${V}_{\\mathrm{inter}}\\gt {V}_{\\mathrm{intra}}$$) reflecting the relation $$\\frac{{{\\rm{\\Delta }}}_{{\\rm{h}}}}{{{\\rm{\\Delta }}}_{{\\rm{e}}}}\\sim \\sqrt{\\frac{{N}_{{\\rm{e}}}}{{N}_{{\\rm{h}}}}}$$ near T c, as in the $${S}_{\\pm }$$-wave pairing state. We also found that this $${\\rm{\\Delta }}C\\;$$ versus T c power law can continuously change from the ideal BNC scaling to a considerable deviation by a moderate variation of the impurity scattering rate $${{\\rm{\\Gamma }}}_{0}$$ (non-pair-breaking). Finally, as a result, our model provides a consistent explanation why the electron-doped Fe-based superconductors follow the ideal BNC scaling very well while the hole-doped systems often show varying degree of deviations.« less

A large-scale perspective on stress-induced alterations in resting-state networks

NASA Astrophysics Data System (ADS)

Maron-Katz, Adi; Vaisvaser, Sharon; Lin, Tamar; Hendler, Talma; Shamir, Ron

2016-02-01

Stress is known to induce large-scale neural modulations. However, its neural effect once the stressor is removed and how it relates to subjective experience are not fully understood. Here we used a statistically sound data-driven approach to investigate alterations in large-scale resting-state functional connectivity (rsFC) induced by acute social stress. We compared rsfMRI profiles of 57 healthy male subjects before and after stress induction. Using a parcellation-based univariate statistical analysis, we identified a large-scale rsFC change, involving 490 parcel-pairs. Aiming to characterize this change, we employed statistical enrichment analysis, identifying anatomic structures that were significantly interconnected by these pairs. This analysis revealed strengthening of thalamo-cortical connectivity and weakening of cross-hemispheral parieto-temporal connectivity. These alterations were further found to be associated with change in subjective stress reports. Integrating report-based information on stress sustainment 20 minutes post induction, revealed a single significant rsFC change between the right amygdala and the precuneus, which inversely correlated with the level of subjective recovery. Our study demonstrates the value of enrichment analysis for exploring large-scale network reorganization patterns, and provides new insight on stress-induced neural modulations and their relation to subjective experience.

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

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.

Experimental Acidification Causes Soil Base-Cation Depletion at the Bear Brook Watershed in Maine

Treesearch

Ivan J. Fernandez; Lindsey E. Rustad; Stephen A. Norton; Jeffrey S. Kahl; Bernard J. Cosby

2003-01-01

There is concern that changes in atmospheric deposition, climate, or land use have altered the biogeochemistry of forests causing soil base-cation depletion, particularly Ca. The Bear Brook Watershed in Maine (BBWM) is a paired watershed experiment with one watershed subjected to elevated N and S deposition through bimonthly additions of (NH4)2SO4. Quantitative soil...

Heritability of changes in brain volume over time in twin pairs discordant for schizophrenia.

PubMed

Brans, Rachel G H; van Haren, Neeltje E M; van Baal, G Caroline M; Schnack, Hugo G; Kahn, René S; Hulshoff Pol, Hilleke E

2008-11-01

Structural brain abnormalities have consistently been found in schizophrenia, with increased familial risk for the disease associated with these abnormalities. Some brain volume changes are progressive over the course of the illness. Whether these progressive brain volume changes are mediated by genetic or disease-related factors is unknown. To investigate whether genetic and/or environmental factors are associated with progressive brain volume changes in schizophrenia. Longitudinal 5-year follow-up in monozygotic (MZ) and dizygotic (DZ) twin pairs discordant for schizophrenia and healthy comparison twin pairs using brain magnetic resonance imaging. Participants were recruited from the twin pair cohort at the University Medical Center Utrecht. A total of 92 participants completed the study: 9 MZ and 10 DZ twin pairs discordant for schizophrenia and 14 MZ and 13 DZ healthy twin pairs. Percentage volume changes of the whole brain; cerebral gray and white matter of the frontal, temporal, parietal, and occipital lobes; cerebellum; and lateral and third ventricles over time between and within twin pairs were compared using repeated measures analysis of covariance. Structural equation modeling was applied to estimate contributions of additive genetic and common and unique environmental factors. Significant decreases over time in whole brain and frontal and temporal lobe volumes were found in patients with schizophrenia and their unaffected co-twins compared with control twins. Bivariate structural equation modeling using cross-trait/cross-twin correlations revealed significant additive genetic influences on the correlations between schizophrenia liability and progressive whole brain (66%; 95% confidence interval [CI], 51%-100%), frontal lobe (76%; 95% CI, 54%-100%), and temporal lobe (79%; CI, 56%-100%) volume change. The progressive brain volume loss found in patients with schizophrenia and their unaffected co-twins is at least partly attributable to genetic factors related to the illness.

Estimating mean change in population salt intake using spot urine samples.

PubMed

Petersen, Kristina S; Wu, Jason H Y; Webster, Jacqui; Grimes, Carley; Woodward, Mark; Nowson, Caryl A; Neal, Bruce

2017-10-01

Spot urine samples are easier to collect than 24-h urine samples and have been used with estimating equations to derive the mean daily salt intake of a population. Whether equations using data from spot urine samples can also be used to estimate change in mean daily population salt intake over time is unknown. We compared estimates of change in mean daily population salt intake based upon 24-h urine collections with estimates derived using equations based on spot urine samples. Paired and unpaired 24-h urine samples and spot urine samples were collected from individuals in two Australian populations, in 2011 and 2014. Estimates of change in daily mean population salt intake between 2011 and 2014 were obtained directly from the 24-h urine samples and by applying established estimating equations (Kawasaki, Tanaka, Mage, Toft, INTERSALT) to the data from spot urine samples. Differences between 2011 and 2014 were calculated using mixed models. A total of 1000 participants provided a 24-h urine sample and a spot urine sample in 2011, and 1012 did so in 2014 (paired samples n = 870; unpaired samples n = 1142). The participants were community-dwelling individuals living in the State of Victoria or the town of Lithgow in the State of New South Wales, Australia, with a mean age of 55 years in 2011. The mean (95% confidence interval) difference in population salt intake between 2011 and 2014 determined from the 24-h urine samples was -0.48g/day (-0.74 to -0.21; P < 0.001). The corresponding result estimated from the spot urine samples was -0.24 g/day (-0.42 to -0.06; P = 0.01) using the Tanaka equation, -0.42 g/day (-0.70 to -0.13; p = 0.004) using the Kawasaki equation, -0.51 g/day (-1.00 to -0.01; P = 0.046) using the Mage equation, -0.26 g/day (-0.42 to -0.10; P = 0.001) using the Toft equation, -0.20 g/day (-0.32 to -0.09; P = 0.001) using the INTERSALT equation and -0.27 g/day (-0.39 to -0.15; P < 0.001) using the INTERSALT equation with potassium. There was no evidence that the changes detected by the 24-h collections and estimating equations were different (all P > 0.058). Separate analysis of the unpaired and paired data showed that detection of change by the estimating equations was observed only in the paired data. All the estimating equations based upon spot urine samples identified a similar change in daily salt intake to that detected by the 24-h urine samples. Methods based upon spot urine samples may provide an approach to measuring change in mean population salt intake, although further investigation in larger and more diverse population groups is required. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

Spatio-temporal changes of seismic anisotropy in seismogenic zones

NASA Astrophysics Data System (ADS)

Saade, M.; Montagner, J.; Roux, P.; Paul, C.; Brenguier, F.; Enescu, B.; Shiomi, K.

2013-12-01

Seismic anisotropy plays a key role in the study of stress and strain fields in the earth. Potential temporal change of seismic anisotropy can be interpreted as change of the orientation of cracks in seismogenic zones and thus change of the stress field. Such temporal changes have been observed in seismogenic zones before and after earthquakes (Durand et al. , 2011) but are still not well understood. In this study, from a numerical point of view, we investigate the variations of the polarization of surface waves in anisotropic media. These variations are related to the elastic properties of the medium, in particular to anisotropy. The technique used is based on the calculation of the whole cross-correlation tensor (CCT) of ambient seismic noise. If the sources are randomly distributed in homogeneous medium, it allows us to reconstruct the Green's tensor between two stations continuously and to monitor the region through the use of its fluctuations. Therefore, the temporal change of the Green's cross-correlation tensor enables the monitoring of stress and strain fields. This technique is applied to synthetic seismograms computed in a transversally isotropic medium with horizontal symmetry axis (hereafter referred to an HTI medium) using a code RegSEM (Cupillard et al. , 2012) based on the spectral element method. We designed an experiment in order to investigate the influence of anisotropy on the CCT. In homogeneous, isotropic medium the off-diagonal terms of the Green's tensor are null. The CCT is computed between each pair of stations and then rotated in order to approximate the Green's tensor by minimizing the off-diagonal components. This procedure permits the calculation of the polarization angle of quasi-Rayleigh and quasi-Love waves, and to observe the azimuthal variation of their polarization. The results show that even a small variation of the azimuth of seismic anisotropy with respect to a certain pair of stations can induce, in some cases, a large variation in the horizontal polarization of surface waves along the direction of this pair of stations. It depends on the relative azimuth angle between the pair of stations and the direction of anisotropy, on the amplitude of anisotropy and the frequency band of the signal. Therefore, it is now possible to explain the large, rapid and very localized variations of surface waves horizontal polarization observed by Durand et al. (2011) during the Parkfield earthquake of 2004. Furthermore, some preliminary results about the investigation of seismic anisotropy change caused by the June 13, 2008 Iwate-Miyagi Nairiku earthquake (Mw = 6.9) will be presented.

Science Teachers' Conceptual Growth within Vygotsky's Zone of Proximal Development.

ERIC Educational Resources Information Center

Jones, M. Gail; Rua, Melissa J.; Carter, Glenda

1998-01-01

Examines how science teachers' (n=14) knowledge of science and science pedagogy changed after participation in a constructivist-based methods course. More-experienced teachers were paired with less-experienced teachers, and pre- and post-instructional concept maps, journals, portfolios, and transcripts revealed that, within the zone of proximal…

Changes in Greenland ice bed conditions inferred from seismology

NASA Astrophysics Data System (ADS)

Toyokuni, Genti; Takenaka, Hiroshi; Takagi, Ryota; Kanao, Masaki; Tsuboi, Seiji; Tono, Yoko; Childs, Dean; Zhao, Dapeng

2018-04-01

Basal conditions of the Greenland Ice Sheet (GrIS) are a key research topic in climate change studies. The recent construction of a seismic network has provided a new opportunity for direct, real-time, and continuous monitoring of the GrIS. Here we use ambient noise surface wave data from seismic stations all over Greenland for a 4.5-year period to detect changes in Rayleigh-wave phase velocity between seismic station pairs. We observe clear seasonal and long-term velocity changes for many pairs, and propose a plausible mechanism for these changes. Dominant factors driving the velocity changes might be seasonal and long-term pressurization/depressurization of the GrIS and shallow bedrock by air and ice mass loading/unloading. However, heterogeneity of the GrIS basal conditions might impose strong regionalities on the results. An interesting feature is that, even at adjacent two station pairs in the inland GrIS, one pair shows velocity decrease while another shows velocity increase as a response to the high air and snow pressure. The former pair might be located on a thawed bed that decreases velocity by increased meltwater due to pressure melting, whereas the latter pair might be located on a frozen bed that increases velocity by compaction of ice and shallow bedrock. The results suggest that surface waves are very sensitive to the GrIS basal conditions, and further observations will contribute to a more direct and quantitative estimation of water balance in the Arctic region.

Characterization of a Chlamydomonas Insertional Mutant that Disrupts Flagellar Central Pair Microtubule-associated Structures

PubMed Central

Mitchell, David R.; Sale, Winfield S.

1999-01-01

Two alleles at a new locus, central pair–associated complex 1 (CPC1), were selected in a screen for Chlamydomonas flagellar motility mutations. These mutations disrupt structures associated with central pair microtubules and reduce flagellar beat frequency, but do not prevent changes in flagellar activity associated with either photophobic responses or phototactic accumulation of live cells. Comparison of cpc1 and pf6 axonemes shows that cpc1 affects a row of projections along C1 microtubules distinct from those missing in pf6, and a row of thin fibers that form an arc between the two central pair microtubules. Electron microscopic images of the central pair in axonemes from radial spoke–defective strains reveal previously undescribed central pair structures, including projections extending laterally toward radial spoke heads, and a diagonal link between the C2 microtubule and the cpc1 projection. By SDS-PAGE, cpc1 axonemes show reductions of 350-, 265-, and 79-kD proteins. When extracted from wild-type axonemes, these three proteins cosediment on sucrose gradients with three other central pair proteins (135, 125, and 56 kD) in a 16S complex. Characterization of cpc1 provides new insights into the structure and biochemistry of the central pair apparatus, and into its function as a regulator of dynein-based motility. PMID:9922455

Tunable electromagnetically induced absorption based on graphene

NASA Astrophysics Data System (ADS)

Cao, Maoyong; Wang, Tongling; Zhang, Huiyun; Zhang, Yuping

2018-04-01

In this paper, an electronically induced absorption (EIA) structure based on graphene at the infrared frequency is proposed. A pair of nanorods is coupled to a ring resonator, resulting in electronically induced transparency (EIT), and then, Babinet's principle is applied to transform the EIT structure into an EIA structure. Based on the bright and dark modes of the coupling schemes, the adjustment of the coupling strength between the dark and bright modes can be achieved by changing the asymmetry degree. In addition, the transparency window and the absorption peak can be tuned by changing the Fermi energy of graphene. This graphene-based EIA structure can develop the path in narrow-band filtering and, absorptive switching in the future.

Training Mentors of Clinical and Translational Research Scholars: A Randomized Controlled Trial

PubMed Central

Pfund, Christine; House, Stephanie C.; Asquith, Pamela; Fleming, Michael F.; Buhr, Kevin A.; Burnham, Ellen L.; Gilmore, Julie M. Eichenberger; Huskins, W. Charles; McGee, Richard; Schurr, Kathryn; Shapiro, Eugene D.; Spencer, Kimberly C.; Sorkness, Christine A.

2014-01-01

Purpose To determine whether a structured mentoring curriculum improves research mentoring skills. Method The authors conducted a randomized controlled trial (RCT) at 16 academic health centers (June 2010 to July 2011). Faculty mentors of trainees who were conducting clinical/translational research ≥50% of the time were eligible. The intervention was an eight-hour, case-based curriculum focused on six mentoring competencies. The primary outcome was the change in mentors’ self-reported pretest to posttest composite scores on the Mentoring Competency Assessment (MCA). Secondary outcomes included changes in the following: mentors’ awareness as measured by their self-reported retrospective change in MCA scores, mentees’ ratings of their mentors’ competency as measured by MCA scores, and mentoring behaviors as reported by mentors and their mentees. Results A total of 283 mentor–mentee pairs were enrolled: 144 mentors were randomized to the intervention; 139 to the control condition. Self-reported pre-/posttest change in MCA composite scores was higher for mentors in the intervention group compared with controls (P < .001). Retrospective changes in MCA composite scores between the two groups were even greater, and extended to all six subscale scores (P < .001). More intervention-group mentors reported changes in their mentoring practices than control mentors (P < .001). Mentees working with intervention-group mentors reported larger changes in retrospective MCA pre-/posttest scores (P = .003) and more changes in their mentors’ behavior (P = .002) than those paired with control mentors. Conclusions This RCT demonstrates that a competency-based research mentor training program can improve mentors’ skills. PMID:24667509

The cyc1-11 mutation in yeast reverts by recombination with a nonallelic gene: composite genes determining the iso-cytochromes c.

PubMed Central

Ernst, J F; Stewart, J W; Sherman, F

1981-01-01

DNA sequence analysis of a cloned fragment directly established that the cyc1-11 mutation of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae is a two-base-pair substitution that changes the CCA proline codon at amino acid position 76 to a UAA nonsense codon. Analysis of 11 revertant proteins and one cloned revertant gene showed that reversion of the cyc1-11 mutation can occur in three ways: a single base-pair substitution, which produces a serine replacement at position 76; recombination with the nonallelic CYC7 gene of iso-2-cytochrome c, which causes replacement of a segment in the cyc1-11 gene by the corresponding segment of the CYC7 gene; and either a two-base-pair substitution or recombination with the CYC7 gene, which causes the formation of the normal iso-1-cytochrome c sequence. These results demonstrate the occurrence of low frequencies of recombination between nonallelic genes having extensive but not complete homology. The formation of composite genes that share sequences from nonallelic genes may be an evolutionary mechanism for producing protein diversities and for maintaining identical sequences at different loci. Images PMID:6273865

[Flicker comparison of optic disc photographs: sensitivity and specificity].

PubMed

Funk, Jens; Lagrèze, Wolf; Zeyen, Thierry

2002-12-01

Examination and documentation of the optic nerve head are essential in monitoring glaucoma patients. Even minor changes in optic nerve head morphology can be visualised using the so-called flicker test: Two optic nerve head photographs, taken at consecutive examinations, are superimposed by projection. When occluding the pictures in a rapid alternating fashion, changes in optic nerve head morphology appear as motion. In this study, we evaluated sensitivity and specificity of the flicker test. A set of 33 pairs of serial optic disc slides was used as gold standard. These 33 pairs had been classified earlier by 3 independent groups of experts. 23 had been classified as "no change over time", 10 had been classified as "change". All 33 pairs were now evaluated by flicker comparison in a masked fashion. Flicker comparison usually took 1 minute per pair of slides. Sensitivity was 90 %, specificity was 65 %. The sensitivity was reasonably high. The moderate specificity was due to some cases showing "change" with the flicker comparison which might have been overlooked by the expert groups. Flicker comparison is an easy, fast and reliable technique to evaluate pairs of consecutive optic disc photographs.

Rotational-translational fourier imaging system

NASA Technical Reports Server (NTRS)

Campbell, Jonathan W. (Inventor)

2004-01-01

This invention has the ability to create Fourier-based images with only two grid pairs. The two grid pairs are manipulated in a manner that allows (1) a first grid pair to provide multiple real components of the Fourier-based image and (2) a second grid pair to provide multiple imaginary components of the Fourier-based image. The novelty of this invention resides in the use of only two grid pairs to provide the same imaging information that has been traditionally collected with multiple grid pairs.

Topological Crystalline Superconductivity in Locally Noncentrosymmetric Multilayer Superconductors

NASA Astrophysics Data System (ADS)

Yoshida, Tomohiro; Sigrist, Manfred; Yanase, Youichi

2015-07-01

Topological crystalline superconductivity in locally noncentrosymmetric multilayer superconductors (SCs) is proposed. We study the odd-parity pair-density wave (PDW) state induced by the spin-singlet pairing interaction through the spin-orbit coupling. It is shown that the PDW state is a topological crystalline SC protected by a mirror symmetry, although it is topologically trivial according to the classification based on the standard topological periodic table. The topological property of the mirror subsectors is intuitively explained by adiabatically changing the Bogoliubov-de Gennes Hamiltonian. A subsector of the bilayer PDW state reduces to the two-dimensional noncentrosymmetric SC, while a subsector of the trilayer PDW state is topologically equivalent to the spinless p -wave SC. Chiral Majorana edge modes in trilayers can be realized without Cooper pairs in the spin-triplet channel and chemical potential tuning.

Topological Crystalline Superconductivity in Locally Noncentrosymmetric Multilayer Superconductors.

PubMed

Yoshida, Tomohiro; Sigrist, Manfred; Yanase, Youichi

2015-07-10

Topological crystalline superconductivity in locally noncentrosymmetric multilayer superconductors (SCs) is proposed. We study the odd-parity pair-density wave (PDW) state induced by the spin-singlet pairing interaction through the spin-orbit coupling. It is shown that the PDW state is a topological crystalline SC protected by a mirror symmetry, although it is topologically trivial according to the classification based on the standard topological periodic table. The topological property of the mirror subsectors is intuitively explained by adiabatically changing the Bogoliubov-de Gennes Hamiltonian. A subsector of the bilayer PDW state reduces to the two-dimensional noncentrosymmetric SC, while a subsector of the trilayer PDW state is topologically equivalent to the spinless p-wave SC. Chiral Majorana edge modes in trilayers can be realized without Cooper pairs in the spin-triplet channel and chemical potential tuning.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

PubMed

Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

2011-03-14

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

A slow-adapting microfluidic-based tactile sensor

NASA Astrophysics Data System (ADS)

Tseng, W.-Y.; Fisher, J. S.; Prieto, J. L.; Rinaldi, K.; Alapati, G.; Lee, A. P.

2009-08-01

We present a microfluidic-based tactile sensor mimicking the human slow-adapting mechanoreceptor such as Merkel's disc. The sensor is composed of a polyimide (PI)/polydimethylsiloxane (PDMS) multilayer structure. The device uses a hemispherical reservoir filled with electrolyte solution in the PDMS layer, a microchannel in the PI layer and a pair of sensing electrodes below the microchannel as the force transducer. The tactile signal is detected as the impedance change resulting predominantly from the resistance variance due to the electrodes coverage by the 1M NaCl solution and is measured across the electrode pair. The sensor response is linear and the working range is shown to be in the range of 0-1.8 N. The characterization results also demonstrate the sensing of various levels of forces and its long-term signal stability.

Efficient Implementation of the Pairing on Mobilephones Using BREW

NASA Astrophysics Data System (ADS)

Yoshitomi, Motoi; Takagi, Tsuyoshi; Kiyomoto, Shinsaku; Tanaka, Toshiaki

Pairing based cryptosystems can accomplish novel security applications such as ID-based cryptosystems, which have not been constructed efficiently without the pairing. The processing speed of the pairing based cryptosystems is relatively slow compared with the other conventional public key cryptosystems. However, several efficient algorithms for computing the pairing have been proposed, namely Duursma-Lee algorithm and its variant ηT pairing. In this paper, we present an efficient implementation of the pairing over some mobilephones. Moreover, we compare the processing speed of the pairing with that of the other standard public key cryptosystems, i. e. RSA cryptosystem and elliptic curve cryptosystem. Indeed the processing speed of our implementation in ARM9 processors on BREW achieves under 100 milliseconds using the supersingular curve over F397. In addition, the pairing is more efficient than the other public key cryptosystems, and the pairing can be achieved enough also on BREW mobilephones. It has become efficient enough to implement security applications, such as short signature, ID-based cryptosystems or broadcast encryption, using the pairing on BREW mobilephones.

Exploring Change Processes in School-Based Mentoring for Bullied Children.

PubMed

Craig, James T; Gregus, Samantha J; Burton, Ally; Hernandez Rodriguez, Juventino; Blue, Mallory; Faith, Melissa A; Cavell, Timothy A

2016-02-01

We examined change processes associated with the school-based, lunchtime mentoring of bullied children. We used data from a one-semester open trial of Lunch Buddy (LB) mentoring (N = 24) to examine changes in bullied children's lunchtime peer relationships. We also tested whether these changes predicted key outcomes (i.e., peer victimization, social preference) post-mentoring. Results provided partial support that bullied children paired with LB mentors experienced improved lunchtime peer relationships and that gains in lunchtime relationships predicted post-mentoring levels of social preference and peer victimization. Neither child nor mentors' ratings of the mentoring relationship predicted post-mentoring outcomes; however, child-rated mentor support and conflict predicted improvements in lunchtime peer relationships. We discuss implications for future research on school-based mentoring as a form of selective intervention for bullied children.

Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket.

PubMed

Keiper, Sonja; Bebenroth, Dirk; Seelig, Burckhard; Westhof, Eric; Jäschke, Andres

2004-09-01

Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.

Influence of pharmacy students on the attitudes of medical students following an interprofessional course.

PubMed

Dabaghzadeh, Fatemeh; Zihayat, Bahare; Sarafzadeh, Farhad

2017-01-01

Clinical interprofessional education (IPE) can promote mutual understanding of other health professions and respectful behaviors among health-care professionals. The aims of this study were to evaluate the effects of IPE on the attitudes of medical and pharmacy students in an inpatient hospital setting and, in particular, the influence of pharmacy students on the attitudes of medical students. The 6th year doctor of pharmacy students and medical students were enrolled in a prospective cohort study. They were paired and each pair was responsible for three beds and all the patients occupying these mentioned beds over the 2-week course. The Readiness for Interprofessional Learning Scale (RIPLS) questionnaire was used to assess the students' attitudes before and after the course. The attitudes of the medical students changed positively after the IPE course based on RIPLS teamwork and collaboration and professional identity subscales. Changes in the attitudes of the pharmacy students were not statistically significant based on the mentioned scale and subscales. IPE could improve the attitudes of the medical students regarding interprofessional teamwork, communication, and sharing learning experience. Based on the current investigation, IPE did not have an effect on pharmacy students.

Optical CO2 sensing with ionic liquid doped electrospun nanofibers.

PubMed

Aydogdu, Sibel; Ertekin, Kadriye; Suslu, Aslihan; Ozdemir, Mehtap; Celik, Erdal; Cocen, Umit

2011-03-01

The first use of electrospun nanofibrous materials as highly responsive fluorescence quenching-based optical CO(2) sensors is reported. Poly(methyl methacrylate) and ethyl cellulose were used as polymeric materials. Sensing slides were fabricated by electrospinning technique. A fiber-optic bundle was used for the gas detection. CO(2) sensors based on the change in the fluorescence signal intensity of ion pair form of 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS). The sensor slides showed high sensitivities due to the high surface area-to-volume ratio of the nanofibrous membrane structures. The preliminary results of Stern-Volmer analysis show that the sensitivities of electrospun nanofibrous membranes to detect CO(2) are 24 to 120 fold higher than those of the thin film based sensors. The response times of the sensing reagents were short and the signal changes were fully reversible. The stability of ion pair form of HPTS in the employed matrix materials was excellent and when stored in the ambient air of the laboratory there was no significant drift in signal intensity after 7 months. Our stability tests are still in progress. © Springer Science+Business Media, LLC 2010

Prospective very young asteroid pairs

NASA Astrophysics Data System (ADS)

Galád, A.; Vokrouhlický, D.; Zizka, J.

2014-07-01

Several tens of asteroid pairs can be discerned from the background main-belt asteroids. The majority of them are thought to have formed within only the last few 10^6 yr. The youngest recognized pairs have formed more than ≈ 10 kyr ago. As some details of pair formation are still not understood well, the study of young pairs is of great importance. It is mainly because the conditions at the time of the pair formation could be deduced much more reliably for young pairs. For example, space weathering on the surfaces of the components, or changes in their rotational properties (in spin rates, tumbling, coordinates of rotational pole) could be negligible since the formation of young pairs. Also, possible strong perturbations by main-belt bodies on pair formation can be reliably studied only for extremely young pairs. Some pairs can quickly blend in with the background asteroids, so even the frequency of asteroid pair formation could be determined more reliably based on young pairs (though only after a statistically significant sample is at disposal). In our regular search for young pairs in the growing asteroid database, only multiopposition asteroids with very similar orbital and proper elements are investigated. Every pair component is represented by a number of clones within orbital uncertainties and drifting in semimajor axis due to the Yarkovsky effect. We found that, if the previously unrecognized pairs (87887) 2000 SS_{286} - 2002 AT_{49} and (355258) 2007 LY_{4} - 2013AF_{40} formed at the recent very close approach of their components, they could become the youngest known pairs. In both cases, the relative encounter velocities of the components were only ˜ 0.1 m s^{-1}. However, the minimum distances between some clones are too large and a few clones of the latter pair did not encounter recently (within ≈ 10 kyr). The age of some prospective young pairs cannot be determined reliably without improved orbital properties (e.g., the second component of a pair (320025) 2007 DT_{76} - 2007 DP_{16}). It is because some components suffered recently repeated close approaches to Ceres or other large main-belt perturbers. In general, the uncertainties in age estimation can be heavily reduced after the physical properties (e.g., sense of rotation, shape, size, binarity) of the pair components are determined.

An ensemble of SVM classifiers based on gene pairs.

PubMed

Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

2013-07-01

In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. Copyright © 2013 Elsevier Ltd. All rights reserved.

Envisaging quantum transport phenomenon in a muddled base pair of DNA

NASA Astrophysics Data System (ADS)

Vohra, Rajan; Sawhney, Ravinder Singh

2018-05-01

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au-AT base pair-Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T( E) and HOMO-LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

PubMed

Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

2015-10-12

A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.

PubMed

Meng, Zhenyu; Kubar, Tomas; Mu, Yuguang; Shao, Fangwei

2018-05-08

Charge transport (CT) through biomolecules is of high significance in the research fields of biology, nanotechnology, and molecular devices. Inspired by our previous work that showed the binding of ionic liquid (IL) facilitated charge transport in duplex DNA, in silico simulation is a useful means to understand the microscopic mechanism of the facilitation phenomenon. Here molecular dynamics simulations (MD) of duplex DNA in water and hydrated ionic liquids were employed to explore the helical parameters. Principal component analysis was further applied to capture the subtle conformational changes of helical DNA upon different environmental impacts. Sequentially, CT rates were calculated by a QM/MM simulation of the flickering resonance model based upon MD trajectories. Herein, MD simulation illustrated that the binding of ionic liquids can restrain dynamic conformation and lower the on-site energy of the DNA base. Confined movement among the adjacent base pairs was highly related to the increase of electronic coupling among base pairs, which may lead DNA to a CT facilitated state. Sequentially combining MD and QM/MM analysis, the rational correlations among the binding modes, the conformational changes, and CT rates illustrated the facilitation effects from hydrated IL on DNA CT and supported a conformational-gating mechanism.

INDIVIDUAL DIFFERENCES IN TASK-SPECIFIC PAIRED ASSOCIATES LEARNING IN OLDER ADULTS: THE ROLE OF PROCESSING SPEED AND WORKING MEMORY

PubMed Central

Kurtz, Tanja; Mogle, Jacqueline; Sliwinski, Martin J.; Hofer, Scott M.

2013-01-01

Background The role of processing speed and working memory was investigated in terms of individual differences in task-specific paired associates learning in a sample of older adults. Task-specific learning, as distinct from content-oriented item-specific learning, refers to gains in performance due to repeated practice on a learning task in which the to-be-learned material changes over trials. Methods Learning trajectories were modeled within an intensive repeated-measures design based on participants obtained from an opt-in internet-based sampling service (Mage = 65.3, SD = 4.81). Participants completed an eight-item paired associates task daily over a seven-day period. Results Results indicated that a three-parameter hyperbolic model (i.e., initial level, learning rate, and asymptotic performance) best described learning trajectory. After controlling for age-related effects, both higher working memory and higher processing speed had a positive effect on all three learning parameters. Conclusion These results emphasize the role of cognitive abilities for individual differences in task-specific learning of older adults. PMID:24151913

Advanced Large Scale Cross Domain Temporal Topic Modeling Algorithms to Infer the Influence of Recent Research on IPCC Assessment Reports

NASA Astrophysics Data System (ADS)

Sleeman, J.; Halem, M.; Finin, T.; Cane, M. A.

2016-12-01

Approximately every five years dating back to 1989, thousands of climate scientists, research centers and government labs volunteer to prepare comprehensive Assessment Reports for the Intergovernmental Panel on Climate Change. These are highly curated reports distributed to 200 nation policy makers. There have been five IPCC Assessment Reports to date, the latest leading to a Paris Agreement in Dec. 2016 signed thus far by 172 nations to limit the amount of global Greenhouse gases emitted to producing no more than a 20 C warming of the atmosphere. These reports are a living evolving big data collection tracing 30 years of climate science research, observations, and model scenario intercomparisons. They contain more than 200,000 citations over a 30 year period that trace the evolution of the physical basis of climate science, the observed and predicted impact, risk and adaptation to increased greenhouse gases and mitigation approaches, pathways, policies for climate change. Document-topic and topic-term probability distributions are built from the vocabularies of the respective assessment report chapters and citations. Using Microsoft Bing, we retrieve 150,000 citations referenced across chapters and convert those citations to text. Using a word n-gram model based on a heterogeneous set of climate change terminology, lemmatization, noise filtering and stopword elimination, we calculate word frequencies for chapters and citations. Temporal document sets are built based on the assessment period. In addition to topic modeling, we employ cross domain correlation measures. Using the Jensen-Shannon divergence and Pearson correlation we build correlation matrices for chapter and citations topics. The shared vocabulary acts as the bridge between domains resulting in chapter-citation point pairs in space. Pairs are established based on a document-topic probability distribution. Each chapter and citation is associated with a vector of topics and based on the n most probable topics, we establish which chapter-citation pairs are most similar. We will perform posterior inferences based on Hastings -Metropolis simulated annealing MCMC algorithm to infer, from the evolution of topics starting from AR1 to AR4, assertions of topics for AR5 and potentially AR6.

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

PubMed

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

1,8-Naphthyridine-2,7-diamine: A Potential Universal Reader of the Watson-Crick Base Pairs for DNA Sequencing by Electron Tunneling

PubMed Central

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2013-01-01

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read the DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs. PMID:23038027

THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides.

PubMed

Wang, Fang; Zhao, Dongbo; Dong, Hao; Jiang, Ling; Huang, Lin; Liu, Yunfei; Li, Shuhua

2018-07-05

The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study. Copyright © 2018 Elsevier B.V. All rights reserved.

Pairing FLUXNET sites to validate model representations of land-use/land-cover change

NASA Astrophysics Data System (ADS)

Chen, Liang; Dirmeyer, Paul A.; Guo, Zhichang; Schultz, Natalie M.

2018-01-01

Land surface energy and water fluxes play an important role in land-atmosphere interactions, especially for the climatic feedback effects driven by land-use/land-cover change (LULCC). These have long been documented in model-based studies, but the performance of land surface models in representing LULCC-induced responses has not been investigated well. In this study, measurements from proximate paired (open versus forest) flux tower sites are used to represent observed deforestation-induced changes in surface fluxes, which are compared with simulations from the Community Land Model (CLM) and the Noah Multi-Parameterization (Noah-MP) land model. Point-scale simulations suggest the CLM can represent the observed diurnal and seasonal changes in net radiation (Rnet) and ground heat flux (G), but difficulties remain in the energy partitioning between latent (LE) and sensible (H) heat flux. The CLM does not capture the observed decreased daytime LE, and overestimates the increased H during summer. These deficiencies are mainly associated with models' greater biases over forest land-cover types and the parameterization of soil evaporation. Global gridded simulations with the CLM show uncertainties in the estimation of LE and H at the grid level for regional and global simulations. Noah-MP exhibits a similar ability to simulate the surface flux changes, but with larger biases in H, G, and Rnet change during late winter and early spring, which are related to a deficiency in estimating albedo. Differences in meteorological conditions between paired sites is not a factor in these results. Attention needs to be devoted to improving the representation of surface heat flux processes in land models to increase confidence in LULCC simulations.

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

PubMed

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

2013-06-17

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Parasitoid, Verticia fasciventris Causes Morphological and Behavioral Changes in Infected Soldiers of the Fungus-Growing Termite, Macrotermes carbonarius

PubMed Central

Neoh, Kok-Boon; Lee, Chow-Yang

2011-01-01

The larval parasitoid Verticia fasciventris Malloch (Diptera: Calliphoridae) develops in the head of soldiers of the fungus-growing termite Macrotermes carbonarius (Hagen) (Isoptera: Termitidae). Morphological and behavioral changes in the host were evaluated and the termite castes and stages that were parasitized were identified. The larval emergence process is also described and possible mechanisms for the parasitoid fly's entry into the host body are discussed based on qualitative observations. Only a single larva per host was found. The mature larva pupated outside the host's body by exiting between the abdominal cerci. Parasitized soldiers possess a short and square-shaped head capsule, a pair of notably short mandibles, and a pair of 18-segmented antennae. Although parasitized soldiers were statistically less aggressive than healthy soldiers (P < 0.05), they expressed varying levels of aggression. Both minor and major soldiers can be parasitized and based on evidence from presoldiers, parasitization may begin during the precursor stages of soldiers. However, the stage at which parasitism first occurs has not been determined. PMID:21861651

A DNA methylation map of human cancer at single base-pair resolution

PubMed Central

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

2017-01-01

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. PMID:28581523

Phylogeny predicts future habitat shifts due to climate change.

PubMed

Kuntner, Matjaž; Năpăruş, Magdalena; Li, Daiqin; Coddington, Jonathan A

2014-01-01

Taxa may respond differently to climatic changes, depending on phylogenetic or ecological effects, but studies that discern among these alternatives are scarce. Here, we use two species pairs from globally distributed spider clades, each pair representing two lifestyles (generalist, specialist) to test the relative importance of phylogeny versus ecology in predicted responses to climate change. We used a recent phylogenetic hypothesis for nephilid spiders to select four species from two genera (Nephilingis and Nephilengys) that match the above criteria, are fully allopatric but combined occupy all subtropical-tropical regions. Based on their records, we modeled each species niche spaces and predicted their ecological shifts 20, 40, 60, and 80 years into the future using customized GIS tools and projected climatic changes. Phylogeny better predicts the species current ecological preferences than do lifestyles. By 2080 all species face dramatic reductions in suitable habitat (54.8-77.1%) and adapt by moving towards higher altitudes and latitudes, although at different tempos. Phylogeny and life style explain simulated habitat shifts in altitude, but phylogeny is the sole best predictor of latitudinal shifts. Models incorporating phylogenetic relatedness are an important additional tool to predict accurately biotic responses to global change.

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

Devadoss, C.; Fessenden, R.W.

The transient that is produced in the quenching of triplet benzophenone by 1,4-diazabicyclo(2.2.2)octane (DABCO) has been examined by use of nano- and picosecond laser photolysis. The initial step in all solvents, both polar and nonpolar, is electron transfer to form a triplet contact ion pair. In nonpolar solvents, the ion pair remains in this form until it decays. For polar solvents, the spectra change somewhat over the first 100 ps showing that the solvation changes and the ion pair becomes solvent separated. The lifetime of the ion pair varies greatly with the solvent. In saturated hydrocarbons it is about 80more » ps. Nonpolar solvents with either {pi} electrons or a lone pair of electrons stabilize the ion pair on the nanosecond to microsecond time scale. A small amount of alcohol in benzene also stabilizes the ion pair by hydrogen bonding. A shift in the peak position with time toward the blue accompanies the formation of hydrogen bonds in this case.« less

Comparison of clinical knowledge bases for summarization of electronic health records.

PubMed

McCoy, Allison B; Sittig, Dean F; Wright, Adam

2013-01-01

Automated summarization tools that create condition-specific displays may improve clinician efficiency. These tools require new kinds of knowledge that is difficult to obtain. We compared five problem-medication pair knowledge bases generated using four previously described knowledge base development approaches. The number of pairs in the resulting mapped knowledge bases varied widely due to differing mapping techniques from the source terminologies, ranging from 2,873 to 63,977,738 pairs. The number of overlapping pairs across knowledge bases was low, with one knowledge base having half of the pairs overlapping with another knowledge base, and most having less than a third overlapping. Further research is necessary to better evaluate the knowledge bases independently in additional settings, and to identify methods to integrate the knowledge bases.

Optimum electrode configuration selection for electrical resistance change based damage detection in composites using an effective independence measure

NASA Astrophysics Data System (ADS)

Escalona, Luis; Díaz-Montiel, Paulina; Venkataraman, Satchi

2016-04-01

Laminated carbon fiber reinforced polymer (CFRP) composite materials are increasingly used in aerospace structures due to their superior mechanical properties and reduced weight. Assessing the health and integrity of these structures requires non-destructive evaluation (NDE) techniques to detect and measure interlaminar delamination and intralaminar matrix cracking damage. The electrical resistance change (ERC) based NDE technique uses the inherent changes in conductive properties of the composite to characterize internal damage. Several works that have explored the ERC technique have been limited to thin cross-ply laminates with simple linear or circular electrode arrangements. This paper investigates a method of optimum selection of electrode configurations for delamination detection in thick cross-ply laminates using ERC. Inverse identification of damage requires numerical optimization of the measured response with a model predicted response. Here, the electrical voltage field in the CFRP composite laminate is calculated using finite element analysis (FEA) models for different specified delamination size and locations, and location of ground and current electrodes. Reducing the number of sensor locations and measurements is needed to reduce hardware requirements, and computational effort needed for inverse identification. This paper explores the use of effective independence (EI) measure originally proposed for sensor location optimization in experimental vibration modal analysis. The EI measure is used for selecting the minimum set of resistance measurements among all possible combinations of selecting a pair of electrodes among the n electrodes. To enable use of EI to ERC required, it is proposed in this research a singular value decomposition SVD to obtain a spectral representation of the resistance measurements in the laminate. The effectiveness of EI measure in eliminating redundant electrode pairs is demonstrated by performing inverse identification of damage using the full set of resistance measurements and the reduced set of measurements. The investigation shows that the EI measure is effective for optimally selecting the electrode pairs needed for resistance measurements in ERC based damage detection.

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

PubMed Central

Serra, Martin J; Baird, John D; Dale, Taraka; Fey, Bridget L; Retatagos, Kimberly; Westhof, Eric

2002-01-01

Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated. PMID:12003491

Three dimensional chiral plasmon rulers based on silver nanorod trimers.

PubMed

Han, Chunrui; Yang, Lechen; Ye, Piao; Parrott, Edward P J; Pickwell-Macpherson, Emma; Tam, Wing Yim

2018-04-16

The symmetry dependences of plasmon excitation modes are studied in 3D silver nanorod trimers. The degenerate plasmon modes split into chiral modes by breaking the inversion and mirror symmetry of the nanorod trimer through translation and/or rotation of the middle rod. With a translation operation, successive evolution of the circular dichroism (CD) spectrum can be achieved through gradual breaking of the inversion symmetry. An additional rotation operation produces even dramatic spectral changes due to breaking a quasi-mirror symmetry resulted from the same angular distance of the middle rod to the top and bottom rods. Especially, pairs of new chiral modes can be excited due to the contact of the middle rod with the top-bottom rod pair. The spectral changes in the simulations, which are also demonstrated experimentally, envision the 3D chiral nanorod trimer system as plasmon ruler for spatial configuration retrieval and dynamic bio-process analysis at the single molecule level.

Optical based tactile shear and normal load sensor

DOEpatents

Salisbury, Curt Michael

2015-06-09

Various technologies described herein pertain to a tactile sensor that senses normal load and/or shear load. The tactile sensor includes a first layer and an optically transparent layer bonded together. At least a portion of the first layer is made of optically reflective material. The optically transparent layer is made of resilient material (e.g., clear silicone rubber). The tactile sensor includes light emitter/light detector pair(s), which respectively detect either normal load or shear load. Light emitter(s) emit light that traverses through the optically transparent layer and reflects off optically reflective material of the first layer, and light detector(s) detect and measure intensity of reflected light. When a normal load is applied, the optically transparent layer compresses, causing a change in reflected light intensity. When shear load is applied, a boundary between optically reflective material and optically absorptive material is laterally displaced, causing a change in reflected light intensity.

The structural impact of DNA mismatches

PubMed Central

Rossetti, Giulia; Dans, Pablo D.; Gomez-Pinto, Irene; Ivani, Ivan; Gonzalez, Carlos; Orozco, Modesto

2015-01-01

The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale. This therefore defines flexible base pairs, where breathing is frequent, and where distortions in helical parameters are strong, resulting in significant alterations in groove dimension. Even if the DNA structure is plastic enough to absorb the structural impact of the mismatch, local structural changes can be propagated far from the mismatch site, following the expected through-backbone and a previously unknown through-space mechanism. The structural changes related to the presence of mismatches help to understand the different susceptibility of mismatches to the action of repairing proteins. PMID:25820425

Higgs Pair Production as a Signal of Enhanced Yukawa Couplings

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

Bauer, Martin; Carena, Marcela; Carmona, Adrián

We present a non-trivial correlation between the enhancement of the Higgs-fermion couplings and the Higgs pair production cross section in two Higgs doublet models with a flavour symmetry. This symmetry suppresses flavour-changing neutral couplings of the Higgs boson and allows for a partial explanation of the hierarchy in the Yukawa sector. After taking into account the constraints from electroweak precision measurements, Higgs coupling strength measurements, and unitarity and perturbativity bounds, we identify an interesting region of parameter space leading to enhanced Yukawa couplings as well as enhanced di-Higgs gluon fusion production at the LHC reach. This effect is visible inmore » both the resonant and non-resonant contributions to the Higgs pair production cross section. We encourage dedicated searches based on differential distributions as a novel way to indirectly probe enhanced Higgs couplings to light fermions.« less

A device that operates within a self-assembled 3D DNA crystal

NASA Astrophysics Data System (ADS)

Hao, Yudong; Kristiansen, Martin; Sha, Ruojie; Birktoft, Jens J.; Hernandez, Carina; Mao, Chengde; Seeman, Nadrian C.

2017-08-01

Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

General theory of the multistage geminate reactions of the isolated pairs of reactants. II. Detailed balance and universal asymptotes of kinetics.

PubMed

Kipriyanov, Alexey A; Doktorov, Alexander B

2014-10-14

The analysis of general (matrix) kinetic equations for the mean survival probabilities of any of the species in a sample (or mean concentrations) has been made for a wide class of the multistage geminate reactions of the isolated pairs. These kinetic equations (obtained in the frame of the kinetic approach based on the concept of "effective" particles in Paper I) take into account various possible elementary reactions (stages of a multistage reaction) excluding monomolecular, but including physical and chemical processes of the change in internal quantum states carried out with the isolated pairs of reactants (or isolated reactants). The general basic principles of total and detailed balance have been established. The behavior of the reacting system has been considered on macroscopic time scales, and the universal long-term kinetics has been determined.

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

Okutsu, N.; Shimamura, K.; Shimizu, E.

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-Cmore » base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.« less

STABILIZED TRANSISTOR AMPLIFIER

DOEpatents

Noe, J.B.

1963-05-01

A temperature stabilized transistor amplifier having a pair of transistors coupled in cascade relation that are capable of providing amplification through a temperature range of - 100 un. Concent 85% F to 400 un. Concent 85% F described. The stabilization of the amplifier is attained by coupling a feedback signal taken from the emitter of second transistor at a junction between two serially arranged biasing resistances in the circuit of the emitter of the second transistor to the base of the first transistor. Thus, a change in the emitter current of the second transistor is automatically corrected by the feedback adjustment of the base-emitter potential of the first transistor and by a corresponding change in the base-emitter potential of the second transistor. (AEC)

Construction typification as the tool for optimizing the functioning of a robotized manufacturing system

NASA Astrophysics Data System (ADS)

Gwiazda, A.; Banas, W.; Sekala, A.; Foit, K.; Hryniewicz, P.; Kost, G.

2015-11-01

Process of workcell designing is limited by different constructional requirements. They are related to technological parameters of manufactured element, to specifications of purchased elements of a workcell and to technical characteristics of a workcell scene. This shows the complexity of the design-constructional process itself. The results of such approach are individually designed workcell suitable to the specific location and specific production cycle. Changing this parameters one must rebuild the whole configuration of a workcell. Taking into consideration this it is important to elaborate the base of typical elements of a robot kinematic chain that could be used as the tool for building Virtual modelling of kinematic chains of industrial robots requires several preparatory phase. Firstly, it is important to create a database element, which will be models of industrial robot arms. These models could be described as functional primitives that represent elements between components of the kinematic pairs and structural members of industrial robots. A database with following elements is created: the base kinematic pairs, the base robot structural elements, the base of the robot work scenes. The first of these databases includes kinematic pairs being the key component of the manipulator actuator modules. Accordingly, as mentioned previously, it includes the first stage rotary pair of fifth stage. This type of kinematic pairs was chosen due to the fact that it occurs most frequently in the structures of industrial robots. Second base consists of structural robot elements therefore it allows for the conversion of schematic structures of kinematic chains in the structural elements of the arm of industrial robots. It contains, inter alia, the structural elements such as base, stiff members - simple or angular units. They allow converting recorded schematic three-dimensional elements. Last database is a database of scenes. It includes elements of both simple and complex: simple models of technological equipment, conveyors models, models of the obstacles and like that. Using these elements it could be formed various production spaces (robotized workcells), in which it is possible to virtually track the operation of an industrial robot arm modelled in the system.

Correlation of RNA secondary structure and attenuation of Sabin vaccine strains of poliovirus in tissue culture.

PubMed

Macadam, A J; Ferguson, G; Burlison, J; Stone, D; Skuce, R; Almond, J W; Minor, P D

1992-08-01

Part of the 5' noncoding regions of all three Sabin vaccine strains of poliovirus contains determinants of attenuation that are shown here to influence the ability of these strains to grow at elevated temperatures in BGM cells. The predicted RNA secondary structure of this region (nt 464-542 in P3/Sabin) suggests that both phenotypes are due to perturbation of base-paired stems. Ts phenotypes of site-directed mutants with defined changes in this region correlated well with predicted secondary structure stabilities. Reversal of base-pair orientation had little effect whereas stem disruption led to marked increases in temperature sensitivity. Phenotypic revertants of such viruses displayed mutations on either side of the stem. Mutations destabilizing stems led to intermediate phenotypes. These results provided evidence for the biological significance of the predicted RNA secondary structure.

Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism

PubMed Central

Yusupov, Marat; Yusupova, Gulnara

2014-01-01

The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes. PMID:24765524

Orbifold E-functions of dual invertible polynomials

NASA Astrophysics Data System (ADS)

Ebeling, Wolfgang; Gusein-Zade, Sabir M.; Takahashi, Atsushi

2016-08-01

An invertible polynomial is a weighted homogeneous polynomial with the number of monomials coinciding with the number of variables and such that the weights of the variables and the quasi-degree are well defined. In the framework of the search for mirror symmetric orbifold Landau-Ginzburg models, P. Berglund and M. Henningson considered a pair (f , G) consisting of an invertible polynomial f and an abelian group G of its symmetries together with a dual pair (f ˜ , G ˜) . We consider the so-called orbifold E-function of such a pair (f , G) which is a generating function for the exponents of the monodromy action on an orbifold version of the mixed Hodge structure on the Milnor fibre of f. We prove that the orbifold E-functions of Berglund-Henningson dual pairs coincide up to a sign depending on the number of variables and a simple change of variables. The proof is based on a relation between monomials (say, elements of a monomial basis of the Milnor algebra of an invertible polynomial) and elements of the whole symmetry group of the dual polynomial.

Pair bond formation leads to a sustained increase in global cerebral glucose metabolism in monogamous male titi monkeys (Callicebus cupreus).

PubMed

Maninger, Nicole; Hinde, Katie; Mendoza, Sally P; Mason, William A; Larke, Rebecca H; Ragen, Benjamin J; Jarcho, Michael R; Cherry, Simon R; Rowland, Douglas J; Ferrer, Emilio; Bales, Karen L

2017-04-21

Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism (GCGM) during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in [ 18 F]-fluorodeoxyglucose (FDG) uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, "motivational" areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on GCGM. They also suggest that more studies should examine how social manipulations affect whole-brain FDG uptake, as opposed to assuming that it does not change across condition. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Pair bond Formation Leads to a Sustained Increase in Global Cerebral Glucose Metabolism in Monogamous Male Titi Monkeys (Callicebus cupreus)

PubMed Central

Maninger, Nicole; Hinde, Katie; Mendoza, Sally P.; Mason, William A.; Larke, Rebecca H.; Ragen, Benjamin J; Jarcho, Michael R.; Cherry, Simon R.; Rowland, Douglas J.; Ferrer, Emilio; Bales, Karen L.

2017-01-01

Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in FDG uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, “motivational” areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on global cerebral glucose metabolism. They also suggest that more studies should examine how social manipulations affect whole brain FDG uptake, as opposed to assuming that it does not change across condition. PMID:28242440

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Retention modeling under organic modifier gradient conditions in ion-pair reversed-phase chromatography. Application to the separation of a set of underivatized amino acids.

PubMed

Pappa-Louisi, A; Agrafiotou, P; Papachristos, K

2010-07-01

The combined effect of the ion-pairing reagent concentration, C(ipr), and organic modifier content, phi, on the retention under phi-gradient conditions at different constant C(ipr) was treated in this study by using two approaches. In the first approach, the prediction of the retention time of a sample solute is based on a direct fitting procedure of a proper retention model to 3-D phi-gradient retention data obtained under the same phi-linear variation but with different slope and time duration of the initial isocratic part and in the presence of various constant C(ipr) values in the eluent. The second approach is based on a retention model describing the combined effect of C(ipr) and phi on the retention of solutes in isocratic mode and consequently analyzes isocratic data obtained in mobile phases containing different C(ipr) values. The effectiveness of the above approaches was tested in the retention prediction of a mixture of 16 underivatized amino acids using mobile phases containing acetonitrile as organic modifier and sodium dodecyl sulfate as ion-pairing reagent. From these approaches, only the first one gives satisfactory predictions and can be successfully used in optimization of ion-pair chromatographic separations under gradient conditions. The failure of the second approach to predict the retention of solutes in the gradient elution mode in the presence of different C(ipr) values was attributed to slow changes in the distribution equilibrium of ion-pairing reagents caused by phi-variation.

Are Drinking Habits Really Changing? A Cross-Generational Test of the "New" Phenomenon of "Binge-Drinking"

ERIC Educational Resources Information Center

McCoy, Sarah Louise; Nieland, Martin Nicholas Stephen

2011-01-01

Aims: To investigate whether "binge-drinking" is new by comparing the behaviour and attitudes of two generations at the same age and of one generation at different ages. Methods: Fifty-six student/parent pairs completed questionnaires partially based on the Adolescent version of the Alcohol Expectancy Questionnaire (Brown, S.A.,…

Using Chem-Wiki to Increase Student Collaboration through Online Lab Reporting

ERIC Educational Resources Information Center

Elliott, Edward W., III; Fraiman, Ana

2010-01-01

The nature of laboratory work has changed in the past decade. One example is a shift from working individually or in pairs on single traditional verification experiments to working collaboratively in larger groups in inquiry and research-based laboratories, over extended periods in and outside of the lab. In this increased era of collaboration, we…

Teaching Aquatic Science as Inquiry through Professional Development: Teacher Characteristics and Student Outcomes

ERIC Educational Resources Information Center

Duncan Seraphin, Kanesa; Harrison, George M.; Philippoff, Joanna; Brandon, Paul R.; Nguyen, Thanh Truc T.; Lawton, Brian E.; Vallin, Lisa M.

2017-01-01

We present an inquiry-based, aquatic science professional development (PD) for upper-elementary, middle, and high school teachers and examine changes in student outcomes in light of participating teachers' characteristics and the grade band of the students. Our study lends support to the assertion that inquiry- and content-focused PD, paired with…

Thermoelectric Transducer Using Bio Nano Process

DTIC Science & Technology

2015-08-01

in which 8 amino acid residues have been removed from all consisted base pairs along the N-terminal direction 38, 39 . Because of this change, Fer8...M. D. V.; Natividad, G.; Rafael, M. and María, T. M. R. Langmuir 22 (16), pp 6993–7000 (2006). (36) Meldrum , F.C.; Douglas, T.; Lei, S.; Arosio, P

Effects of two-stage and total vs. fence-line weaning on the physiology and performance of beef calves

USDA-ARS?s Scientific Manuscript database

Calves weaned using a two-stage method where nursing is prevented between cow-calf pairs prior to separation (Stage 1) experience less weaning stress after separation (Stage 2) based on behavior and growth measures. The aim of this study was to document changes in various physiological measures of s...

The OECD program to validate the rat Hershberger bioassay to screen compounds for in vivo and androgen and antiandrogen responses: Phase-2 dose-response studies

EPA Science Inventory

DESIGN: The Hershberger bioassay is designed to identify suspected androgens and antiandrogens based on changes in the weights of five androgen-responsive tissues (ventral prostate, paired seminal vesicles and coagulating glands, the levator ani and bulbocavernosus muscles, the g...

The early-type multiple system QZ Carinae

NASA Astrophysics Data System (ADS)

Mayer, P.; Lorenz, R.; Drechsel, H.; Abseim, A.

2001-02-01

We present an analysis of the early-type quadruple system QZ Car, consisting of an eclipsing and a non-eclipsing binary. The spectroscopic investigation is based on new high dispersion echelle and CAT/CES spectra of H and He lines. The elements for the orbit of the non-eclipsing pair could be refined. Lines of the brighter component of the eclipsing binary were detected in near-quadrature spectra, while signatures of the fainter component could be identified in only few spectra. Lines of the primary component of the non-eclipsing pair and of both components of the eclipsing pair were found to be variable in position and strength; in particular, the He ii 4686 emission line of the brighter eclipsing component is strongly variable. An ephemeris for the eclipsing binary QZ Car valid at present was derived Prim. Min. = hel. JD 2448687.16 + 5fd9991 * E. The relative orbit of the two binary constituents of the multiple system is discussed. In contrast to earlier investigations we found radial velocity changes of the systemic velocities of both binaries, which were used - together with an O-C analysis of the expected light-time effect - to derive approximate parameters of the mutual orbit of the two pairs. It is shown that this orbit and the distance to QZ Car can be further refined by minima timing and interferometry. Based on observations collected at the European Southern Observatory, La Silla, Chile.

Splitting efficiency and interference effects in a Cooper pair splitter based on a triple quantum dot with ferromagnetic contacts

NASA Astrophysics Data System (ADS)

Bocian, Kacper; Rudziński, Wojciech; Weymann, Ireneusz

2018-05-01

We theoretically study the spin-resolved subgap transport properties of a Cooper pair splitter based on a triple quantum dot attached to superconducting and ferromagnetic leads. Using the Keldysh Green's function formalism, we analyze the dependence of the Andreev conductance, Cooper pair splitting efficiency, and tunnel magnetoresistance on the gate and bias voltages applied to the system. We show that the system's transport properties are strongly affected by spin dependence of tunneling processes and quantum interference between different local and nonlocal Andreev reflections. We also study the effects of finite hopping between the side quantum dots on the Andreev current. This allows for identifying the optimal conditions for enhancing the Cooper pair splitting efficiency of the device. We find that the splitting efficiency exhibits a nonmonotonic dependence on the degree of spin polarization of the leads and the magnitude and type of hopping between the dots. An almost perfect splitting efficiency is predicted in the nonlinear response regime when the energies of the side quantum dots are tuned to the energies of the corresponding Andreev bound states. In addition, we analyzed features of the tunnel magnetoresistance (TMR) for a wide range of the gate and bias voltages, as well as for different model parameters, finding the corresponding sign changes of the TMR in certain transport regimes. The mechanisms leading to these effects are thoroughly discussed.

OFFSETTING TOMORROW’S ADVERSARY IN A CONTESTED ENVIRONMENT: DEFENDING EXPEDITIONARY ADVANCE BASES IN 2025 AND BEYOND

DTIC Science & Technology

2017-04-06

action by keeping a foot in the door in contested environments. The integration of game -changing technology in force development paired with an...domain synergy, and emerging " game -changing" technologies. The intent of this report is not to define but rather describe what has been coined as the...Energy as possible “ game changers” in the implementation of future offset strategies and each lends distinct capabilities in defense of EABs.23 The

Sequence dependency of canonical base pair opening in the DNA double helix

PubMed Central

Villa, Alessandra

2017-01-01

The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. PMID:28369121

A two-dimensional 1H-NMR study of the dam methylase site: comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence. The sequence dependence of methylation upon base-pair lifetimes.

PubMed

Fazakerley, G V; Quignard, E; Teoule, R; Guy, A; Guschlbauer, W

1987-09-15

We report two-dimensional NOE (NOESY) spectra on the sequence d(GCGATCATGG).d(CCATGATCGC) which contains the unmethylated dam site. As expected the DNA adopts a B-form conformation but appears to be distorted at the TG step of the second strand. This distorsion, probably bending, is not seen on the opposite strand. When the first strand is methylated on adenine in the GATC or CATG sequence the NOESY spectra indicate little or no change in the conformation. However the single strand-duplex exchange is slowed down to the slow-exchange region on a proton NMR time scale. We have assigned the exchangeable imino and cytidine amino resonances of the three duplexes. From the imino linewidths as a function of temperature, we observe that the unmethylated and the hemimethylated Gm6ATC duplexes melt normally from the ends. However, this is not so for the hemimethylated Cm6ATG duplex which, apart from the terminal base pairs, melts cooperatively and at higher temperature. In spectra recorded in H2O a second duplex is observed, for the Gm6ATC sequence, which we have not been able to identify. It is however unlikely to be a hairpin structure. Ultraviolet-melting curves also indicate the presence of two transitions for this duplex. The effect of methylation upon base-pair lifetimes has been studied by comparing the above three duplexes. Little effect is observed upon methylation in the GATC sequence but a drastic increase in the lifetimes of all base pairs is observed upon methylation in the CATG sequence.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs.

PubMed

McCoy, A B; Wright, A; Krousel-Wood, M; Thomas, E J; McCoy, J A; Sittig, D F

2015-01-01

Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs

PubMed Central

Wright, A.; Krousel-Wood, M.; Thomas, E. J.; McCoy, J. A.; Sittig, D. F.

2015-01-01

Summary Background Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. Objective We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. Methods We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. Results The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. Conclusions We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes. PMID:26171079

Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations.

PubMed

Ishida, Hisashi; Matsumoto, Atsushi

2016-09-01

In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base-pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base-pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide-binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS-mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA-repair reaction step. Moreover, MM-PBSA/GBSA showed that the MutS-homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base-pairs. Proteins 2016; 84:1287-1303. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Bilocal current densities and mean trajectories in a Young interferometer with two Gaussian slits and two detectors

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

Withers, L. P., E-mail: lpwithers@mitre.org; Narducci, F. A., E-mail: francesco.narducci@navy.mil

2015-06-15

The recent single-photon double-slit experiment of Steinberg et al., based on a weak measurement method proposed by Wiseman, showed that, by encoding the photon’s transverse momentum behind the slits into its polarization state, the momentum profile can subsequently be measured on average, from a difference of the separated fringe intensities for the two circular polarization components. They then integrated the measured average velocity field, to obtain the average trajectories of the photons enroute to the detector array. In this paper, we propose a modification of their experiment, to demonstrate that the average particle velocities and trajectories change when the modemore » of detection changes. The proposed experiment replaces a single detector by a pair of detectors with a given spacing between them. The pair of detectors is configured so that it is impossible to distinguish which detector received the particle. The pair of detectors is then analogous to the simple pair of slits, in that it is impossible to distinguish which slit the particle passed through. To establish the paradoxical outcome of the modified experiment, the theory and explicit three-dimensional formulas are developed for the bilocal probability and current densities, and for the average velocity field and trajectories as the particle wavefunction propagates in the volume of space behind the Gaussian slits. Examples of these predicted results are plotted. Implementation details of the proposed experiment are discussed.« less

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

Energy of charged states in the acetanilide crystal: Trapping of charge-transfer states at vacancies as a possible mechanism for optical damage

NASA Astrophysics Data System (ADS)

Tsiaousis, D.; Munn, R. W.

2004-04-01

Calculations for the acetanilide crystal yield the effective polarizability (16.6 Å3), local electric field tensor, effective dipole moment (5.41 D), and dipole-dipole energy (-12.8 kJ/mol). Fourier-transform techniques are used to calculate the polarization energy P for a single charge in the perfect crystal (-1.16 eV); the charge-dipole energy WD is zero if the crystal carries no bulk dipole moment. Polarization energies for charge-transfer (CT) pairs combine with the Coulomb energy EC to give the screened Coulomb energy Escr; screening is nearly isotropic, with Escr≈EC/2.7. For CT pairs WD reduces to a term δWD arising from the interaction of the charge on each ion with the change in dipole moment on the other ion relative to the neutral molecule. The dipole moments calculated by density-functional theory methods with the B3LYP functional at the 6-311++G** level are 3.62 D for the neutral molecule, changing to 7.13 D and 4.38 D for the anion and cation, relative to the center of mass. Because of the large change in the anion, δWD reaches -0.9 eV and modifies the sequence of CT energies markedly from that of Escr, giving the lowest two CT pairs at -1.98 eV and -1.41 eV. The changes in P and WD near a vacancy are calculated; WD changes for the individual charges because the vacancy removes a dipole moment and modifies the crystal dielectric response, but δWD and EC do not change. A vacancy yields a positive change ΔP that scatters a charge or CT pair, but the change ΔWD can be negative and large enough to outweigh ΔP, yielding traps with depths that can exceed 150 meV for single charges and for CT pairs. Divacancies yield traps with depths nearly equal to the sum of those produced by the separate vacancies and so they can exceed 300 meV. These results are consistent with a mechanism of optical damage in which vacancies trap optically generated CT pairs that recombine and release energy; this can disrupt the lattice around the vacancy, thereby favoring trapping and recombination of CT pairs generated by subsequent photon absorption, leading to further lattice disruption. Revisions to previous calculations on trapping of CT pairs in anthracene are reported.

Behavior of visual field index in advanced glaucoma.

PubMed

Rao, Harsha L; Senthil, Sirisha; Choudhari, Nikhil S; Mandal, Anil K; Garudadri, Chandra S

2013-01-14

To evaluate the magnitude of Visual Field Index (VFI) change attributable to change in the estimation algorithm from the pattern deviation probability plot (PDPP) to the total deviation probability plot (TDPP) when the mean deviation (MD) crosses -20 decibels (dB). In a retrospective study, 37 stable glaucoma eyes in which MD of the VFs crossed -20 dB were identified. For each eye, a pair of VFs was selected so that one VF of the pair had a MD better than but close to -20 dB and the other had a MD worse than but again close to -20 dB. The change in VFI in the VF pairs and its associations with the number of points in probability plots with normal threshold sensitivities were evaluated. Similar pairs of VFs from 28 stable glaucoma eyes where the MD crossed -10 dB were chosen as controls. The change in VFI in VF pairs when the MD crossed 20 dB ranged from 3% to 33% (median: 15%), while the change when MD crossed -10 dB ranged from 1% to 8% (median: 4%). Difference in the number of points with normal threshold sensitivities in PDPP when MD was better than -20 dB compared to those in TDPP when MD crossed -20 dB significantly influenced the VFI change (R(2) = 0.65). Considering the eccentricity of these points further explained the VFI change (R(2) = 0.81). The decrease in VFI when MD crosses -20 dB can be highly variable. This has to be considered with the use of VFI in clinical and research settings.

Changes in rat parotid saliva protein composition following chronic reserpine treatment and their relation to inanition.

PubMed

Johnson, D A

1988-01-01

Chronic administration of the catecholamine-depleting agent, reserpine (0.5 mg/kg), resulted in a reduction in food intake after 3 days. To differentiate effects of the drug from those of reduced food intake a pair-fed group, whose daily caloric intake was restricted to the amount consumed by the reserpine-treated rats, was included. After 7 days, both the reserpine-treated and pair-fed control exhibited a marked reduction in the volume of saliva collected in a 30 min interval following a secretory stimulus compared to untreated ad libitum-fed controls, and the proportion of salivary proteins attributable to acidic and basic proline-rich proteins and to minor 1b protein were decreased whereas deoxyribonuclease was increased. For two of the salivary proteins (fractions I and V) changes for the reserpine-treated and pair-fed groups were different. Fraction I was reduced in both groups, but exhibited a greater decrease in the pair-fed than in the reserpine-treated, whereas fraction V was significantly increased only in the pair-fed group. Thus many of the salivary changes associated with reserpine treatment may have resulted from the change in feeding habits and not from reserpine treatment per se. The study demonstrates the importance of controlling for food intake under experimental circumstances which may lead to a marked change in daily feeding habits.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

A comparison of transmission characteristics of Salmonella enterica serovar Enteritidis between pair-housed and group-housed laying hens.

PubMed

Thomas, Ekelijn; Bouma, Annemarie; Klinkenberg, Don

2011-02-23

Human cases of bacterial gastro-enteritis are often caused by the consumption of eggs contaminated with Salmonella species, mainly Salmonella enterica serovar Enteriditis (Salmonella Enteritidis). To reduce human exposure, in several countries worldwide surveillance programmes are implemented to detect colonized layer flocks. The sampling schemes are based on the within-flock prevalence, and, as this changes over time, knowledge of the within-flock dynamics of Salmonella Enteritidis is required. Transmission of Salmonella Enteritidis has been quantified in pairs of layers, but the question is whether the dynamics in pairs is comparable to transmission in large groups, which are more representative for commercial layer flocks. The aim of this study was to compare results of transmission experiments between pairs and groups of laying hens. Experimental groups of either 2 or 200 hens were housed at similar densities, and 1 or 4 hens were inoculated with Salmonella Enteritidis, respectively. Excretion was monitored by regularly testing of fecal samples for the presence of Salmonella Enteritidis. Using mathematical modeling, the group experiments were simulated with transmission parameter estimates from the pairwise experiments. Transmission of the bacteria did not differ significantly between pairs or groups. This finding suggests that the transmission parameter estimates from small-scale experiments might be extrapolated to the field situation.

Unidirectional adaptation in tempo in pairs of chimpanzees during simultaneous tapping movement: an examination under face-to-face setup.

PubMed

Yu, Lira; Tomonaga, Masaki

2016-04-01

Many studies have reported a spontaneous nature to synchronized movement in humans and in non-human primates. However, it is not yet clear whether individuals mutually adapt their movement to each other or whether one individual significantly changes to synchronize with the other. In the current study, we examined a directionality of the tempo adaptation to understand an introductive process of interactional synchrony in pairs of chimpanzees. Four pairs, consisting of five female chimpanzees, produced a finger-tapping movement under a face-to-face experimental setup where both auditory and visual cues of the partner's movement were available. Two test conditions were prepared: alone and paired. An analysis of the tapping tempo depending on condition showed that only one chimpanzee in each pair significantly changed their tapping tempo in the direction of the partner's tapping tempo in the paired condition compared with the alone condition. The current study demonstrated that unidirectional adaptation in tempo occurs in pairs of chimpanzees when they simultaneously produce the tapping movement under auditory and visual interaction.

[Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

PubMed

Brovarets', O O

2013-01-01

At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

Repeat Photography of Alaskan Glaciers and Landscapes as Both Art and as a Means of Communicating Climat Change

NASA Astrophysics Data System (ADS)

Molnia, B. F.

2013-12-01

For nearly 15 years, I have used repeat photography of Alaskan glaciers and landscapes to communicate to fellow scientists, policymakers, the media, and society that Alaskan glaciers and landscapes have been experiencing significant change in response to post-Little Ice Age climate change. I began this pursuit after being contacted by a U.S. Department of the Interior senior official who requested unequivocal and unambiguous documentation that climate change was real and underway. After considering several options as to how best respond to this challenge, I decided that if a picture is worth a thousand words, then a pair of photographs, both with the same field of view, spanning a century or more, and showing dramatic differences, would speak volumes to documenting that dynamic climate change is occurring over a very broad region of Alaska. To me, understating the obvious with photographic pairs was the best mechanism to present irrefutable, unambiguous, nonjudgmental, as well as unequivocal visual documentation that climate change was both underway and real. To date, more than 150 pairs that meet these criteria have been produced. What has surprised me most is that the many of the photographs contained in the pairs present beautiful images of stark, remote landscapes that convey the majestic nature of this dynamic region with its unique topography and landscapes. Typically, over periods of just several decades, the photographed landscapes change from black and white to blue and green. White ice becomes blue water and dark rock becomes lush vegetation. Repeat photography is a technique in which a historical photograph and a modern photograph, both having the same field of view, are compared and contrasted to quantitatively and qualitatively determine their similarities and differences. I have used this technique from both ground-based photo stations and airborne platforms at Alaskan locations in Kenai Fjords National Park, Glacier Bay National Park and Preserve, Wrangell-St. Elias National Park and Preserve, Denali National Park and Preserve, the northern and northwestern Prince William Sound area of the Chugach National Forest, and the Mendenhall Glacier area of the Tongass National Forest to document and determine the extent of changing glaciers and landscapes. The use of repeat photography to document temporal change is not new. It originated as a glacier-monitoring technique in the European Alps more than 150 years ago. What is unique in this Alaskan application of repeat photography is the systematic approach being used to obtain photographic documentation of glacier and landscape change for every glacier-hosting fiord in western southcentral Alaska, as well as at many Alaskan valley glacier sites. What is also unique is the development of an annotated website which presents many pairs of these photographs as well as ancillary materials to help convey the basics of Alaskan glaciers and climate change. The website, titled 'Glacier and Landscape Change in Response to Changing Climate', (http://www.usgs.gov/climate_landuse/glaciers/) was awarded the 2010 USGS Shoemaker External Communications Award.

Short-term change detection for UAV video

NASA Astrophysics Data System (ADS)

Saur, Günter; Krüger, Wolfgang

2012-11-01

In the last years, there has been an increased use of unmanned aerial vehicles (UAV) for video reconnaissance and surveillance. An important application in this context is change detection in UAV video data. Here we address short-term change detection, in which the time between observations ranges from several minutes to a few hours. We distinguish this task from video motion detection (shorter time scale) and from long-term change detection, based on time series of still images taken between several days, weeks, or even years. Examples for relevant changes we are looking for are recently parked or moved vehicles. As a pre-requisite, a precise image-to-image registration is needed. Images are selected on the basis of the geo-coordinates of the sensor's footprint and with respect to a certain minimal overlap. The automatic imagebased fine-registration adjusts the image pair to a common geometry by using a robust matching approach to handle outliers. The change detection algorithm has to distinguish between relevant and non-relevant changes. Examples for non-relevant changes are stereo disparity at 3D structures of the scene, changed length of shadows, and compression or transmission artifacts. To detect changes in image pairs we analyzed image differencing, local image correlation, and a transformation-based approach (multivariate alteration detection). As input we used color and gradient magnitude images. To cope with local misalignment of image structures we extended the approaches by a local neighborhood search. The algorithms are applied to several examples covering both urban and rural scenes. The local neighborhood search in combination with intensity and gradient magnitude differencing clearly improved the results. Extended image differencing performed better than both the correlation based approach and the multivariate alternation detection. The algorithms are adapted to be used in semi-automatic workflows for the ABUL video exploitation system of Fraunhofer IOSB, see Heinze et. al. 2010.1 In a further step we plan to incorporate more information from the video sequences to the change detection input images, e.g., by image enhancement or by along-track stereo which are available in the ABUL system.

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

Application of Powder Diffraction Methods to the Analysis of Short- and Long-Range Atomic Order in Nanocrystalline Diamond and SiC: The Concept of the Apparent Lattice Parameter (alp)

NASA Technical Reports Server (NTRS)

Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.

2003-01-01

Two methods of the analysis of powder diffraction patterns of diamond and SiC nanocrystals are presented: (a) examination of changes of the lattice parameters with diffraction vector Q ('apparent lattice parameter', alp) which refers to Bragg scattering, and (b), examination of changes of inter-atomic distances based on the analysis of the atomic Pair Distribution Function, PDF. Application of these methods was studied based on the theoretical diffraction patterns computed for models of nanocrystals having (i) a perfect crystal lattice, and (ii), a core-shell structure, i.e. constituting a two-phase system. The models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the shell. X-ray and neutron experimental diffraction data of nanocrystalline SiC and diamond powders of the grain diameter from 4 nm up to micrometers were used. The effects of the internal pressure and strain at the grain surface on the structure are discussed based on the experimentally determined dependence of the alp values on the Q-vector, and changes of the interatomic distances with the grain size determined experimentally by the atomic Pair Distribution Function (PDF) analysis. The experimental results lend a strong support to the concept of a two-phase, core and the surface shell structure of nanocrystalline diamond and SiC.

Developing a patient-centered outcome measure for complementary and alternative medicine therapies II: Refining content validity through cognitive interviews

PubMed Central

2011-01-01

Background Available measures of patient-reported outcomes for complementary and alternative medicine (CAM) inadequately capture the range of patient-reported treatment effects. The Self-Assessment of Change questionnaire was developed to measure multi-dimensional shifts in well-being for CAM users. With content derived from patient narratives, items were subsequently focused through interviews on a new cohort of participants. Here we present the development of the final version in which the content and format is refined through cognitive interviews. Methods We conducted cognitive interviews across five iterations of questionnaire refinement with a culturally diverse sample of 28 CAM users. In each iteration, participant critiques were used to revise the questionnaire, which was then re-tested in subsequent rounds of cognitive interviews. Following all five iterations, transcripts of cognitive interviews were systematically coded and analyzed to examine participants' understanding of the format and content of the final questionnaire. Based on this data, we established summary descriptions and selected exemplar quotations for each word pair on the final questionnaire. Results The final version of the Self-Assessment of Change questionnaire (SAC) includes 16 word pairs, nine of which remained unchanged from the original draft. Participants consistently said that these stable word pairs represented opposite ends of the same domain of experience and the meanings of these terms were stable across the participant pool. Five pairs underwent revision and two word pairs were added. Four word pairs were eliminated for redundancy or because participants did not agree on the meaning of the terms. Cognitive interviews indicate that participants understood the format of the questionnaire and considered each word pair to represent opposite poles of a shared domain of experience. Conclusions We have placed lay language and direct experience at the center of questionnaire revision and refinement. In so doing, we provide an innovative model for the development of truly patient-centered outcome measures. Although this instrument was designed and tested in a CAM-specific population, it may be useful in assessing multi-dimensional shifts in well-being across a broader patient population. PMID:22206409

Thermal transport in topological-insulator-based superconducting hybrid structures with mixed singlet and triplet pairing states.

PubMed

Li, Hai; Zhao, Yuan Yuan

2017-11-22

In the framework of the Bogoliubov-de Gennes equation, we investigate the thermal transport properties in topological-insulator-based superconducting hybrid structures with mixed spin-singlet and spin-triplet pairing states, and emphasize the different manifestations of the spin-singlet and spin-triplet pairing states in the thermal transport signatures. It is revealed that the temperature-dependent differential thermal conductance strongly depends on the components of the pairing state, and the negative differential thermal conductance only occurs in the spin-singlet pairing state dominated regime. It is also found that the thermal conductance is profoundly sensitive to the components of the pairing state. In the spin-singlet pairing state controlled regime, the thermal conductance obviously oscillates with the phase difference and junction length. With increasing the proportion of the spin-triplet pairing state, the oscillating characteristic of the thermal conductance fades out distinctly. These results suggest an alternative route for distinguishing the components of pairing states in topological-insulator-based superconducting hybrid structures.

Black holes, information, and the universal coefficient theorem

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

Patrascu, Andrei T.

2016-07-15

General relativity is based on the diffeomorphism covariant formulation of the laws of physics while quantum mechanics is based on the principle of unitary evolution. In this article, I provide a possible answer to the black hole information paradox by means of homological algebra and pairings generated by the universal coefficient theorem. The unitarity of processes involving black holes is restored by the demanding invariance of the laws of physics to the change of coefficient structures in cohomology.

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

The longitudinal effects of neighbourhood social and material deprivation change on psychological distress in urban, community-dwelling Canadian adults.

PubMed

Blair, A; Gariépy, G; Schmitz, N

2015-07-01

The purpose of this study was to assess how longitudinal changes in neighbourhood material and social deprivation affect distress outcomes in adult Canadians. This study used a prospective cohort approach. We paired data from 2745 urban participants of Canada's National Population Health Survey-who completed the Kessler 6-Item psychological distress screening tool at baseline and follow-up-with neighbourhood social and material deprivation data from the census-based Pampalon Deprivation Index. Data were paired using participants' postal code. We conducted multiple linear regression models, which were stratified by baseline deprivation level and controlled for key confounders. Most participants lived in neighbourhoods that did not change drastically in social or material deprivation level during the six years between baseline and follow-up. We found that a worsening of material settings was significantly associated with worsening distress scores at follow-up. This finding is discussed in the context of existing literature, and made relevant for urban health research and policy. Copyright © 2015 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Urban transitions: on urban resilience and human-dominated ecosystems.

PubMed

Ernstson, Henrik; van der Leeuw, Sander E; Redman, Charles L; Meffert, Douglas J; Davis, George; Alfsen, Christine; Elmqvist, Thomas

2010-12-01

Urbanization is a global multidimensional process paired with increasing uncertainty due to climate change, migration of people, and changes in the capacity to sustain ecosystem services. This article lays a foundation for discussing transitions in urban governance, which enable cities to navigate change, build capacity to withstand shocks, and use experimentation and innovation in face of uncertainty. Using the three concrete case cities--New Orleans, Cape Town, and Phoenix--the article analyzes thresholds and cross-scale interactions, and expands the scale at which urban resilience has been discussed by integrating the idea from geography that cities form part of "system of cities" (i.e., they cannot be seen as single entities). Based on this, the article argues that urban governance need to harness social networks of urban innovation to sustain ecosystem services, while nurturing discourses that situate the city as part of regional ecosystems. The article broadens the discussion on urban resilience while challenging resilience theory when addressing human-dominated ecosystems. Practical examples of harnessing urban innovation are presented, paired with an agenda for research and policy.

Silver(I)-Mediated Base Pairs in DNA Sequences Containing 7-Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson-Crick Base Pairs.

PubMed

Méndez-Arriaga, José M; Maldonado, Carmen R; Dobado, José A; Galindo, Miguel A

2018-03-26

DNA sequences comprising noncanonical 7-deazaguanine ( 7C G) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplexes I and II containing 7C G and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV spectroscopy, circular dichroism, and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7C G-Ag I -C Watson-Crick base pairs that preserve the original B-type conformation. Furthermore, additional studies performed on duplex III indicated that, in the presence of Ag I ions, 7C G-C and 7C A-T Watson-Crick base pairs ( 7C A, 7-deazadenine; T, thymine) can be converted to metallated 7C G-Ag I -C and 7C A-Ag I -T base pairs inside the same DNA molecule whilst maintaining its initial double helix conformation. These findings are very important for the development of customized silver-DNA nanostructures based on a Watson-Crick complementarity pattern. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

PubMed

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-08

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

PubMed Central

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-01

The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs

PubMed Central

Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N.; Sathyamoorthy, Bharathwaj; Grazioli, Gianmarc; McSally, James; Bai, Tianyu; Wunderlich, Christoph H.; Kreutz, Christoph; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2016-01-01

The B-DNA double helix can dynamically accommodate G–C and A–T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G–C+ and A–U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result, N1-methyl adenosine and N1-methyl guanosine, which occur in DNA as a form of alkylation damage, and in RNA as a posttranscriptional modification, have dramatically different consequences. They create G–C+ and A–U Hoogsteen base pairs in duplex DNA that maintain the structural integrity of the double helix, but block base pairing all together and induce local duplex melting in RNA, providing a mechanism for potently disrupting RNA structure through posttranscriptional modifications. The markedly different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help meet the opposing requirements of maintaining genome stability on one hand, and dynamically modulating the structure of the epitranscriptome on the other. PMID:27478929

Solution structure of a GAAA tetraloop receptor RNA.

PubMed Central

Butcher, S E; Dieckmann, T; Feigon, J

1997-01-01

The GAAA tetraloop receptor is an 11-nucleotide RNA sequence that participates in the tertiary folding of a variety of large catalytic RNAs by providing a specific binding site for GAAA tetraloops. Here we report the solution structure of the isolated tetraloop receptor as solved by multidimensional, heteronuclear magnetic resonance spectroscopy. The internal loop of the tetraloop receptor has three adenosines stacked in a cross-strand or zipper-like fashion. This arrangement produces a high degree of base stacking within the asymmetric internal loop without extrahelical bases or kinking the helix. Additional interactions within the internal loop include a U. U mismatch pair and a G.U wobble pair. A comparison with the crystal structure of the receptor RNA bound to its tetraloop shows that a conformational change has to occur upon tetraloop binding, which is in good agreement with previous biochemical data. A model for an alternative binding site within the receptor is proposed based on the NMR structure, phylogenetic data and previous crystallographic structures of tetraloop interactions. PMID:9405377

Is evaluative conditioning really resistant to extinction? Evidence for changes in evaluative judgements without changes in evaluative representations.

PubMed

Gawronski, Bertram; Gast, Anne; De Houwer, Jan

2015-01-01

Evaluative conditioning (EC) is defined as the change in the evaluation of a conditioned stimulus (CS) due to its pairing with a positive or negative unconditioned stimulus (US). Although several individual studies suggest that EC is unaffected by unreinforced presentations of the CS without the US, a recent meta-analysis indicates that EC effects are less pronounced for post-extinction measurements than post-acquisition measurements. The disparity in research findings suggests that extinction of EC may depend on yet unidentified conditions. In an attempt to uncover these conditions, three experiments (N = 784) investigated the influence of unreinforced post-acquisition CS presentations on EC effects resulting from simultaneous versus sequential pairings and pairings with single versus multiple USs. For all four types of CS-US pairings, EC effects on self-reported evaluations were reduced by unreinforced CS presentations, but only when the CSs had been rated after the initial presentation of CS-US pairings. EC effects on an evaluative priming measure remained unaffected by unreinforced CS presentations regardless of whether the CSs had been rated after acquisition. The results suggest that reduced EC effects resulting from unreinforced CS presentations are due to judgement-related processes during the verbal expression of CS evaluations rather than genuine changes in the underlying evaluative representations.

Real-time line matching from stereo images using a nonparametric transform of spatial relations and texture information

NASA Astrophysics Data System (ADS)

Park, Jonghee; Yoon, Kuk-Jin

2015-02-01

We propose a real-time line matching method for stereo systems. To achieve real-time performance while retaining a high level of matching precision, we first propose a nonparametric transform to represent the spatial relations between neighboring lines and nearby textures as a binary stream. Since the length of a line can vary across images, the matching costs between lines are computed within an overlap area (OA) based on the binary stream. The OA is determined for each line pair by employing the properties of a rectified image pair. Finally, the line correspondence is determined using a winner-takes-all method with a left-right consistency check. To reduce the computational time requirements further, we filter out unreliable matching candidates in advance based on their rectification properties. The performance of the proposed method was compared with state-of-the-art methods in terms of the computational time, matching precision, and recall. The proposed method required 47 ms to match lines from an image pair in the KITTI dataset with an average precision of 95%. We also verified the proposed method under image blur, illumination variation, and viewpoint changes.

Evaluative Conditioning Can Be Modulated by Memory of the CS-US Pairings at the Time of Testing

ERIC Educational Resources Information Center

Gast, Anne; De Houwer, Jan; De Schryver, Maarten

2012-01-01

Evaluative conditioning (EC) is the valence change of a (typically neutral) stimulus (CS) that is due to the previous pairing with another (typically valent) stimulus (US). It has been repeatedly shown that EC effects are stronger or existent only if participants know which US was paired with which CS. Knowledge of the CS-US pairings is usually…

How the manner of presentation of data influences older patients in determining their treatment preferences.

PubMed

Mazur, D J; Merz, J F

1993-03-01

To assess how the manner of presentation of graphic data to older patients influences their treatment preferences. Cross-sectional structured interviews with patients. A university-based Department of Veterans Affairs Medical Center. One hundred sixty-six consecutive patients (mean age = 64.8 years, range of ages 29-82) seen in a Department of Veterans Affairs general medicine clinic. Five pairs of 5-year survival curves were presented to patients. Each pair was composed of two survival curves for alternative unidentified treatments for an unidentified medical condition. Curve A (LT = better long-term, worse short-term survival) was fixed throughout all curve pairs. Curve B (ST = better short-term, worse long-term survival) changed in each curve pair, showing incrementally better chances of short-term survival across the five curve pairs. Patients were randomly assigned to view the curve pairs in forward (increasing short-term survival) or backward (decreasing short-term survival) order. Order is a significant predictor of patients' initial preferences for the short-term survival curve (P = 0.0004) as well as their willingness to shift preferences during presentation of the five curve pairs. Patients > or = 65 were more likely to initially choose the ST curve in forward order presentation than patients < 65. More educated patients generally were less likely to prefer the ST curve under both elicitation orders. The data indicate that the method of eliciting patients' preferences strongly influenced their expressed preferences, and that these preferences may have predictable relationships with demographic characteristics such as age.

Differential optical shadow sensor for sub-nanometer displacement measurement and its application to drag-free satellites.

PubMed

Zoellner, Andreas; Tan, Si; Saraf, Shailendhar; Alfauwaz, Abdul; DeBra, Dan; Buchman, Sasha; Lipa, John A

2017-10-16

We present a method for 3D sub-nanometer displacement measurement using a set of differential optical shadow sensors. It is based on using pairs of collimated beams on opposite sides of an object that are partially blocked by it. Applied to a sphere, our 3-axis sensor module consists of 8 parallel beam-detector sets for redundancy. The sphere blocks half of each beam's power in the nominal centered position, and any displacement can be measured by the differential optical power changes amongst the pairs of detectors. We have experimentally demonstrated a displacement sensitivity of 0.87nm/Hz at 1 Hz and 0.39nm/Hz at 10 Hz. We describe the application of the module to the inertial sensor of a drag-free satellite, which can potentially be used for navigation, geodesy and fundamental science experiments as well as ground based applications.

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.

Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

PubMed Central

Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

2014-01-01

The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

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 Development of Inhibitory Control in Early Childhood: A Twin Study from 2-3 Years

ERIC Educational Resources Information Center

Gagne, Jeffrey R.; Saudino, Kimberly J.

2016-01-01

Parent- and lab-based observer ratings were employed to examine genetic and environmental influences on continuity and change in inhibitory control (IC) in over 300 twin-pairs assessed longitudinally at 2 and 3 years of age. Genetic influences accounted for approximately 60% of the variance in parent-rated IC at both ages. Although many of the…

Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

PubMed Central

Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

2018-01-01

Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

Urban growth in American cities : glimpses of U.S. urbanization

USGS Publications Warehouse

Auch, Roger; Taylor, Janis; Acevedo, William

2004-01-01

The Earth's surface is changing rapidly. Changes are local, regional, national, and even global in scope. Some changes have natural causes, such as earthquakes or drought. Other changes, such as urban expansion, agricultural intensification, resource extraction, and water resources development, are examples of human-induced change that have significant impact upon people, the economy, and resources. The consequences that result from these changes are often dramatic and widespread (Buchanan, Acevedo, and Zirbes, 2002)It is the role of the U.S. Geological Survey (USGS) to provide useful and relevant scientific information both to the agencies within the Department of the Interior and to the Nation in general. In an effort to comply with this task, USGS scientists are assessing the status of, and the trends in, the Nation's land surface. This assessment provides useful information for regional and national land use decisionmaking. This knowledge can be used to deal with issues of significance to the Nation, such as quality-of-life, ecology of urban environments, ecosystem health, ecological integrity, water quality and quantity concerns, resource availability, vulnerability to natural hazards, safeguards to human health, air and land quality, and accessibility to scientific information. Results of these assessments can also be analyzed to reveal rates and trends in land use change. Results from urban growth studies provide a firm foundation for continuing research that explores the consequences of human modification of the landscape.The USGS seeks to illustrate and explain the spatial history of urban growth and corresponding land use change. Scientists are studying urban environments from a regional perspective and a time scale of decades to measure the changes that have occurred in order to help understand the impact of anticipated changes in the future.Within this booklet are pairs of images of selected urbanized regions from across the Nation. These image pairs illustrate the transformation that these areas have undergone over two decades. Specifically, they depict changes in the extent of urban land. Each change pair is composed of one image from the 1970s and one image from the 1990s. Accompanying each image pair is a brief historical geography of factors that helped facilitate major changes that have occurred since the founding of the main city and the consequences and challenges of regional urban growth. The goal of this publication is to provide an illustration of urban change that is easily understood by a broad audience.The images used throughout this booklet were generated from land cover data developed by the USGS. The data sources include the Geographic Information Retrieval and Analysis System (GIRAS) for the 1970s images and the National Land Cover Dataset (NLCD) for the 1990s images. GIRAS digital maps are based on photointerpretations completed in the mid-1970s. The NLCD is a land cover dataset for the conterminous United States based on 1992 Landsat thematic mapper (TM) satellite imagery and supplemental data (fig. 1a and fig. 1b). The USGS distributes both of these land use and land cover digital datasets.The images were developed by using a geographic information system (GIS). The GIRAS and NLCD datasets were used to identify urban land within each region. In the final images all urban areas are shown in red. A shaded-relief map of each region was used to display the topographic context of the red polygon coverage. For all of these images, urban land is defined as areas transformed into a built-up environment for human use. It includes residential areas, commercial and industrial developments, transportation features, and institutions.

Stacking interactions and DNA intercalation

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

Li, Dr. Shen; Cooper, Valentino R; Thonhauser, Prof. Timo

2009-01-01

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair base-pair interactions and that of the stacked intercalator base pair system. Most notable result is the paucity of torque which so distinctively defines the Twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observedmore » proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.« less

Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions.

PubMed

Lopez-Gomollon, Sara; Mohorianu, Irina; Szittya, Gyorgy; Moulton, Vincent; Dalmay, Tamas

2012-12-01

MicroRNAs negatively regulate the accumulation of mRNAs therefore when they are expressed in the same cells their expression profiles show an inverse correlation. We previously described one positively correlated miRNA/target pair, but it is not known how widespread this phenomenon is. Here, we investigated the correlation between the expression profiles of differentially expressed miRNAs and their targets during tomato fruit development using deep sequencing, Northern blot and RT-qPCR. We found an equal number of positively and negatively correlated miRNA/target pairs indicating that positive correlation is more frequent than previously thought. We also found that the correlation between microRNA and target expression profiles can vary between mRNAs belonging to the same gene family and even for the same target mRNA at different developmental stages. Since microRNAs always negatively regulate their targets, the high number of positively correlated microRNA/target pairs suggests that mutual exclusion could be as widespread as temporal regulation. The change of correlation during development suggests that the type of regulatory circuit directed by a microRNA can change over time and can be different for individual gene family members. Our results also highlight potential problems for expression profiling-based microRNA target identification/validation.

Cortical Power-Density Changes of Different Frequency Bands in Visually Guided Associative Learning: A Human EEG-Study

PubMed Central

Puszta, András; Katona, Xénia; Bodosi, Balázs; Pertich, Ákos; Nyujtó, Diána; Braunitzer, Gábor; Nagy, Attila

2018-01-01

The computer-based Rutgers Acquired Equivalence test (RAET) is a widely used paradigm to test the function of subcortical structures in visual associative learning. The test consists of an acquisition (pair learning) and a test (rule transfer) phase, associated with the function of the basal ganglia and the hippocampi, respectively. Obviously, such a complex task also requires cortical involvement. To investigate the activity of different cortical areas during this test, 64-channel EEG recordings were recorded in 24 healthy volunteers. Fast-Fourier and Morlet wavelet convolution analyses were performed on the recordings. The most robust power changes were observed in the theta (4–7 Hz) and gamma (>30 Hz) frequency bands, in which significant power elevation was observed in the vast majority of the subjects, over the parieto-occipital and temporo-parietal areas during the acquisition phase. The involvement of the frontal areas in the acquisition phase was remarkably weaker. No remarkable cortical power elevations were found in the test phase. In fact, the power of the alpha and beta bands was significantly decreased over the parietooccipital areas. We conclude that the initial acquisition of the image pairs requires strong cortical involvement, but once the pairs have been learned, neither retrieval nor generalization requires strong cortical contribution. PMID:29867412

Cortical Power-Density Changes of Different Frequency Bands in Visually Guided Associative Learning: A Human EEG-Study.

PubMed

Puszta, András; Katona, Xénia; Bodosi, Balázs; Pertich, Ákos; Nyujtó, Diána; Braunitzer, Gábor; Nagy, Attila

2018-01-01

The computer-based Rutgers Acquired Equivalence test (RAET) is a widely used paradigm to test the function of subcortical structures in visual associative learning. The test consists of an acquisition (pair learning) and a test (rule transfer) phase, associated with the function of the basal ganglia and the hippocampi, respectively. Obviously, such a complex task also requires cortical involvement. To investigate the activity of different cortical areas during this test, 64-channel EEG recordings were recorded in 24 healthy volunteers. Fast-Fourier and Morlet wavelet convolution analyses were performed on the recordings. The most robust power changes were observed in the theta (4-7 Hz) and gamma (>30 Hz) frequency bands, in which significant power elevation was observed in the vast majority of the subjects, over the parieto-occipital and temporo-parietal areas during the acquisition phase. The involvement of the frontal areas in the acquisition phase was remarkably weaker. No remarkable cortical power elevations were found in the test phase. In fact, the power of the alpha and beta bands was significantly decreased over the parietooccipital areas. We conclude that the initial acquisition of the image pairs requires strong cortical involvement, but once the pairs have been learned, neither retrieval nor generalization requires strong cortical contribution.

Thermodynamic characterization of a triple-helical three-way junction containing a Hoogsteen branch point.

PubMed

Hüsler, P L; Klump, H H

1995-09-10

We have designed a Hoogsteen (HG) triple-helical three-way junction (ternary complex) constructed from three 33-mer oligonucleotides based on the same subset of sequences used for the Watson-Crick (WC) triple-helical three-way junction, characterized previously (P. L. Hüsler and H. H. Klump (1994) Arch. Biochem. Biophys., 313, 29-38). The junction differs primarily in the assembly of the branch point and the ends of the arms. The three oligonucleotides can each fold into a WC hairpin, linked by a four-member cytosine loop, each containing a homo-pyrimidine 10-mer single-strand extension. On lowering the pH (between 6 and 4), the extensions mutually associate to one of the other hairpins via Hoogsteen (HG) hydrogen bonding. Collectively, this process results in the formation of the branch point and the triple-helical arms. The HG triple-helical three-way junction is characterized by gel electrophoresis, circular dichroism, uv melting, and differential scanning calorimetry. The junction undergoes thermal unfolding in two distinct temperature regions. In the temperature range 15 to 50 degrees C loss of HG base pairing results in the dissociation of the three-way junction. Between 55 and 95 degrees C the resulting hairpins undergo further successive unfolding. The overall calorimetric unfolding enthalpy and entropy changes associated with the loss of HG base pairing are approximately equal to the sum of the enthalpy and entropy changes associated with the dissociation of the HG base pairing in the isolated arms (170.6 kcal.mol-1; 540.1 cal.mol-1.K-1). It is apparent from these results that in the proximity of the branch point the structure is not perturb or strain. This result is contrary to the results obtained for the WC triple-helical three-way and for three-way junctions constructed from canonical double-helical DNA. Complete folding of the junction requires either high Na+ (600 mM) ion concentrations or 40-60 mM Mg2+.

Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications

PubMed Central

Wright, Adam; Laxmisan, Archana; Ottosen, Madelene J; McCoy, Jacob A; Butten, David; Sittig, Dean F

2012-01-01

Objective We describe a novel, crowdsourcing method for generating a knowledge base of problem–medication pairs that takes advantage of manually asserted links between medications and problems. Methods Through iterative review, we developed metrics to estimate the appropriateness of manually entered problem–medication links for inclusion in a knowledge base that can be used to infer previously unasserted links between problems and medications. Results Clinicians manually linked 231 223 medications (55.30% of prescribed medications) to problems within the electronic health record, generating 41 203 distinct problem–medication pairs, although not all were accurate. We developed methods to evaluate the accuracy of the pairs, and after limiting the pairs to those meeting an estimated 95% appropriateness threshold, 11 166 pairs remained. The pairs in the knowledge base accounted for 183 127 total links asserted (76.47% of all links). Retrospective application of the knowledge base linked 68 316 medications not previously linked by a clinician to an indicated problem (36.53% of unlinked medications). Expert review of the combined knowledge base, including inferred and manually linked problem–medication pairs, found a sensitivity of 65.8% and a specificity of 97.9%. Conclusion Crowdsourcing is an effective, inexpensive method for generating a knowledge base of problem–medication pairs that is automatically mapped to local terminologies, up-to-date, and reflective of local prescribing practices and trends. PMID:22582202

Longitudinal assessment of childhood optic gliomas: relationship between flicker visual evoked potentials and magnetic resonance imaging findings.

PubMed

Falsini, Benedetto; Ziccardi, Lucia; Lazzareschi, Ilaria; Ruggiero, Antonio; Placentino, Luca; Dickmann, Anna; Liotti, Lucia; Piccardi, Marco; Balestrazzi, Emilio; Colosimo, Cesare; Di Rocco, Concezio; Riccardi, Riccardo

2008-05-01

The aim of this study was to evaluate longitudinally functional and neuro-radiologic findings in childhood optic gliomas (OG), by comparing flicker visual evoked potentials (F-VEPs) with brain magnetic resonance imaging (MRI) changes. Fourteen children (age range: 1-13 years) with OGs underwent serial F-VEP, MRI and neuro-ophthalmic examinations over a 38 month (median, range: 6-76) follow-up. F-VEPs were elicited by 8 Hz sine-wave flicker stimuli presented in a mini-Ganzfeld. Contrast-enhanced MRI examinations were performed. Results of both tests were blindly assessed by independent evaluators. F-VEPs were judged to be improved, stable or worsened if changes in the amplitude and/or phase angle of the response exceeded the limits of test-retest variability (+/-90th percentile) established for the same patients. MRI results were judged to show regression, stabilization or progression of OG based on its changes in size (+/-20%) or extension. Two to seven pairs of F-VEP/MRI examinations per patient (median: 4) were collected. Based on a total of 38 pairs of F-VEP/MRI examinations, both tests agreed in showing worsening (progression), stabilization and improvement (regression) in 5, 15 and 10 cases, respectively. In 3 cases, F-VEPs showed a worsening and MRI a stabilization, while in 5 cases F-VEPs showed an improvement and MRI a stabilization. Agreement between F-VEP and MRI changes was 78.9% (95% CI: +/- 37%, K statistics = 0.67, P < 0.001). The results indicate that longitudinal F-VEP changes can predict changes in MRI-assessed OG size and extension, providing a non-invasive functional assay, complementary to neuro-imaging, for OG follow-up.

Hydrological Footprints of Urban Developments in the Lake Simcoe Watershed, Canada: A Combined Paired-Catchment and Change Detection Modeling Approach

NASA Astrophysics Data System (ADS)

Oni, S. K.; Futter, M. N.; Buttle, J. M.; Dillon, P.

2014-12-01

Urban sprawl and regional climate variability are major stresses on surface water resources in many places. The Lake Simcoe watershed (LSW) Ontario, Canada, is no exception. The LSW is predominantly agricultural but is experiencing rapid population growth due to its proximity to the greater Toronto area. This has led to extensive land use changes which have impacted its water resources and altered runoff patterns in some rivers draining to the lake. Here, we use a paired-catchment approach, hydrological change detection modelling and remote sensing analysis of satellite images to evaluate the impacts of land use change on the hydrology of the LSW (1994 to 2008). Results show that urbanization increased up to 16% in Lovers Creek, the most-urban impacted catchment. Annual runoff from Lovers Creek increased from 239 to 442 mm/yr in contrast to the reference catchment (Black River at Washago) where runoff was relatively stable with an annual mean of 474 mm/yr. Increased annual runoff from Lovers Creek was not accompanied by an increase in annual precipitation. Discriminant function analysis suggests that early (1992-1997; pre-major development) and late (2004-2009; fully urbanized) periods for Lovers Creek separated mainly based on model parameter sets related to runoff flashiness and evapotranspiration. As a result, parameterization in either period cannot be used interchangeably to produce credible runoff simulations in Lovers Creek due to greater scatter between the parameters in canonical space. Separation of early and late period parameter sets for the reference catchment was based on climate and snowmelt related processes. This suggests that regional climatic variability could be influencing hydrologic change in the reference catchment whereas urbanization amplified the regional natural hydrologic changes in urbanizing catchments of the LSW.

Brood size and its importance for nestling growth in the Biscutate Swift (Streptoprocne biscutata, Aves: Apodidae).

PubMed

Pichorim, M; Monteiro-Filho, E L A

2008-11-01

Many Apodidae, including Streptoprocne biscutata (Sclater, 1866), drop eggs from their nests during incubation. This is interpreted as nest site competition or accident. We provide evidence that egg ejection is deliberate and that this behaviour controls the brood size. Brood sizes were manipulated and nestling growth was measured to test the hypothesis that pairs can regulate brood size during incubation based on current ability to rear nestlings. Natural (control) broods with one, two and three nestlings, and manipulated (experimental) broods reduced to one and increased to two and three young were monitored. Growth rates were measured based on weight, and wing, tail and tarsus lengths of natural and manipulated broods. We compared the slopes of each measure's regression lines of the nestlings of each brood size by t-test. Nestling growth of control nests was similar and relatively little associated with brood size. In broods reduced to one nestling, weight, wing and tail had greater growth rates, and in broods increased to three nestlings growth rates were lower. Weight was most, and tarsus length least influenced by brood size. In general, nestling growth of manipulated nests was inversely proportional to brood size. The results suggest that pairs with larger clutches are in better physical conditions than others. Thus, in experimental broods, pairs are over or under-loaded because feeding activities increase or decrease and these changes affect the growth rate of the nestlings. The present study suggests that egg ejection can control brood size. This behaviour is probably stimulated by physical changes in the adult birds during incubation.

Acuity of a Cryptochrome and Vision-Based Magnetoreception System in Birds

PubMed Central

Solov'yov, Ilia A.; Mouritsen, Henrik; Schulten, Klaus

2010-01-01

Abstract The magnetic compass of birds is embedded in the visual system and it has been hypothesized that the primary sensory mechanism is based on a radical pair reaction. Previous models of magnetoreception have assumed that the radical pair-forming molecules are rigidly fixed in space, and this assumption has been a major objection to the suggested hypothesis. In this article, we investigate theoretically how much disorder is permitted for the radical pair-forming, protein-based magnetic compass in the eye to remain functional. Our study shows that only one rotational degree of freedom of the radical pair-forming protein needs to be partially constrained, while the other two rotational degrees of freedom do not impact the magnetoreceptive properties of the protein. The result implies that any membrane-associated protein is sufficiently restricted in its motion to function as a radical pair-based magnetoreceptor. We relate our theoretical findings to the cryptochromes, currently considered the likeliest candidate to furnish radical pair-based magnetoreception. PMID:20655831

A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs

PubMed Central

Lee, Dong-Hoon; Liu, Yinling; Lee, Hyun-Wook; Xia, Bo; Brice, Allyn R.; Park, Sung-Hyun; Balduf, Hunter; Dominy, Brian N.; Cao, Weiguo

2015-01-01

The uracil DNA glycosylase superfamily consists of several distinct families. Family 2 mismatch-specific uracil DNA glycosylase (MUG) from Escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, T/U, G/U and C/U. Family 1 uracil N-glycosylase (UNG) from E. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the A/U base pair. Here, we report the identification of an important structural determinant that underlies the functional difference between MUG and UNG. Substitution of a Lys residue at position 68 with Asn in MUG not only accelerates the removal of uracil from mismatched base pairs but also enables the enzyme to gain catalytic activity on A/U base pairs. Binding and kinetic analysis demonstrate that the MUG-K68N substitution results in enhanced ground state binding and transition state interactions. Molecular modeling reveals that MUG-K68N, UNG-N123 and family 5 Thermus thermophiles UDGb-A111N can form bidentate hydrogen bonds with the N3 and O4 moieties of the uracil base. Genetic analysis indicates the gain of function for A/U base pairs allows the MUG-K68N mutant to remove uracil incorporated into the genome during DNA replication. The implications of this study in the origin of life are discussed. PMID:25550433

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Perturbations in DNA structure upon interaction with porphyrins revealed by chemical probes, DNA footprinting and molecular modelling.

PubMed

Ford, K G; Neidle, S

1995-06-01

The interactions of several porphyrins with a 74 base-pair DNA sequence have been examined by footprinting and chemical protection methods. Tetra-(4-N-methyl-(pyridyl)) porphyrin (TMPy), two of its metal complexes and tetra-(4-trimethylanilinium) porphyrin (TMAP) bind to closely similar AT-rich sequences. The three TMPy ligands produce modest changes in DNA structure and base accessibility on binding, in contrast to the large-scale conformational changes observed with TMAP. Molecular modelling studies have been performed on TMPy and TMAP bound in the AT-rich minor groove of an oligonucleotide. These have shown that significant structural change is needed to accommodate the bulky trimethyl substituent groups of TMAP, in contrast to the facile minor groove fit of TMPy.

Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials.

PubMed

Kékedy-Nagy, László; Ferapontova, Elena E; Brand, Izabella

2017-02-23

Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT) 25 or cytosine-guanine (dGdC) 20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C 6 alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT) 25 molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC) 20 helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.

Anticipating changes to future connectivity within a network of marine protected areas.

PubMed

Coleman, Melinda A; Cetina-Heredia, Paulina; Roughan, Moninya; Feng, Ming; van Sebille, Erik; Kelaher, Brendan P

2017-09-01

Continental boundary currents are projected to be altered under future scenarios of climate change. As these currents often influence dispersal and connectivity among populations of many marine organisms, changes to boundary currents may have dramatic implications for population persistence. Networks of marine protected areas (MPAs) often aim to maintain connectivity, but anticipation of the scale and extent of climatic impacts on connectivity are required to achieve this critical conservation goal in a future of climate change. For two key marine species (kelp and sea urchins), we use oceanographic modelling to predict how continental boundary currents are likely to change connectivity among a network of MPAs spanning over 1000 km of coastline off the coast of eastern Australia. Overall change in predicted connectivity among pairs of MPAs within the network did not change significantly over and above temporal variation within climatic scenarios, highlighting the need for future studies to incorporate temporal variation in dispersal to robustly anticipate likely change. However, the intricacies of connectivity between different pairs of MPAs were noteworthy. For kelp, poleward connectivity among pairs of MPAs tended to increase in the future, whereas equatorward connectivity tended to decrease. In contrast, for sea urchins, connectivity among pairs of MPAs generally decreased in both directions. Self-seeding within higher-latitude MPAs tended to increase, and the role of low-latitude MPAs as a sink for urchins changed significantly in contrasting ways. These projected changes have the potential to alter important genetic parameters with implications for adaptation and ecosystem vulnerability to climate change. Considering such changes, in the context of managing and designing MPA networks, may ensure that conservation goals are achieved into the future. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Development of a spatial analysis method using ground-based repeat photography to detect changes in the alpine treeline ecotone, Glacier National Park, Montana, U.S.A.

USGS Publications Warehouse

Roush, W.; Munroe, Jeffrey S.; Fagre, D.B.

2007-01-01

Repeat photography is a powerful tool for detection of landscape change over decadal timescales. Here a novel method is presented that applies spatial analysis software to digital photo-pairs, allowing vegetation change to be categorized and quantified. This method is applied to 12 sites within the alpine treeline ecotone of Glacier National Park, Montana, and is used to examine vegetation changes over timescales ranging from 71 to 93 years. Tree cover at the treeline ecotone increased in 10 out of the 12 photo-pairs (mean increase of 60%). Establishment occurred at all sites, infilling occurred at 11 sites. To demonstrate the utility of this method, patterns of tree establishment at treeline are described and the possible causes of changes within the treeline ecotone are discussed. Local factors undoubtedly affect the magnitude and type of the observed changes, however the ubiquity of the increase in tree cover implies a common forcing mechanism. Mean minimum summer temperatures have increased by 1.5??C over the past century and, coupled with variations in the amount of early spring snow water equivalent, likely account for much of the increase in tree cover at the treeline ecotone. Lastly, shortcomings of this method are presented along with possible solutions and areas for future research. ?? 2007 Regents of the University of Colorado.

Energy of charged states in the acetanilide crystal: trapping of charge-transfer states at vacancies as a possible mechanism for optical damage.

PubMed

Tsiaousis, D; Munn, R W

2004-04-15

Calculations for the acetanilide crystal yield the effective polarizability (16.6 A(3)), local electric field tensor, effective dipole moment (5.41 D), and dipole-dipole energy (-12.8 kJ/mol). Fourier-transform techniques are used to calculate the polarization energy P for a single charge in the perfect crystal (-1.16 eV); the charge-dipole energy W(D) is zero if the crystal carries no bulk dipole moment. Polarization energies for charge-transfer (CT) pairs combine with the Coulomb energy E(C) to give the screened Coulomb energy E(scr); screening is nearly isotropic, with E(scr) approximately E(C)/2.7. For CT pairs W(D) reduces to a term deltaW(D) arising from the interaction of the charge on each ion with the change in dipole moment on the other ion relative to the neutral molecule. The dipole moments calculated by density-functional theory methods with the B3LYP functional at the 6-311++G(**) level are 3.62 D for the neutral molecule, changing to 7.13 D and 4.38 D for the anion and cation, relative to the center of mass. Because of the large change in the anion, deltaW(D) reaches -0.9 eV and modifies the sequence of CT energies markedly from that of E(scr), giving the lowest two CT pairs at -1.98 eV and -1.41 eV. The changes in P and W(D) near a vacancy are calculated; W(D) changes for the individual charges because the vacancy removes a dipole moment and modifies the crystal dielectric response, but deltaW(D) and E(C) do not change. A vacancy yields a positive change DeltaP that scatters a charge or CT pair, but the change DeltaW(D) can be negative and large enough to outweigh DeltaP, yielding traps with depths that can exceed 150 meV for single charges and for CT pairs. Divacancies yield traps with depths nearly equal to the sum of those produced by the separate vacancies and so they can exceed 300 meV. These results are consistent with a mechanism of optical damage in which vacancies trap optically generated CT pairs that recombine and release energy; this can disrupt the lattice around the vacancy, thereby favoring trapping and recombination of CT pairs generated by subsequent photon absorption, leading to further lattice disruption. Revisions to previous calculations on trapping of CT pairs in anthracene are reported. (c) 2004 American Institute of Physics.

Ultrasound of the fingers for human identification using biometrics.

PubMed

Narayanasamy, Ganesh; Fowlkes, J Brian; Kripfgans, Oliver D; Jacobson, Jon A; De Maeseneer, Michel; Schmitt, Rainer M; Carson, Paul L

2008-03-01

It was hypothesized that the use of internal finger structure as imaged using commercially available ultrasound (US) scanners could act as a supplement to standard methods of biometric identification, as well as a means of assessing physiological and cardiovascular status. Anatomical structures in the finger including bone contour, tendon and features along the interphalangeal joint were investigated as potential biometric identifiers. Thirty-six pairs of three-dimensional (3D) gray-scale images of second to fourth finger (index, middle and ring) data taken from 20 individuals were spatially registered using MIAMI-Fuse software developed at our institution and also visually matched by four readers. The image-based registration met the criteria for matching successfully in 14 out of 15 image pairs on the same individual and did not meet criteria for matching in any of the 12 image pairs from different subjects, providing a sensitivity and specificity of 0.93 and 1.00, respectively. Visual matching of all image pairs by four readers yielded 96% successful match. Power Doppler imaging was performed to calculate the change in color pixel density due to physical exercise as a surrogate of stress level and to provide basic physiological information. (E-mail: gnarayan@umich.edu).

Pairing-induced speedup of nuclear spontaneous fission

NASA Astrophysics Data System (ADS)

Sadhukhan, Jhilam; Dobaczewski, J.; Nazarewicz, W.; Sheikh, J. A.; Baran, A.

2014-12-01

Background: Collective inertia is strongly influenced at the level crossing at which the quantum system changes its microscopic configuration diabatically. Pairing correlations tend to make the large-amplitude nuclear collective motion more adiabatic by reducing the effect of these configuration changes. Competition between pairing and level crossing is thus expected to have a profound impact on spontaneous fission lifetimes. Purpose: To elucidate the role of nucleonic pairing on spontaneous fission, we study the dynamic fission trajectories of 264Fm and 240Pu using the state-of-the-art self-consistent framework. Methods: We employ the superfluid nuclear density functional theory with the Skyrme energy density functional SkM* and a density-dependent pairing interaction. Along with shape variables, proton and neutron pairing correlations are taken as collective coordinates. The collective inertia tensor is calculated within the nonperturbative cranking approximation. The fission paths are obtained by using the least action principle in a four-dimensional collective space of shape and pairing coordinates. Results: Pairing correlations are enhanced along the minimum-action fission path. For the symmetric fission of 264Fm, where the effect of triaxiality on the fission barrier is large, the geometry of the fission pathway in the space of the shape degrees of freedom is weakly impacted by pairing. This is not the case for 240Pu, where pairing fluctuations restore the axial symmetry of the dynamic fission trajectory. Conclusions: The minimum-action fission path is strongly impacted by nucleonic pairing. In some cases, the dynamical coupling between shape and pairing degrees of freedom can lead to a dramatic departure from the static picture. Consequently, in the dynamical description of nuclear fission, particle-particle correlations should be considered on the same footing as those associated with shape degrees of freedom.

Pairing-induced speedup of nuclear spontaneous fission

DOE PAGES

Sadhukhan, Jhilam; Dobaczewski, J.; Nazarewicz, W.; ...

2014-12-22

Collective inertia is strongly influenced at the level crossing at which the quantum system changes its microscopic configuration diabatically. Pairing correlations tend to make the large-amplitude nuclear collective motion more adiabatic by reducing the effect of these configuration changes. Competition between pairing and level crossing is thus expected to have a profound impact on spontaneous fission lifetimes. To elucidate the role of nucleonic pairing on spontaneous fission, we study the dynamic fission trajectories of 264Fm and 240Pu using the state-of-the-art self-consistent framework. We employ the superfluid nuclear density functional theory with the Skyrme energy density functional SkM* and a density-dependentmore » pairing interaction. Along with shape variables, proton and neutron pairing correlations are taken as collective coordinates. The collective inertia tensor is calculated within the nonperturbative cranking approximation. The fission paths are obtained by using the least action principle in a four-dimensional collective space of shape and pairing coordinates. Pairing correlations are enhanced along the minimum-action fission path. For the symmetric fission of 264Fm, where the effect of triaxiality on the fission barrier is large, the geometry of the fission pathway in the space of the shape degrees of freedom is weakly impacted by pairing. This is not the case for 240Pu, where pairing fluctuations restore the axial symmetry of the dynamic fission trajectory. The minimum-action fission path is strongly impacted by nucleonic pairing. In some cases, the dynamical coupling between shape and pairing degrees of freedom can lead to a dramatic departure from the static picture. As a result, in the dynamical description of nuclear fission, particle-particle correlations should be considered on the same footing as those associated with shape degrees of freedom.« less

Theory of nodal s ±-wave pairing symmetry in the Pu-based 115 superconductor family

DOE PAGES

Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

2015-02-27

The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-T c superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scatteringmore » channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

Rapid Delivery of Cocaine Facilitates Acquisition of Self-Administration in Rats: An Effect Masked by Paired Stimuli

PubMed Central

Schindler, Charles W.; Cogan, Elizabeth S.; Thorndike, Eric B.; Panlilio, Leigh V.

2011-01-01

In general, faster infusions of cocaine are more likely to support behavior related to abuse than are slower infusions. However, some studies of cocaine self-administration in rats have failed to support this finding, possibly because the effect was masked by other factors. One such factor may be the pairing of a stimulus with the infusion, a procedure that is known to facilitate acquisition of drug self-administration. We compared fast and slow infusions by allowing groups of rats to acquire cocaine self-administration at a dose of 1 mg/kg/infusion, delivered over different durations (1.8 or 100 sec). Two groups were trained with either short or long infusions paired with a visual stimulus change (lights off), and two other groups were trained with short or long durations but with no stimulus change. Both groups trained with a paired stimulus acquired cocaine self-administration. With no stimulus change, the rats trained with the 1.8-sec infusion acquired cocaine self-administration at a rate comparable to the two groups that were trained with a paired stimulus. However, most rats in the group trained with the 100-sec infusion that was not accompanied by a stimulus change failed to acquire cocaine self-administration. The stimulus itself did not support responding. These results indicate that infusing a given dose of cocaine over a longer duration reduces its ability to support self-administration, but drug-paired stimuli can partially mask this effect by enhancing the effectiveness of slow infusions. PMID:21600912

Rapid delivery of cocaine facilitates acquisition of self-administration in rats: an effect masked by paired stimuli.

PubMed

Schindler, Charles W; Cogan, Elizabeth S; Thorndike, Eric B; Panlilio, Leigh V

2011-09-01

In general, faster infusions of cocaine are more likely to support behavior related to abuse than are slower infusions. However, some studies of cocaine self-administration in rats have failed to support this finding, possibly because the effect was masked by other factors. One such factor may be the pairing of a stimulus with the infusion, a procedure that is known to facilitate acquisition of drug self-administration. We compared fast and slow infusions by allowing groups of rats to acquire cocaine self-administration at a dose of 1mg/kg/infusion, delivered over different durations (1.8 or 100 s). Two groups were trained with either short or long infusions paired with a visual stimulus change (lights off), and two other groups were trained with short or long durations but with no stimulus change. Both groups trained with a paired stimulus acquired cocaine self-administration. With no stimulus change, the rats trained with the 1.8-s infusion acquired cocaine self-administration at a rate comparable to the two groups that were trained with a paired stimulus. However, most rats in the group trained with the 100-s infusion that was not accompanied by a stimulus change failed to acquire cocaine self-administration. The stimulus itself did not support responding. These results indicate that infusing a given dose of cocaine over a longer duration reduces its ability to support self-administration, but drug-paired stimuli can partially mask this effect by enhancing the effectiveness of slow infusions. Published by Elsevier Inc.

Growth properties associated with A-U replacement of specific G-C base pairs in 16S rRNA from Escherichia coli.

PubMed Central

Triman, K L

1995-01-01

Mutations that disrupt each of seven specific G-C base pairs in 16S rRNA from Escherichia coli confer loss of expression of a plasmid-encoded 16S rRNA selectable marker (spectinomycin resistance). However, A-U replacement of G-C base pairs at nucleotides 359/52 or 1292/1245 in 16S rRNA permits normal expression of the marker. By contrast, A-U replacements at 146/176, 153/168, 350/339, or 1293/1244 are associated with loss of expression of the marker. These genetic studies are designed to determine the importance of specific base pairs by assessment of the structural and functional impairments of 16S rRNA molecules resulting from expression of base pair substitutions at these positions. PMID:7543481

Quantitative determination of pairing interactions for high-temperature superconductivity in cuprates

PubMed Central

Bok, Jin Mo; Bae, Jong Ju; Choi, Han-Yong; Varma, Chandra M.; Zhang, Wentao; He, Junfeng; Zhang, Yuxiao; Yu, Li; Zhou, X. J.

2016-01-01

A profound problem in modern condensed matter physics is discovering and understanding the nature of fluctuations and their coupling to fermions in cuprates, which lead to high-temperature superconductivity and the invariably associated strange metal state. We report the quantitative determination of normal and pairing self-energies, made possible by laser-based angle-resolved photoemission measurements of unprecedented accuracy and stability. Through a precise inversion procedure, both the effective interactions in the attractive d-wave symmetry and the repulsive part in the full symmetry are determined. The latter is nearly angle-independent. Near Tc, both interactions are nearly independent of frequency and have almost the same magnitude over the complete energy range of up to about 0.4 eV, except for a low-energy feature at around 50 meV that is present only in the repulsive part, which has less than 10% of the total spectral weight. Well below Tc, they both change similarly, with superconductivity-induced features at low energies. Besides finding the pairing self-energy and the attractive interactions for the first time, these results expose the central paradox of the problem of high Tc: how the same frequency-independent fluctuations can dominantly scatter at angles ±π/2 in the attractive channel to give d-wave pairing and lead to angle-independent repulsive scattering. The experimental results are compared with available theoretical calculations based on antiferromagnetic fluctuations, the Hubbard model, and quantum-critical fluctuations of the loop-current order. PMID:26973872

Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation.

PubMed

Dion-Côté, Anne-Marie; Symonová, Radka; Lamaze, Fabien C; Pelikánová, Šárka; Ráb, Petr; Bernatchez, Louis

2017-01-01

The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation. © 2016 John Wiley & Sons Ltd.

The Effect of Differences in Day and Night Lighting Distributions on Drivers' Speed Perception.

PubMed

Kim, Jonathan D; Perrone, John A; Isler, Robert B

2017-06-01

Previous research has shown that changes to contrast levels in the visual environment caused by fog can affect drivers' perceptions of speed. It is not easy, however, to extrapolate these results to other driving scenarios in which contrast is affected, such as during nighttime driving, because the measure of contrast is more complex when considering factors such as the illumination provided by headlights. Therefore, we investigated the differences in lighting distribution patterns between day- and nighttime driving on speed perception using prerendered 3D scenarios representing driving on a rural road. A two-alternative forced-choice design based on the method of constant stimuli was utilised, with 32 participants viewing a series of pairs of scenarios (day vs. night driving) from a driver's perspective while indicating for each pair whether the second scenario was faster or slower than the first scenario. Our results indicated that speed discrimination accuracy was minimally affected by changes in lighting distribution patterns between day and night.

Demographic mechanisms of inbreeding adjustment through extra-pair reproduction.

PubMed

Reid, Jane M; Duthie, A Bradley; Wolak, Matthew E; Arcese, Peter

2015-07-01

One hypothesis explaining extra-pair reproduction is that socially monogamous females mate with extra-pair males to adjust the coefficient of inbreeding (f) of extra-pair offspring (EPO) relative to that of within-pair offspring (WPO) they would produce with their socially paired male. Such adjustment of offspring f requires non-random extra-pair reproduction with respect to relatedness, which is in turn often assumed to require some mechanism of explicit pre-copulatory or post-copulatory kin discrimination. We propose three demographic processes that could potentially cause mean f to differ between individual females' EPO and WPO given random extra-pair reproduction with available males without necessarily requiring explicit kin discrimination. Specifically, such a difference could arise if social pairings formed non-randomly with respect to relatedness or persisted non-randomly with respect to relatedness, or if the distribution of relatedness between females and their sets of potential mates changed during the period through which social pairings persisted. We used comprehensive pedigree and pairing data from free-living song sparrows (Melospiza melodia) to quantify these three processes and hence investigate how individual females could adjust mean offspring f through instantaneously random extra-pair reproduction. Female song sparrows tended to form social pairings with unrelated or distantly related males slightly less frequently than expected given random pairing within the defined set of available males. Furthermore, social pairings between more closely related mates tended to be more likely to persist across years than social pairings between less closely related mates. However, these effects were small and the mean relatedness between females and their sets of potential extra-pair males did not change substantially across the years through which social pairings persisted. Our framework and analyses illustrate how demographic and social structuring within populations might allow females to adjust mean f of offspring through random extra-pair reproduction without necessarily requiring explicit kin discrimination, implying that adjustment of offspring f might be an inevitable consequence of extra-pair reproduction. New theoretical and empirical studies are required to explore the general magnitude of such effects and quantify the degree to which they could facilitate or constrain long-term evolution of extra-pair reproduction. © 2015 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Experimental demonstration of wavelength domain rogue-free ONU based on wavelength-pairing for TDM/WDM optical access networks.

PubMed

Lee, Jie Hyun; Park, Heuk; Kang, Sae-Kyoung; Lee, Joon Ki; Chung, Hwan Seok

2015-11-30

In this study, we propose and experimentally demonstrate a wavelength domain rogue-free ONU based on wavelength-pairing of downstream and upstream signals for time/wavelength division-multiplexed optical access networks. The wavelength-pairing tunable filter is aligned to the upstream wavelength channel by aligning it to one of the downstream wavelength channels. Wavelength-pairing is implemented with a compact and cyclic Si-AWG integrated with a Ge-PD. The pairing filter covered four 100 GHz-spaced wavelength channels. The feasibility of the wavelength domain rogue-free operation is investigated by emulating malfunction of the misaligned laser. The wavelength-pairing tunable filter based on the Si-AWG blocks the upstream signal in the non-assigned wavelength channel before data collision with other ONUs.

Orbital selective pairing and gap structures of iron-based superconductors

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

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Orbital selective pairing and gap structures of iron-based superconductors

DOE PAGES

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.; ...

2017-05-08

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Causal Entropies – a measure for determining changes in the temporal organization of neural systems

PubMed Central

Waddell, Jack; Dzakpasu, Rhonda; Booth, Victoria; Riley, Brett; Reasor, Jonathan; Poe, Gina; Zochowski, Michal

2009-01-01

We propose a novel measure to detect temporal ordering in the activity of individual neurons in a local network, which is thought to be a hallmark of activity-dependent synaptic modifications during learning. The measure, called Causal Entropy, is based on the time-adaptive detection of asymmetries in the relative temporal patterning between neuronal pairs. We characterize properties of the measure on both simulated data and experimental multiunit recordings of hippocampal neurons from the awake, behaving rat, and show that the metric can more readily detect those asymmetries than standard cross correlation-based techniques, especially since the temporal sensitivity of causal entropy can detect such changes rapidly and dynamically. PMID:17275095

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.

I like it because I said that I like it: evaluative conditioning effects can be based on stimulus-response learning.

PubMed

Gast, Anne; Rothermund, Klaus

2011-10-01

Evaluative conditioning (EC) effects are often assumed to be based on a learned mental link between the CS (conditioned stimulus) and the US (unconditioned stimulus). We demonstrate that this link is not the only one that can underlie EC effects, but that if evaluative responses are actually given during the learning phase also a direct link between the CS and an evaluative response-a CS-ER link-can be learned and lead to EC effects. In Experiment 1, CSs were paired with USs and participants were asked to evaluate the pairs during the conditioning phase. Resulting EC effects were unaffected by a later revaluation of the USs, suggesting that these EC effects can be attributed to CS-ER learning rather than to CS-US learning. Experiment 2 replicated Experiment 1 with the difference that no evaluative responses were given during the learning phase. EC effects in this study were influenced by US revaluation, suggesting that these EC effects are mainly based on CS-US learning. In Experiment 3, it was shown that EC effects can be found even if the USs are entirely removed from the procedure and the CSs are only paired with enforced evaluative responses. Together the experiments show that the valence of a stimulus can change because of a contingency with an evaluative response. (PsycINFO Database Record (c) 2011 APA, all rights reserved).

Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2Ile

PubMed Central

Köhrer, Caroline; Mandal, Debabrata; Gaston, Kirk W.; Grosjean, Henri; Limbach, Patrick A.; RajBhandary, Uttam L.

2014-01-01

Translation of the isoleucine codon AUA in most prokaryotes requires a modified C (lysidine or agmatidine) at the wobble position of tRNA2Ile to base pair specifically with the A of the AUA codon but not with the G of AUG. Recently, a Bacillus subtilis strain was isolated in which the essential gene encoding tRNAIle-lysidine synthetase was deleted for the first time. In such a strain, C34 at the wobble position of tRNA2Ile is expected to remain unmodified and cells depend on a mutant suppressor tRNA derived from tRNA1Ile, in which G34 has been changed to U34. An important question, therefore, is how U34 base pairs with A without also base pairing with G. Here, we show (i) that unlike U34 at the wobble position of all B. subtilis tRNAs of known sequence, U34 in the mutant tRNA is not modified, and (ii) that the mutant tRNA binds strongly to the AUA codon on B. subtilis ribosomes but only weakly to AUG. These in vitro data explain why the suppressor strain displays only a low level of misreading AUG codons in vivo and, as shown here, grows at a rate comparable to that of the wild-type strain. PMID:24194599

Capacitive proximity sensor

DOEpatents

Kronberg, James W.

1994-01-01

A proximity sensor based on a closed field circuit. The circuit comprises a ring oscillator using a symmetrical array of plates that creates an oscillating displacement current. The displacement current varies as a function of the proximity of objects to the plate array. Preferably the plates are in the form of a group of three pair of symmetric plates having a common center, arranged in a hexagonal pattern with opposing plates linked as a pair. The sensor produces logic level pulses suitable for interfacing with a computer or process controller. The proximity sensor can be incorporated into a load cell, a differential pressure gauge, or a device for measuring the consistency of a characteristic of a material where a variation in the consistency causes the dielectric constant of the material to change.

Developing Topological Insulator Fiber Based Photon Pairs Source for Ultrafast Optoelectronic Applications

DTIC Science & Technology

2016-04-01

DEVELOPING TOPOLOGICAL INSULATOR FIBER BASED PHOTON PAIRS SOURCE FOR ULTRAFAST OPTOELECTRONIC APPLICATIONS NORTHWESTERN UNIVERSITY...REPORT TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) APRIL 2015 – DEC 2015 4. TITLE AND SUBTITLE DEVELOPING TOPOLOGICAL INSULATOR FIBER BASED...in developing a new source for the production of correlated/entangled photon pairs based on the unique nanolayer properties of topological insulator

Modeling of light distribution in the brain for topographical imaging

NASA Astrophysics Data System (ADS)

Okada, Eiji; Hayashi, Toshiyuki; Kawaguchi, Hiroshi

2004-07-01

Multi-channel optical imaging system can obtain a topographical distribution of the activated region in the brain cortex by a simple mapping algorithm. Near-infrared light is strongly scattered in the head and the volume of tissue that contributes to the change in the optical signal detected with source-detector pair on the head surface is broadly distributed in the brain. This scattering effect results in poor resolution and contrast in the topographic image of the brain activity. We report theoretical investigations on the spatial resolution of the topographic imaging of the brain activity. The head model for the theoretical study consists of five layers that imitate the scalp, skull, subarachnoid space, gray matter and white matter. The light propagation in the head model is predicted by Monte Carlo simulation to obtain the spatial sensitivity profile for a source-detector pair. The source-detector pairs are one dimensionally arranged on the surface of the model and the distance between the adjoining source-detector pairs are varied from 4 mm to 32 mm. The change in detected intensity caused by the absorption change is obtained by Monte Carlo simulation. The position of absorption change is reconstructed by the conventional mapping algorithm and the reconstruction algorithm using the spatial sensitivity profiles. We discuss the effective interval between the source-detector pairs and the choice of reconstruction algorithms to improve the topographic images of brain activity.

Comparison of endoscopic endonasal and bifrontal craniotomy approaches for olfactory groove meningiomas: A matched pair analysis of outcomes and frontal lobe changes on MRI.

PubMed

de Almeida, John R; Carvalho, Felipe; Vaz Guimaraes Filho, Francisco; Kiehl, Tim-Rasmus; Koutourousiou, Maria; Su, Shirley; Vescan, Allan D; Witterick, Ian J; Zadeh, Gelareh; Wang, Eric W; Fernandez-Miranda, Juan C; Gardner, Paul A; Gentili, Fred; Snyderman, Carl H

2015-11-01

We compare the outcomes and postoperative MRI changes of endoscopic endonasal (EEA) and bifrontal craniotomy (BFC) approaches for olfactory groove meningiomas (OGM). All patients who underwent either BFC or EEA for OGM were eligible. Matched pairs were created by matching tumor volumes of an EEA patient with a BFC patient, and matching the timing of the postoperative scans. The tumor dimensions, peritumoral edema, resectability issues, and frontal lobe changes were recorded based on preoperative and postoperative MRI. Postoperative fluid-attenuated inversion recovery (FLAIR) hyperintensity and residual cystic cavity (porencephalic cave) volume were compared using univariable and multivariable analyses. From a total of 70 patients (46 EEA, 24 BFC), 10 matched pairs (20 patients) were created. Three patients (30%) in the EEA group and two (20%) in the BFC had postoperative cerebrospinal fluid leaks (p=0.61). Gross total resections were achieved in seven (70%) of the EEA group and nine (90%) of the BFC group (p=0.26), and one patient from each group developed a recurrence. On postoperative MRI, there was no significant difference in FLAIR signal volumes between EEA and BFC approaches (6.9 versus 13.3 cm(3); p=0.17) or in porencephalic cave volumes (1.7 versus 5.0 cm(3); p=0.11) in univariable analysis. However, in a multivariable analysis, EEA was associated with less postoperative FLAIR change (p=0.02) after adjusting for the volume of preoperative edema. This study provides preliminary evidence that EEA is associated with quantifiable improvements in postoperative frontal lobe imaging. Copyright © 2015 Elsevier Ltd. All rights reserved.

A neuronal network model for context-dependence of pitch change perception.

PubMed

Huang, Chengcheng; Englitz, Bernhard; Shamma, Shihab; Rinzel, John

2015-01-01

Many natural stimuli have perceptual ambiguities that can be cognitively resolved by the surrounding context. In audition, preceding context can bias the perception of speech and non-speech stimuli. Here, we develop a neuronal network model that can account for how context affects the perception of pitch change between a pair of successive complex tones. We focus especially on an ambiguous comparison-listeners experience opposite percepts (either ascending or descending) for an ambiguous tone pair depending on the spectral location of preceding context tones. We developed a recurrent, firing-rate network model, which detects frequency-change-direction of successively played stimuli and successfully accounts for the context-dependent perception demonstrated in behavioral experiments. The model consists of two tonotopically organized, excitatory populations, E up and E down, that respond preferentially to ascending or descending stimuli in pitch, respectively. These preferences are generated by an inhibitory population that provides inhibition asymmetric in frequency to the two populations; context dependence arises from slow facilitation of inhibition. We show that contextual influence depends on the spectral distribution of preceding tones and the tuning width of inhibitory neurons. Further, we demonstrate, using phase-space analysis, how the facilitated inhibition from previous stimuli and the waning inhibition from the just-preceding tone shape the competition between the E up and E down populations. In sum, our model accounts for contextual influences on the pitch change perception of an ambiguous tone pair by introducing a novel decoding strategy based on direction-selective units. The model's network architecture and slow facilitating inhibition emerge as predictions of neuronal mechanisms for these perceptual dynamics. Since the model structure does not depend on the specific stimuli, we show that it generalizes to other contextual effects and stimulus types.

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription.

PubMed

Liu, Ning; Tian, Ru; Loeb, Daniel D

2003-02-18

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis.

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.

PubMed

Cojocaru, Vlad; Klement, Reinhard; Jovin, Thomas M

2005-01-01

Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation.

PubMed

Wu, Wen-Jin; Su, Mei-I; Wu, Jian-Li; Kumar, Sandeep; Lim, Liang-Hin; Wang, Chun-Wei Eric; Nelissen, Frank H T; Chen, Ming-Chuan Chad; Doreleijers, Jurgen F; Wijmenga, Sybren S; Tsai, Ming-Daw

2014-04-02

A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix αE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.

Major merging history in CANDELS. I. Evolution of the incidence of massive galaxy-galaxy pairs from z = 3 to z ˜ 0

NASA Astrophysics Data System (ADS)

Mantha, Kameswara Bharadwaj; McIntosh, Daniel H.; Brennan, Ryan; Ferguson, Henry C.; Kodra, Dritan; Newman, Jeffrey A.; Rafelski, Marc; Somerville, Rachel S.; Conselice, Christopher J.; Cook, Joshua S.; Hathi, Nimish P.; Koo, David C.; Lotz, Jennifer M.; Simmons, Brooke D.; Straughn, Amber N.; Snyder, Gregory F.; Wuyts, Stijn; Bell, Eric F.; Dekel, Avishai; Kartaltepe, Jeyhan; Kocevski, Dale D.; Koekemoer, Anton M.; Lee, Seong-Kook; Lucas, Ray A.; Pacifici, Camilla; Peth, Michael A.; Barro, Guillermo; Dahlen, Tomas; Finkelstein, Steven L.; Fontana, Adriano; Galametz, Audrey; Grogin, Norman A.; Guo, Yicheng; Mobasher, Bahram; Nayyeri, Hooshang; Pérez-González, Pablo G.; Pforr, Janine; Santini, Paola; Stefanon, Mauro; Wiklind, Tommy

2018-04-01

The rate of major galaxy-galaxy merging is theoretically predicted to steadily increase with redshift during the peak epoch of massive galaxy development (1 ≤ z ≤ 3). We use close-pair statistics to objectively study the incidence of massive galaxies (stellar M1 > 2 × 1010 M⊙) hosting major companions (1 ≤ M1/M2 ≤ 4; i.e. <4:1) at six epochs spanning 0 < z < 3. We select companions from a nearly complete, mass-limited (≥5 × 109 M⊙) sample of 23 696 galaxies in the five Cosmic Assembly Near-Infrared Deep Extragalactic Legacy Survey fields and the Sloan Digital Sky Survey. Using 5-50 kpc projected separation and close redshift proximity criteria, we find that the major companion fraction fmc(z) based on stellar mass-ratio (MR) selection increases from 6 per cent (z ˜ 0) to 16 per cent (z ˜ 0.8), then turns over at z ˜ 1 and decreases to 7 per cent (z ˜ 3). Instead, if we use a major F160W flux-ratio (FR) selection, we find that fmc(z) increases steadily until z = 3 owing to increasing contamination from minor (MR > 4:1) companions at z > 1. We show that these evolutionary trends are statistically robust to changes in companion proximity. We find disagreements between published results are resolved when selection criteria are closely matched. If we compute merger rates using constant fraction-to-rate conversion factors (Cmerg,pair = 0.6 and Tobs,pair = 0.65 Gyr), we find that MR rates disagree with theoretical predictions at z > 1.5. Instead, if we use an evolving Tobs,pair(z) ∝ (1 + z)-2 from Snyder et al., our MR-based rates agree with theory at 0 < z < 3. Our analysis underscores the need for detailed calibration of Cmerg,pair and Tobs,pair as a function of redshift, mass, and companion selection criteria to better constrain the empirical major merger history.

Pairing images of unhealthy and healthy foods with images of negative and positive health consequences: Impact on attitudes and food choice.

PubMed

Hollands, Gareth J; Marteau, Theresa M

2016-08-01

To examine the impact of presenting images of foods paired with images of positive and negative health consequences of their consumption on food choice and attitudes. Participants (N = 711) were randomly allocated in a 2 × 3 factorial design (Food Type × Affective Valence) to 1 of 6 conditioning procedures that paired images of either energy-dense snack foods or fruit, with (a) images of negative health outcomes, (b) images of positive health outcomes, or (c) a no image control. The primary outcome was food choice assessed postintervention with a behavioral choice task. Secondary outcomes were implicit attitudes (assessed pre- and postintervention) and explicit attitudes (assessed postintervention). Presenting images of negative health outcomes led to more healthy food choices relative to control and positive image conditions, irrespective of whether they were paired with images of energy-dense snack foods or fruit. This relationship was partially mediated by changes in implicit and explicit attitudes. Images of positive health outcomes did not alter food choices. This study replicates and extends previous research showing that presenting images of negative health consequences increases healthy food choices. Because effects were elicited by manipulating affective valence irrespective of paired food type, these results appear more consistent with an explanation based on priming than on evaluative conditioning. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

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

[Mass spectrometric and quantum chemical study of dimeric associates of nucleosides].

PubMed

Sukhodub, L F; Aksenov, S A; Boldeskul, A I

1995-01-01

Deoxyribonucleosides H-bonded pairs were investigated using fast atom bombardment mass spectrometry and MNDO/H quantum chemistry method. It was shown that "rare" (enol or imin) forms of the nitrogen bases could form pairs with energy comparable with "canonical" base pair energy. It was shown that pair stability rows, which are measured using different experimental techniques, were in conformity each with other.

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

Automating Performance Measures and Clinical Practice Guidelines: Differences and Complementarities.

PubMed

Tu, Samson W; Martins, Susana; Oshiro, Connie; Yuen, Kaeli; Wang, Dan; Robinson, Amy; Ashcraft, Michael; Heidenreich, Paul A; Goldstein, Mary K

2016-01-01

Through close analysis of two pairs of systems that implement the automated evaluation of performance measures (PMs) and guideline-based clinical decision support (CDS), we contrast differences in their knowledge encoding and necessary changes to a CDS system that provides management recommendations for patients failing performance measures. We trace the sources of differences to the implementation environments and goals of PMs and CDS.

Effects of social contact and zygosity on 21-y weight change in male twins.

PubMed

McCaffery, Jeanne M; Franz, Carol E; Jacobson, Kristen; Leahey, Tricia M; Xian, Hong; Wing, Rena R; Lyons, Michael J; Kremen, William S

2011-08-01

Recent evidence indicates that social contact is related to similarities in weight gain over time. However, no studies have examined this effect in a twin design, in which genetic and other environmental effects can also be estimated. We determined whether the frequency of social contact is associated with similarity in weight change from young adulthood (mean age: 20 y) to middle age (mean age: 41 y) in twins and quantified the percentage of variance in weight change attributable to social contact, genetic factors, and other environmental influences. Participants were 1966 monozygotic and 1529 dizygotic male twin pairs from the Vietnam-Era Twin Registry. Regression models tested whether frequency of social contact and zygosity predicted twin pair similarity in body mass index (BMI) change and weight change. Twin modeling was used to partition the percentage variance attributable to social contact, genetic, and other environmental effects. Twins gained an average of 3.99 BMI units, or 13.23 kg (29.11 lb), over 21 y. In regression models, both zygosity (P < 0.001) and degree of social contact (P < 0.02) significantly predicted twin pair similarity in BMI change. In twin modeling, social contact between twins contributed 16% of the variance in BMI change (P < 0.001), whereas genetic factors contributed 42%, with no effect of additional shared environmental factors (1%). Similar results were obtained for weight change. Frequency of social contact significantly predicted twin pair similarity in BMI and weight change over 21 y, independent of zygosity and other shared environmental influences.

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.

The electrostatic characteristics of G·U wobble base pairs

PubMed Central

Xu, Darui; Landon, Theresa; Greenbaum, Nancy L.; Fenley, Marcia O.

2007-01-01

G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands. PMID:17526525

Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence

PubMed Central

Turriani, Elisa; Höbartner, Claudia; Jovin, Thomas M.

2015-01-01

Among the deoxyribozymes catalyzing the ligation of two RNA substrates, 7S11 generates a branched RNA containing a 2′,5′-linkage. We have attached the small fluorogenic probe Bimane to the triphosphate terminated RNA substrate and utilized emission intensity and anisotropy to follow structural rearrangements leading to a catalytically active complex upon addition of Mg2+. Bimane coupled to synthetic oligonucleotides is quenched by nearby guanines via photoinduced electron transfer. The degree of quenching is sensitive to changes in the base pairing of the residues involved and in their distances to the probe. These phenomena permit the characterization of various sequential processes in the assembly and function of 7S11: binding of Mg2+ to the triphosphate moiety, release of quenching of the probe by the 5′-terminal G residues of R-RNA as they engage in secondary base-pair interactions, local rearrangement into a distinct active conformation, and continuous release of the Bimane-labeled pyrophosphate during the course of reaction at 37°C. It was possible to assign equilibrium and rate constants and structural interpretations to the sequence of conformational transitions and catalysis, information useful for optimizing the design of next generation deoxyribozymes. The fluorescent signatures, thermodynamic equilibria and catalytic function of numerous mutated (base/substituted) molecules were examined. PMID:25505142

Lessons learned for applying a paired-catchment approach in drought analysis

NASA Astrophysics Data System (ADS)

Van Loon, Anne; Rangecroft, Sally; Coxon, Gemma; Agustín Breña Naranjo, José; Van Ogtrop, Floris; Croghan, Danny; Van Lanen, Henny

2017-04-01

Ongoing research is looking to quantify the human impact on hydrological drought using observed data. One potentially suitable method is the paired-catchment approach. Paired catchments have been successfully used for quantifying the impact of human actions (e.g. forest treatment and wildfires) on various components of a catchment's water balance. However, it is unclear whether this method could successfully be applied to drought. In this study, we used a paired-catchment approach to quantify the effects of reservoirs, groundwater abstraction and urbanisation on hydrological drought in the UK, Mexico, and Australia. Following recommendations in literature, we undertook a thorough catchment selection and identified catchments of similar size, climate, geology, and topography. One catchment of the pair was affected by either reservoirs, groundwater abstraction or urbanisation. For the selected catchment pairs, we standardised streamflow time series to catchment area, calculated a drought threshold from the natural catchment and applied it to the human-influenced catchment. The underlying assumption being that the differences in drought severity between catchments can then be attributed to the anthropogenic activity. In some catchments we had local knowledge about human influences, and therefore we could compare our paired-catchment results with hydrological model scenarios. However, we experienced that detailed data on human influences usually are not well recorded. The results showed us that it is important to account for variation in average annual precipitation between the paired catchments to be able to transfer the drought threshold of the natural catchment to the human-influenced catchment. This can be achieved by scaling the discharge by the difference in annual average precipitation. We also found that the temporal distribution of precipitation is important, because if meteorological droughts differ between the paired catchments, this may mask changes caused by human activities. This issue can generally be overcome by selecting adjacent or nearby catchments. Finally, we found that geology is much more important for paired-catchment analysis of drought than we anticipated based upon the experiences in flood research. For example, in two of the UK pairs, we could not use the results due to differences in geology overruling the human influence. We learned that in the selection of catchments for drought analysis, (hydro)geology should be considered in even more detail. Taking these aspects into account, we concluded that the paired-catchment approach works for evaluating the effects of reservoirs and groundwater abstraction on streamflow drought, but is more challenging for urbanisation. The reasons are more problems in catchment selection, lack of results, and complexity of processes making attribution more difficult. Urbanisation is not a simple land cover change influencing only infiltration and runoff, but it involves all kinds of indirect effects, such as artificial inputs (drainage, sewage return flows) that are very important during low flow periods. For this we would suggest starting in small, well-measured urban catchments, of which all artificial inputs are known. We believe that with the careful selection criteria and accounting for variations in climate and landscape, there is scope for using a paired-catchment approach in hydrological drought research.

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

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sensory specificity and speciation: a potential neuronal pathway for host fruit odour discrimination in Rhagoletis pomonella

PubMed Central

Batra, Srishti; Ramaswamy, Sree Subha; Feder, Jeffrey L.

2016-01-01

Behavioural changes in habitat or mate choice can trigger population divergence, leading to speciation. However, little is known about the neurological bases for such changes. Rhagoletis pomonella (Diptera: Tephritidae) is a model for ecological speciation via host plant shifts. Within the past 180 years, Rhagoletis flies infesting hawthorn (Crataegus spp.) shifted to attack domesticated apple (Malus pumila). The two populations differ in their olfactory preferences for apple versus hawthorn fruit. Here, we looked for patterns of sensory organization that may have contributed to this shift by characterizing the morphology, specificity and distribution of olfactory sensory neurons (OSNs) on the antennae of Rhagoletis responding to host fruit and non-host volatiles. Of 28 OSN classes identified, two colocalized OSN pairs were found that specifically responded to the major behavioural attractant and antagonist volatiles for each fly population. A reversal in the response of these OSNs to fruit volatiles, either through a switch in receptor expression between these paired neurons or changes in neuronal projections in the brain, could therefore account for the behavioural difference between apple and hawthorn flies. The finding supports the hypothesis that relatively minor changes in olfactory sensory pathways may contribute to rapid host shifting and divergence in Rhagoletis. PMID:28003447

Somatic Pairing of Chromosome 19 in Renal Oncocytoma Is Associated with Deregulated ELGN2-Mediated Oxygen-Sensing Response

PubMed Central

Petillo, David; Westphal, Michael; Koelzer, Katherine; Metcalf, Julie L.; Zhang, Zhongfa; Matsuda, Daisuke; Dykema, Karl J.; Houseman, Heather L.; Kort, Eric J.; Furge, Laura L.; Kahnoski, Richard J.; Richard, Stéphane; Vieillefond, Annick; Swiatek, Pamela J.; Teh, Bin Tean; Ohh, Michael; Furge, Kyle A.

2008-01-01

Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. Somatic pairing was associated with significant disruption of gene expression within the paired regions and resulted in the deregulation of the prolyl-hydroxylase ELGN2, a key protein that regulates the oxygen-dependent degradation of hypoxia-inducible factor (HIF). Overexpression of ELGN2 in renal oncocytoma increased ubiquitin-mediated destruction of HIF and concomitantly suppressed the expression of several HIF-target genes, including the pro-death BNIP3L gene. The transcriptional changes that are associated with somatic pairing of chromosome 19 mimic the transcriptional changes that occur following DNA amplification. Therefore, in addition to numerical and structural chromosomal abnormalities, alterations in chromosomal spatial dynamics should be considered as genomic events that are associated with tumorigenesis. The identification of EGLN2 as a significantly deregulated gene that maps within the paired chromosome region directly implicates defects in the oxygen-sensing network to the biology of renal oncocytoma. PMID:18773095

Similarity in genetic alterations between paired well-differentiated and dedifferentiated components of dedifferentiated liposarcoma.

PubMed

Horvai, Andrew E; DeVries, Sandy; Roy, Ritu; O'Donnell, Richard J; Waldman, Frederic

2009-11-01

Liposarcoma represents a unique model insofar as some well-differentiated liposarcomas progress to non-lipogenic, so-called 'dedifferentiated,' forms. The well-differentiated and dedifferentiated family of liposarcomas demonstrates amplification of the chromosome subregion 12q13-q15 with resultant amplification of the MDM2 and CDK4 genes. However, the specific genetic changes that distinguish between well-differentiated and dedifferentiated liposarcomas are less well understood. To study the genetic changes in dedifferentiated liposarcomas, paired well-differentiated and dedifferentiated components of 29 tumors were analyzed separately by array-based comparative genomic hybridization. A bacterial artificial chromosome array at approximately 1-Mb resolution was used. The genetic changes were compared with clinical presentation, grade of the dedifferentiated component and overexpression of MDM2 and CDK4. Most tumors (n=21, 72%) were retroperitoneal, with both components present at initial diagnosis (n=25, 86%). Eight tumors (28%) were classified as low-grade dedifferentiation. In four cases (14%), a well-differentiated liposarcoma preceded the presentation of the dedifferentiated tumor by 1-5 years. 12q13-q15 was amplified in all tumors. Using unsupervised hierarchical clustering of copy-number changes, all but two tumors showed close similarities between well-differentiated and dedifferentiated components, and segregated as pairs. Dedifferentiated components had more total amplifications (P=0.008) and a trend for gain at 19q13.2, but no genetic changes were significant in distinguishing between the two components. High-level amplifications of 1p21-32 (n=7, 24%), 1q21-23 (n=9, 31%), 6q23-24 (n=6, 21%) and 12q24 (n=3, 10%) were common, but none significantly correlated with differentiation. Presentation and grade correlated with the frequency of changes at a number of genetic loci (P<0.001), whereas CDK4 immunostaining showed negative correlation with 12q13.13 amplification. The genotypic similarity, at the limit of the array's resolution, between components implies that most genetic changes precede phenotypic 'progression,' early in tumorigenesis. The relationship between genetic changes and presentation or grade may reflect differences in factors that control genomic instability or the background genotype of the tumor.

Discordant inflammatory changes in the apophyseal and sacroiliac joints: serial observations in enthesitis-related arthritis.

PubMed

Bray, Timothy J P; Amies, Thomas; Vendhan, Kanimozhi; Humphries, Paul; Sen, Debajit; Ioannou, Yiannis; Hall-Craggs, Margaret A

2016-09-01

To determine the extent to which inflammation of the sacroiliac joints (SIJs) and apophyseal joints (AJs) changes concordantly after treatment in enthesitis-related arthritis (ERA). A retrospective study was performed with institutional review board approval. 31 young patients with ERA who had been scanned between March 2009 and November 2014 were included. All patients had post-contrast imaging of the SIJs and lumbar spine and short tau inversion-recovery (STIR) images of the SIJs. The severity of sacroiliitis was scored using a modification of an established technique, and inflammation of the AJs was evaluated using a recently described grading system. The changes in SIJ and AJ scores after treatment were classified as either concordant or discordant, and the proportion of scan pairs in these groups was recorded. In addition, the correlation between change in SIJ STIR score (Δnfla) and change in AJ score (ΔAJ) was assessed using Spearman's correlation coefficient. Of a total of 43 scan pairs, the changes in inflammation were concordant in 16 scan pairs and discordant in 27 scan pairs. There was no significant correlation between Δnfla and ΔAJ (R = 0.14, p = 0.37). Inflammatory changes in the SIJs and AJs are often discordant. This may be a reason why patients experience ongoing back pain despite apparent improvement in one or the other site. Inflammation may behave differently at different anatomical sites. The SIJs and AJs should both be imaged in patients with ERA with back pain.

Skin self-examination education for early detection of melanoma: a randomized controlled trial of Internet, workbook, and in-person interventions.

PubMed

Robinson, June K; Gaber, Rikki; Hultgren, Brittney; Eilers, Steven; Blatt, Hanz; Stapleton, Jerod; Mallett, Kimberly; Turrisi, Rob; Duffecy, Jenna; Begale, Mark; Martini, Mary; Bilimoria, Karl; Wayne, Jeffrey

2014-01-13

Early detection of melanoma improves survival. Since many melanoma patients and their spouses seek the care of a physician after discovering their melanoma, an ongoing study will determine the efficacy of teaching at-risk melanoma patients and their skin check partner how to conduct skin self-examinations (SSEs). Internet-based health behavior interventions have proven efficacious in creating behavior change in patients to better prevent, detect, or cope with their health issues. The efficacy of electronic interactive SSE educational intervention provided on a tablet device has not previously been determined. The electronic interactive educational intervention was created to develop a scalable, effective intervention to enhance performance and accuracy of SSE among those at-risk to develop melanoma. The intervention in the office was conducted using one of the following three methods: (1) in-person through a facilitator, (2) with a paper workbook, or (3) with a tablet device used in the clinical office. Differences related to method of delivery were elucidated by having the melanoma patient and their skin check partner provide a self-report of their confidence in performing SSE and take a knowledge-based test immediately after receiving the intervention. The three interventions used 9 of the 26 behavioral change techniques defined by Abraham and Michie to promote planning of monthly SSE, encourage performing SSE, and reinforce self-efficacy by praising correct responses to knowledge-based decision making and offering helpful suggestions to improve performance. In creating the electronic interactive SSE educational intervention, the educational content was taken directly from both the scripted in-person presentation delivered with Microsoft PowerPoint by a trained facilitator and the paper workbook training arms of the study. Enrollment totaled 500 pairs (melanoma patient and their SSE partner) with randomization of 165 pairs to the in-person, 165 pairs to the workbook, and 70 pairs to electronic interactive SSE educational intervention. The demographic survey data showed no significant mean differences between groups in age, education, or income. The tablet usability survey given to the first 30 tablet pairs found that, overall, participants found the electronic interactive intervention easy to use and that the video of the doctor-patient-partner dialogue accompanying the dermatologist's examination was particularly helpful in understanding what they were asked to do for the study. The interactive group proved to be just as good as the workbook group in self-confidence of scoring moles, and just as good as both the workbook and the in-person intervention groups in self-confidence of monitoring their moles. While the in-person intervention performed significantly better on a skill-based quiz, the electronic interactive group performed significantly better than the workbook group. The electronic interactive and in-person interventions were more efficient (30 minutes), while the workbook took longer (45 minutes). This study suggests that an electronic interactive intervention can deliver skills training comparable to other training methods, and the experience can be accommodated during the customary outpatient office visit with the physician. Further testing of the electronic interactive intervention's role in the anxiety of the pair and pair-discovered melanomas upon self-screening will elucidate the impact of these tools on outcomes in at-risk patient populations. ClinicalTrials.gov NCT01013844; http://clinicaltrials.gov/show/NCT01013844 (Archived by WebCite at http://www.webcitation.org/6LvGGSTKK).

The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

ERIC Educational Resources Information Center

Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

2010-01-01

This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

Weak nanoscale chaos and anomalous relaxation in DNA

NASA Astrophysics Data System (ADS)

Mazur, Alexey K.

2017-06-01

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Pólya Counting to a Physical System

NASA Astrophysics Data System (ADS)

Hillebrand, Malcolm; Paterson-Jones, Guy; Kalosakas, George; Skokos, Charalampos

2018-03-01

In modeling DNA chains, the number of alternations between Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability distribution function of the number of these alternations is derived for circular or periodic DNA. Since there are several symmetries to account for in the periodic chain, necklace counting methods are used. In particular, Polya's Enumeration Theorem is extended for the case of a group action that preserves partitioned necklaces. This, along with the treatment of generating functions as formal power series, allows for the direct calculation of the number of possible necklaces with a given number of AT base pairs, GC base pairs and alternations. The theoretically obtained probability distribution functions of the number of alternations are accurately reproduced by Monte Carlo simulations and fitted by Gaussians. The effect of the number of base pairs on the characteristics of these distributions is also discussed, as well as the effect of the ratios of the numbers of AT and GC base pairs.

Weak nanoscale chaos and anomalous relaxation in DNA.

PubMed

Mazur, Alexey K

2017-06-01

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Think Pair Share: A Teaching Learning Strategy to Enhance Students' Critical Thinking

ERIC Educational Resources Information Center

Kaddoura, Mahmoud

2013-01-01

This study investigated the change in critical thinking (CT) skills of baccalaureate nursing students who were educated using a Think-Pair-Share (TPS) or an equivalent Non-Think-Pair-Share (Non-TPS) teaching method. Critical thinking has been an essential outcome of nursing students to prepare them to provide effective and safe quality care for…

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

Attention-related changes in correlated neuronal activity arise from normalization mechanisms

PubMed Central

Verhoef, Bram-Ernst; Maunsell, John H.R.

2017-01-01

Attention is believed to enhance perception by altering the correlations between pairs of neurons. How attention changes neuronal correlations is unknown. Using multi-electrodes in primate visual cortex, we measured spike-count correlations when single or multiple stimuli were presented, and stimuli were attended or unattended. When stimuli were unattended, adding a suppressive, non-preferred, stimulus beside a preferred stimulus increased spike-count correlations between pairs of similarly-tuned neurons, but decreased spike-count correlations between pairs of oppositely-tuned neurons. These changes are explained by a stochastic normalization model containing populations of oppositely-tuned, mutually-suppressive neurons. Importantly, this model also explains why attention decreased (attend preferred stimulus) or increased (attend non-preferred stimulus) correlations: as an indirect consequence of attention-related changes in the inputs to normalization mechanisms. Our findings link normalization mechanisms to correlated neuronal activity and attention, showing that normalization mechanisms shape response correlations and that these correlations change when attention biases normalization mechanisms. PMID:28553943

Spaceborne radar interferometry for coastal DEM construction

USGS Publications Warehouse

Hong, S.-H.; Lee, C.-W.; Won, J.-S.; Kwoun, Oh-Ig; Lu, Z.

2005-01-01

Topographic features in coastal regions including tidal flats change more significantly than landmass, and are characterized by extremely low slopes. High precision DEMs are required to monitor dynamic changes in coastal topography. It is difficult to obtain coherent interferometric SAR pairs especially over tidal flats mainly because of variation of tidal conditions. Here we focus on i) coherence of multi-pass ERS SAR interferometric pairs and ii) DEM construction from ERS-ENVISAT pairs. Coherences of multi-pass ERS interferograms were good enough to construct DEM under favorable tidal conditions. Coherence in sand dominant area was generally higher than that in muddy surface. The coarse grained coastal areas are favorable for multi-pass interferometry. Utilization of ERS-ENVISAT interferometric pairs is taken a growing interest. We carried out investigation using a cross-interferometric pair with a normal baseline of about 1.3 km, a 30 minutes temporal separation and the height sensitivity of about 6 meters. Preliminary results of ERS-ENVISAT interferometry were not successful due to baseline and unfavorable scattering conditions. ?? 2005 IEEE.

Layer-Based Approach for Image Pair Fusion.

PubMed

Son, Chang-Hwan; Zhang, Xiao-Ping

2016-04-20

Recently, image pairs, such as noisy and blurred images or infrared and noisy images, have been considered as a solution to provide high-quality photographs under low lighting conditions. In this paper, a new method for decomposing the image pairs into two layers, i.e., the base layer and the detail layer, is proposed for image pair fusion. In the case of infrared and noisy images, simple naive fusion leads to unsatisfactory results due to the discrepancies in brightness and image structures between the image pair. To address this problem, a local contrast-preserving conversion method is first proposed to create a new base layer of the infrared image, which can have visual appearance similar to another base layer such as the denoised noisy image. Then, a new way of designing three types of detail layers from the given noisy and infrared images is presented. To estimate the noise-free and unknown detail layer from the three designed detail layers, the optimization framework is modeled with residual-based sparsity and patch redundancy priors. To better suppress the noise, an iterative approach that updates the detail layer of the noisy image is adopted via a feedback loop. This proposed layer-based method can also be applied to fuse another noisy and blurred image pair. The experimental results show that the proposed method is effective for solving the image pair fusion problem.

Changes in beta-actin mRNA expression in remodeling canine myocardium.

PubMed

Carlyle, W C; Toher, C A; Vandervelde, J R; McDonald, K M; Homans, D C; Cohn, J N

1996-01-01

Beta-actin, a cytoskeletal protein important in the maintenance of cytoarchitecture, has long been thought to be expressed constitutively in myocardial tissue. As such, beta-actin mRNA has been used as a control gene in a wide range of experiments. However, we have uncovered consistent changes in beta-actin mRNA expression in canine myocardium remodeling as a result of insult to the left ventricle. The experimental canine models used were either DC shock damage to the left ventricle or volume overload resulting from severe mitral regurgitation. The remodeling process in both canine models is characterized by an increase in left ventricular mass. PCR amplification using primers designed to selectively amplify the 3' end and a portion of the 3' untranslated region of beta-actin mRNA resulted in the generation of a 297 base pair product predominant only in normal canine myocardium and a 472 base pair product that became increasingly prominent from 1 to 30 days after DC shock damage to the left ventricle and from 10 to 90 days after creation of mitral regurgitation. Northern analysis showed a three-fold increase in beta-actin mRNA after either DC shock or creation of mitral regurgitation. Western analysis revealed an early increase in beta-actin protein followed by an apparent decrease to below baseline levels. These observations suggest that changes in beta-actin mRNA expression accompany the structural alterations that occur in response to myocardial damage. Whether or not the changes in beta-actin mRNA expression play a role in mediating these structural alterations remains to be determined.

Temperature-induced Lifshitz transition in WTe 2

DOE PAGES

Wu, Yun; Jo, Na Hyun; Ochi, Masayuki; ...

2015-10-12

In this study, we use ultrahigh resolution, tunable, vacuum ultraviolet laser-based, angle-resolved photoemission spectroscopy (ARPES), temperature- and field-dependent resistivity, and thermoelectric power (TEP) measurements to study the electronic properties of WTe 2, a compound that manifests exceptionally large, temperature-dependent magnetoresistance. The Fermi surface consists of two pairs of electron and two pairs of hole pockets along the X–Γ–X direction. Using detailed ARPES temperature scans, we find a rare example of a temperature-induced Lifshitz transition at T≃160 K, associated with the complete disappearance of the hole pockets. Our electronic structure calculations show a clear and substantial shift of the chemical potentialmore » μ(T) due to the semimetal nature of this material driven by modest changes in temperature. This change of Fermi surface topology is also corroborated by the temperature dependence of the TEP that shows a change of slope at T≈175 K and a breakdown of Kohler’s rule in the 70–140 K range. Our results and the mechanisms driving the Lifshitz transition and transport anomalies are relevant to other systems, such as pnictides, 3D Dirac semimetals, and Weyl semimetals.« less

Repeated evaluative pairings and evaluative statements: How effectively do they shift implicit attitudes?

PubMed

Kurdi, Benedek; Banaji, Mahzarin R

2017-02-01

Six experiments, involving a total of 6,492 participants, were conducted to investigate the relative effectiveness of repeated evaluative pairings (REP; exposure to category members paired with pleasant or unpleasant images), evaluative statements (ES; verbally signaling upcoming pairings without actual exposure), and their combination (ES + REP) in shifting implicit social and nonsocial attitudes. Learning modality (REP, ES, and ES + REP) was varied between participants and implicit attitudes were assessed using an Implicit Association Test (IAT). Study 1 (N = 675) used fictitious social groups (NIFFs and LAAPs), Study 2 (N = 1,034) used novel social groups (humans with long vs. square faces), Study 3 (N = 1,072) used nonsocial stimuli (squares vs. rectangles), and Study 4 (N = 848) and Study 5 (N = 958) used known social groups (young vs. elderly; American vs. foreign). ES were more effective than REP and no less superior than ES + REP in producing implicit attitude change. Results were robust across social and nonsocial domains and for known and novel groups. Study 6 (N = 1,905) eliminated time on intervention, levels of construal, and expectancy effects as possible explanations for these findings. Associative theories of implicit evaluation posit that implicit attitudes should shift piecemeal over time; yet, in these experiments, one-shot language-based learning led to larger shifts in implicit attitude than exposure to stimulus pairings. Moreover, the redundancy observed in REP + ES suggests that attitude acquisition from repeated pairings and evaluative instructions may rely on shared mental representations. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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.

Galápagos hydroclimate of the Common Era from paired microalgal and mangrove biomarker 2H/1H values

NASA Astrophysics Data System (ADS)

Nelson, Daniel B.; Sachs, Julian P.

2016-03-01

Tropical maritime precipitation affects global atmospheric circulation, influencing storm tracks and the size and location of subtropical deserts. Paleoclimate evidence suggests centuries-long changes in rainfall in the tropical Pacific over the past 2,000 y, but these remain poorly characterized across most of the ocean where long, continuous proxy records capable of resolving decadal-to-centennial climate changes are still virtually nonexistent despite substantial efforts to develop them. Here we apply a new climate proxy based on paired hydrogen isotope ratios from microalgal and mangrove-derived sedimentary lipids in the Galápagos to reconstruct maritime precipitation changes during the Common Era. We show that increased rainfall during the Little Ice Age (LIA) (∼1400-1850 CE) was likely caused by a southward migration of the Intertropical Convergence Zone (ITCZ), and that this shift occurred later than previously recognized, coeval with dynamically linked precipitation changes in South America and the western tropical Pacific. Before the LIA, we show that drier conditions at the onset of the Medieval Warm Period (∼800-1300 CE) and wetter conditions ca. 2 ka were caused by changes in the El Niño/Southern Oscillation (ENSO). Collectively, the large natural variations in tropical rainfall we detect, each linked to a multicentury perturbation of either ENSO-like variability or the ITCZ, imply a high sensitivity of tropical Pacific rainfall to climate forcings.

Spatially Correlated Sparse MIMO Channel Path Delay Estimation in Scattering Environments Based on Signal Subspace Tracking

PubMed Central

Chargé, Pascal; Bazzi, Oussama; Ding, Yuehua

2018-01-01

A parametric scheme for spatially correlated sparse multiple-input multiple-output (MIMO) channel path delay estimation in scattering environments is presented in this paper. In MIMO outdoor communication scenarios, channel impulse responses (CIRs) of different transmit–receive antenna pairs are often supposed to be sparse due to a few significant scatterers, and share a common sparse pattern, such that path delays are assumed to be equal for every transmit–receive antenna pair. In some existing works, an exact common support condition is exploited, where the path delays are considered equal for every transmit–receive antenna pair, meanwhile ignoring the influence of scattering. A more realistic channel model is proposed in this paper, where due to scatterers in the environment, the received signals are modeled as clusters of multi-rays around a nominal or mean time delay at different antenna elements, resulting in a non-strictly exact common support phenomenon. A method for estimating the channel mean path delays is then derived based on the subspace approach, and the tracking of the effective dimension of the signal subspace that changes due to the wireless environment. The proposed method shows an improved channel mean path delays estimation performance in comparison with the conventional estimation methods. PMID:29734797

Spatially Correlated Sparse MIMO Channel Path Delay Estimation in Scattering Environments Based on Signal Subspace Tracking.

PubMed

Mohydeen, Ali; Chargé, Pascal; Wang, Yide; Bazzi, Oussama; Ding, Yuehua

2018-05-06

A parametric scheme for spatially correlated sparse multiple-input multiple-output (MIMO) channel path delay estimation in scattering environments is presented in this paper. In MIMO outdoor communication scenarios, channel impulse responses (CIRs) of different transmit⁻receive antenna pairs are often supposed to be sparse due to a few significant scatterers, and share a common sparse pattern, such that path delays are assumed to be equal for every transmit⁻receive antenna pair. In some existing works, an exact common support condition is exploited, where the path delays are considered equal for every transmit⁻receive antenna pair, meanwhile ignoring the influence of scattering. A more realistic channel model is proposed in this paper, where due to scatterers in the environment, the received signals are modeled as clusters of multi-rays around a nominal or mean time delay at different antenna elements, resulting in a non-strictly exact common support phenomenon. A method for estimating the channel mean path delays is then derived based on the subspace approach, and the tracking of the effective dimension of the signal subspace that changes due to the wireless environment. The proposed method shows an improved channel mean path delays estimation performance in comparison with the conventional estimation methods.

Evaluative conditioning: A brief computer-delivered intervention to reduce college student drinking.

PubMed

Tello, Nina; Bocage-Barthélémy, Yvana; Dandaba, Meira; Jaafari, Nematollah; Chatard, Armand

2018-07-01

Recent research suggests that a brief computer-delivered intervention based on evaluative conditioning (EC) can change the implicit evaluation of alcohol and reduce drinking behaviors among college students. We tested whether we could obtain similar findings in a high-powered preregistered study and whether hazardous drinking moderates these effects. Before the intervention, 122 French college students were screened for hazardous drinking using the Alcohol Use Disorder Identification Test (AUDIT). Implicit evaluation of alcohol was assessed before and immediately after the intervention using an Implicit Association Test (IAT). Drinking behavior was assessed before the intervention and approximately two weeks after using the TimeLine Follow Back (TLFB) method. The EC consisted of 120 trials of words (related to alcoholic beverages, soft drinks or neutral) paired with pictures (neutral, positive or negative). In the EC condition, alcohol-related words were systematically paired with negative pictures. In the control condition, alcohol-related words were systematically paired with neutral pictures. The EC did not change the implicit evaluation of alcohol, Cohen's d = 0.01, 95CI [-0.35, 0.35]. However, the EC reduced drinking behavior, Cohen's d = 0.37, 95CI [0.01, 0.72]. This effect was independent of hazardous drinking behavior, but it was especially pronounced among participants with the most positive implicit evaluation of alcohol before the intervention. This preregistered study suggests that evaluative conditioning can successfully reduce drinking behavior among college students by 31% (compared to 4% in the control condition) without causing an immediate change in the implicit evaluation of alcohol. Copyright © 2018 Elsevier Ltd. All rights reserved.

Are behaviors at one alternative in concurrent schedules independent of contingencies at the other alternative?

PubMed

MacDonall, James S

2017-09-01

Some have reported changing the schedule at one alternative of a concurrent schedule changed responding at the other alternative (Catania, 1969), which seems odd because no contingencies were changed there. When concurrent schedules are programmed using two schedules, one associated with each alternative that operate continuously, changing the schedule at one alternative also changes the switch schedule at the other alternative. Thus, changes in responding at the constant alternative could be due to the change in the switch schedule. To assess this possibility, six rats were exposed to a series of conditions that alternated between pairs of interval schedules at both alternatives and a pair of interval schedules at one, constant, alternative and a pair of extinction schedules at the other alternative. Comparing run lengths, visit durations and response rates at the constant alternative in the alternating conditions did not show consistent increases and decreases when a strict criterion for changes was used. Using a less stringent definition (any change in mean values) showed changes. The stay/switch analysis suggests it may be inaccurate to apply behavioral contrast to procedures that change from concurrent variable-interval variable-interval schedules to concurrent variable-interval extinction schedules because the contingencies in neither alternative are constant. © 2017 Society for the Experimental Analysis of Behavior.

Ecological relationships of breeding blue-winged teal to prairie potholes

USGS Publications Warehouse

Drewien, R.C.; Springer, P.F.

1969-01-01

Ecology of breeding blue-winged teal (Anas discors) was studied on the Waubay Study Area in Day County, South Dakota, in 1965 and 1966. Breeding pair use of the wetland habitat and importance of Type 1 ponds in the wetland complex were evaluated. Changes in breeding pair densities and wetland habitat conditions on the study area were compared for the 16-year period, 1950-66.Blue-winged teal pair densities of 30.7 and 33.0 per square mile in 1965 and 1966, respectively, were above the 16-year average from 1950 to 1966 and near the maximum for this period. Blue-winged teal comprised 46.7 per cent of the waterfowl breeding population in 1965 and 51.7 per cent in 1966. Number of water areas per square mile through mid-spring 1965 was comparable to the average for the 16-year period, whereas during late spring 1965 and throughout the 1966 spring breeding seasons the number of water areas increased to near optimum conditions.Annual breeding-pair densities from 1950 to 1966 appeared to be largely influenced by water conditions, and pair-density fluctuations resulted from changes in number of wet ponds from late April through mid-May. Variations in water conditions after this period did not appear to have as great an effect on numbers of breeding teal.Use of wetland habitat by pairs changed throughout the spring breeding seasons. During the post-arrival period, teal congregated on larger wetlands. With onset of egg-laying, pairs dispersed into ponds throughout the wetland complex to establish breeding home ranges. Other factors that influenced changes in habitat use included: 1) pond type and size, 2) breeding cycle phenology, 3) availability of wet ponds, and 4) land use. Number of blue-winged teal pairs per unit area of water was highest in 1965 and 1966 on Type 1B ponds, followed in decreasing order by Types 3, 1A, and 4 and 5. Greater use of Type 1B ponds was probably related to larger ratio of edge or shore line to unit area of water. Interspersion of many small wetlands throughout the breeding habitat provided for maximum pair dispersal during egg-laying and early incubation stages of the reproductive cycle.

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription

PubMed Central

Liu, Ning; Tian, Ru; Loeb, Daniel D.

2003-01-01

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis. PMID:12578983

A health promotion program at a Japanese newspaper undergoing restructuring.

PubMed

Ariyoshi, Hiromi; Suzaki, Yoshika; Takayama, Naoko; Wakeshima, Ruriko; Ishitake, Tatsuya

2010-09-01

Occupational health activities based on a health promotion philosophy and focused on primary and secondary prevention were introduced at a Japanese newspaper company where restructuring had occurred. Japanese metabolic syndrome diagnostic standards were used to determine changes in certain lifestyle disease risk factors over 10 years. The amount of change from 1998 to 2007 was determined, and two groups (i.e., 1998 and 2007) were compared using paired t-tests. Results suggested that the occupational health activities focused on primary prevention had been effective. The authors concluded that, in situations where industrial change and corporate restructuring are occurring, occupational health activities based on a health promotion philosophy and focused on primary and secondary prevention are more effective than diagnostic activities and other types of health management focused on tertiary prevention. Copyright 2010, SLACK Incorporated.

Population size and trends for nesting ospreys in northwestern Mexico: Region-wide surveys, 1977, 1992/1993 and 2006

USGS Publications Warehouse

Henny, Charles J.; Anderson, Daniel W.; Vera, Aradit Castellanos; Carton, Jean-Luc E.

2007-01-01

We used a double-sampling technique (air plus ground survey) in 2006, with partial double coverage, to estimate the present size of the osprey (Pandion haliaetus) nesting population in northwestern Mexico. With the exception of Natividad, Cedros, and San Benito Islands along the Pacific Coast of Baja California, all three excluded from our coverage in 2006 due to fog, this survey was a repeat of previous surveys conducted by us with the same protocol in 1977 and 1992/1993 (Baja California surveyed in 1992, Sonora and Sinaloa 1993), allowing for estimates of regional population trends. Population estimates at the 'time of aerial survey' include those nesting, but missed from the air. The population estimate for our coverage area in 2006 was 1,343 nesting pairs, or an 81% increase since 1977, but only a 3% increase since 1992/1993. The population on the Gulf side of Baja California generally remained stable during the three surveys (255, 236 and 252 pairs, respectively). The overall Midriff Islands population remained similar from 1992/1993 (308 pairs) to 2006 (289 pairs), but with notable population changes on the largest two islands (Isla Angel de la Guarda: 45 to 105 pairs [+ 60 pairs]; Isla Tiburon: 164 to 109 pairs [- 55 pairs, or -34%]). The estimated osprey population on the Sonora mainland decreased in a manner similar to adjacent Isla Tiburon, i.e., by 26%, from 214 pairs in 1993 to 158 pairs in 2006. In contrast, the population in Sinaloa, which had increased by 150% between 1977 and 1993, grew again by 58% between 1993 and 2006, from 180 to 285 pairs. Our survey confirmed previously described patterns of rapid population changes at a local level, coupled with apparent shifts in spatial distribution. The large ground nesting population that until recently nested on two islands in San Ignacio Lagoon was no longer present on the islands in 2006, but an equivalent number of pairs were found to the north and south of the lagoon, nesting in small towns and along adjoining power-lines, with no overall change in population size for that general area (198 pairs in 1992; 199 in 2006). Use of artificial nesting structures was 4.3% in 1977 and 6.2% in 1992/1993, but jumped to 26.4% in 2006. Use of power poles poses a risk of electrocution to ospreys as well as causes power outages and fires; modification of power poles to safely accommodate osprey nests has been successful in many countries.

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

Wahl, Daniel E.; Yocky, David A.; Jakowatz, Jr., Charles V.

In previous research, two-pass repeat-geometry synthetic aperture radar (SAR) coherent change detection (CCD) predominantly utilized the sample degree of coherence as a measure of the temporal change occurring between two complex-valued image collects. Previous coherence-based CCD approaches tend to show temporal change when there is none in areas of the image that have a low clutter-to-noise power ratio. Instead of employing the sample coherence magnitude as a change metric, in this paper, we derive a new maximum-likelihood (ML) temporal change estimate—the complex reflectance change detection (CRCD) metric to be used for SAR coherent temporal change detection. The new CRCD estimatormore » is a surprisingly simple expression, easy to implement, and optimal in the ML sense. As a result, this new estimate produces improved results in the coherent pair collects that we have tested.« less

Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes.

PubMed

Patel, D J; Canuel, L L

1977-07-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex.

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

PubMed Central

Patel, Dinshaw J.; Canuel, Lita L.

1977-01-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. PMID:268613

Base drive circuit

DOEpatents

Lange, A.C.

1995-04-04

An improved base drive circuit having a level shifter for providing bistable input signals to a pair of non-linear delays. The non-linear delays provide gate control to a corresponding pair of field effect transistors through a corresponding pair of buffer components. The non-linear delays provide delayed turn-on for each of the field effect transistors while an associated pair of transistors shunt the non-linear delays during turn-off of the associated field effect transistor. 2 figures.

An Intelligent Model for Pairs Trading Using Genetic Algorithms.

PubMed

Huang, Chien-Feng; Hsu, Chi-Jen; Chen, Chi-Chung; Chang, Bao Rong; Li, Chen-An

2015-01-01

Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

An Intelligent Model for Pairs Trading Using Genetic Algorithms

PubMed Central

Hsu, Chi-Jen; Chen, Chi-Chung; Li, Chen-An

2015-01-01

Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice. PMID:26339236

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.

Light-dependent magnetoreception: orientation behaviour of migratory birds under dim red light.

PubMed

Wiltschko, Roswitha; Munro, Ursula; Ford, Hugh; Stapput, Katrin; Wiltschko, Wolfgang

2008-10-01

Magnetic compass orientation in migratory birds has been shown to be based on radical pair processes and to require light from the short wavelength part of the spectrum up to 565 nm Green. Under dim red light of 645 nm wavelength and 1 mW m(-2) intensity, Australian silvereyes and European robins showed a westerly tendency that did not change between spring and autumn, identifying it as a 'fixed direction' response. A thorough analysis revealed that this orientation did not involve the inclination compass, but was a response based on the polarity of the magnetic field. Furthermore, in contrast to the orientation under short-wavelength light, it could be disrupted by local anaesthesia of the upper beak where iron-containing receptors are located, indicating that it is controlled by these receptors. The similarity of the response under dim red light to the response in total darkness suggests that the two responses may be identical. These findings indicate that the observed 'fixed direction' response under dim red light is fundamentally different from the normal compass orientation, which is based on radical pair processes.

Learning and memory associated with aggression in Drosophila melanogaster

PubMed Central

Yurkovic, Alexandra; Wang, Oulu; Basu, Alo C.; Kravitz, Edward A.

2006-01-01

Male Drosophila melanogaster (Canton-S strain) exhibit aggression in competition for resources, to defend territory, and for access to mates. In the study reported here, we asked: (i) how long flies fight; (ii) whether flies adopt distinct winning and losing strategies as hierarchical relationships are established; (iii) whether flies exhibit experience-dependent changes in fighting strategies in later fights; and (iv) whether flies fight differently in second fights against familiar or unfamiliar opponents. The results showed that flies fought for up to 5 h. As hierarchical relationships were established, behavioral strategies changed: winners progressively lunged more and retreated less, whereas losers progressively lunged less and retreated more. Encounters between flies were frequent during the first 10 min of pairing and then dropped significantly. To ask whether flies remembered previous fights, they were re-paired with familiar or unfamiliar opponents after 30 min of separation. In familiar pairings, there were fewer encounters during the first 10 min of fighting than in unfamiliar pairings, and former losers fought differently against familiar winners than unfamiliar winners. Former losers lost or no decision was reached in all second fights in pairings with familiar or unfamiliar winners or with naive flies. Winner/winner, loser/loser, and naive/naive pairings revealed that losers used low-intensity strategies in later fights and were unlikely to form new hierarchical relationships, compared with winners or socially naive flies. These results strongly support the idea that learning and memory accompany the changes in social status that result from fruit fly fights. PMID:17088536

Functional cross‐hemispheric shift between object‐place paired associate memory and spatial memory in the human hippocampus

PubMed Central

Lee, Choong‐Hee; Ryu, Jungwon; Lee, Sang‐Hun; Kim, Hakjin

2016-01-01

ABSTRACT The hippocampus plays critical roles in both object‐based event memory and spatial navigation, but it is largely unknown whether the left and right hippocampi play functionally equivalent roles in these cognitive domains. To examine the hemispheric symmetry of human hippocampal functions, we used an fMRI scanner to measure BOLD activity while subjects performed tasks requiring both object‐based event memory and spatial navigation in a virtual environment. Specifically, the subjects were required to form object‐place paired associate memory after visiting four buildings containing discrete objects in a virtual plus maze. The four buildings were visually identical, and the subjects used distal visual cues (i.e., scenes) to differentiate the buildings. During testing, the subjects were required to identify one of the buildings when cued with a previously associated object, and when shifted to a random place, the subject was expected to navigate to the previously chosen building. We observed that the BOLD activity foci changed from the left hippocampus to the right hippocampus as task demand changed from identifying a previously seen object (object‐cueing period) to searching for its paired‐associate place (object‐cued place recognition period). Furthermore, the efficient retrieval of object‐place paired associate memory (object‐cued place recognition period) was correlated with the BOLD response of the left hippocampus, whereas the efficient retrieval of relatively pure spatial memory (spatial memory period) was correlated with the right hippocampal BOLD response. These findings suggest that the left and right hippocampi in humans might process qualitatively different information for remembering episodic events in space. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc. PMID:27009679

Asynchronous inputs alter excitability, spike timing, and topography in primary auditory cortex

PubMed Central

Pandya, Pritesh K.; Moucha, Raluca; Engineer, Navzer D.; Rathbun, Daniel L.; Vazquez, Jessica; Kilgard, Michael P.

2010-01-01

Correlation-based synaptic plasticity provides a potential cellular mechanism for learning and memory. Studies in the visual and somatosensory systems have shown that behavioral and surgical manipulation of sensory inputs leads to changes in cortical organization that are consistent with the operation of these learning rules. In this study, we examine how the organization of primary auditory cortex (A1) is altered by tones designed to decrease the average input correlation across the frequency map. After one month of separately pairing nucleus basalis stimulation with 2 and 14 kHz tones, a greater proportion of A1 neurons responded to frequencies below 2 kHz and above 14 kHz. Despite the expanded representation of these tones, cortical excitability was specifically reduced in the high and low frequency regions of A1, as evidenced by increased neural thresholds and decreased response strength. In contrast, in the frequency region between the two paired tones, driven rates were unaffected and spontaneous firing rate was increased. Neural response latencies were increased across the frequency map when nucleus basalis stimulation was associated with asynchronous activation of the high and low frequency regions of A1. This set of changes did not occur when pulsed noise bursts were paired with nucleus basalis stimulation. These results are consistent with earlier observations that sensory input statistics can shape cortical map organization and spike timing. PMID:15855025

Karyotype differentiation of four Cestrum species (Solanaceae) revealed by fluorescent chromosome banding and FISH

PubMed Central

2009-01-01

The karyotypes of four South American species of Cestrum (C. capsulare,C. corymbosum,C. laevigatum and C. megalophylum) were studied using conventional staining, C-CMA/DAPI chromosome banding and FISH with 45S and 5S rDNA probes. The karyotypes showed a chromosome number of 2n = 2x = 16, with metacentric chromosomes, except for the eighth submeta- to acrocentric pair. Several types of heterochromatin were detected, which varied in size, number, distribution and base composition. The C-CMA+ bands and 45S rDNA were located predominantly in terminal regions. The C-CMA + /DAPI + bands appeared in interstitial and terminal regions, and the C-DAPI + bands were found in all chromosome regions. The 5S rDNA sites were observed on the long arm of pair 8 in all species except C. capsulare, where they were found in the paracentromeric region of the long arm of pair 4. The differences in band patterns among the species studied here, along with data from other nine species reported in the literature, suggest that the bands are dispersed in an equilocal and non-equilocal manner and that structural rearrangements can be responsible for internal karyotype diversification. However, it is important to point out that the structural changes involving repetitive segments did not culminate in substantial changes in the general karyotype structure concerning chromosome size and morphology. PMID:21637687

Progression in disability and regional grey matter atrophy in relapsing-remitting multiple sclerosis.

PubMed

Hofstetter, Louis; Naegelin, Yvonne; Filli, Lukas; Kuster, Pascal; Traud, Stefan; Smieskova, Renata; Mueller-Lenke, Nicole; Kappos, Ludwig; Gass, Achim; Sprenger, Till; Penner, Iris-Katharina; Nichols, Thomas E; Vrenken, Hugo; Barkhof, Frederik; Polman, Chris; Radue, Ernst-Wilhelm; Borgwardt, Stefan J; Bendfeldt, Kerstin

2014-02-01

In multiple sclerosis (MS) regional grey matter (GM) atrophy has been associated with disability progression. The aim of this study was to compare regional GM volume changes in relapsing-remitting MS (RRMS) patients with progressive and stable disability, using voxel-based morphometry (VBM). We acquired baseline and 1-year follow-up 3-dimensional (3D) T1-weighted magnetic resonance imaging (MRI) data of RRMS patients, using two 1.5-Tesla scanners. Patients were matched pair-wise with respect to age, gender, disease duration, medication, scanner and baseline Expanded Disability Status Scale (EDSS) into 13 pairs, with either progressive EDSS (≥ 1 point change y(-1)) or stable EDSS, as well as into 29 pairs with either progressive Multiple Sclerosis Functional Composite (MSFC) at ≥ 0.25% decrease in y(-1) in any component, or stable MSFC. We analysed longitudinal regional differences in GM volumes in the progressive and stable EDSS and MSFC groups, respectively, using VBM. Significant GM volume reductions occurred in the right precuneus, in the progressive EDSS group. Differential between-group effects occurred in the right precuneus and in the postcentral gyrus. Further longitudinal GM volume reductions occurred in the right orbicular gyrus, in the progressive MSFC group, but no between-group differences were observed (non-stationary cluster-wise inference, all P(corrected) < 0.05). These results suggested a direct association of disability progression and regional GM atrophy in RRMS.

The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase

PubMed Central

2004-01-01

With the goal of constructing a genetic alphabet consisting of a set of three base pairs, the fidelity of replication of the three base pairs TH (5-methyl-2-pyrimidinone)/HS (6-thiopurine; thiohypoxanthine), C/H (hypoxanthine) and T/A was evaluated using T7 DNA polymerase, a polymerase with a strong 3′→5′ exonuclease activity. An evaluation of the suitability of a new base pair for replication should include both the contribution of the fidelity of a polymerase activity and the contribution of proofreading by a 3′→5′ exonuclease activity. Using a steady-state kinetics method that included the contribution of the 3′→5′ exonuclease activity, the fidelity of replication was determined. The method determined the ratio of the apparent rate constant for the addition of a deoxynucleotide to the primer across from a template base by the polymerase activity and the rate constant for removal of the added deoxynucleotide from the primer by the 3′→5′ exonuclease activity. This ratio was designated the eni (efficiency of net incorporation). The eni of the base pair C/H was equal to or greater than the eni of T/A. The eni of the base pair TH/HS was 0.1 times that of A/T for TH in the template and 0.01 times that of A/T for HS in the template. The ratio of the eni of a mismatched deoxynucleotide to the eni of a matched deoxynucleotide was a measure of the error frequency. The error frequencies were as follows: thymine or TH opposite a template hypoxanthine, 2×10−6; HS opposite a template cytosine, <3×10−4. The remaining 24 mismatched combinations of bases gave no detectable net incorporation. Two mismatches, hypoxanthine opposite a template thymine or a template TH, showed trace incorporation in the presence of a standard dNTP complementary to the next template base. T7 DNA polymerase extended the primer beyond each of the matched base pairs of the set. The level of fidelity of replication of the three base pairs with T7 DNA polymerase suggests that they are adequate for a three-base-pair alphabet for DNA replication. PMID:15078225

A Pharmacovigilance Signaling System Based on FDA Regulatory Action and Post-Marketing Adverse Event Reports.

PubMed

Hoffman, Keith B; Dimbil, Mo; Tatonetti, Nicholas P; Kyle, Robert F

2016-06-01

Many serious drug adverse events (AEs) only manifest well after regulatory approval. Therefore, the development of signaling methods to use with post-approval AE databases appears vital to comprehensively assess real-world drug safety. However, with millions of potential drug-AE pairs to analyze, the issue of focus is daunting. Our objective was to develop a signaling platform that focuses on AEs with historically demonstrated regulatory interest and to analyze such AEs with a disproportional reporting method that offers broad signal detection and acceptable false-positive rates. We analyzed over 1500 US FDA regulatory actions (safety communications and drug label changes) from 2008 to 2015 to construct a list of eligible signal AEs. The FDA Adverse Event Reporting System (FAERS) was used to evaluate disproportional reporting rates, constrained by minimum case counts and confidence interval limits, of these selected AEs for 109 training drugs. This step led to 45 AEs that appeared to have a low likelihood of being added to a label by FDA, so they were removed from the signal eligible list. We measured disproportional reporting for the final group of eligible AEs on a test group of 29 drugs that were not used in either the eligible list construction or the training steps. In a group of 29 test drugs, our model reduced the number of potential drug-AE signals from 41,834 to 97 and predicted 73 % of individual drug label changes. The model also predicted at least one AE-drug pair label change in 66 % of all the label changes for the test drugs. By concentrating on AE types with already demonstrated interest to FDA, we constructed a signaling system that provided focus regarding drug-AE pairs and suitable accuracy with regard to the issuance of FDA labeling changes. We suggest that focus on historical regulatory actions may increase the utility of pharmacovigilance signaling systems.

Pairing States of Spin-3/2 Fermions: Symmetry-Enforced Topological Gap Functions

NASA Astrophysics Data System (ADS)

Venderbos, Jörn W. F.; Savary, Lucile; Ruhman, Jonathan; Lee, Patrick A.; Fu, Liang

2018-01-01

We study the topological properties of superconductors with paired j =3/2 quasiparticles. Higher spin Fermi surfaces can arise, for instance, in strongly spin-orbit coupled band-inverted semimetals. Examples include the Bi-based half-Heusler materials, which have recently been established as low-temperature and low-carrier density superconductors. Motivated by this experimental observation, we obtain a comprehensive symmetry-based classification of topological pairing states in systems with higher angular momentum Cooper pairing. Our study consists of two main parts. First, we develop the phenomenological theory of multicomponent (i.e., higher angular momentum) pairing by classifying the stationary points of the free energy within a Ginzburg-Landau framework. Based on the symmetry classification of stationary pairing states, we then derive the symmetry-imposed constraints on their gap structures. We find that, depending on the symmetry quantum numbers of the Cooper pairs, different types of topological pairing states can occur: fully gapped topological superconductors in class DIII, Dirac superconductors, and superconductors hosting Majorana fermions. Notably, we find a series of nematic fully gapped topological superconductors, as well as double- and triple-Dirac superconductors, with quadratic and cubic dispersion, respectively. Our approach, applied here to the case of j =3/2 Cooper pairing, is rooted in the symmetry properties of pairing states, and can therefore also be applied to other systems with higher angular momentum and high-spin pairing. We conclude by relating our results to experimentally accessible signatures in thermodynamic and dynamic probes.

A new maximum-likelihood change estimator for two-pass SAR coherent change detection

DOE PAGES

Wahl, Daniel E.; Yocky, David A.; Jakowatz, Jr., Charles V.; ...

2016-01-11

In previous research, two-pass repeat-geometry synthetic aperture radar (SAR) coherent change detection (CCD) predominantly utilized the sample degree of coherence as a measure of the temporal change occurring between two complex-valued image collects. Previous coherence-based CCD approaches tend to show temporal change when there is none in areas of the image that have a low clutter-to-noise power ratio. Instead of employing the sample coherence magnitude as a change metric, in this paper, we derive a new maximum-likelihood (ML) temporal change estimate—the complex reflectance change detection (CRCD) metric to be used for SAR coherent temporal change detection. The new CRCD estimatormore » is a surprisingly simple expression, easy to implement, and optimal in the ML sense. As a result, this new estimate produces improved results in the coherent pair collects that we have tested.« less

FUNDAMENTAL AREAS OF PHENOMENOLOGY (INCLUDING APPLICATIONS): Teleportation of Entangled States through Divorce of Entangled Pair Mediated by a Weak Coherent Field in a High-Q Cavity

NASA Astrophysics Data System (ADS)

Cardoso B., W.; Almeida G. de, N.

2008-07-01

We propose a scheme to partially teleport an unknown entangled atomic state. A high-Q cavity, supporting one mode of a weak coherent state, is needed to accomplish this process. By partial teleportation we mean that teleportation will occur by changing one of the partners of the entangled state to be teleported. The entangled state to be teleported is composed by one pair of particles, we called this surprising characteristic of maintaining the entanglement, even when one of the particle of the entangled pair being teleported is changed, of divorce of entangled states.

Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

NASA Technical Reports Server (NTRS)

Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

2011-01-01

We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

Using social-emotional and character development to improve academic outcomes: a matched-pair, cluster-randomized controlled trial in low-income, urban schools

PubMed Central

Lewis, Kendra M.; DuBois, David L.; Acock, Alan; Vuchinich, Samuel; Silverthorn, Naida; Snyder, Frank J.; Day, Joseph; Ji, Peter; Flay, Brian R.

2013-01-01

BACKGROUND School-based social-emotional and character development (SECD) programs can influence not only SECD, but also academic-related outcomes. This study evaluated the impact of one SECD program, Positive Action (PA), on educational outcomes among low-income, urban youth. METHODS The longitudinal study used a matched-pair, cluster-randomized controlled design. Student-reported disaffection with learning and academic grades, and teacher ratings of academic ability and motivation were assessed for a cohort followed from grades 3 to 8. Aggregate school records were used to assess standardized test performance (for entire school, cohort, and demographic subgroups) and absenteeism (entire school). Multilevel growth-curve analyses tested program effects. RESULTS PA significantly improved growth in academic motivation and mitigated disaffection with learning. There was a positive impact of PA on absenteeism and marginally significant impact on math performance of all students. There were favorable program effects on reading for African American boys and cohort students transitioning between grades 7 and 8, and on math for girls and low-income students. CONCLUSIONS A school-based SECD program was found to influence academic outcomes among students living in low-income, urban communities. Future research should examine mechanisms by which changes in SECD influence changes in academic outcomes. PMID:24138347

Using social-emotional and character development to improve academic outcomes: a matched-pair, cluster-randomized controlled trial in low-income, urban schools.

PubMed

Bavarian, Niloofar; Lewis, Kendra M; Dubois, David L; Acock, Alan; Vuchinich, Samuel; Silverthorn, Naida; Snyder, Frank J; Day, Joseph; Ji, Peter; Flay, Brian R

2013-11-01

School-based social-emotional and character development (SECD) programs can influence not only SECD but also academic-related outcomes. This study evaluated the impact of one SECD program, Positive Action (PA), on educational outcomes among low-income, urban youth. The longitudinal study used a matched-pair, cluster-randomized controlled design. Student-reported disaffection with learning and academic grades, and teacher ratings of academic ability and motivation were assessed for a cohort followed from grades 3 to 8. Aggregate school records were used to assess standardized test performance (for entire school, cohort, and demographic subgroups) and absenteeism (entire school). Multilevel growth-curve analyses tested program effects. PA significantly improved growth in academic motivation and mitigated disaffection with learning. There was a positive impact of PA on absenteeism and marginally significant impact on math performance of all students. There were favorable program effects on reading for African American boys and cohort students transitioning between grades 7 and 8, and on math for girls and low-income students. A school-based SECD program was found to influence academic outcomes among students living in low-income, urban communities. Future research should examine mechanisms by which changes in SECD influence changes in academic outcomes. © 2013, American School Health Association.

Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides.

PubMed

Lacy, Eilyn R; Nguyen, Binh; Le, Minh; Cox, Kari K; OHare, Caroline; Hartley, John A; Lee, Moses; Wilson, W David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.

Energetic basis for selective recognition of T·G mismatched base pairs in DNA by imidazole-rich polyamides

PubMed Central

Lacy, Eilyn R.; Nguyen, Binh; Le, Minh; Cox, Kari K.; O'Hare, Caroline; Hartley, John A.; Lee, Moses; Wilson, W. David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T·G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T·G–polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T·G mismatch containing DNA hairpin duplex and a similar DNA with only Watson–Crick base pairs. Large negative binding enthalpies for all of the polyamide–DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T·G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T·G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T·G mismatch sites. PMID:15064359

How Adolescents with Autism Spectrum Disorder (ASD) Spontaneously Attend to Real-World Scenes: Use of a Change Blindness Paradigm

ERIC Educational Resources Information Center

Hochhauser, Michal; Aran, Adi; Grynszpan, Ouriel

2018-01-01

Visual attention of adolescents with autism spectrum disorder (ASD) was assessed using a change blindness paradigm. Twenty-five adolescents with ASD aged 12-18 years and 25 matched typically developing (TD) adolescents viewed 36 pairs of digitized real-world images. Each pair of images was displayed in a "flicker paradigm" whereby a…

N-H Stretching Excitations in Adenosine-Thymidine Base Pairs in Solution: Base Pair Geometries, Infrared Line Shapes and Ultrafast Vibrational Dynamics

PubMed Central

Greve, Christian; Preketes, Nicholas K.; Fidder, Henk; Costard, Rene; Koeppe, Benjamin; Heisler, Ismael A.; Mukamel, Shaul; Temps, Friedrich; Nibbering, Erik T. J.; Elsaesser, Thomas

2013-01-01

We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen configurations with similar probability. Steady-state concentration- and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH2 bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes. PMID:23234439

Long-term population dynamics of a managed burrowing owl colony

USGS Publications Warehouse

Barclay, John H.; Korfanta, Nicole M.; Kauffman, Matthew J.

2011-01-01

We analyzed the population dynamics of a burrowing owl (Athene cunicularia) colony at Mineta San Jose International Airport in San Jose, California, USA from 1990-2007. This colony was managed by using artificial burrows to reduce the occurrence of nesting owls along runways and within major airport improvement projects during the study period. We estimated annual reproduction in natural and artificial burrows and age-specific survival rates with mark-recapture techniques, and we estimated the relative contribution of these vital rates to population dynamics using a life table response experiment. The breeding colony showed 2 distinct periods of change: high population growth from 7 nesting pairs in 1991 to 40 pairs in 2002 and population decline to 17 pairs in 2007. Reproduction was highly variable: annual nesting success (pairs that raised =1 young) averaged 79% and ranged from 36% to 100%, whereas fecundity averaged 3.36 juveniles/pair and ranged from 1.43 juveniles/pair to 4.54 juveniles/pair. We estimated annual adult survival at 0.710 during the period of colony increase from 1996 to 2001 and 0.465 during decline from 2002 to 2007, but there was no change in annual survival of juveniles between the 2 time periods. Long-term population growth rate (lambda) estimated from average vital rates was lambdaa=1.072 with lambdai=1.288 during colony increase and lambdad=0.921 (DELTA lambda=0.368) during decline. A life table response experiment showed that change in adult survival rate during increasing and declining phases explained more than twice the variation in growth rate than other vital rates. Our findings suggest that management and conservation of declining burrowing owl populations should address factors that influence adult survival.

Simultaneous master-slave Omega pairs. [navigation system featuring low cost receiver

NASA Technical Reports Server (NTRS)

Burhans, R. W.

1974-01-01

Master-slave sequence ordering of the Omega system is suggested as a method of improving the pair geometry for low-cost receiver user benefit. The sequence change will not affect present sophisticated processor users other than require new labels for some pair combinations, but may require worldwide transmitter operators to slightly alter their long-range synchronizing techniques.

Think Pair Share: A Teaching Learning Strategy to Enhance Students' Critical Thinking

ERIC Educational Resources Information Center

Kaddoura, Mahmoud

2013-01-01

This study investigated the change in critical thinking (CT) skills of baccalaureate nursing students who were educated using a Think-Pair-Share (TPS) or an equivalent Non-Think-Pair-Share (Non-TPS) teaching method. Critical thinking has been an essential outcome of nursing students to prepare them to provide effective and safe quality care for…

Longitudinal Changes in Intellectual Development in Children with Fragile X Syndrome

ERIC Educational Resources Information Center

Hall, Scott S.; Burns, David D.; Lightbody, Amy A.; Reiss, Allan L.

2008-01-01

Structural equation modeling (SEM) was used to examine the development of intellectual functioning in 145 school-age pairs of siblings. Each pair included one child with Fragile X syndrome (FXS) and one unaffected sibling. All pairs of children were evaluated on the Wechsler Intelligence Scale for Children-Third Edition (WISC-III) at time 1 and 80…

Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer.

PubMed

Zhou, Xionghui; Liu, Juan

2014-01-01

Although many methods have been proposed to reconstruct gene regulatory network, most of them, when applied in the sample-based data, can not reveal the gene regulatory relations underlying the phenotypic change (e.g. normal versus cancer). In this paper, we adopt phenotype as a variable when constructing the gene regulatory network, while former researches either neglected it or only used it to select the differentially expressed genes as the inputs to construct the gene regulatory network. To be specific, we integrate phenotype information with gene expression data to identify the gene dependency pairs by using the method of conditional mutual information. A gene dependency pair (A,B) means that the influence of gene A on the phenotype depends on gene B. All identified gene dependency pairs constitute a directed network underlying the phenotype, namely gene dependency network. By this way, we have constructed gene dependency network of breast cancer from gene expression data along with two different phenotype states (metastasis and non-metastasis). Moreover, we have found the network scale free, indicating that its hub genes with high out-degrees may play critical roles in the network. After functional investigation, these hub genes are found to be biologically significant and specially related to breast cancer, which suggests that our gene dependency network is meaningful. The validity has also been justified by literature investigation. From the network, we have selected 43 discriminative hubs as signature to build the classification model for distinguishing the distant metastasis risks of breast cancer patients, and the result outperforms those classification models with published signatures. In conclusion, we have proposed a promising way to construct the gene regulatory network by using sample-based data, which has been shown to be effective and accurate in uncovering the hidden mechanism of the biological process and identifying the gene signature for phenotypic change.

Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase

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

Wang, Lan; Chakravarthy, Srinivas; Verdine, Gregory L.

The highly mutagenic A:8-oxoguanine (oxoG) base pair is generated mainly by misreplication of the C:oxoG base pair, the oxidation product of the C:G base pair. The A:oxoG base pair is particularly insidious because neither base in it carries faithful information to direct the repair of the other. The bacterial MutY (MUTYH in humans) adenine DNA glycosylase is able to initiate the repair of A:oxoG by selectively cleaving the A base from the A:oxoG base pair. The difference between faithful repair and wreaking mutagenic havoc on the genome lies in the accurate discrimination between two structurally similar base pairs: A:oxoG andmore » A:T. Here we present two crystal structures of the MutY N-terminal domain in complex with either undamaged DNA or DNA containing an intrahelical lesion. These structures have captured for the first time a DNA glycosylase scanning the genome for a damaged base in the very first stage of lesion recognition and the base extrusion pathway. The mode of interaction observed here has suggested a common lesion-scanning mechanism across the entire helix-hairpin-helix superfamily to which MutY belongs. In addition, small angle X-ray scattering studies together with accompanying biochemical assays have suggested a possible role played by the C-terminal oxoG-recognition domain of MutY in lesion scanning.« less

Social Competition in Rats: Cell Proliferation and Behavior

PubMed Central

Hoshaw, Brian A.; Evans, Jennifer C.; Mueller, Bridget; Valentino, Rita J.; Lucki, Irwin

2007-01-01

Behavioral and physiological changes were studied following prolonged exposure to social competition in pairs of non food-deprived rats competing daily for a limited supply of graham cracker crumbs. Stable dominant-subordinate relationships developed in most pairs, as measured by feeding time, which were maintained over a 5–6-week study period. In other behavioral tests, subordinates demonstrated a decreased latency to immobility in the forced swim test compared with dominants, but no difference in locomotor activity. Subordinates had increased bladder size, decreased adrenal gland size, and a 35% reduction of hippocampus cell proliferation compared with the dominant member. Therefore, prolonged social competition, based on restricted access to palatable substances, produced hierarchies among individuals that were associated with differences in behavior, physiology and hippocampal cell proliferation. PMID:17045347

Capacitive proximity sensor

DOEpatents

Kronberg, J.W.

1994-05-31

A proximity sensor based on a closed field circuit is disclosed. The circuit comprises a ring oscillator using a symmetrical array of plates that creates an oscillating displacement current. The displacement current varies as a function of the proximity of objects to the plate array. Preferably the plates are in the form of a group of three pair of symmetric plates having a common center, arranged in a hexagonal pattern with opposing plates linked as a pair. The sensor produces logic level pulses suitable for interfacing with a computer or process controller. The proximity sensor can be incorporated into a load cell, a differential pressure gauge, or a device for measuring the consistency of a characteristic of a material where a variation in the consistency causes the dielectric constant of the material to change. 14 figs.

Bioassays Based on Molecular Nanomechanics

DOE PAGES

Majumdar, Arun

2002-01-01

Recent experiments have shown that when specific biomolecular interactions are confined to one surface of a microcantilever beam, changes in intermolecular nanomechanical forces provide sufficient differential torque to bend the cantilever beam. This has been used to detect single base pair mismatches during DNA hybridization, as well as prostate specific antigen (PSA) at concentrations and conditions that are clinically relevant for prostate cancer diagnosis. Since cantilever motion originates from free energy change induced by specific biomolecular binding, this technique is now offering a common platform for label-free quantitative analysis of protein-protein binding, DNA hybridization DNA-protein interactions, and in general receptor-ligandmore » interactions. Current work is focused on developing “universal microarrays” of microcantilever beams for high-throughput multiplexed bioassays.« less

Influence of seismic anisotropy on the cross correlation tensor: numerical investigations

NASA Astrophysics Data System (ADS)

Saade, M.; Montagner, J. P.; Roux, P.; Cupillard, P.; Durand, S.; Brenguier, F.

2015-05-01

Temporal changes in seismic anisotropy can be interpreted as variations in the orientation of cracks in seismogenic zones, and thus as variations in the stress field. Such temporal changes have been observed in seismogenic zones before and after earthquakes, although they are still not well understood. In this study, we investigate the azimuthal polarization of surface waves in anisotropic media with respect to the orientation of anisotropy, from a numerical point of view. This technique is based on the observation of the signature of anisotropy on the nine-component cross-correlation tensor (CCT) computed from seismic ambient noise recorded on pairs of three-component sensors. If noise sources are spatially distributed in a homogeneous medium, the CCT allows the reconstruction of the surface wave Green's tensor between the station pairs. In homogeneous, isotropic medium, four off-diagonal terms of the surface wave Green's tensor are null, but not in anisotropic medium. This technique is applied to three-component synthetic seismograms computed in a transversely isotropic medium with a horizontal symmetry axis, using a spectral element code. The CCT is computed between each pair of stations and then rotated, to approximate the surface wave Green's tensor by minimizing the off-diagonal components. This procedure allows the calculation of the azimuthal variation of quasi-Rayleigh and quasi-Love waves. In an anisotropic medium, in some cases, the azimuth of seismic anisotropy can induce a large variation in the horizontal polarization of surface waves. This variation depends on the relative angle between a pair of stations and the direction of anisotropy, the amplitude of the anisotropy, the frequency band of the signal and the depth of the anisotropic layer.

Cytogenetic landscape of paired neurospheres and traditional monolayer cultures in pediatric malignant brain tumors.

PubMed

Zhao, Xiumei; Zhao, Yi-Jue; Lin, Qi; Yu, Litian; Liu, Zhigang; Lindsay, Holly; Kogiso, Mari; Rao, Pulivarthi; Li, Xiao-Nan; Lu, Xinyan

2015-07-01

New therapeutic targets are needed to eliminate cancer stem cells (CSCs). We hypothesize that direct comparison of paired CSCs and nonstem tumor cells (NSTCs) will facilitate identification of primary "driver" chromosomal aberrations that can serve as diagnostic markers and/or therapeutic targets. We applied spectral karyotyping and G-banding to matched pairs of neurospheres (CSC-enriched cultures) and fetal bovine serum-based monolayer cultures (enriched with NSTCs) from 16 patient-derived orthotopic xenograft mouse models, including 9 medulloblastomas (MBs) and 7 high-grade gliomas (HGGs), followed by direct comparison of their numerical and structural abnormalities. Chromosomal aberrations were detected in neurospheres of all 16 models, and 82.0% numerical and 82.4% structural abnormalities were maintained in their matching monolayer cultures. Among the shared abnormalities, recurrent clonal changes were identified including gain of chromosomes 18 and 7 and loss of chromosome 10/10q (5/16 models), isochromosome 17q in 2 MBs, and a new breakpoint of 13q14 in 3 HGGs. Chromothripsis-like evidence was also observed in 3 HGG pairs. Additionally, we noted 20 numerical and 15 structural aberrations that were lost from the neurospheres and found 26 numerical and 23 structural aberrations that were only present in the NSTCs. Compared with MBs, the neurosphere karyotypes of HGG were more complex, with fewer chromosomal aberrations preserved in their matching NSTCs. Self-renewing CSCs in MBs and pediatric HGGs harbor recurrent numerical and structural aberrations that were maintained in the matching monolayer cultures. These primary chromosomal changes may represent new markers for anti-CSC therapies. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

On-chip plasmon-induced transparency based on plasmonic coupled nanocavities

PubMed Central

Zhu, Yu; Hu, Xiaoyong; Yang, Hong; Gong, Qihuang

2014-01-01

On-chip plasmon-induced transparency offers the possibility of realization of ultrahigh-speed information processing chips. Unfortunately, little experimental progress has been made to date because it is difficult to obtain on-chip plasmon-induced transparency using only a single meta-molecule in plasmonic circuits. Here, we report a simple and efficient strategy to realize on-chip plasmon-induced transparency in a nanoscale U-shaped plasmonic waveguide side-coupled nanocavity pair. High tunability in the transparency window is achieved by covering the pair with different organic polymer layers. It is possible to realize ultrafast all-optical tunability based on pump light-induced refractive index change of a graphene cover layer. Compared with previous reports, the overall feature size of the plasmonic nanostructure is reduced by more than three orders of magnitude, while ultrahigh tunability of the transparency window is maintained. This work also provides a superior platform for the study of the various physical effects and phenomena of nonlinear optics and quantum optics. PMID:24435059

On-chip plasmon-induced transparency based on plasmonic coupled nanocavities.

PubMed

Zhu, Yu; Hu, Xiaoyong; Yang, Hong; Gong, Qihuang

2014-01-17

On-chip plasmon-induced transparency offers the possibility of realization of ultrahigh-speed information processing chips. Unfortunately, little experimental progress has been made to date because it is difficult to obtain on-chip plasmon-induced transparency using only a single meta-molecule in plasmonic circuits. Here, we report a simple and efficient strategy to realize on-chip plasmon-induced transparency in a nanoscale U-shaped plasmonic waveguide side-coupled nanocavity pair. High tunability in the transparency window is achieved by covering the pair with different organic polymer layers. It is possible to realize ultrafast all-optical tunability based on pump light-induced refractive index change of a graphene cover layer. Compared with previous reports, the overall feature size of the plasmonic nanostructure is reduced by more than three orders of magnitude, while ultrahigh tunability of the transparency window is maintained. This work also provides a superior platform for the study of the various physical effects and phenomena of nonlinear optics and quantum optics.

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.

The mechanism of the emergence of distinct overstretched DNA states

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

Zhu, You-Liang; Sun, Zhao-Yan, E-mail: zysun@ciac.ac.cn; Lu, Zhong-Yuan

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model whichmore » prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.« less

Discriminating tastes

PubMed Central

Storz, Gisela

2011-01-01

Hfq-binding small RNAs (sRNAs) are critical regulators that form limited base-pairing interactions with target mRNAs in bacteria. These sRNAs have been linked to diverse environmental responses, yet little is known how Hfq-binding sRNAs participate in the regulatory networks associated with each response. We recently described how the Hfq-binding sRNA Spot 42 in Escherichia coli contributes to catabolite repression, a regulatory phenomenon that allows bacteria to consume some carbon sources over others. Spot 42 base pairs with numerous mRNAs encoding enzymes in central and secondary metabolism, redox balancing, and the uptake and consumption of non-preferred carbon sources. Many of the corresponding genes are transcriptionally activated by the Spot 42-repressor CRP, forming a regulatory circuit called a multi-output feedforward loop. We found that this loop influences both the steady-state levels and dynamics of gene regulation. In this article, we discuss how the CRP-Spot 42 feedforward loop is integrated into encompassing networks and how this loop may benefit enteric bacteria facing uncertain and changing nutrient conditions. PMID:21788732

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

PubMed

Betz, Karin; Malyshev, Denis A; Lavergne, Thomas; Welte, Wolfram; Diederichs, Kay; Dwyer, Tammy J; Ordoukhanian, Phillip; Romesberg, Floyd E; Marx, Andreas

2012-07-01

Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

MR-assisted PET motion correction in simultaneous PET/MRI studies of dementia subjects.

PubMed

Chen, Kevin T; Salcedo, Stephanie; Chonde, Daniel B; Izquierdo-Garcia, David; Levine, Michael A; Price, Julie C; Dickerson, Bradford C; Catana, Ciprian

2018-03-08

Subject motion in positron emission tomography (PET) studies leads to image blurring and artifacts; simultaneously acquired magnetic resonance imaging (MRI) data provides a means for motion correction (MC) in integrated PET/MRI scanners. To assess the effect of realistic head motion and MR-based MC on static [ 18 F]-fluorodeoxyglucose (FDG) PET images in dementia patients. Observational study. Thirty dementia subjects were recruited. 3T hybrid PET/MR scanner where EPI-based and T 1 -weighted sequences were acquired simultaneously with the PET data. Head motion parameters estimated from high temporal resolution MR volumes were used for PET MC. The MR-based MC method was compared to PET frame-based MC methods in which motion parameters were estimated by coregistering 5-minute frames before and after accounting for the attenuation-emission mismatch. The relative changes in standardized uptake value ratios (SUVRs) between the PET volumes processed with the various MC methods, without MC, and the PET volumes with simulated motion were compared in relevant brain regions. The absolute value of the regional SUVR relative change was assessed with pairwise paired t-tests testing at the P = 0.05 level, comparing the values obtained through different MR-based MC processing methods as well as across different motion groups. The intraregion voxelwise variability of regional SUVRs obtained through different MR-based MC processing methods was also assessed with pairwise paired t-tests testing at the P = 0.05 level. MC had a greater impact on PET data quantification in subjects with larger amplitude motion (higher than 18% in the medial orbitofrontal cortex) and greater changes were generally observed for the MR-based MC method compared to the frame-based methods. Furthermore, a mean relative change of ∼4% was observed after MC even at the group level, suggesting the importance of routinely applying this correction. The intraregion voxelwise variability of regional SUVRs was also decreased using MR-based MC. All comparisons were significant at the P = 0.05 level. Incorporating temporally correlated MR data to account for intraframe motion has a positive impact on the FDG PET image quality and data quantification in dementia patients. 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Heterochronic shift in Hox-mediated activation of sonic hedgehog leads to morphological changes during fin development.

PubMed

Sakamoto, Koji; Onimaru, Koh; Munakata, Keijiro; Suda, Natsuno; Tamura, Mika; Ochi, Haruki; Tanaka, Mikiko

2009-01-01

We explored the molecular mechanisms of morphological transformations of vertebrate paired fin/limb evolution by comparative gene expression profiling and functional analyses. In this study, we focused on the temporal differences of the onset of Sonic hedgehog (Shh) expression in paired appendages among different vertebrates. In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, concomitant with Hoxd10 expression. In dogfish (Scyliorhinus canicula), however, we found that Shh was transcribed late in fin development, concomitant with Hoxd13 expression. We utilized zebrafish as a model to determine whether quantitative changes in hox expression alter the timing of shh expression in pectoral fins of zebrafish embryos. We found that the temporal shift of Shh activity altered the size of endoskeletal elements in paired fins of zebrafish and dogfish. Thus, a threshold level of hox expression determines the onset of shh expression, and the subsequent heterochronic shift of Shh activity can affect the size of the fin endoskeleton. This process may have facilitated major morphological changes in paired appendages during vertebrate limb evolution.

High-speed volume measurement system and method

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

Lane, Michael H.; Doyle, Jr., James L.; Brinkman, Michael J.

2017-12-12

Disclosed is a volume sensor having first, second, and third laser sources emitting first, second, and third laser beams; first, second, and third beam splitters splitting the first, second, and third laser beams into first, second, and third beam pairs; first, second, and third optical assemblies expanding the first, second, and third beam pairs into first, second, and third pairs of parallel beam sheets; fourth, fifth, and sixth optical assemblies focusing the first, second, and third beam sheet pairs into fourth, fifth, and sixth beam pairs; and first, second, and third detector pairs receiving the fourth, fifth, and sixth beammore » pairs and converting a change in intensity of at least one of the beam pairs resulting from an object passing through at least one of the first, second, and third parallel beam sheets into at least one electrical signal proportional to a three-dimensional representation of the object.« less

The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β

PubMed Central

Koag, Myong-Chul; Nam, Kwangho; Lee, Seongmin

2014-01-01

To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β (polβ), we report four crystal structures of polβ complexed with dG•dTTP and dA•dCTP mismatches in the presence of Mg2+ or Mn2+. The Mg2+-bound ground-state structures show that the dA•dCTP-Mg2+ complex adopts an ‘intermediate’ protein conformation while the dG•dTTP-Mg2+ complex adopts an open protein conformation. The Mn2+-bound ‘pre-chemistry-state’ structures show that the dA•dCTP-Mn2+ complex is structurally very similar to the dA•dCTP-Mg2+ complex, whereas the dG•dTTP-Mn2+ complex undergoes a large-scale conformational change to adopt a Watson–Crick-like dG•dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polβ increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polβ appears to allow only a Watson–Crick-like conformation for purine•pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson–Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polβ. PMID:25200079

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

Egli, Martin; Pallan, Pradeep S.; Pattanayek, Rekha

An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4{prime} {yields} 6{prime})-linked oligo(2{prime},3{prime}-dideoxy-{beta}-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4{prime} {yields} 6{prime})more » family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.« less

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

PubMed Central

Qi, Zhi; Pugh, Robert A; Spies, Maria; Chemla, Yann R

2013-01-01

Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be understood. This necessitates monitoring helicase activity directly, at high spatio-temporal resolution. Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwinding by XPD helicase, a Superfamily 2 (SF2) DNA helicase involved in DNA repair and transcription initiation. We show that monomeric XPD unwinds duplex DNA in 1-bp steps, yet exhibits frequent backsteps and undergoes conformational transitions manifested in 5-bp backward and forward steps. Quantifying the sequence dependence of XPD stepping dynamics with near base pair resolution, we provide the strongest and most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spontaneous opening of the duplex. The proposed unwinding mechanism may be a universal feature of DNA helicases that move along DNA phosphodiester backbones. DOI: http://dx.doi.org/10.7554/eLife.00334.001 PMID:23741615

Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units.

PubMed

Ren, Shanshan; Bertels, Koen; Al-Ars, Zaid

2018-01-01

GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm. It also analyzes the performance bottlenecks of the implementations on an NVIDIA Tesla K40 card with various data sets. Based on these results and the characteristics of GATK HC, we are able to identify the GPU-based implementations with the highest performance for the various analyzed data sets. Experimental results show that the GPU-based implementations of the pair-HMMs forward algorithm achieve a speedup of up to 5.47× over existing GPU-based implementations.

DNA bases ring-expanded with a cyclopentadiene free radical: a theoretical investigation of building blocks with diradical character.

PubMed

Zhao, Peiwen; Bu, Yuxiang

2016-01-14

In this work, we computationally design radical nucleobases which possess improved electronic properties, especially diradical properties through introducing a cyclopentadiene radical. We predict that the detailed electromagnetic features of base assemblies are based on the orientation of the extra five-membered cyclopentadiene ring. Broken symmetry DFT calculations take into account the relevant structures and properties. Our results reveal that both the radicalized DNA bases and the base pairs formed when they combine with their counterparts remain stable and display larger spin delocalization. The mode of embedding the cyclopentadiene free radical in the structures has some influence on the degree of π-conjugation, which results in various diradical characteristics. Single-layered radical base pairs all have an open-shell singlet ground state, but the energy difference between singlet and triplet is not significant. For two-layered radical base pairs, the situation is more complex. All of them have an open-shell state as their ground state, including an open-shell singlet state and an open-shell triplet state. That is, the majority of radical base pairs possess anti-ferromagnetic or ferromagnetic characteristics. We present here a more in-depth discussion and analyses to study the magnetic characteristics of radical bases and base pairs. As an important factor, two-layered radical base pairs also have been carefully analyzed. We hope that all the measurements and results presented here will stimulate further detailed insights into the related mechanisms in modified DNA bases and the design of better ring-expanded DNA magnetic materials.

Contingent choice. Exploring the relationship between sweetened beverages and vegetable consumption.

PubMed

Cornwell, T Bettina; McAlister, Anna R

2013-03-01

Adults and children are repeatedly exposed to the pairing of food and drink as found in meal deals and "combos". There may arise from this indoctrination, a contingent relationship between drink context and food preference. Our multi-method research examines food and drink combining. A survey-based study examines the food and drink pairing preferences of adults (N=60), while a laboratory study with young children (N=75, aged three to five) examines the role of drink context on vegetable consumption. The adult survey finds strong food and drink combining preferences. The pairing of soft drinks with calorie dense foods is regarded favorably, while the pairing of soft drinks with vegetables is not. In child food trials, vegetable consumption is not influenced by the child's fussiness but is influenced by the drink accompaniment. In limited contexts, these findings demonstrate the contingent relationship between drink context and food consumption. Both palate preference and associative learning may be mechanisms driving the effects of drink context on food consumption. The findings suggest simple consumer strategies that might be employed to change dietary patterns (e.g., drink water with meals), and hold straightforward policy implications (e.g., increase water as the default option in meal deals). Copyright © 2012 Elsevier Ltd. All rights reserved.

[Separation of p-aminobenzenearsonic acid and its oxide by ion-pair reversed-phase high performance liquid chromatography].

PubMed

Kang, J; Ma, X; Meng, L; Ma, D

1999-05-01

To study the separation of p-aminobenzenearsonic acid (PABAA) and its oxide, p-aminophenylarsine oxide (PAPAO), both the absorption spectra were scanned at the wavelengths from 200 nm to 380 nm. PABAA had absorption maximum at 254 nm and PAPAO 258 nm. The effects of salt concentration, column temperature, methanol and ion-pair agent concentrations on the capacity factor were investigated. Compounds of high polarity showed almost no retention on reversed-phase column; as the volume fraction of the methanol decreased from 90% to 10%, the retention time of PABAA gradually increased with broad peak, and partially eluted when methanol volume fraction being below 20%. With temperature rising, the retention time of PABAA was decreased. But PABAA capacity factor can be increased by selecting an appropriate salt concentration for the mobile phase. The cetyltrimethyl and tetrabutyl ammonium ions were separately added as ion-pair agents to the mobile phase containing methanol in phosphate buffer of 10 mmol/L, the changes of retention time were observed. The mechanism of retention based on reversed phase ion-pair model is proposed. Besides, the retention behaviour is also influenced by size exclusion in stationary phase as well as polar interactions with residual silanol group on the silica surface.

Electron attraction mediated by Coulomb repulsion.

PubMed

Hamo, A; Benyamini, A; Shapir, I; Khivrich, I; Waissman, J; Kaasbjerg, K; Oreg, Y; von Oppen, F; Ilani, S

2016-07-21

One of the defining properties of electrons is their mutual Coulomb repulsion. However, in solids this basic property may change; for example, in superconductors, the coupling of electrons to lattice vibrations makes the electrons attract one another, leading to the formation of bound pairs. Fifty years ago it was proposed that electrons can be made attractive even when all of the degrees of freedom in the solid are electronic, by exploiting their repulsion from other electrons. This attraction mechanism, termed 'excitonic', promised to achieve stronger and more exotic superconductivity. Yet, despite an extensive search, experimental evidence for excitonic attraction has yet to be found. Here we demonstrate this attraction by constructing, from the bottom up, the fundamental building block of the excitonic mechanism. Our experiments are based on quantum devices made from pristine carbon nanotubes, combined with cryogenic precision manipulation. Using this platform, we demonstrate that two electrons can be made to attract each other using an independent electronic system as the 'glue' that mediates attraction. Owing to its tunability, our system offers insights into the underlying physics, such as the dependence of the emergent attraction on the underlying repulsion, and the origin of the pairing energy. We also demonstrate transport signatures of excitonic pairing. This experimental demonstration of excitonic pairing paves the way for the design of exotic states of matter.

Electron attraction mediated by Coulomb repulsion

NASA Astrophysics Data System (ADS)

Hamo, A.; Benyamini, A.; Shapir, I.; Khivrich, I.; Waissman, J.; Kaasbjerg, K.; Oreg, Y.; von Oppen, F.; Ilani, S.

2016-07-01

One of the defining properties of electrons is their mutual Coulomb repulsion. However, in solids this basic property may change; for example, in superconductors, the coupling of electrons to lattice vibrations makes the electrons attract one another, leading to the formation of bound pairs. Fifty years ago it was proposed that electrons can be made attractive even when all of the degrees of freedom in the solid are electronic, by exploiting their repulsion from other electrons. This attraction mechanism, termed ‘excitonic’, promised to achieve stronger and more exotic superconductivity. Yet, despite an extensive search, experimental evidence for excitonic attraction has yet to be found. Here we demonstrate this attraction by constructing, from the bottom up, the fundamental building block of the excitonic mechanism. Our experiments are based on quantum devices made from pristine carbon nanotubes, combined with cryogenic precision manipulation. Using this platform, we demonstrate that two electrons can be made to attract each other using an independent electronic system as the ‘glue’ that mediates attraction. Owing to its tunability, our system offers insights into the underlying physics, such as the dependence of the emergent attraction on the underlying repulsion, and the origin of the pairing energy. We also demonstrate transport signatures of excitonic pairing. This experimental demonstration of excitonic pairing paves the way for the design of exotic states of matter.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies.

PubMed

Novosjolova, Irina; Kennedy, Scott D; Rozners, Eriks

2017-11-02

The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrically tunable g factors in quantum dot molecular spin states.

PubMed

Doty, M F; Scheibner, M; Ponomarev, I V; Stinaff, E A; Bracker, A S; Korenev, V L; Reinecke, T L; Gammon, D

2006-11-10

We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

Electrically Tunable g Factors in Quantum Dot Molecular Spin States

NASA Astrophysics Data System (ADS)

Doty, M. F.; Scheibner, M.; Ponomarev, I. V.; Stinaff, E. A.; Bracker, A. S.; Korenev, V. L.; Reinecke, T. L.; Gammon, D.

2006-11-01

We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

Polymerase chain reaction with phase change as intrinsic thermal control

NASA Astrophysics Data System (ADS)

Hsieh, Yi-Fan; Yonezawa, Eri; Kuo, Long-Sheng; Yeh, Shiou-Hwei; Chen, Pei-Jer; Chen, Ping-Hei

2013-04-01

This research demonstrated that without any external temperature controller, the capillary convective polymerase chain reaction (ccPCR) powered by a candle can operate with the help of phase change. The candle ccPCR system productively amplified hepatitis B virus 122 base-pairs DNA fragment. The detection sensitivity can achieve at an initial DNA concentration to 5 copies per reaction. The results also show that the candle ccPCR system can operate functionally even the ambient temperature varies from 7 °C to 45 °C. These features imply that the candle ccPCR system can provide robust medical detection services.

Comparative evaluation of the effect of denture cleansers on the surface topography of denture base materials: An in-vitro study.

PubMed

Jeyapalan, Karthigeyan; Kumar, Jaya Krishna; Azhagarasan, N S

2015-08-01

The aim was to evaluate and compare the effects of three chemically different commercially available denture cleansing agents on the surface topography of two different denture base materials. Three chemically different denture cleansers (sodium perborate, 1% sodium hypochlorite, 0.2% chlorhexidine gluconate) were used on two denture base materials (acrylic resin and chrome cobalt alloy) and the changes were evaluated at 3 times intervals (56 h, 120 h, 240 h). Changes from baseline for surface roughness were recorded using a surface profilometer and standard error of the mean (SEM) both quantitatively and qualitatively, respectively. Qualitative surface analyses for all groups were done by SEM. The values obtained were analyzed statistically using one-way ANOVA and paired t-test. All three denture cleanser solutions showed no statistically significant surface changes on the acrylic resin portions at 56 h, 120 h, and 240 h of immersion. However, on the alloy portion changes were significant at the end of 120 h and 240 h. Of the three denture cleansers used in the study, none produced significant changes on the two denture base materials for the short duration of immersion, whereas changes were seen as the immersion periods were increased.

Comparative evaluation of the effect of denture cleansers on the surface topography of denture base materials: An in-vitro study

PubMed Central

Jeyapalan, Karthigeyan; Kumar, Jaya Krishna; Azhagarasan, N. S.

2015-01-01

Aims: The aim was to evaluate and compare the effects of three chemically different commercially available denture cleansing agents on the surface topography of two different denture base materials. Materials and Methods: Three chemically different denture cleansers (sodium perborate, 1% sodium hypochlorite, 0.2% chlorhexidine gluconate) were used on two denture base materials (acrylic resin and chrome cobalt alloy) and the changes were evaluated at 3 times intervals (56 h, 120 h, 240 h). Changes from baseline for surface roughness were recorded using a surface profilometer and standard error of the mean (SEM) both quantitatively and qualitatively, respectively. Qualitative surface analyses for all groups were done by SEM. Statistical Analysis Used: The values obtained were analyzed statistically using one-way ANOVA and paired t-test. Results: All three denture cleanser solutions showed no statistically significant surface changes on the acrylic resin portions at 56 h, 120 h, and 240 h of immersion. However, on the alloy portion changes were significant at the end of 120 h and 240 h. Conclusion: Of the three denture cleansers used in the study, none produced significant changes on the two denture base materials for the short duration of immersion, whereas changes were seen as the immersion periods were increased. PMID:26538915

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

PubMed

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-11-01

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Comparison of the conformation of an oligonucleotide containing a central G-T base pair with the non-mismatch sequence by proton NMR.

PubMed Central

Quignard, E; Fazakerley, G V; van der Marel, G; van Boom, J H; Guschlbauer, W

1987-01-01

We have recorded NOESY spectra of two non-selfcomplementary undecanucleotide duplexes. From the observed NOEs we do not detect any significant distortion of the helix when a G-C pair is replaced by a G-T pair and the normal interresidue connectivities can be followed through the mismatch site. We conclude that the 2D spectra of the non-exchangeable protons do not allow differentiation between a wobble or rare tautomer form for the mismatch. NOE measurements in H2O, however, clearly show that the mismatch adopts a wobble structure and give information on the hydration in the minor groove for the G-T base pair which is embedded between two A-T base pairs in the sequence. PMID:3033602

Discordant inflammatory changes in the apophyseal and sacroiliac joints: serial observations in enthesitis-related arthritis

PubMed Central

Amies, Thomas; Vendhan, Kanimozhi; Humphries, Paul; Sen, Debajit; Ioannou, Yiannis; Hall-Craggs, Margaret A

2016-01-01

Objective: To determine the extent to which inflammation of the sacroiliac joints (SIJs) and apophyseal joints (AJs) changes concordantly after treatment in enthesitis-related arthritis (ERA). Methods: A retrospective study was performed with institutional review board approval. 31 young patients with ERA who had been scanned between March 2009 and November 2014 were included. All patients had post-contrast imaging of the SIJs and lumbar spine and short tau inversion-recovery (STIR) images of the SIJs. The severity of sacroiliitis was scored using a modification of an established technique, and inflammation of the AJs was evaluated using a recently described grading system. The changes in SIJ and AJ scores after treatment were classified as either concordant or discordant, and the proportion of scan pairs in these groups was recorded. In addition, the correlation between change in SIJ STIR score (Δnfla) and change in AJ score (ΔAJ) was assessed using Spearman's correlation coefficient. Results: Of a total of 43 scan pairs, the changes in inflammation were concordant in 16 scan pairs and discordant in 27 scan pairs. There was no significant correlation between Δnfla and ΔAJ (R = 0.14, p = 0.37). Conclusion: Inflammatory changes in the SIJs and AJs are often discordant. This may be a reason why patients experience ongoing back pain despite apparent improvement in one or the other site. Advances in knowledge: Inflammation may behave differently at different anatomical sites. The SIJs and AJs should both be imaged in patients with ERA with back pain. PMID:27376529

Changes in the zero-point energy of the protons as the source of the binding energy of water to A-phase DNA.

PubMed

Reiter, G F; Senesi, R; Mayers, J

2010-10-01

The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6  water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Å.

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position.

PubMed

Liu, Wei; Shin, Dongwon; Ng, Martin; Sanbonmatsu, Karissa Y; Tor, Yitzhak; Cooperman, Barry S

2017-08-29

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5'- and 3'-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.

Characterization of the Trans Watson-Crick GU Base Pair Located in the Catalytic Core of the Antigenomic HDV Ribozyme

PubMed Central

Lévesque, Dominique; Reymond, Cédric; Perreault, Jean-Pierre

2012-01-01

The HDV ribozyme’s folding pathway is, by far, the most complex folding pathway elucidated to date for a small ribozyme. It includes 6 different steps that have been shown to occur before the chemical cleavage. It is likely that other steps remain to be discovered. One of the most critical of these unknown steps is the formation of the trans Watson-Crick GU base pair within loop III. The U23 and G28 nucleotides that form this base pair are perfectly conserved in all natural variants of the HDV ribozyme, and therefore are considered as being part of the signature of HDV-like ribozymes. Both the formation and the transformation of this base pair have been studied mainly by crystal structure and by molecular dynamic simulations. In order to obtain physical support for the formation of this base pair in solution, a set of experiments, including direct mutagenesis, the site-specific substitution of chemical groups, kinetic studies, chemical probing and magnesium-induced cleavage, were performed with the specific goal of characterizing this trans Watson-Crick GU base pair in an antigenomic HDV ribozyme. Both U23 and G28 can be substituted for nucleotides that likely preserve some of the H-bond interactions present before and after the cleavage step. The formation of the more stable trans Watson-Crick base pair is shown to be a post-cleavage event, while a possibly weaker trans Watson-Crick/Hoogsteen interaction seems to form before the cleavage step. The formation of this unusually stable post-cleavage base pair may act as a driving force on the chemical cleavage by favouring the formation of a more stable ground state of the product-ribozyme complex. To our knowledge, this represents the first demonstration of a potential stabilising role of a post-cleavage conformational switch event in a ribozyme-catalyzed reaction. PMID:22768274

A change detection method for remote sensing image based on LBP and SURF feature

NASA Astrophysics Data System (ADS)

Hu, Lei; Yang, Hao; Li, Jin; Zhang, Yun

2018-04-01

Finding the change in multi-temporal remote sensing image is important in many the image application. Because of the infection of climate and illumination, the texture of the ground object is more stable relative to the gray in high-resolution remote sensing image. And the texture features of Local Binary Patterns (LBP) and Speeded Up Robust Features (SURF) are outstanding in extracting speed and illumination invariance. A method of change detection for matched remote sensing image pair is present, which compares the similarity by LBP and SURF to detect the change and unchanged of the block after blocking the image. And region growing is adopted to process the block edge zone. The experiment results show that the method can endure some illumination change and slight texture change of the ground object.

Articular cartilage degeneration classification by means of high-frequency ultrasound.

PubMed

Männicke, N; Schöne, M; Oelze, M; Raum, K

2014-10-01

To date only single ultrasound parameters were regarded in statistical analyses to characterize osteoarthritic changes in articular cartilage and the potential benefit of using parameter combinations for characterization remains unclear. Therefore, the aim of this work was to utilize feature selection and classification of a Mankin subset score (i.e., cartilage surface and cell sub-scores) using ultrasound-based parameter pairs and investigate both classification accuracy and the sensitivity towards different degeneration stages. 40 punch biopsies of human cartilage were previously scanned ex vivo with a 40-MHz transducer. Ultrasound-based surface parameters, as well as backscatter and envelope statistics parameters were available. Logistic regression was performed with each unique US parameter pair as predictor and different degeneration stages as response variables. The best ultrasound-based parameter pair for each Mankin subset score value was assessed by highest classification accuracy and utilized in receiver operating characteristics (ROC) analysis. The classifications discriminating between early degenerations yielded area under the ROC curve (AUC) values of 0.94-0.99 (mean ± SD: 0.97 ± 0.03). In contrast, classifications among higher Mankin subset scores resulted in lower AUC values: 0.75-0.91 (mean ± SD: 0.84 ± 0.08). Variable sensitivities of the different ultrasound features were observed with respect to different degeneration stages. Our results strongly suggest that combinations of high-frequency ultrasound-based parameters exhibit potential to characterize different, particularly very early, degeneration stages of hyaline cartilage. Variable sensitivities towards different degeneration stages suggest that a concurrent estimation of multiple ultrasound-based parameters is diagnostically valuable. In-vivo application of the present findings is conceivable in both minimally invasive arthroscopic ultrasound and high-frequency transcutaneous ultrasound. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Estimates of electronic coupling for excess electron transfer in DNA

NASA Astrophysics Data System (ADS)

Voityuk, Alexander A.

2005-07-01

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31G* and extended 6-31++G** basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.

Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic web technologies.

PubMed

Jiang, Guoqian; Wang, Liwei; Liu, Hongfang; Solbrig, Harold R; Chute, Christopher G

2013-01-01

A semantically coded knowledge base of adverse drug events (ADEs) with severity information is critical for clinical decision support systems and translational research applications. However it remains challenging to measure and identify the severity information of ADEs. The objective of the study is to develop and evaluate a semantic web based approach for building a knowledge base of severe ADEs based on the FDA Adverse Event Reporting System (AERS) reporting data. We utilized a normalized AERS reporting dataset and extracted putative drug-ADE pairs and their associated outcome codes in the domain of cardiac disorders. We validated the drug-ADE associations using ADE datasets from SIDe Effect Resource (SIDER) and the UMLS. We leveraged the Common Terminology Criteria for Adverse Event (CTCAE) grading system and classified the ADEs into the CTCAE in the Web Ontology Language (OWL). We identified and validated 2,444 unique Drug-ADE pairs in the domain of cardiac disorders, of which 760 pairs are in Grade 5, 775 pairs in Grade 4 and 2,196 pairs in Grade 3.

Daughters and mothers exercising together: effects of home- and community-based programs.

PubMed

Ransdell, Lynda B; Taylor, Alison; Oakland, Darcie; Schmidt, Jenny; Moyer-Mileur, Laurie; Shultz, Barry

2003-02-01

This pilot study compares the effectiveness of home- and community-based physical activity interventions that target mothers and daughters to increase physical activity and improve health-related fitness. Mothers (45.18 +/- 7.49 yr) and daughters (15.41 +/- 1.33 yr) were randomly assigned to a community-based (CB) (N = 20 participants) or home-based (HB) (N = 14 participants) program. CB participants attended three instructor-led sessions per week for 12 wk. HB participants were asked to participate in 3 sessions per week for 12 wk in a program similar to the CB program. The main difference between the programs was that CB activities were completed at a fitness facility within a university and HB activities were completed in or near the home. Before and after the intervention, changes in health-related fitness and physical activity were assessed. A series of 2 (group assignment) x 2 (time) ANOVAs were conducted to assess changes separately for mothers and daughters. CB participants attended 77% of the sessions, and none of the pairs dropped out. HB participants completed 70% of the recommended sessions, and three pairs dropped out. Mothers and daughters in both groups significantly increased their participation in aerobic, muscular strength, and flexibility activities (P = 0.02 to 0.000). Daughters in both groups significantly improved their muscular endurance (sit-ups,P = 0.000). Mothers in both groups improved their muscular strength (push-ups, P = 0.003), muscular endurance (sit-ups, P = 0.000), flexibility (sit-and-reach, P = 0.008), and aerobic capacity (1-mile walk, P = 0.002). Positive changes in diastolic blood pressure also occurred (P = 0.008). Mothers and daughters responded positively to CB and HB physical activity programs. Home-based physical activity programming is a cost-effective means to increase physical activity and improve health-related fitness in these groups.

Many intercity travelers face longer travel schedules

DOT National Transportation Integrated Search

2003-10-01

Since 1995, scheduled travel times for direct : intercity air, bus, and rail service without an en : route transfer have measurably lengthened in : most major-market city-pairs. : Long-haul rail city-pairs affected by service : changes and short-...

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.

PubMed

Chen, Xianfeng; Johnson, Stephen; Jeraldo, Patricio; Wang, Junwen; Chia, Nicholas; Kocher, Jean-Pierre A; Chen, Jun

2018-03-01

Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than single-end reads due to a longer read length. However, the reverse read (R2) often has significant low base quality, and a large proportion of R2s will be discarded after quality control, resulting in a mixture of paired-end and single-end reads. A typical 16S analysis pipeline usually processes either paired-end or single-end reads but not a mixture. Thus, the quantification accuracy and statistical power will be reduced due to the loss of a large amount of reads. As a result, rare taxa may not be detectable with the paired-end approach, or low taxonomic resolution will result in a single-end approach. To have both the higher phylogenetic resolution provided by paired-end reads and the higher sequence coverage by single-end reads, we propose a novel OTU-picking pipeline, hybrid-denovo, that can process a hybrid of single-end and paired-end reads. Using high-quality paired-end reads as a gold standard, we show that hybrid-denovo achieved the highest correlation with the gold standard and performed better than the approaches based on paired-end or single-end reads in terms of quantifying the microbial diversity and taxonomic abundances. By applying our method to a rheumatoid arthritis (RA) data set, we demonstrated that hybrid-denovo captured more microbial diversity and identified more RA-associated taxa than a paired-end or single-end approach. Hybrid-denovo utilizes both paired-end and single-end 16S sequencing reads and is recommended for 16S rRNA gene targeted paired-end sequencing data.

Investigation of focused and unfocused transducer beam patterns in moderately nonlinear absorbing media

NASA Astrophysics Data System (ADS)

Kharin, Nikolay A.

2001-05-01

The novel solution of the KZK equation for acoustic pressure of the second harmonic in slightly focused beam of a circular transducer was obtained in a closed form for moderately nonlinear absorbing media (Gol'dberg numbers ~ 1). The solution is based on the method of slowly changing wave profile in combination with the method of successive approximations. Two pairs of transducers (Valpey-Fisher Corp.) Were compared to investigate the influence of focusing on the applicability of the moderate nonlinearity approach. The first pair was of 0.25' diameter and the second was of 0.5' diameter. Both pairs has one transducer with flat surface and the other geometrically focused at 4'. The central frequency for all transducers was 5 MHz. Measurements were undertaken in the blood-mimicking solution of water and glycerine. The results demonstrated that for slightly focused transducers with circular apertures, the moderate nonlinearity approach is still valid, as it was proved for flat sources with the same source level, despite the higher pressures in the focal region. The peak pressure for the weakly focused system occurs at a shorter range than focal length.

Coherence of beam arrays propagating in the turbulent atmosphere

NASA Astrophysics Data System (ADS)

Charnotskii, Mikhail

2010-04-01

We analyze some recent publications addressing propagation of the partially coherent polarized beams and beam arrays in the turbulent atmosphere. We show that the published results are limited to the scalar propagation model, and are not particular to the beam polarization. Therefore these results are equally relevant for the scalar beam pairs and arrays discriminated by some parameters such as small frequency shift, time delay or geometry, but not necessary the polarization. We use the virtual incoherent source model to derive the general form of the mutual coherence function of the two Schell-type beams. We discuss some physical stochastic models that result in the creation of the Schell-type beams and beam arrays. New classes of the uniformly, nonuniformly and nonlocally coherent beam pairs emerge naturally from this analysis. Rigorous, Markov approximation-based, propagation model provides relatively simple analytic results for the second-order moments of the optical field of the partially-coherent individual beams and beam pairs. We examine the changes of the beam mutual coherence in the process of the free-space propagation and propagation through the turbulent atmosphere.

Designed Reduction of Streptococcus pneumoniae Pathogenicity via Synthetic Changes in Virulence Factor Codon-pair Bias

PubMed Central

Coleman, J. Robert; Papamichail, Dimitris; Yano, Masahide; García-Suárez, María del Mar

2011-01-01

In this study, we used a previously described method of controlling gene expression with computer-based gene design and de novo DNA synthesis to attenuate the virulence of Streptococcus pneumoniae. We produced 2 S. pneumoniae serotype 3 (SP3) strains in which the pneumolysin gene (ply) was recoded with underrepresented codon pairs while retaining its amino acid sequence and determined their ply expression and pneumolysin production in vitro and their virulence in a mouse pulmonary infection model. Expression of ply and production of pneumolysin of the recoded SP3 strains were decreased, and the recoded SP3 strains were less virulent in mice than the wild-type SP3 strain or a Δply SP3 strain. Further studies showed that the least virulent recoded strain induced a markedly reduced inflammatory response in the lungs compared with the wild-type or Δply strain. These findings suggest that reducing pneumococcal virulence gene expression by altering codon-pair bias could hold promise for rational design of live-attenuated pneumococcal vaccines. PMID:21343143

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

An Ultra-Sensitive Electrometer based on the Cavity-Embedded Cooper-Pair Transistor

NASA Astrophysics Data System (ADS)

Li, Juliang; Miller, Marco; Rimberg, Alex

2015-03-01

We discuss use of a cavity-embedded Cooper-pair transistor (cCPT) as a potentially quantum-limited electrometer. The cCPT consists of a Cooper pair transistor placed at the voltage antinode of a 5.7 GHz shorted quarter-wave resonator so that the CPT provides a galvanic connection between the cavity's central conductor and ground plane. The quantum inductance of the CPT, which appears in parallel with the effective inductance of the cavity resonance, can be modulated by application of either a gate voltage to the CPT island or a flux bias to the CPT/cavity loop. Changes in the CPT inductance shift the cavity resonant frequency, and therefore the phase of a microwave signal reflected from the cavity. The reflected wave is amplified by both SLUG and HEMT amplifiers before its phase is measured. Results of recent measurements on the cCPT electrometer will be compared with theoretical predictions. This work was supported by the NSF under Grant No. DMR-1104821, by the ARO under Contract No, W911NF-13-1-0377 and by AFOSR/DARPA under Agreement No. FA8750-12-2-0339.

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

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

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

On twelve types of covering-based rough sets.

PubMed

Safari, Samira; Hooshmandasl, Mohammad Reza

2016-01-01

Covering approximation spaces are a generalization of equivalence-based rough set theories. In this paper, we will consider twelve types of covering based approximation operators by combining four types of covering lower approximation operators and three types of covering upper approximation operators. Then, we will study the properties of these new pairs and show they have most of the common properties among existing covering approximation pairs. Finally, the relation between these new pairs is studied.

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.

Two-Dimensional Versus Three-Dimensional Conceptualization in Astronomy Education

NASA Astrophysics Data System (ADS)

Reynolds, Michael David

Numerous science conceptual issues are naturally three-dimensional. Classroom presentations are often two -dimensional or at best multidimensional. Several astronomy topics are of this nature, e. g. mechanics of the phases of the moon. Textbooks present this three-dimensional topic in two-dimensions; such is often the case in the classroom. This study was conducted to examine conceptions exhibited by pairs of like-sex 11th grade standard physics students as they modeled the lunar phases. Student pairs, 13 male and 13 female, were randomly selected and assigned. Pairing comes closer to classroom emulation, minimizes needs for direct probes, and pair discussion is more likely to display variety and depth. Four hypotheses were addressed: (1) Participants who model three-dimensionally will more likely achieve a higher explanation score. (2) Students who experienced more earth or physical science exposure will more likely model three-dimensionally. (3) Pairs that exhibit a strong science or mathematics preference will more likely model three-dimensionally. (4) Males will model in three dimensions more than females. Students provided background information, including science course exposure and subject preference. Each pair laid out a 16-card set representing two complete lunar phase changes. The pair was asked to explain why the phases occur. Materials were provided for use, including disks, spheres, paper and pen, and flashlight. Activities were videotaped for later evaluation. Statistics of choice was a correlation determination between course preference and model type and ANOVA for the other hypotheses. It was determined that pairs who modeled three -dimensionally achieved a higher score on their phases mechanics explanation at p <.05 level. Pairs with earth science or physical science exposure, those who prefer science or mathematics, and male participants were not more likely to model three-dimensionally. Possible reasons for lack of significance was small sample size and in the case of course preferences, small differences in course preference means. Based on this study, instructors should be aware of dimensionality and student misconceptions. Whenever possible, three-dimensional concepts should be modeled as such. Authors and publishers should consider modeling suggestions and three-dimensional ancillaries.

Gel-Based Hippocampal Proteomic Analysis 2 Weeks following Traumatic Brain Injury to Immature Rats Using Controlled Cortical Impact

PubMed Central

Kochanek, Ashley R.; Kline, Anthony E.; Gao, Wei-Min; Chadha, Mandeep; Lai, Yichen; Clark, Robert S.B.; Dixon, C. Edward; Jenkins, Larry W.

2009-01-01

Traumatic brain injury (TBI) to postnatal day 17 rats has been shown to produce acute changes in hippocampal global protein levels and spatial learning and memory deficits. The purpose of the present study was to analyze global hippocampal protein changes 2 weeks after a moderate ipsilateral controlled cortical impact in postnatal day 17 rats using 2-dimensional difference gel electrophoresis and mass spectrometry. Paired sham and ipsilateral injured hippocampal lysates were independently labeled with different fluorescent cyanine dyes and coseparated within the same immobilized pH gradient strips and slab gel based on isoelectric point and molecular mass. Significant changes in key proteins involved in glial and neuronal stress, oxidative metabolism, calcium uptake and neurotransmitter function were found 2 weeks after injury, and their potential roles in hippocampal plasticity and cognitive dysfunction were discussed. PMID:16943664

Urban Change Detection of Pingtan City based on Bi-temporal Remote Sensing Images

NASA Astrophysics Data System (ADS)

Degang, JIANG; Jinyan, XU; Yikang, GAO

2017-02-01

In this paper, a pair of SPOT 5-6 images with the resolution of 0.5m is selected. An object-oriented classification method is used to the two images and five classes of ground features were identified as man-made objects, farmland, forest, waterbody and unutilized land. An auxiliary ASTER GDEM was used to improve the classification accuracy. And the change detection based on the classification results was performed. Accuracy assessment was carried out finally. Consequently, satisfactory results were obtained. The results show that great changes of the Pingtan city have been detected as the expansion of the city area and the intensity increase of man-made buildings, roads and other infrastructures with the establishment of Pingtan comprehensive experimental zone. Wide range of open sea area along the island coast zones has been reclaimed for port and CBDs construction.

Phase Transition in Biopolymer Hydrogels Based on Glycine (g), Valine (v), Proline (p), and Isoleucine (i)

NASA Astrophysics Data System (ADS)

Lee, Jonghwi; Urry, Dan W.; Macosko, Christopher W.

2000-03-01

Selectively modified elastic protein-based polymers demonstrate diverse energy conversions by means of the control of a phase transition resulting from the sensitivity to stimuli of the hydrophobic association. Among these polymers, poly(GVGVP), poly(GVGIP) and analogues of poly(GVGVP) containing carboxylic acid or amino functional groups as side chains were cross-linked and their swelling behavior was studied. Regardless of cross-linking method, reversible phase transitions can be observed in the swelling of all cross-linked polymers by changing temperature and pH, where relevant. Decreased cross-link density leads to increased swelling ratio as the transition becomes more pronounced. Fibers, chemically cross-linked after formation, exhibit anisotropic dimensional changes on changing the temperature. Gamma-irradiation cross-linked poly(GVGVP) exhibited a more distinct phase transition than modified poly(GVGVP) with ion pairs between side chains, which were partially converted to amide cross-links.

Impact of LANDSAT MSS sensor differences on change detection analysis

NASA Technical Reports Server (NTRS)

Likens, W. C.; Wrigley, R. C.

1983-01-01

Some 512 by 512 pixel subwindows for simultaneously acquired scene pairs obtained by LANDSAT 2,3 and 4 multispectral band scanners were coregistered using LANDSAT 4 scenes as the base to which the other images were registered. Scattergrams between the coregistered scenes (a form of contingency analysis) were used to radiometrically compare data from the various sensors. Mode values were derived and used to visually fit a linear regression. Root mean square errors of the registration varied between .1 and 1.5 pixels. There appear to be no major problem preventing the use of LANDSAT 4 MSS with previous MSS sensors for change detection, provided the noise interference can be removed or minimized. Data normalizations for change detection should be based on the data rather than solely on calibration information. This allows simultaneous normalization of the atmosphere as well as the radiometry.

Initial estimate of NOAA-9 SBUV/2 total ozone drift: Based on comparison with re-calibrated TOMS measurements and pair justification of SBUV/2

NASA Technical Reports Server (NTRS)

Wellemeyer, C. G.; Taylor, S. L.; Gu, X. U.; Mcpeters, Richard D.; Hudson, R. D.

1990-01-01

Newly recalibrated version 6 Total Ozone Mapping Spectrometer (TOMS) data are used as a reference measurement in a comparison of monthly means of total ozone in 10 degree latitude zones from SBUV/2 and the nadir measurements from TOMS. These comparisons indicate a roughly linear long-term drift in SBUV/2 total ozone relative to TOMS of about 2.5 Dobson units per year at the equator over the first three years of SBUV/2. The pari justification technique is also applied to the SBUV/2 measurements in a manner similar to that used for SBUV and TOMS. The higher solar zenith angles associated with the afternoon orbit of NOAA-9 and the large changes in solar zenith angle associated with its changing equator crossing time degrade the accuracy of the pair justification method relative to its application to SBUV and TOMS, but the results are consistent with the SBUV/2-TOMS comparisons, and show a roughly linear drift in SBUV/2 of 2.5 to 4.5 Dobson units per year in equatorial ozone.

Identification of a novel mutation in the paired domain of PAX3 in an Iranian family with waardenburg syndrome type I.

PubMed

Sotirova, V N; Rezaie, T M; Khoshsorour, M M; Sarfarazi, M

2000-03-01

Waardenburg syndrome Type I (WS1) is an autosomal dominant disorder that has previously been associated with mutations in the PAX3 gene on the 2q35 region. In this study, we used an Iranian WS1 family with seven affected individuals in three generations. The phenotypic characteristics of the family include sensorineural deafness, dystopia canthorum, hypopigmented skin patches of the upper limbs, congenital white forelock, confluent white eyebrows, nonpigmented iris, poliosis, and hypopigmentation of the retina. Herein, we report a previously unidentified single-base substitution in exon II (C-->T at position 218) that results in a change of serine to leucine (S73L) in this family. This change was not observed in 100 chromosomes of healthy unrelated individuals. This mutation is within the PAX3 paired domain region, a structure that is highly conserved and implicated in DNA binding. This is the first identification of a PAX3 mutation for this phenotype in the Iranian population. This also provides additional confirmation for the involvement of this gene in the etiology of WS1.

[Network of plastic neurons capable of forming conditioned reflexes ("membrane" model of learning)].

PubMed

Litvinov, E G; Frolov, A A

1978-01-01

Simple net neuronal model was suggested which was able to form the conditioning due to changes of the neuron excitability. The model was based on the following main concepts: (a) the conditioning formation should result in reduction of the firing threshold in the same neurons where the conditioning and reinforcement stimuli were converged, (b) neuron threshold may have only two possible states: initial and final ones, these were identical for all cells, the threshold may be changed only once from the initial value to the final one, (c) isomorphous relation may be introduced between some pair of arbitrary stimuli and some subset of the net neurons; any two pairs differing at least in one stimulus have unlike subsets of the convergent neurons. Stochastically organized neuronal net was used for analysis of the model. Considerable information capacity of the net gives the opportunity to consider that the conditioning formation is possible on the basis of the nervous cells. The efficienty of the model turn out to be comparable with the well known models where the conditioning formation was due to the modification of the synapses.

The three-dimensional evolution of a plane mixing layer. Part 2: Pairing and transition to turbulence

NASA Technical Reports Server (NTRS)

Moser, Robert D.; Rogers, Michael M.

1992-01-01

The evolution of three-dimensional temporally evolving plane mixing layers through as many as three pairings was simulated numerically. Initial conditions for all simulations consisted of a few low-wavenumber disturbances, usually derived from linear stability theory, in addition to the mean velocity. Three-dimensional perturbations were used with amplitudes ranging from infinitesimal to large enough to trigger a rapid transition to turbulence. Pairing is found both to inhibit the growth of infinitesimal three-dimensional disturbances and to trigger the transition to turbulence in highly three dimensional flows. The mechanisms responsible for the growth of three-dimensionality as well as the initial phases of the transition to turbulence are described. The transition to turbulence is accompanied by the formation of thin sheets of span wise vorticity, which undergo a secondary roll up. Transition also produces an increase in the degree of scalar mixing, in agreement with experimental observations of mixing transition. Simulations were also conducted to investigate changes in span wise length scale that may occur in response to the change in stream wise length scale during a pairing. The linear mechanism for this process was found to be very slow, requiring roughly three pairings to complete a doubling of the span wise scale. Stronger three-dimensionality can produce more rapid scale changes but is also likely to trigger transition to turbulence. No evidence was found for a change from an organized array of rib vortices at one span wise scale to a similar array at a larger span wise scale.

Changes in health insurance for US children and their parents: comparing 2003 to 2008.

PubMed

Angier, Heather; DeVoe, Jennifer E; Tillotson, Carrie; Wallace, Lorraine

2013-01-01

Recent policy changes have affected access to health insurance for families in the United States. Private health insurance premiums have increased, and state Medicaid programs have cut back coverage for adults. Concurrently, the Children's Health Insurance Program has made public insurance available to more children. We aimed to better understand how child and parent health insurance coverage patterns may have changed as a result of these policies. We analyzed data from the nationally representative Medical Expenditure Panel Survey, comparing cohorts from 2003 and 2008. We assessed cross-sectional and full-year coverage patterns for child/parent pairs, stratified by income. We conducted chi-square tests to assess significant differences in coverage over time. Middle-income child/parent pairs had the most significant changes in their coverage patterns. For example, those with full-year health insurance coverage significantly decreased from 85.4% in 2003 to 80.6% in 2008. There was also an increase in uninsured middle-income child/parent pairs for the full year (5.6% in 2003 to 8.3% in 2008) and an increase in pairs who had a gap in coverage (9.7% in 2003 to 13.0% in 2008). The percentage of middle-income child/parent pairs who were lacking insurance, for part or all of the year, has risen, suggesting that these families may be caught between affording private coverage and being eligible for public coverage. Unless private coverage becomes more affordable, insurance instability among middle-income families may persist despite the passage of the Patient Protection and Affordable Care Act.

Sample project: establishing a global forest monitoring capability using multi-resolution and multi-temporal remotely sensed data sets

USGS Publications Warehouse

Hansen, Matt; Stehman, Steve; Loveland, Tom; Vogelmann, Jim; Cochrane, Mark

2009-01-01

Quantifying rates of forest-cover change is important for improved carbon accounting and climate change modeling, management of forestry and agricultural resources, and biodiversity monitoring. A practical solution to examining trends in forest cover change at global scale is to employ remotely sensed data. Satellite-based monitoring of forest cover can be implemented consistently across large regions at annual and inter-annual intervals. This research extends previous research on global forest-cover dynamics and land-cover change estimation to establish a robust, operational forest monitoring and assessment system. The approach integrates both MODIS and Landsat data to provide timely biome-scale forest change estimation. This is achieved by using annual MODIS change indicator maps to stratify biomes into low, medium and high change categories. Landsat image pairs can then be sampled within these strata and analyzed for estimating area of forest cleared.

Mis-segmentation in voxel-based morphometry due to a signal intensity change in the putamen.

PubMed

Goto, Masami; Abe, Osamu; Miyati, Tosiaki; Aoki, Shigeki; Gomi, Tsutomu; Takeda, Tohoru

2017-12-01

The aims of this study were to demonstrate an association between changes in the signal intensity of the putamen on three-dimensional T1-weighted magnetic resonance images (3D-T1WI) and mis-segmentation, using the voxel-based morphometry (VBM) 8 toolbox. The sagittal 3D-T1WIs of 22 healthy volunteers were obtained for VBM analysis using the 1.5-T MR scanner. We prepared five levels of 3D-T1WI signal intensity (baseline, same level, background level, low level, and high level) in regions of interest containing the putamen. Groups of smoothed, spatially normalized tissue images were compared to the baseline group using a paired t test. The baseline was compared to the other four levels. In all comparisons, significant volume changes were observed around and outside the area that included the signal intensity change. The present study demonstrated an association between a change in the signal intensity of the putamen on 3D-T1WI and changed volume in segmented tissue images.

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.

COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.

PubMed

Cui, Licong

Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on the knowledge provided within the targeted ontology. This paper proposes a novel cross-ontology analysis method, Cross-Ontology Hierarchical Relation Examination (COHeRE), to detect inconsistencies and possible errors in hierarchical relations across multiple ontologies. COHeRE leverages the Unified Medical Language System (UMLS) knowledge source and the MapReduce cloud computing technique for systematic, large-scale ontology quality assurance work. COHeRE consists of three main steps with the UMLS concepts and relations as the input. First, the relations claimed in source vocabularies are filtered and aggregated for each pair of concepts. Second, inconsistent relations are detected if a concept pair is related by different types of relations in different source vocabularies. Finally, the uncovered inconsistent relations are voted according to their number of occurrences across different source vocabularies. The voting result together with the inconsistent relations serve as the output of COHeRE for possible ontological change. The highest votes provide initial suggestion on how such inconsistencies might be fixed. In UMLS, 138,987 concept pairs were found to have inconsistent relationships across multiple source vocabularies. 40 inconsistent concept pairs involving hierarchical relationships were randomly selected and manually reviewed by a human expert. 95.8% of the inconsistent relations involved in these concept pairs indeed exist in their source vocabularies rather than being introduced by mistake in the UMLS integration process. 73.7% of the concept pairs with suggested relationship were agreed by the human expert. The effectiveness of COHeRE indicates that UMLS provides a promising environment to enhance qualities of biomedical ontologies by performing cross-ontology examination.

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.

Freezing transition of the random bond RNA model: Statistical properties of the pairing weights

NASA Astrophysics Data System (ADS)

Monthus, Cécile; Garel, Thomas

2007-03-01

To characterize the pairing specificity of RNA secondary structures as a function of temperature, we analyze the statistics of the pairing weights as follows: for each base (i) of the sequence of length N , we consider the (N-1) pairing weights wi(j) with the other bases (j≠i) of the sequence. We numerically compute the probability distributions P1(w) of the maximal weight wimax=maxj[wi(j)] , the probability distribution Π(Y2) of the parameter Y2(i)=∑jwi2(j) , as well as the average values of the moments Yk(i)=∑jwik(j) . We find that there are two important temperatures TcTgap , the distribution P1(w) vanishes at some value w0(T)<1 , and accordingly the moments Yk(i)¯ decay exponentially as [w0(T)]k in k . For T

Low-temperature thermally regenerative electrochemical system

DOEpatents

Loutfy, R.O.; Brown, A.P.; Yao, N.P.

1982-04-21

A thermally regenerative electrochemical system is described including an electrochemical cell with two water-based electrolytes separated by an ion exchange membrane, at least one of the electrolytes containing a complexing agent and a salt of a multivalent metal whose respective order of potentials for a pair of its redox couples is reversible by a change in the amount of the ocmplexing agent in the electrolyte, the complexing agent being removable by distillation to cause the reversal.

Low temperature thermally regenerative electrochemical system

DOEpatents

Loutfy, Raouf O.; Brown, Alan P.; Yao, Neng-Ping

1983-01-01

A thermally regenerative electrochemical system including an electrochemical cell with two water-based electrolytes separated by an ion exchange membrane, at least one of the electrolytes containing a complexing agent and a salt of a multivalent metal whose respective order of potentials for a pair of its redox couples is reversible by a change in the amount of the complexing agent in the electrolyte, the complexing agent being removable by distillation to cause the reversal.

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

Wang, Yujie; Gong, Sha; Wang, Zhen

The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption ofmore » hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.« less

Can tautomerization of the A·T Watson-Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis.

PubMed

Brovarets, Ol'ha O; Hovorun, Dmytro M

2014-01-01

Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and density functional theory levels of QM theory with quantum theory of atoms in molecules analysis, the tautomerization of the A·T Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4) corresponding to a hydrophobic interfaces of protein-nucleic acid interactions. Based on the sweeps of the electron-topological, geometric, and energetic parameters, which describe the course of the tautomerization along its intrinsic reaction coordinate (IRC), it was proved that the A·T → A(∗)·T(∗) tautomerization through the DPT is a concerted (i.e. the pathway without an intermediate) and asynchronous (i.e. protons move with a time gap) process. The limiting stage of this phenomenon is the final PT along the N6H⋯O4 hydrogen bond (H-bond). The continuum with ϵ = 4 does not affect qualitatively the course of the tautomerization reaction: similar to that observed in vacuo, it proceeds via a concerted asynchronous process with the same structure of the transition state (TS). For the first time, the nine key points along the IRC of the A·T base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These nine key points have been used to define the reactant, TS, and product regions of the DPT in the A·T base pair. Considering the energy dependence of each of the three H-bonds, which stabilize the Watson-Crick and Löwdin's base pairs, along the IRC of the tautomerization, it was found that all these H-bonds in the А·Т base pair are cooperative, reinforcing each other, whereas the C2H⋯O2 H-bond in the А(∗)·Т(∗) base pair behaves anticooperatively, in other words it gets weakened while two others get strengthened. From a quantum-mechanical point of view, the A(∗)·T(∗) Löwdin's base pair appeared to be dynamically unstable because the electronic energy of the back-reaction barrier of the A·T → A(∗)·T(∗) tautomerization does not exceed zero-point vibrational energy associated with the mode for which vibrational frequency becomes imaginary in the TS of tautomerization. Additionally, it was demonstrated using the conductor-like polarizable continuum model that the effects of biomolecular environment (ϵ = 4) cannot ensure dynamic stabilization of the A(∗)·T(∗) Löwdin's base pair. These findings, together with data available from the literature, indicate that the tautomerization of the A·T Watson-Crick base pair to the A(∗)·T(∗) Löwdin's base pair through the DPT cannot be a source of spontaneous point errors that occur during DNA replication.

A fast method for searching for repeating earthquakes, applied to the northern San Francisco Bay area

NASA Astrophysics Data System (ADS)

Shakibay Senobari, N.; Funning, G.

2016-12-01

Repeating earthquakes (REs) are the regular or semi-regular failures of the same patch on a fault, producing near-identical waveforms at a given station. Sequences of REs are commonly interpreted as slip on small locked patches surrounded by large areas of fault that are creeping (Nadeau and McEvilly, 1999). Detecting them, therefore, places important constraints on the extent of fault creep at depth. In addition, the magnitude and recurrence interval of these RE sequences can be related to the creep rate and used as constraints on slip models. In this study we search for REs in northern California fault systems upon which creep is suspected, but not well constrained, including the Rodgers Creek, Maacama, Bartlett Springs, Concord-Green Valley, West Napa and Greenville faults, targeting events recorded at stations where the instrument was not changed for 10 years or more. A pair of events can be identified as REs based on a high cross-correlation coefficient (CCC) between their waveforms. Thus a fundamental step in RE searches is calculating the CCC for all event waveform pairs recorded at common stations. This becomes computationally expensive for large data sets. To expedite our search, we use a fast and accurate similarity search algorithm developed by the computer science community (Mueen et al., 2015; Zhu et al., 2016). Our initial tests on a data set including 1500 waveforms suggest it is around 40 times faster than the algorithm that we used previously (Shakibay Senobari and Funning, AGU Fall Meeting 2014). We search for event pairs with CCC>0.85 and cluster them based on their similarity. A second, location based filter, based on the differential S-P times for each event pair at 5 or more stations, is used as an independent check. We consider a cluster of events a RE sequence if the source location separation distance for each pair is less than the estimated circular size of the source (e.g. Chen et al., 2008); these are gathered into an RE catalogue. In future, we plan to use this information in combination with geodetic data to produce a robust creep distribution model for all of the faults in this region.

Quantum entanglement and quantum information in biological systems (DNA)

NASA Astrophysics Data System (ADS)

Hubač, Ivan; Švec, Miloslav; Wilson, Stephen

2017-12-01

Recent studies of DNA show that the hydrogen bonds between given base pairs can be treated as diabatic systems with spin-orbit coupling. For solid state systems strong diabaticity and spin-orbit coupling the possibility of forming Majorana fermions has been discussed. We analyze the hydrogen bonds in the base pairs in DNA from this perspective. Our analysis is based on a quasiparticle supersymmetric transformation which couples electronic and vibrational motion and includes normal coordinates and the corresponding momenta. We define qubits formed by Majorana fermions in the hydrogen bonds and also discuss the entangled states in base pairs. Quantum information and quantum entropy are introduced. In addition to the well-known classical information connected with the DNA base pairs, we also consider quantum information and show that the classical and quantum information are closely connected.

Hyperthyroidism is associated with work disability and loss of labour market income. A Danish register-based study in singletons and disease-discordant twin pairs.

PubMed

Brandt, Frans; Thvilum, Marianne; Hegedüs, Laszlo; Brix, Thomas Heiberg

2015-11-01

To examine the risk of disability pension and changes in labour market income in patients with hyperthyroidism. From a 5% random sample of the Danish population and twins from the Danish Twin Registry we identified 1942 hyperthyroid singletons and 7768 non-hyperthyroid (matched 1:4) controls as well as 584 same-sex twin pairs discordant for hyperthyroidism. Singletons and twins were followed for a mean of 9 years (range 1-20). Cox regression analysis was used to examine the risk of disability pension and a difference-in-differences model was used to evaluate changes in labour market income. Hyperthyroid individuals had an increased risk of receiving disability pension: hazard ratio (HR) was 1.88, (95% CI: 1.57-2.24). Subdividing as to the cause of hyperthyroidism did not change this finding: Graves' disease (GD) HR was 1.51 (95% CI: 0.87-2.63) and toxic nodular goitre (TNG) HR was 2.10 (95% CI: 1.02-4.36). With respect to labour market income, the income of hyperthyroid individuals increased on average 1189 € less than their controls (P<0.001). This difference in income was more pronounced in GD (2539 €) than in TNG (132 €). Essentially similar results, with respect to disability pension and labour market income, were seen within monozygotic twin pairs discordant for hyperthyroidism. Hyperthyroidism is associated with severe work disability as reflected by an 88% increased risk of receiving disability pension and a significant loss of labour market income. Similar results in monozygotic twins discordant for hyperthyroidism suggest that genetic confounding is unlikely. © 2015 European Society of Endocrinology.

Heterogeneity in the spatial receptive field architecture of multisensory neurons of the superior colliculus and its effects on multisensory integration

PubMed Central

Ghose, Dipanwita; Wallace, Mark T.

2013-01-01

Multisensory integration has been widely studied in neurons of the mammalian superior colliculus (SC). This has led to the description of various determinants of multisensory integration, including those based on stimulus- and neuron-specific factors. The most widely characterized of these illustrate the importance of the spatial and temporal relationships of the paired stimuli as well as their relative effectiveness in eliciting a response in determining the final integrated output. Although these stimulus-specific factors have generally been considered in isolation (i.e., manipulating stimulus location while holding all other factors constant), they have an intrinsic interdependency that has yet to be fully elucidated. For example, changes in stimulus location will likely also impact both the temporal profile of response and the effectiveness of the stimulus. The importance of better describing this interdependency is further reinforced by the fact that SC neurons have large receptive fields, and that responses at different locations within these receptive fields are far from equivalent. To address these issues, the current study was designed to examine the interdependency between the stimulus factors of space and effectiveness in dictating the multisensory responses of SC neurons. The results show that neuronal responsiveness changes dramatically with changes in stimulus location – highlighting a marked heterogeneity in the spatial receptive fields of SC neurons. More importantly, this receptive field heterogeneity played a major role in the integrative product exhibited by stimulus pairings, such that pairings at weakly responsive locations of the receptive fields resulted in the largest multisensory interactions. Together these results provide greater insight into the interrelationship of the factors underlying multisensory integration in SC neurons, and may have important mechanistic implications for multisensory integration and the role it plays in shaping SC mediated behaviors. PMID:24183964

Paired peer review of university classroom teaching in a school of nursing and midwifery.

PubMed

Bennett, Paul N; Parker, Steve; Smigiel, Heather

2012-08-01

Peer review of university classroom teaching can increase the quality of teaching but is not universally practiced in Australian universities. To report an evaluation of paired peer-review process using both paper and web based teaching evaluation tools. Twenty university teachers in one metropolitan Australian School of Nursing and Midwifery were randomly paired and then randomly assigned to a paper based or web-based peer review tool. Each teacher reviewed each other's classroom teaching as part of a peer review program. The participants then completed an 18 question survey evaluating the peer review tool and paired evaluation process. Responses were analyzed using frequencies and percentages. Regardless of the tool used, participants found this process of peer review positive (75%), collegial (78%), supportive (61%) and non-threatening (71%). Participants reported that the peer review will improve their own classroom delivery (61%), teaching evaluation (61%) and planning (53%). The web-based tool was found to be easier to use and allowed more space than the paper-based tool. Implementation of a web-based paired peer review system can be a positive method of peer review of university classroom teaching. Pairing of teachers to review each other's classroom teaching is a promising strategy and has the potential to improve teaching in teaching universities. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Cocaine decreases saccharin preference without altering sweet taste sensitivity.

PubMed

Roebber, Jennifer K; Izenwasser, Sari; Chaudhari, Nirupa

2015-06-01

In rodents, saccharin consumption is suppressed when the sweet taste stimulus is paired with moderate doses of cocaine. Several hypotheses have been used to explain the seemingly contradictory effect of decreased consumption of a normally preferred substance following a highly rewarding drug. A common theme across these hypotheses is that saccharin is interpreted as less rewarding after cocaine pairing. We considered the alternative possibility that suppression is caused not by a change in reward circuitry, but rather by a change in taste detection, for instance by altering the afferent taste response and decreasing sensitivity to sweet taste stimuli. To evaluate this possibility, we measured saccharin taste sensitivity of mice before and after a standard cocaine-pairing paradigm. We measured taste sensitivity using a brief-access lickometer equipped with multiple concentrations of saccharin solution and established concentration-response curves before and after saccharin-cocaine pairing. Our results indicate that the EC50 for saccharin was unaltered following pairing. Instead, the avidity of licking saccharin, an indicator of motivation, was depressed. Latency to first-lick, a negative indicator of motivation, was also dramatically increased. Thus, our findings are consistent with the interpretation that saccharin-cocaine pairing results in devaluing of the sweet taste reward. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparison of Novel and Known Neuroprotectants for Treating Exposure to Different Types of Toxins

DTIC Science & Technology

2000-09-01

NMDA for 30 s followed by rapid quenching with the antagonist AP5. Immunoassays of the experimental samples indicated that concentrations of NCAM...for anti-NCAM immunoblotting; the migration pattern for the three isoforms is shown. (B) Paired samples of experimental and control slices were...used to determine the change in NCAM-180 immunoreactivity in experimental samples as compared to control samples ; the mean change (± SEM) among paired

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position

PubMed Central

Liu, Wei; Shin, Dongwon; Ng, Martin; Sanbonmatsu, Karissa Y.; Tor, Yitzhak; Cooperman, Barry S.

2017-01-01

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5′- and 3′-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix. PMID:28850078

Patterns of call communication between group-housed zebra finches change during the breeding cycle.

PubMed

Gill, Lisa F; Goymann, Wolfgang; Ter Maat, Andries; Gahr, Manfred

2015-10-06

Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems.

Amplitude fluctuations driven by the density of electron pairs within nanosize granular structures inside strongly disordered superconductors: evidence for a shell-like effect.

PubMed

Ghosh, Sanjib; Mandal, Sudhansu S

2013-11-15

Motivated by the recent observation of the shell effect in a nanoscale pure superconductor by Bose et al. [Nat. Mater. 9, 550 (2010)], we explore the possible shell-like effect in a strongly disordered superconductor as it is known to produce nanosize superconducting puddles (SPs). We find a remarkable change in the texture of the pairing amplitudes that is responsible for forming the SP, upon monotonic tuning of the average electron density, , and keeping the disorder landscape unaltered. Both the spatially averaged pairing amplitude and the quasiparticle excitation gap oscillate with . This oscillation is due to a rapid change in the low-lying quasiparticle energy spectra and thereby a change in the shapes and positions of the SPs. We establish a correlation between the formation of SPs and the shell-like effect. The experimental consequences of our theory are also discussed.

Pair Cascades and Deathlines in Magnetic Fields with Offset Polar Caps

NASA Technical Reports Server (NTRS)

Harding, Alice K.; Muslimov, Alex G.

2012-01-01

We present results of electron-positron pair cascade simulations in a dipole magnetic field whose polar cap is offset from the dipole axis. In such a field geometry, the polar cap is displaced a small fraction of the neutron star radius from the star symmetry axis and the field line radius of curvature is modified. Using the modified parallel electric field near the offset polar cap, we simulate pair cascades to determine the pair deathlines and pair multiplicities as a function of the offset. We find that the pair multiplicity can change dr;unatically with a modest offset, with a significant increase on one side of the polar cap. Lower pair deathlines allow a larger fraction of the pulsar population, that include old and millisecond pulsars, to produce cascades with high multiplicity. The results have some important implications for pulsar particle production, high-energy emission and cosmic-ray contribution.

Galápagos hydroclimate of the Common Era from paired microalgal and mangrove biomarker 2H/1H values

PubMed Central

Sachs, Julian P.

2016-01-01

Tropical maritime precipitation affects global atmospheric circulation, influencing storm tracks and the size and location of subtropical deserts. Paleoclimate evidence suggests centuries-long changes in rainfall in the tropical Pacific over the past 2,000 y, but these remain poorly characterized across most of the ocean where long, continuous proxy records capable of resolving decadal-to-centennial climate changes are still virtually nonexistent despite substantial efforts to develop them. Here we apply a new climate proxy based on paired hydrogen isotope ratios from microalgal and mangrove-derived sedimentary lipids in the Galápagos to reconstruct maritime precipitation changes during the Common Era. We show that increased rainfall during the Little Ice Age (LIA) (∼1400–1850 CE) was likely caused by a southward migration of the Intertropical Convergence Zone (ITCZ), and that this shift occurred later than previously recognized, coeval with dynamically linked precipitation changes in South America and the western tropical Pacific. Before the LIA, we show that drier conditions at the onset of the Medieval Warm Period (∼800–1300 CE) and wetter conditions ca. 2 ka were caused by changes in the El Niño/Southern Oscillation (ENSO). Collectively, the large natural variations in tropical rainfall we detect, each linked to a multicentury perturbation of either ENSO-like variability or the ITCZ, imply a high sensitivity of tropical Pacific rainfall to climate forcings. PMID:26976574

Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

PubMed

Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

2014-01-01

DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

The Effects of Reinforcer Pairing and Fading on Preschoolers' Snack Selections

ERIC Educational Resources Information Center

Solberg, Katherine M.; Hanley, Gregory P.; Layer, Stacy A.; Ingvarsson, Einar T.

2007-01-01

The effects of reinforcement pairing and fading on preschoolers' snack selections were evaluated in a multiple baseline design. Baseline preferences for snack options were assessed via repeated paired-item preference assessments. Edible, social, and activity-based reinforcers were then exclusively paired with a less preferred snack option. Once…

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

PubMed Central

Lavery, Richard; Zakrzewska, Krystyna; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dixit, Surjit; Jayaram, B.; Lankas, Filip; Laughton, Charles; Maddocks, John H.; Michon, Alexis; Osman, Roman; Orozco, Modesto; Perez, Alberto; Singh, Tanya; Spackova, Nada; Sponer, Jiri

2010-01-01

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein–DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50–100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA. PMID:19850719

Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase ι: Hoogsteen or Watson-Crick base pairing?†

PubMed Central

Donny-Clark, Kerry; Shapiro, Robert; Broyde, Suse

2009-01-01

Bypass across DNA lesions by specialized polymerases is essential for maintenance of genomic stability. Human DNA polymerase ι (polι) is a bypass polymerase of the Y family. Crystal structures of polι suggest that Hoogsteen base pairing is employed to bypass minor groove DNA lesions, placing them on the spacious major groove side of the enzyme. Primer extension studies have shown that polι is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetyl-aminofluorene (dG-AAF). We present molecular dynamics simulations and free energy calculations suggesting that Watson-Crick base pairing could be employed in polι for bypass of dG-AAF. In polι with Hoogsteen paired dG-AAF the bulky AAF moiety would reside on the cramped minor groove side of the template. The Hoogsteen-capable conformation distorts the active site, disrupting interactions necessary for error-free incorporation of dC opposite the lesion. Watson-Crick pairing places the AAF rings on the spacious major groove side, similar to the position of minor groove adducts observed with Hoogsteen pairing. Watson-Crick paired structures show a well-ordered active site, with a near reaction-ready ternary complex. Thus our results suggest that polι would utilize the same spacious region for lesion bypass of both major and minor groove adducts. Therefore, purine adducts with bulk on the minor groove side would use Hoogsteen pairing, while adducts with the bulky lesion on the major groove side would utilize Watson-Crick base pairing as indicated by our MD simulations for dG-AAF. This suggests the possibility of an expanded role for polι in lesion bypass. PMID:19072536

Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?

PubMed

Donny-Clark, Kerry; Shapiro, Robert; Broyde, Suse

2009-01-13

Bypass across DNA lesions by specialized polymerases is essential for maintenance of genomic stability. Human DNA polymerase iota (poliota) is a bypass polymerase of the Y family. Crystal structures of poliota suggest that Hoogsteen base pairing is employed to bypass minor groove DNA lesions, placing them on the spacious major groove side of the enzyme. Primer extension studies have shown that poliota is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF). We present molecular dynamics simulations and free energy calculations suggesting that Watson-Crick base pairing could be employed in poliota for bypass of dG-AAF. In poliota with Hoogsteen-paired dG-AAF the bulky AAF moiety would reside on the cramped minor groove side of the template. The Hoogsteen-capable conformation distorts the active site, disrupting interactions necessary for error-free incorporation of dC opposite the lesion. Watson-Crick pairing places the AAF rings on the spacious major groove side, similar to the position of minor groove adducts observed with Hoogsteen pairing. Watson-Crick-paired structures show a well-ordered active site, with a near reaction-ready ternary complex. Thus our results suggest that poliota would utilize the same spacious region for lesion bypass of both major and minor groove adducts. Therefore, purine adducts with bulk on the minor groove side would use Hoogsteen pairing, while adducts with the bulky lesion on the major groove side would utilize Watson-Crick base pairing as indicated by our MD simulations for dG-AAF. This suggests the possibility of an expanded role for poliota in lesion bypass.

STS 118 Return Samples: Assessment of Air Quality aboard the Shuttle (STS-118) and International Space Station

NASA Technical Reports Server (NTRS)

James, John T.

2007-01-01

The toxicological assessments of 2 grab sample canisters (GSCs) and one pair of formaldehyde badges from the Shuttle are reported. Analytical methods have not changed from earlier reports. The recoveries of the 3 surrogates (C-13-acetone, fluorobenzene, and chlorobenzene) from the 2 GSCs averaged 120, 117, and 122 %, respectively. Three formaldehyde controls averaged 98% recovery. The Shuttle atmosphere was acceptable for human respiration. The toxicological assessment of 8 GSCs and 6 pairs of formaldehyde badges from the ISS is shown. The recoveries of the 3 standards (as listed above) from the GSCs averaged 99, 99 and 99%, respectively. Three formaldehyde control badges averaged 98% recovery. Based on these limited samples, the ISS atmosphere is acceptable for human respiration. The alcohol levels were well controlled throughout the period of sampling.

Base drive circuit

DOEpatents

Lange, Arnold C.

1995-01-01

An improved base drive circuit (10) having a level shifter (24) for providing bistable input signals to a pair of non-linear delays (30, 32). The non-linear delays (30, 32) provide gate control to a corresponding pair of field effect transistors (100, 106) through a corresponding pair of buffer components (88, 94). The non-linear delays (30, 32) provide delayed turn-on for each of the field effect transistors (100, 106) while an associated pair of transistors (72, 80) shunt the non-linear delays (30, 32) during turn-off of the associated field effect transistor (100, 106).

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.

Mutations That Improve the pRE Promoter of Coliphage Lambda

PubMed Central

Mahoney, Michael E.; Wulff, Daniel L.

1987-01-01

The dya5 mutation, a C→T change at position -43 of the λ pRE promoter, results in a twofold increase in pRE activity in vivo. Smaller increases in pRE activity are found for the dya2 mutation, a T→C change at position -1 of pRE, and the dya3 mutation, an A→G change at +5 of pRE. The mutant p RE promoters retain complete dependence on cII protein for activity. These observations argue, at least for pRE-like promoters, that promoter activities are influenced by nucleotide sequences at least eight nucleotides to the 5'-side of the conventional -35 region consensus sequence, and by nucleotide sequences near the start-site of transcription. Although Hawley and McClure (1983) found A·T pairs more frequently than G·TC pairs in the region of -40 to -45 of prokaryotic promoters, other mutations that change a G·TC pair to an A·T pair at positions -41, -44 and -45 of pRE do not result in increased promoter activity. We also found that a T→C change at position -42 results in a mild decrease in promoter activity. These observations argue that Ts at positions -42 and -43 of pRE are required for maximum promoter activity, but do not support the hypothesis that As and Ts in the -40 to -45 region generally lead to higher promoter activities. PMID:2953648

Split-Ring Resonator-Based Strain Sensor on Flexible Substrates for Glaucoma Detection

NASA Astrophysics Data System (ADS)

Ekinci, Gizem; Deniz Yalcinkaya, Arda; Dundar, Gunhan; Torun, Hamdi

2016-10-01

This paper presents split-ring resonator-based strain sensors designed and characterized for glaucoma detection application. The geometry of the sensor is optimized such that it can be embedded in a contact lens. Silver conductive paint is to form the sensors realized on flexible substrates made of cellulose acetate and latex rubber. The devices are excited and interrogated using a pair of monopole antennas and the characteristics of devices with different curvature profiles are obtained. The sensitivity of the device, i.e. the change in resonant frequency for a unit change in radius of curvature, on acetate film is calculated as -4.73 MHz/mm and the sensitivity of the device on latex is 33.2 MHz/mm. The results indicate that the demonstrated device is suitable for glaucoma diagnosis.

Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

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

Carra,J.; McHugh, C.; Mulligan, S.

2007-01-01

We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding tomore » a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.« less

Stroke Health and Risk Education (SHARE): Design, methods, and theoretical basis

PubMed Central

Brown, Devin L.; Conley, Kathleen M.; Resnicow, Kenneth; Murphy, Jillian; Sánchez, Brisa N.; Cowdery, Joan E.; Sais, Emma; Lisabeth, Lynda D.; Skolarus, Lesli E.; Zahuranec, Darin B.; Williams, Geoffrey C.; Morgenstern, Lewis B.

2012-01-01

Background Stroke is a disease with tremendous individual, family, and societal impact across all race/ethnic groups. Mexican Americans, the largest subgroup of Hispanic Americans, are at even higher risk of stroke than European Americans. Aim To test the effectiveness of a culturally sensitive, church-based, multicomponent, motivational enhancement intervention for Mexican Americans and European Americans in reducing stroke risk factors. Methods Participants enroll in family or friendship pairs, from the same Catholic church in the Corpus Christi Texas area, and are encouraged to change diet and physical activity behaviors and provide support for behavior change to their partners. Churches are randomized to either the intervention or control group. Goal enrollment for each of the 10 participating churches is 40 participant pairs. The intervention consists of self-help materials (including a motivational short film, cookbook/healthy eating guide, physical activity guide with pedometer, and photonovella), five motivational interviewing calls, two tailored newsletters, parish health promotion activities and environmental changes, and a peer support workshop where participants learn to provide autonomy supportive counseling to their partner. SHARE’s three primary outcomes are self-reported sodium intake, fruit and vegetable intake, and level of physical activity. Participants complete questionnaires and have measurements at baseline, six months, and twelve months. Persistence testing is performed at 18 months in the intervention group. PMID:22421317

Leisure-time physical inactivity and association with body mass index: a Finnish Twin Study with a 35-year follow-up.

PubMed

Piirtola, Maarit; Kaprio, Jaakko; Waller, Katja; Heikkilä, Kauko; Koskenvuo, Markku; Svedberg, Pia; Silventoinen, Karri; Kujala, Urho M; Ropponen, Annina

2017-02-01

We investigated the stability and change of leisure-time physical inactivity in adult men and women during a 35-year follow-up. We also analysed the impact of long-term physical inactivity on the development of body mass index (BMI). : In this population-based cohort study, 5254 Finnish twin individuals (59% women) participated in four surveys in 1975, 1981, 1990 and 2011. Mean age at baseline was 23.9 years. Individual long-term leisure-time physical activity (LTPA) was categorized into seven classes varying from 'persistently inactive' to 'persistently active'. We used the multivariate multilevel mixed-effects linear regression model and paired-sample t-test in the analyses. Co-twin control design was used for examining within-pair associations. : Of men 11%, and of women 8%, were persistently inactive. Among both sexes, the mean BMI slope trajectories were steeper among the persistently inactive and those who became inactive than among those who were persistently active. Overall, the inactive participants gained 1.4 kg/m 2 [95% confidence interval (CI) 1.2 to 1.7] more in weight than did the active participants from 1975 to 2011. Among twin pairs discordant for LTPA, the corresponding difference was 1.4 kg/m 2 (95% CI 0.83 to 2.0) in dizygotic pairs and 0.68 kg/m 2 (95% CI 0.05 to1.3) in monozygotic pairs. Over a 35-year time span from young adulthood, persistently inactive participants and those who had become inactive had greater weight increases than those who were persistently active. This association was also found in twin-pair analyses, although attenuated in monozygotic pairs. This may support the importance of LTPA in weight management, although further causal inference is required. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

Fully gapped superconductivity with no sign change in the prototypical heavy-fermion CeCu2Si2.

PubMed

Yamashita, Takuya; Takenaka, Takaaki; Tokiwa, Yoshifumi; Wilcox, Joseph A; Mizukami, Yuta; Terazawa, Daiki; Kasahara, Yuichi; Kittaka, Shunichiro; Sakakibara, Toshiro; Konczykowski, Marcin; Seiro, Silvia; Jeevan, Hirale S; Geibel, Christoph; Putzke, Carsten; Onishi, Takafumi; Ikeda, Hiroaki; Carrington, Antony; Shibauchi, Takasada; Matsuda, Yuji

2017-06-01

In exotic superconductors, including high- T c copper oxides, the interactions mediating electron Cooper pairing are widely considered to have a magnetic rather than a conventional electron-phonon origin. Interest in this exotic pairing was initiated by the 1979 discovery of heavy-fermion superconductivity in CeCu 2 Si 2 , which exhibits strong antiferromagnetic fluctuations. A hallmark of unconventional pairing by anisotropic repulsive interactions is that the superconducting energy gap changes sign as a function of the electron momentum, often leading to nodes where the gap goes to zero. We report low-temperature specific heat, thermal conductivity, and magnetic penetration depth measurements in CeCu 2 Si 2 , demonstrating the absence of gap nodes at any point on the Fermi surface. Moreover, electron irradiation experiments reveal that the superconductivity survives even when the electron mean free path becomes substantially shorter than the superconducting coherence length. This indicates that superconductivity is robust against impurities, implying that there is no sign change in the gap function. These results show that, contrary to long-standing belief, heavy electrons with extremely strong Coulomb repulsions can condense into a fully gapped s-wave superconducting state, which has an on-site attractive pairing interaction.

Multi-hop teleportation based on W state and EPR pairs

NASA Astrophysics Data System (ADS)

Hai-Tao, Zhan; Xu-Tao, Yu; Pei-Ying, Xiong; Zai-Chen, Zhang

2016-05-01

Multi-hop teleportation has significant value due to long-distance delivery of quantum information. Many studies about multi-hop teleportation are based on Bell pairs, partially entangled pairs or W state. The possibility of multi-hop teleportation constituted by partially entangled pairs relates to the number of nodes. The possibility of multi-hop teleportation constituted by double W states is after n-hop teleportation. In this paper, a multi-hop teleportation scheme based on W state and EPR pairs is presented and proved. The successful possibility of quantum information transmitted hop by hop through intermediate nodes is deduced. The possibility of successful transmission is after n-hop teleportation. Project supported by the National Natural Science Foundation of China (Grant No. 61571105), the Prospective Future Network Project of Jiangsu Province, China (Grant No. BY2013095-1-18), and the Independent Project of State Key Laboratory of Millimeter Waves, China (Grant No. Z201504).

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.

Activity and milk compositional changes following experimentally induced Streptococcus uberis bovine mastitis.

PubMed

Kester, H J; Sorter, D E; Hogan, J S

2015-02-01

Milk constituents and physical activity of cows experimentally infected with Streptococcus uberis mastitis were compared with those of uninfected cows. Twelve late-lactation Holsteins cows were paired based on milk production and parity. One cow in each pair was experimentally infected in the right front mammary gland with Strep. uberis. The remaining cow in each pair served as an uninfected control. Real-time analyses of milk constituents provided fat, protein, and lactose percentages at each milking. Pedometers were placed on the left front leg of all cows and activity was measured. Intramammary infections with Strep. uberis reduced milk yield in experimental cows by approximately 1.6kg/d in the first week after challenge compared with control cows. Lactose percentage in milk was reduced on d 3, 4, 5, and 6 after challenge in treatment cows compared with controls. Percentages of fat and protein in milk did not differ between infected and uninfected cows the week after infections were induced. Total steps per day were reduced and minutes resting per day were increased the week after experimental challenge in infected cows compared with control cows. The number of resting bouts did not differ between infected and uninfected cows. Changes in percentage of lactose in milk and animal activity caused by experimentally induced Strep. uberis mastitis were detected by the automated milk analyzer and pedometer systems. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Changes in liver stiffness measurement using acoustic radiation force impulse elastography after antiviral therapy in patients with chronic hepatitis C.

PubMed

Chen, Sheng-Hung; Lai, Hsueh-Chou; Chiang, I-Ping; Su, Wen-Pang; Lin, Chia-Hsin; Kao, Jung-Ta; Chuang, Po-Heng; Hsu, Wei-Fan; Wang, Hung-Wei; Chen, Hung-Yao; Huang, Guan-Tarn; Peng, Cheng-Yuan

2018-01-01

To compare on-treatment and off-treatment parameters acquired using acoustic radiation force impulse elastography, the Fibrosis-4 (FIB-4) index, and aspartate aminotransferase-to-platelet ratio index (APRI) in patients with chronic hepatitis C (CHC). Patients received therapies based on pegylated interferon or direct-acting antiviral agents. The changes in paired patient parameters, including liver stiffness (LS) values, the FIB-4 index, and APRI, from baseline to sustained virologic response (SVR) visit (24 weeks after the end of treatment) were compared. Multiple regression models were used to identify significant factors that explained the correlations with LS, FIB-4, and APRI values and SVR. A total of 256 patients were included, of which 219 (85.5%) achieved SVR. The paired LS values declined significantly from baseline to SVR visit in all groups and subgroups except the nonresponder subgroup (n = 10). Body mass index (P = 0.0062) and baseline LS (P < 0.0001) were identified as independent factors that explained the LS declines. Likewise, the baseline FIB-4 (P < 0.0001) and APRI (P < 0.0001) values independently explained the declines in the FIB-4 index and APRI, respectively. Moreover, interleukin-28B polymorphisms, baseline LS, and rapid virologic response were identified as independent correlates with SVR. Paired LS measurements in patients treated for CHC exhibited significant declines comparable to those in FIB-4 and APRI values. These declines may have correlated with the resolution of necroinflammation. Baseline LS values predicted SVR.

Treatment retention in a prison-based residential sex offender treatment program.

PubMed

Pelissier, Bernadette

2007-12-01

This study assessed the role of static factors, a dynamic factor (motivation to change sexually deviant behavior), and an administrative factor in predicting treatment retention within a prison-based sex offender treatment program. The analyses also included assessing differences in initial levels of motivation and differences in beginning-versus end-of-treatment motivation scores for various types of program discharges. The sample consisted of 251 individuals who were admitted to a residential prison-based sex offender treatment program where 46% completed the program. Paired comparison t-tests showed higher motivation scores at the end of treatment only among treatment completers. Multivariate analyses showed that treatment retention was associated with higher initial motivation scores, higher levels of education and admission to treatment within 3 months of initial commitment to prison. Implications for motivational enhancement programming as well as for changes in admission criteria are discussed.

Long-Term Visuo-Gustatory Appetitive and Aversive Conditioning Potentiate Human Visual Evoked Potentials

PubMed Central

Christoffersen, Gert R. J.; Laugesen, Jakob L.; Møller, Per; Bredie, Wender L. P.; Schachtman, Todd R.; Liljendahl, Christina; Viemose, Ida

2017-01-01

Human recognition of foods and beverages are often based on visual cues associated with flavors. The dynamics of neurophysiological plasticity related to acquisition of such long-term associations has only recently become the target of investigation. In the present work, the effects of appetitive and aversive visuo-gustatory conditioning were studied with high density EEG-recordings focusing on late components in the visual evoked potentials (VEPs), specifically the N2-P3 waves. Unfamiliar images were paired with either a pleasant or an unpleasant juice and VEPs evoked by the images were compared before and 1 day after the pairings. In electrodes located over posterior visual cortex areas, the following changes were observed after conditioning: the amplitude from the N2-peak to the P3-peak increased and the N2 peak delay was reduced. The percentage increase of N2-to-P3 amplitudes was asymmetrically distributed over the posterior hemispheres despite the fact that the images were bilaterally symmetrical across the two visual hemifields. The percentage increases of N2-to-P3 amplitudes in each experimental subject correlated with the subject’s evaluation of positive or negative hedonic valences of the two juices. The results from 118 scalp electrodes gave surface maps of theta power distributions showing increased power over posterior visual areas after the pairings. Source current distributions calculated from swLORETA revealed that visual evoked currents rose as a result of conditioning in five cortical regions—from primary visual areas and into the inferior temporal gyrus (ITG). These learning-induced changes were seen after both appetitive and aversive training while a sham trained control group showed no changes. It is concluded that long-term visuo-gustatory conditioning potentiated the N2-P3 complex, and it is suggested that the changes are regulated by the perceived hedonic valence of the US. PMID:28983243

Comparison of two color-difference formulas using the Bland-Altman approach based on gingiva color space.

PubMed

Gómez Polo, Cristina; Montero, Javier; Martín Casado, Ana Maria

2018-04-23

The objectives of this study were to determine the relationship between the results provided by the classical CIELab (ΔE ab *) and the CIEDE2000 (ΔE00) formulas and the gingival color space using the Bland and Altman limits of agreement, to use this relationship to establish the equivalences between the gingival color thresholds of perceptibility of both formulas, and to evaluate whether the relationship between ΔE ab * and ΔE00 is modified depending on the axis in which the changes occur. The means of the L*, a*, and b* coordinates of the 21 gingiva porcelain samples (Heraceram, Heraeus Kulzer Mitsui Chemical Groups) were used and the differences in color were calculated in 210 pairs of samples using the CIELab (ΔE*ab) and CIEDE2000 (ΔE00) color-difference formulas. The results obtained with these formulas were compared and the limits of agreement after a logarithmic transformation of the data were obtained. The relationship between both formulas was ln ΔE 00  = - 0.22 + ln ΔE ab *. The results obtained with the CIELab formula were between 1.01 (95% confidence interval 0.98-1.03) and 1.54 (95% confidence interval 1.52-1.59) times higher than those obtained with the CIEDE200 formula. In the gingiva color space, the scale factor between the CIEDE2000 and CIELab values changes from 0.63 to 1.02, such that providing an accurate scale factor between both values proves difficult. The pairs with the highest ratio were those where the difference in color was mainly due to changes in lightness, whereas the pairs with the smallest ratio were those where the difference in color was mainly due to changes in the blue-yellow or green-red axes.

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