Using response time distributions to examine top-down influences on attentional capture.

PubMed

Burnham, Bryan R

2013-02-01

Three experiments examined contingent attentional capture, which is the finding that cuing effects are larger when cues are perceptually similar to a target than when they are dissimilar to the target. This study also analyzed response times (RTs) in terms of the underlying distributions for valid cues and invalid cues. Specifically, an ex-Gaussian analysis and a vincentile analysis examined the influence of top-down attentional control settings on the shift and skew of RT distributions and how the shift and the skew contributed to the cuing effects in the mean RTs. The results showed that cue/target similarity influenced the size of cuing effects. The RT distribution analyses showed that the cuing effects reflected only a shifting effect, not a skewing effect, in the RT distribution between valid cues and invalid cues. That is, top-down attentional control moderated the cuing effects in the mean RTs through distribution shifting, not distribution skewing. The results support the contingent orienting hypothesis (Folk, Remington, & Johnston, Journal of Experimental Psychology: Human Perception and Performance, 18, 1030-1044, 1992) over the attentional disengagement account (Theeuwes, Atchley, & Kramer, 2000) as an explanation for when top-down attentional settings influence the selection of salient stimuli.

Impacts of Streambed Heterogeneity and Anisotropy on Residence Time of Hyporheic Zone.

PubMed

Liu, Suning; Chui, Ting Fong May

2018-05-01

The hyporheic zone (HZ), which is the region beneath or alongside a streambed, plays an important role in the stream's ecology. The duration that a water molecule or a solute remains within the HZ, or residence time (RT), is one of the most common metrics used to evaluate the function of the HZ. The RT is greatly influenced by the streambed's hydraulic conductivity (K), which is intrinsically difficult to characterize due to its heterogeneity and anisotropy. Many laboratory and numerical studies of the HZ have simplified the streambed K to a constant, thus producing RT values that may differ from those gathered from the field. Some studies have considered the heterogeneity of the HZ, but very few have accounted for anisotropy or the natural K distributions typically found in real streambeds. This study developed numerical models in MODFLOW to examine the influence of heterogeneity and anisotropy, and that of the natural K distribution in a streambed, on the RT of the HZ. Heterogeneity and anisotropy were both found to shorten the mean and median RTs while increasing the range of the RTs. Moreover, heterogeneous K fields arranged in a more orderly pattern had longer RTs than those with random K distributions. These results could facilitate the design of streambed K values and distributions to achieve the desired RT during river restoration. They could also assist the translation of results from the more commonly considered homogeneous and/or isotropic conditions into heterogeneous and anisotropic field situations. © 2017, National Ground Water Association.

Display size effects in visual search: analyses of reaction time distributions as mixtures.

PubMed

Reynolds, Ann; Miller, Jeff

2009-05-01

In a reanalysis of data from Cousineau and Shiffrin (2004) and two new visual search experiments, we used a likelihood ratio test to examine the full distributions of reaction time (RT) for evidence that the display size effect is a mixture-type effect that occurs on only a proportion of trials, leaving RT in the remaining trials unaffected, as is predicted by serial self-terminating search models. Experiment 1 was a reanalysis of Cousineau and Shiffrin's data, for which a mixture effect had previously been established by a bimodal distribution of RTs, and the results confirmed that the likelihood ratio test could also detect this mixture. Experiment 2 applied the likelihood ratio test within a more standard visual search task with a relatively easy target/distractor discrimination, and Experiment 3 applied it within a target identification search task within the same types of stimuli. Neither of these experiments provided any evidence for the mixture-type display size effect predicted by serial self-terminating search models. Overall, these results suggest that serial self-terminating search models may generally be applicable only with relatively difficult target/distractor discriminations, and then only for some participants. In addition, they further illustrate the utility of analysing full RT distributions in addition to mean RT.

An RT distribution analysis of relatedness proportion effects in lexical decision and semantic categorization reveals different mechanisms.

PubMed

de Wit, Bianca; Kinoshita, Sachiko

2015-01-01

The magnitude of the semantic priming effect is known to increase as the proportion of related prime-target pairs in an experiment increases. This relatedness proportion (RP) effect was studied in a lexical decision task at a short prime-target stimulus onset asynchrony (240 ms), which is widely assumed to preclude strategic prospective usage of the prime. The analysis of the reaction time (RT) distribution suggested that the observed RP effect reflected a modulation of a retrospective semantic matching process. The pattern of the RP effect on the RT distribution found here is contrasted to that reported in De Wit and Kinoshita's (2014) semantic categorization study, and it is concluded that the RP effect is driven by different underlying mechanisms in lexical decision and semantic categorization.

A reliability analysis of cardiac repolarization time markers.

PubMed

Scacchi, S; Franzone, P Colli; Pavarino, L F; Taccardi, B

2009-06-01

Only a limited number of studies have addressed the reliability of extracellular markers of cardiac repolarization time, such as the classical marker RT(eg) defined as the time of maximum upslope of the electrogram T wave. This work presents an extensive three-dimensional simulation study of cardiac repolarization time, extending the previous one-dimensional simulation study of a myocardial strand by Steinhaus [B.M. Steinhaus, Estimating cardiac transmembrane activation and recovery times from unipolar and bipolar extracellular electrograms: a simulation study, Circ. Res. 64 (3) (1989) 449]. The simulations are based on the bidomain - Luo-Rudy phase I system with rotational fiber anisotropy and homogeneous or heterogeneous transmural intrinsic membrane properties. The classical extracellular marker RT(eg) is compared with the gold standard of fastest repolarization time RT(tap), defined as the time of minimum derivative during the downstroke of the transmembrane action potential (TAP). Additionally, a new extracellular marker RT90(eg) is compared with the gold standard of late repolarization time RT90(tap), defined as the time when the TAP reaches 90% of its resting value. The results show a good global match between the extracellular and transmembrane repolarization markers, with small relative mean discrepancy (or=0.92), ensuring a reasonably good global match between the associated repolarization sequences. However, large local discrepancies of the extracellular versus transmembrane markers may ensue in regions where the curvature of the repolarization front changes abruptly (e.g. near front collisions) or is negligible (e.g. where repolarization proceeds almost uniformly across fiber). As a consequence, the spatial distribution of activation-recovery intervals (ARI) may provide an inaccurate estimate of (and weakly correlated with) the spatial distribution of action potential durations (APD).

Flow Residence Time and Regions of Intraluminal Thrombus Deposition in Intracranial Aneurysms

PubMed Central

Boussel, L.; Ge, L.; Leach, J. R.; Martin, A. J.; Lawton, M. T.; McCulloch, C.; Saloner, D.

2010-01-01

Thrombus formation in intracranial aneurysms, while sometimes stabilizing lesion growth, can present additional risk of thrombo-embolism. The role of hemodynamics in the progression of aneurysmal disease can be elucidated by patient-specific computational modeling. In our previous work, patient-specific computational fluid dynamics (CFD) models were constructed from MRI data for three patients who had fusiform basilar aneurysms that were thrombus-free and then proceeded to develop intraluminal thrombus. In this study, we investigated the effect of increased flow residence time (RT) by modeling passive scalar advection in the same aneurysmal geometries. Non-Newtonian pulsatile flow simulations were carried out in base-line geometries and a new postprocessing technique, referred to as “virtual ink” and based on the passive scalar distribution maps, was used to visualize the flow and estimate the flow RT. The virtual ink technique clearly depicted regions of flow separation. The flow RT at different locations adjacent to aneurysmal walls was calculated as the time the virtual ink scalar remained above a threshold value. The RT values obtained in different areas were then correlated with the location of intra-aneurysmal thrombus observed at a follow-up MR study. For each patient, the wall shear stress (WSS) distribution was also obtained from CFD simulations and correlated with thrombus location. The correlation analysis determined a significant relationship between regions where CFD predicted either an increased RT or low WSS and the regions where thrombus deposition was observed to occur in vivo. A model including both low WSS and increased RT predicted thrombus-prone regions significantly better than the models with RT or WSS alone. PMID:20499185

Discrete-Slots Models of Visual Working-Memory Response Times

PubMed Central

Donkin, Christopher; Nosofsky, Robert M.; Gold, Jason M.; Shiffrin, Richard M.

2014-01-01

Much recent research has aimed to establish whether visual working memory (WM) is better characterized by a limited number of discrete all-or-none slots or by a continuous sharing of memory resources. To date, however, researchers have not considered the response-time (RT) predictions of discrete-slots versus shared-resources models. To complement the past research in this field, we formalize a family of mixed-state, discrete-slots models for explaining choice and RTs in tasks of visual WM change detection. In the tasks under investigation, a small set of visual items is presented, followed by a test item in 1 of the studied positions for which a change judgment must be made. According to the models, if the studied item in that position is retained in 1 of the discrete slots, then a memory-based evidence-accumulation process determines the choice and the RT; if the studied item in that position is missing, then a guessing-based accumulation process operates. Observed RT distributions are therefore theorized to arise as probabilistic mixtures of the memory-based and guessing distributions. We formalize an analogous set of continuous shared-resources models. The model classes are tested on individual subjects with both qualitative contrasts and quantitative fits to RT-distribution data. The discrete-slots models provide much better qualitative and quantitative accounts of the RT and choice data than do the shared-resources models, although there is some evidence for “slots plus resources” when memory set size is very small. PMID:24015956

Adult age differences in wrap-up during sentence comprehension: evidence from ex-Gaussian distributional analyses of reading time.

PubMed

Payne, Brennan R; Stine-Morrow, Elizabeth A L

2014-06-01

We report a secondary data analysis investigating age differences in the effects of clause and sentence wrap-up on reading time distributions during sentence comprehension. Residual word-by-word self-paced reading times were fit to the ex-Gaussian distribution to examine age differences in the effects of clause and sentence wrap-up on both the location and shape of participants' reaction time (RT) distributions. The ex-Gaussian distribution showed good fit to the data in both younger and older adults. Sentence wrap-up increased the central tendency, the variability, and the tail of the distribution, and these effects were exaggerated among the old. In contrast, clause wrap-up influenced the tail of the distribution only, and did so differentially for older adults. Effects were confirmed via nonparametric vincentile plots. Individual differences in visual acuity, working memory, speed of processing, and verbal ability were differentially related to ex-Gaussian parameters reflecting wrap-up effects on underlying reading time distributions. These findings argue against simple pause mechanisms to explain end-of-clause and end-of-sentence reading time patterns; rather, the findings are consistent with a cognitively effortful view of wrap-up and suggest that age and individual differences in attentional allocation to semantic integration during reading, as revealed by RT distribution analyses, play an important role in sentence understanding. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Decreased reaction time variability is associated with greater cardiovascular responses to acute stress

PubMed Central

Hamer, Mark; Steptoe, Andrew; Endrighi, Romano

2016-01-01

Abstract Cardiovascular (CV) responses to mental stress are prospectively associated with poor CV outcomes. The association between CV responses to mental stress and reaction times (RTs) in aging individuals may be important but warrants further investigation. The present study assessed RTs to examine associations with CV responses to mental stress in healthy, older individuals using robust regression techniques. Participants were 262 men and women (mean age = 63.3 ± 5.5 years) from the Whitehall II cohort who completed a RT task (Stroop) and underwent acute mental stress (mirror tracing) to elicit CV responses. Blood pressure, heart rate, and heart rate variability were measured at baseline, during acute stress, and through a 75‐min recovery. RT measures were generated from an ex‐Gaussian distribution that yielded three predictors: mu‐RT, sigma‐RT, and tau‐RT, the mean, standard deviation, and mean of the exponential component of the normal distribution, respectively. Decreased intraindividual RT variability was marginally associated with greater systolic (B = −.009, SE = .005, p = .09) and diastolic (B = −.004, SE = .002, p = .08) blood pressure reactivity. Decreased intraindividual RT variability was associated with impaired systolic blood pressure recovery (B = −.007, SE = .003, p = .03) and impaired vagal tone (B = −.0047, SE = .0024, p = .045). Study findings offer tentative support for an association between RTs and CV responses. Despite small effect sizes and associations not consistent across predictors, these data may point to a link between intrinsic neuronal plasticity and CV responses. PMID:26894967

Peripheral visual response time to colored stimuli imaged on the horizontal meridian

NASA Technical Reports Server (NTRS)

Haines, R. F.; Gross, M. M.; Nylen, D.; Dawson, L. M.

1974-01-01

Two male observers were administered a binocular visual response time task to small (45 min arc), flashed, photopic stimuli at four dominant wavelengths (632 nm red; 583 nm yellow; 526 nm green; 464 nm blue) imaged across the horizontal retinal meridian. The stimuli were imaged at 10 deg arc intervals from 80 deg left to 90 deg right of fixation. Testing followed either prior light adaptation or prior dark adaptation. Results indicated that mean response time (RT) varies with stimulus color. RT is faster to yellow than to blue and green and slowest to red. In general, mean RT was found to increase from fovea to periphery for all four colors, with the curve for red stimuli exhibiting the most rapid positive acceleration with increasing angular eccentricity from the fovea. The shape of the RT distribution across the retina was also found to depend upon the state of light or dark adaptation. The findings are related to previous RT research and are discussed in terms of optimizing the color and position of colored displays on instrument panels.

Time and Frequency Synchronization on the Virac Radio Telescope RT-32

NASA Astrophysics Data System (ADS)

Bezrukovs, V.

2016-04-01

One of the main research directions of Ventspils International Radio Astronomy Centre (VIRAC) is radio astronomy and astrophysics. The instrumental base for the centre comprised two fully steerable parabolic antennas, RT-16 and RT-32 (i.e. with the mirror diameter of 16 m and 32 m). After long reconstruction, radio telescope RT-32 is currently equipped with the receiving and data acquisition systems that allow observing in a wide frequency range from 327 MHz to 9 GHz. New Antenna Control Unit (ACU) allows stable, fast and precise pointing of antenna. Time and frequency distribution service provide 5, 10 and 100 MHz reference frequency, 1PPS signals and precise time stamps by NTP protocol and in the IRIG-B format by coaxial cable. For the radio astronomical observations, main requirement of spatially Very Long Base Line Interferometric (VLBI) observations for the observatory is precise synchronization of the received and sampled data and linking to the exact time stamps. During October 2015, radio telescope RT-32 performance was tested in several successful VLBI experiments. The obtained results confirm the efficiency of the chosen methods of synchronization and the ability to reproduce them on similar antennas.

Decreased reaction time variability is associated with greater cardiovascular responses to acute stress.

PubMed

Wawrzyniak, Andrew J; Hamer, Mark; Steptoe, Andrew; Endrighi, Romano

2016-05-01

Cardiovascular (CV) responses to mental stress are prospectively associated with poor CV outcomes. The association between CV responses to mental stress and reaction times (RTs) in aging individuals may be important but warrants further investigation. The present study assessed RTs to examine associations with CV responses to mental stress in healthy, older individuals using robust regression techniques. Participants were 262 men and women (mean age = 63.3 ± 5.5 years) from the Whitehall II cohort who completed a RT task (Stroop) and underwent acute mental stress (mirror tracing) to elicit CV responses. Blood pressure, heart rate, and heart rate variability were measured at baseline, during acute stress, and through a 75-min recovery. RT measures were generated from an ex-Gaussian distribution that yielded three predictors: mu-RT, sigma-RT, and tau-RT, the mean, standard deviation, and mean of the exponential component of the normal distribution, respectively. Decreased intraindividual RT variability was marginally associated with greater systolic (B = -.009, SE = .005, p = .09) and diastolic (B = -.004, SE = .002, p = .08) blood pressure reactivity. Decreased intraindividual RT variability was associated with impaired systolic blood pressure recovery (B = -.007, SE = .003, p = .03) and impaired vagal tone (B = -.0047, SE = .0024, p = .045). Study findings offer tentative support for an association between RTs and CV responses. Despite small effect sizes and associations not consistent across predictors, these data may point to a link between intrinsic neuronal plasticity and CV responses. © 2016 The Authors. Psychophysiology published by Wiley Periodicals, Inc. on behalf of Society for Psychophysiological Research.

Scheduling of network access for feedback-based embedded systems

NASA Astrophysics Data System (ADS)

Liberatore, Vincenzo

2002-07-01

nd communication capabilities. Examples range from smart dust embedded in building materials to networks of appliances in the home. Embedded devices will be deployed in unprecedented numbers, will enable pervasive distributed computing, and will radically change the way people interact with the surrounding environment [EGH00a]. The paper targets embedded systems and their real-time (RT) communication requirements. RT requirements arise from the

Effects of healthy aging and early stage dementia of the Alzheimer's type on components of response time distributions in three attention tasks.

PubMed

Tse, Chi-Shing; Balota, David A; Yap, Melvin J; Duchek, Janet M; McCabe, David P

2010-05-01

The characteristics of response time (RT) distributions beyond measures of central tendency were explored in 3 attention tasks across groups of young adults, healthy older adults, and individuals with very mild dementia of the Alzheimer's type (DAT). Participants were administered computerized Stroop, Simon, and switching tasks, along with psychometric tasks that tap various cognitive abilities and a standard personality inventory (NEO-FFI). Ex-Gaussian (and Vincentile) analyses were used to capture the characteristics of the RT distributions for each participant across the 3 tasks, which afforded 3 components: mu and sigma (mean and standard deviation of the modal portion of the distribution) and tau (the positive tail of the distribution). The results indicated that across all 3 attention tasks, healthy aging produced large changes in the central tendency mu parameter of the distribution along with some change in sigma and tau (mean etap(2) = .17, .08, and .04, respectively). In contrast, early stage DAT primarily produced an increase in the tau component (mean etap(2) = .06). tau was also correlated with the psychometric measures of episodic/semantic memory, working memory, and processing speed, and with the personality traits of neuroticism and conscientiousness. Structural equation modeling indicated a unique relation between a latent tau construct (-.90), as opposed to sigma (-.09) and mu constructs (.24), with working memory measures. The results suggest a critical role of attentional control systems in discriminating healthy aging from early stage DAT and the utility of RT distribution analyses to better specify the nature of such change.

Factoring out nondecision time in choice reaction time data: Theory and implications.

PubMed

Verdonck, Stijn; Tuerlinckx, Francis

2016-03-01

Choice reaction time (RT) experiments are an invaluable tool in psychology and neuroscience. A common assumption is that the total choice response time is the sum of a decision and a nondecision part (time spent on perceptual and motor processes). While the decision part is typically modeled very carefully (commonly with diffusion models), a simple and ad hoc distribution (mostly uniform) is assumed for the nondecision component. Nevertheless, it has been shown that the misspecification of the nondecision time can severely distort the decision model parameter estimates. In this article, we propose an alternative approach to the estimation of choice RT models that elegantly bypasses the specification of the nondecision time distribution by means of an unconventional convolution of data and decision model distributions (hence called the D*M approach). Once the decision model parameters have been estimated, it is possible to compute a nonparametric estimate of the nondecision time distribution. The technique is tested on simulated data, and is shown to systematically remove traditional estimation bias related to misspecified nondecision time, even for a relatively small number of observations. The shape of the actual underlying nondecision time distribution can also be recovered. Next, the D*M approach is applied to a selection of existing diffusion model application articles. For all of these studies, substantial quantitative differences with the original analyses are found. For one study, these differences radically alter its final conclusions, underlining the importance of our approach. Additionally, we find that strongly right skewed nondecision time distributions are not at all uncommon. (c) 2016 APA, all rights reserved).

HIV-1 subtypes D and F are prevalent in Guinea Conakry.

PubMed

Freimanis, G L; Loua, A; Allain, J P

2012-04-01

Limited data is available upon the distribution of different HIV-1/2 genotypes in the blood donor population from Guinea Conakry. To investigate the prevalence of HIV-1/2 subtypes in asymptomatic blood donors in Guinea Conakry, in order to update knowledge of HIV-1/2 epidemiology within this country. Samples from 104 blood donors seropositive for HIV-1/2 were tested for HIV-1 by real-time RT-PCR. Those negative for HIV-1 were tested with HIV-2 nested RT-PCR. Positive samples were further amplified in the HIV-1 gag and pol regions and sequenced. Subtypes were determined by phylogenetic analysis on amplicon sequences. 61 samples were positive by HIV-1 real-time RT-PCR. Of the 43 negative, 2 (4.6%) were positive for HIV-2. 52/61 (85.3%) samples were positive by nested RT-PCR. Of the 52, 43 (70.5%) and 31(59.6%) sequences were obtained in the gag and pol regions, respectively; 23 for both regions. HIV-1 subtype distribution was 1 B (2.1%), 8 F (17%), 8 D (17%) and 28 CRF02_AG (59.6%) with 2 unclassified recombinants (4.3%). Unique clusters for subtype D and F distinguished Guinea from HIV-1 subtype distribution in neighboring countries. Subtype F and subtype D strains, uncommon in West Africa, are a substantial part of HIV-1 epidemiology in Guinea. Copyright © 2011 Elsevier B.V. All rights reserved.

The DICOM-based radiation therapy information system

NASA Astrophysics Data System (ADS)

Law, Maria Y. Y.; Chan, Lawrence W. C.; Zhang, Xiaoyan; Zhang, Jianguo

2004-04-01

Similar to DICOM for PACS (Picture Archiving and Communication System), standards for radiotherapy (RT) information have been ratified with seven DICOM-RT objects and their IODs (Information Object Definitions), which are more than just images. This presentation describes how a DICOM-based RT Information System Server can be built based on the PACS technology and its data model for a web-based distribution. Methods: The RT information System consists of a Modality Simulator, a data format translator, a RT Gateway, the DICOM RT Server, and the Web-based Application Server. The DICOM RT Server was designed based on a PACS data model and was connected to a Web application Server for distribution of the RT information including therapeutic plans, structures, dose distribution, images and records. Various DICOM RT objects of the patient transmitted to the RT Server were routed to the Web Application Server where the contents of the DICOM RT objects were decoded and mapped to the corresponding location of the RT data model for display in the specially-designed Graphic User Interface. The non-DICOM objects were first rendered to DICOM RT Objects in the translator before they were sent to the RT Server. Results: Ten clinical cases have been collected from different hopsitals for evaluation of the DICOM-based RT Information System. They were successfully routed through the data flow and displayed in the client workstation of the RT information System. Conclusion: Using the DICOM-RT standards, integration of RT data from different vendors is possible.

On the Impact of Multi-GNSS Observations on Real-Time Precise Point Positioning Zenith Total Delay Estimates

NASA Astrophysics Data System (ADS)

Ding, Wenwu; Teferle, Norman; Kaźmierski, Kamil; Laurichesse, Denis; Yuan, Yunbin

2017-04-01

Observations from multiple Global Navigation Satellite System (GNSS) can improve the performance of real-time (RT) GNSS meteorology, in particular of the Zenith Total Delay (ZTD) estimates. RT ZTD estimates in combination with derived precipitable water vapour estimates can be used for weather now-casting and the tracking of severe weather events. While a number of published literature has already highlighted this positive development, in this study we describe an operational RT system for extracting ZTD using a modified version of the PPP-wizard (with PPP denoting Precise Point Positioning). Multi-GNSS, including GPS, GLONASS and Galileo, observation streams are processed using a RT PPP strategy based on RT satellite orbit and clock products from the Centre National d'Etudes Spatiales (CNES). A continuous experiment for 30 days was conducted, in which the RT observation streams of 20 globally distributed stations were processed. The initialization time and accuracy of the RT troposphere products using single and/or multi-system observations were evaluated. The effect of RT PPP ambiguity resolution was also evaluated. The results revealed that the RT troposphere products based on single system observations can fulfill the requirements of the meteorological application in now-casting systems. We noted that the GPS-only solution is better than the GLONASS-only solution in both initialization and accuracy. While the ZTD performance can be improved by applying RT PPP ambiguity resolution, the inclusion of observations from multiple GNSS has a more profound effect. Specifically, we saw that the ambiguity resolution is more effective in improving the accuracy, whereas the initialization process can be better accelerated by multi-GNSS observations. Combining all systems, RT troposphere products with an average accuracy of about 8 mm in ZTD were achieved after an initialization process of approximately 9 minutes, which supports the application of multi-GNSS observations and ambiguity resolution for RT meteorological applications.

Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI.

PubMed

Bester, Rachelle; Jooste, Anna E C; Maree, Hans J; Burger, Johan T

2012-09-27

Grapevine leafroll-associated virus 3 (GLRaV-3) is the main contributing agent of leafroll disease worldwide. Four of the six GLRaV-3 variant groups known have been found in South Africa, but their individual contribution to leafroll disease is unknown. In order to study the pathogenesis of leafroll disease, a sensitive and accurate diagnostic assay is required that can detect different variant groups of GLRaV-3. In this study, a one-step real-time RT-PCR, followed by high-resolution melting (HRM) curve analysis for the simultaneous detection and identification of GLRaV-3 variants of groups I, II, III and VI, was developed. A melting point confidence interval for each variant group was calculated to include at least 90% of all melting points observed. A multiplex RT-PCR protocol was developed to these four variant groups in order to assess the efficacy of the real-time RT-PCR HRM assay. A universal primer set for GLRaV-3 targeting the heat shock protein 70 homologue (Hsp70h) gene of GLRaV-3 was designed that is able to detect GLRaV-3 variant groups I, II, III and VI and differentiate between them with high-resolution melting curve analysis. The real-time RT-PCR HRM and the multiplex RT-PCR were optimized using 121 GLRaV-3 positive samples. Due to a considerable variation in melting profile observed within each GLRaV-3 group, a confidence interval of above 90% was calculated for each variant group, based on the range and distribution of melting points. The intervals of groups I and II could not be distinguished and a 95% joint confidence interval was calculated for simultaneous detection of group I and II variants. An additional primer pair targeting GLRaV-3 ORF1a was developed that can be used in a subsequent real-time RT-PCR HRM to differentiate between variants of groups I and II. Additionally, the multiplex RT-PCR successfully validated 94.64% of the infections detected with the real-time RT-PCR HRM. The real-time RT-PCR HRM provides a sensitive, automated and rapid tool to detect and differentiate different variant groups in order to study the epidemiology of leafroll disease.

Stimulant Treatment Reduces Lapses in Attention among Children with ADHD: The Effects of Methylphenidate on Intra-Individual Response Time Distributions

ERIC Educational Resources Information Center

Spencer, Sarah V.; Hawk, Larry W., Jr.; Richards, Jerry B.; Shiels, Keri; Pelham, William E., Jr.; Waxmonsky, James G.

2009-01-01

Recent research has suggested that intra-individual variability in reaction time (RT) distributions of children with ADHD is characterized by a particularly large rightward skew that may reflect lapses in attention. The purpose of the study was to provide the first randomized, placebo-controlled test of the effects of the stimulant methylphenidate…

Movement is the glue connecting home ranges and habitat selection.

PubMed

Van Moorter, Bram; Rolandsen, Christer M; Basille, Mathieu; Gaillard, Jean-Michel

2016-01-01

Animal space use has been studied by focusing either on geographic (e.g. home ranges, species' distribution) or on environmental (e.g. habitat use and selection) space. However, all patterns of space use emerge from individual movements, which are the primary means by which animals change their environment. Individuals increase their use of a given area by adjusting two key movement components: the duration of their visit and/or the frequency of revisits. Thus, in spatially heterogeneous environments, animals exploit known, high-quality resource areas by increasing their residence time (RT) in and/or decreasing their time to return (TtoR) to these areas. We expected that spatial variation in these two movement properties should lead to observed patterns of space use in both geographic and environmental spaces. We derived a set of nine predictions linking spatial distribution of movement properties to emerging space-use patterns. We predicted that, at a given scale, high variation in RT and TtoR among habitats leads to strong habitat selection and that long RT and short TtoR result in a small home range size. We tested these predictions using moose (Alces alces) GPS tracking data. We first modelled the relationship between landscape characteristics and movement properties. Then, we investigated how the spatial distribution of predicted movement properties (i.e. spatial autocorrelation, mean, and variance of RT and TtoR) influences home range size and hierarchical habitat selection. In landscapes with high spatial autocorrelation of RT and TtoR, a high variation in both RT and TtoR occurred in home ranges. As expected, home range location was highly selective in such landscapes (i.e. second-order habitat selection); RT was higher and TtoR lower within the selected home range than outside, and moose home ranges were small. Within home ranges, a higher variation in both RT and TtoR was associated with higher selectivity among habitat types (i.e. third-order habitat selection). Our findings show how patterns of geographic and environmental space use correspond to the two sides of a coin, linked by movement responses of individuals to environmental heterogeneity. By demonstrating the potential to assess the consequences of altering RT or TtoR (e.g. through human disturbance or climatic changes) on home range size and habitat selection, our work sets the basis for new theoretical and methodological advances in movement ecology. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Groundwater age, life expectancy and transit time distributions in advective dispersive systems; 2. Reservoir theory for sub-drainage basins

NASA Astrophysics Data System (ADS)

Cornaton, F.; Perrochet, P.

2006-09-01

Groundwater age and life expectancy probability density functions (pdf) have been defined, and solved in a general three-dimensional context by means of forward and backward advection-dispersion equations [Cornaton F, Perrochet P. Groundwater age, life expectancy and transit time distributions in advective-dispersive systems; 1. Generalized reservoir theory. Adv Water Res (xxxx)]. The discharge and recharge zones transit time pdfs were then derived by applying the reservoir theory (RT) to the global system, thus considering as ensemble the union of all inlet boundaries on one hand, and the union of all outlet boundaries on the other hand. The main advantages in using the RT to calculate the transit time pdf is that the outlet boundary geometry does not represent a computational limiting factor (e.g. outlets of small sizes), since the methodology is based on the integration over the entire domain of each age, or life expectancy, occurrence. In the present paper, we extend the applicability of the RT to sub-drainage basins of groundwater reservoirs by treating the reservoir flow systems as compartments which transfer the water fluxes to a particular discharge zone, and inside which mixing and dispersion processes can take place. Drainage basins are defined by the field of probability of exit at outlet. In this way, we make the RT applicable to each sub-drainage system of an aquifer of arbitrary complexity and configuration. The case of the well-head protection problem is taken as illustrative example, and sensitivity analysis of the effect of pore velocity variations on the simulated ages is carried out.

GNSS in real-time: Demonstration experiment at Berlin Airport International

NASA Astrophysics Data System (ADS)

Wickert, Jens; Dick, Galina; Ge, Maorong; Heise, Stefan; Li, XingXing; Ming, Shangguan; Nischan, Thomas; Ramatschi, Markus; Schuh, Harald; Alberding, Jürgen; Weigmann, Uwe

2013-04-01

Real-time (RT) applications are in focus of recent GNSS research. International activities related to the RT data collection and distribution, as well as provision of specific RT data products (e.g., satellite orbits and clocks, station coordinates) are coordinated within the Real-Time Project of the International GNSS Service (IGS). Currently IGS provides real-time data from more than 100 globally distributed GNSS ground stations. This number, in parallel with the extension of various additional international real-time networks, is continuously increasing. In parallel to the rapid development of GNSS RT activities also innovative geophysical applications were pioneered by GNSS research groups and institutions, including GFZ. One prominent example is the use of GNSS components in early warning systems. GNSS measurements can be used there for the rapid detection and characterization of deformation fields, related to earthquakes, which induce Tsunamis. Such deformation data cannot be provided by seismometer measurements, but are important for the prediction of the tsunami wave propagation caused by earthquakes. The GNSS real-time group at GFZ is involved in several research projects related to geophysical RT GNSS applications, and also operates one of the RT analysis centers of the IGS. We introduce results of a real-time GNSS demonstration project, which was performed in 2012 at the new Berlin International Airport BER at Schönefeld, south-east of Berlin city center. The main goal of the project was the demonstration of the functionality of a complex RT-PPP server-client solution for dynamic applications which was developed within a joint research project of GFZ and the company Alberding GmbH. Compared to the standard PPP (clock & orbit) this solution uses additional information (ionosphere, uncalibrated phase delays UPD) to increase the positioning accuracy and to reduce the convergence time. The major challenges of the experiment were the stable operation of the entire server-client system, the implementation of a mainly for scientific purposes developed software to a potentially commercial positioning solution, the real-time GNSS data management, and the generation and usage of the correction data. We evaluate the server-client system functionality and PPP results of the experiment in view of the project goals and indicate problems to be focused in future work. In addition, the GNSS data from a temporary ground station at the air-field was used to derive vertically integrated water vapor (IWV) data to demonstrate the potential of real-time water vapor data to improve the weather forecast at the airport. The IWV data are compared with measurements from nearby stations of the permanent German GNSS network for atmosphere sounding and with a water vapor radiometer, operated at GFZ.

A reach-to-touch investigation on the nature of reading in the Stroop task.

PubMed

Tillman, Gabriel; Eidels, Ami; Finkbeiner, Matthew

2016-11-01

In a Stroop task, participants can be presented with a color name printed in color and need to classify the print color while ignoring the word. The Stroop effect is typically calculated as the difference in mean response time (RT) between congruent (e.g., the word RED printed in red) and incongruent (GREEN in red) trials. Delta plots compare not just mean performance, but the entire RT distributions of congruent and incongruent conditions. However, both mean RT and delta plots have some limitations. Arm-reaching trajectories allow a more continuous measure for assessing the time course of the Stroop effect. We compared arm movements to congruent and incongruent stimuli in a standard Stroop task and a control task that encourages processing of each and every word. The Stroop effect emerged over time in the control task, but not in the standard Stroop, suggesting words may be processed differently in the two tasks.

Associations between number of consecutive night shifts and impairment of neurobehavioral performance during a subsequent simulated night shift.

PubMed

Magee, Michelle; Sletten, Tracey L; Ferguson, Sally A; Grunstein, Ronald R; Anderson, Clare; Kennaway, David J; Lockley, Steven W; Rajaratnam, Shantha Mw

2016-05-01

This study aimed to investigate sleep and circadian phase in the relationships between neurobehavioral performance and the number of consecutive shifts worked. Thirty-four shift workers [20 men, mean age 31.8 (SD 10.9) years] worked 2-7 consecutive night shifts immediately prior to a laboratory-based, simulated night shift. For 7 days prior, participants worked their usual shift sequence, and sleep was assessed with logs and actigraphy. Participants completed a 10-minute auditory psychomotor vigilance task (PVT) at the start (~21:00 hours) and end (~07:00 hours) of the simulated night shift. Mean reaction times (RT), number of lapses and RT distribution was compared between those who worked 2-3 consecutive night shifts versus those who worked 4-7 shifts. Following 4-7 shifts, night shift workers had significantly longer mean RT at the start and end of shift, compared to those who worked 2-3 shifts. The slowest and fastest 10% RT were significantly slower at the start, but not end, of shift among participants who worked 4-7 nights. Those working 4-7 nights also demonstrated a broader RT distribution at the start and end of shift and had significantly slower RT based on cumulative distribution analysis (5 (th), 25 (th), 50 (th), 75 (th)percentiles at the start of shift; 75th percentile at the end of shift). No group differences in sleep parameters were found for 7 days and 24 hours prior to the simulated night shift. A greater number of consecutive night shifts has a negative impact on neurobehavioral performance, likely due to cognitive slowing.

Operational Data Quality Assessment of the Combined PBO, TLALOCNet and COCONet Real-Time GNSS Networks

NASA Astrophysics Data System (ADS)

Hodgkinson, K. M.; Mencin, D.; Fox, O.; Walls, C. P.; Mann, D.; Blume, F.; Berglund, H. T.; Phillips, D.; Meertens, C. M.; Mattioli, G. S.

2015-12-01

The GAGE facility, managed by UNAVCO, currently operates a network of ~460, real-time, high-rate GNSS stations (RT-GNSS). The majority of these RT stations are part of the Earthscope PBO network, which spans the western US Pacific North-American plate boundary. Approximately 50 are distributed throughout the Mexico and Caribbean region funded by the TLALOCNet and COCONet projects. The entire network is processed in real-time at UNAVCO using Precise Point Positioning (PPP). The real-time streams are freely available to all and user demand has grown almost exponentially since 2010. Data usage is multidisciplinary, including tectonic and volcanic deformation studies, meteorological applications, atmospheric science research in addition to use by national, state and commercial entities. 21 RT-GNSS sites in California now include 200-sps accelerometers for the development of Earthquake Early Warning systems. All categories of users of real-time streams have similar requirements, reliable, low-latency, high-rate, and complete data sets. To meet these requirements, UNAVCO tracks the latency and completeness of the incoming raw observations and also is developing tools to monitor the quality of the processed data streams. UNAVCO is currently assessing the precision, accuracy and latency of solutions from various PPP software packages. Also under review are the data formats UNAVCO distributes; for example, the PPP solutions are currently distributed in NMEA format, but other formats such as SEED or GeoJSON may be preferred by different user groups to achieve specific mission objectives. In this presentation we will share our experiences of the challenges involved in the data operations of a continental-scale, multi-project, real-time GNSS network, summarize the network's performance in terms of latency and completeness, and present the comparisons of PPP solutions using different PPP processing techniques.

Propagation Aspects of Frequency Sharing, Interference and System Diversity

DTIC Science & Technology

1983-03-01

DRSEL-COM-RN-1 Fort Monmouth, N.J. 07703 USA 11.Pages 432 12. Distribution Statement This document is distributed in accordance with AGARD policies ...OD ■rtCMCO •«^ CD CD -rt ■rtCU -T CD coo-^in vinNoi CDCOOO cDhvcno CMCUOO cncD o o oooo oooo CO oo o -rtCOCD N N X X 2: z o o in o

Intraindividual variability in inhibitory function in adults with ADHD--an ex-Gaussian approach.

PubMed

Gmehlin, Dennis; Fuermaier, Anselm B M; Walther, Stephan; Debelak, Rudolf; Rentrop, Mirjam; Westermann, Celina; Sharma, Anuradha; Tucha, Lara; Koerts, Janneke; Tucha, Oliver; Weisbrod, Matthias; Aschenbrenner, Steffen

2014-01-01

Attention deficit disorder (ADHD) is commonly associated with inhibitory dysfunction contributing to typical behavioral symptoms like impulsivity or hyperactivity. However, some studies analyzing intraindividual variability (IIV) of reaction times in children with ADHD (cADHD) question a predominance of inhibitory deficits. IIV is a measure of the stability of information processing and provides evidence that longer reaction times (RT) in inhibitory tasks in cADHD are due to only a few prolonged responses which may indicate deficits in sustained attention rather than inhibitory dysfunction. We wanted to find out, whether a slowing in inhibitory functioning in adults with ADHD (aADHD) is due to isolated slow responses. Computing classical RT measures (mean RT, SD), ex-Gaussian parameters of IIV (which allow a better separation of reaction time (mu), variability (sigma) and abnormally slow responses (tau) than classical measures) as well as errors of omission and commission, we examined response inhibition in a well-established GoNogo task in a sample of aADHD subjects without medication and healthy controls matched for age, gender and education. We did not find higher numbers of commission errors in aADHD, while the number of omissions was significantly increased compared with controls. In contrast to increased mean RT, the distributional parameter mu did not document a significant slowing in aADHD. However, subjects with aADHD were characterized by increased IIV throughout the entire RT distribution as indicated by the parameters sigma and tau as well as the SD of reaction time. Moreover, we found a significant correlation between tau and the number of omission errors. Our findings question a primacy of inhibitory deficits in aADHD and provide evidence for attentional dysfunction. The present findings may have theoretical implications for etiological models of ADHD as well as more practical implications for neuropsychological testing in aADHD.

Intraindividual Variability in Inhibitory Function in Adults with ADHD – An Ex-Gaussian Approach

PubMed Central

Gmehlin, Dennis; Fuermaier, Anselm B. M.; Walther, Stephan; Debelak, Rudolf; Rentrop, Mirjam; Westermann, Celina; Sharma, Anuradha; Tucha, Lara; Koerts, Janneke; Tucha, Oliver; Weisbrod, Matthias; Aschenbrenner, Steffen

2014-01-01

Objective Attention deficit disorder (ADHD) is commonly associated with inhibitory dysfunction contributing to typical behavioral symptoms like impulsivity or hyperactivity. However, some studies analyzing intraindividual variability (IIV) of reaction times in children with ADHD (cADHD) question a predominance of inhibitory deficits. IIV is a measure of the stability of information processing and provides evidence that longer reaction times (RT) in inhibitory tasks in cADHD are due to only a few prolonged responses which may indicate deficits in sustained attention rather than inhibitory dysfunction. We wanted to find out, whether a slowing in inhibitory functioning in adults with ADHD (aADHD) is due to isolated slow responses. Methods Computing classical RT measures (mean RT, SD), ex-Gaussian parameters of IIV (which allow a better separation of reaction time (mu), variability (sigma) and abnormally slow responses (tau) than classical measures) as well as errors of omission and commission, we examined response inhibition in a well-established GoNogo task in a sample of aADHD subjects without medication and healthy controls matched for age, gender and education. Results We did not find higher numbers of commission errors in aADHD, while the number of omissions was significantly increased compared with controls. In contrast to increased mean RT, the distributional parameter mu did not document a significant slowing in aADHD. However, subjects with aADHD were characterized by increased IIV throughout the entire RT distribution as indicated by the parameters sigma and tau as well as the SD of reaction time. Moreover, we found a significant correlation between tau and the number of omission errors. Conclusions Our findings question a primacy of inhibitory deficits in aADHD and provide evidence for attentional dysfunction. The present findings may have theoretical implications for etiological models of ADHD as well as more practical implications for neuropsychological testing in aADHD. PMID:25479234

Neural substrates of behavioral variability in attention deficit hyperactivity disorder: based on ex-Gaussian reaction time distribution and diffusion spectrum imaging tractography.

PubMed

Lin, H-Y; Gau, S S-F; Huang-Gu, S L; Shang, C-Y; Wu, Y-H; Tseng, W-Y I

2014-06-01

Increased intra-individual variability (IIV) in reaction time (RT) across various tasks is one ubiquitous neuropsychological finding in attention deficit hyperactivity disorder (ADHD). However, neurobiological underpinnings of IIV in individuals with ADHD have not yet been fully delineated. The ex-Gaussian distribution has been proved to capture IIV in RT. The authors explored the three parameters [μ (mu), σ (sigma), τ (tau)] of an ex-Gaussian RT distribution derived from the Conners' continuous performance test (CCPT) and their correlations with the microstructural integrity of the frontostriatal-caudate tracts and the cingulum bundles. We assessed 28 youths with ADHD (8-17 years; 25 males) and 28 age-, sex-, IQ- and handedness-matched typically developing (TD) youths using the CCPT, Wechsler Intelligence Scale for Children, 3rd edition and magnetic resonance imaging (MRI). Microstructural integrity, indexed by generalized fractional anisotropy (GFA), was measured by diffusion spectrum imaging tractrography on a 3-T MRI system. Youths with ADHD had larger σ (s.d. of Gaussian distribution) and τ (mean of exponential distribution) and reduced GFA in four bilateral frontostriatal tracts. With increased inter-stimulus intervals of CCPT, the magnitude of greater τ in ADHD than TD increased. In ADHD youths, the cingulum bundles and frontostriatal integrity were associated with three ex-Gaussian parameters and with μ (mean of Gaussian distribution) and τ, respectively; while only frontostriatal GFA was associated with μ and τ in TD youths. Our findings suggest the crucial role of the integrity of the cingulum bundles in accounting for IIV in ADHD. Involvement of different brain systems in mediating IIV may relate to a distinctive pathophysiological processing and/or adaptive compensatory mechanism.

The location-, word-, and arrow-based Simon effects: An ex-Gaussian analysis.

PubMed

Luo, Chunming; Proctor, Robert W

2018-04-01

Task-irrelevant spatial information, conveyed by stimulus location, location word, or arrow direction, can influence the response to task-relevant attributes, generating the location-, word-, and arrow-based Simon effects. We examined whether different mechanisms are involved in the generation of these Simon effects by fitting a mathematical ex-Gaussian function to empirical response time (RT) distributions. Specifically, we tested whether which ex-Gaussian parameters (μ, σ, and τ) show Simon effects and whether the location-, word, and arrow-based effects are on different parameters. Results show that the location-based Simon effect occurred on mean RT and μ but not on τ, and a reverse Simon effect occurred on σ. In contrast, a positive word-based Simon effect was obtained on all these measures (including σ), and a positive arrow-based Simon effect was evident on mean RT, σ, and τ but not μ. The arrow-based Simon effect was not different from the word-based Simon effect on τ or σ but was on μ and mean RT. These distinct results on mean RT and ex-Gaussian parameters provide evidence that spatial information conveyed by the various location modes are different in the time-course of activation.

Using hazard functions to assess changes in processing capacity in an attentional cuing paradigm.

PubMed

Wenger, Michael J; Gibson, Bradley S

2004-08-01

Processing capacity--defined as the relative ability to perform mental work in a unit of time--is a critical construct in cognitive psychology and is central to theories of visual attention. The unambiguous use of the construct, experimentally and theoretically, has been hindered by both conceptual confusions and the use of measures that are at best only coarsely mapped to the construct. However, more than 25 years ago, J. T. Townsend and F. G. Ashby (1978) suggested that the hazard function on the response time (RT) distribution offered a number of conceptual advantages as a measure of capacity. The present study suggests that a set of statistical techniques, well-known outside the cognitive and perceptual literatures, offers the ability to perform hypothesis tests on RT-distribution hazard functions. These techniques are introduced, and their use is illustrated in application to data from the contingent attentional capture paradigm.

Performance Lapses in Children with Attention-Deficit/Hyperactivity Disorder Contribute to Poor Reading Fluency

PubMed Central

Jacobson, Lisa A.; Ryan, Matthew; Denckla, Martha B.; Mostofsky, Stewart H.; Mahone, E. Mark

2013-01-01

Children with Attention-Deficit/Hyperactivity Disorder (ADHD) demonstrate increased response variability compared with controls, which is thought to be associated with deficits in attention regulation and response control that subsequently affect performance of more cognitively demanding tasks, such as reading. The present study examined response variability during a computerized simple reaction time (RT) task in 67 children. Ex-Gaussian analyses separated the response time distribution into normal (mu and sigma) and exponential (tau) components; the association of each with reading fluency was examined. Children with ADHD had significantly slower, more variable, and more skewed RTs compared with controls. After controlling for ADHD symptom severity, tau (but not mu or mean RT) was significantly associated with reduced reading fluency, but not with single word reading accuracy. These data support the growing evidence that RT variability, but not simply slower mean response speed, is the characteristic of youth with ADHD and that longer response time latencies (tau) may be implicated in the poorer academic performance associated with ADHD. PMID:23838684

Performance lapses in children with attention-deficit/hyperactivity disorder contribute to poor reading fluency.

PubMed

Jacobson, Lisa A; Ryan, Matthew; Denckla, Martha B; Mostofsky, Stewart H; Mahone, E Mark

2013-11-01

Children with Attention-Deficit/Hyperactivity Disorder (ADHD) demonstrate increased response variability compared with controls, which is thought to be associated with deficits in attention regulation and response control that subsequently affect performance of more cognitively demanding tasks, such as reading. The present study examined response variability during a computerized simple reaction time (RT) task in 67 children. Ex-Gaussian analyses separated the response time distribution into normal (mu and sigma) and exponential (tau) components; the association of each with reading fluency was examined. Children with ADHD had significantly slower, more variable, and more skewed RTs compared with controls. After controlling for ADHD symptom severity, tau (but not mu or mean RT) was significantly associated with reduced reading fluency, but not with single word reading accuracy. These data support the growing evidence that RT variability, but not simply slower mean response speed, is the characteristic of youth with ADHD and that longer response time latencies (tau) may be implicated in the poorer academic performance associated with ADHD.

Parallel Distributed Processing and Lexical-Semantic Effects in Visual Word Recognition: Are a Few Stages Necessary?

ERIC Educational Resources Information Center

Borowsky, Ron; Besner, Derek

2006-01-01

D. C. Plaut and J. R. Booth presented a parallel distributed processing model that purports to simulate human lexical decision performance. This model (and D. C. Plaut, 1995) offers a single mechanism account of the pattern of factor effects on reaction time (RT) between semantic priming, word frequency, and stimulus quality without requiring a…

Kinetic Energy and Angular Distributions of He and Ar Atoms Evaporating from Liquid Dodecane.

PubMed

Patel, Enamul-Hasan; Williams, Mark A; Koehler, Sven P K

2017-01-12

We report both kinetic energy and angular distributions for He and Ar atoms evaporating from C 12 H 26 . All results were obtained by performing molecular dynamics simulations of liquid C 12 H 26 with around 10-20 noble gas atoms dissolved in the liquid and by subsequently following the trajectories of the noble gas atoms after evaporation from the liquid. Whereas He evaporates with a kinetic energy distribution of (1.05 ± 0.03) × 2RT (corrected for the geometry used in experiments: (1.08 ± 0.03) × 2RT, experimentally obtained value: (1.14 ± 0.01) × 2RT), Ar displays a kinetic energy distribution that better matches a Maxwell-Boltzmann distribution at the temperature of the liquid ((0.99 ± 0.04) × 2RT). This behavior is also reflected in the angular distributions, which are close to a cosine distribution for Ar but slightly narrower, especially for faster atoms, in the case of He. This behavior of He is most likely due to the weak interaction potential between He and the liquid hydrocarbon.

Avalanches and power-law behaviour in lung inflation

NASA Astrophysics Data System (ADS)

Suki, Béla; Barabási, Albert-László; Hantos, Zoltán; Peták, Ferenc; Stanley, H. Eugene

1994-04-01

WHEN lungs are emptied during exhalation, peripheral airways close up1. For people with lung disease, they may not reopen for a significant portion of inhalation, impairing gas exchange2,3. A knowledge of the mechanisms that govern reinflation of collapsed regions of lungs is therefore central to the development of ventilation strategies for combating respiratory problems. Here we report measurements of the terminal airway resistance, Rt , during the opening of isolated dog lungs. When inflated by a constant flow, Rt decreases in discrete jumps. We find that the probability distribution of the sizes of the jumps and of the time intervals between them exhibit power-law behaviour over two decades. We develop a model of the inflation process in which 'avalanches' of airway openings are seen-with power-law distributions of both the size of avalanches and the time intervals between them-which agree quantitatively with those seen experimentally, and are reminiscent of the power-law behaviour observed for self-organized critical systems4. Thus power-law distributions, arising from avalanches associated with threshold phenomena propagating down a branching tree structure, appear to govern the recruitment of terminal airspaces.

A Single-Boundary Accumulator Model of Response Times in an Addition Verification Task

PubMed Central

Faulkenberry, Thomas J.

2017-01-01

Current theories of mathematical cognition offer competing accounts of the interplay between encoding and calculation in mental arithmetic. Additive models propose that manipulations of problem format do not interact with the cognitive processes used in calculation. Alternatively, interactive models suppose that format manipulations have a direct effect on calculation processes. In the present study, we tested these competing models by fitting participants' RT distributions in an arithmetic verification task with a single-boundary accumulator model (the shifted Wald distribution). We found that in addition to providing a more complete description of RT distributions, the accumulator model afforded a potentially more sensitive test of format effects. Specifically, we found that format affected drift rate, which implies that problem format has a direct impact on calculation processes. These data give further support for an interactive model of mental arithmetic. PMID:28769853

Across-task priming revisited: response and task conflicts disentangled using ex-Gaussian distribution analysis.

PubMed

Moutsopoulou, Karolina; Waszak, Florian

2012-04-01

The differential effects of task and response conflict in priming paradigms where associations are strengthened between a stimulus, a task, and a response have been demonstrated in recent years with neuroimaging methods. However, such effects are not easily disentangled with only measurements of behavior, such as reaction times (RTs). Here, we report the application of ex-Gaussian distribution analysis on task-switching RT data and show that conflict related to stimulus-response associations retrieved after a switch of tasks is reflected in the Gaussian component. By contrast, conflict related to the retrieval of stimulus-task associations is reflected in the exponential component. Our data confirm that the retrieval of stimulus-task and -response associations affects behavior differently. Ex-Gaussian distribution analysis is a useful tool for pulling apart these different levels of associative priming that are not distinguishable in analyses of RT means.

Motivational salience signal in the basal forebrain is coupled with faster and more precise decision speed.

PubMed

Avila, Irene; Lin, Shih-Chieh

2014-03-01

The survival of animals depends critically on prioritizing responses to motivationally salient stimuli. While it is generally believed that motivational salience increases decision speed, the quantitative relationship between motivational salience and decision speed, measured by reaction time (RT), remains unclear. Here we show that the neural correlate of motivational salience in the basal forebrain (BF), defined independently of RT, is coupled with faster and also more precise decision speed. In rats performing a reward-biased simple RT task, motivational salience was encoded by BF bursting response that occurred before RT. We found that faster RTs were tightly coupled with stronger BF motivational salience signals. Furthermore, the fraction of RT variability reflecting the contribution of intrinsic noise in the decision-making process was actively suppressed in faster RT distributions with stronger BF motivational salience signals. Artificially augmenting the BF motivational salience signal via electrical stimulation led to faster and more precise RTs and supports a causal relationship. Together, these results not only describe for the first time, to our knowledge, the quantitative relationship between motivational salience and faster decision speed, they also reveal the quantitative coupling relationship between motivational salience and more precise RT. Our results further establish the existence of an early and previously unrecognized step in the decision-making process that determines both the RT speed and variability of the entire decision-making process and suggest that this novel decision step is dictated largely by the BF motivational salience signal. Finally, our study raises the hypothesis that the dysregulation of decision speed in conditions such as depression, schizophrenia, and cognitive aging may result from the functional impairment of the motivational salience signal encoded by the poorly understood noncholinergic BF neurons.

Motivational Salience Signal in the Basal Forebrain Is Coupled with Faster and More Precise Decision Speed

PubMed Central

Avila, Irene; Lin, Shih-Chieh

2014-01-01

The survival of animals depends critically on prioritizing responses to motivationally salient stimuli. While it is generally believed that motivational salience increases decision speed, the quantitative relationship between motivational salience and decision speed, measured by reaction time (RT), remains unclear. Here we show that the neural correlate of motivational salience in the basal forebrain (BF), defined independently of RT, is coupled with faster and also more precise decision speed. In rats performing a reward-biased simple RT task, motivational salience was encoded by BF bursting response that occurred before RT. We found that faster RTs were tightly coupled with stronger BF motivational salience signals. Furthermore, the fraction of RT variability reflecting the contribution of intrinsic noise in the decision-making process was actively suppressed in faster RT distributions with stronger BF motivational salience signals. Artificially augmenting the BF motivational salience signal via electrical stimulation led to faster and more precise RTs and supports a causal relationship. Together, these results not only describe for the first time, to our knowledge, the quantitative relationship between motivational salience and faster decision speed, they also reveal the quantitative coupling relationship between motivational salience and more precise RT. Our results further establish the existence of an early and previously unrecognized step in the decision-making process that determines both the RT speed and variability of the entire decision-making process and suggest that this novel decision step is dictated largely by the BF motivational salience signal. Finally, our study raises the hypothesis that the dysregulation of decision speed in conditions such as depression, schizophrenia, and cognitive aging may result from the functional impairment of the motivational salience signal encoded by the poorly understood noncholinergic BF neurons. PMID:24642480

Distinct Response Time Distributions in Attention Deficit Hyperactivity Disorder Subtypes

ERIC Educational Resources Information Center

Querne, Laurent; Berquin, Patrick

2009-01-01

Objective: To address the issue of response time (RT) profiles in hyperactive-impulsive (ADHD-HI), inattentive (ADHD-IA), and combined (ADHD-C) subtypes of ADHD. We hypothesized that children with ADHD-HI should respond more rapidly than children without ADHD and children with ADHD-IA and ADHD-C should respond more slowly than children without…

Cortical Components of Reaction-Time during Perceptual Decisions in Humans.

PubMed

Dmochowski, Jacek P; Norcia, Anthony M

2015-01-01

The mechanisms of perceptual decision-making are frequently studied through measurements of reaction time (RT). Classical sequential-sampling models (SSMs) of decision-making posit RT as the sum of non-overlapping sensory, evidence accumulation, and motor delays. In contrast, recent empirical evidence hints at a continuous-flow paradigm in which multiple motor plans evolve concurrently with the accumulation of sensory evidence. Here we employ a trial-to-trial reliability-based component analysis of encephalographic data acquired during a random-dot motion task to directly image continuous flow in the human brain. We identify three topographically distinct neural sources whose dynamics exhibit contemporaneous ramping to time-of-response, with the rate and duration of ramping discriminating fast and slow responses. Only one of these sources, a parietal component, exhibits dependence on strength-of-evidence. The remaining two components possess topographies consistent with origins in the motor system, and their covariation with RT overlaps in time with the evidence accumulation process. After fitting the behavioral data to a popular SSM, we find that the model decision variable is more closely matched to the combined activity of the three components than to their individual activity. Our results emphasize the role of motor variability in shaping RT distributions on perceptual decision tasks, suggesting that physiologically plausible computational accounts of perceptual decision-making must model the concurrent nature of evidence accumulation and motor planning.

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

PubMed Central

Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

2008-01-01

Background The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. Methodology/Principal Findings By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. Conclusions/Significance We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses. PMID:19052647

Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.

PubMed

Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

2008-01-01

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.

Design and performance of the CDC real-time reverse transcriptase PCR swine flu panel for detection of 2009 A (H1N1) pandemic influenza virus.

PubMed

Shu, Bo; Wu, Kai-Hui; Emery, Shannon; Villanueva, Julie; Johnson, Roy; Guthrie, Erica; Berman, LaShondra; Warnes, Christine; Barnes, Nathelia; Klimov, Alexander; Lindstrom, Stephen

2011-07-01

Swine influenza viruses (SIV) have been shown to sporadically infect humans and are infrequently identified by the Influenza Division of the Centers for Disease Control and Prevention (CDC) after being received as unsubtypeable influenza A virus samples. Real-time reverse transcriptase PCR (rRT-PCR) procedures for detection and characterization of North American lineage (N. Am) SIV were developed and implemented at CDC for rapid identification of specimens from cases of suspected infections with SIV. These procedures were utilized in April 2009 for detection of human cases of 2009 A (H1N1) pandemic (pdm) influenza virus infection. Based on genetic sequence data derived from the first two viruses investigated, the previously developed rRT-PCR procedures were optimized to create the CDC rRT-PCR Swine Flu Panel for detection of the 2009 A (H1N1) pdm influenza virus. The analytical sensitivity of the CDC rRT-PCR Swine Flu Panel was shown to be 5 copies of RNA per reaction and 10(-1.3 - -0.7) 50% infectious doses (ID(50)) per reaction for cultured viruses. Cross-reactivity was not observed when testing human clinical specimens or cultured viruses that were positive for human seasonal A (H1N1, H3N2) and B influenza viruses. The CDC rRT-PCR Swine Flu Panel was distributed to public health laboratories in the United States and internationally from April 2009 until June 2010. The CDC rRT-PCR Swine Flu Panel served as an effective tool for timely and specific detection of 2009 A (H1N1) pdm influenza viruses and facilitated subsequent public health response implementation.

Design and Performance of the CDC Real-Time Reverse Transcriptase PCR Swine Flu Panel for Detection of 2009 A (H1N1) Pandemic Influenza Virus▿†‡

PubMed Central

Shu, Bo; Wu, Kai-Hui; Emery, Shannon; Villanueva, Julie; Johnson, Roy; Guthrie, Erica; Berman, LaShondra; Warnes, Christine; Barnes, Nathelia; Klimov, Alexander; Lindstrom, Stephen

2011-01-01

Swine influenza viruses (SIV) have been shown to sporadically infect humans and are infrequently identified by the Influenza Division of the Centers for Disease Control and Prevention (CDC) after being received as unsubtypeable influenza A virus samples. Real-time reverse transcriptase PCR (rRT-PCR) procedures for detection and characterization of North American lineage (N. Am) SIV were developed and implemented at CDC for rapid identification of specimens from cases of suspected infections with SIV. These procedures were utilized in April 2009 for detection of human cases of 2009 A (H1N1) pandemic (pdm) influenza virus infection. Based on genetic sequence data derived from the first two viruses investigated, the previously developed rRT-PCR procedures were optimized to create the CDC rRT-PCR Swine Flu Panel for detection of the 2009 A (H1N1) pdm influenza virus. The analytical sensitivity of the CDC rRT-PCR Swine Flu Panel was shown to be 5 copies of RNA per reaction and 10−1.3∼−0.7 50% infectious doses (ID50) per reaction for cultured viruses. Cross-reactivity was not observed when testing human clinical specimens or cultured viruses that were positive for human seasonal A (H1N1, H3N2) and B influenza viruses. The CDC rRT-PCR Swine Flu Panel was distributed to public health laboratories in the United States and internationally from April 2009 until June 2010. The CDC rRT-PCR Swine Flu Panel served as an effective tool for timely and specific detection of 2009 A (H1N1) pdm influenza viruses and facilitated subsequent public health response implementation. PMID:21593260

Examining procedural working memory processing in obsessive-compulsive disorder.

PubMed

Shahar, Nitzan; Teodorescu, Andrei R; Anholt, Gideon E; Karmon-Presser, Anat; Meiran, Nachshon

2017-07-01

Previous research has suggested that a deficit in working memory might underlie the difficulty of obsessive-compulsive disorder (OCD) patients to control their thoughts and actions. However, a recent meta-analyses found only small effect sizes for working memory deficits in OCD. Recently, a distinction has been made between declarative and procedural working memory. Working memory in OCD was tested mostly using declarative measurements. However, OCD symptoms typically concerns actions, making procedural working-memory more relevant. Here, we tested the operation of procedural working memory in OCD. Participants with OCD and healthy controls performed a battery of choice reaction tasks under high and low procedural working memory demands. Reaction-times (RT) were estimated using ex-Gaussian distribution fitting, revealing no group differences in the size of the RT distribution tail (i.e., τ parameter), known to be sensitive to procedural working memory manipulations. Group differences, unrelated to working memory manipulations, were found in the leading-edge of the RT distribution and analyzed using a two-stage evidence accumulation model. Modeling results suggested that perceptual difficulties might underlie the current group differences. In conclusion, our results suggest that procedural working-memory processing is most likely intact in OCD, and raise a novel, yet untested assumption regarding perceptual deficits in OCD. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Motor selection dynamics in FEF explain the reaction time variance of saccades to single targets

PubMed Central

Hauser, Christopher K; Zhu, Dantong; Stanford, Terrence R

2018-01-01

In studies of voluntary movement, a most elemental quantity is the reaction time (RT) between the onset of a visual stimulus and a saccade toward it. However, this RT demonstrates extremely high variability which, in spite of extensive research, remains unexplained. It is well established that, when a visual target appears, oculomotor activity gradually builds up until a critical level is reached, at which point a saccade is triggered. Here, based on computational work and single-neuron recordings from monkey frontal eye field (FEF), we show that this rise-to-threshold process starts from a dynamic initial state that already contains other incipient, internally driven motor plans, which compete with the target-driven activity to varying degrees. The ensuing conflict resolution process, which manifests in subtle covariations between baseline activity, build-up rate, and threshold, consists of fundamentally deterministic interactions, and explains the observed RT distributions while invoking only a small amount of intrinsic randomness. PMID:29652247

Using Lunar Impact Basin Relaxation to Test Impact Flux Models

NASA Astrophysics Data System (ADS)

Nimmo, F.; Conrad, J. W.; Neumann, G. A.; Kamata, S.; Fassett, C.

2017-12-01

Gravity data obtained by the GRAIL mission [1] has constrained the number and distribution of lunar impact basins [2]. We analyzed crater densities for newly-proposed basins to assign relative ages. The extent to which a basin is relaxed is calculated using GRAIL-derived crustal thickness models [3] by comparing the mantle uplift under basins to the surrounding region. With our catalog we can investigate the distribution of basin properties through relative time. We identify a relaxation state transition (RT) around the pre-Nectarian 4 relative age group for basins with diameters > 450 km, similar to previous results using a pre-GRAIL basin catalog [4]. This RT likely signals a change in the global thermal state of the crust, representing the time at which the lunar moho temperature fell below 1400 K [4]. This transition happens 50-100 million years (Myr) after the lunar magma ocean (LMO) solidifies [4]. Based on models and inferences of LMO solidification [5, 6] the RT is expected to occur at 4.25-4.50 Ga, depending on the rate of cooling once a crustal lid has formed [5] and the amount of tidal heating in the early crust [6]. Monotonically declining impact flux models, such as [7] and [8] predict a younger RT; 4.07-4.08 and 4.24-4.27 Ga respectively. A scaled-down version of [8] can fit the RT but fails to match the observed number of younger, unrelaxed basins. Models that invoke a later transient increase in impact flux can reproduce the inferred RT time; for instance, the model of [9] gives a RT age of 4.43-4.46 Ga. This model matches the number of younger basins and implies that basin preservation started at 4.49 Ga, likely before the LMO completely solidified. [1] Zuber M.T. et al. (2013) Science, 339, 668-671. [2] Neumann G.A. et al. (2015) Science Advances, 1, e1500852. [3] Wieczorek M.A. (2013) Science, 339, 671-675. [4] Kamata S. et al. (2015) Icarus, 250, 492-504. [5] Elkins-Tanton L.T. et al. (2011) Earth Planet. Sci. Lett., 304, 326-336. [6] Meyer, J. et al. (2010) Icarus, 208, 1-10. [7] Robbins S.J. (2014) Earth Planet. Sci. Lett., 403, 188-198. [8] Neukum G. et al. (2001) Space Sci. Rev., 96, 55-86. [9] Morbidelli A. et al. (2012) Earth Planet. Sci. Lett., 355, 144-151.

Effects of Healthy Aging and Early-Stage Dementia of the Alzheimer’s Type on Components of Response Time Distributions in Three Attention Tasks

PubMed Central

Tse, Chi-Shing; Balota, David A.; Yap, Melvin J.; Duchek, Janet M.; McCabe, David P.

2009-01-01

Objective The characteristics of response time (RT) distributions beyond measures of central tendency were explored in three attention tasks across groups of young, healthy older adults and individuals with very mild dementia of the Alzheimer’s type (DAT). Method Participants were administered computerized Stroop, Simon, and Switching tasks, along with psychometric tasks that tap various cognitive abilities, and a standard personality inventory (NEO-FFI). Ex-Gaussian (and Vincentile) analyses were used to capture the characteristics of the RT distributions for each participant across the three tasks, which afforded three components: Mu, Sigma (mean and standard deviation of the modal portion of the distribution), and Tau (the positive tail of the distribution). Results The results indicated that across all three attention tasks, healthy aging produced large changes in the central tendency Mu parameter of the distribution along with some change in Sigma and Tau (mean ηp2=.17, .08, and .04, respectively). In contrast, early stage DAT primarily produced an increase in the Tau component (mean ηp2=.06). Tau was also correlated with the psychometric measures of episodic/semantic memory, working memory, and processing speed, and with the personality traits of Neuroticism and Conscientiousness. Structural equation modeling indicated a unique relation between a latent Tau construct (−.90), as opposed to Sigma (−.09) and Mu constructs (.24), with working memory measures. Conclusions The results suggest a critical role of attentional control systems in discriminating healthy aging from early stage DAT and the utility of reaction time distribution analyses to better specify the nature of such change. PMID:20438208

Response time distributions in rapid chess: a large-scale decision making experiment.

PubMed

Sigman, Mariano; Etchemendy, Pablo; Slezak, Diego Fernández; Cecchi, Guillermo A

2010-01-01

Rapid chess provides an unparalleled laboratory to understand decision making in a natural environment. In a chess game, players choose consecutively around 40 moves in a finite time budget. The goodness of each choice can be determined quantitatively since current chess algorithms estimate precisely the value of a position. Web-based chess produces vast amounts of data, millions of decisions per day, incommensurable with traditional psychological experiments. We generated a database of response times (RTs) and position value in rapid chess games. We measured robust emergent statistical observables: (1) RT distributions are long-tailed and show qualitatively distinct forms at different stages of the game, (2) RT of successive moves are highly correlated both for intra- and inter-player moves. These findings have theoretical implications since they deny two basic assumptions of sequential decision making algorithms: RTs are not stationary and can not be generated by a state-function. Our results also have practical implications. First, we characterized the capacity of blunders and score fluctuations to predict a player strength, which is yet an open problem in chess softwares. Second, we show that the winning likelihood can be reliably estimated from a weighted combination of remaining times and position evaluation.

Response Time Distributions in Rapid Chess: A Large-Scale Decision Making Experiment

PubMed Central

Sigman, Mariano; Etchemendy, Pablo; Slezak, Diego Fernández; Cecchi, Guillermo A.

2010-01-01

Rapid chess provides an unparalleled laboratory to understand decision making in a natural environment. In a chess game, players choose consecutively around 40 moves in a finite time budget. The goodness of each choice can be determined quantitatively since current chess algorithms estimate precisely the value of a position. Web-based chess produces vast amounts of data, millions of decisions per day, incommensurable with traditional psychological experiments. We generated a database of response times (RTs) and position value in rapid chess games. We measured robust emergent statistical observables: (1) RT distributions are long-tailed and show qualitatively distinct forms at different stages of the game, (2) RT of successive moves are highly correlated both for intra- and inter-player moves. These findings have theoretical implications since they deny two basic assumptions of sequential decision making algorithms: RTs are not stationary and can not be generated by a state-function. Our results also have practical implications. First, we characterized the capacity of blunders and score fluctuations to predict a player strength, which is yet an open problem in chess softwares. Second, we show that the winning likelihood can be reliably estimated from a weighted combination of remaining times and position evaluation. PMID:21031032

A Quantitative Analysis of the Relationship Between Radiation Therapy Use and Travel Time.

PubMed

Liu, Emma; Santibáñez, Pablo; Puterman, Martin L; Weber, Leah; Ma, Xiang; Sauré, Antoine; Olivotto, Ivo A; Halperin, Ross; French, John; Tyldesley, Scott

2015-11-01

To model and quantify the relationship between radiation therapy (RT) use and travel time to RT services. Population-based registries and databases were used to identify both incident cancer patient and patients receiving RT within 1 year of diagnosis (RT1y) in British Columbia, Canada, between 1992 and 2011. The effects of age, gender, diagnosis year, income, prevailing wait time, and travel duration for RT on RT1y were assessed. Significant factors from univariate analyses were included in a multivariable logistic regression model. The shape of the travel time-RT1y curve was represented by generalized additive and segmented regression models. Analyses were conducted for breast, lung, and genitourinary cancer separately and for all cancer sites combined. After adjustment for age, gender, diagnosis year, income, and prevailing wait times, increasing travel time to the closest RT facility had a negative impact RT1y. The shape of the travel time-RT1y curve varied with cancer type. For breast cancer, the odds of RT1y were constant for the first 2 driving hours and decreased at 17% per hour thereafter. For lung cancer, the odds of RT1y decreased by 16% after 20 minutes and then decreased at 6% per hour. Genitourinary cancer RT1y was relatively independent of travel time. For all cancer sites combined, the odds of RT1y were constant within the first 2 driving hours and decreased at 7% per hour thereafter. Travel time to receive RT has a different impact on RT1y for different tumor sites. The results provide evidence-based insights for the configuration of catchment areas for new and existing cancer centers providing RT. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Rapid and sensitive detection of Zika virus by reverse transcription loop-mediated isothermal amplification.

PubMed

Wang, Xuan; Yin, Fenggui; Bi, Yuhai; Cheng, Gong; Li, Jing; Hou, Lidan; Li, Yunlong; Yang, Baozhi; Liu, Wenjun; Yang, Limin

2016-12-01

Zika virus (ZIKV) is an arbovirus that recently emerged and has expanded worldwide, causing a global threat and raising international concerns. Current molecular diagnostics, e.g., real-time PCR and reverse transcription PCR (RT-PCR), are time consuming, expensive, and can only be deployed in a laboratory instead of for field diagnostics. This study aimed to develop a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform showing sensitivity, specificity, and more convenience than previous methods, being easily distributed and implemented. Specific primers were designed and screened to target the entire ZIKV genome. The analytical sensitivity and specificity of the assay were evaluated and compared with traditional PCR and quantitative real-time PCR. Three different simulated clinical sample quick preparation protocols were evaluated to establish a rapid and straightforward treatment procedure for clinical specimens in open field detection. The RT-LAMP assay for detection of ZIKV demonstrated superior specificity and sensitivity compared to traditional PCR at the optimum reaction temperature. For the ZIKV RNA standard, the limit of detection was 20 copies/test. For the simulated ZIKV clinical samples, the limit of detection was 0.02 pfu/test, which was one order of magnitude higher than RT-PCR and similar to real-time PCR. The detection limit of simulated ZIKV specimens prepared using a protease quick processing method was consistent with that of samples prepared using commercial nucleic acid extraction kits, indicating that our ZIKV detection method could be used in point-of-care testing. The RT-LAMP assay had excellent sensitivity and specificity for detecting ZIKV and can be deployed together with a rapid specimen processing method, offering the possibility for ZIKV diagnosis outside of the laboratory. Copyright © 2016 Elsevier B.V. All rights reserved.

Cranial nerve involvement in nasopharyngeal carcinoma: response to radiotherapy and its clinical impact.

PubMed

Li, Jian-Cheng; Mayr, Nina A; Yuh, William T C; Wang, Jian Z; Jiang, Guo-Liang

2006-05-01

To evaluate the cranial nerve (CN) palsy associated with nasopharyngeal carcinoma (NPC), we studied factors that influenced the neurologic outcome of radiotherapy (RT), and the patterns and time course of neurologic recovery of CN palsy. Between July 1987 and July 1989, 93 patients who presented with CN palsy at the time of diagnosis of NPC were studied. All patients underwent external-beam RT with either cobalt-60 or 6-MV photon beams to a dose of 69 to 84 Gy at 2 Gy per fraction. The time course and pattern of neurologic recovery (complete, partial, or none) from CN palsy were evaluated. Age, sex, stage, histology, incidence and distribution of types of CNs involved, duration of CN palsy, and time course of tumor response during RT were correlated with the patterns and the time course of neurologic CN recovery by univariate and multivariate analyses. The cases of CN palsy most commonly involved CN V (38%), CN VI (26%), and CN XII (11%), which accounted for the majority of the cases (75%). The time course of CN recovery was variable and protracted. Most patients showed significant improvement upon completion of RT (51%, 19%, and 30% complete, partial, and no recovery, respectively) and further improvement 6 months after RT (58%, 17%, and 25%, respectively). Cranial nerves V, VI, and XII accounted for 75% of cases with no recovery. Recovery was best for CNs II, IX, and XI and the sympathetic nerve (100%, 87%, 100%, and 100%, respectively) and worst for CNs IV, VII, and XII (67%, 60%, and 40%, respectively, with no recovery). Neurologic CN recovery correlated significantly with the pretherapy duration (<3 months versus > or =3 months) of CN palsy (88% versus 62%; p = .002, multivariate analysis), the time course of clinical tumor regression, and neurologic symptom improvement during RT. Age, sex, T stage, N stage, histology, anterior versus posterior CN palsies, and base of skull involvement were not significant. According to our limited data, most patients with CN palsy respond well to RT. That the time course of neurologic recovery is variable and can be protracted indicates a need for continuous and close neurologic surveillance. The poorer neurologic outcome associated with a longer duration of CN symptoms may be related to a more severe longterm CN compression that results in irreversible damage. Timely diagnosis of NPC and fast institution of therapy are therefore critical to improving the neurologic outcome.

A Quantitative Analysis of the Relationship Between Radiation Therapy Use and Travel Time

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

Liu, Emma; Santibáñez, Pablo; Puterman, Martin L.

Purpose: To model and quantify the relationship between radiation therapy (RT) use and travel time to RT services. Methods and Materials: Population-based registries and databases were used to identify both incident cancer patient and patients receiving RT within 1 year of diagnosis (RT1y) in British Columbia, Canada, between 1992 and 2011. The effects of age, gender, diagnosis year, income, prevailing wait time, and travel duration for RT on RT1y were assessed. Significant factors from univariate analyses were included in a multivariable logistic regression model. The shape of the travel time–RT1y curve was represented by generalized additive and segmented regression models. Analysesmore » were conducted for breast, lung, and genitourinary cancer separately and for all cancer sites combined. Results: After adjustment for age, gender, diagnosis year, income, and prevailing wait times, increasing travel time to the closest RT facility had a negative impact RT1y. The shape of the travel time–RT1y curve varied with cancer type. For breast cancer, the odds of RT1y were constant for the first 2 driving hours and decreased at 17% per hour thereafter. For lung cancer, the odds of RT1y decreased by 16% after 20 minutes and then decreased at 6% per hour. Genitourinary cancer RT1y was relatively independent of travel time. For all cancer sites combined, the odds of RT1y were constant within the first 2 driving hours and decreased at 7% per hour thereafter. Conclusions: Travel time to receive RT has a different impact on RT1y for different tumor sites. The results provide evidence-based insights for the configuration of catchment areas for new and existing cancer centers providing RT.« less

Effectiveness of motor sequential learning according to practice schedules in healthy adults; distributed practice versus massed practice

PubMed Central

Kwon, Yong Hyun; Kwon, Jung Won; Lee, Myoung Hee

2015-01-01

[Purpose] The purpose of the current study was to compare the effectiveness of motor sequential learning according to two different types of practice schedules, distributed practice schedule (two 12-hour inter-trial intervals) and massed practice schedule (two 10-minute inter-trial intervals) using a serial reaction time (SRT) task. [Subjects and Methods] Thirty healthy subjects were recruited and then randomly and evenly assigned to either the distributed practice group or the massed practice group. All subjects performed three consecutive sessions of the SRT task following one of the two different types of practice schedules. Distributed practice was scheduled for two 12-hour inter-session intervals including sleeping time, whereas massed practice was administered for two 10-minute inter-session intervals. Response time (RT) and response accuracy (RA) were measured in at pre-test, mid-test, and post-test. [Results] For RT, univariate analysis demonstrated significant main effects in the within-group comparison of the three tests as well as the interaction effect of two groups × three tests, whereas the between-group comparison showed no significant effect. The results for RA showed no significant differences in neither the between-group comparison nor the interaction effect of two groups × three tests, whereas the within-group comparison of the three tests showed a significant main effect. [Conclusion] Distributed practice led to enhancement of motor skill acquisition at the first inter-session interval as well as at the second inter-interval the following day, compared to massed practice. Consequentially, the results of this study suggest that a distributed practice schedule can enhance the effectiveness of motor sequential learning in 1-day learning as well as for two days learning formats compared to massed practice. PMID:25931727

Dissociations of spatial congruence effects across response measures: an examination of delta plots.

PubMed

Miller, Jeff; Roüast, Nora M

2016-09-01

Spatial congruence ("Simon") effects on reaction time (RT) and response force (RF) were studied in two experiments requiring speeded choice responses to the color of a stimulus located irrelevantly to the left or right of fixation. In Experiment 1 with unimanual responses, both RT and incorrect-hand RF were sensitive to spatial congruence, and both showed larger Simon effects following a congruent trial than following an incongruent one. RT and incorrect-hand RF were dissociated in distributional (i.e., delta plot) analyses, however. As in previous studies, the Simon effect on RT was largest for the fastest responses and diminished as RT increased (i.e., decreasing delta plot). In contrast, Simon effects on RF did not decrease for slower responses; if anything, they increased slightly. In Experiment 2 participants made bimanual responses, allowing measurement of the spatial congruence effect for each trial. Responses were both faster and more forceful with the spatially congruent hand than with the spatially incongruent one, but neither of these effects decreased for slower responses. Overall, the results demonstrate that at least some motor-level effects of irrelevant spatial location persist for slower responses.

Fluoride tracer test for the performance analysis of a basin used as a lagooning pre-treatment facility in a WTP.

PubMed

Ruffino, Barbara

2015-07-01

The water treatment plant (WTP) of the city of Torino (NW Italy), which treats about 40 · 10(6) m(3)/year of raw water from Po river, has a 15-ha basin used as a lagooning pre-treatment facility. Since the efficiency of the lagooning process in the removal of pollutants from raw water depends on the internal hydrodynamics of the basin, the hydraulic performance of the basin was studied by combining the results of a stimulus-response tracer test with the monitoring of the tracer (fluoride) concentration throughout the basin at different times. The outcomes of the test demonstrated that the system was efficiently mixed and could be assimilated to a continuous stirred reactor presenting no flow anomalies, with an actual mean residence time (RT) of 12.7 days, compared with a nominal RT of 18 days. This assured that dissolved contaminants (such as fluoride) coming from the river were efficiently diluted before entering the WTP. The axial dispersion coefficient calculated from the RT distribution was approximately 47,300 m(2)/day. Three of the most popular formulae developed for the calculation of the axial dispersion coefficient provided results spreading over three orders of magnitude, thus showing their limitations. Finally, because of the width extent of the basin and the characteristics of its inflow, the 1-D advection-dispersion model failed in predicting the tracer concentration values in time at the outlet channel. On the contrary, the analytical solution of the 2-D advection-dispersion model proved to be suitable to fit the tracer concentration data over time at the outlet channel but it failed in describing the tracer distribution throughout the basin on the monitoring dates.

Dose distribution in the thyroid gland following radiation therapy of breast cancer--a retrospective study.

PubMed

Johansen, S; Reinertsen, K V; Knutstad, K; Olsen, D R; Fosså, S D

2011-06-09

To relate the development of post-treatment hypothyroidism with the dose distribution within the thyroid gland in breast cancer (BC) patients treated with loco-regional radiotherapy (RT). In two groups of BC patients postoperatively irradiated by computer tomography (CT)-based RT, the individual dose distributions in the thyroid gland were compared with each other; Cases developed post-treatment hypothyroidism after multimodal treatment including 4-field RT technique. Matched patients in Controls remained free for hypothyroidism. Based on each patient's dose volume histogram (DVH) the volume percentages of the thyroid absorbing respectively 20, 30, 40 and 50 Gy were then estimated (V20, V30, V40 and V50) together with the individual mean thyroid dose over the whole gland (MeanTotGy). The mean and median thyroid dose for the included patients was about 30 Gy, subsequently the total volume of the thyroid gland (VolTotGy) and the absolute volumes (cm3) receiving respectively <30 Gy and ≥30 Gy were calculated (Vol<30 and Vol≥30) and analyzed. No statistically significant inter-group differences were found between V20, V30, V40 and V50Gy or the median of MeanTotGy. The median VolTotGy in Controls was 2.3 times above VolTotGy in Cases (ρ=0.003), with large inter-individual variations in both groups. The volume of the thyroid gland receiving<30 Gy in Controls was almost 2.5 times greater than the comparable figure in Cases. We concluded that in patients with small thyroid glands after loco-radiotherapy of BC, the risk of post-treatment hypothyroidism depends on the volume of the thyroid gland.

Effects of Aging and IQ on Item and Associative Memory

ERIC Educational Resources Information Center

Ratcliff, Roger; Thapar, Anjali; McKoon, Gail

2011-01-01

The effects of aging and IQ on performance were examined in 4 memory tasks: item recognition, associative recognition, cued recall, and free recall. For item and associative recognition, accuracy and the response time (RT) distributions for correct and error responses were explained by Ratcliff's (1978) diffusion model at the level of individual…

Proactive Control Processes in Event-Based Prospective Memory: Evidence from Intraindividual Variability and Ex-Gaussian Analyses

ERIC Educational Resources Information Center

Ball, B. Hunter; Brewer, Gene A.

2018-01-01

The present study implemented an individual differences approach in conjunction with response time (RT) variability and distribution modeling techniques to better characterize the cognitive control dynamics underlying ongoing task cost (i.e., slowing) and cue detection in event-based prospective memory (PM). Three experiments assessed the relation…

Magnetic nanoparticle hyperthermia enhances radiation therapy: A study in mouse models of human prostate cancer

PubMed Central

Attaluri, Anilchandra; Kandala, Sri Kamal; Wabler, Michele; Zhou, Haoming; Cornejo, Christine; Armour, Michael; Hedayati, Mohammad; Zhang, Yonggang; DeWeese, Theodore L.; Herman, Cila; Ivkov, Robert

2015-01-01

Purpose We aimed to characterise magnetic nanoparticle hyperthermia (mNPH) with radiation therapy (RT) for prostate cancer. Methods Human prostate cancer subcutaneous tumours, PC3 and LAPC-4, were grown in nude male mice. When tumours measured 150 mm3 magnetic iron oxide nanoparticles (MIONPs) were injected into tumours to a target dose of 5.5 mg Fe/cm3 tumour, and treated 24 h later by exposure to alternating magnetic field (AMF). Mice were randomly assigned to one of four cohorts to characterise (1) intratumour MIONP distribution, (2) effects of variable thermal dose mNPH (fixed AMF peak amplitude 24 kA/m at 160±5 kHz) with/without RT (5 Gy), (3) effects of RT (RT5: 5 Gy; RT8: 8 Gy), and (4) fixed thermal dose mNPH (43 °C for 20min) with/without RT (5 Gy). MIONP concentration and distribution were assessed following sacrifice and tissue harvest using inductively coupled plasma mass spectrometry (ICP-MS) and Prussian blue staining, respectively. Tumour growth was monitored and compared among treated groups. Results LAPC-4 tumours retained higher MIONP concentration and more uniform distribution than did PC3 tumours. AMF power modulation provided similar thermal dose for mNPH and combination therapy groups (CEM43: LAPC-4: 33.6 ± 3.4 versus 25.9 ± 0.8, and PC3: 27.19 ± 0.7 versus 27.50 ± 0.6), thereby overcoming limitations of MIONP distribution and yielding statistically significant tumour growth delay. Conclusion PC3 and LAPC-4 tumours represent two biological models that demonstrate different patterns of nanoparticle retention and distribution, offering a model to make comparisons of these effects for mNPH. Modulating power for mNPH offers potential to overcome limitations of MIONP distribution to enhance mNPH. PMID:25811736

Magnetic nanoparticle hyperthermia enhances radiation therapy: A study in mouse models of human prostate cancer.

PubMed

Attaluri, Anilchandra; Kandala, Sri Kamal; Wabler, Michele; Zhou, Haoming; Cornejo, Christine; Armour, Michael; Hedayati, Mohammad; Zhang, Yonggang; DeWeese, Theodore L; Herman, Cila; Ivkov, Robert

2015-06-01

We aimed to characterise magnetic nanoparticle hyperthermia (mNPH) with radiation therapy (RT) for prostate cancer. Human prostate cancer subcutaneous tumours, PC3 and LAPC-4, were grown in nude male mice. When tumours measured 150 mm3 magnetic iron oxide nanoparticles (MIONPs) were injected into tumours to a target dose of 5.5 mg Fe/cm3 tumour, and treated 24 h later by exposure to alternating magnetic field (AMF). Mice were randomly assigned to one of four cohorts to characterise (1) intratumour MIONP distribution, (2) effects of variable thermal dose mNPH (fixed AMF peak amplitude 24 kA/m at 160 ± 5 kHz) with/without RT (5 Gy), (3) effects of RT (RT5: 5 Gy; RT8: 8 Gy), and (4) fixed thermal dose mNPH (43 °C for 20 min) with/without RT (5 Gy). MIONP concentration and distribution were assessed following sacrifice and tissue harvest using inductively coupled plasma mass spectrometry (ICP-MS) and Prussian blue staining, respectively. Tumour growth was monitored and compared among treated groups. LAPC-4 tumours retained higher MIONP concentration and more uniform distribution than did PC3 tumours. AMF power modulation provided similar thermal dose for mNPH and combination therapy groups (CEM43: LAPC-4: 33.6 ± 3.4 versus 25.9 ± 0.8, and PC3: 27.19 ± 0.7 versus 27.50 ± 0.6), thereby overcoming limitations of MIONP distribution and yielding statistically significant tumour growth delay. PC3 and LAPC-4 tumours represent two biological models that demonstrate different patterns of nanoparticle retention and distribution, offering a model to make comparisons of these effects for mNPH. Modulating power for mNPH offers potential to overcome limitations of MIONP distribution to enhance mNPH.

Stereotactic radiotherapy for locally recurrent nasopharyngeal carcinoma.

PubMed

Leung, To-Wai; Wong, Victy Y W; Tung, Stewart Y

2009-11-01

To study the treatment outcome in patients with locally recurrent nasopharyngeal carcinoma (NPC) who were treated with stereotactic radiotherapy (SRT). Thirty patients with non-metastatic, locally recurrent NPC who were treated with curative intent between 1998 and 2002 were retrospectively analyzed. The International Union Against Cancer T-stage distribution at recurrence (rT) was as follows: rT1-14, rT2-7, rT3-3, and rT4-6. All patients were treated with SRT with a daily fractional dose of 2.5-4.5 Gy (median, 3 Gy) in 8-22 fractions (median, 18 fractions). Total equivalent dose (TED) was calculated by the linear-quadratic formula without a time factor correction. The 5-year actuarial overall survival rate, disease-specific survival rate, and local failure-free survival (LFFS) rate for the whole group were 40%, 41.4%, and 56.8%, respectively. The 3-year LFFS rates of rT1-2 and rT3-4 diseases were 65% and 66.7%, respectively. Seven of nine patients who received a TED <55 Gy recurred locally compared with 4 of 21 patients who received > or =55 Gy. Their corresponding 5-year LFFS rates were 22.2% and 75.8% (p = 0.005). The TED was the only factor significant in affecting the local control on univariate analyses. SRT is an effective treatment for locally recurrent NPC. TED > or =55 Gy should be given to secure a higher local control rate. The late complication rates were acceptable for patients with rT1-2 disease. For patients with rT3-4 disease, more works need to be done to further decrease the late complications.

Development of recombinase polymerase amplification assays for the rapid detection of peste des petits ruminants virus.

PubMed

Zhang, Yongning; Wang, Jianchang; Zhang, Zhou; Mei, Lin; Wang, Jinfeng; Wu, Shaoqiang; Lin, Xiangmei

2018-04-01

Peste des petits ruminants (PPR) is a severe infectious disease of small ruminants caused by PPR virus (PPRV). Rapid and sensitive detection of PPRV is critical for controlling PPR. This report describes the development and evaluation of a conventional reverse transcription recombinase polymerase amplification (RT-RPA) assay and a real-time RT-RPA assay, targeting the PPRV N gene. Sensitivity analysis revealed that the conventional RT-RPA assay could detect 852 copies of standard PPRV RNA per reaction at 95% probability within 20 min at 41 °C, and the real-time RT-RPA assay could detect 103 copies of RNA molecules per reaction at 95% probability. Specificity analysis showed that both assays have no cross-reactivity with nucleic acid templates prepared from other selected viruses or common pathogens. Clinical evaluation using 162 ovine and hircine serum and nasal swab samples showed that the performance of both the real-time RT-RPA assay and the conventional RT-RPA assay were comparable to that of real-time RT-PCR. The overall agreements between real-time RT-PCR and real-time RT-RPA, and conventional RT-RPA were 99.4% (161/162) and 98.8% (160/162), respectively. The R 2 value of real-time RT-RPA and real-time RT-PCR was 0.900 by linear regression analysis. Our results suggest that both RT-RPA assays have a potential application in the rapid, sensitive and specific detection of PPRV. Copyright © 2018 Elsevier B.V. All rights reserved.

Speaker diarization system on the 2007 NIST rich transcription meeting recognition evaluation

NASA Astrophysics Data System (ADS)

Sun, Hanwu; Nwe, Tin Lay; Koh, Eugene Chin Wei; Bin, Ma; Li, Haizhou

2007-09-01

This paper presents a speaker diarization system developed at the Institute for Infocomm Research (I2R) for NIST Rich Transcription 2007 (RT-07) evaluation task. We describe in details our primary approaches for the speaker diarization on the Multiple Distant Microphones (MDM) conditions in conference room scenario. Our proposed system consists of six modules: 1). Least-mean squared (NLMS) adaptive filter for the speaker direction estimate via Time Difference of Arrival (TDOA), 2). An initial speaker clustering via two-stage TDOA histogram distribution quantization approach, 3). Multiple microphone speaker data alignment via GCC-PHAT Time Delay Estimate (TDE) among all the distant microphone channel signals, 4). A speaker clustering algorithm based on GMM modeling approach, 5). Non-speech removal via speech/non-speech verification mechanism and, 6). Silence removal via "Double-Layer Windowing"(DLW) method. We achieves error rate of 31.02% on the 2006 Spring (RT-06s) MDM evaluation task and a competitive overall error rate of 15.32% for the NIST Rich Transcription 2007 (RT-07) MDM evaluation task.

The Temporal Dynamics of Visual Search: Evidence for Parallel Processing in Feature and Conjunction Searches

PubMed Central

McElree, Brian; Carrasco, Marisa

2012-01-01

Feature and conjunction searches have been argued to delineate parallel and serial operations in visual processing. The authors evaluated this claim by examining the temporal dynamics of the detection of features and conjunctions. The 1st experiment used a reaction time (RT) task to replicate standard mean RT patterns and to examine the shapes of the RT distributions. The 2nd experiment used the response-signal speed–accuracy trade-off (SAT) procedure to measure discrimination (asymptotic detection accuracy) and detection speed (processing dynamics). Set size affected discrimination in both feature and conjunction searches but affected detection speed only in the latter. Fits of models to the SAT data that included a serial component overpredicted the magnitude of the observed dynamics differences. The authors concluded that both features and conjunctions are detected in parallel. Implications for the role of attention in visual processing are discussed. PMID:10641310

Investigating the neural bases for intra-subject cognitive efficiency changes using functional magnetic resonance imaging

PubMed Central

Rao, Neena K.; Motes, Michael A.; Rypma, Bart

2014-01-01

Several fMRI studies have examined brain regions mediating inter-subject variability in cognitive efficiency, but none have examined regions mediating intra-subject variability in efficiency. Thus, the present study was designed to identify brain regions involved in intra-subject variability in cognitive efficiency via participant-level correlations between trial-level reaction time (RT) and trial-level fMRI BOLD percent signal change on a processing speed task. On each trial, participants indicated whether a digit-symbol probe-pair was present or absent in an array of nine digit-symbol probe-pairs while fMRI data were collected. Deconvolution analyses, using RT time-series models (derived from the proportional scaling of an event-related hemodynamic response function model by trial-level RT), were used to evaluate relationships between trial-level RTs and BOLD percent signal change. Although task-related patterns of activation and deactivation were observed in regions including bilateral occipital, bilateral parietal, portions of the medial wall such as the precuneus, default mode network regions including anterior cingulate, posterior cingulate, bilateral temporal, right cerebellum, and right cuneus, RT-BOLD correlations were observed in a more circumscribed set of regions. Positive RT-BOLD correlations, where fast RTs were associated with lower BOLD percent signal change, were observed in regions including bilateral occipital, bilateral parietal, and the precuneus. RT-BOLD correlations were not observed in the default mode network indicating a smaller set of regions associated with intra-subject variability in cognitive efficiency. The results are discussed in terms of a distributed area of regions that mediate variability in the cognitive efficiency that might underlie processing speed differences between individuals. PMID:25374527

Investigating the neural bases for intra-subject cognitive efficiency changes using functional magnetic resonance imaging.

PubMed

Rao, Neena K; Motes, Michael A; Rypma, Bart

2014-01-01

Several fMRI studies have examined brain regions mediating inter-subject variability in cognitive efficiency, but none have examined regions mediating intra-subject variability in efficiency. Thus, the present study was designed to identify brain regions involved in intra-subject variability in cognitive efficiency via participant-level correlations between trial-level reaction time (RT) and trial-level fMRI BOLD percent signal change on a processing speed task. On each trial, participants indicated whether a digit-symbol probe-pair was present or absent in an array of nine digit-symbol probe-pairs while fMRI data were collected. Deconvolution analyses, using RT time-series models (derived from the proportional scaling of an event-related hemodynamic response function model by trial-level RT), were used to evaluate relationships between trial-level RTs and BOLD percent signal change. Although task-related patterns of activation and deactivation were observed in regions including bilateral occipital, bilateral parietal, portions of the medial wall such as the precuneus, default mode network regions including anterior cingulate, posterior cingulate, bilateral temporal, right cerebellum, and right cuneus, RT-BOLD correlations were observed in a more circumscribed set of regions. Positive RT-BOLD correlations, where fast RTs were associated with lower BOLD percent signal change, were observed in regions including bilateral occipital, bilateral parietal, and the precuneus. RT-BOLD correlations were not observed in the default mode network indicating a smaller set of regions associated with intra-subject variability in cognitive efficiency. The results are discussed in terms of a distributed area of regions that mediate variability in the cognitive efficiency that might underlie processing speed differences between individuals.

Evaluation of TRMM satellite-based precipitation indexes for flood forecasting over Riyadh City, Saudi Arabia

NASA Astrophysics Data System (ADS)

Tekeli, Ahmet Emre; Fouli, Hesham

2016-10-01

Floods are among the most common disasters harming humanity. In particular, flash floods cause hazards to life, property and any type of structures. Arid and semi-arid regions are equally prone to flash floods like regions with abundant rainfall. Despite rareness of intensive and frequent rainfall events over Kingdom of Saudi Arabia (KSA); an arid/semi-arid region, occasional flash floods occur and result in large amounts of damaging surface runoff. The flooding of 16 November, 2013 in Riyadh; the capital city of KSA, resulted in killing some people and led to much property damage. The Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA) Real Time (RT) data (3B42RT) are used herein for flash flood forecasting. 3B42RT detected high-intensity rainfall events matching with the distribution of observed floods over KSA. A flood early warning system based on exceedance of threshold limits on 3B42RT data is proposed for Riyadh. Three different indexes: Constant Threshold (CT), Cumulative Distribution Functions (CDF) and Riyadh Flood Precipitation Index (RFPI) are developed using 14-year 3B42RT data from 2000 to 2013. RFPI and CDF with 90% captured the three major flooding events that occurred in February 2005, May 2010 and November 2013 in Riyadh. CT with 3 mm/h intensity indicated the 2013 flooding, but missed those of 2005 and 2010. The methodology implemented herein is a first-step simple and accurate way for flash flood forecasting over Riyadh. The simplicity of the methodology enables its applicability for the TRMM follow-on missions like Global Precipitation Measurement (GPM) mission.

Risk of radiation-induced malignancy with heterotopic ossification prophylaxis: a case-control analysis.

PubMed

Sheybani, Arshin; TenNapel, Mindi J; Lack, William D; Clerkin, Patrick; Hyer, Daniel E; Sun, Wenqing; Jacobson, Geraldine M

2014-07-01

To determine the risk of radiation-induced malignancy after prophylactic treatment for heterotopic ossification (HO). A matched case-control study was conducted within a population-based cohort of 3489 patients treated either for acetabular fractures with acetabular open reduction internal fixation or who underwent total hip arthroplasty from 1990 to 2009. Record-linkage techniques identified patients who were diagnosed with a malignancy from our state health registry. Patients with a prior history of malignancy were excluded from the cohort. For each documented case of cancer, 2 controls were selected by stratified random sampling from the cohort that did not develop a malignancy. Matching factors were sex, age at time of hip treatment, and duration of follow-up. A total of 243 patients were diagnosed with a malignancy after hip treatment. Five patients were excluded owing to inadequate follow-up time in the corresponding control cohort. A cohort of 238 cases (control, 476 patients) was included. Mean follow-up was 10 years, 12 years in the control group. In the cancer cohort, 4% of patients had radiation therapy (RT), compared with 7% in the control group. Of the 9 patients diagnosed with cancer after RT, none occurred within the field. The mean latency period was 5.9 years in the patients who received RT and 6.6 years in the patients who did not. Median (range) age at time of cancer diagnosis in patients who received RT was 62 (43-75) years, compared with 70 (32-92) years in the non-RT patients. An ad hoc analysis was subsequently performed in all 2749 patients who were not matched and found neither an increased incidence of malignancy nor a difference in distribution of type of malignancy. We were unable to demonstrate an increased risk of malignancy in patients who were treated with RT for HO prophylaxis compared with those who were not. Copyright © 2014 Elsevier Inc. All rights reserved.

Risk of Radiation-Induced Malignancy With Heterotopic Ossification Prophylaxis: A Case–Control Analysis

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

Sheybani, Arshin, E-mail: arshin-sheybani@uiowa.edu; TenNapel, Mindi J.; Lack, William D.

2014-07-01

Purpose: To determine the risk of radiation-induced malignancy after prophylactic treatment for heterotopic ossification (HO). Methods and Materials: A matched case–control study was conducted within a population-based cohort of 3489 patients treated either for acetabular fractures with acetabular open reduction internal fixation or who underwent total hip arthroplasty from 1990 to 2009. Record-linkage techniques identified patients who were diagnosed with a malignancy from our state health registry. Patients with a prior history of malignancy were excluded from the cohort. For each documented case of cancer, 2 controls were selected by stratified random sampling from the cohort that did not developmore » a malignancy. Matching factors were sex, age at time of hip treatment, and duration of follow-up. Results: A total of 243 patients were diagnosed with a malignancy after hip treatment. Five patients were excluded owing to inadequate follow-up time in the corresponding control cohort. A cohort of 238 cases (control, 476 patients) was included. Mean follow-up was 10 years, 12 years in the control group. In the cancer cohort, 4% of patients had radiation therapy (RT), compared with 7% in the control group. Of the 9 patients diagnosed with cancer after RT, none occurred within the field. The mean latency period was 5.9 years in the patients who received RT and 6.6 years in the patients who did not. Median (range) age at time of cancer diagnosis in patients who received RT was 62 (43-75) years, compared with 70 (32-92) years in the non-RT patients. An ad hoc analysis was subsequently performed in all 2749 patients who were not matched and found neither an increased incidence of malignancy nor a difference in distribution of type of malignancy. Conclusion: We were unable to demonstrate an increased risk of malignancy in patients who were treated with RT for HO prophylaxis compared with those who were not.« less

Breath-holding times in various phases of respiration and effect of respiratory training in lung cancer patients.

PubMed

Tibdewal, Anil; Munshi, Anusheel; Pathak, Rima; Misra, Shagun; Daptardar, Anuradha; Singh, Vincent; Agarwal, Jai Prakash

2015-08-01

Breath-holding (BH) technique is used for reducing the intrafraction-tumour motion in mobile lung tumours treated with radiotherapy (RT). There is paucity of literature evaluating differences in BH times in various phases of respiration in patients with lung cancer. One hundred consecutive patients with lung cancer planned for radical RT/chemoradiation were accrued in the study. Eighty-seven patients were eligible for analysis at RT conclusion. Baseline pulmonary function test (PFT) were performed in all patients, and respiratory training was given from the day of RT planning. Deep inspiration breath hold (DIBH), deep expiration breath hold (DEBH) and mid-ventilation breath hold (MVBH) were recorded manually with a stopwatch for each patient at four time points (RT planning/baseline, RT starting, during RT and RT conclusion). Median DIBH times at RT planning, RT starting, during RT and RT conclusion were 21.2, 20.6, 20.1 and 21.1 s, respectively. The corresponding median DEBH and MVBH times were 16.3, 18.2, 18.3, 18.5 s and 19.9, 20.5, 21.3, 22.1 s, respectively. Respiratory training increased MVBH time at RT conclusion compared to baseline, which was statistically significant (19.9-22.1 s, P = 0.002). DIBH or DEBH times were stable at various time points with neither a significant improvement nor decline. Among various patient and tumour factors Forced Vital Capacity pre-bronchodilation (FVCpre ) was the only factor that consistently predicted DIBH, DEBH and MVBH at all four time points with P value <0.05. BH was well tolerated by most lung cancer patients with minimum median BH time of at least 16 s in any of the three phases of respiration. Respiratory training improved MVBH time while consistently maintaining DIBH and DEBH times throughout the course of radiotherapy. © 2015 The Royal Australian and New Zealand College of Radiologists.

Online versus offline: The Web as a medium for response time data collection.

PubMed

Chetverikov, Andrey; Upravitelev, Philipp

2016-09-01

The Internet provides a convenient environment for data collection in psychology. Modern Web programming languages, such as JavaScript or Flash (ActionScript), facilitate complex experiments without the necessity of experimenter presence. Yet there is always a question of how much noise is added due to the differences between the setups used by participants and whether it is compensated for by increased ecological validity and larger sample sizes. This is especially a problem for experiments that measure response times (RTs), because they are more sensitive (and hence more susceptible to noise) than, for example, choices per se. We used a simple visual search task with different set sizes to compare laboratory performance with Web performance. The results suggest that although the locations (means) of RT distributions are different, other distribution parameters are not. Furthermore, the effect of experiment setting does not depend on set size, suggesting that task difficulty is not important in the choice of a data collection method. We also collected an additional online sample to investigate the effects of hardware and software diversity on the accuracy of RT data. We found that the high diversity of browsers, operating systems, and CPU performance may have a detrimental effect, though it can partly be compensated for by increased sample sizes and trial numbers. In sum, the findings show that Web-based experiments are an acceptable source of RT data, comparable to a common keyboard-based setup in the laboratory.

Modeling Real-Time Applications with Reusable Design Patterns

NASA Astrophysics Data System (ADS)

Rekhis, Saoussen; Bouassida, Nadia; Bouaziz, Rafik

Real-Time (RT) applications, which manipulate important volumes of data, need to be managed with RT databases that deal with time-constrained data and time-constrained transactions. In spite of their numerous advantages, RT databases development remains a complex task, since developers must study many design issues related to the RT domain. In this paper, we tackle this problem by proposing RT design patterns that allow the modeling of structural and behavioral aspects of RT databases. We show how RT design patterns can provide design assistance through architecture reuse of reoccurring design problems. In addition, we present an UML profile that represents patterns and facilitates further their reuse. This profile proposes, on one hand, UML extensions allowing to model the variability of patterns in the RT context and, on another hand, extensions inspired from the MARTE (Modeling and Analysis of Real-Time Embedded systems) profile.

Automated selection of brain regions for real-time fMRI brain-computer interfaces

NASA Astrophysics Data System (ADS)

Lührs, Michael; Sorger, Bettina; Goebel, Rainer; Esposito, Fabrizio

2017-02-01

Objective. Brain-computer interfaces (BCIs) implemented with real-time functional magnetic resonance imaging (rt-fMRI) use fMRI time-courses from predefined regions of interest (ROIs). To reach best performances, localizer experiments and on-site expert supervision are required for ROI definition. To automate this step, we developed two unsupervised computational techniques based on the general linear model (GLM) and independent component analysis (ICA) of rt-fMRI data, and compared their performances on a communication BCI. Approach. 3 T fMRI data of six volunteers were re-analyzed in simulated real-time. During a localizer run, participants performed three mental tasks following visual cues. During two communication runs, a letter-spelling display guided the subjects to freely encode letters by performing one of the mental tasks with a specific timing. GLM- and ICA-based procedures were used to decode each letter, respectively using compact ROIs and whole-brain distributed spatio-temporal patterns of fMRI activity, automatically defined from subject-specific or group-level maps. Main results. Letter-decoding performances were comparable to supervised methods. In combination with a similarity-based criterion, GLM- and ICA-based approaches successfully decoded more than 80% (average) of the letters. Subject-specific maps yielded optimal performances. Significance. Automated solutions for ROI selection may help accelerating the translation of rt-fMRI BCIs from research to clinical applications.

Systematic Analysis of the Effect of Small Scale Permeability Heterogeneity on Hyporheic Exchange Flux and Residence Times

NASA Astrophysics Data System (ADS)

Laube, G.; Schmidt, C.; Fleckenstein, J. H.

2014-12-01

The hyporheic zone (HZ) contributes significantly to whole stream biogeochemical cycling. Biogeochemical reactions within the HZ are often transport limited, thus, understanding these reactions requires knowledge about the magnitude of hyporheic fluxes (HF) and the residence time (RT) of these fluxes within the HZ. While the hydraulics of HF are relatively well understood, studies addressing the influence of permeability heterogeneity lack systematic analysis and have even produced contradictory results (e.g. [1] vs. [2]). In order to close this gap, this study uses a statistical numerical approach to elucidate the influence of permeability heterogeneity on HF and RT. We simulated and evaluated 3750 2D-scenarios of sediment heterogeneity by means of Gaussian random fields with focus on total HF and RT distribution. The scenarios were based on ten realizations of each of all possible combinations of 15 different correlation lengths, 5 dipping angles and 5 permeability variances. Roughly 500 hyporheic stream traces were analyzed per simulation, for a total of almost two million stream traces analyzed for correlations between permeability heterogeneity, HF, and RT. Total HF and the RT variance positively correlated with permeability variance while the mean RT negatively correlated with permeability variance. In contrast, changes in correlation lengths and dipping angles had little effect on the examined properties RT and HF. These results provide a possible explanation of the seemingly contradictory conclusions of recent studies, given that the permeability variances in these studies differ by several orders of magnitude. [1] Bardini, L., Boano, F., Cardenas, M.B, Sawyer, A.H, Revelli, R. and Ridolfi, L. "Small-Scale Permeability Heterogeneity Has Negligible Effects on Nutrient Cycling in Streambeds." Geophysical Research Letters, 2013. doi:10.1002/grl.50224. [2] Zhou, Y., Ritzi, R. W., Soltanian, M. R. and Dominic, D. F. "The Influence of Streambed Heterogeneity on Hyporheic Flow in Gravelly Rivers." Groundwater, 2013. doi:10.1111/gwat.12048.

The ex-Gaussian distribution of reaction times in adolescents with attention-deficit/hyperactivity disorder.

PubMed

Gu, Shoou-Lian Hwang; Gau, Susan Shur-Fen; Tzang, Shyh-Weir; Hsu, Wen-Yau

2013-11-01

We investigated the three parameters (mu, sigma, tau) of ex-Gaussian distribution of RT derived from the Conners' continuous performance test (CCPT) and examined the moderating effects of the energetic factors (the inter-stimulus intervals (ISIs) and Blocks) among these three parameters, especially tau, an index describing the positive skew of RT distribution. We assessed 195 adolescents with DSM-IV ADHD, and 90 typically developing (TD) adolescents, aged 10-16. Participants and their parents received psychiatric interviews to confirm the diagnosis of ADHD and other psychiatric disorders. Participants also received intelligence (WISC-III) and CCPT assessments. We found that participants with ADHD had a smaller mu, and larger tau. As the ISI/Block increased, the magnitude of group difference in tau increased. Among the three ex-Gaussian parameters, tau was positively associated with omission errors, and mu was negatively associated with commission errors. The moderating effects of ISIs and Blocks on tau parameters suggested that the ex-Gaussian parameters could offer more information about the attention state in vigilance task, especially in ADHD. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evaluation of a simple test of reaction time for baseline concussion testing in a population of high school athletes.

PubMed

MacDonald, James; Wilson, Julie; Young, Julie; Duerson, Drew; Swisher, Gail; Collins, Christy L; Meehan, William P

2015-01-01

A common sequela of concussions is impaired reaction time. Computerized neurocognitive tests commonly measure reaction time. A simple clinical test for reaction time has been studied previously in college athletes; whether this test is valid and reliable when assessing younger athletes remains unknown. Our study examines the reliability and validity of this test in a population of high school athletes. Cross-sectional study. Two American High Schools. High school athletes (N = 448) participating in American football or soccer during the academic years 2011 to 2012 and 2012 to 2013. All study participants completed a computerized baseline neurocognitive assessment that included a measure of reaction time (RT comp), in addition to a clinical measure of reaction time that assessed how far a standard measuring device would fall prior to the athlete catching it (RT clin). Validity was assessed by determining the correlation between RT clin and RT comp. Reliability was assessed by measuring the intraclass correlation coefficients (ICCs) between the repeated measures of RT clin and RT comp taken 1 year apart. In the first year of study, RT clin and RT comp were positively but weakly correlated (rs = 0.229, P < 0.001). In the second year, there was no significant correlation between RT clin and RT comp (rs = 0.084, P = 0.084). Both RT clin [ICC = 0.608; 95% confidence interval (CI), 0.434-0.728] and RT comp (ICC = 0.691; 95% CI, 0.554-0.786) had marginal reliability. In a population of high school athletes, RT clin had poor validity when compared with RT comp as a standard. Both RT clin and RT comp had marginal test-retest reliability. Before considering the clinical use of RT clin in the assessment of sport-related concussions sustained by high school athletes, the factors affecting reliability and validity should be investigated further. Reaction time impairment commonly results from concussion and is among the most clinically important measures of the condition. The device evaluated in this study has previously been investigated as a reaction time measure in college athletes. This study investigates the clinical generalizability of the device in a younger population. A video abstract showing how the RT clin device is used in practice is available as Supplemental Digital Content 1, http://links.lww.com/JSM/A43.

Investigating the role of feedback and motivation in clinical reaction time assessment.

PubMed

Eckner, James T; Chandran, Srikrishna; Richardson, James K

2011-12-01

To investigate the influence of performance feedback and motivation during 2 tests of simple visuomotor reaction time (RT). Cross-sectional, observational study. Outpatient academic physiatry clinic. Thirty-one healthy adults (mean [SD], 54 ± 15 years). Participants completed a clinical test of RT (RT(clin)) and a computerized test of RT with and without performance feedback (RT(compFB) and RT(compNoFB), respectively) in randomly assigned order. They then ranked their degree of motivation during each test. RT(clin) measured the time required to catch a suspended vertical shaft by hand closure after release of the shaft by the examiner. RT(compFB) and RT(compNoFB) both measured the time required to press a computer key in response to a visual cue displayed on a computer monitor. Performance feedback (visual display of the previous trial and summary results) was provided for RT(compFB), but not for RT(compNoFB). Means and standard deviations of RT(clin), RT(compFB), and RT(compNoFB) and participants' self-reported motivation on a 5-point Likert scale for each test. There were significant differences in both the means and standard deviations of RT(clin), RT(compFB), and RT(compNoFB) (F(2,60) = 81.66, P < .0001; F(2,60) = 32.46, P < .0001, respectively), with RT(clin) being both the fastest and least variable of the RT measurements. RT(clin) was more strongly correlated with RT(compFB) (r = 0.449, P = .0011) than with RT(compNoFB) (r = 0.314, P = .086). The participants reported similar levels of motivation between RT(clin) and RT(compFB), both of which were reported to be more motivating than RT(compNoFB). The stronger correlation between RT(clin) and RT(compFB) as well as the higher reported motivation during RT(clin) and RT(compFB) testing suggest that performance feedback is a positive motivating factor that is inherent to RT(clin) testing. RT(clin) is a simple, inexpensive technique for measuring RT and appears to be an intrinsically motivating task. This motivation may promote faster, more consistent RT performance compared with currently available computerized programs, which do not typically provide performance feedback. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

Drifting from slow to "D'oh!": working memory capacity and mind wandering predict extreme reaction times and executive control errors.

PubMed

McVay, Jennifer C; Kane, Michael J

2012-05-01

A combined experimental, individual-differences, and thought-sampling study tested the predictions of executive attention (e.g., Engle & Kane, 2004) and coordinative binding (e.g., Oberauer, Süβ, Wilhelm, & Sander, 2007) theories of working memory capacity (WMC). We assessed 288 subjects' WMC and their performance and mind-wandering rates during a sustained-attention task; subjects completed either a go/no-go version requiring executive control over habit or a vigilance version that did not. We further combined the data with those from McVay and Kane (2009) to (1) gauge the contributions of WMC and attentional lapses to the worst performance rule and the tail, or τ parameter, of reaction time (RT) distributions; (2) assess which parameters from a quantitative evidence-accumulation RT model were predicted by WMC and mind-wandering reports; and (3) consider intrasubject RT patterns--particularly, speeding--as potential objective markers of mind wandering. We found that WMC predicted action and thought control in only some conditions, that attentional lapses (indicated by task-unrelated-thought reports and drift-rate variability in evidence accumulation) contributed to τ, performance accuracy, and WMC's association with them and that mind-wandering experiences were not predicted by trial-to-trial RT changes, and so they cannot always be inferred from objective performance measures. (c) 2012 APA, all rights reserved.

Drifting from Slow to “D’oh!” Working Memory Capacity and Mind Wandering Predict Extreme Reaction Times and Executive-Control Errors

PubMed Central

McVay, Jennifer C.; Kane, Michael J.

2012-01-01

A combined experimental, individual-differences, and thought-sampling study tested the predictions of executive attention (e.g., Engle & Kane, 2004) and coordinative binding (e.g., Oberauer, Süß, Wilhelm, & Sander, 2007) theories of working memory capacity (WMC). We assessed 288 subjects’ WMC and their performance and mind-wandering rates during a sustained-attention task; subjects completed either a go/no-go version requiring executive control over habit, or a vigilance version that did not. We further combined the data with those from McVay and Kane (2009) to: (1) gauge the contributions of WMC and attentional lapses to the worst-performance rule and the tail, or τ parameter, of response time (RT) distributions; (2) assess which parameters from a quantitative evidence-accumulation RT model were predicted by WMC and mind-wandering reports, and (3) consider intra-subject RT patterns – particularly, speeding – as potential objective markers of mind wandering. We found that WMC predicted action and thought control in only some conditions, that attentional lapses (indicated by TUT reports and drift-rate variability in evidence accumulation) contributed to τ, performance accuracy, and WMC’s association with them, and that mind-wandering experiences were not predicted by trial-to-trial RT changes, and so they cannot always be inferred from objective performance measures. PMID:22004270

Recent advances in radiation oncology.

PubMed

Garibaldi, Cristina; Jereczek-Fossa, Barbara Alicja; Marvaso, Giulia; Dicuonzo, Samantha; Rojas, Damaris Patricia; Cattani, Federica; Starzyńska, Anna; Ciardo, Delia; Surgo, Alessia; Leonardi, Maria Cristina; Ricotti, Rosalinda

2017-01-01

Radiotherapy (RT) is very much a technology-driven treatment modality in the management of cancer. RT techniques have changed significantly over the past few decades, thanks to improvements in engineering and computing. We aim to highlight the recent developments in radiation oncology, focusing on the technological and biological advances. We will present state-of-the-art treatment techniques, employing photon beams, such as intensity-modulated RT, volumetric-modulated arc therapy, stereotactic body RT and adaptive RT, which make possible a highly tailored dose distribution with maximum normal tissue sparing. We will analyse all the steps involved in the treatment: imaging, delineation of the tumour and organs at risk, treatment planning and finally image-guidance for accurate tumour localisation before and during treatment delivery. Particular attention will be given to the crucial role that imaging plays throughout the entire process. In the case of adaptive RT, the precise identification of target volumes as well as the monitoring of tumour response/modification during the course of treatment is mainly based on multimodality imaging that integrates morphological, functional and metabolic information. Moreover, real-time imaging of the tumour is essential in breathing adaptive techniques to compensate for tumour motion due to respiration. Brief reference will be made to the recent spread of particle beam therapy, in particular to the use of protons, but also to the yet limited experience of using heavy particles such as carbon ions. Finally, we will analyse the latest biological advances in tumour targeting. Indeed, the effectiveness of RT has been improved not only by technological developments but also through the integration of radiobiological knowledge to produce more efficient and personalised treatment strategies.

Academic and Resident Radiation Oncologists' Attitudes and Intentions Regarding Radiation Therapy near the End of Life.

PubMed

Lloyd, Shane; Dosoretz, Arie P; Yu, James B; Evans, Suzanne B; Decker, Roy H

2016-02-01

There has been increasing scrutiny about cancer treatment for patients very near the end of life (EoL), yet a substantial number receive palliative radiation therapy (RT) in this setting. Our aim was to document the attitudes and intentions of thought leaders and trainees in giving RT near the EoL. We distributed an anonymous survey to 473 radiation oncologists and residents. The survey examined the clinical and psychosocial factors considered as well as intentions and expectations in the delivery of RT near the EoL. Factors surrounding unfinished treatment courses, and the formative factors that shape opinions about RT at the EoL were also explored. We received 139 responses (29%). Eighty-nine percent of respondents worked at academic institutions. The factors that respondents most often consider very or extremely important to offer RT near the EoL were the preference of the patient to be treated (94%), the ability to tolerate treatment (88%), and palliative intent (70%). After instances when their patients were unable to complete treatment near the EoL, 42% of respondents said they would prescribe a shorter treatment the next time they see a similar patient. Personal experience (71%) was most often listed as very or extremely important in shaping their opinions about RT near the EoL. Survey respondents, 89% of whom were academic radiation oncologists, have a positive view of palliative RT near the EoL. They favor shorter fractionation for patients near the EoL. Personal experience is most important in shaping practices and attitudes.

Validation of a HLA-A2 tetramer flow cytometric method, IFNgamma real time RT-PCR, and IFNgamma ELISPOT for detection of immunologic response to gp100 and MelanA/MART-1 in melanoma patients

PubMed Central

Xu, Yuanxin; Theobald, Valerie; Sung, Crystal; DePalma, Kathleen; Atwater, Laura; Seiger, Keirsten; Perricone, Michael A; Richards, Susan M

2008-01-01

Background HLA-A2 tetramer flow cytometry, IFNγ real time RT-PCR and IFNγ ELISPOT assays are commonly used as surrogate immunological endpoints for cancer immunotherapy. While these are often used as research assays to assess patient's immunologic response, assay validation is necessary to ensure reliable and reproducible results and enable more accurate data interpretation. Here we describe a rigorous validation approach for each of these assays prior to their use for clinical sample analysis. Methods Standard operating procedures for each assay were established. HLA-A2 (A*0201) tetramer assay specific for gp100209(210M) and MART-126–35(27L), IFNγ real time RT-PCR and ELISPOT methods were validated using tumor infiltrating lymphocyte cell lines (TIL) isolated from HLA-A2 melanoma patients. TIL cells, specific for gp100 (TIL 1520) or MART-1 (TIL 1143 and TIL1235), were used alone or spiked into cryopreserved HLA-A2 PBMC from healthy subjects. TIL/PBMC were stimulated with peptides (gp100209, gp100pool, MART-127–35, or influenza-M1 and negative control peptide HIV) to further assess assay performance characteristics for real time RT-PCR and ELISPOT methods. Validation parameters included specificity, accuracy, precision, linearity of dilution, limit of detection (LOD) and limit of quantification (LOQ). In addition, distribution was established in normal HLA-A2 PBMC samples. Reference ranges for assay controls were established. Results The validation process demonstrated that the HLA-A2 tetramer, IFNγ real time RT-PCR, and IFNγ ELISPOT were highly specific for each antigen, with minimal cross-reactivity between gp100 and MelanA/MART-1. The assays were sensitive; detection could be achieved at as few as 1/4545–1/6667 cells by tetramer analysis, 1/50,000 cells by real time RT-PCR, and 1/10,000–1/20,000 by ELISPOT. The assays met criteria for precision with %CV < 20% (except ELISPOT using high PBMC numbers with %CV < 25%) although flow cytometric assays and cell based functional assays are known to have high assay variability. Most importantly, assays were demonstrated to be effective for their intended use. A positive IFNγ response (by RT-PCR and ELISPOT) to gp100 was demonstrated in PBMC from 3 melanoma patients. Another patient showed a positive MART-1 response measured by all 3 validated methods. Conclusion Our results demonstrated the tetramer flow cytometry assay, IFNγ real-time RT-PCR, and INFγ ELISPOT met validation criteria. Validation approaches provide a guide for others in the field to validate these and other similar assays for assessment of patient T cell response. These methods can be applied not only to cancer vaccines but to other therapeutic proteins as part of immunogenicity and safety analyses. PMID:18945350

Clinical utility of RT-PCR in assessing HER 2 gene expression versus traditional IHC and FISH in breast cancer patients.

PubMed

Suryavanshi, Moushumi; Mehta, Anurag; Jaipuria, Jiten; Kumar, Dushyant; Vishwakarma, Gayatri; Panigrahi, Manoj Kumar; Verma, Haristuti; Saifi, Mumtaz; Sharma, Sanjeev; Tandon, Simran; Doval, D C; Das, Bhudev C

2018-02-09

IHC and FISH are used for categorizing HER 2 status in breast cancer at the protein and DNA level, respectively. HER 2 expression at the RNA level is quantitative, cheaper, easier to standardize and free from interobserver variation. 115 consecutive patients were tested by IHC, FISH and RT-PCR (test cohort). Assuming FISH result to be the response variable, ROC curves for RT-PCR ratio were analyzed to label HER 2 negative, equivocal and positive cases as RT-PCR score 1, 2 and 3, respectively. Inter-relationships between RT-PCR, IHC and FISH were defined. 'Clinical benefit' of a test was defined as proportion of patients labeled unequivocally as HER 2 positive or negative. Population for 1 year was simulated constraint to previous reports of HER 2 positivity and IHC category distribution by a meta-analysis of previous studies that evaluated concordance between IHC and FISH to determine HER 2 status (simulation cohort). Four diagnostic pathways in the simulation cohort were defined-(1) initial IHC, followed by FISH (conventional pathway); (2) initial RT-PCR, followed by FISH; (3) initial IHC, followed by RT-PCR and then by FISH; (4) initial RT-PCR, followed by IHC and then by FISH. The clinical benefit of IHC and RT-PCR in the four pathways was analyzed and sensitivity analysis for incremental cost-effectiveness ratio and cost-benefit comapring RT-PCR against IHC, both as first-line tests and among those with IHC score 2 as a reflex second-line test was performed by the Monte Carlo technique. 115 patients comprised the study population. While none with IHC score of 0 or 1 was FISH positive for HER 2, all cases with IHC score of 3 were FISH positive. 43 cases were assigned IHC score of 2. Thus, 72 patients benefited from the initial IHC testing [clinical benefit 62.6%], with the overall concordance between IHC and FISH being 100% for those with IHC score of 0, 1 and 3 (conclusive IHC categories). For RT-PCR with 100% concordance, 15.7% (115-97 = 18) patients would have benefited from RT-PCR testing if it was used as a first-line test. If RT-PCR would have been used as a second-line test among those with IHC score 2 (n = 43), then only 6 patients would have been assigned a conclusive RT-PCR category (category 1 or 3) translating to a clinical benefit of 14% (6/43) as a second-line test. As a second-line test it had 51% probability to prove more cost-effective than the conventional pathway, provided the cost of RT-PCR was 0.4 times the cost of IHC. Also in a three-step pathway, RT-PCR upfront would have 56% probability of higher cost-benefit provided the cost of RT-PCR was 0.1 times the cost of IHC. RT-PCR results were found to be suboptimal to IHC in terms of discriminative ability and clinical benefit; thus, it is unlikely to replace IHC as a first-line test in the near future.

Current status of 3D EPID-based in vivo dosimetry in The Netherlands Cancer Institute

NASA Astrophysics Data System (ADS)

Mijnheer, B.; Olaciregui-Ruiz, I.; Rozendaal, R.; Spreeuw, H.; van Herk, M.; Mans, A.

2015-01-01

3D in vivo dose verification using a-Si EPIDs is performed routinely in our institution for almost all RT treatments. The EPID-based 3D dose distribution is reconstructed using a back-projection algorithm and compared with the planned dose distribution using 3D gamma evaluation. Dose-reconstruction and gamma-evaluation software runs automatically, and deviations outside the alert criteria are immediately available and investigated, in combination with inspection of cone-beam CT scans. The implementation of our 3D EPID- based in vivo dosimetry approach was able to replace pre-treatment verification for more than 90% of the patient treatments. Clinically relevant deviations could be detected for approximately 1 out of 300 patient treatments (IMRT and VMAT). Most of these errors were patient related anatomical changes or deviations from the routine clinical procedure, and would not have been detected by pre-treatment verification. Moreover, 3D EPID-based in vivo dose verification is a fast and accurate tool to assure the safe delivery of RT treatments. It provides clinically more useful information and is less time consuming than pre-treatment verification measurements. Automated 3D in vivo dosimetry is therefore a prerequisite for large-scale implementation of patient-specific quality assurance of RT treatments.

Soil Tillage Management Affects Maize Grain Yield by Regulating Spatial Distribution Coordination of Roots, Soil Moisture and Nitrogen Status.

PubMed

Wang, Xinbing; Zhou, Baoyuan; Sun, Xuefang; Yue, Yang; Ma, Wei; Zhao, Ming

2015-01-01

The spatial distribution of the root system through the soil profile has an impact on moisture and nutrient uptake by plants, affecting growth and productivity. The spatial distribution of the roots, soil moisture, and fertility are affected by tillage practices. The combination of high soil density and the presence of a soil plow pan typically impede the growth of maize (Zea mays L.).We investigated the spatial distribution coordination of the root system, soil moisture, and N status in response to different soil tillage treatments (NT: no-tillage, RT: rotary-tillage, SS: subsoiling) and the subsequent impact on maize yield, and identify yield-increasing mechanisms and optimal soil tillage management practices. Field experiments were conducted on the Huang-Huai-Hai plain in China during 2011 and 2012. The SS and RT treatments significantly reduced soil bulk density in the top 0-20 cm layer of the soil profile, while SS significantly decreased soil bulk density in the 20-30 cm layer. Soil moisture in the 20-50 cm profile layer was significantly higher for the SS treatment compared to the RT and NT treatment. In the 0-20 cm topsoil layer, the NT treatment had higher soil moisture than the SS and RT treatments. Root length density of the SS treatment was significantly greater than density of the RT and NT treatments, as soil depth increased. Soil moisture was reduced in the soil profile where root concentration was high. SS had greater soil moisture depletion and a more concentration root system than RT and NT in deep soil. Our results suggest that the SS treatment improved the spatial distribution of root density, soil moisture and N states, thereby promoting the absorption of soil moisture and reducing N leaching via the root system in the 20-50 cm layer of the profile. Within the context of the SS treatment, a root architecture densely distributed deep into the soil profile, played a pivotal role in plants' ability to access nutrients and water. An optimal combination of deeper deployment of roots and resource (water and N) availability was realized where the soil was prone to leaching. The correlation between the depletion of resources and distribution of patchy roots endorsed the SS tillage practice. It resulted in significantly greater post-silking biomass and grain yield compared to the RT and NT treatments, for summer maize on the Huang-Huai-Hai plain.

Soil Tillage Management Affects Maize Grain Yield by Regulating Spatial Distribution Coordination of Roots, Soil Moisture and Nitrogen Status

PubMed Central

Wang, Xinbing; Zhou, Baoyuan; Sun, Xuefang; Yue, Yang; Ma, Wei; Zhao, Ming

2015-01-01

The spatial distribution of the root system through the soil profile has an impact on moisture and nutrient uptake by plants, affecting growth and productivity. The spatial distribution of the roots, soil moisture, and fertility are affected by tillage practices. The combination of high soil density and the presence of a soil plow pan typically impede the growth of maize (Zea mays L.).We investigated the spatial distribution coordination of the root system, soil moisture, and N status in response to different soil tillage treatments (NT: no-tillage, RT: rotary-tillage, SS: subsoiling) and the subsequent impact on maize yield, and identify yield-increasing mechanisms and optimal soil tillage management practices. Field experiments were conducted on the Huang-Huai-Hai plain in China during 2011 and 2012. The SS and RT treatments significantly reduced soil bulk density in the top 0–20 cm layer of the soil profile, while SS significantly decreased soil bulk density in the 20–30 cm layer. Soil moisture in the 20–50 cm profile layer was significantly higher for the SS treatment compared to the RT and NT treatment. In the 0-20 cm topsoil layer, the NT treatment had higher soil moisture than the SS and RT treatments. Root length density of the SS treatment was significantly greater than density of the RT and NT treatments, as soil depth increased. Soil moisture was reduced in the soil profile where root concentration was high. SS had greater soil moisture depletion and a more concentration root system than RT and NT in deep soil. Our results suggest that the SS treatment improved the spatial distribution of root density, soil moisture and N states, thereby promoting the absorption of soil moisture and reducing N leaching via the root system in the 20–50 cm layer of the profile. Within the context of the SS treatment, a root architecture densely distributed deep into the soil profile, played a pivotal role in plants’ ability to access nutrients and water. An optimal combination of deeper deployment of roots and resource (water and N) availability was realized where the soil was prone to leaching. The correlation between the depletion of resources and distribution of patchy roots endorsed the SS tillage practice. It resulted in significantly greater post-silking biomass and grain yield compared to the RT and NT treatments, for summer maize on the Huang-Huai-Hai plain. PMID:26098548

Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus.

PubMed

Mari, Viviana; Losurdo, Michele; Lucente, Maria Stella; Lorusso, Eleonora; Elia, Gabriella; Martella, Vito; Patruno, Giovanni; Buonavoglia, Domenico; Decaro, Nicola

2016-03-01

HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)-10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. Copyright © 2015 Elsevier B.V. All rights reserved.

The 2014 Mw 6.0 Napa Earthquake, California: Observations from Real-time GPS-enhanced Earthquake Early Warning

NASA Astrophysics Data System (ADS)

Johanson, I. A.; Grapenthin, R.; Allen, R. M.

2014-12-01

Recently, progress has been made to demonstrate feasibility and benefits of including real-time GPS (rtGPS) in earthquake early warning and rapid response systems. While most concepts have yet to be integrated into operational environments, the Berkeley Seismological Laboratory is currently running an rtGPS based finite fault inversion scheme in true real-time, which is triggered by the seismic-based ShakeAlert system and then sends updated earthquake alerts to a test receiver. The Geodetic Alarm System (G-larmS) was online and responded to the 2014 Mw6.0 South Napa earthquake in California. We review G-larmS' performance during this event and for 13 aftershocks, and we present rtGPS observations and real-time modeling results for the main shock. The first distributed slip model and a magnitude estimate of Mw5.5 were available 24 s after the event origin time, which could be reduced to 14 s after a bug fix (~8 s S-wave travel time, ~6 s data latency). The system continued to re-estimate the magnitude once every second: it increased to Mw5.9 3 s after the first alert and stabilized at Mw5.8 after 15 s. G-larmS' solutions for the subsequent small magnitude aftershocks demonstrate that Mw~6.0 is the current limit for alert updates to contribute back to the seismic-based early warning system.

Avian influenza virus detection and quantitation by real-time RT-PCR

USDA-ARS?s Scientific Manuscript database

Real-time RT-PCR (rRT-PCR) has been used for avian influenza virus (AIV) detection since the early 2000’s for routine surveillance, during outbreaks and for research. Some of the advantages of rRT-PCR are: high sensitivity, high specificity, rapid time-to-result, scalability, cost, and its inherentl...

Workload Capacity: A Response Time-Based Measure of Automation Dependence.

PubMed

Yamani, Yusuke; McCarley, Jason S

2016-05-01

An experiment used the workload capacity measure C(t) to quantify the processing efficiency of human-automation teams and identify operators' automation usage strategies in a speeded decision task. Although response accuracy rates and related measures are often used to measure the influence of an automated decision aid on human performance, aids can also influence response speed. Mean response times (RTs), however, conflate the influence of the human operator and the automated aid on team performance and may mask changes in the operator's performance strategy under aided conditions. The present study used a measure of parallel processing efficiency, or workload capacity, derived from empirical RT distributions as a novel gauge of human-automation performance and automation dependence in a speeded task. Participants performed a speeded probabilistic decision task with and without the assistance of an automated aid. RT distributions were used to calculate two variants of a workload capacity measure, COR(t) and CAND(t). Capacity measures gave evidence that a diagnosis from the automated aid speeded human participants' responses, and that participants did not moderate their own decision times in anticipation of diagnoses from the aid. Workload capacity provides a sensitive and informative measure of human-automation performance and operators' automation dependence in speeded tasks. © 2016, Human Factors and Ergonomics Society.

Simultaneous detection of papaya ringspot virus, papaya leaf distortion mosaic virus, and papaya mosaic virus by multiplex real-time reverse transcription PCR.

PubMed

Huo, P; Shen, W T; Yan, P; Tuo, D C; Li, X Y; Zhou, P

2015-12-01

Both the single infection of papaya ringspot virus (PRSV), papaya leaf distortion mosaic virus (PLDMV) or papaya mosaic virus (PapMV) and double infection of PRSV and PLDMV or PapMV which cause indistinguishable symptoms, threaten the papaya industry in Hainan Island, China. In this study, a multiplex real-time reverse transcription PCR (RT-PCR) was developed to detect simultaneously the three viruses based on their distinctive melting temperatures (Tms): 81.0±0.8°C for PRSV, 84.7±0.6°C for PLDMV, and 88.7±0.4°C for PapMV. The multiplex real-time RT-PCR method was specific and sensitive in detecting the three viruses, with a detection limit of 1.0×10(1), 1.0×10(2), and 1.0×10(2) copies for PRSV, PLDMV, and PapMV, respectively. Indeed, the reaction was 100 times more sensitive than the multiplex RT-PCR for PRSV, and 10 times more sensitive than multiplex RT-PCR for PLDMV. Field application of the multiplex real-time RT-PCR demonstrated that some non-symptomatic samples were positive for PLDMV by multiplex real-time RT-PCR but negative by multiplex RT-PCR, whereas some samples were positive for both PRSV and PLDMV by multiplex real-time RT-PCR assay but only positive for PLDMV by multiplex RT-PCR. Therefore, this multiplex real-time RT-PCR assay provides a more rapid, sensitive and reliable method for simultaneous detection of PRSV, PLDMV, PapMV and their mixed infections in papaya.

Manual choice reaction times in the rate-domain

PubMed Central

Harris, Christopher M.; Waddington, Jonathan; Biscione, Valerio; Manzi, Sean

2014-01-01

Over the last 150 years, human manual reaction times (RTs) have been recorded countless times. Yet, our understanding of them remains remarkably poor. RTs are highly variable with positively skewed frequency distributions, often modeled as an inverse Gaussian distribution reflecting a stochastic rise to threshold (diffusion process). However, latency distributions of saccades are very close to the reciprocal Normal, suggesting that “rate” (reciprocal RT) may be the more fundamental variable. We explored whether this phenomenon extends to choice manual RTs. We recorded two-alternative choice RTs from 24 subjects, each with 4 blocks of 200 trials with two task difficulties (easy vs. difficult discrimination) and two instruction sets (urgent vs. accurate). We found that rate distributions were, indeed, very close to Normal, shifting to lower rates with increasing difficulty and accuracy, and for some blocks they appeared to become left-truncated, but still close to Normal. Using autoregressive techniques, we found temporal sequential dependencies for lags of at least 3. We identified a transient and steady-state component in each block. Because rates were Normal, we were able to estimate autoregressive weights using the Box-Jenkins technique, and convert to a moving average model using z-transforms to show explicit dependence on stimulus input. We also found a spatial sequential dependence for the previous 3 lags depending on whether the laterality of previous trials was repeated or alternated. This was partially dissociated from temporal dependency as it only occurred in the easy tasks. We conclude that 2-alternative choice manual RT distributions are close to reciprocal Normal and not the inverse Gaussian. This is not consistent with stochastic rise to threshold models, and we propose a simple optimality model in which reward is maximized to yield to an optimal rate, and hence an optimal time to respond. We discuss how it might be implemented. PMID:24959134

The identification of unfolding facial expressions.

PubMed

Fiorentini, Chiara; Schmidt, Susanna; Viviani, Paolo

2012-01-01

We asked whether the identification of emotional facial expressions (FEs) involves the simultaneous perception of the facial configuration or the detection of emotion-specific diagnostic cues. We recorded at high speed (500 frames s-1) the unfolding of the FE in five actors, each expressing six emotions (anger, surprise, happiness, disgust, fear, sadness). Recordings were coded every 10 frames (20 ms of real time) with the Facial Action Coding System (FACS, Ekman et al 2002, Salt Lake City, UT: Research Nexus eBook) to identify the facial actions contributing to each expression, and their intensity changes over time. Recordings were shown in slow motion (1/20 of recording speed) to one hundred observers in a forced-choice identification task. Participants were asked to identify the emotion during the presentation as soon as they felt confident to do so. Responses were recorded along with the associated response times (RTs). The RT probability density functions for both correct and incorrect responses were correlated with the facial activity during the presentation. There were systematic correlations between facial activities, response probabilities, and RT peaks, and significant differences in RT distributions for correct and incorrect answers. The results show that a reliable response is possible long before the full FE configuration is reached. This suggests that identification is reached by integrating in time individual diagnostic facial actions, and does not require perceiving the full apex configuration.

Differential distribution of the KCl cotransporter KCC2 in thalamic relay and reticular nuclei

PubMed Central

Barthó, P.; Payne, J. A.; Freund, T. F.; Acsády, L.

2009-01-01

In the thalamus of the rat the reversal potential of GABA-induced anion currents is more negative in relay cells than in neurones of the reticular nucleus (nRt) due to different chloride extrusion mechanisms operating in these cells. The distribution of KCl cotransporter type 2 (KCC2), the major neuronal chloride transporter that may underlie this effect, is unknown in the thalamus. In this study the precise regional and ultrastructural localization of KCC2 was examined in the thalamus using immunocytochemical methods. The neuropil of all relay nuclei was found to display intense KCC2 immunostaining to varying degrees. In sharp contrast, the majority of the nRt was negative for KCC2. In the anterior and dorsal part of the nRt, however, KCC2 immunostaining was similar to relay nuclei and parvalbumin and calretinin were found to colocalize with KCC2. At the ultrastructural level, KCC2 immunoreactivity was mainly located in the extrasynaptic membranes of thick and thin dendrites and the somata of relay cells but was also found in close association with asymmetrical synapses formed by cortical afferents. Quantitative evaluation of KCC2 distribution at the electron microscopic level demonstrated that the density of KCC2 did not correlate with dendritic diameter or synaptic coverage but is 1.7 times higher on perisynaptic membrane surfaces than on extrasynaptic membranes. Our data demonstrate that the regional distribution of KCC2 is compatible with the difference in GABA-A reversal potential between relay and reticular nuclei. At the ultrastructural level, abundant extrasynaptic KCC2 expression will probably play a role in the regulation of extrasynaptic GABA-A receptor-mediated inhibition. PMID:15305865

Integrating impairments in reaction time and executive function using a diffusion model framework

PubMed Central

Karalunas, Sarah L.; Huang-Pollock, Cynthia L.

2013-01-01

Using Ratcliff’s diffusion model and ex-Gaussian decomposition, we directly evaluate the role individual differences in reaction time (RT) distribution components play in the prediction of inhibitory control and working memory (WM) capacity in children with and without ADHD. Children with (n=92, x̄ age= 10.2 years, 67% male) and without ADHD (n=62, x̄ age=10.6 years, 46% male) completed four tasks of WM and a stop signal reaction time (SSRT) task. Children with ADHD had smaller WM capacities and less efficient inhibitory control. Diffusion model analyses revealed that children with ADHD had slower drift rates (v) and faster non-decision times (Ter), but there were no group differences in boundary separations (a). Similarly, using an ex-Gaussian approach, children with ADHD had larger τ values than non-ADHD controls, but did not differ in µ or σ distribution components. Drift rate mediated the association between ADHD status and performance on both inhibitory control and WM capacity. τ also mediated the ADHD-executive function impairment associations; however, models were a poorer fit to the data. Impaired performance on RT and executive functioning tasks has long been associated with childhood ADHD. Both are believed to be important cognitive mechanisms to the disorder. We demonstrate here that drift rate, or the speed at which information accumulates towards a decision, is able to explain both. PMID:23334775

Prediction of Liver Function by Using Magnetic Resonance-based Portal Venous Perfusion Imaging

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

Cao Yue, E-mail: yuecao@umich.edu; Department of Radiology, University of Michigan, Ann Arbor, Michigan; Wang Hesheng

2013-01-01

Purpose: To evaluate whether liver function can be assessed globally and spatially by using volumetric dynamic contrast-enhanced magnetic resonance imaging MRI (DCE-MRI) to potentially aid in adaptive treatment planning. Methods and Materials: Seventeen patients with intrahepatic cancer undergoing focal radiation therapy (RT) were enrolled in institution review board-approved prospective studies to obtain DCE-MRI (to measure regional perfusion) and indocyanine green (ICG) clearance rates (to measure overall liver function) prior to, during, and at 1 and 2 months after treatment. The volumetric distribution of portal venous perfusion in the whole liver was estimated for each scan. We assessed the correlation betweenmore » mean portal venous perfusion in the nontumor volume of the liver and overall liver function measured by ICG before, during, and after RT. The dose response for regional portal venous perfusion to RT was determined using a linear mixed effects model. Results: There was a significant correlation between the ICG clearance rate and mean portal venous perfusion in the functioning liver parenchyma, suggesting that portal venous perfusion could be used as a surrogate for function. Reduction in regional venous perfusion 1 month after RT was predicted by the locally accumulated biologically corrected dose at the end of RT (P<.0007). Regional portal venous perfusion measured during RT was a significant predictor for regional venous perfusion assessed 1 month after RT (P<.00001). Global hypovenous perfusion pre-RT was observed in 4 patients (3 patients with hepatocellular carcinoma and cirrhosis), 3 of whom had recovered from hypoperfusion, except in the highest dose regions, post-RT. In addition, 3 patients who had normal perfusion pre-RT had marked hypervenous perfusion or reperfusion in low-dose regions post-RT. Conclusions: This study suggests that MR-based volumetric hepatic perfusion imaging may be a biomarker for spatial distribution of liver function, which could aid in individualizing therapy, particularly for patients at risk for liver injury after RT.« less

Real-Time Reverse-Transcription Quantitative Polymerase Chain Reaction Assay Is a Feasible Method for the Relative Quantification of Heregulin Expression in Non-Small Cell Lung Cancer Tissue.

PubMed

Kristof, Jessica; Sakrison, Kellen; Jin, Xiaoping; Nakamaru, Kenji; Schneider, Matthias; Beckman, Robert A; Freeman, Daniel; Spittle, Cindy; Feng, Wenqin

2017-01-01

In preclinical studies, heregulin ( HRG ) expression was shown to be the most relevant predictive biomarker for response to patritumab, a fully human anti-epidermal growth factor receptor 3 monoclonal antibody. In support of a phase 2 study of erlotinib ± patritumab in non-small cell lung cancer (NSCLC), a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay for relative quantification of HRG expression from formalin-fixed paraffin-embedded (FFPE) NSCLC tissue samples was developed and validated and described herein. Test specimens included matched FFPE normal lung and NSCLC and frozen NSCLC tissue, and HRG -positive and HRG -negative cell lines. Formalin-fixed paraffin-embedded tissue was examined for functional performance. Heregulin distribution was also analyzed across 200 NSCLC commercial samples. Applied Biosystems TaqMan Gene Expression Assays were run on the Bio-Rad CFX96 real-time PCR platform. Heregulin RT-qPCR assay specificity, PCR efficiency, PCR linearity, and reproducibility were demonstrated. The final assay parameters included the Qiagen FFPE RNA Extraction Kit for RNA extraction from FFPE NSCLC tissue, 50 ng of RNA input, and 3 reference (housekeeping) genes ( HMBS, IPO8 , and EIF2B1 ), which had expression levels similar to HRG expression levels and were stable among FFPE NSCLC samples. Using the validated assay, unimodal HRG distribution was confirmed across 185 evaluable FFPE NSCLC commercial samples. Feasibility of an RT-qPCR assay for the quantification of HRG expression in FFPE NSCLC specimens was demonstrated.

Real-time Implementation of the Waveloc Technique for Monitoring Earthquake Swarms

NASA Astrophysics Data System (ADS)

Maggi, A.; Langet, N.; Michelini, A.

2013-12-01

Monitoring regions with high swarm-type seismicity (e.g. volcanoes, certain tectonic regions) is a challenge for the traditional pick-associate-locate type algorithms that form the basis of most seismicity monitoring software. Over the past few years, new approaches that avoid the association phase by direct migration of some characteristic function of the recorded seismograms have started to be implemented, and have shown great promise (see related abstract on the Waveloc method applied to Piton de la Fournaise volcano). Implementing such methods in real-time is an essential step in proving their usefulness and robustness in swarm-monitoring situations. Here we describe the work in progress on adapting the Waveloc migration technique to real-time operation. The resulting software package, RT-Waveloc, is currently in the prototype stage, and we hope to have a version that can be distributed to the scientific community for beta-testing within a year. The development of RT-Waveloc is financed by the EU NERA project.

Variability in reaction time performance of younger and older adults.

PubMed

Hultsch, David F; MacDonald, Stuart W S; Dixon, Roger A

2002-03-01

Age differences in three basic types of variability were examined: variability between persons (diversity), variability within persons across tasks (dispersion), and variability within persons across time (inconsistency). Measures of variability were based on latency performance from four measures of reaction time (RT) performed by a total of 99 younger adults (ages 17--36 years) and 763 older adults (ages 54--94 years). Results indicated that all three types of variability were greater in older compared with younger participants even when group differences in speed were statistically controlled. Quantile-quantile plots showed age and task differences in the shape of the inconsistency distributions. Measures of within-person variability (dispersion and inconsistency) were positively correlated. Individual differences in RT inconsistency correlated negatively with level of performance on measures of perceptual speed, working memory, episodic memory, and crystallized abilities. Partial set correlation analyses indicated that inconsistency predicted cognitive performance independent of level of performance. The results indicate that variability of performance is an important indicator of cognitive functioning and aging.

Logical-rule models of classification response times: a synthesis of mental-architecture, random-walk, and decision-bound approaches.

PubMed

Fific, Mario; Little, Daniel R; Nosofsky, Robert M

2010-04-01

We formalize and provide tests of a set of logical-rule models for predicting perceptual classification response times (RTs) and choice probabilities. The models are developed by synthesizing mental-architecture, random-walk, and decision-bound approaches. According to the models, people make independent decisions about the locations of stimuli along a set of component dimensions. Those independent decisions are then combined via logical rules to determine the overall categorization response. The time course of the independent decisions is modeled via random-walk processes operating along individual dimensions. Alternative mental architectures are used as mechanisms for combining the independent decisions to implement the logical rules. We derive fundamental qualitative contrasts for distinguishing among the predictions of the rule models and major alternative models of classification RT. We also use the models to predict detailed RT-distribution data associated with individual stimuli in tasks of speeded perceptual classification. PsycINFO Database Record (c) 2010 APA, all rights reserved.

Real-time RT-PCR, a necessary tool to support the diagnosis and surveillance of rotavirus in Mexico.

PubMed

De La Cruz Hernández, Sergio Isaac; Anaya Molina, Yazmin; Gómez Santiago, Fabián; Terán Vega, Heidi Lizbeth; Monroy Leyva, Elda; Méndez Pérez, Héctor; García Lozano, Herlinda

2018-04-01

Rotavirus produces diarrhea in children under 5 years old. Most of those conventional methods such as polyacrylamide gel electrophoresis (PAGE) and reverse transcription-polymerase chain reaction (RT-PCR) have been used for rotavirus detection. However, these techniques need a multi-step process to get the results. In comparison with conventional methods, the real-time RT-PCR is a highly sensitive method, which allows getting the results in only one day. In this study a real-time RT-PCR assay was tested using a panel of 440 samples from patients with acute gastroenteritis, and characterized by PAGE and RT-PCR. The results show that the real-time RT-PCR detected rotavirus from 73% of rotavirus-negative samples analyzed by PAGE and RT-PCR; thus, the percentage of rotavirus-positive samples increased to 81%. The results indicate that this real-time RT-PCR should be part of a routine analysis, and as a support of the diagnosis of rotavirus in Mexico. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of resistance training and protein intake pattern on myofibrillar protein synthesis and proteome kinetics in older men in energy restriction.

PubMed

Murphy, Caoileann H; Shankaran, Mahalakshmi; Churchward-Venne, Tyler A; Mitchell, Cameron J; Kolar, Nathan M; Burke, Louise M; Hawley, John A; Kassis, Amira; Karagounis, Leonidas G; Li, Kelvin; King, Chelsea; Hellerstein, Marc; Phillips, Stuart M

2018-06-01

Strategies to enhance the loss of fat while preserving muscle mass during energy restriction are of great importance to prevent sarcopenia in overweight older adults. We show for the first time that the integrated rate of synthesis of numerous individual contractile, cytosolic and mitochondrial skeletal muscle proteins was increased by resistance training (RT) and unaffected by dietary protein intake pattern during energy restriction in free-living, obese older men. We observed a correlation between the synthetic rates of skeletal muscle-derived proteins obtained in serum (creatine kinase M-type, carbonic anhydrase 3) and the synthetic rates of proteins obtained via muscle sampling; and that the synthesis rates of these proteins in serum revealed the stimulatory effects of RT. These results have ramifications for understanding the influence of RT on skeletal muscle and are consistent with the role of RT in maintaining muscle protein synthesis and potentially supporting muscle mass preservation during weight loss. We determined how the pattern of protein intake and resistance training (RT) influenced longer-term (2 weeks) integrated myofibrillar protein synthesis (MyoPS) during energy restriction (ER). MyoPS and proteome kinetics were measured during 2 weeks of ER alone and 2 weeks of ER plus RT (ER + RT) in overweight/obese older men. Participants were randomized to consume dietary protein in a balanced (BAL: 25% daily protein per meal × 4 meals) or skewed (SKEW: 7:17:72:4% daily protein per meal) pattern (n = 10 per group). Participants ingested deuterated water during the consecutive 2-week periods, and skeletal muscle biopsies and serum were obtained at the beginning and conclusion of ER and ER + RT. Bulk MyoPS (i.e. synthesis of the myofibrillar protein sub-fraction) and the synthetic rates of numerous individual skeletal muscle proteins were quantified. Bulk MyoPS was not affected by protein distribution during ER or ER + RT (ER: BAL = 1.24 ± 0.31%/day, SKEW = 1.26 ± 0.37%/day; ER + RT: BAL = 1.64 ± 0.48%/day, SKEW = 1.52 ± 0.66%/day) but was ∼26% higher during ER + RT than during ER (P = 0.023). The synthetic rates of 175 of 190 contractile, cytosolic and mitochondrial skeletal muscle proteins, as well as synthesis of muscle-derived proteins measured in serum, creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3), were higher during ER + RT than during ER (P < 0.05). In addition, the synthetic rates of CK-M and CA-3 measured in serum correlated with the synthetic rates of proteins obtained via muscle sampling (P < 0.05). This study provides novel data on the skeletal muscle adaptations to RT and dietary protein distribution. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

Rapid and sensitive detection of canine distemper virus by real-time reverse transcription recombinase polymerase amplification.

PubMed

Wang, Jianchang; Wang, Jinfeng; Li, Ruiwen; Liu, Libing; Yuan, Wanzhe

2017-08-15

Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Recombinase polymerase amplification (RPA), as an isothermal gene amplification technique, has been explored for the molecular detection of diverse pathogens. A real-time reverse transcription RPA (RT-RPA) assay for the detection of canine distemper virus (CDV) using primers and exo probe targeting the CDV nucleocapsid protein gene was developed. A series of other viruses were tested by the RT-RPA.Thirty-two field samples were further tested by RT-RPA, and the resuts were compared with those obtained by the real-time RT-PCR. The RT-RPA assay was performed successfully at 40 °C, and the results were obtained within 3 min-12 min. The assay could detect CDV, but did not show cross-detection of canine parvovirus-2 (CPV-2), canine coronavirus (CCoV), canine parainfluenza virus (CPIV), pseudorabies virus (PRV) or Newcastle disease virus (NDV), demonstrating high specificity. The analytical sensitivity of RT-RPA was 31.8 copies in vitro transcribed CDV RNA, which is 10 times lower than the real-time RT-PCR. The assay performance was validated by testing 32 field samples and compared to real-time RT-PCR. The results indicated an excellent correlation between RT-RPA and a reference real-time RT-PCR method. Both assays provided the same results, and R 2 value of the positive results was 0.947. The results demonstrated that the RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of CDV both in the laboratory and point-of-care facility, especially in the resource-limited settings.

Comprehensive phylogenetic analysis of bacterial reverse transcriptases.

PubMed

Toro, Nicolás; Nisa-Martínez, Rafael

2014-01-01

Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

PubMed Central

Toro, Nicolás; Nisa-Martínez, Rafael

2014-01-01

Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology. PMID:25423096

Detection and genetic analysis of human sapoviruses in river water in Japan.

PubMed

Kitajima, Masaaki; Oka, Tomoichiro; Haramoto, Eiji; Katayama, Hiroyuki; Takeda, Naokazu; Katayama, Kazuhiko; Ohgaki, Shinichiro

2010-04-01

We investigated the prevalence of sapoviruses (SaVs) in the Tamagawa River in Japan from April 2003 to March 2004 and performed genetic analysis of the SaV genes identified in river water. A total of 60 river water samples were collected from five sites along the river, and 500 ml was concentrated using the cation-coated filter method. By use of a real-time reverse transcription (RT)-PCR assay, 12 (20%) of the 60 samples were positive for SaV. SaV sequences were obtained from 15 (25%) samples, and a total of 30 SaV strains were identified using six RT-PCR assays followed by cloning and sequence analysis. A newly developed nested RT-PCR assay utilizing a broadly reactive forward primer showed the highest detection efficiency and amplified more diverse SaV genomes in the samples. SaV sequences were frequently detected from November to March, whereas none were obtained in April, July, September, or October. No SaV sequences were detected in the upstream portion of the river, whereas the midstream portion showed high positive rates. Based on phylogenetic analysis, SaV strains identified in the river water samples were classified into nine genotypes, namely, GI/1, GI/2, GI/3, GI/5, GI/untyped, GII/1, GII/2, GII/3, and GV/1. To our knowledge, this is the first study describing seasonal and spatial distributions and genetic diversity of SaVs in river water. A combination of real-time RT-PCR assay and newly developed nested RT-PCR assay is useful for identifying and characterizing SaV strains in a water environment.

Recent advances in radiation oncology

PubMed Central

Garibaldi, Cristina; Jereczek-Fossa, Barbara Alicja; Marvaso, Giulia; Dicuonzo, Samantha; Rojas, Damaris Patricia; Cattani, Federica; Starzyńska, Anna; Ciardo, Delia; Surgo, Alessia; Leonardi, Maria Cristina; Ricotti, Rosalinda

2017-01-01

Radiotherapy (RT) is very much a technology-driven treatment modality in the management of cancer. RT techniques have changed significantly over the past few decades, thanks to improvements in engineering and computing. We aim to highlight the recent developments in radiation oncology, focusing on the technological and biological advances. We will present state-of-the-art treatment techniques, employing photon beams, such as intensity-modulated RT, volumetric-modulated arc therapy, stereotactic body RT and adaptive RT, which make possible a highly tailored dose distribution with maximum normal tissue sparing. We will analyse all the steps involved in the treatment: imaging, delineation of the tumour and organs at risk, treatment planning and finally image-guidance for accurate tumour localisation before and during treatment delivery. Particular attention will be given to the crucial role that imaging plays throughout the entire process. In the case of adaptive RT, the precise identification of target volumes as well as the monitoring of tumour response/modification during the course of treatment is mainly based on multimodality imaging that integrates morphological, functional and metabolic information. Moreover, real-time imaging of the tumour is essential in breathing adaptive techniques to compensate for tumour motion due to respiration. Brief reference will be made to the recent spread of particle beam therapy, in particular to the use of protons, but also to the yet limited experience of using heavy particles such as carbon ions. Finally, we will analyse the latest biological advances in tumour targeting. Indeed, the effectiveness of RT has been improved not only by technological developments but also through the integration of radiobiological knowledge to produce more efficient and personalised treatment strategies. PMID:29225692

Interval between surgery and radiotherapy: effect on local control of soft tissue sarcoma.

PubMed

Ballo, Matthew T; Zagars, Gunar K; Cormier, Janice N; Hunt, Kelly K; Feig, Barry W; Patel, Shreyaskumar R; Pisters, Peter W T

2004-04-01

To evaluate the clinical significance of the interval between surgery and postoperative radiotherapy (RT) for patients with soft tissue sarcoma. The records of 799 patients who underwent postoperative RT for soft tissue sarcoma between 1960 and 2000 were retrospectively reviewed. Univariate and multivariate analyses were used to evaluate the potential impact of the timing of postoperative RT on the rate of local control (LC). The actuarial overall LC rate was 79% at 10 years and 78% at 15 years. Univariate analysis indicated that the factors associated with an inferior 10-year LC rate were positive resection margins (p <0.0001); treatment for recurrent disease (p <0.0001); primary location in the head and neck or deep trunk (p <0.0001); age >64 years (p <0.0001); histopathologic subtype of malignant fibrous histiocytoma, neurogenic sarcoma, or epithelioid sarcoma (p = 0.01); tumor size >10 cm (p = 0.02); postoperative radiation dose <64 Gy (p = 0.03); and high histologic grade (p = 0.05). On multivariate analysis, all these factors remained statistically significant, except for high histologic grade and large size. A delay between surgery and the start of RT of >30 days was associated with a decreased 10-year LC rate, but this association was not statistically significant (76% vs. 83%, p = 0.07). The potential association between RT delay and inferior LC could be explained by an imbalance in the distribution of other prognostic factors. The interval between surgery and RT did not significantly impact the 10-year LC rate. These findings indicate that an RT delay should not be viewed as an independent adverse factor for LC and that treatment intensification may not be necessary for patients in whom a treatment delay has already occurred.

Detection of Citrus leprosis virus C using specific primers and TaqMan probe in one-step real-time reverse-transcription polymerase chain reaction assays.

PubMed

Choudhary, Nandlal; Wei, G; Govindarajulu, A; Roy, Avijit; Li, Wenbin; Picton, Deric D; Nakhla, M K; Levy, L; Brlansky, R H

2015-11-01

Citrus leprosis virus C (CiLV-C), a causal agent of the leprosis disease in citrus, is mostly present in the South and Central America and spreading toward the North America. To enable better diagnosis and inhibit the further spread of this re-emerging virus a quantitative (q) real-time reverse transcription polymerase chain reaction (qRT-PCR) assay is needed for early detection of CiLV-C when the virus is present in low titer in citrus leprosis samples. Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene. A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. The one-step qRT-PCR detection assays for CiLV-C were determined to be 1000 times more sensitive when compared to the one-step conventional reverse transcription polymerase chain reaction (RT-PCR) CiLV-C detection method. To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. The one-step qRT-PCR specificity was successfully validated by testing for the presence of CiLV-C in the total RNA extracts of the citrus leprosis samples collected from Belize, Costa Rica, Mexico and Panama. Implementation of the one-step qRT-PCR assays for CiLV-C diagnosis should assist regulatory agencies in surveillance activities to monitor the distribution pattern of CiLV-C in countries where it is present and to prevent further dissemination into citrus growing countries where there is no report of CiLV-C presence. Published by Elsevier B.V.

Quality of Life and Survival Outcome for Patients With Nasopharyngeal Carcinoma Receiving Three-Dimensional Conformal Radiotherapy vs. Intensity-Modulated Radiotherapy-A Longitudinal Study

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

Fang, F.-M.; Kaohsiung Chang Gung Head and Neck Oncology Group, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung Hsien, Taiwan; Chien, C.-Y.

2008-10-01

Purpose: To investigate the changes of quality of life (QoL) and survival outcomes for patients with nasopharyngeal carcinoma (NPC) treated by three-dimensional conformal radiotherapy (3D-CRT) vs. intensity-modulated radiotherapy (IMRT). Methods and Materials: Two hundred and three newly diagnosed NPC patients, who were curatively treated by 3D-CRT (n = 93) or IMRT (n = 110) between March 2002 and July 2004, were analyzed. The distributions of clinical stage according to American Joint Committee on Cancer 1997 were I: 15 (7.4%), II: 78 (38.4%), III: 74 (36.5%), and IV: 36 (17.7%). QoL was longitudinally assessed by the European Organization for Research andmore » Treatment of Cancer (EORTC) QLQ-C30 and the EORTC QLQ-H and N35 questionnaires at the five time points: before RT, during RT (36 Gy), and 3 months, 12 months, and 24 months after RT. Results: The 3-year locoregional control, metastasis-free survival, and overall survival rates were 84.8%, 76.7%, and 81.7% for the 3D-CRT group, respectively, compared with 84.2%, 82.6%, and 85.4% for the IMRT group (p value > 0.05). A general trend of maximal deterioration in most QoL scales was observed during RT, followed by a gradual recovery thereafter. There was no significant difference in most scales between the two groups at each time point. The exception was that patients treated by IMRT had a both statistically and clinically significant improvement in global QoL, fatigue, taste/smell, dry mouth, and feeling ill at the time point of 3 months after RT. Conclusions: The potential advantage of IMRT over 3D-CRT in treating NPC patients might occur in QoL outcome during the recovery phase of acute toxicity.« less

Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus

NASA Astrophysics Data System (ADS)

Huang, Su-Hua; Yang, Tsuey-Ching; Tsai, Ming-Hong; Tsai, I.-Shou; Lu, Huang-Chih; Chuang, Pei-Hsin; Wan, Lei; Lin, Ying-Ju; Lai, Chih-Ho; Lin, Cheng-Wen

2008-10-01

Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples.

Using iRT, a normalized retention time for more targeted measurement of peptides

PubMed Central

Escher, Claudia; Reiter, Lukas; MacLean, Brendan; Ossola, Reto; Herzog, Franz; Chilton, John; MacCoss, Michael J.; Rinner, Oliver

2014-01-01

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than 4 times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments. PMID:22577012

Use of short-term real-time continuous glucose monitoring in type 1 diabetes patients on continuous intraperitoneal insulin infusion: a feasibility study.

PubMed

Logtenberg, Susan J J; Kleefstra, Nanne; Groenier, Klaas H; Gans, Rijk O B; Bilo, Henk J G

2009-05-01

In diabetes, strict glycemic control reduces risk of complications. One mode of therapy is continuous intraperitoneal insulin infusion (CIPII). With CIPII, like all intensified treatment strategies, frequent assessment of glucose levels is mandatory. Real-time (RT)-continuous glucose monitoring (CGM) gives RT information without the need for multiple invasive measurements. In theory, CIPII combined with RT-CGM could provide near normal glucose profiles. The objective of this study is to investigate effectiveness and safety of RT-CGM in patients treated with intraperitoneal insulin through an implanted pump. In an open-label, crossover, randomized study, effects of 6-day open RT-CGM use were studied in 12 type 1 diabetes patients on CIPII, with blinded RT-CGM used as a control. Primary outcome was time in euglycemia. Secondary outcomes included time in other glucose ranges, incidence of adverse events, and patient satisfaction. Agreement of self-measurement of blood glucose (SMBG) and RT-CGM measurements was assessed. Median time spent in euglycemia was 68.2% (55.9-72.3%) with open RT-CGM and 64.9% (55.3-71.2%) with blinded RT-CGM (P = 0.25). Time spent in other glucose ranges did not differ (P > 0.05). There were no serious adverse events. Patient satisfaction was good. Median relative absolute difference of SMBG and RT-CGM values was 13.9%. Bland-Altman analysis showed a mean difference of -0.31 mg/dL with lower and upper limits of agreement of -77.0 and +76.4 mg/dL, respectively. Short-term use of RT-CGM, although safe and with good patient satisfaction, does not result in more time spent in euglycemia, nor does it change time spent in other glucose ranges in our population of type 1 diabetes patients receiving CIPII.

The Plate Boundary Observatory Cascadia Network: Development and Installation of a Large Scale Real-time GPS Network

NASA Astrophysics Data System (ADS)

Austin, K. E.; Blume, F.; Berglund, H. T.; Feaux, K.; Gallaher, W. W.; Hodgkinson, K. M.; Mattioli, G. S.; Mencin, D.

2014-12-01

The EarthScope Plate Boundary Observatory (PBO), through a NSF-ARRA supplement, has enhanced the geophysical infrastructure in in the Pacific Northwest by upgrading a total of 282 Plate Boundary Observatory GPS stations to allow the collection and distribution of high-rate (1 Hz), low-latency (<1 s) data streams (RT-GPS). These upgraded stations supplemented the original 100 RT-GPS stations in the PBO GPS network. The addition of the new RT-GPS sites in Cascadia should spur new volcano and earthquake research opportunities in an area of great scientific interest and high geophysical hazard. Streaming RT-GPS data will enable researchers to detect and investigate strong ground motion during large geophysical events, including a possible plate-interface earthquake, which has implications for earthquake hazard mitigation. A Mw 6.9 earthquake occurred on March 10, 2014, off the coast of northern California. As a response, UNAVCO downloaded high-rate GPS data from Plate Boundary Observatory stations within 500 km of the epicenter of the event, providing a good test of network performance.In addition to the 282 stations upgraded to real-time, 22 new meteorological instruments were added to existing PBO stations. Extensive testing of BGAN satellite communications systems has been conducted to support the Cascadia RT-GPS upgrades and the installation of three BGAN satellite fail over systems along the Cascadia margin will allow for the continuation of data flow in the event of a loss of primary communications during in a large geophysical event or other interruptions in commercial cellular networks. In summary, with these additional upgrades in the Cascadia region, the PBO RT-GPS network will increase to 420 stations. Upgrades to the UNAVCO data infrastructure included evaluation and purchase of the Trimble Pivot Platform, servers, and additional hardware for archiving the high rate data, as well as testing and implementation of GLONASS and Trimble RTX positioning on the receivers. UNAVCO staff is working closely with the UNAVCO community to develop data standards, protocols, and a science plan for the use of RT-GPS data.

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

PubMed

Goldman, N

1994-09-01

The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)

The Electron Density Features Revealed by the GNSS-Based Radio Tomography in the Different Latitudinal and Longitudinal Sectors of the Ionosphere

NASA Astrophysics Data System (ADS)

Andreeva, Elena; Tereshchenko, Evgeniy; Nazarenko, Marina; Nesterov, Ivan; Kozharin, Maksim; Padokhin, Artem; Tumanova, Yulia

2016-04-01

The ionospheric radio tomography is an efficient method for electron density imaging in the different geographical regions of the world under different space weather conditions. The input for the satellite-based ionospheric radio tomography is provided by the signals that are transmitted from the navigational satellites and recorded by the chains or networks of ground receivers. The low-orbiting (LO) radio tomography employs the 150/400 MHz radio transmissions from the Earth's orbiters (like the Russian Tsikada/Parus and American Transit) flying at a height of ~1000 km above the Earth in the nearly polar orbits. The phases of the signals from a moving satellite which are recorded by the chains of ground receivers oriented along the satellite path form the families of linear integrals of electron density along the satellite-receiver rays that are used as the input data for LORT. The LO tomographic inversion of these data by phase difference method yields the 2D distributions of the ionospheric plasma in the vertical plane containing the receiving chain and the satellite path. LORT provides vertical resolution of 20-30 km and horizontal resolution of 30-40 km. The high-orbiting (HO) radio tomography employs the radio transmissions from the GPS/GLONASS satellites and enables 4D imaging of the ionosphere (3 spatial coordinates and time). HORT has a much wider spatial coverage (almost worldwide) and provides continuous time series of the reconstructions. However, the spatial resolution of HORT is lower (~100 km horizontally with a time step 60-20 min). In the regions with dense receiving networks (Europe, USA, Alaska, Japan), the resolution can be increased to 30-50 km with a time interval of 30-10 min. To date, the extensive RT data collected from the existing RT chains and networks enable a thorough analysis of both the regular and sporadic ionospheric features which are observed systematically or appear spontaneously, whose origin is fairly well understood or requires a dedicated study. We present the examples of the both types of the structures. We show a collection of different ionospheric structures under different space weather conditions: the ionization troughs, with their widely varying shapes, depths, positions, and internal distributions of plasma; isolated spots of the increased or decreased electron density, sharp wall-like density gradients, blobs, wavelike disturbances on different spatiotemporal scales etc. We demonstrate the series of the local isolated irregularities which are observed during both the quiet and disturbed days. We show the examples of the ionospheric plasma distributions strikingly varying during the geomagnetic storms. Some of the RT data are compared to the independent observations by the ionosondes. We also present the examples of RT images comparison with the UV spectroscopy data.

TMPA Products 3B42RT & 3B42V6: Evaluation and Application in Qinghai-Tibet Plateau

NASA Astrophysics Data System (ADS)

Hao, Z.; Sun, L.; Wang, J.

2012-04-01

Hydrological researchers in Qinghai-Tibet Plateau tend to be haunted by deficiency of station gauged precipitation data for the sparse and uneven distribution of local meteorological stations. Fortunately, alternative data can be obtained from TRMM (Tropic Rainfall Measurement Mission) satellite. Preliminary evaluation and necessary correction of TRMM satellite rainfall products is required for the sake of reliability and suitability considering that TRMM precipitation is unconventional and natural condition in Qinghai-Tibet Plateau is unusually complicated. 3B42RT and 3B42V6 products from TRMM Multisatellite Precipitation Analysis(TMPA) are evaluated in northeast Qinghai-Tibet Plateau with 50 stations quality-controlled gauged daily precipitation as the benchmark precipitation set. It is found that the RT data overestimates the actual precipitation greatly while V6 only overestimates it slightly. RT data shows different seasonal and inter-annual accuracies. Summer and autumn see better accuracies than winter and spring and wet years see higher accuracies than dry years. Latitude is believed to be an important factor that influences the accuracy of satellite precipitation. Both RT and V6 can reflect the general pattern of the spatial distribution of precipitation even though RT overestimates the quantity greatly. A new parameter, accumulated precipitation weight point (APWP), was introduced to describe the temporal-spatial pattern evolution of precipitation. The APWP of both RT and V6 were moving from south to north in the past decade, but they are all in the west of station gauged precipitation APWP(s).V6 APWP track fit gauged precipitation perfectly while RT APWP track has over-exaggerated legs, indicating that spatial distribution of RT precipitation experienced unreasonable sharp changes. A practical and operational procedure to correct satellite precipitation data is developed. For RT, there are two steps. Step 1, the downscaling, original daily precipitation was multiplied by a ratio of its monthly satellite/station precipitation gauged precipitation. Step2, objective analysis, Barnes/Cressman successive correction as well as Optimal Interpolation was applied to refine the processed daily results. Step 1 is unnecessary for V6 correction. The accuracy of RT can be improved significantly and the spatial details of satellite precipitation can be obtained as much as possible while quite little improvement showed in V6 correction. Besides, the iteration of successive correction should not be more than twice and the ideal influence radius for Optimal Interpolation is R=5. The original/corrected RT and V6 data sets were used as precipitation inputs to drive a newly developed hydrological model DHM-SP in the headwater region of the Yellow river so as to assess their applicability in simulating the daily runoff. V6 simulation result is qualified even though it is uncorrected. The bias in RT is too much to make use of RT as model input directly while quite satisfied results can be derived from corrected RT input. The simulation results of corrected RT are even better than that of station gauged and V6.

Real-time modeling and simulation of distribution feeder and distributed resources

NASA Astrophysics Data System (ADS)

Singh, Pawan

The analysis of the electrical system dates back to the days when analog network analyzers were used. With the advent of digital computers, many programs were written for power-flow and short circuit analysis for the improvement of the electrical system. Real-time computer simulations can answer many what-if scenarios in the existing or the proposed power system. In this thesis, the standard IEEE 13-Node distribution feeder is developed and validated on a real-time platform OPAL-RT. The concept and the challenges of the real-time simulation are studied and addressed. Distributed energy resources include some of the commonly used distributed generation and storage devices like diesel engine, solar photovoltaic array, and battery storage system are modeled and simulated on a real-time platform. A microgrid encompasses a portion of an electric power distribution which is located downstream of the distribution substation. Normally, the microgrid operates in paralleled mode with the grid; however, scheduled or forced isolation can take place. In such conditions, the microgrid must have the ability to operate stably and autonomously. The microgrid can operate in grid connected and islanded mode, both the operating modes are studied in the last chapter. Towards the end, a simple microgrid controller modeled and simulated on the real-time platform is developed for energy management and protection for the microgrid.

The conditional power of randomization tests for single-case effect sizes in designs with randomized treatment order: A Monte Carlo simulation study.

PubMed

Michiels, Bart; Heyvaert, Mieke; Onghena, Patrick

2018-04-01

The conditional power (CP) of the randomization test (RT) was investigated in a simulation study in which three different single-case effect size (ES) measures were used as the test statistics: the mean difference (MD), the percentage of nonoverlapping data (PND), and the nonoverlap of all pairs (NAP). Furthermore, we studied the effect of the experimental design on the RT's CP for three different single-case designs with rapid treatment alternation: the completely randomized design (CRD), the randomized block design (RBD), and the restricted randomized alternation design (RRAD). As a third goal, we evaluated the CP of the RT for three types of simulated data: data generated from a standard normal distribution, data generated from a uniform distribution, and data generated from a first-order autoregressive Gaussian process. The results showed that the MD and NAP perform very similarly in terms of CP, whereas the PND performs substantially worse. Furthermore, the RRAD yielded marginally higher power in the RT, followed by the CRD and then the RBD. Finally, the power of the RT was almost unaffected by the type of the simulated data. On the basis of the results of the simulation study, we recommend at least 20 measurement occasions for single-case designs with a randomized treatment order that are to be evaluated with an RT using a 5% significance level. Furthermore, we do not recommend use of the PND, because of its low power in the RT.

Using iRT, a normalized retention time for more targeted measurement of peptides.

PubMed

Escher, Claudia; Reiter, Lukas; MacLean, Brendan; Ossola, Reto; Herzog, Franz; Chilton, John; MacCoss, Michael J; Rinner, Oliver

2012-04-01

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrating impairments in reaction time and executive function using a diffusion model framework.

PubMed

Karalunas, Sarah L; Huang-Pollock, Cynthia L

2013-07-01

Using Ratcliff's diffusion model and ex-Gaussian decomposition, we directly evaluate the role individual differences in reaction time (RT) distribution components play in the prediction of inhibitory control and working memory (WM) capacity in children with and without ADHD. Children with (n = 91, [Formula: see text] age = 10.2 years, 67 % male) and without ADHD (n = 62, [Formula: see text] age = 10.6 years, 46 % male) completed four tasks of WM and a stop signal reaction time (SSRT) task. Children with ADHD had smaller WM capacities and less efficient inhibitory control. Diffusion model analyses revealed that children with ADHD had slower drift rates (v) and faster non-decision times (Ter), but there were no group differences in boundary separations (a). Similarly, using an ex-Gaussian approach, children with ADHD had larger τ values than non-ADHD controls, but did not differ in μ or σ distribution components. Drift rate mediated the association between ADHD status and performance on both inhibitory control and WM capacity. τ also mediated the ADHD-executive function impairment associations; however, models were a poorer fit to the data. Impaired performance on RT and executive functioning tasks has long been associated with childhood ADHD. Both are believed to be important cognitive mechanisms to the disorder. We demonstrate here that drift rate, or the speed at which information accumulates towards a decision, is able to explain both.

Prediction of Malaysian monthly GDP

NASA Astrophysics Data System (ADS)

Hin, Pooi Ah; Ching, Soo Huei; Yeing, Pan Wei

2015-12-01

The paper attempts to use a method based on multivariate power-normal distribution to predict the Malaysian Gross Domestic Product next month. Letting r(t) be the vector consisting of the month-t values on m selected macroeconomic variables, and GDP, we model the month-(t+1) GDP to be dependent on the present and l-1 past values r(t), r(t-1),…,r(t-l+1) via a conditional distribution which is derived from a [(m+1)l+1]-dimensional power-normal distribution. The 100(α/2)% and 100(1-α/2)% points of the conditional distribution may be used to form an out-of sample prediction interval. This interval together with the mean of the conditional distribution may be used to predict the month-(t+1) GDP. The mean absolute percentage error (MAPE), estimated coverage probability and average length of the prediction interval are used as the criterions for selecting the suitable lag value l-1 and the subset from a pool of 17 macroeconomic variables. It is found that the relatively better models would be those of which 2 ≤ l ≤ 3, and involving one or two of the macroeconomic variables given by Market Indicative Yield, Oil Prices, Exchange Rate and Import Trade.

Rapid detection of highly pathogenic porcine reproductive and respiratory syndrome virus by a fluorescent probe-based isothermal recombinase polymerase amplification assay.

PubMed

Yang, Yang; Qin, Xiaodong; Sun, Yingjun; Chen, Ting; Zhang, Zhidong

2016-12-01

A novel fluorescent probe-based real-time reverse transcription recombinase polymerase amplification (real-time RT-RPA) assay was developed for rapid detection of highly pathogenic type 2 porcine reproductive and respiratory syndrome virus (HP-PRRSV). The sensitivity analysis showed that the detection limit of RPA was 70 copies of HP-PRRSV RNA/reaction. The real-time RT-RPA highly specific amplified HP-PRRSV with no cross-reaction with classic PRRSV, classic swine fever virus, pseudorabies virus, and foot-and-mouth disease virus. Assessment with 125 clinical samples showed that the developed real-time RT-RPA assay was well correlated with real-time RT-qPCR assays for detection of HP-PRRSV. These results suggest that the developed real-time RT-RPA assay is suitable for rapid detection of HP-PRRSV.

The BCD of response time analysis in experimental economics.

PubMed

Spiliopoulos, Leonidas; Ortmann, Andreas

2018-01-01

For decisions in the wild, time is of the essence. Available decision time is often cut short through natural or artificial constraints, or is impinged upon by the opportunity cost of time. Experimental economists have only recently begun to conduct experiments with time constraints and to analyze response time (RT) data, in contrast to experimental psychologists. RT analysis has proven valuable for the identification of individual and strategic decision processes including identification of social preferences in the latter case, model comparison/selection, and the investigation of heuristics that combine speed and performance by exploiting environmental regularities. Here we focus on the benefits, challenges, and desiderata of RT analysis in strategic decision making. We argue that unlocking the potential of RT analysis requires the adoption of process-based models instead of outcome-based models, and discuss how RT in the wild can be captured by time-constrained experiments in the lab. We conclude that RT analysis holds considerable potential for experimental economics, deserves greater attention as a methodological tool, and promises important insights on strategic decision making in naturally occurring environments.

Simplest chronoscope. III. Further comparisons between reaction times obtained by meterstick versus machine.

PubMed

Montare, Alberto

2013-06-01

The three classical Donders' reaction time (RT) tasks (simple, choice, and discriminative RTs) were employed to compare reaction time scores from college students obtained by use of Montare's simplest chronoscope (meterstick) methodology to scores obtained by use of a digital-readout multi-choice reaction timer (machine). Five hypotheses were tested. Simple RT, choice RT, and discriminative RT were faster when obtained by meterstick than by machine. The meterstick method showed higher reliability than the machine method and was less variable. The meterstick method of the simplest chronoscope may help to alleviate the longstanding problems of low reliability and high variability of reaction time performances; while at the same time producing faster performance on Donders' simple, choice and discriminative RT tasks than the machine method.

Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR.

PubMed

Kamau, Everlyn; Agoti, Charles N; Lewa, Clement S; Oketch, John; Owor, Betty E; Otieno, Grieven P; Bett, Anne; Cane, Patricia A; Nokes, D James

2017-03-01

Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples. N gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses. An emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Changes of uterine blood flow after vaginal radical trachelectomy (VRT) in patients with early-stage uterine invasive cervical cancer.

PubMed

Umemura, Kota; Ishioka, Shin-ichi; Endo, Toshiaki; Baba, Tsuyoshi; Ezaka, Yoshiaki; Nagasawa, Kunihiko; Takahashi, Madoka; Mizuuchi, Masahito; Iwami, Nanako; Adachi, Hidefumi; Takeda, Noriko; Tamagawa, Mitsuharu; Saito, Tsuyoshi

2010-08-05

Vaginal radical trachectomy (RT) ligates and cuts several arteries supplying the uterus. Changes of blood supply to the uterus in two patients who experienced pregnancy and delivery were studied by using 3-D CT scanning. Effects of changes of blood supply to the uterus on the pregnancy courses were also examined. Vascular distribution in the uterus was studied in two patients who received vaginal RT after delivery. Effects of changes of vascular distribution after vaginal RT were studied with respect to pregnancy courses and cervical functions. New arterial vascularization from the ascending branches of uterine arteries or other arteries occurred, and these new vessels seemed to supply blood to the remaining cervix. Differences of fetal growth and histopathological changes in the placenta between the two patients could not be detected. Ligation and cutting of several supplying arteries by RT induces new arterial vascularization and it does not seem to affect fetal growth and placental function.

Decomposing ADHD-Related Effects in Response Speed and Variability

PubMed Central

Karalunas, Sarah L.; Huang-Pollock, Cynthia L.; Nigg, Joel T.

2012-01-01

Objective Slow and variable reaction times (RTs) on fast tasks are such a prominent feature of Attention Deficit Hyperactivity Disorder (ADHD) that any theory must account for them. However, this has proven difficult because the cognitive mechanisms responsible for this effect remain unexplained. Although speed and variability are typically correlated, it is unclear whether single or multiple mechanisms are responsible for group differences in each. RTs are a result of several semi-independent processes, including stimulus encoding, rate of information processing, speed-accuracy trade-offs, and motor response, which have not been previously well characterized. Method A diffusion model was applied to RTs from a forced-choice RT paradigm in two large, independent case-control samples (NCohort 1= 214 and N Cohort 2=172). The decomposition measured three validated parameters that account for the full RT distribution, and assessed reproducibility of ADHD effects. Results In both samples, group differences in traditional RT variables were explained by slow information processing speed, and unrelated to speed-accuracy trade-offs or non-decisional processes (e.g. encoding, motor response). Conclusions RT speed and variability in ADHD may be explained by a single information processing parameter, potentially simplifying explanations that assume different mechanisms are required to account for group differences in the mean and variability of RTs. PMID:23106115

Present Status of Radiotherapy in Clinical Practice

NASA Astrophysics Data System (ADS)

Duehmke, Eckhart

Aims of radiation oncology are cure from malignant diseases and - at the same time preservation of anatomy (e.g. female breast, uterus, prostate) and organ functions (e.g. brain, eye, voice, sphincter ani). At present, methods and results of clinical radiotherapy (RT) are based on experiences with natural history and radiobiology of malignant tumors in properly defined situations as well as on technical developments since World War II in geometrical and biological treatment planning in teletherapy and brachytherapy. Radiobiological research revealed tolerance limits of healthy tissues to be respected, effective total treatment doses of high cure probability depending on histology and tumor volume, and - more recently - altered fractionation schemes to be adapted to specific growth fractions and intrinsic radiosensitivities of clonogenic tumor cells. In addition, Biological Response Modifiers (BRM), such as cis-platinum, oxygen and hyperthermia may steepen cell survival curves of hypoxic tumor cells, others - such as tetrachiordekaoxid (TCDO) - may enhance repair of normal tissues. Computer assisted techniques in geometrical RT-planning based on individual healthy and pathologic anatomy (CT, MRT) provide high precision RT for well defined brain lesions by using dedicated linear accelerators (Stereotaxy). CT-based individual tissue compensators help with homogenization of distorted dose distributions in magna field irradiation for malignant lymphomas and with total body irradiation (TBI) before allogeneic bone marrow transplantation, e.g. for leukemia. RT with fast neutrons, Boron Neutron Capture Therapy (BNCT), RT with protons and heavy ions need to be tested in randomized trials before implementation into clinical routine.

[Clinical efficacy of alternating chemo-radiotherapy for locally advanced nasopharyngeal carcinoma].

PubMed

You, Xi; Yang, Yucheng

2014-03-01

The purpose of this study is to investigate the effective of alternating Chemo-radiotherapy for locally Advanced Nasopharyngeal Carcinoma. Retrospective analysis 106 cases of patients with locally advanced nasopharyngeal carcinoma between November 2005 and March 2007. All patients received cisplatin-based chemotherapy but 15 patients received radiotherapy(RT) alone. Inducing chemotherapy (IC) + RT + adju-vant chemotherapy (AC) regimen in 36 patients, IC+RT regimen was delivered in 25 patients and AC + RT regimen in 30 patients. 61 patients received 1 to 2 cycles of inducing chemotherapy and 66 patients received 3 to 6 cycles of adjuvant chemotherapy after radiotherapy. Chemotherapy started on the first day after the end of the induction chemotherapy, adjuvant chemotherapy begun after radiotherapy for a week. All patients were treated by radiotherapy using 60 Co r-ray, the nasophyarynx primary site was given a total does of 68 -74 Gy. The lymph nodes of the neck was given 60 to 70 Gy. The prophylactic irradiation does of the neck was 48-50 Gy. RESCULT: The median follow up time was 51 months. A total of 58 patients died, the overall survival rate was 45% in whole groups. The 5-year overall survival rates were 33%, 63%, 60% and 50% in RT, IC + RT + AC, IC + RT and RT+AC group, respectively. The 5-year disease-free survival rates were 13%, 56%, 48% and 40% in RT, IC + RT + AC, IC + RT and RT + AC group, respectively. The 5-year relapse-free survival rates were 13%, 53%, 48% and 50% in RT, IC + RT + AC, IC + RT and RT + AC group, respectively. The 5-year metastasis-free survival rates were 6%, 50%, 44% and 47% in RT, IC + RT + AC, IC+ RT and RT + AC group, respectively. There was significant difference in all groups (P < 0.05). The median time to relapses were 22 months, 29 months, 28 months and 25 months in RT, IC + RT + AC, IC + RT and RT + AC group, respectively. The median time to first distant metastasis were 10 months, 19 months, 15 months and 12 months in RT, IC + RT + AC, IC + RT and RT + AC group, respectively. There was no significant difference in all groups (P > 0.05). IC + RT + AC group had heavier acute toxicity effects than other groups, but it did not affect the treatment process, all patients could be tolerated. This retrospective study has demonstrated that alternating Chemo-radiotherapy and early radiotherapy not only can improve the survival rate for locally Advanced Nasopharyngeal Carcinoma, but also have slight toxicities and side reaction, all patients may tolerated.

Evaluating the 4-hour and 30-minute rules: effects of room temperature exposure on red blood cell quality and bacterial growth.

PubMed

Ramirez-Arcos, Sandra; Mastronardi, Cherie; Perkins, Heather; Kou, Yuntong; Turner, Tracey; Mastronardi, Emily; Hansen, Adele; Yi, Qi-Long; McLaughlin, Natasha; Kahwash, Eiad; Lin, Yulia; Acker, Jason

2013-04-01

A 30-minute rule was established to limit red blood cell (RBC) exposure to uncontrolled temperatures during storage and transportation. Also, RBC units issued for transfusion should not remain at room temperature (RT) for more than 4 hours (4-hour rule). This study was aimed at determining if single or multiple RT exposures affect RBC quality and/or promote bacterial growth. Growth and RT exposure experiments were performed in RBCs inoculated with Serratia liquefaciens and Serratia marcescens. RBCs were exposed once to RT for 5 hours (S. liquefaciens) or five times to RT for 30 minutes (S. marcescens) with periodic sampling for bacterial counts. Noncontaminated units were exposed to RT once (5 hr) or five times (30 min each) and sampled to measure in vitro quality variables. RBC core temperature was monitored using mock units with temperature loggers. Growth and RT exposure experiments were repeated three and at least six times, respectively. Statistical analysis was done using mixed-model analysis. RBC core temperature ranged from 7.3 to 11.6°C during 30-minute RT exposures and the time to reach 10°C varied from 22 to 55 minutes during 5-hour RT exposures. RBC quality was preserved after single or multiple RT exposures. Increased growth of S. liquefaciens was only observed after 2 hours of continuous RT exposure. S. marcescens concentration increased significantly in multiple-exposed units compared to the controls but did not reach clinically important levels. Single or multiple RT exposures did not affect RBC quality but slightly promoted bacterial growth in contaminated units. The clinical significance of these results remains unclear and needs further investigation. © 2012 American Association of Blood Banks.

Radio Tomography of Ionospheric Structures (probably) due to Underground-Surface-Atmosphere-Ionosphere Coupling

NASA Astrophysics Data System (ADS)

Kunitsyn, V.; Nesterov, I.; Andreeva, E.; Rekenthaler, D. A.

2012-12-01

Ionospheric radio-tomography (RT) utilizes radio signals transmitted from the global navigational satellite systems (GNSS), including low-orbiting (LO) navigational systems such as Transit, Tsikada, etc., and high-orbiting (HO) navigational systems such as GPS, GLONASS, Galileo, Beidou, etc. The signals that are transmitted from the LO navigational satellites and recorded by ground receiving chains can be inverted for almost instantaneous (5-8 min) 2D snapshots of electron density. The data from the networks of ground receivers that record the signals of the HO satellites are suitable for implementing high-orbital RT (HORT), i.e. reconstructing the 4D distributions of the ionospheric electron density (one 3D image every 20-30 min). In the regions densely covered by the GNSS receivers, it is currently possible to get a time step of 2-4 min. The LORT and HORT approaches have a common methodical basis: in both these techniques, the integrals of electron density along the ray between the satellite and the receiver are measured, and then the tomographic procedures are applied to reconstruct the distributions of electron density. We present several examples of the experiments on the ionospheric RT, which are related to the Underground-Surface-Atmosphere-Ionosphere (USAI) coupling. In particular, we demonstrate examples of RT images of the ionosphere after industrial explosions, rocket launches, and modification of the ionosphere by high-power radio waves. We also show RT cross sections reflecting ionospheric disturbances caused by the earthquakes (EQ) and tsunami waves. In these cases, there is an evident cause-and-effect relationship. The perturbations are transferred between the geospheres predominantly by acoustic gravity waves (AGW), whose amplitudes increase with increasing height. As far as EQ are concerned, the cause of the USAI coupling mechanism is not obvious. It is clear, however, that the regular RT studies can promote the solution of this challenging problem. The single-point measurements (by ionosondes or by isolated receivers) are not amenable to unambiguous interpretation; based on these data, it is impossible to distinguish the contribution of USAI coupling from the ionospheric effects induced by the "ordinary" impacts (the Sun, the solar wind, geomagnetic perturbations, galactic cosmic rays, etc.). In order to localize sources of the ionospheric disturbances, the geophysicist needs information on the spatial structure and dynamics of the ionospheric perturbations. This information (2D-4D RT images) is optimally provided by RT methods. We present examples of the ionospheric disturbances caused by EQs as well as the ionospheric precursors of these EQs in the form of specific ionospheric irregularities: AGW- and soliton-like wave disturbances, which we identified using RT methods. Based on the results of the RT studies in the Alaska and Taiwan regions, we have detected several dozen AGW-related precursors of EQs. These data allow us to attempt to locate the source of these perturbations. We discuss the possibilities and prospects of further research aimed at identifying and analyzing precursors of EQs and establishing the mechanisms of USAI coupling. We are grateful to Northwest Research Associates, Inc., and Dr. L.-C.Tsai for providing raw RT data for Alaska and Taiwan.

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

Lévy/Anomalous Diffusion as a Mean-Field Theory for 3D Cloud Effects in SW-RT: Empirical Support, New Analytical Formulation, and Impact on Atmospheric Absorption

NASA Astrophysics Data System (ADS)

Pfeilsticker, K.; Davis, A.; Marshak, A.; Suszcynsky, D. M.; Buldryrev, S.; Barker, H.

2001-12-01

2-stream RT models, as used in all current GCMs, are mathematically equivalent to standard diffusion theory where the physical picture is a slow propagation of the diffuse radiation by Gaussian random walks. In other words, after the conventional van de Hulst rescaling by 1/(1-g) in R3 and also by (1-g) in t, solar photons follow convoluted fractal trajectories in the atmosphere. For instance, we know that transmitted light is typically scattered about (1-g)τ 2 times while reflected light is scattered on average about τ times, where τ is the optical depth of the column. The space/time spread of this diffusion process is described exactly by a Gaussian distribution; from the statistical physics viewpoint, this follows from the convergence of the sum of many (rescaled) steps between scattering events with a finite variance. This Gaussian picture follows from directly from first principles (the RT equation) under the assumptions of horizontal uniformity and large optical depth, i.e., there is a homogeneous plane-parallel cloud somewhere in the column. The first-order effect of 3D variability of cloudiness, the main source of scattering, is to perturb the distribution of single steps between scatterings which, modulo the '1-g' rescaling, can be assumed effectively isotropic. The most natural generalization of the Gaussian distribution is the 1-parameter family of symmetric Lévy-stable distributions because the sum of many zero-mean random variables with infinite variance, but finite moments of order q < α (0 < α < 2), converge to them. It has been shown on heuristic grounds that for these Lévy-based random walks the typical number of scatterings is now (1-g)τ α for transmitted light. The appearance of a non-rational exponent is why this is referred to as anomalous diffusion. Note that standard/Gaussian diffusion is retrieved in the limit α = 2-. Lévy transport theory has been successfully used in the statistical physics to investigate a wide variety of systems with strongly nonlinear dynamics; these applications range from random advection in turbulent fluids to the erratic behavior of financial time-series and, most recently, self-regulating ecological systems. We will briefly survey the state-of-the-art observations that offer compelling empirical support for the Lévy/anomalous diffusion model in atmospheric radiation: (1) high-resolution spectroscopy of differential absorption in the O2 A-band from ground; (2) temporal transient records of lightning strokes transmitted through clouds to a sensitive detector in space; and (3) the Gamma-distributions of optical depths derived from Landsat cloud scenes at 30-m resolution. We will then introduce a rigorous analytical formulation of anomalous transport through finite media based on fractional derivatives and Sonin calculus. A remarkable result from this new theoretical development is an extremal property of the α = 1+ case (divergent mean-free-path), as is observed in the cloudy atmosphere. Finally, we will discuss the implications of anomalous transport theory for bulk 3D effects on the current enhanced absorption problem as well as its role as the basis of a next-generation GCM RT parameterization.

A Prolonged Time Interval Between Trauma and Prophylactic Radiation Therapy Significantly Increases the Risk of Heterotopic Ossification

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

Mourad, Waleed F., E-mail: Waleed246@gmail.com; Department of Radiation Oncology, Beth Israel Medical Center, New York, NY; Packianathan, Satyaseelan

2012-03-01

Purpose: To ascertain whether the time from injury to prophylactic radiation therapy (RT) influences the rate of heterotopic ossification (HO) after operative treatment of displaced acetabular fractures. Methods and Materials: This is a single-institution, retrospective analysis of patients referred for RT for the prevention of HO. Between January 2000 and January 2009, 585 patients with displaced acetabular fractures were treated surgically followed by RT for HO prevention. We analyzed the effect of time from injury on prevention of HO by RT. In all patients, 700 cGy was prescribed in a single fraction and delivered within 72 hours postsurgery. The patientsmore » were stratified into five groups according to time interval (in days) from the date of their accident to the date of RT: Groups A {<=}3, B {<=}7, C {<=}14, D {<=}21, and E >21days. Results: Of the 585 patients with displaced acetabular fractures treated with RT, (18%) 106 patients developed HO within the irradiated field. The risk of HO after RT increased from 10% for RT delivered {<=}3 days to 92% for treatment delivered >21 days after the initial injury. Wilcoxon test showed a significant correlation between the risk of HO and the length of time from injury to RT (p < 0.0001). Chi-square test and multiple logistic regression analysis showed no significant association between all other factors and the risk of HO (race, gender, cause and type of fracture, surgical approach, or the use of indomethacin). Conclusions: Our data suggest that there is higher incidence and risk of HO if prophylactic RT is significantly delayed after a displaced acetabular fracture. Thus, RT should be administered as early as clinically possible after the trauma. Patients undergoing RT >3 weeks from their displaced acetabular fracture should be informed of the higher risk (>90%) of developing HO despite prophylaxis.« less

Adequacy of TRMM satellite rainfall data in driving the SWAT modeling of Tiaoxi catchment (Taihu lake basin, China)

NASA Astrophysics Data System (ADS)

Li, Dan; Christakos, George; Ding, Xinxin; Wu, Jiaping

2018-01-01

Spatial rainfall data is an essential input to Distributed Hydrological Models (DHM), and a significant contributor to hydrological model uncertainty. Model uncertainty is higher when rain gauges are sparse, as is often the case in practice. Currently, satellite-based precipitation products increasingly provide an alternative means to ground-based rainfall estimates, in which case a rigorous product assessment is required before implementation. Accordingly, the twofold objective of this work paper was the real-world assessment of both (a) the Tropical Rainfall Measuring Mission (TRMM) rainfall product using gauge data, and (b) the TRMM product's role in forcing data for hydrologic simulations in the area of the Tiaoxi catchment (Taihu lake basin, China). The TRMM rainfall products used in this study are the Version-7 real-time 3B42RT and the post-real-time 3B42. It was found that the TRMM rainfall data showed a superior performance at the monthly and annual scales, fitting well with surface observation-based frequency rainfall distributions. The Nash-Sutcliffe Coefficient of Efficiency (NSCE) and the relative bias ratio (BIAS) were used to evaluate hydrologic model performance. The satisfactory performance of the monthly runoff simulations in the Tiaoxi study supports the view that the implementation of real-time 3B42RT allows considerable room for improvement. At the same time, post-real-time 3B42 can be a valuable tool of hydrologic modeling, water balance analysis, and basin water resource management, especially in developing countries or at remote locations in which rainfall gauges are scarce.

TU-G-BRA-03: Predicting Radiation Therapy Induced Ventilation Changes Using 4DCT Jacobian Calculations

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

Patton, T; Du, K; Bayouth, J

2015-06-15

Purpose: Longitudinal changes in lung ventilation following radiation therapy can be mapped using four-dimensional computed tomography(4DCT) and image registration. This study aimed to predict ventilation changes caused by radiation therapy(RT) as a function of pre-RT ventilation and delivered dose. Methods: 4DCT images were acquired before and 3 months after radiation therapy for 13 subjects. Jacobian ventilation maps were calculated from the 4DCT images, warped to a common coordinate system, and a Jacobian ratio map was computed voxel-by-voxel as the ratio of post-RT to pre-RT Jacobian calculations. A leave-one-out method was used to build a response model for each subject: post-RTmore » to pre-RT Jacobian ratio data and dose distributions of 12 subjects were applied to the subject’s pre-RT Jacobian map to predict the post-RT Jacobian. The predicted Jacobian map was compared to the actual post-RT Jacobian map to evaluate efficacy. Within this cohort, 8 subjects had repeat pre-RT scans that were compared as a reference for no ventilation change. Maps were compared using gamma pass rate criteria of 2mm distance-to-agreement and 6% ventilation difference. Gamma pass rates were compared using paired t-tests to determine significant differences. Further analysis masked non-radiation induced changes by excluding voxels below specified dose thresholds. Results: Visual inspection demonstrates the predicted post-RT ventilation map is similar to the actual map in magnitude and distribution. Quantitatively, the percentage of voxels in agreement when excluding voxels receiving below specified doses are: 74%/20Gy, 73%/10Gy, 73%/5Gy, and 71%/0Gy. By comparison, repeat scans produced 73% of voxels within the 6%/2mm criteria. The agreement of the actual post-RT maps with the predicted maps was significantly better than agreement with pre-RT maps (p<0.02). Conclusion: This work validates that significant changes to ventilation post-RT can be predicted. The differences between the predicted and actual outcome are similar to differences between repeat scans with equivalent ventilation. This work was supported by NIH grant CA166703 and a Pilot Grant from University of Iowa Carver College of Medicine.« less

Searching for the best real-time RT-PCRs to detect Zika virus infections: the importance of comparing several protocols.

PubMed

de Moraes, F M; Espósito, D L A; Klein, T M; da Fonseca, B A L

2018-01-01

Clinical manifestations of Zika, dengue, and chikungunya virus infections are very similar, making it difficult to reach a diagnosis based only on clinical grounds. In addition, there is an intense cross-reactivity between antibodies directed to Zika virus and other flaviviruses, and an accurate Zika diagnosis is best achieved by real-time RT-PCR. However, some real-time RT-PCR show better performance than others. To reach the best possible Zika diagnosis, the analytic sensitivity of some probe-based real-time RT-PCR amplifying Zika virus RNA was evaluated in spiked and clinical samples. We evaluated primers and probes to detect Zika virus, which had been published before, and tested sensitivity using serum spiked and patient samples by real-time RT-PCR. When tested against spiked samples, the previously described primers showed different sensitivity, with very similar results when samples from patients (serum and urine) were analyzed. Real-time RT-PCR designed to amplify Zika virus NS1 showed the best analytical sensitivity for all samples.

Is thyroid gland an organ at risk in breast cancer patients treated with locoregional radiotherapy? Results of a pilot study.

PubMed

Tunio, Mutahir Ali; Al Asiri, Mushabbab; Bayoumi, Yasser; Stanciu, Laura G; Al Johani, Naji; Al Saeed, Eyad Fawzi

2015-01-01

Aim was to evaluate the dose distribution within the thyroid gland its association with hypothyroidism in breast cancer (BC) patients receiving supraclavicular (SC) radiation therapy (RT). Consecutive 40 BC patients with baseline normal thyroid function tests (TFTs), were randomized into two groups: (a) Adjuvant chest wall/breast with SC-RT (20 patients) and (b) control group (adjuvant chest wall/breast RT only); 20 patients. The thyroid gland was contoured for each patient. Each patient's dose volume histogram (DVH), mean thyroid volume, the volume percentages of the thyroid absorbing respectively 5, 10, 20, 30, 40, and 50 Gy (V5, V10, V20, V30, V40, and V50), and Dmean (average dose in whole volume of thyroid) were then estimated. TFTs were performed at the time of the last follow-up and compared. Mean thyroid volume of cohort was 19.6 cm(3) (4.02-93.52) and Dmean of thyroid gland in SC-RT and control group was 25.8 Gy (16.4-52.2) and 5.6 Gy (0.7-12.8), respectively. Median values of V5, V10, V20, V30, V40, and V50 were 54%, 51%, 42.8%, 30.8%, 27.8%, and 7.64%, respectively, in SC-RT as compared to control group (V5;4.9%, V10;2.4%, V20;1.75%, V301%, V40;0%, and V50;0%, respectively) with P < 0.0001. At 52 months, a majority of patients (90%) had a normal thyroid function whereas four patients (10%) had hypothyroidism; 3/20 (15%) patients in SC-RT and 1/20 (5%) in control group with P < 0.001. Significant prognostic factors were; SC-RT (P = 0.001), V30 above 50% (P = 0.001), and smaller thyroid volume (P = 0.03). The risk of hypothyroidism in BC patients after SC-RT depends on the thyroid gland volume and V30 >50% and the risk can be minimized by thyroid gland shielding during RT.

Planning of visually guided reach-to-grasp movements: inference from reaction time and contingent negative variation (CNV).

PubMed

Zaepffel, Manuel; Brochier, Thomas

2012-01-01

We performed electroencephalogram (EEG) recording in a precuing task to investigate the planning processes of reach-to-grasp movements in human. In this reaction time (RT) task, subjects had to reach, grasp, and pull an object as fast as possible after a visual GO signal. We manipulated two parameters: the hand shape for grasping (precision grip or side grip) and the force required to pull the object (high or low). Three seconds before the GO onset, a cue provided advance information about force, grip, both parameters, or no information at all. EEG data show that reach-to-grasp movements generate differences in the topographic distribution of the late Contingent Negative Variation (ICNV) amplitude between the 4 precuing conditions. Along with RT data, it confirms that two distinct functional networks are involved with different time courses in the planning of grip and force. Finally, we outline the composite nature of the lCNV that might reflect both high- and low-level planning processes. Copyright © 2011 Society for Psychophysiological Research.

Jitter Reduces Response-Time Variability in ADHD: An Ex-Gaussian Analysis.

PubMed

Lee, Ryan W Y; Jacobson, Lisa A; Pritchard, Alison E; Ryan, Matthew S; Yu, Qilu; Denckla, Martha B; Mostofsky, Stewart; Mahone, E Mark

2015-09-01

"Jitter" involves randomization of intervals between stimulus events. Compared with controls, individuals with ADHD demonstrate greater intrasubject variability (ISV) performing tasks with fixed interstimulus intervals (ISIs). Because Gaussian curves mask the effect of extremely slow or fast response times (RTs), ex-Gaussian approaches have been applied to study ISV. This study applied ex-Gaussian analysis to examine the effects of jitter on RT variability in children with and without ADHD. A total of 75 children, aged 9 to 14 years (44 ADHD, 31 controls), completed a go/no-go test with two conditions: fixed ISI and jittered ISI. ADHD children showed greater variability, driven by elevations in exponential (tau), but not normal (sigma) components of the RT distribution. Jitter decreased tau in ADHD to levels not statistically different than controls, reducing lapses in performance characteristic of impaired response control. Jitter may provide a nonpharmacologic mechanism to facilitate readiness to respond and reduce lapses from sustained (controlled) performance. © 2012 SAGE Publications.

N08C9 (Alliance): A Phase 3 Randomized Study of Sulfasalazine Versus Placebo in the Prevention of Acute Diarrhea in Patients Receiving Pelvic Radiation Therapy

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

Miller, Robert C., E-mail: miller.robert@mayo.edu; Petereit, Daniel G.; Sloan, Jeff A.

Purpose: To provide confirmatory evidence on the use of sulfasalazine to reduce enteritis during pelvic radiation therapy (RT), following 2 prior single-institution trials suggestive that benefit existed. Methods and Materials: A multi-institution, randomized, double-blind, placebo-controlled phase 3 trial was designed to assess the efficacy of sulfasalazine versus placebo in the treatment of RT-related enteritis during RT including the posterior pelvis (45.0-53.5 Gy) and conducted through a multicenter national cooperative research alliance. Patients received 1000 mg of sulfasalazine or placebo orally twice daily during and for 4 weeks after RT. The primary endpoint was maximum severity of diarrhea (Common Terminology Criteria for Adverse Events versionmore » 4.0). Toxicity and bowel function were assessed by providers through a self-administered bowel function questionnaire taken weekly during RT and for 6 weeks afterward. Results: Eighty-seven patients were enrolled in the trial between April 29, 2011, and May 13, 2013, with evenly distributed baseline factors. At the time of a planned interim toxicity analysis, more patients with grade ≥3 diarrhea received sulfasalazine than received placebo (29% vs 11%, P=.04). A futility analysis showed that trial continuation would be unlikely to yield a positive result, and a research board recommended halting study treatment. Final analysis of the primary endpoint showed no significant difference in maximum diarrhea severity between the sulfasalazine and placebo arms (P=.41). Conclusions: Sulfasalazine does not reduce enteritis during pelvic RT and may be associated with a higher risk of adverse events than placebo. This trial illustrates the importance of confirmatory phase 3 trials in the evaluation of symptom-control agents.« less

Development of duplex real-time RT-PCR based on Taqman technology for detecting simultaneously the genome of pan-enterovirus and enterovirus 71.

PubMed

Hwang, Seoyeon; Kang, Byunghak; Hong, Jiyoung; Kim, Ahyoun; Kim, Hyejin; Kim, Kisang; Cheon, Doo-Sung

2013-07-01

Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia-Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real-time RT-PCR assay was developed in order to simultaneously detect pan-EV and EV71. EV71-specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real-time RT-PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross-reactions were observed in this duplex real-time RT-PCR. The EV71-specific duplex real-time RT-PCR was more sensitive than conventional RT-PCR, and detected viral titers that were 10-fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan-EV-positive, of which 170 (86.7%) were EV71-positive when tested by pan-EV and EV71-specific duplex real-time RT-PCR. EV71-specific duplex real-time RT-PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. Copyright © 2013 Wiley Periodicals, Inc.

Effects of elastic band resistance training and nutritional supplementation on physical performance of institutionalised elderly--A randomized controlled trial.

PubMed

Oesen, Stefan; Halper, Barbara; Hofmann, Marlene; Jandrasits, Waltraud; Franzke, Bernhard; Strasser, Eva-Maria; Graf, Alexandra; Tschan, Harald; Bachl, Norbert; Quittan, Michael; Wagner, Karl Heinz; Wessner, Barbara

2015-12-01

To evaluate the effects of elastic band resistance training in combination with nutrient supplementation on muscular strength and the ability to perform mobility-related activities of daily living in older adults living in retirement care facilities. Randomized controlled trial, with a 6-month intervention period. A retirement care facility, Vienna, Austria. One hundred and seventeen older adults (14 males (12%) and 103 females (88%)), aged 65 to 97 years (mean age: 82.8 ± 6.0), having a mini-mental state examination score ≥ 23 and no chronic diseases posing a medical contraindication to training therapy. Participants were randomly assigned, but stratified by sex, to one of three intervention groups: supervised resistance exercise training (RT), RT in combination with nutrient supplementation (RTS), or cognitive training group (CT). All interventions were performed two times a week for 6 months. RT was designed to train all major muscle groups using elastic bands. The nutrient supplement (rich in proteins, vitamin D, B2, B12) was distributed every morning as well as after each RT session. A battery of motor ability tests and functional test were performed prior to as well as following 3 months and finally after 6 months of intervention. These tests included isokinetic torque measurements of the knee extensors and flexors in concentric mode at 60 and 120°/s, isometric handgrip strength, senior arm-lifting test, chair stand test, maximum walking speed and a 6-minute walking test (6 MWT). A repeated-measures ANOVA analysis revealed significant improvements in physical function of lower (p=0.002) and upper extremities (p=0.006) for RT and/or RTS in comparison to CT. For isokinetic measurements, 6 MWT, and gait speed time effects (p<0.05) were detected without any group × time interaction effects. Dropouts showed lower performance in chair stand test (p=0.012), 6 MWT (p=0.003), and gait speed (p=0.013) at baseline than that of the finishers of the study. Six months of a low intensity resistance exercise using elastic bands and own body weight is safe and beneficial in improving functional performance of institutionalised older people. Multinutrient supplementation did not offer additional benefits to the effects of RT in improving muscular performance. Copyright © 2015 Elsevier Inc. All rights reserved.

Imaging water velocity and volume fraction distributions in water continuous multiphase flows using inductive flow tomography and electrical resistance tomography

NASA Astrophysics Data System (ADS)

Meng, Yiqing; Lucas, Gary P.

2017-05-01

This paper presents the design and implementation of an inductive flow tomography (IFT) system, employing a multi-electrode electromagnetic flow meter (EMFM) and novel reconstruction techniques, for measuring the local water velocity distribution in water continuous single and multiphase flows. A series of experiments were carried out in vertical-upward and upward-inclined single phase water flows and ‘water continuous’ gas-water and oil-gas-water flows in which the velocity profiles ranged from axisymmetric (single phase and vertical-upward multiphase flows) to highly asymmetric (upward-inclined multiphase flows). Using potential difference measurements obtained from the electrode array of the EMFM, local axial velocity distributions of the continuous water phase were reconstructed using two different IFT reconstruction algorithms denoted RT#1, which assumes that the overall water velocity profile comprises the sum of a series of polynomial velocity components, and RT#2, which is similar to RT#1 but which assumes that the zero’th order velocity component may be replaced by an axisymmetric ‘power law’ velocity distribution. During each experiment, measurement of the local water volume fraction distribution was also made using the well-established technique of electrical resistance tomography (ERT). By integrating the product of the local axial water velocity and the local water volume fraction in the cross section an estimate of the water volumetric flow rate was made which was compared with a reference measurement of the water volumetric flow rate. In vertical upward flows RT#2 was found to give rise to water velocity profiles which are consistent with the previous literature although the profiles obtained in the multiphase flows had relatively higher central velocity peaks than was observed for the single phase profiles. This observation was almost certainly a result of the transfer of axial momentum from the less dense dispersed phases to the water, which occurred preferentially at the pipe centre. For upward inclined multiphase flows RT#1 was found to give rise to water velocity profiles which are more consistent with results in the previous literature than was the case for RT#2—which leads to the tentative conclusion that the upward inclined multiphase flows investigated in the present study did not contain significant axisymmetric velocity components.

Inter-patient image registration algorithms to disentangle regional dose bioeffects.

PubMed

Monti, Serena; Pacelli, Roberto; Cella, Laura; Palma, Giuseppe

2018-03-20

Radiation therapy (RT) technological advances call for a comprehensive reconsideration of the definition of dose features leading to radiation induced morbidity (RIM). In this context, the voxel-based approach (VBA) to dose distribution analysis in RT offers a radically new philosophy to evaluate local dose response patterns, as an alternative to dose-volume-histograms for identifying dose sensitive regions of normal tissue. The VBA relies on mapping patient dose distributions into a single reference case anatomy which serves as anchor for local dosimetric evaluations. The inter-patient elastic image registrations (EIRs) of the planning CTs provide the deformation fields necessary for the actual warp of dose distributions. In this study we assessed the impact of EIR on the VBA results in thoracic patients by identifying two state-of-the-art EIR algorithms (Demons and B-Spline). Our analysis demonstrated that both the EIR algorithms may be successfully used to highlight subregions with dose differences associated with RIM that substantially overlap. Furthermore, the inclusion for the first time of covariates within a dosimetric statistical model that faces the multiple comparison problem expands the potential of VBA, thus paving the way to a reliable voxel-based analysis of RIM in datasets with strong correlation of the outcome with non-dosimetric variables.

Novel HBV recombinants between genotypes B and C in 3'-terminal reverse transcriptase (RT) sequences are associated with enhanced viral DNA load, higher RT point mutation rates and place of birth among Chinese patients.

PubMed

Liu, Baoming; Yang, Jing-Xian; Yan, Ling; Zhuang, Hui; Li, Tong

2018-01-01

As one of the major global public health concerns, hepatitis B virus (HBV) can be divided into at least eight genotypes, which may be related to disease severity and treatment response. We previously demonstrated that genotypes B and C HBV, with distinct geographical distribution in China, had divergent genotype-dependent amino acid polymorphisms and variations in reverse transcriptase (RT) gene region, a target of antiviral therapy using nucleos(t)ide analogues. Recently recombination between HBV genotypes B and C was reported to occur in the RT region. However, their frequency and clinical significance is poorly understood. Here full-length HBV RT sequences from 201 Chinese chronic hepatitis B (CHB) patients were amplified and sequenced, among which 31.34% (63/201) were genotype B whereas 68.66% (138/201) genotype C. Although no intergenotypic recombination was detected among C-genotype HBV, 38.10% (24/63) of B-genotype HBV had recombination with genotype C in the 3'-terminal RT sequences. The patients with B/C intergenotypic recombinants had significantly (P<0.05) higher serum HBV DNA level than the "pure" B-genotype cohort did. Moreover, the B/C intergenotypic recombinants were prone to more substitutions at several specific residues in the RT region than genotype B or C. Besides, unlike their parental genotypes, the recombinant HBV appeared to display an altered geographic distribution feature in China. Our findings provide novel insight into the virological, clinical and epidemiological features of new HBV B/C intergenotypic recombinants at the 3' end of RT sequences among Chinese CHB patients. The highly complex genetic background of the novel recombinant HBV carrying new mutations affecting RT protein may contribute to an enhanced heterogeneity in treatment response or prognosis among CHB patients. Published by Elsevier B.V.

Evaluation of the utilization of external radiotherapy in the treatment of localized prostate cancer in Andalusia, Spain.

PubMed

Expósito, José; Linares, Isabel; Castillo, Isabel; Martínez, Miguel; Vargas, Pilar; Herruzo, Ismael; Medina, José Antonio; Palacios, Amalia; Bayo, Eloísa; Peracaula, Francisco; Jaén, Javier; Sánchez, José Antonio; Ortiz, María José

2015-12-30

Around 27,000 new cases of prostate cancer are diagnosed every year in Spain and 5400 die from this disease. Radiotherapy (RT), alone or combined, has proven to be effective as initial treatment in patients with localized disease. Our objective was to evaluate the use of external beam RT (EBRT) in our region, comparing the indication rate and irradiation rate and examining variability in its application among hospitals. We conducted a review of RT guidelines and indication studies for prostate cancer (% expected irradiation). Data were gathered from all twelve public healthcare centers in Andalusia (Spain) on RT-treated prostate cancer patients during 2013 (% actual irradiation) and from nine of the centers on RT discharge reports. Information was classified according to type of hospital, tumor risk category and RT treatment (technique, dosage, volume, toxicity). The estimated RT rate was 67 % (1289/1917), 43 % were aged > 70 years, 44.7 % had ECOG performance status of 0); 44.7 % had high-risk tumors; 57 % underwent RT associated with hormone therapy; 70 % of patients receiving RT were treated with 3D planning (30 % IGRT); and doses were 70-76 Gy in 70 % of cases and >76 Gy in 10.7 %. Acute gastrointestinal and genitourinary toxicities were < grade 2 in 79 and 89 % of patients, respectively. An irradiation rate significantly below the mean for the study was found in four provinces. There was a significant difference among provinces in the distribution of risk groups. Underutilization of EBRT was estimated to be around 30 % in prostate cancer patients, with an elevated variability in irradiation rates among hospitals related to differences in available technology and in the distribution of patients with different risk levels. These data should be a matter of concern to regional health managers, given the negative and measurable impact on the survival of patients.

On the efficacy of procedures to normalize Ex-Gaussian distributions.

PubMed

Marmolejo-Ramos, Fernando; Cousineau, Denis; Benites, Luis; Maehara, Rocío

2014-01-01

Reaction time (RT) is one of the most common types of measure used in experimental psychology. Its distribution is not normal (Gaussian) but resembles a convolution of normal and exponential distributions (Ex-Gaussian). One of the major assumptions in parametric tests (such as ANOVAs) is that variables are normally distributed. Hence, it is acknowledged by many that the normality assumption is not met. This paper presents different procedures to normalize data sampled from an Ex-Gaussian distribution in such a way that they are suitable for parametric tests based on the normality assumption. Using simulation studies, various outlier elimination and transformation procedures were tested against the level of normality they provide. The results suggest that the transformation methods are better than elimination methods in normalizing positively skewed data and the more skewed the distribution then the transformation methods are more effective in normalizing such data. Specifically, transformation with parameter lambda -1 leads to the best results.

The influence of emotion on lexical processing: insights from RT distributional analysis.

PubMed

Yap, Melvin J; Seow, Cui Shan

2014-04-01

In two lexical decision experiments, the present study was designed to examine emotional valence effects on visual lexical decision (standard and go/no-go) performance, using traditional analyses of means and distributional analyses of response times. Consistent with an earlier study by Kousta, Vinson, and Vigliocco (Cognition 112:473-481, 2009), we found that emotional words (both negative and positive) were responded to faster than neutral words. Finer-grained distributional analyses further revealed that the facilitation afforded by valence was reflected by a combination of distributional shifting and an increase in the slow tail of the distribution. This suggests that emotional valence effects in lexical decision are unlikely to be entirely mediated by early, preconscious processes, which are associated with pure distributional shifting. Instead, our results suggest a dissociation between early preconscious processes and a later, more task-specific effect that is driven by feedback from semantically rich representations.

A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System

PubMed Central

Coudray-Meunier, Coralie; Fraisse, Audrey; Martin-Latil, Sandra; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie

2016-01-01

Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log10. Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log10. Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log10 lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log10. Conversely, sensitivity was only 0.30 log10 better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health. PMID:26824897

Application of High- and Low-Orbiting Radio Tomography for Exploring the Ionospheric Structures on Different Scales

NASA Astrophysics Data System (ADS)

Andreeva, Elena; Padokhin, Artem; Nazarenko, Marina; Nesterov, Ivan; Tumanova, Yulia; Tereshchenko, Evgeniy; Kozharin, Maksim

2016-07-01

The methods of ionospheric radio tomography (RT) are actively developing at present. These methods are suitable for reconstructing the spatial distributions of electron density from radio signals transmitted from the navigational satellite systems and recorded by the networks of ground-based receivers. The RT systems based on the low-orbiting (LO) (Parus/Transit) navigational systems have been in operation since the early 1990s. Recently, the RT methods employing the signals from high-orbiting (HO) satellite navigational systems such as GPS/GLONASS have come into play. In our presentation, we discuss the accuracies, advantages, and limitations of LORT and HORT as well as the possibilities of their combined application fro reconstructing the structure of the ionosphere in the same region during the same time interval on the different spatiotemporal scales. The LORT reconstructions provide practically instantaneous (spanning 5-10 min) 2D snapshots of the ionosphere within a spatial interval with a length of up to a few thousand km. The vertical resolution of LORT is 25-30 km and the horizontal resolution, 15-25 km. The HORT methods are capable of reconstructing the 4D structure of the ionosphere (three spatial coordinates and time). The spatial resolution of HORT is generally not better than 100 km with a 60-20 min interval between the successive reconstructions. In the regions of dense receiving networks, the resolution can be improved to 30-50 km and the time step can be reduced to 30-10 min. In California and Japan which are covered by extremely dense receiving networks the resolution can be even higher (10-30 km) and the time interval between the reconstruction even shorter (up to 2 min). In the presentation, we discuss the LORT and HORT reconstructions of the ionosphere during different time periods of the 23rd and 24th solar cycles in the different regions of the world. We analyze the spatiotemporal features and dynamics of the ionosphere depending on the solar and geophysical conditions. Particular attention is attached to the periods of the strong geomagnetic disturbances. The stormy ionosphere is characterized by extremely sophisticated structure and rapid dynamics. Being affected by a variety of the perturbing factors, the ionospheric parameters experience striking variations which can be traced by the RT methods. The RT reconstructions revealed multi-extremal plasma structures, steep wall-like gradients of electron density, and spots of enhanced ionization. A complicated structure of the main ionization trough with its polar wall moving equatorwards was observed. In contrast to the middle and lower latitudes where the magnetic field largely shields the Earth from the energetic particle fluxes, the RT reconstructions in the northern high latitudes demonstrate the presence of localized highly ionized features and wavelike disturbances associated with the injections of corpuscular radiation into the ionosphere. We present and discuss the examples of the qualitative comparisons of the RT ionospheric images with the data on the ionizing particle fluxes measured by the DMSP satellite. The examples of RT data comparison with the ionosonde measurements are demonstrated.

Rapid group-, serotype-, and vaccine strain-specific identification of poliovirus isolates by real-time reverse transcription-PCR using degenerate primers and probes containing deoxyinosine residues.

PubMed

Kilpatrick, David R; Yang, Chen-Fu; Ching, Karen; Vincent, Annelet; Iber, Jane; Campagnoli, Ray; Mandelbaum, Mark; De, Lina; Yang, Su-Ju; Nix, Allan; Kew, Olen M

2009-06-01

We have adapted our previously described poliovirus diagnostic reverse transcription-PCR (RT-PCR) assays to a real-time RT-PCR (rRT-PCR) format. Our highly specific assays and rRT-PCR reagents are designed for use in the WHO Global Polio Laboratory Network for rapid and large-scale identification of poliovirus field isolates.

Transit Fare Prepayment Distribution Methods in Sacramento, CA

DOT National Transportation Integrated Search

1985-06-01

This demonstration tested the use of new methods to distribute transit fare prepayment (TFP) instruments at the Sacramento Regional Transit district (RT). Five new distribution methods were implemented to supplement a network of public, private, and ...

Development of a highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus 71 in hand, foot, and mouth disease.

PubMed

Niu, Peihua; Qi, Shunxiang; Yu, Benzhang; Zhang, Chen; Wang, Ji; Li, Qi; Ma, Xuejun

2016-11-01

Enterovirus 71 (EV71) is one of the major causative agents of outbreaks of hand, foot, and mouth disease (HFMD). A commercial TaqMan probe-based real-time PCR assay has been widely used for the differential detection of EV71 despite its relatively high cost and failure to detect samples with a low viral load (Ct value > 35). In this study, a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of EV71 in HFMD was developed. The sensitivity and specificity of this assay were evaluated using a reference EV71 stock and a panel of controls consisting of coxsackievirus A16 (CVA16) and common respiratory viruses, respectively. The clinical performance of this assay was evaluated and compared with those of a commercial TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional two-step nested RT-PCR assay. The limit of detection for the RTN RT-PCR assay was 0.01 TCID50/ml, with a Ct value of 38.3, which was the same as that of the traditional two-step nested RT-PCR assay and approximately tenfold lower than that of the qRT-PCR assay. When testing the reference strain EV71, this assay showed favorable detection reproducibility and no obvious cross-reactivity. The testing results of 100 clinical throat swabs from HFMD-suspected patients revealed that 41 samples were positive for EV71 by both RTN RT-PCR and traditional two-step nested RT-PCR assays, whereas only 29 were EV71 positive by qRT-PCR assay.

The timing of surgery after neoadjuvant radiotherapy influences tumor dissemination in a preclinical model

PubMed Central

Leroi, Natacha; Sounni, Nor Eddine; Van Overmeire, Eva; Blacher, Silvia; Marée, Raphael; Van Ginderachter, Jo; Lallemand, François; Lenaerts, Eric; Coucke, Philippe; Noel, Agnès; Martinive, Philippe

2015-01-01

Neoadjuvant radiotherapy (neoRT) used in cancer treatments aims at improving local tumor control and patient overall survival. The neoRT schedule and the timing of the surgical treatment (ST) are empirically based and influenced by the clinician's experience. The current study examines how the sequencing of neoRT and ST affects metastatic dissemination. In a breast carcinoma model, tumors were exposed to different neoRT schedules (2x5Gy or 5x2Gy) followed by surgery at day 4 or 11 post-RT. The impact on the tumor microenvironment and lung metastases was evaluated through immunohistochemical and flow cytometry analyses. After 2x5Gy, early ST (at day 4 post-RT) led to increased size and number of lung metastases as compared to ST performed at day 11. Inversely, after 5x2Gy neoRT, early ST protected the mice against lung metastases. This intriguing relationship between tumor aggressiveness and ST timing could not be explained by differences in classical parameters studied such as hypoxia, vessel density and matrix remodeling. The study of tumor-related inflammation and immunity reveals an increased circulating NK cell percentage following neoRT as compared to non irradiated mice. Then, radiation treatment and surgery were applied to tumor-bearing NOD/SCID mice. In the absence of NK cells, neoRT appears to increase lung metastatic dissemination as compared to non irradiated tumor-bearing mice. Altogether our data demonstrate that the neoRT schedule and the ST timing affect metastasis formation in a pre-clinical model and points out the potential role of NK cells. These findings highlight the importance to cautiously tailor the optimal window for ST following RT. PMID:26440148

Impact of a radio frequency management information system on the process and timing of providing respiratory care services.

PubMed

Stoller, James K; Kester, Lucy; Orens, Douglas K; McCarthy, Kevin

2002-08-01

Although radio frequency (RF) systems have proliferated and are designed to simplify care delivery in many clinical settings, little information is available on the impact of such RF systems on the delivery of patient care. Having used a hand-held-device-based management information system in our Respiratory Therapy Section for 16 years, we assessed the impact of an RF system on the delivery of respiratory therapy (RT) services. A single nursing unit dedicated to pulmonary and ear, nose, and throat care was selected for the RF system trial. Baseline (pre-RF) data were collected over 2 separate 1-month intervals (February 1999 and February 2000). The main outcome measures were (1) the amount of time needed at the beginning of the shift to organize and assign orders for RT services, (2) the time interval between notification of an RT consult order and completion of the RT consult, and (3) the time interval between notification of an RT treatment order and completion of the RT treatment. The activities required for organizing and assigning the orders were manually timed. Starting 6 weeks after therapists were trained to use the RF system, similar data were collected while using the RF system for two 1-month intervals (February and March 2001). The mean +/- SD time interval between receiving an RT consult order and completing the consult was reduced from 7.8 +/- 18.9 h to 2.8 +/- 2.4 h (p = 0.002). The percentage of patients who waited longer than 8 hours between receipt of a consult order and completion of the consult decreased from 18% to 4.7% (p = 0.026). The total time required for organizing and assigning RT work was reduced from 81.6 min to 43.6 min. The RF system had several advantages over the hand-held-device-based system: (1) shorter interval between the order for and completion of an RT consult, (2) lower percentage of patients for whom the interval between the order and the consult exceeded 8 hours, and (3) less time required to make shift assignments. These results invite assessment of whether accelerated delivery of RT services confers clinical benefits.

Concurrent versus sequential sorafenib therapy in combination with radiation for hepatocellular carcinoma.

PubMed

Wild, Aaron T; Gandhi, Nishant; Chettiar, Sivarajan T; Aziz, Khaled; Gajula, Rajendra P; Williams, Russell D; Kumar, Rachit; Taparra, Kekoa; Zeng, Jing; Cades, Jessica A; Velarde, Esteban; Menon, Siddharth; Geschwind, Jean F; Cosgrove, David; Pawlik, Timothy M; Maitra, Anirban; Wong, John; Hales, Russell K; Torbenson, Michael S; Herman, Joseph M; Tran, Phuoc T

2013-01-01

Sorafenib (SOR) is the only systemic agent known to improve survival for hepatocellular carcinoma (HCC). However, SOR prolongs survival by less than 3 months and does not alter symptomatic progression. To improve outcomes, several phase I-II trials are currently examining SOR with radiation (RT) for HCC utilizing heterogeneous concurrent and sequential treatment regimens. Our study provides preclinical data characterizing the effects of concurrent versus sequential RT-SOR on HCC cells both in vitro and in vivo. Concurrent and sequential RT-SOR regimens were tested for efficacy among 4 HCC cell lines in vitro by assessment of clonogenic survival, apoptosis, cell cycle distribution, and γ-H2AX foci formation. Results were confirmed in vivo by evaluating tumor growth delay and performing immunofluorescence staining in a hind-flank xenograft model. In vitro, concurrent RT-SOR produced radioprotection in 3 of 4 cell lines, whereas sequential RT-SOR produced decreased colony formation among all 4. Sequential RT-SOR increased apoptosis compared to RT alone, while concurrent RT-SOR did not. Sorafenib induced reassortment into less radiosensitive phases of the cell cycle through G1-S delay and cell cycle slowing. More double-strand breaks (DSBs) persisted 24 h post-irradiation for RT alone versus concurrent RT-SOR. In vivo, sequential RT-SOR produced the greatest tumor growth delay, while concurrent RT-SOR was similar to RT alone. More persistent DSBs were observed in xenografts treated with sequential RT-SOR or RT alone versus concurrent RT-SOR. Sequential RT-SOR additionally produced a greater reduction in xenograft tumor vascularity and mitotic index than either concurrent RT-SOR or RT alone. In conclusion, sequential RT-SOR demonstrates greater efficacy against HCC than concurrent RT-SOR both in vitro and in vivo. These results may have implications for clinical decision-making and prospective trial design.

Concurrent versus Sequential Sorafenib Therapy in Combination with Radiation for Hepatocellular Carcinoma

PubMed Central

Chettiar, Sivarajan T.; Aziz, Khaled; Gajula, Rajendra P.; Williams, Russell D.; Kumar, Rachit; Taparra, Kekoa; Zeng, Jing; Cades, Jessica A.; Velarde, Esteban; Menon, Siddharth; Geschwind, Jean F.; Cosgrove, David; Pawlik, Timothy M.; Maitra, Anirban; Wong, John; Hales, Russell K.; Torbenson, Michael S.; Herman, Joseph M.; Tran, Phuoc T.

2013-01-01

Sorafenib (SOR) is the only systemic agent known to improve survival for hepatocellular carcinoma (HCC). However, SOR prolongs survival by less than 3 months and does not alter symptomatic progression. To improve outcomes, several phase I-II trials are currently examining SOR with radiation (RT) for HCC utilizing heterogeneous concurrent and sequential treatment regimens. Our study provides preclinical data characterizing the effects of concurrent versus sequential RT-SOR on HCC cells both in vitro and in vivo. Concurrent and sequential RT-SOR regimens were tested for efficacy among 4 HCC cell lines in vitro by assessment of clonogenic survival, apoptosis, cell cycle distribution, and γ-H2AX foci formation. Results were confirmed in vivo by evaluating tumor growth delay and performing immunofluorescence staining in a hind-flank xenograft model. In vitro, concurrent RT-SOR produced radioprotection in 3 of 4 cell lines, whereas sequential RT-SOR produced decreased colony formation among all 4. Sequential RT-SOR increased apoptosis compared to RT alone, while concurrent RT-SOR did not. Sorafenib induced reassortment into less radiosensitive phases of the cell cycle through G1-S delay and cell cycle slowing. More double-strand breaks (DSBs) persisted 24 h post-irradiation for RT alone versus concurrent RT-SOR. In vivo, sequential RT-SOR produced the greatest tumor growth delay, while concurrent RT-SOR was similar to RT alone. More persistent DSBs were observed in xenografts treated with sequential RT-SOR or RT alone versus concurrent RT-SOR. Sequential RT-SOR additionally produced a greater reduction in xenograft tumor vascularity and mitotic index than either concurrent RT-SOR or RT alone. In conclusion, sequential RT-SOR demonstrates greater efficacy against HCC than concurrent RT-SOR both in vitro and in vivo. These results may have implications for clinical decision-making and prospective trial design. PMID:23762417

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus.

PubMed

Kang, Xiao-ping; Jiang, Tao; Li, Yong-qiang; Lin, Fang; Liu, Hong; Chang, Guo-hui; Zhu, Qing-yu; Qin, E-de; Qin, Cheng-feng; Yang, Yin-hui

2010-06-02

A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose) for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis.

Response time variability under slow and fast-incentive conditions in children with ASD, ADHD and ASD+ADHD.

PubMed

Tye, Charlotte; Johnson, Katherine A; Kelly, Simon P; Asherson, Philip; Kuntsi, Jonna; Ashwood, Karen L; Azadi, Bahare; Bolton, Patrick; McLoughlin, Gráinne

2016-12-01

Attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) show significant behavioural and genetic overlap. Both ADHD and ASD are characterised by poor performance on a range of cognitive tasks. In particular, increased response time variability (RTV) is a promising indicator of risk for both ADHD and ASD. However, it is not clear whether different indices of RTV and changes to RTV according to task conditions are able to discriminate between the two disorders. Children with ASD (n = 19), ADHD (n = 18), ASD + ADHD (n = 29) and typically developing controls (TDC; n = 26) performed a four-choice RT task with slow-baseline and fast-incentive conditions. Performance was characterised by mean RT (MRT), standard deviation of RT (SD-RT), coefficient of variation (CV) and ex-Gaussian distribution measures of Mu, Sigma and Tau. In the slow-baseline condition, categorical diagnoses and trait measures converged to indicate that children with ADHD-only and ASD + ADHD demonstrated increased MRT, SD-RT, CV and Tau compared to TDC and ASD-only. Importantly, greater improvement in MRT, SD-RT and Tau was demonstrated in ADHD and ASD + ADHD from slow-baseline to fast-incentive conditions compared to TDC and ASD-only. Slower and more variable RTs are markers of ADHD compared to ASD and typically developing controls during slow and less rewarding conditions. Energetic factors and rewards improve task performance to a greater extent in children with ADHD compared to children with ASD. These findings suggest that RTV can be distinguished in ASD, ADHD and ASD + ADHD based on the indices of variability used and the conditions in which they are elicited. Further work identifying neural processes underlying increased RTV is warranted, in order to elucidate disorder-specific and disorder-convergent aetiological pathways. © 2016 The Authors. Journal of Child Psychology and Psychiatry published by John Wiley & Sons Ltd on behalf of Association for Child and Adolescent Mental Health.

Phase II multi-institutional clinical trial on a new mixed beam RT scheme of IMRT on pelvis combined with a carbon ion boost for high-risk prostate cancer patients.

PubMed

Marvaso, Giulia; Jereczek-Fossa, Barbara A; Vischioni, Barbara; Ciardo, Delia; Giandini, Tommaso; Hasegawa, Azusa; Cattani, Federica; Carrara, Mauro; Ciocca, Mario; Bedini, Nice; Villa, Sergio; Morlino, Sara; Russo, Stefania; Zerini, Dario; Colangione, Sarah Pia; Panaino, Costanza Maria Vittoria; Fodor, Cristiana; Santoro, Luigi; Pignoli, Emanuele; Valvo, Francesca; Valdagni, Riccardo; De Cobelli, Ottavio; Orecchia, Roberto

2017-05-12

Definition of the optimal treatment schedule for high-risk prostate cancer is under debate. A combination of photon intensity modulated radiotherapy (IMRT) on pelvis with a carbon ion boost might be the optimal treatment scheme to escalate the dose on prostate and deliver curative dose with respect to normal tissue and quality of dose distributions. In fact, carbon ion beams offer the advantage to deliver hypofractionated radiotherapy (RT) using a significantly smaller number of fractions compared to conventional RT without increasing risks of late effects. This study is a prospective phase II clinical trial exploring safety and feasibility of a mixed beam scheme of carbon ion prostate boost followed by photon IMRT on pelvis. The study is designed to enroll 65 patients with localized high-risk prostate cancer at 3 different oncologic hospitals: Istituto Europeo di Oncologia, Fondazione IRCCS Istituto Nazionale dei Tumori, and Centro Nazionale di Adroterapia Oncologica. The primary endpoint is the evaluation of safety and feasibility with acute toxicity scored up to 1 month after the end of RT. Secondary endpoints are treatment early (3 months after the end of RT) and long-term tolerability, quality of life, and efficacy. The study is not yet recruiting; in silico studies are ongoing and we expect to start recruitment by 2017. The present clinical trial aims at improving the current treatment for high-risk prostate cancer, evaluating safety and feasibility of a new RT mixed-beam scheme including photons and carbon ions. Encouraging results are coming from carbon ion facilities worldwide on the treatment of different tumors including prostate cancers. Carbon ions combine physical properties allowing for high dose conformity and advantageous radiobiological characteristics. The proposed mixed beam treatment has the advantage to combine a photon high conformity standard of care IMRT phase with a hypofractionated carbon ion RT boost delivered in a short overall treatment time.

Decoupling of reaction time-related default mode network activity with cognitive demand.

PubMed

Barber, Anita D; Caffo, Brian S; Pekar, James J; Mostofsky, Stewart H

2017-06-01

Reaction Time (RT) is associated with increased amplitude of the Blood Oxygen-Level Dependent (BOLD) response in task positive regions. Few studies have focused on whether opposing RT-related suppression of task activity also occurs. The current study used two Go/No-go tasks with different cognitive demands to examine regions that showed greater BOLD suppression for longer RT trials. These RT-related suppression effects occurred within the DMN and were task-specific, localizing to separate regions for the two tasks. In the task requiring working memory, RT-related de-coupling of the DMN occurred. This was reflected by opposing RT-BOLD effects for different DMN regions, as well as by reduced positive RT-related Psycho-Physiological Interaction (PPI) connectivity within the DMN and a lack of negative RT-related PPI connectivity between DMN and task positive regions. The results suggest that RT-related DMN suppression is task-specific. RT-related de-coupling of the DMN with more complex task demands may contribute to lapses of attention and performance decrements that occur during cognitively-demanding tasks.

Optimization of the elution buffer and concentration method for detecting hepatitis E virus in swine liver using a nested reverse transcription-polymerase chain reaction and real-time reverse transcription-polymerase chain reaction.

PubMed

Son, Na Ry; Seo, Dong Joo; Lee, Min Hwa; Seo, Sheungwoo; Wang, Xiaoyu; Lee, Bog-Hieu; Lee, Jeong-Su; Joo, In-Sun; Hwang, In-Gyun; Choi, Changsun

2014-09-01

The aim of this study was to develop an optimal technique for detecting hepatitis E virus (HEV) in swine livers. Here, three elution buffers and two concentration methods were compared with respect to enhancing recovery of HEV from swine liver samples. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR were performed to detect HEV RNA. When phosphate-buffered saline (PBS, pH 7.4) was used to concentrate HEV in swine liver samples using ultrafiltration, real-time RT-PCR detected HEV in 6 of the 26 samples. When threonine buffer was used to concentrate HEV using polyethylene glycol (PEG) precipitation and ultrafiltration, real-time RT-PCR detected HEV in 1 and 3 of the 26 samples, respectively. When glycine buffer was used to concentrate HEV using ultrafiltration and PEG precipitation, real-time RT-PCR detected HEV in 1 and 3 samples of the 26 samples, respectively. When nested RT-PCR was used to detect HEV, all samples tested negative regardless of the type of elution buffer or concentration method used. Therefore, the combination of real-time RT-PCR and ultrafiltration with PBS buffer was the most sensitive and reliable method for detecting HEV in swine livers. Copyright © 2014 Elsevier B.V. All rights reserved.

Development and comparative evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantification of West Nile virus in human patients.

PubMed

Kumar, Jyoti S; Saxena, Divyasha; Parida, Manmohan

2014-01-01

The recent outbreaks of West Nile Virus (WNV) in the Northeastern American continents and other regions of the world have made it essential to develop an efficient protocol for surveillance of WN virus. Nucleic acid based techniques like, RT-PCR have the advantage of sensitivity, specificity and rapidity. A one step single tube Env gene specific real-time RT-PCR was developed for early and reliable clinical diagnosis of WNV infection in clinical samples. The applicability of this assay for clinical diagnosis was validated with 105 suspected acute-phase serum and plasma samples from the recent epidemic of mysterious fever in Tamil Nadu, India in 2009-10. The comparative evaluation revealed the higher sensitivity of real-time RT-PCR assay by picking up 4 additional samples with low copy number of template in comparison to conventional RT-PCR. All the real-time positive samples further confirmed by CDC reported TaqMan real-time RT-PCR and quantitative real-time RT-PCR assays for the simultaneous detection of WNV lineage 1 and 2 strains. The quantitation of the viral load samples was done using a standard curve. These findings demonstrated that the assay has the potential usefulness for clinical diagnosis due to detection and quantification of WNV in acute-phase patient serum samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

A novel and highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus.

PubMed

Shen, Xin-Xin; Qiu, Fang-Zhou; Zhao, Huai-Long; Yang, Meng-Jie; Hong, Liu; Xu, Song-Tao; Zhou, Shuai-Feng; Li, Gui-Xia; Feng, Zhi-Shan; Ma, Xue-Jun

2018-03-01

The sensitivity of qRT-PCR assay is not adequate for the detection of the samples with lower viral load, particularly in the cerebrospinal fluid (CSF) of patients. Here, we present the development of a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of human enterovirus (HEV). The clinical performance of both RTN RT-PCR and qRT-PCR was also tested and compared using 140 CSF and fecal specimens. The sensitivities of RTN RT-PCR assay for EV71, Coxsackievirus A (CVA)16, CVA6 and CVA10 achieved 10 -8 dilution with a corresponding Ct value of 38.20, 36.45, 36.75, and 36.45, respectively, which is equal to traditional two-step nested RT-PCR assay and approximately 2-10-fold lower than that of qRT-PCR assay. The specificity of RTN RT-PCR assay was extensively analyzed insilico and subsequently verified using the reference isolates and clinical samples. Sixteen qRT-PCR-negative samples were detected by RTN RT-PCR and a variety of enterovirus serotypes was identified by sequencing of inner PCR products. We conclude RTN RT-PCR is more sensitive than qRT-PCR for the detection of HEV in clinical samples. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of travel distance and time to radiotherapy on likelihood of receiving mastectomy.

PubMed

Goyal, Sharad; Chandwani, Sheenu; Haffty, Bruce G; Demissie, Kitaw

2015-04-01

Breast-conserving surgery (BCS) followed by adjuvant radiation therapy (RT) is the standard of care for women with early-stage breast cancer as an alternative to mastectomy. The purpose of this study was to examine the relationship between receipt of mastectomy and travel distance and time to RT facility in New Jersey (NJ). Data were collected from a cohort of 634 NJ women diagnosed with early-stage breast cancer. In patients receiving RT, the precise RT facility was used, whereas in patients not receiving RT, surgeons were contacted to determine the location of RT referral. Travel distance and time to RT facility from the patients' residential address were modeled separately using multiple binomial regression to examine their association with choice of surgery while adjusting for clinical and sociodemographic factors. Overall, 58.5 % patients underwent BCS with median travel distance to the radiation facility of 4.8 miles (vs. 6.6 miles for mastectomy) and median travel time of 12.0 min (vs. 15.0 min for mastectomy). Patients residing > 9.2 miles compared with ≤ 9.2 miles from radiation facility were 44 % more likely to receive mastectomy. Additionally, patients requiring > 19 min compared with ≤ 19 min of travel time were 36 % more likely to receive mastectomy. These data found that travel distance and time from RT facility act as barriers to undergoing BCS in women with early-stage breast cancer. Despite being in an urban region, a significant number of women in NJ with early-stage breast cancer did not receive BCS.

Need for Resourcefulness Training for Women Caregivers of Elders with Dementia.

PubMed

Zauszniewski, Jaclene A; Lekhak, Nirmala; Yolpant, Wichiya; Morris, Diana L

2015-01-01

Nearly ten million American women are caregivers of elders with dementia and may experience overwhelming stress that adversely affects their mental health. Interventions to teach them resourcefulness skills for managing stress can promote optimal mental health and facilitate continued caregiving. However, effectiveness of resourcefulness training (RT) cannot be examined until its need is established. This pilot trial with 138 women caregivers of someone with dementia examined the need for RT using subjective and objective data. Data were collected before and after RT. Data analysis focused on baseline resourcefulness scores (higher scores = lower need); scores in relation to attrition; correlations among resourcefulness, stress, and depressive symptoms; and post-RT evaluation of the need for RT. Baseline resourcefulness scores were normally distributed and showed that 74% of the caregivers had a moderate to high need for RT. Reasons for attrition were unrelated to the need for RT; however, caregivers who dropped out had resourcefulness scores that averaged two points higher than those who remained in the study. Lower resourcefulness was associated greater stress (r = -.37, p < .001) and depressive symptoms (r = -.52, p < .001). Of the 63 caregivers who received RT, 82% (n = 52) reported a felt need for RT and 94% (n = 59) believed that other caregivers need RT. The results suggest a substantial need for resourcefulness training in women dementia caregivers and support moving forward to test RT's effectiveness for reducing caregiver stress and depressive symptoms.

Interval Between Hysterectomy and Start of Radiation Treatment Is Predictive of Recurrence in Patients With Endometrial Carcinoma

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

Cattaneo, Richard; Hanna, Rabbie K.; Jacobsen, Gordon

Purpose: Adjuvant radiation therapy (RT) has been shown to improve local control in patients with endometrial carcinoma. We analyzed the impact of the time interval between hysterectomy and RT initiation in patients with endometrial carcinoma. Methods and Materials: In this institutional review board-approved study, we identified 308 patients with endometrial carcinoma who received adjuvant RT after hysterectomy. All patients had undergone hysterectomy, oophorectomy, and pelvic and para-aortic lymph node evaluation from 1988 to 2010. Patients' demographics, pathologic features, and treatments were compared. The time interval between hysterectomy and the start of RT was calculated. The effects of time interval onmore » recurrence-free (RFS), disease-specific (DSS), and overall survival (OS) were calculated. Following univariate analysis, multivariate modeling was performed. Results: The median age and follow-up for the study cohort was 65 years and 72 months, respectively. Eighty-five percent of the patients had endometrioid carcinoma. RT was delivered with high-dose-rate brachytherapy alone (29%), pelvic RT alone (20%), or both (51%). Median time interval to start RT was 42 days (range, 21-130 days). A total of 269 patients (74%) started their RT <9 weeks after undergoing hysterectomy (group 1) and 26% started ≥9 weeks after surgery (group 2). There were a total of 43 recurrences. Tumor recurrence was significantly associated with treatment delay of ≥9 weeks, with 5-year RFS of 90% for group 1 compared to only 39% for group 2 (P<.001). On multivariate analysis, RT delay of ≥9 weeks (P<.001), presence of lymphovascular space involvement (P=.001), and higher International Federation of Gynecology and Obstetrics grade (P=.012) were independent predictors of recurrence. In addition, RT delay of ≥9 weeks was an independent significant predictor for worse DSS and OS (P=.001 and P=.01, respectively). Conclusions: Delay in administering adjuvant RT after hysterectomy was associated with worse survival endpoints. Our data suggest that shorter time interval between hysterectomy and start of RT may be beneficial.« less

Benefits of Resistance Training with Blood Flow Restriction in Knee Osteoarthritis.

PubMed

Ferraz, Rodrigo Branco; Gualano, Bruno; Rodrigues, Reynaldo; Kurimori, Ceci Obara; Fuller, Ricardo; Lima, Fernanda Rodrigues; DE Sá-Pinto, Ana Lúcia; Roschel, Hamilton

2018-05-01

Evaluate the effects of a low-intensity resistance training (LI-RT) program associated with partial blood flow restriction on selected clinical outcomes in patients with knee osteoarthritis (OA). Forty-eight women with knee OA were randomized into one of the three groups: LI-RT (30% one repetition maximum [1-RM]) associated (blood flow restriction training [BFRT]) or not (LI-RT) with partial blood flow restriction, and high-intensity resistance training (HI-RT, 80% 1-RM). Patients underwent a 12-wk supervised training program and were assessed for lower-limb 1-RM, quadriceps cross-sectional area, functionality (timed-stands test and timed-up-and-go test), and disease-specific inventory (Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC]) before (PRE) and after (POST) the protocol. Similar within-group increases were observed in leg press (26% and 33%, all P < 0.0001), knee extension 1-RM (23% and 22%; all P < 0.0001) and cross-sectional area (7% and 8%; all P < 0.0001) in BFRT and HI-RT, respectively, and these were significantly greater (all P < 0.05) than those of LI-RT. The BFRT and HI-RT showed comparable improvements in timed-stands test (7% and 14%, respectively), with the latter showing greater increases than LI-RT. Timed-up-and-go test scores were not significantly changed within or between groups. WOMAC physical function was improved in BFRT and HI-RT (-49% and -42%, respectively; all P < 0.05), and WOMAC pain was improved in BFRT and LI-RT (-45% and -39%, respectively; all P < 0.05). Four patients (of 16) were excluded due to exercise-induced knee pain in HI-RT. Blood flow restriction training and HI-RT were similarly effective in increasing muscle strength, quadriceps muscle mass, and functionality in knee OA patients. Importantly, BFRT was also able to improve pain while inducing less joint stress, emerging as a feasible and effective therapeutic adjuvant in OA management.

Effective Analysis of Reaction Time Data

ERIC Educational Resources Information Center

Whelan, Robert

2008-01-01

Most analyses of reaction time (RT) data are conducted by using the statistical techniques with which psychologists are most familiar, such as analysis of variance on the sample mean. Unfortunately, these methods are usually inappropriate for RT data, because they have little power to detect genuine differences in RT between conditions. In…

A novel duplex real time quantitative reverse transcription polymerase chain reaction for rubella virus with armored RNA as a noncompetitive internal positive control.

PubMed

Zhao, Lihong; Li, Ruiying; Liu, Aihua; Zhao, Shuping

2015-07-01

The objective of this study was to build and apply a duplex real time quantitative reverse transcription-polymerase chain reaction (RT-PCR) for rubella virus. Firstly, a 60-bp-long armored RV RNA was constructed in the laboratory. Secondly, a duplex real time RT-PCR assay was established. Thirdly, the 60-bp-long armored RV RNA was used as an internal positive control (IPC) for the duplex real time RT-PCR. And finally the duplex real time RT-PCR assay was applied to detect RV RNA in clinical specimens. The in-house assay has a high amplification efficiency (0.99), a high analytical sensitivity (200 copies/mL), and a good reproducibility. The diagnostic specificity and sensitivity of the in-house assay were both 100%, due to the monitoring of the armored RV RNA IPC. Therefore, the in-house duplex real time quantitative RT-PCR assay is a specific, sensitive, reproducible and accurate assay for quantitation of RV RNA in clinical specimens. And noncompetitive armored RV RNA IPC can monitor RT-PCR inhibition and prevent false-negative and inaccurate results in the real time detection system. Copyright © 2015 Elsevier B.V. All rights reserved.

Blind estimation of reverberation time

NASA Astrophysics Data System (ADS)

Ratnam, Rama; Jones, Douglas L.; Wheeler, Bruce C.; O'Brien, William D.; Lansing, Charissa R.; Feng, Albert S.

2003-11-01

The reverberation time (RT) is an important parameter for characterizing the quality of an auditory space. Sounds in reverberant environments are subject to coloration. This affects speech intelligibility and sound localization. Many state-of-the-art audio signal processing algorithms, for example in hearing-aids and telephony, are expected to have the ability to characterize the listening environment, and turn on an appropriate processing strategy accordingly. Thus, a method for characterization of room RT based on passively received microphone signals represents an important enabling technology. Current RT estimators, such as Schroeder's method, depend on a controlled sound source, and thus cannot produce an online, blind RT estimate. Here, a method for estimating RT without prior knowledge of sound sources or room geometry is presented. The diffusive tail of reverberation was modeled as an exponentially damped Gaussian white noise process. The time-constant of the decay, which provided a measure of the RT, was estimated using a maximum-likelihood procedure. The estimates were obtained continuously, and an order-statistics filter was used to extract the most likely RT from the accumulated estimates. The procedure was illustrated for connected speech. Results obtained for simulated and real room data are in good agreement with the real RT values.

Online estimation of room reverberation time

NASA Astrophysics Data System (ADS)

Ratnam, Rama; Jones, Douglas L.; Wheeler, Bruce C.; Feng, Albert S.

2003-04-01

The reverberation time (RT) is an important parameter for characterizing the quality of an auditory space. Sounds in reverberant environments are subject to coloration. This affects speech intelligibility and sound localization. State-of-the-art signal processing algorithms for hearing aids are expected to have the ability to evaluate the characteristics of the listening environment and turn on an appropriate processing strategy accordingly. Thus, a method for the characterization of room RT based on passively received microphone signals represents an important enabling technology. Current RT estimators, such as Schroeder's method or regression, depend on a controlled sound source, and thus cannot produce an online, blind RT estimate. Here, we describe a method for estimating RT without prior knowledge of sound sources or room geometry. The diffusive tail of reverberation was modeled as an exponentially damped Gaussian white noise process. The time constant of the decay, which provided a measure of the RT, was estimated using a maximum-likelihood procedure. The estimates were obtained continuously, and an order-statistics filter was used to extract the most likely RT from the accumulated estimates. The procedure was illustrated for connected speech. Results obtained for simulated and real room data are in good agreement with the real RT values.

Respiratory Therapy Faculty Knowledge of and Attitudes Toward Interprofessional Education.

PubMed

Vernon, Marlo M; Moore, Nicole M; Cummins, Lisa-Anne; Reyes, Stephanie E; Mazzoli, Andrew J; Heboyan, Vahe; De Leo, Gianluca

2017-07-01

Interprofessional education (IPE) improves collaboration and patient care through joint education between health professions. Respiratory therapy (RT) faculty were surveyed to evaluate their knowledge and attitudes toward IPE. We report current opportunities for IPE from faculty and compare responses from associate's, bachelor's, and master's degree programs and profit versus nonprofit institutions. We developed an online survey based on IPE literature and questions modified for the RT discipline. The survey was distributed by email to 874 faculty from the Commission on Accreditation for Respiratory Care accredited programs. The response rate was 33%. Faculty identified IPE as an important component of RT education ( n = 207, 80%) but reported challenges in integrating IPE into current curriculum. Overall, communication was ranked as the most important IPE competency ( n = 104, 39%) and ethics least important ( n = 131, 49%). When asked how many credit hours are required to teach IPE, 48% of respondents reported that they were unsure of an appropriate time requirement. Significant differences between associate's and bachelor's/master's degree program faculty were found on the following topics: institutional resources needed for IPE ( P < .001), faculty availability ( P < .001), curriculum availability for IPE ( P = .02), and importance of including IPE at academic health center campuses ( P < .001). IPE is recognized as an important component of RT education by all faculty respondents. However, significant differences in knowledge and attitudes toward IPE exist between faculty in associate's versus bachelor's/master's degree programs. Revisiting the current accreditation standards program may allow IPE to take a more prominent role in RT curricula. Copyright © 2017 by Daedalus Enterprises.

Comparisons of vegetarian and beef-containing diets on hematological indexes and iron stores during a period of resistive training in older men

PubMed Central

Wells, Amanda M.; Haub, Mark D.; Fluckey, James; Williams, D. Keith; Chernoff, Ronni; Campbell, Wayne W.

2008-01-01

Objective To test the hypothesis that older men who consumed a vegetarian (lacto-ovo) diet would develop a lower iron status compared with older men who consumed a beef-containing diet during a period of resistive training (RT). Design Experimental, repeated measures study. Subjects Twenty-one healthy men aged 59 to 78 years, with a BMI range of 24 to 33 kg/m2, completed the study. Intervention All men consumed a vegetarian diet for 2 weeks (baseline). After this, the men were randomly assigned to one of two dietary groups. Eleven men consumed a beef-containing diet, and 10 men continued to consume a vegetarian diet for 12 weeks. During this time all subjects participated in RT three days per week, designated as RT1 to RT12. Main outcome measures Serum ferritin and serum iron concentrations, transferrin saturation, transferrin receptor, total iron binding capacity, and selected hematological variables, as well as selected nutrient intakes and estimated iron bioavailability from three-day diet records, were determined at baseline, RT5, and RT12. Statistical analyses A general linear model repeated-measures ANOVA was used to examine the effects of group, time, and group×time interactions for iron status and dietary data. Results Total iron intake was not different between the two groups; however, the beef group had a three to four times greater intake of bioavailable iron (P<.01) than the vegetarian group. Serum iron, total iron binding capacity, transferrin saturation, and transferrin receptor were not significantly different between the beef and vegetarian groups, or changed over time with RT. Serum ferritin decreased over time in both the beef and vegetarian groups during RT (P<.01). Re-introduction of beef into the diets of the beef group increased hemoglobin concentration and hematocrit compared with the vegetarian group during the 12 weeks of RT (group×time, P<.05). These changes were within clinically normal limits. Applications/Conclusions Older men who consume a beef-containing, higher-bioavailable-iron diet, compared with a vegetarian, lower-bioavailable-iron diet, have an increased hematological profile during a 12-week period of RT. Older men who consume either a beef-containing or a vegetarian diet maintain a hematological profile within clinically normal limits during 12 weeks of RT. PMID:12728219

Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species.

PubMed

Soltan, Mohamed A; Tsai, Yun-Long; Lee, Pei-Yu A; Tsai, Chuan-Fu; Chang, Hsiao-Fen G; Wang, Hwa-Tang T; Wilkes, Rebecca P

2016-09-01

There is no gold standard for detection of Rotavirus Group A (RVA), one of the main causes of diarrhea in neonatal animals. Sensitive and specific real-time RT-PCR (rtRT-PCR) assays are available for RVA but require submission of the clinical samples to diagnostic laboratories. Patient-side immunoassays for RVA protein detection have shown variable results, particularly with samples from unintended species. A sensitive and specific test for detection of RVA on the farm would facilitate rapid management decisions. The insulated isothermal RT-PCR (RT-iiPCR) assay works in a portable machine to allow sensitive and specific on-site testing. The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. This assay was compared to an in-house rtRT-PCR assay and a commercially available rtRT-PCR kit, as well as an ELISA and EM for RVA detection. All three PCR assays targeted the well-conserved NSP5 gene. Clinical fecal samples from 108 diarrheic animals (mainly cattle and horses) were tested. The percentage of positive samples by ELISA, EM, in-house rtRT-PCR, commercial rtRT-PCR, and RT-iiPCR was 29.4%, 31%, 36.7%, 51.4%, 56.9%, respectively. The agreement between different assays was high (81.3-100%) in samples containing high viral loads. The sensitivity of the RT-iiPCR assay appeared to be higher than the commercially available rtRT-PCR assay, with a limit of detection (95% confidence index) of 3-4 copies of in vitro transcribed dsRNA. In conclusion, the user-friendly, field-deployable RT-iiPCR system holds substantial promise for on-site detection of RVA. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Charge-Coupled Devices for Analog Signal Processing -- A Circuit Study

DTIC Science & Technology

1976-03-01

FNG( T+H/2) ) /H (X2»Y3»Z2) 1*2*K2-^2*K3*’ɜ) /o.3 ECK TO SEE IF IT’S TIME TO PRINT OUT. SGN(L)*1.’.5E-9>=i^«𔃽 THEN 1120 80 ^^^^ LEI rt=b 113^ LEI a...DISTRIBUTION LIST No. Copies 1. Defense Docmnentation Center 2 Cameron Station Alexandria, Virginia 22314 2. Library, Code 0212 2 Naval Postgraduate School

Intra-Individual Response Variability Assessed by Ex-Gaussian Analysis may be a New Endophenotype for Attention-Deficit/Hyperactivity Disorder.

PubMed

Henríquez-Henríquez, Marcela Patricia; Billeke, Pablo; Henríquez, Hugo; Zamorano, Francisco Javier; Rothhammer, Francisco; Aboitiz, Francisco

2014-01-01

Intra-individual variability of response times (RTisv) is considered as potential endophenotype for attentional deficit/hyperactivity disorder (ADHD). Traditional methods for estimating RTisv lose information regarding response times (RTs) distribution along the task, with eventual effects on statistical power. Ex-Gaussian analysis captures the dynamic nature of RTisv, estimating normal and exponential components for RT distribution, with specific phenomenological correlates. Here, we applied ex-Gaussian analysis to explore whether intra-individual variability of RTs agrees with criteria proposed by Gottesman and Gould for endophenotypes. Specifically, we evaluated if normal and/or exponential components of RTs may (a) present the stair-like distribution expected for endophenotypes (ADHD > siblings > typically developing children (TD) without familiar history of ADHD) and (b) represent a phenotypic correlate for previously described genetic risk variants. This is a pilot study including 55 subjects (20 ADHD-discordant sibling-pairs and 15 TD children), all aged between 8 and 13 years. Participants resolved a visual Go/Nogo with 10% Nogo probability. Ex-Gaussian distributions were fitted to individual RT data and compared among the three samples. In order to test whether intra-individual variability may represent a correlate for previously described genetic risk variants, VNTRs at DRD4 and SLC6A3 were identified in all sibling-pairs following standard protocols. Groups were compared adjusting independent general linear models for the exponential and normal components from the ex-Gaussian analysis. Identified trends were confirmed by the non-parametric Jonckheere-Terpstra test. Stair-like distributions were observed for μ (p = 0.036) and σ (p = 0.009). An additional "DRD4-genotype" × "clinical status" interaction was present for τ (p = 0.014) reflecting a possible severity factor. Thus, normal and exponential RTisv components are suitable as ADHD endophenotypes.

Predictive Models for Regional Hepatic Function Based on 99mTc-IDA SPECT and Local Radiation Dose for Physiologic Adaptive Radiation Therapy

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

Wang, Hesheng, E-mail: hesheng@umich.edu; Feng, Mary; Frey, Kirk A.

2013-08-01

Purpose: High-dose radiation therapy (RT) for intrahepatic cancer is limited by the development of liver injury. This study investigated whether regional hepatic function assessed before and during the course of RT using 99mTc-labeled iminodiacetic acid (IDA) single photon emission computed tomography (SPECT) could predict regional liver function reserve after RT. Methods and Materials: Fourteen patients treated with RT for intrahepatic cancers underwent dynamic 99mTc-IDA SPECT scans before RT, during, and 1 month after completion of RT. Indocyanine green (ICG) tests, a measure of overall liver function, were performed within 1 day of each scan. Three-dimensional volumetric hepatic extraction fraction (HEF)more » images of the liver were estimated by deconvolution analysis. After coregistration of the CT/SPECT and the treatment planning CT, HEF dose–response functions during and after RT were generated. The volumetric mean of the HEFs in the whole liver was correlated with ICG clearance time. Three models, dose, priori, and adaptive models, were developed using multivariate linear regression to assess whether the regional HEFs measured before and during RT helped predict regional hepatic function after RT. Results: The mean of the volumetric liver HEFs was significantly correlated with ICG clearance half-life time (r=−0.80, P<.0001), for all time points. Linear correlations between local doses and regional HEFs 1 month after RT were significant in 12 patients. In the priori model, regional HEF after RT was predicted by the planned dose and regional HEF assessed before RT (R=0.71, P<.0001). In the adaptive model, regional HEF after RT was predicted by regional HEF reassessed during RT and the remaining planned local dose (R=0.83, P<.0001). Conclusions: 99mTc-IDA SPECT obtained during RT could be used to assess regional hepatic function and helped predict post-RT regional liver function reserve. This could support individualized adaptive radiation treatment strategies to maximize tumor control and minimize the risk of liver damage.« less

Predictive models for regional hepatic function based on 99mTc-IDA SPECT and local radiation dose for physiologic adaptive radiation therapy.

PubMed

Wang, Hesheng; Feng, Mary; Frey, Kirk A; Ten Haken, Randall K; Lawrence, Theodore S; Cao, Yue

2013-08-01

High-dose radiation therapy (RT) for intrahepatic cancer is limited by the development of liver injury. This study investigated whether regional hepatic function assessed before and during the course of RT using 99mTc-labeled iminodiacetic acid (IDA) single photon emission computed tomography (SPECT) could predict regional liver function reserve after RT. Fourteen patients treated with RT for intrahepatic cancers underwent dynamic 99mTc-IDA SPECT scans before RT, during, and 1 month after completion of RT. Indocyanine green (ICG) tests, a measure of overall liver function, were performed within 1 day of each scan. Three-dimensional volumetric hepatic extraction fraction (HEF) images of the liver were estimated by deconvolution analysis. After coregistration of the CT/SPECT and the treatment planning CT, HEF dose-response functions during and after RT were generated. The volumetric mean of the HEFs in the whole liver was correlated with ICG clearance time. Three models, dose, priori, and adaptive models, were developed using multivariate linear regression to assess whether the regional HEFs measured before and during RT helped predict regional hepatic function after RT. The mean of the volumetric liver HEFs was significantly correlated with ICG clearance half-life time (r=-0.80, P<.0001), for all time points. Linear correlations between local doses and regional HEFs 1 month after RT were significant in 12 patients. In the priori model, regional HEF after RT was predicted by the planned dose and regional HEF assessed before RT (R=0.71, P<.0001). In the adaptive model, regional HEF after RT was predicted by regional HEF reassessed during RT and the remaining planned local dose (R=0.83, P<.0001). 99mTc-IDA SPECT obtained during RT could be used to assess regional hepatic function and helped predict post-RT regional liver function reserve. This could support individualized adaptive radiation treatment strategies to maximize tumor control and minimize the risk of liver damage. Published by Elsevier Inc.

ScriptingRT: A Software Library for Collecting Response Latencies in Online Studies of Cognition

PubMed Central

Schubert, Thomas W.; Murteira, Carla; Collins, Elizabeth C.; Lopes, Diniz

2013-01-01

ScriptingRT is a new open source tool to collect response latencies in online studies of human cognition. ScriptingRT studies run as Flash applets in enabled browsers. ScriptingRT provides the building blocks of response latency studies, which are then combined with generic Apache Flex programming. Six studies evaluate the performance of ScriptingRT empirically. Studies 1–3 use specialized hardware to measure variance of response time measurement and stimulus presentation timing. Studies 4–6 implement a Stroop paradigm and run it both online and in the laboratory, comparing ScriptingRT to other response latency software. Altogether, the studies show that Flash programs developed in ScriptingRT show a small lag and an increased variance in response latencies. However, this did not significantly influence measured effects: The Stroop effect was reliably replicated in all studies, and the found effects did not depend on the software used. We conclude that ScriptingRT can be used to test response latency effects online. PMID:23805326

The influence of pretreatment characteristics and radiotherapy parameters on time interval to development of radiation-associated meningioma.

PubMed

Paulino, Arnold C; Ahmed, Irfan M; Mai, Wei Y; Teh, Bin S

2009-12-01

To identify pretreatment characteristics and radiotherapy parameters which may influence time interval to development of radiation-associated meningioma (RAM). A Medline/PUBMED search of articles dealing with RAM yielded 66 studies between 1981 and 2006. Factors analyzed included patient age and gender, type of initial tumor treated, radiotherapy (RT) dose and volume, and time interval from RT to development of RAM. A total of 143 patients with a median age at RT of 12 years form the basis of this report. The most common initial tumors or conditions treated with RT were medulloblastoma (n = 27), pituitary adenoma (n = 20), acute lymphoblastic leukemia (n = 20), low-grade astrocytoma (n = 19), and tinea capitis (n = 14). In the 116 patients whose RT fields were known, 55 (47.4%) had a portion of the brain treated, whereas 32 (27.6%) and 29 (25.0%) had craniospinal and whole-brain fields. The median time from RT to develop a RAM or latent time (LT) was 19 years (range, 1-63 years). Male gender (p = 0.001), initial diagnosis of leukemia (p = 0.001), and use of whole brain or craniospinal field (p

The Influence of Pretreatment Characteristics and Radiotherapy Parameters on Time Interval to Development of Radiation-Associated Meningioma

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

Paulino, Arnold C., E-mail: apaulino@tmhs.or; Ahmed, Irfan M.; Mai, Wei Y.

2009-12-01

Purpose: To identify pretreatment characteristics and radiotherapy parameters which may influence time interval to development of radiation-associated meningioma (RAM). Methods and Materials: A Medline/PUBMED search of articles dealing with RAM yielded 66 studies between 1981 and 2006. Factors analyzed included patient age and gender, type of initial tumor treated, radiotherapy (RT) dose and volume, and time interval from RT to development of RAM. Results: A total of 143 patients with a median age at RT of 12 years form the basis of this report. The most common initial tumors or conditions treated with RT were medulloblastoma (n = 27), pituitarymore » adenoma (n = 20), acute lymphoblastic leukemia (n = 20), low-grade astrocytoma (n = 19), and tinea capitis (n = 14). In the 116 patients whose RT fields were known, 55 (47.4%) had a portion of the brain treated, whereas 32 (27.6%) and 29 (25.0%) had craniospinal and whole-brain fields. The median time from RT to develop a RAM or latent time (LT) was 19 years (range, 1-63 years). Male gender (p = 0.001), initial diagnosis of leukemia (p = 0.001), and use of whole brain or craniospinal field (p <= 0.0001) were associated with a shorter LT, whereas patients who received lower doses of RT had a longer LT (p < 0.0001). Conclusions: The latent time to develop a RAM was related to gender, initial tumor type, radiotherapy volume, and radiotherapy dose.« less

A Graphics Processing Unit Accelerated Motion Correction Algorithm and Modular System for Real-time fMRI

PubMed Central

Scheinost, Dustin; Hampson, Michelle; Qiu, Maolin; Bhawnani, Jitendra; Constable, R. Todd; Papademetris, Xenophon

2013-01-01

Real-time functional magnetic resonance imaging (rt-fMRI) has recently gained interest as a possible means to facilitate the learning of certain behaviors. However, rt-fMRI is limited by processing speed and available software, and continued development is needed for rt-fMRI to progress further and become feasible for clinical use. In this work, we present an open-source rt-fMRI system for biofeedback powered by a novel Graphics Processing Unit (GPU) accelerated motion correction strategy as part of the BioImage Suite project (www.bioimagesuite.org). Our system contributes to the development of rt-fMRI by presenting a motion correction algorithm that provides an estimate of motion with essentially no processing delay as well as a modular rt-fMRI system design. Using empirical data from rt-fMRI scans, we assessed the quality of motion correction in this new system. The present algorithm performed comparably to standard (non real-time) offline methods and outperformed other real-time methods based on zero order interpolation of motion parameters. The modular approach to the rt-fMRI system allows the system to be flexible to the experiment and feedback design, a valuable feature for many applications. We illustrate the flexibility of the system by describing several of our ongoing studies. Our hope is that continuing development of open-source rt-fMRI algorithms and software will make this new technology more accessible and adaptable, and will thereby accelerate its application in the clinical and cognitive neurosciences. PMID:23319241

A graphics processing unit accelerated motion correction algorithm and modular system for real-time fMRI.

PubMed

Scheinost, Dustin; Hampson, Michelle; Qiu, Maolin; Bhawnani, Jitendra; Constable, R Todd; Papademetris, Xenophon

2013-07-01

Real-time functional magnetic resonance imaging (rt-fMRI) has recently gained interest as a possible means to facilitate the learning of certain behaviors. However, rt-fMRI is limited by processing speed and available software, and continued development is needed for rt-fMRI to progress further and become feasible for clinical use. In this work, we present an open-source rt-fMRI system for biofeedback powered by a novel Graphics Processing Unit (GPU) accelerated motion correction strategy as part of the BioImage Suite project ( www.bioimagesuite.org ). Our system contributes to the development of rt-fMRI by presenting a motion correction algorithm that provides an estimate of motion with essentially no processing delay as well as a modular rt-fMRI system design. Using empirical data from rt-fMRI scans, we assessed the quality of motion correction in this new system. The present algorithm performed comparably to standard (non real-time) offline methods and outperformed other real-time methods based on zero order interpolation of motion parameters. The modular approach to the rt-fMRI system allows the system to be flexible to the experiment and feedback design, a valuable feature for many applications. We illustrate the flexibility of the system by describing several of our ongoing studies. Our hope is that continuing development of open-source rt-fMRI algorithms and software will make this new technology more accessible and adaptable, and will thereby accelerate its application in the clinical and cognitive neurosciences.

Anxiety and its time courses during radiotherapy for non-metastatic breast cancer: a longitudinal study.

PubMed

Lewis, Florence; Merckaert, Isabelle; Liénard, Aurore; Libert, Yves; Etienne, Anne-Marie; Reynaert, Christine; Slachmuylder, Jean-Louis; Scalliet, Pierre; Paul, Van Houtte; Coucke, Philippe; Salamon, Emile; Razavi, Darius

2014-05-01

To our knowledge, no study has specifically assessed the time course of anxiety during radiotherapy (RT). The objective of this study was to assess anxiety time courses in patients with non-metastatic breast cancer. This multicenter, descriptive longitudinal study included 213 consecutive patients with breast cancer who completed visual analog scales (VASs) assessing state anxiety before and after the RT simulation and the first and last five RT sessions. Pre- and post-session anxiety mean levels were highest at the RT simulation (respectively, 2.9±2.9 and 1.6±2.5) and first RT session (respectively, 3.4±2.9 and 2.0±2.4), then declined rapidly. Clinically relevant mean differences (⩾1cm on the VAS) between pre- and post-simulation/session VAS scores were found only for the RT simulation (-1.3±2.7; p<0.001) and first RT session (-1.4±2.4; p<0.001). Five percent to 16% of patients presented clinically relevant anxiety (pre- and post-simulation/session VAS scores⩾4cm) throughout treatment. To optimize care, RT team members should offer all patients appropriate information about treatment at the simulation, check patients' understanding, and identify patients with clinically relevant anxiety requiring appropriate support throughout RT. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Rapid and sensitive detection of canine distemper virus by one-tube reverse transcription-insulated isothermal polymerase chain reaction.

PubMed

Wilkes, Rebecca P; Tsai, Yun-Long; Lee, Pei-Yu; Lee, Fu-Chun; Chang, Hsiao-Fen Grace; Wang, Hwa-Tang Thomas

2014-09-09

Canine distemper virus (CDV) has been associated with outbreaks of canine infectious respiratory disease in shelters and boarding kennel environments. POCKITTM Nucleic Acid Analyzer is a field-deployable device capable of generating automatically interpreted insulated isothermal polymerase chain reaction (iiPCR) results from extracted nucleic acid within one hour. In this study, reverse transcription iiPCR (RT-iiPCR) was developed to facilitate point-of-need diagnosis of CDV infection. Analytical sensitivity (limit of detection 95%) of the established CDV RT-iiPCR was about 11 copies of in vitro transcribed RNA per reaction. CDV RT-iiPCR generated positive signals from CDV, but not Bordetella bronchiseptica, canine parvovirus, canine herpesvirus, canine adenovirus 2, canine influenza virus (subtype H3N8), canine parainfluenza virus, and canine respiratory coronavirus. To evaluate accuracy of the established reaction in canine distemper clinical diagnosis, 110 specimens from dogs, raccoons, and foxes suspected with CDV infection were tested simultaneously by CDV RT-iiPCR and real-time RT-PCR. CDV RT-iiPCR demonstrated excellent sensitivity (100%) and specificity (100%), compared to real-time RT-PCR. The results indicated an excellent correlation between RT-iiPCR and a reference real time RT-PCR method. Working in a lyophilized format, the established method has great potential to be used for point-of-care diagnosis of canine distemper in animals, especially in resource-limited facilities.

Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler's murine encephalomyelitis virus and rat theilovirus.

PubMed

Yuan, Wen; Wang, Jing; Xu, Fengjiao; Huang, Bihong; Lian, Yuexiao; Rao, Dan; Yin, Xueqin; Wu, Miaoli; Zhu, Yujun; Zhang, Yu; Huang, Ren; Guo, Pengju

2016-10-01

Theiler's murine encephalomyelitis virus (TMEV) and rat theilovirus (RTV), the member of the genus Cardiovirus, are widespread in laboratory mice and rats, and are potential contaminants of biological materials. Cardioviruses infection may cause serious complications in biomedical research. To improve the efficiency of routine screening for Cardioviruses infection, a duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection and differentiation of TMEV and RTV. The duplex assay was specific for reference strains of TMEV and RTV, and no cross-reaction was found with seven other rodent viruses. The limits of detection of both TMEV and RTV were 4×10(1) copies RNA/reaction. Reproducibility was estimated using standard dilutions, with coefficients of variation <3.1%. 439 clinical samples were evaluated by both duplex real-time RT-PCR and conventional RT-PCR. For 439 clinical samples，95 samples were positive for TMEV and 72 samples were positive for RTV using duplex real-time RT-PCR approach, whereas only 77 samples were positive for TMEV and 66 samples were positive for RTV when conventional RT-PCR was applied. Mixed infections were found in 20 samples when analyzed by conventional RT-PCR whereas 30 samples were found to be mixed infection when duplex real-time RT-PCR was applied. This duplex assay provides a useful tool for routine health monitoring and screening of contaminated biological materials of these two viruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Sequence Optimized Real-Time RT-PCR Assay for Detection of Crimean-Congo Hemorrhagic Fever Virus

DTIC Science & Technology

2017-03-21

19-23]. Real-56 time reverse-transcription PCR remains the gold standard for quantitative , sensitive, and specific 57 detection of CCHFV; however...five-fold in two different series , and samples were run by real- time RT-PCR 116 in triplicate. The preliminary LOD was the lowest RNA dilution where...1 Sequence optimized real- time RT-PCR assay for detection of Crimean-Congo hemorrhagic fever 1 virus 2 3 JW Koehler1, KL Delp1, AT Hall1, SP

Stability of Spinal Bone Lesions in Patients With Multiple Myeloma After Radiotherapy-A Retrospective Analysis of 130 Cases.

PubMed

Lang, Kristin; König, Laila; Bruckner, Thomas; Förster, Robert; Sprave, Tanja; Schlampp, Ingmar; Bostel, Tilman; Welte, Stefan; Nicolay, Nils H; Debus, Jürgen; Rief, Harald

2017-12-01

The objective of the present retrospective analysis was the response evaluation regarding bone density and stability of patients with osteolytic spinal bone lesions due to multiple myeloma after palliative radiotherapy (RT). Patients with multiple myeloma who had undergone spinal RT from March 2003 to May 2016 were analyzed before and 3 and 6 months after RT. Assessment of spinal stability and bone density was performed using the internationally recognized Taneichi scoring system and measurement of bone density using computed tomography imaging-based Hounsfield units. For statistical analysis, we used the Bowker test, McNemar test, and κ statistics to detect possible asymmetries in the distribution of the Taneichi score over time. We used the Student t test for comparison of the density values (Hounsfield units) before and after treatment. Toxicity was evaluated using the Common Terminology Criteria for Adverse Events, version 4.0. Additionally, overall survival was calculated using the Kaplan-Meier method. We evaluated 130 patients (69% male; 31% female) with multiple myeloma and a median age of 58 years. The median follow-up period was 41 months. Before treatment, 51% of the lesions were classified as unstable. At 3 and 6 months after RT, this rate had decreased to 41% (P = .0047) and 24% (P = .2393), respectively. The computed tomography measurements showed a significant increase in bone density at 3 and 6 months after RT. Acute RT-related grade 1 and 2 complications were detected in 34% of patients. Late side effects (grade 1-2) were detected in 23% of the patients. No severe grade 3 or 4 acute or late toxicities were identified. The median overall survival was 19.7 months for all patients and 6.6 months for patients with a Karnofsky performance score of ≤ 70%. To the best of our knowledge, ours is the first report to analyze the bone density and stability in patients with multiple myeloma after RT using a validated scoring system and computed tomography imaging. Palliative RT is an effective method resulting in a significant increase in bone density for local response and stability without severe RT-related toxicity. Furthermore, recalcification could already be detected at 3 months after treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP), a light for mammalian transcript analysis in low-input laboratories.

PubMed

Pandey, Mamta; Singh, Dheer; Onteru, Suneel K

2018-06-01

Transcript analysis is usually performed by costly, time-consuming, and expertise intensive methods, like real time-PCR, microarray, etc. However, they are not much feasible in low-input laboratories. Therefore, we implemented the reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a means of mammalian transcript analysis. Particularly, RT-LAMP was developed for buffalo aromatase cytochrome P450 (CYP19) transcript, to study its expression in 3D-cultured buffalo granulosa cells, which were exposed to lipopolysaccharide (LPS). The CYP19-RT-LAMP assay rapidly identified the LPS-induced downregulation of the CYP19 gene within 30 min at 63°C in a water bath. The assay was visualized via unaided eye by observing the change in turbidity and fluorescence, which were decreased by increasing the LPS exposure time to granulosa cells. Overall, the developed CYP19-RT-LAMP assay provided a hope on the application of RT-LAMP for mammalian transcript analysis in low-input laboratories. © 2017 Wiley Periodicals, Inc.

Expansion of the Real-Time SPoRT-Land Information System for NOAA/National Weather Service Situational Awareness and Local Modeling Applications

NASA Technical Reports Server (NTRS)

Case, Jonathan L; White, Kristopher D.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center in Huntsville, AL is running a real-time configuration of the Noah land surface model (LSM) within the NASA Land Information System (LIS) framework (hereafter referred to as the "SPoRT-LIS"). Output from the real-time SPoRT-LIS is used for (1) initializing land surface variables for local modeling applications, and (2) displaying in decision support systems for situational awareness and drought monitoring at select NOAA/National Weather Service (NWS) partner offices. The experimental CONUS run incorporates hourly quantitative precipitation estimation (QPE) from the National Severe Storms Laboratory Multi- Radar Multi-Sensor (MRMS) which will be transitioned into operations at the National Centers for Environmental Prediction (NCEP) in Fall 2014.This paper describes the current and experimental SPoRT-LIS configurations, and documents some of the limitations still remaining through the advent of MRMS precipitation analyses in the SPoRT-LIS land surface model (LSM) simulations.

Energy balance in a Z pinch with suppressed Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Baksht, R. B.; Oreshkin, V. I.; Rousskikh, A. G.; Zhigalin, A. S.

2018-03-01

At present Z-pinch has evolved into a powerful plasma source of soft x-ray. This paper considers the energy balance in a radiating metallic gas-puff Z pinch. In this type of Z pinch, a power-law density distribution is realized, promoting suppression of Rayleigh-Taylor (RT) instabilities that occur in the pinch plasma during compression. The energy coupled into the pinch plasma, is determined as the difference between the total energy delivered to the load from the generator and the magnetic energy of the load inductance. A calibrated voltage divider and a Rogowski coil were used to determine the coupled energy and the load inductance. Time-gated optical imaging of the pinch plasma showed its stable compression up to the stagnation phase. The pinch implosion was simulated using a 1D two-temperature radiative magnetohydrodynamic code. Comparison of the experimental and simulation results has shown that the simulation adequately describes the pinch dynamics for conditions in which RT instability is suppressed. It has been found that the proportion of the Ohmic heating in the energy balance of a Z pinch with suppressed RT instability is determined by Spitzer resistance and makes no more than ten percent.

[Molecular characterization of heterozygous beta-thalassemia in Lanzarote, Spain].

PubMed

Calvo-Villas, José Manuel; de la Iglesia Iñigo, Silvia; Ropero Gradilla, Paloma; Zapata Ramos, María Francisca; Cuesta Tovar, Jorge; Sicilia Guillén, Francisco

2008-04-05

The aim of this study was to determine the molecular defects of heterozygous beta thalassaemia and to ascertain their distribution in Lanzarote. Molecular characterization was achieved by real time polymerase chain reaction (RT-PCR LightCycler, Roche), PCR-ARMS (PCR-amplification reaction mutations system) and DNA sequencing on an automated DNA sequencer. Two hundred forty-three heterozygous beta thalassaemia carriers were included between July 1991 and February 2007. RT-PCR detected the molecular defect in 81% of the beta thalassaemia chromosomes analyzed [113 codon CD 39 (C --> T); 41 IVS-1-nt-110 (G --> A), 25 IVS 1-nt-1 (G --> A) and 19 IVS 1-nt-6 (T --> C)]. The remaining 12 molecular defects included the deletion 619 bp (7.8%) and the mutations -28 (A --> G), IVS1-nt-2 (T --> G), CD 41/42 (-TTCT), CD 8/9 (+G), CD 51 (-C), CD 22 (G --> T) and CD 24 (T --> A), CD 67 (-TG) and the novel mutation CD 20/21-TGGA. The distribution of the mutations is similar to that found in the Mediterranean area. The increasing migratory flow received in the Canary Islands may explain the emergence of new mutations not reported before in our area.

Thermal annealing behavior of hydrogen and surface topography of H 2 + ion implanted tungsten

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

Zhang, Jiandong; Jiang, Weilin; Zhu, Zihua

2018-01-25

Tungsten (W) has been proposed as a plasma-facing material (PFM) in fusion reactors due to its outstanding properties. Degradation of the material properties is expected to occur as a result of hydrogen (H) isotope permeation and trapping in W. In this study, two polycrystalline W plates were implanted with 80 keV H 2 + ions to a fluence of 2E21 H+/m2 at room temperature (RT). Time-of-flight secondary ion mass spectrometry (ToF-SIMS), focused ion beam (FIB) and scanning electron microscopy (SEM) were used for sample characterization. The SIMS data shows that H atoms are distributed well beyond the ion projected range.more » Isochronal annealing appears to suggest two H release stages that might be associated with the reported activation energies. H release at RT was observed between days 10 and 70 following ion implantation, and the level was maintained over the next 60 days. In addition, FIB/SEM results exhibit H2 blister formation near the surface of the as-implanted W. The blister distribution remains unchanged after thermal annealing up to 600 °C.« less

Nonlinear responses of chiral fluids from kinetic theory

NASA Astrophysics Data System (ADS)

Hidaka, Yoshimasa; Pu, Shi; Yang, Di-Lun

2018-01-01

The second-order nonlinear responses of inviscid chiral fluids near local equilibrium are investigated by applying the chiral kinetic theory (CKT) incorporating side-jump effects. It is shown that the local equilibrium distribution function can be nontrivially introduced in a comoving frame with respect to the fluid velocity when the quantum corrections in collisions are involved. For the study of anomalous transport, contributions from both quantum corrections in anomalous hydrodynamic equations of motion and those from the CKT and Wigner functions are considered under the relaxation-time (RT) approximation, which result in anomalous charge Hall currents propagating along the cross product of the background electric field and the temperature (or chemical-potential) gradient and of the temperature and chemical-potential gradients. On the other hand, the nonlinear quantum correction on the charge density vanishes in the classical RT approximation, which in fact satisfies the matching condition given by the anomalous equation obtained from the CKT.

Outlines of a multiple trace theory of temporal preparation.

PubMed

Los, Sander A; Kruijne, Wouter; Meeter, Martijn

2014-01-01

We outline a new multiple trace theory of temporal preparation (MTP), which accounts for behavior in reaction time (RT) tasks in which the participant is presented with a warning stimulus (S1) followed by a target stimulus (S2) that requires a speeded response. The theory assumes that during the foreperiod (FP; the S1-S2 interval) inhibition is applied to prevent premature response, while a wave of activation occurs upon the presentation of S2. On each trial, these actions are stored in a separate memory trace, which, jointly with earlier formed memory traces, starts contributing to preparation on subsequent trials. We show that MTP accounts for classic effects in temporal preparation, including mean RT-FP functions observed under a variety of FP distributions and asymmetric sequential effects. We discuss the advantages of MTP over other accounts of these effects (trace-conditioning and hazard-based explanations) and suggest a critical experiment to empirically distinguish among them.

Selective attention and response set in the Stroop task.

PubMed

Lamers, Martijn J M; Roelofs, Ardi; Rabeling-Keus, Inge M

2010-10-01

Response set membership contributes much to the interference in the color-word Stroop task. This may be due to selective allocation of attention to eligible responses or, alternatively, to greater inhibition of distractors that are not responses. In the present article, we report two experiments that were designed to adjudicate between these accounts. In Experiment 1, membership was manipulated on a trial-by-trial basis by cuing the possible responses for each trial. Response time (RT) was longer for distractors that corresponded to a cued, eligible response than to an ineligible one. This cuing effect was independent of the number of different responses. In Experiment 2, the distractor was cued on half the trials. Cuing the distractor decreased RTs on both incongruent and congruent trials. Vincentile analyses in both experiments revealed that the effects were constant throughout the entire RT distributions. These results suggest that response set effects arise because of selective allocation of attention to eligible responses.

Cortical topography of intracortical inhibition influences the speed of decision making.

PubMed

Wilimzig, Claudia; Ragert, Patrick; Dinse, Hubert R

2012-02-21

The neocortex contains orderly topographic maps; however, their functional role remains controversial. Theoretical studies have suggested a role in minimizing computational costs, whereas empirical studies have focused on spatial localization. Using a tactile multiple-choice reaction time (RT) task before and after the induction of perceptual learning through repetitive sensory stimulation, we extend the framework of cortical topographies by demonstrating that the topographic arrangement of intracortical inhibition contributes to the speed of human perceptual decision-making processes. RTs differ among fingers, displaying an inverted U-shaped function. Simulations using neural fields show the inverted U-shaped RT distribution as an emergent consequence of lateral inhibition. Weakening inhibition through learning shortens RTs, which is modeled through topographically reorganized inhibition. Whereas changes in decision making are often regarded as an outcome of higher cortical areas, our data show that the spatial layout of interaction processes within representational maps contributes to selection and decision-making processes.

Cortical topography of intracortical inhibition influences the speed of decision making

PubMed Central

Wilimzig, Claudia; Ragert, Patrick; Dinse, Hubert R.

2012-01-01

The neocortex contains orderly topographic maps; however, their functional role remains controversial. Theoretical studies have suggested a role in minimizing computational costs, whereas empirical studies have focused on spatial localization. Using a tactile multiple-choice reaction time (RT) task before and after the induction of perceptual learning through repetitive sensory stimulation, we extend the framework of cortical topographies by demonstrating that the topographic arrangement of intracortical inhibition contributes to the speed of human perceptual decision-making processes. RTs differ among fingers, displaying an inverted U-shaped function. Simulations using neural fields show the inverted U-shaped RT distribution as an emergent consequence of lateral inhibition. Weakening inhibition through learning shortens RTs, which is modeled through topographically reorganized inhibition. Whereas changes in decision making are often regarded as an outcome of higher cortical areas, our data show that the spatial layout of interaction processes within representational maps contributes to selection and decision-making processes. PMID:22315409

Response time as a discriminator between true- and false-positive responses in suprathreshold perimetry.

PubMed

Artes, Paul H; McLeod, David; Henson, David B

2002-01-01

To report on differences between the latency distributions of responses to stimuli and to false-positive catch trials in suprathreshold perimetry. To describe an algorithm for defining response time windows and to report on its performance in discriminating between true- and false-positive responses on the basis of response time (RT). A sample of 435 largely inexperienced patients underwent suprathreshold visual field examination on a perimeter that was modified to record RTs. Data were analyzed from 60,500 responses to suprathreshold stimuli and from 523 false-positive responses to catch trials. False-positive responses had much more variable latencies than responses to suprathreshold stimuli. An algorithm defining RT windows on the basis of z-transformed individual latency samples correctly identified more than 70% of false-positive responses to catch trials, whereas fewer than 3% of responses to suprathreshold stimuli were classified as false-positive responses. Latency analysis can be used to detect a substantial proportion of false-positive responses in suprathreshold perimetry. Rejection of such responses may increase the reliability of visual field screening by reducing variability and bias in a small but clinically important proportion of patients.

Effect of the flexibility training performed immediately before resistance training on muscle hypertrophy, maximum strength and flexibility.

PubMed

Junior, Roberto Moriggi; Berton, Ricardo; de Souza, Thiago Mattos Frota; Chacon-Mikahil, Mara Patrícia Traina; Cavaglieri, Cláudia Regina

2017-04-01

It has been suggested that flexibility training may reduce the total volume of training during resistance trainings. The purpose of this study was to compare the effect of flexibility training immediately before resistance training (FLEX-RT) versus resistance training without flexibility training (RT) on maximum strength and the vastus lateralis muscle cross-sectional area (CSA). Participants had each leg assigned to RT or FLEX-RT. Both groups performed four sets of leg extensions to voluntary failure of 80% of one repetition maximum (1RM); however, FLEX-RT performed two sets of 25 s of static stretching before resistance training. Number of repetitions and total volume were calculated during weeks 1-5 and 6-10. Vastus lateralis muscle CSA, 1RM, and flexibility were assessed at baseline and after 10 weeks. The number of repetitions and total training volume were greater for RT than FLEX-RT for weeks 1-5 and 6-10. Regarding the vastus lateralis muscle CSA, a main time effect was observed, however, greater change was observed for RT than FLEX-RT (12.7 and 7.4%, respectively). A main time effect for 1RM was also observed with similar changes for RT and FLEX-RT (12.7 and 12.9%, respectively). Flexibility was increased pre- to post-training for FLEX-RT with greater change for FLEX-RT (10.1%) than RT (2.1%). These results show that performing flexibility training immediately before resistance training can contribute to a lower number of repetitions, total volume, and muscle hypertrophy.

Patterns of care and treatment outcomes of patients with Craniopharyngioma in the national cancer database.

PubMed

Rao, Yuan J; Hassanzadeh, Comron; Fischer-Valuck, Benjamin; Chicoine, Michael R; Kim, Albert H; Perkins, Stephanie M; Huang, Jiayi

2017-03-01

To investigate the patterns of care and outcomes in patients with craniopharyngioma in the National Cancer Data Base (NCDB). This study included 697 patients (166 pediatric and 531 adult cases) treated for craniopharyngioma between 2004 and 2012 in the NCDB. Adjuvant radiotherapy (RT) was defined if within 6 months of surgery. Limited surgery (LS) was defined as biopsy or subtotal resection. Proportional-hazards models were used to evaluate associations between covariates and overall survival (OS). A time-dependent analysis of RT was performed to account for early deaths after surgery. Median follow-up was 46 months. Overall, 21% of patients received adjuvant RT. Of patients with known surgical extent (n = 195), 71% had LS. Utilization of adjuvant RT increased from 18% in 2004-2007 to 24% in 2008-2012. Patterns of care regarding adjuvant RT or LS were not significantly different between adult and pediatric patients. Tumor size, low comorbidity, and LS were associated with increased utilization of adjuvant RT. The 5-year OS among patients treated with LS, LS+RT, and gross total resection were 75, 85, and 82% (p = 0.02). On multivariate analysis of the 195 patients with known surgical extent, LS+RT was associated with improved OS compared to LS (HR 0.22, 95% CI 0.05-0.99, p = 0.04), but was not significant when early deaths (<2 months from surgery) were removed to adjust for immortal-time bias. Medical practice regarding surgical approach and adjuvant RT are similar for pediatric and adult craniopharyngiomas. Immortal-time bias may confound assessment of OS for adjuvant RT. Prospective studies comparing adjuvant RT versus observation after LS are warranted.

Real-Time Three-Dimensional Echocardiography: Characterization of Cardiac Anatomy and Function-Current Clinical Applications and Literature Review Update.

PubMed

Velasco, Omar; Beckett, Morgan Q; James, Aaron W; Loehr, Megan N; Lewis, Taylor G; Hassan, Tahmin; Janardhanan, Rajesh

2017-01-01

Our review of real-time three-dimensional echocardiography (RT3DE) discusses the diagnostic utility of RT3DE and provides a comparison with two-dimensional echocardiography (2DE) in clinical cardiology. A Pubmed literature search on RT3DE was performed using the following key words: transthoracic, two-dimensional, three-dimensional, real-time, and left ventricular (LV) function. Articles included perspective clinical studies and meta-analyses in the English language, and focused on the role of RT3DE in human subjects. Application of RT3DE includes analysis of the pericardium, right ventricular (RV) and LV cavities, wall motion, valvular disease, great vessels, congenital anomalies, and traumatic injury, such as myocardial contusion. RT3DE, through a transthoracic echocardiography (TTE), allows for increasingly accurate volume and valve motion assessment, estimated LV ejection fraction, and volume measurements. Chamber motion and LV mass approximation have been more accurately evaluated by RT3DE by improved inclusion of the third dimension and quantification of volumetric movement. Moreover, RT3DE was shown to have no statistical significance when comparing the ejection fractions of RT3DE to cardiac magnetic resonance (CMR). Analysis of RT3DE data sets of the LV endocardial exterior allows for the volume to be directly quantified for specific phases of the cardiac cycle, ranging from end systole to end diastole, eliminating error from wall motion abnormalities and asymmetrical left ventricles. RT3DE through TTE measures cardiac function with superior diagnostic accuracy in predicting LV mass, systolic function, along with LV and RV volume when compared with 2DE with comparable results to CMR.

The Diffusion Model Is Not a Deterministic Growth Model: Comment on Jones and Dzhafarov (2014)

PubMed Central

Smith, Philip L.; Ratcliff, Roger; McKoon, Gail

2015-01-01

Jones and Dzhafarov (2014) claim that several current models of speeded decision making in cognitive tasks, including the diffusion model, can be viewed as special cases of other general models or model classes. The general models can be made to match any set of response time (RT) distribution and accuracy data exactly by a suitable choice of parameters and so are unfalsifiable. The implication of their claim is that models like the diffusion model are empirically testable only by artificially restricting them to exclude unfalsifiable instances of the general model. We show that Jones and Dzhafarov’s argument depends on enlarging the class of “diffusion” models to include models in which there is little or no diffusion. The unfalsifiable models are deterministic or near-deterministic growth models, from which the effects of within-trial variability have been removed or in which they are constrained to be negligible. These models attribute most or all of the variability in RT and accuracy to across-trial variability in the rate of evidence growth, which is permitted to be distributed arbitrarily and to vary freely across experimental conditions. In contrast, in the standard diffusion model, within-trial variability in evidence is the primary determinant of variability in RT. Across-trial variability, which determines the relative speed of correct responses and errors, is theoretically and empirically constrained. Jones and Dzhafarov’s attempt to include the diffusion model in a class of models that also includes deterministic growth models misrepresents and trivializes it and conveys a misleading picture of cognitive decision-making research. PMID:25347314

The incidence and distribution characteristics of MLL rearrangements in Chinese acute myeloid leukemia patients by multiplex nested RT-PCR.

PubMed

Yang, Hua; Cao, Tingting; Gao, Li; Wang, Lili; Zhu, Chengying; Xu, Yuanyuan; Jing, Yu; Zhu, Haiyan; Lv, Na; Yu, Li

2017-07-20

Occurrence of MLL (Mixed Lineage Leukemia) gene rearrangements indicates poor prognosis in acute myeloid leukemia (AML) patients. This is the first study to report the positive rate and distribution characteristics of MLL rearrangements in AML patients in north China. We used multiplex nested real time PCR (RT-PCR) to screen for incidence of 11 MLL rearrangements in 433 AML patients. Eleven MLL rearrangements included (MLL-PTD, MLL-AF9, MLL-ELL, MLL-AF10, MLL-AF17, MLL-AF6, MLL-ENL, MLL-AF1Q, MLL-CBP, MLL-AF1P, MLL-AFX1). There were 68 AML patients with MLL rearrangements, and the positive rate was 15.7%. MLL-PTD (4.84%) was detected in 21 patients, MLL-AF9 in 15, (3.46%), MLL-ELL in 10 (2.31%), MLL-AF10 in 8 (1.85%), MLL-AF1Q in 2 (0.46%), 3 cases each of MLL-AF17, MLL-AF6, MLL-ENL (0.69% each), a and single case each of MLL-CBP, MLL-AF1P, and MLL-AFX1 (0.23% each). The highest rate of MLL rearrangements was found in 24 patients with M5 subtype AML, occurring in 24 cases (35.3%). MLL rearrangements occurred in 21 patients with M2 subtype AML (30.9%), and in 10 patients with M4 subtype AML (14.7%). Screening fusion genes by multiplex nested RT-PCR is a convenient, fast, economical, and accurate method for diagnosis and predicting prognosis of AML.

Evidence for higher reaction time variability for children with ADHD on a range of cognitive tasks including reward and event rate manipulations

PubMed Central

Epstein, Jeffery N.; Langberg, Joshua M.; Rosen, Paul J.; Graham, Amanda; Narad, Megan E.; Antonini, Tanya N.; Brinkman, William B.; Froehlich, Tanya; Simon, John O.; Altaye, Mekibib

2012-01-01

Objective The purpose of the research study was to examine the manifestation of variability in reaction times (RT) in children with Attention Deficit Hyperactivity Disorder (ADHD) and to examine whether RT variability presented differently across a variety of neuropsychological tasks, was present across the two most common ADHD subtypes, and whether it was affected by reward and event rate (ER) manipulations. Method Children with ADHD-Combined Type (n=51), ADHD-Predominantly Inattentive Type (n=53) and 47 controls completed five neuropsychological tasks (Choice Discrimination Task, Child Attentional Network Task, Go/No-Go task, Stop Signal Task, and N-back task), each allowing trial-by-trial assessment of reaction times. Multiple indicators of RT variability including RT standard deviation, coefficient of variation and ex-Gaussian tau were used. Results Children with ADHD demonstrated greater RT variability than controls across all five tasks as measured by the ex-Gaussian indicator tau. There were minimal differences in RT variability across the ADHD subtypes. Children with ADHD also had poorer task accuracy than controls across all tasks except the Choice Discrimination task. Although ER and reward manipulations did affect children’s RT variability and task accuracy, these manipulations largely did not differentially affect children with ADHD compared to controls. RT variability and task accuracy were highly correlated across tasks. Removing variance attributable to RT variability from task accuracy did not appreciably affect between-group differences in task accuracy. Conclusions High RT variability is a ubiquitous and robust phenomenon in children with ADHD. PMID:21463041

Sero-epidemiological survey of Crimean-Congo hemorrhagic fever virus in Tunisia

PubMed Central

Wasfi, Fares; Dowall, Stuart; Ghabbari, Tayssir; Bosworth, Andrew; Chakroun, Mohamed; Varghese, Anitha; Tiouiri, Hanene; Ben Jemaa, Mounir; Znazen, Abir; Hewson, Roger; Zhioua, Elyes; Letaief, Amel

2016-01-01

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease associated with a high case fatality rate and transmitted mainly by Hyalomma marginatum. The geographical distribution of H. marginatum covers most of the Western Mediterranean basin. We aimed to investigate whether CCHF virus (CCHFv) is circulating in Tunisia. Samples from unexplained acute febrile patients (n = 181) and a high risk group of humans, mainly slaughter workers (n = 38), were collected in the summer of 2014 and analyzed for exposure to CCHFv using serological tests and real-time RT-PCR. Ticks were collected from Northern and Southern Tunisia during May–June 2014 and examined for the presence of CCHFv by real-time RT-PCR. Of the 181 febrile patients, 5 showed only high titers of IgM suggesting a recent exposure to CCHFv. Among 38 slaughter workers, 2 had IgG anti-CCHFv responses yielding a seroprevalence of 5.2%. No CCHFv was detected in ticks and sera. Our results provide evidence of human exposure to CCHFv in Tunisia. PMID:26956221

Sero-epidemiological survey of Crimean-Congo hemorrhagic fever virus in Tunisia.

PubMed

Wasfi, Fares; Dowall, Stuart; Ghabbari, Tayssir; Bosworth, Andrew; Chakroun, Mohamed; Varghese, Anitha; Tiouiri, Hanene; Ben Jemaa, Mounir; Znazen, Abir; Hewson, Roger; Zhioua, Elyes; Letaief, Amel

2016-01-01

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease associated with a high case fatality rate and transmitted mainly by Hyalomma marginatum. The geographical distribution of H. marginatum covers most of the Western Mediterranean basin. We aimed to investigate whether CCHF virus (CCHFv) is circulating in Tunisia. Samples from unexplained acute febrile patients (n = 181) and a high risk group of humans, mainly slaughter workers (n = 38), were collected in the summer of 2014 and analyzed for exposure to CCHFv using serological tests and real-time RT-PCR. Ticks were collected from Northern and Southern Tunisia during May-June 2014 and examined for the presence of CCHFv by real-time RT-PCR. Of the 181 febrile patients, 5 showed only high titers of IgM suggesting a recent exposure to CCHFv. Among 38 slaughter workers, 2 had IgG anti-CCHFv responses yielding a seroprevalence of 5.2%. No CCHFv was detected in ticks and sera. Our results provide evidence of human exposure to CCHFv in Tunisia. © F. Wasfi et al., published by EDP Sciences, 2016.

TaqMan real-time RT-PCR detection of infectious salmon anaemia virus (ISAV) from formalin-fixed paraffin-embedded Atlantic salmon Salmo salar tissues.

PubMed

Godoy, M G; Kibenge, F S; Kibenge, M J; Olmos, P; Ovalle, L; Yañez, A J; Avendaño-Herrera, R

2010-05-18

The objective of this study was to evaluate the application of a TaqMan real-time reverse transcriptase PCR (RT-PCR) assay for the detection of infectious salmon anaemia virus (ISAV) in formalin-fixed paraffin-embedded (FFPE) fish tissues from Atlantic salmon Salmo salar with and without clinical signs of infection, and to compare it with histological and immunohistochemical (IHC) techniques. Sixteen fish samples obtained in 2007 and 2008 from 4 different farms in Chile were examined. The real-time RT-PCR allowed the detection of ISAV in FFPE samples from 9 of 16 fish, regardless of the organs analyzed, whereas 4 of the real-time RT-PCR negative fish were positive as indicated by histological examination and 3 of the real-time RT-PCR positive fish were negative as indicated by immunohistochemistry evaluation. The presence of ISAV in RT-PCR positive samples was confirmed by amplicon sequencing. This work constitutes the first report on the use of real-time RT-PCR for the detection of ISAV in FFPE sections. The assay is very useful for the examination of archival wax-embedded tissues, and allows for both prospective and retrospective evaluation of tissue samples for the presence of ISAV. However, the method only confirms the presence of the pathogen and should be used in combination with histopathology, which is a more precise tool. The combination of both techniques would be invaluable for confirmatory diagnosis of infectious salmon anaemia (ISA), which is essential for solving salmon farm problems.

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

Witkowski, Peter T.; Charite Universitaetsmedizin, CCM, Institut fuer Virologie, Helmut Ruska Haus, Chariteplatz 1, 10117 Berlin; Schuenadel, Livia, E-mail: SchuenadelL@rki.de

Research highlights: {yields} Real-time data acquisition by RT-CES requires low operative effort. {yields} Time to result is reduced by using RT-CES instead of conventional methods. {yields} RT-CES enables quantification of virus titers in unknown samples. {yields} RT-CES is a useful tool for high-throughput characterization of antiviral agents. {yields} An RT-CES-based virus neutralization test was established. -- Abstract: Impedance-based biosensing known as real-time cell electronic sensing (RT-CES) belongs to an emerging technology for analyzing the status of cells in vitro. In the present study protocols were developed for an RT-CES-based system (xCELLigence{sup TM}, Roche Applied Science, ACEA Biosciences Inc.) to supplementmore » conventional techniques in pox virology. First, proliferation of cells susceptible to orthopoxviruses was monitored. For virus titration cells were infected with vaccinia virus and cell status, represented by the dimensionless impedance-based cell index (CI), was monitored. A virus-dose dependent decrease in electrical impedance could be shown. Calculation of calibration curves at a suitable CI covering a dynamic range of 4 log enabled the quantification of virus titers in unknown samples. Similarly, antiviral effects could be determined as shown for anti-poxviral agents ST-246 and Cidofovir. Published values for the in vitro concentration that inhibited virus replication by 50% (IC{sub 50}) could be confirmed while cytotoxicity in effective concentrations was excluded in long-term incubation experiments. Finally, an RT-CES-based virus neutralization test was established. Various poxvirus-specific antibodies were examined for their neutralizing activity and a calculation mode for the neutralizing antibody titer was introduced. In summary, the presented RT-CES-based methods outmatch end-point assays by observing the cell population throughout the entire experiment while workload and time to result are reduced.« less

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus.

PubMed

Qin, Shaomin; Underwood, Darren; Driver, Luke; Kistler, Carol; Diallo, Ibrahim; Kirkland, Peter D

2018-06-01

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Impact of timing of radiotherapy in patients with newly diagnosed glioblastoma.

PubMed

Randolph, David M; McTyre, Emory R; Paulsson, Anna K; Holmes, Jordan A; Hinson, William H; Lesser, Glenn J; Strowd, Roy; Lo, Hui-Wen; Laxton, Adrian W; Tatter, Stephen B; Debinski, Waldemar; Chan, Michael D

2016-12-01

To further evaluate if a delay in the start of radiation therapy (RT) affects patient outcomes for glioblastoma (GBM). From May 1999 to May 2010, a total of 161 patients underwent surgery followed by RT for GBM. We assessed overall survival (OS) and progression free survival (PFS), stratified by extent of surgical resection. Included in the analysis were genomic predictors of progression. Median time from surgery to start of RT was 20days for biopsy alone, 28days for subtotal resection (STR) and 28days for gross total resection (GTR). For all patients, a delay >28days did not result in a difference in PFS when compared to no delay (6.7 vs. 6.9 months, p=0.07). PFS was improved in biopsy or STR patients with a >28day delay to start of RT (4.2 vs. 6.7 months, p=0.006). OS was also improved in patients receiving biopsy or STR with a >28day delay to start of RT (12.3 vs. 7.8 months, p=0.005). Multivariable analysis (MVA) demonstrated an improvement in OS and PFS with time to RT >28days for biopsy or STR patients (HR 0.52 p=0.008 and HR 0.48 p=0.02, respectively). In this retrospective review of GBM patients treated at a single institution, OS and PFS were not different between time to RT >28days compared to <28 days. There was a modest improvement in both PFS and OS in patients who received biopsy or STR with time to RT >28 days. Copyright © 2016 Elsevier B.V. All rights reserved.

Planning for RtI

ERIC Educational Resources Information Center

Robins, Jennifer; Antrim, Patricia

2013-01-01

In 2004 the Individuals with Disabilities Education Act authorized funding for Response to Intervention (RtI) instruction in the United States. By 2011, 71 percent of school districts had adopted RtI (Institute of Education Sciences 2011). The goal of RtI is to provide personalized, just-in-time intervention in reading and math for students who…

Real-time continuous glucose monitoring systems in the classroom/school environment.

PubMed

Benassi, Kari; Drobny, Jessica; Aye, Tandy

2013-05-01

Children with type 1 diabetes (T1D) spend 4-7 h/day in school with very little supervision of their diabetes management. Therefore, families have become more dependent on technology, such as use of real-time continuous glucose monitoring (RT-CGM), to provide increased supervision of their diabetes management. We sought to assess the impact of RT-CGM use in the classroom/school environment. Children with T1D using RT-CGM, their parents, and teachers completed a questionnaire about RT-CGM in the classroom/school environment. The RT-CGM was tolerated well in the classroom/school environment. Seventy percent of parents, 75% of students, and 51% of teachers found RT-CGM useful in the classroom/school environment. The students found the device to be more disruptive than did their parents and teachers. However, all three groups agreed that RT-CGM increased their comfort with diabetes management at school. Our study suggests that RT-CGM is useful and not disruptive in the classroom/school environment. The development of education materials for teachers could further increase its acceptance in the classroom/school environment.

In search of late time evolution self-similar scaling laws of Rayleigh-Taylor and Richtmyer-Meshkov hydrodynamic instabilities - recent theorical advance and NIF Discovery-Science experiments

NASA Astrophysics Data System (ADS)

Shvarts, Dov

2017-10-01

Hydrodynamic instabilities, and the mixing that they cause, are of crucial importance in describing many phenomena, from very large scales such as stellar explosions (supernovae) to very small scales, such as inertial confinement fusion (ICF) implosions. Such mixing causes the ejection of stellar core material in supernovae, and impedes attempts at ICF ignition. The Rayleigh-Taylor instability (RTI) occurs at an accelerated interface between two fluids with the lower density accelerating the higher density fluid. The Richtmyer-Meshkov (RM) instability occurs when a shock wave passes an interface between the two fluids of different density. In the RTI, buoyancy causes ``bubbles'' of the light fluid to rise through (penetrate) the denser fluid, while ``spikes'' of the heavy fluid sink through (penetrate) the lighter fluid. With realistic multi-mode initial conditions, in the deep nonlinear regime, the mixing zone width, H, and its internal structure, progress through an inverse cascade of spatial scales, reaching an asymptotic self-similar evolution: hRT =αRT Agt2 for RT and hRM =αRM tθ for RM. While this characteristic behavior has been known for years, the self-similar parameters αRT and θRM and their dependence on dimensionality and density ratio have continued to be intensively studied and a relatively wide distribution of those values have emerged. This talk will describe recent theoretical advances in the description of this turbulent mixing evolution that sheds light on the spread in αRT and θRM. Results of new and specially designed experiments, done by scientists from several laboratories, were performed recently using NIF, the only facility that is powerful enough to reach the self-similar regime, for quantitative testing of this theoretical advance, will be presented.

On the efficacy of procedures to normalize Ex-Gaussian distributions

PubMed Central

Marmolejo-Ramos, Fernando; Cousineau, Denis; Benites, Luis; Maehara, Rocío

2015-01-01

Reaction time (RT) is one of the most common types of measure used in experimental psychology. Its distribution is not normal (Gaussian) but resembles a convolution of normal and exponential distributions (Ex-Gaussian). One of the major assumptions in parametric tests (such as ANOVAs) is that variables are normally distributed. Hence, it is acknowledged by many that the normality assumption is not met. This paper presents different procedures to normalize data sampled from an Ex-Gaussian distribution in such a way that they are suitable for parametric tests based on the normality assumption. Using simulation studies, various outlier elimination and transformation procedures were tested against the level of normality they provide. The results suggest that the transformation methods are better than elimination methods in normalizing positively skewed data and the more skewed the distribution then the transformation methods are more effective in normalizing such data. Specifically, transformation with parameter lambda -1 leads to the best results. PMID:25709588

The linear transformation model with frailties for the analysis of item response times.

PubMed

Wang, Chun; Chang, Hua-Hua; Douglas, Jeffrey A

2013-02-01

The item response times (RTs) collected from computerized testing represent an underutilized source of information about items and examinees. In addition to knowing the examinees' responses to each item, we can investigate the amount of time examinees spend on each item. In this paper, we propose a semi-parametric model for RTs, the linear transformation model with a latent speed covariate, which combines the flexibility of non-parametric modelling and the brevity as well as interpretability of parametric modelling. In this new model, the RTs, after some non-parametric monotone transformation, become a linear model with latent speed as covariate plus an error term. The distribution of the error term implicitly defines the relationship between the RT and examinees' latent speeds; whereas the non-parametric transformation is able to describe various shapes of RT distributions. The linear transformation model represents a rich family of models that includes the Cox proportional hazards model, the Box-Cox normal model, and many other models as special cases. This new model is embedded in a hierarchical framework so that both RTs and responses are modelled simultaneously. A two-stage estimation method is proposed. In the first stage, the Markov chain Monte Carlo method is employed to estimate the parametric part of the model. In the second stage, an estimating equation method with a recursive algorithm is adopted to estimate the non-parametric transformation. Applicability of the new model is demonstrated with a simulation study and a real data application. Finally, methods to evaluate the model fit are suggested. © 2012 The British Psychological Society.

Expansion of the Real-time Sport-land Information System for NOAA / National Weather Service Situational Awareness and Local Modeling Applications

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; White, Kristopher D.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center in Huntsville, AL (Jedlovec 2013; Ralph et al. 2013; Merceret et al. 2013) is running a real-time configuration of the Noah land surface model (LSM) within the NASA Land Information System (LIS) framework (hereafter referred to as the "SPoRT-LIS"). Output from the real-time SPoRT-LIS is used for (1) initializing land surface variables for local modeling applications, and (2) displaying in decision support systems for situational awareness and drought monitoring at select NOAA/National Weather Service (NWS) partner offices. The SPoRT-LIS is currently run over a domain covering the southeastern half of the Continental United States (CONUS), with an additional experimental real-time run over the entire CONUS and surrounding portions of southern Canada and northern Mexico. The experimental CONUS run incorporates hourly quantitative precipitation estimation (QPE) from the National Severe Storms Laboratory Multi- Radar Multi-Sensor (MRMS) product (Zhang et al. 2011, 2014), which will be transitioned into operations at the National Centers for Environmental Prediction (NCEP) in Fall 2014. This paper describes the current and experimental SPoRT-LIS configurations, and documents some of the limitations still remaining through the advent of MRMS precipitation analyses in the SPoRT-LIS land surface model (LSM) simulations. Section 2 gives background information on the NASA LIS and describes the realtime SPoRT-LIS configurations being compared. Section 3 presents recent work done to develop a training module on situational awareness applications of real-time SPoRT-LIS output. Comparisons between output from the two SPoRT-LIS runs are shown in Section 4, including a documentation of issues encountered in using the MRMS precipitation dataset. A summary and future work in given in Section 5, followed by acknowledgements and references.

Esthesioneuroblastoma of the nasal cavity.

PubMed

Hollen, Tyler R; Morris, Christopher G; Kirwan, Jessica M; Amdur, Robert J; Werning, John W; Vaysberg, Mikhail; Mendenhall, William M

2015-06-01

Esthesioneuroblastoma is an uncommon cancer of the nasal cavity. We describe the outcomes for 26 patients treated with curative intent with photon radiotherapy (RT) at the University of Florida. Between May 1972 and June 2007, 26 patients received RT for previously untreated esthesioneuroblastoma of the nasal cavity. Sixteen patients were males and 10 were females with a median age of 55 years (range, 3 to 82 y). The modified Kadish stage distribution was: B, 7 patients; C, 17 patients; and D, 2 patients. Treatment modalities included the following: definitive RT, 5 patients; preoperative RT, 2 patients; and postoperative RT after resection, 19 patients. Elective neck irradiation (ENI) was performed in 17 (71%) of 24 N0 patients. Rates of local control, cause-specific survival, and absolute overall survival at 5 years were 79%, 72%, and 69%, respectively. Overall survival among patients treated with definitive RT was 20% at 5 years, compared with 81% among those who underwent surgery and adjuvant RT (P=0.01). One (6%) of 17 patients who received ENI developed a recurrence in the neck and was successfully salvaged. Ultimate neck control was 100% at 5 years for patients who received ENI versus 69% among those not receiving ENI (P=0.0173). Resection combined with adjuvant RT is more effective than surgery or RT alone in the treatment of esthesioneuroblastoma. ENI reduces the risk of regional relapse in patients with Kadish stage B and C cancers.

Benefit from the inclusion of radiation therapy in the treatment of patients with stage III classical Hodgkin lymphoma: A propensity matched analysis of the Surveillance, Epidemiology, and End Results database.

PubMed

Bates, James E; Dhakal, Sughosh; Mazloom, Ali; Casulo, Carla; Constine, Louis S

2017-08-01

While stage III and IV classical Hodgkin lymphoma (HL) patients are often combined and defined as "advanced stage," there are significant differences in disease distribution and burden between the two stages. This may obscure advantages of radiotherapy (RT) in a combined modality therapy strategy in stage III disease due to the relative lack of benefit in stage IV patients. We queried the Surveillance, Epidemiology, and End Results (SEER) database, restricting our search to patients with stage III classical HL diagnosed from 2004 to 2012, to examine the difference in overall and cause-specific survival (OS and CSS) between patients who did or did not receive RT. Patients treated with RT had improved OS and CSS relative to those treated without RT (5-year OS 91.6% with RT compared to 71.4% without RT, HR=0.34, p<0.001) and CSS (5-year OS 95.4% with RT compared to 84.7% without RT, HR=0.32, p<0.001). A benefit in OS and/or CSS was seen in all patient subgroups except for older adults (>64years). These data support at least a cautionary approach to omitting RT from treatment strategies for patients with advanced stage HL. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of a novel virus inactivation method for a multicenter avian influenza real-time reverse transcriptase-polymerase chain reaction proficiency study.

PubMed

Spackman, Erica; Suarez, David L

2005-01-01

Proficiency assessments are important elements in quality control for diagnostic laboratories. Traditionally, proficiency testing for polymerase chain reaction (PCR)-based assays has involved the use of clinical samples, samples "spiked" with live agents or DNA plasmids. Because of government regulations and biosecurity concerns, distribution of live high-consequence pathogens of livestock and poultry, such as avian influenza, is not possible, and DNA plasmids are not technically suitable for evaluating RNA virus detection. Therefore, a proficiency testing panel using whole avian influenza in a diluent containing a phenolic disinfectant that inactivates the virus while preserving the RNA for at least 8 weeks at -70 C was developed and used in a multicenter proficiency assessment for a type A influenza real-time reverse transcriptase (RT)-PCR test. The test, which was highly standardized, except for variation in the real-time RT-PCR equipment used, was shown to be highly reproducible by proficiency testing in 12 laboratories in the United States, Canada, and Hong Kong. Variation in cycle threshold values among 35 data sets and 490 samples was minimal (CV = 5.19%), and sample identifications were highly accurate (96.7% correct identifications) regardless of real-time PCR instrumentation.

Palliative radiation therapy practice for advanced esophageal carcinoma in Africa.

PubMed

Sharma, V; Gaye, P M; Wahab, S A; Ndlovu, N; Ngoma, T; Vanderpuye, V; Sowuhami, A; Dawotola, D A; Kigula-Mugambe, J; Jeremic, B

2010-04-01

While numerous surveys of pattern of practices of palliative radiotherapy (RT) in advanced esophageal cancers have been published in developed countries, there is no such survey in African countries. During and after a regional training course by the International Atomic Energy Agency (IAEA) in palliative cancer care, a questionnaire was distributed to African RT centers to gather information about infrastructure and human resources available, and the pattern of practice of palliative RT for esophageal cancers. Twenty-four of the 35 centers (60%) completed the questionnaire. Twenty out of 23 (87%) centers treat patients with esophageal cancer presenting with dysphagia using external beam RT (16 centers external beam RT alone and 4 centers also use brachytherapy as a boost). Twelve (60%) centers prescribe RT doses of 30 Gy in 10 fractions and 2 centers 20 Gy in 5 fractions. Eighteen centers (78%) have low dose rate (LDR) brachytherapy, and 9 (39%) centers have high dose rate (HDR) brachytherapy. One center only used HDR brachytherapy alone to a dose of 16 Gy in 2 fractions over 8 days. RT remains a major component of treatment of patients with esophageal cancers in African countries. Still, there is a great variety among centers in both indications for RT and its characteristics for a treatment indication.

Characterizing the utility of the TMPA real-time product for hydrologic predictions over global river basins across scales

NASA Astrophysics Data System (ADS)

Gao, H.; Zhang, S.; Nijssen, B.; Zhou, T.; Voisin, N.; Sheffield, J.; Lee, K.; Shukla, S.; Lettenmaier, D. P.

2017-12-01

Despite its errors and uncertainties, the Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis real-time product (TMPA-RT) has been widely used for hydrological monitoring and forecasting due to its timely availability for real-time applications. To evaluate the utility of TMPA-RT in hydrologic predictions, many studies have compared modeled streamflows driven by TMPA-RT against gauge data. However, because of the limited availability of streamflow observations in data sparse regions, there is still a lack of comprehensive comparisons for TMPA-RT based hydrologic predictions at the global scale. Furthermore, it is expected that its skill is less optimal at the subbasin scale than the basin scale. In this study, we evaluate and characterize the utility of the TMPA-RT product over selected global river basins during the period of 1998 to 2015 using the TMPA research product (TMPA-RP) as a reference. The Variable Infiltration Capacity (VIC) model, which was calibrated and validated previously, is adopted to simulate streamflows driven by TMPA-RT and TMPA-RP, respectively. The objective of this study is to analyze the spatial and temporal characteristics of the hydrologic predictions by answering the following questions: (1) How do the precipitation errors associated with the TMPA-RT product transform into streamflow errors with respect to geographical and climatological characteristics? (2) How do streamflow errors vary across scales within a basin?

Quantifying human response capabilities towards tsunami threats at community level

NASA Astrophysics Data System (ADS)

Post, J.; Mück, M.; Zosseder, K.; Wegscheider, S.; Taubenböck, H.; Strunz, G.; Muhari, A.; Anwar, H. Z.; Birkmann, J.; Gebert, N.

2009-04-01

Decision makers at the community level need detailed information on tsunami risks in their area. Knowledge on potential hazard impact, exposed elements such as people, critical facilities and lifelines, people's coping capacity and recovery potential are crucial to plan precautionary measures for adaptation and to mitigate potential impacts of tsunamis on society and the environment. A crucial point within a people-centred tsunami risk assessment is to quantify the human response capabilities towards tsunami threats. Based on this quantification and spatial representation in maps tsunami affected and safe areas, difficult-to-evacuate areas, evacuation target points and evacuation routes can be assigned and used as an important contribution to e.g. community level evacuation planning. Major component in the quantification of human response capabilities towards tsunami impacts is the factor time. The human response capabilities depend on the estimated time of arrival (ETA) of a tsunami, the time until technical or natural warning signs (ToNW) can be received, the reaction time (RT) of the population (human understanding of a tsunami warning and the decision to take appropriate action), the evacuation time (ET, time people need to reach a safe area) and the actual available response time (RsT = ETA - ToNW - RT). If RsT is larger than ET, people in the respective areas are able to reach a safe area and rescue themselves. Critical areas possess RsT values equal or even smaller ET and hence people whin these areas will be directly affected by a tsunami. Quantifying the factor time is challenging and an attempt to this is presented here. The ETA can be derived by analyzing pre-computed tsunami scenarios for a respective area. For ToNW we assume that the early warning center is able to fulfil the Indonesian presidential decree to issue a warning within 5 minutes. RT is difficult as here human intrinsic factors as educational level, believe, tsunami knowledge and experience besides others play a role. An attempt to quantify this variable under high uncertainty is also presented. Quantifying ET is based on a GIS modelling using a Cost Weighted Distance approach. Basic principle is to define the best evacuation path from a given point to the next safe area (shelter location). Here the fastest path from that point to the shelter location has to be found. Thereby the impact of land cover, slope, population density, population age and gender distribution are taken into account as literature studies prove these factors as highly important. Knowing the fastest path and the distance to the next safe area together with a spatially distributed pattern of evacuation speed delivers the time needed from each location to a safe area. By considering now the obtained time value for RsT the coverage area of an evacuation target point (safe area) can be assigned. Incorporating knowledge on people capacity of an evacuation target point the respective coverage area is refined. Hence areas with weak, moderate and good human response capabilities can be detected. This allows calculation of potential amount of people affected (dead or injured) and amount of people dislocated. First results for Kuta (Bali) for a worst case tsunami event deliver people affected of approx. 25 000 when RT = 0 minutes (direct evacuation when receiving a tsunami warning to 120 000 when RT > ETA (no evacuation action until tsunami hits the land). Additionally fastest evacuation routes to the evacuation target points can be assigned. Areas with weak response capabilities can be assigned as priority areas to install e.g. additional evacuation target points or to increase tsunami knowledge and awareness to promote a faster reaction time. Especially in analyzing underlying socio-economic properties causing deficiencies in responding to a tsunami threat can lead to valuable information and direct planning of adaptation measures. Keywords: Community level, Risk and vulnerability assessment, Early warning, Disaster management, Tsunami, Indonesia

Corrective response times in a coordinated eye-head-arm countermanding task.

PubMed

Tao, Gordon; Khan, Aarlenne Z; Blohm, Gunnar

2018-06-01

Inhibition of motor responses has been described as a race between two competing decision processes of motor initiation and inhibition, which manifest as the reaction time (RT) and the stop signal reaction time (SSRT); in the case where motor initiation wins out over inhibition, an erroneous movement occurs that usually needs to be corrected, leading to corrective response times (CRTs). Here we used a combined eye-head-arm movement countermanding task to investigate the mechanisms governing multiple effector coordination and the timing of corrective responses. We found a high degree of correlation between effector response times for RT, SSRT, and CRT, suggesting that decision processes are strongly dependent across effectors. To gain further insight into the mechanisms underlying CRTs, we tested multiple models to describe the distribution of RTs, SSRTs, and CRTs. The best-ranked model (according to 3 information criteria) extends the LATER race model governing RTs and SSRTs, whereby a second motor initiation process triggers the corrective response (CRT) only after the inhibition process completes in an expedited fashion. Our model suggests that the neural processing underpinning a failed decision has a residual effect on subsequent actions. NEW & NOTEWORTHY Failure to inhibit erroneous movements typically results in corrective movements. For coordinated eye-head-hand movements we show that corrective movements are only initiated after the erroneous movement cancellation signal has reached a decision threshold in an accelerated fashion.

Evaluation of the Abbott RealTime MTB and RealTime MTB INH/RIF Assays for Direct Detection of Mycobacterium tuberculosis Complex and Resistance Markers in Respiratory and Extrapulmonary Specimens.

PubMed

Hofmann-Thiel, Sabine; Molodtsov, Nikolay; Antonenka, Uladzimir; Hoffmann, Harald

2016-12-01

The Abbott RealTime MTB (RT MTB) assay is a new automated nucleic acid amplification test for the detection of Mycobacterium tuberculosis complex (MTBC) in clinical specimens. In combination with the RealTime MTB INH/RIF (RT MTB INH/RIF) resistance assay, which can be applied to RT MTB-positive specimens as an add-on assay, the tests also indicate the genetic markers of resistance to isoniazid (INH) and rifampin (RIF). We aimed to evaluate the diagnostic sensitivity and specificity of RT MTB using different types of respiratory and extrapulmonary specimens and to compare performance characteristics directly with those of the FluoroType MTB assay. The resistance results obtained by RT MTB INH/RIF were compared to those from the GenoType MTBDRplus and from phenotypic drug susceptibility testing. A total of 715 clinical specimens were analyzed. Compared to culture, the overall sensitivity of RT MTB was 92.1%; the sensitivity rates for smear-positive and smear-negative samples were 100% and 76.2%, respectively. The sensitivities of smear-negative specimens were almost identical for respiratory (76.3%) and extrapulmonary (76%) specimens. Specificity rates were 100% and 95.8% for culture-negative specimens and those that grew nontuberculous mycobacteria, respectively. RT MTB INH/RIF was applied to 233 RT MTB-positive samples and identified resistance markers in 7.7% of samples. Agreement with phenotypic and genotypic drug susceptibility testing was 99.5%. In conclusion, RT MTB and RT MTB INH/RIF allow for the rapid and accurate diagnosis of tuberculosis (TB) in different types of specimens and reliably indicate resistance markers. The strengths of this system are the comparably high sensitivity with paucibacillary specimens, its ability to detect INH and RIF resistance, and its high-throughput capacities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Kozlowski, Danielle; Case, Jonathan; Molthan, Andrew

2012-01-01

Short-term Prediction Research and Transition (SPoRT) seeks to improve short-term, regional weather forecasts using unique NASA products and capabilities SPoRT has developed a unique, real-time configuration of the NASA Unified Weather Research and Forecasting (WRF)WRF (ARW) that integrates all SPoRT modeling research data: (1) 2-km SPoRT Sea Surface Temperature (SST) Composite, (2) 3-km LIS with 1-km Greenness Vegetation Fraction (GVFs) (3) 45-km AIRS retrieved profiles. Transitioned this real-time forecast to NOAA's Hazardous Weather Testbed (HWT) as deterministic model at Experimental Forecast Program (EFP). Feedback from forecasters/participants and internal evaluation of SPoRT-WRF shows a cool, dry bias that appears to suppress convection likely related to methodology for assimilation of AIRS profiles Version 2 of the SPoRT-WRF will premier at the 2012 EFP and include NASA physics, cycling data assimilation methodology, better coverage of precipitation forcing, and new GVFs

Radiation therapy in the last month of life.

PubMed

Patel, Anand; Dunmore-Griffith, Jacquelyn; Lutz, Stephen; Johnstone, Peter A S

2014-05-01

We sought to survey a large, multi-center patient sample to better characterize/quantify RT utilization at the end of life. Few objective data exist for radiation therapy (RT) delivery at end of life (EOL). Data were retrieved for all patients receiving RT in calendar year 2010 in the Department of Radiation Oncology at Indiana University (IU) and Howard University (HU) hospitals. Specific attention was made of the group of patients receiving RT in the last 30 days of life. A total of 852 patients received all or part of their RT during 2010 (HU: 139, IU: 713). At time of analysis in early 2012, 179 patients had died (21%). Fifty-four patients (6.3% of total; 30% of expired patients) died within 30 days of receiving their last treatment. Twenty patients (2.3% of total; 11.2% of expired patients) received RT within their last week of life. For both sites, the median time until death from completion of therapy was 12.5 days (range 2-30 days). Radiation in the last month of life is likely to provide minimal palliation or survival benefit. This, coupled with the financial implications, time investment, and physical costs, suggests that physicians and patients should more strongly consider hospice, and minimize duration of palliative RT courses as far as possible. As with chemotherapy, RT utilization at EOL should be considered for collection as an overuse metric.

Patient education using virtual reality increases knowledge and positive experience for breast cancer patients undergoing radiation therapy.

PubMed

Jimenez, Yobelli A; Cumming, Steven; Wang, Wei; Stuart, Kirsty; Thwaites, David I; Lewis, Sarah J

2018-03-13

Improved access to technology in the radiation therapy (RT) workforce education has resulted in opportunities for innovative patient education methods. This study investigated the impact of a newly developed education tool using the Virtual Environment for Radiotherapy Training (VERT) system on patients' RT knowledge and anxiety. Breast cancer patients were recruited into a control group (CG) (n = 18) who underwent the standard pre-RT education package at a targeted cancer therapy centre, followed by a VERT group (VG) (n = 19). VG patients attended a VERT-based education session detailing RT immobilisation, planning and treatment. All patients completed questionnaires at four time points throughout their treatment, with survey sub-sections on RT knowledge, experience and anxiety. For both groups, anxiety levels were highest at time point 1(T1 after initial radiation oncologist consultation) (CG, 41.2; VG, 43.1), with a gradual decrease observed thereafter at time points before simulation, at the beginning of treatment and at the end of treatment (p > 0.05). The VG's RT knowledge scores were statistically significantly higher than those of the CG scores at all time points following VERT education (p < 0.05). This study reports the high value of VERT breast cancer-targeted education programs in improving RT knowledge and perhaps decreasing patient anxiety. Continued efforts are required to improve patients' accessibility to VERT in Australia, and to better understand the effect of VERT's unique educational features on patients' emotional and physical needs throughout their RT.

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins

PubMed Central

Hartard, C.; Rivet, R.; Banas, S.

2015-01-01

F-specific RNA bacteriophages (FRNAPH) have been widely studied as tools for evaluating fecal or viral pollution in water. It has also been proposed that they can be used to differentiate human from animal fecal contamination. While FRNAPH subgroup I (FRNAPH-I) and FRNAPH-IV are often associated with animal pollution, FRNAPH-II and -III prevail in human wastewater. However, this distribution is not absolute, and variable survival rates in these subgroups lead to misinterpretation of the original distribution. In this context, we studied FRNAPH distribution in urban wastewater and animal feces/wastewater. To increase the specificity, we partially sequenced the genomes of phages of urban and animal origins. The persistence of the genomes and infectivity were also studied, over time in wastewater and during treatment, for each subgroup. FRNAPH-I genome sequences did not show any specific urban or animal clusters to allow development of molecular tools for differentiation. They were the most resistant and as such may be used as fecal or viral indicators. FRNAPH-II's low prevalence and low sequence variability in animal stools, combined with specific clusters formed by urban strains, allowed differentiation between urban and animal pollution by using a specific reverse transcription-PCR (RT-PCR) method. The subgroup's resistance over time was comparable to that of FRNAPH-I, but its surface properties allowed higher elimination rates during activated-sludge treatment. FRNAPH-III's low sequence variability in animal wastewater and specific cluster formation by urban strains also allowed differentiation by using a specific RT-PCR method. Nevertheless, its low resistance restricted it to being used only for recent urban pollution detection. FRNAPH-IV was too rare to be used. PMID:26162878

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins.

PubMed

Hartard, C; Rivet, R; Banas, S; Gantzer, C

2015-09-01

F-specific RNA bacteriophages (FRNAPH) have been widely studied as tools for evaluating fecal or viral pollution in water. It has also been proposed that they can be used to differentiate human from animal fecal contamination. While FRNAPH subgroup I (FRNAPH-I) and FRNAPH-IV are often associated with animal pollution, FRNAPH-II and -III prevail in human wastewater. However, this distribution is not absolute, and variable survival rates in these subgroups lead to misinterpretation of the original distribution. In this context, we studied FRNAPH distribution in urban wastewater and animal feces/wastewater. To increase the specificity, we partially sequenced the genomes of phages of urban and animal origins. The persistence of the genomes and infectivity were also studied, over time in wastewater and during treatment, for each subgroup. FRNAPH-I genome sequences did not show any specific urban or animal clusters to allow development of molecular tools for differentiation. They were the most resistant and as such may be used as fecal or viral indicators. FRNAPH-II's low prevalence and low sequence variability in animal stools, combined with specific clusters formed by urban strains, allowed differentiation between urban and animal pollution by using a specific reverse transcription-PCR (RT-PCR) method. The subgroup's resistance over time was comparable to that of FRNAPH-I, but its surface properties allowed higher elimination rates during activated-sludge treatment. FRNAPH-III's low sequence variability in animal wastewater and specific cluster formation by urban strains also allowed differentiation by using a specific RT-PCR method. Nevertheless, its low resistance restricted it to being used only for recent urban pollution detection. FRNAPH-IV was too rare to be used. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Head movement compensation in real-time magnetoencephalographic recordings.

PubMed

Little, Graham; Boe, Shaun; Bardouille, Timothy

2014-01-01

Neurofeedback- and brain-computer interface (BCI)-based interventions can be implemented using real-time analysis of magnetoencephalographic (MEG) recordings. Head movement during MEG recordings, however, can lead to inaccurate estimates of brain activity, reducing the efficacy of the intervention. Most real-time applications in MEG have utilized analyses that do not correct for head movement. Effective means of correcting for head movement are needed to optimize the use of MEG in such applications. Here we provide preliminary validation of a novel analysis technique, real-time source estimation (rtSE), that measures head movement and generates corrected current source time course estimates in real-time. rtSE was applied while recording a calibrated phantom to determine phantom position localization accuracy and source amplitude estimation accuracy under stationary and moving conditions. Results were compared to off-line analysis methods to assess validity of the rtSE technique. The rtSE method allowed for accurate estimation of current source activity at the source-level in real-time, and accounted for movement of the source due to changes in phantom position. The rtSE technique requires modifications and specialized analysis of the following MEG work flow steps.•Data acquisition•Head position estimation•Source localization•Real-time source estimation This work explains the technical details and validates each of these steps.

Top-down guidance in visual search for facial expressions.

PubMed

Hahn, Sowon; Gronlund, Scott D

2007-02-01

Using a visual search paradigm, we investigated how a top-down goal modified attentional bias for threatening facial expressions. In two experiments, participants searched for a facial expression either based on stimulus characteristics or a top-down goal. In Experiment 1 participants searched for a discrepant facial expression in a homogenous crowd of faces. Consistent with previous research, we obtained a shallower response time (RT) slope when the target face was angry than when it was happy. In Experiment 2, participants searched for a specific type of facial expression (allowing a top-down goal). When the display included a target, we found a shallower RT slope for the angry than for the happy face search. However, when an angry or happy face was present in the display in opposition to the task goal, we obtained equivalent RT slopes, suggesting that the mere presence of an angry face in opposition to the task goal did not support the well-known angry face superiority effect. Furthermore, RT distribution analyses supported the special status of an angry face only when it was combined with the top-down goal. On the basis of these results, we suggest that a threatening facial expression may guide attention as a high-priority stimulus in the absence of a specific goal; however, in the presence of a specific goal, the efficiency of facial expression search is dependent on the combined influence of a top-down goal and the stimulus characteristics.

Decline of Tumor Vascular Function as Assessed by Dynamic Contrast-Enhanced Magnetic Resonance Imaging Is Associated With Poor Responses to Radiation Therapy and Chemotherapy

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

Chen, Fang-Hsin; Wang, Chun-Chieh; Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan

Purpose: To investigate whether changes in the volume transfer coefficient (K{sup trans}) in a growing tumor could be used as a surrogate marker for predicting tumor responses to radiation therapy (RT) and chemotherapy (CT). Methods and Materials: Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was consecutively performed on tumor-bearing mice, and temporal and spatial changes of K{sup trans} values were measured along with tumor growth. Tumor responses to RT and CT were studied before and after observed changes in K{sup trans} values with time. Results: Dynamic changes with an initial increase and subsequent decline in K{sup trans} values were found tomore » be associated with tumor growth. When each tumor was divided into core and peripheral regions, the K{sup trans} decline was greater in core, although neither vascular structure or necrosis could be linked to this spatial difference. Tumor responses to RT were worse if applied after the decline of K{sup trans}, and there was less drug distribution and cell death in the tumor core after CT. Conclusion: The K{sup trans} value in growing tumors, reflecting the changes of tumor microenvironment and vascular function, is strongly associated with tumor responses to RT and CT and could be a potential surrogate marker for predicting the tumor response to these treatments.« less

Real-Time PCR (RT-PCR) Assays for Burkholderia mallei and B. pseudomallei

DTIC Science & Technology

2005-10-01

1 Real-time PCR (RT-PCR) Assays for Burkholderia mallei and B. pseudomallei Vipin K. Rastogi1, Tu-chen Cheng1, Lisa Collins1 and Jennifer Bagley2 1...A 3. DATES COVERED - 4. TITLE AND SUBTITLE Real-time PCR (RT-PCR) Assays for Burkholderia mallei and B.pseudomallei 5a. CONTRACT NUMBER 5b...pseudomallei and B. mallei , respectively are the causative agents of meliodosis and glanders , primarily in animals (both pathogens), and in humans

US geographic distribution of rt-PA utilization by hospital for acute ischemic stroke.

PubMed

Kleindorfer, Dawn; Xu, Yingying; Moomaw, Charles J; Khatri, Pooja; Adeoye, Opeolu; Hornung, Richard

2009-11-01

Previously, we have estimated US national rates of recombinant tissue plasminogen activator (rt-PA) use to be 1.8% to 3.0% of all ischemic stroke patients. However, we hypothesized that the rate of rt-PA use may vary widely depending on regional variation, and that a large percentage of the US population likely does not have access to hospitals using rt-PA regularly. We describe the US geographic distribution of hospitals using rt-PA for acute ischemic stroke. This analysis used the MEDPAR database, which is a claims-based dataset that contains every fee-for-service Medicare-eligible hospital discharge in the US. Cases potentially eligible for rt-PA treatment based on diagnosis were defined as those with a hospital DRG code of 14, 15, or 559, and that also had an ICD-9 code of 433, 434, or 436. Thrombolysis use was defined as an ICD-9 code of 99.1. Study interval was July 1, 2005 to June 30, 2007. Hospital locations were mapped using ArcView software; population densities and regions of the US are based on US Census 2000. There were 4750 hospitals in the MEDPAR database, which included 495 186 ischemic stroke admissions during the study period. Of these hospitals, 64% had no reported treatments with rt-PA for ischemic stroke, and 0.9% reported >10% treatment rates within the MEDPAR dataset. Bed size, rural or underserved designation, and population density were significantly associated with reported rt-PA treatment rates, and remained significant in the multivariable regression. Approximately 162 million US citizens reside in counties containing a hospital reporting a >or=2.4% treatment rate within the MEDPAR dataset. We report the first description of US hospital rt-PA treatment rates by hospital. Unfortunately, we found that 64% of US hospitals did not report giving rt-PA at all within the MEDPAR database within a 2-year period. These tended to be hospitals that were smaller (average bed size of 95), located in less densely populated areas, or located in the South or Midwest. In addition, 40% of the US population resides in counties without a hospital that administered rt-PA to at least 2.4% of ischemic stroke patients, although distinguishing transferred patients is problematic within administrative datasets. Such national-based resource-utilization data is important for planning at the local and national level, especially for such initiatives as telemedicine, to reach underserved areas.

Single-pair fluorescence resonance energy transfer analysis of mRNA transcripts for highly sensitive gene expression profiling in near real time.

PubMed

Peng, Zhiyong; Young, Brandon; Baird, Alison E; Soper, Steven A

2013-08-20

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with online single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10-10,000 copies) with an R(2) = 0.9995 for RT-LDR/spFRET and R(2) = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a two thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics.

Single-Pair Fret Analysis of mRNA Transcripts for Highly Sensitive Gene Expression Profiling in Near Real Time

PubMed Central

Peng, Zhiyong; Young, Brandon; Baird, Alison E.; Soper, Steven A.

2013-01-01

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with on-line single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10 − 10,000 copies) with an R2 = 0.9995 for RT-LDR/spFRET and R2 = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a 2 thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics. PMID:23869556

Obesity and Risk of Biochemical Failure for Patients Receiving Salvage Radiotherapy After Prostatectomy

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

King, Christopher R.; Spiotto, Michael T.; Kapp, Daniel S.

Purpose: Obesity has been proposed as an independent risk factor for patients undergoing surgery or radiotherapy (RT) for prostate cancer. Using body mass index (BMI) as a measure of obesity, we tested its role as a risk factor for patients receiving salvage RT after prostatectomy. Methods and Materials: Rates of subsequent biochemical relapse were examined in 90 patients who underwent salvage RT between 1984 and 2004 for biochemical failure after radical prostatectomy. Median follow-up was 3.7 years. The BMI was tested as a continuous and categorical variable (stratified as <25, 25-<30, and {>=}30 kg/m{sup 2}). Univariate and multivariate proportional hazardsmore » regression analyses were performed for clinical, pathologic, and treatment factors associated with time to relapse after salvage RT. Results: There were 40 biochemical failures after salvage RT with a median time to failure of 1.2 years. The BMI was not associated with adverse clinical, pathologic, or treatment factors. On multivariate analysis, obesity was independently significant (hazard ratio [HR], 1.2; p = 0.01), along with RT dose (HR, 0.7; p = 0.003) and pre-RT prostate-specific antigen level (HR, 1.2; p = 0.0003). Conclusions: This study is weakly suggestive that obesity may be a risk factor for salvage RT patients. Whether this results from greater biologic aggressiveness or technical inadequacies cannot be answered by this study. Given the very high failure rate observed for severely obese patients, we propose that technical difficulties with RT are at play. This hypothesis is supported by the RT literature and could be prospectively investigated. Techniques that optimize targeting, especially in obese patients, perhaps seem warranted at this time.« less

Obstructed bi-leaflet prosthetic mitral valve imaging with real-time three-dimensional transesophageal echocardiography.

PubMed

Shimbo, Mai; Watanabe, Hiroyuki; Kimura, Shunsuke; Terada, Mai; Iino, Takako; Iino, Kenji; Ito, Hiroshi

2015-01-01

Real-time three-dimensional transesophageal echocardiography (RT3D-TEE) can provide unique visualization and better understanding of the relationship among cardiac structures. Here, we report the case of an 85-year-old woman with an obstructed mitral prosthetic valve diagnosed promptly by RT3D-TEE, which clearly showed a leaflet stuck in the closed position. The opening and closing angles of the valve leaflets measured by RT3D-TEE were compatible with those measured by fluoroscopy. Moreover, RT3D-TEE revealed, in the ring of the prosthetic valve, thrombi that were not visible on fluoroscopy. RT3D-TEE might be a valuable diagnostic technique for prosthetic mitral valve thrombosis. © 2014 Wiley Periodicals, Inc.

Phase III randomized study of radiation and temozolomide versus radiation and nitrosourea therapy for anaplastic astrocytoma: results of NRG Oncology RTOG 9813.

PubMed

Chang, Susan; Zhang, Peixin; Cairncross, J Gregory; Gilbert, Mark R; Bahary, Jean-Paul; Dolinskas, Carol A; Chakravarti, Arnab; Aldape, Kenneth D; Bell, Erica H; Schiff, David; Jaeckle, Kurt; Brown, Paul D; Barger, Geoffrey R; Werner-Wasik, Maria; Shih, Helen; Brachman, David; Penas-Prado, Marta; Robins, H Ian; Belanger, Karl; Schultz, Christopher; Hunter, Grant; Mehta, Minesh

2017-02-01

The primary objective of this study was to compare the overall survival (OS) of patients with anaplastic astrocytoma (AA) treated with radiotherapy (RT) and either temozolomide (TMZ) or a nitrosourea (NU). Secondary endpoints were time to tumor progression (TTP), toxicity, and the effect of IDH1 mutation status on clinical outcome. Eligible patients with centrally reviewed, histologically confirmed, newly diagnosed AA were randomized to receive either RT+TMZ (n = 97) or RT+NU (n = 99). The study closed early because the target accrual rate was not met. Median follow-up time for patients still alive was 10.1 years (1.9-12.6 y); 66% of the patients died. Median survival time was 3.9 years in the RT/TMZ arm (95% CI, 3.0-7.0) and 3.8 years in the RT/NU arm (95% CI, 2.2-7.0), corresponding to a hazard ratio (HR) of 0.94 (P = .36; 95% CI, 0.67-1.32). The differences in progression-free survival (PFS) and TTP between the 2 arms were not statistically significant. Patients in the RT+NU arm experienced more grade ≥3 toxicity (75.8% vs 47.9%, P < .001), mainly related to myelosuppression. Of the 196 patients, 111 were tested for IDH1-R132H status (60 RT+TMZ and 51 RT+NU). Fifty-four patients were IDH negative and 49 were IDH positive with a better OS in IDH-positive patients (median survival time 7.9 vs 2.8 y; P = .004, HR = 0.50; 95% CI, 0.31-0.81). RT+TMZ did not appear to significantly improve OS or TTP for AA compared with RT+ NU. RT+TMZ was better tolerated. IDH1-R132H mutation was associated with longer survival. © The Author(s) 2016. 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

Potential Utility of the Real-Time TMPA-RT Precipitation Estimates in Streamflow Prediction

NASA Technical Reports Server (NTRS)

Su, Fengge; Gao, Huilin; Huffman, George J.; Lettenmaier, Dennis P.

2010-01-01

We investigate the potential utility of the real-time Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA-RT) data for streamflow prediction, both through direct comparisons of TMPA-RT estimates with a gridded gauge product, and through evaluation of streamflow simulations over four tributaries of La Plata Basin (LPB) in South America using the two precipitation products. Our assessments indicate that the relative accuracy and the hydrologic performance of TMPA-RT-based streamflow simulations generally improved after February 2005. The improvements in TMPA-RT since 2005 are closely related to upgrades in the TMPA-RT algorithm in early February, 2005 which include use of additional microwave sensors (AMSR-E and AMSU-B) and implementation of different calibration schemes. Our work suggests considerable potential for hydrologic prediction using purely satellite-derived precipitation estimates (no adjustments by in situ gauges) in parts of the globe where in situ observations are sparse.

Characterization of efficacy and toxicity after high-dose pelvic reirradiation with palliative intent for genitourinary second malignant neoplasms or local recurrences after full-dose radiation therapy in the pelvis: A high-volume cancer center experience.

PubMed

Kamran, Sophia C; Harshman, Lauren C; Bhagwat, Mandar S; Muralidhar, Vinayak; Nguyen, Paul L; Martin, Neil E; La Follette, Stephanie; Faso, Sarah; Viswanathan, Akila N; Efstathiou, Jason A; Beard, Clair J

2017-01-01

The use of large-field external beam reirradiation (re-RT) after pelvic radiation therapy (RT) for genitourinary (GU) cancers has not been reported. We report the results of such treatment in patients with either symptomatic GU second malignant neoplasms or locally recurrent pelvic tumors after initial RT for whom surgery or further systemic therapy was not an option. The records of 28 consecutive patients with advanced, bulky GU malignancies treated with high-dose, large-field re-RT with palliative intent between 2008 and 2014 were retrospectively reviewed. Descriptive outcome analyses focused on toxicities and symptom control, and responses were evaluated by 2 independent observers. Twenty-seven male patients (96%) were included. Median initial external beam RT dose was 64 Gy (range, 30-75.6 Gy). The median time between initial RT and re-RT was 9.5 years (range, 0.2-32 years). At the time of re-RT, there were 16 local recurrences and 12 second malignant neoplasms together comprising 16 bladder, 10 prostate, 1 ureteral, and 1 penile cancer. Indications for re-RT were pain and bleeding/hemorrhage. The median equivalent sphere diameter planning target volume for re-RT was 8.6 cm (range, 4.7-16.3 cm). Given the severity of the symptoms and the bulk of the disease at the time of re-RT, a higher dose of RT was administered. The median re-RT dose was 50 Gy (range, 27.5-66 Gy). For patients who received <60 Gy, hypofractionation of 250 cGy was used. The median cumulative dose was 113.9 Gy (range, 81.5-132.8 Gy). Re-RT was well tolerated with no Radiation Therapy Oncology Group grade 3-4 toxicities. Twenty-four patients (92%) had complete resolution of symptoms, and relief was durable in 67% of patients. The median overall survival was 5.8 months (range, 0.3-38.9 months). Of those patients who are still alive, 100% remain free of initial symptoms. This small series suggests that aggressive re-RT of inoperable and symptomatic GU malignancies that is undertaken with meticulous treatment planning is well tolerated and provides excellent, durable relief without undue short-term toxicity. Validation in a larger prospective cohort is required.

SU-E-T-335: Dosimetric Investigation of An Advanced Rotating Gamma Ray System for Imaged Guided Radiation Therapy

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

Ma, C; Eldib, A; Chibani, O

2015-06-15

Purpose: Co-60 beams have unique dosimetric properties for cranial treatments and thoracic cancers. The conventional concern about the high surface dose is overcome by modern system designs with rotational treatment techniques. This work investigates a novel rotational Gamma ray system for image-guided, external beam radiotherapy. Methods: The CybeRT system (Cyber Medical Corp., China) consists of a ring gantry with either one or two treatment heads containing a Gamma source and a multileaf collimator (MLC). The MLC has 60 paired leaves, and the maximum field size is either 40cmx40cm (40 pairs of 0.5cm central leaves, 20 pairs of 1cm outer leaves),more » or 22cmx40cm (32 pairs of 0.25cm central leaves, 28 pairs of 0.5cm outer leaves). The treatment head(s) can swing 35° superiorly and 8° inferiorly, allowing a total of 43° non-coplanar beam incident. The treatment couch provides 6-degrees-of-freedom motion compensation and the kV cone-beam CT system has a spatial resolution of 0.4mm. Monte Carlo simulations were used to compute dose distributions and compare with measurements. A retrospective study of 98 previously treated patients was performed to compare CybeRT with existing RT systems. Results: Monte Carlo results confirmed the CybeRT design parameters including output factors and 3D dose distributions. Its beam penumbra/dose gradient was similar to or better than that of 6MV photon beams and its isocenter accuracy is 0.3mm. Co-60 beams produce lower-energy secondary electrons that exhibit better dose properties in low-density lung tissues. Because of their rapid depth dose falloff, Co-60 beams are favorable for peripheral lung tumors with half-arc arrangements to spare the opposite lung and critical structures. Superior dose distributions were obtained for head and neck, breast, spine and lung tumors. Conclusion: Because of its accurate dose delivery and unique dosimetric properties of C-60 sources, CybeRT is ideally suited for advanced SBRT as well as conventional RT. This work was partially supported by Cyber Medical Corp.« less

Alteration of GABAergic synapses and gephyrin clusters in the thalamic reticular nucleus of GABAA receptor alpha3 subunit-null mice.

PubMed

Studer, Remo; von Boehmer, Lotta; Haenggi, Tatjana; Schweizer, Claude; Benke, Dietmar; Rudolph, Uwe; Fritschy, Jean-Marc

2006-09-01

Multiple GABAA-receptor subtypes are assembled from alpha, beta and gamma subunit variants. GABAA receptors containing the alpha3 subunit represent a minor population with a restricted distribution in the CNS. In addition, they predominate in monoaminergic neurons and in the nucleus reticularis thalami (nRT), suggesting a role in the regulation of cortical function and sleep. Mice with a targeted deletion of the alpha3 subunit gene (alpha3(0/0)) are viable and exhibit a subtle behavioural phenotype possibly related to dopaminergic hyperfunction. Here, we investigated immunohistochemically the consequences of the loss of alpha3 subunit for maturation of GABAA receptors and formation of GABAergic synapses in the nRT. Throughout postnatal development, the regional distribution of the alpha1, alpha2, or alpha5 subunit was unaltered in alpha3(0/0) mice and the prominent alpha3 subunit staining of nRT neurons in wildtype mice was not replaced. Subcellularly, as seen by double immunofluorescence, the alpha3 and gamma2 subunit were clustered at postsynaptic sites in the nRT of adult wildtype mice along with the scaffolding protein gephyrin. In alpha3(0/0) mice, gamma2 subunit clustering was disrupted and gephyrin formed large aggregates localized at the cell surface, but unrelated to postsynaptic sites, indicating that nRT neurons lack postsynaptic GABAA receptors in mutant mice. Furthermore, GABAergic terminals were enlarged and reduced in number, suggesting a partial deficit of GABAergic synapses. Therefore, GABAA receptors are required for gephyrin clustering and long-term synapse maintenance. The absence of GABAA-mediated transmission in the nRT may have a significant impact on the function of the thalamo-cortical loop of alpha3(0/0) mice.

Multi-objective optimization of radiotherapy: distributed Q-learning and agent-based simulation

NASA Astrophysics Data System (ADS)

Jalalimanesh, Ammar; Haghighi, Hamidreza Shahabi; Ahmadi, Abbas; Hejazian, Hossein; Soltani, Madjid

2017-09-01

Radiotherapy (RT) is among the regular techniques for the treatment of cancerous tumours. Many of cancer patients are treated by this manner. Treatment planning is the most important phase in RT and it plays a key role in therapy quality achievement. As the goal of RT is to irradiate the tumour with adequately high levels of radiation while sparing neighbouring healthy tissues as much as possible, it is a multi-objective problem naturally. In this study, we propose an agent-based model of vascular tumour growth and also effects of RT. Next, we use multi-objective distributed Q-learning algorithm to find Pareto-optimal solutions for calculating RT dynamic dose. We consider multiple objectives and each group of optimizer agents attempt to optimise one of them, iteratively. At the end of each iteration, agents compromise the solutions to shape the Pareto-front of multi-objective problem. We propose a new approach by defining three schemes of treatment planning created based on different combinations of our objectives namely invasive, conservative and moderate. In invasive scheme, we enforce killing cancer cells and pay less attention about irradiation effects on normal cells. In conservative scheme, we take more care of normal cells and try to destroy cancer cells in a less stressed manner. The moderate scheme stands in between. For implementation, each of these schemes is handled by one agent in MDQ-learning algorithm and the Pareto optimal solutions are discovered by the collaboration of agents. By applying this methodology, we could reach Pareto treatment plans through building different scenarios of tumour growth and RT. The proposed multi-objective optimisation algorithm generates robust solutions and finds the best treatment plan for different conditions.

Relationship between daily rumination time and estrus of dairy cows.

PubMed

Reith, S; Hoy, S

2012-11-01

The aim of the study was to investigate whether rumination time (RT) was related to estrus in dairy cattle. On 4 farms, cows were equipped with a microphone-based sensor system that allowed continuous recording (in blocks of 2 h) of RT. The analyzed data set consisted of 265 verified estrus cycles of 224 animals with artificial insemination leading to conception. The day of estrus (d 0) was defined as the day when estrus was identified either by measurement of physical activity or by visual observation. In estrous cows, RT was significantly reduced. With a duration of 355 min/d, the minimum RT was found on the day of estrus compared with the base level of 429 min/d during the reference period (the mean of 3 d before and 3 d after estrus). The average decrease in RT was 17% (74 min), ranging between -71 and +16% among animals. Herd and parity affected the RT decrease during estrus. Among the 4 analyzed herds, the RT decrease of cows in estrus ranged between 14% (60 min/d) and 24% (94 min/d). The decrease in RT was more pronounced in primiparous than in mature cows. In conclusion, RT is reduced on the day of estrus on average. The RT decrease during estrus was characterized by high variation among cows. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Portable Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of Foot-and-Mouth Disease Virus

PubMed Central

Abd El Wahed, Ahmed; El-Deeb, Ayman; El-Tholoth, Mohamed; Abd El Kader, Hanaa; Ahmed, Abeer; Hassan, Sayed; Hoffmann, Bernd; Haas, Bernd; Shalaby, Mohamed A.; Hufert, Frank T.; Weidmann, Manfred

2013-01-01

Foot-and-mouth disease (FMD) is a trans-boundary viral disease of livestock, which causes huge economic losses and constitutes a serious infectious threat for livestock farming worldwide. Early diagnosis of FMD helps to diminish its impact by adequate outbreak management. In this study, we describe the development of a real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of FMD virus (FMDV). The FMDV RT-RPA design targeted the 3D gene of FMDV and a 260 nt molecular RNA standard was used for assay validation. The RT-RPA assay was fast (4–10 minutes) and the analytical sensitivity was determined at 1436 RNA molecules detected by probit regression analysis. The FMDV RT-RPA assay detected RNA prepared from all seven FMDV serotypes but did not detect classical swine fever virus or swine vesicular disease virus. The FMDV RT-RPA assay was used in the field during the recent FMD outbreak in Egypt. In clinical samples, reverse transcription polymerase chain reaction (RT-PCR) and RT-RPA showed a diagnostic sensitivity of 100% and 98%, respectively. In conclusion, FMDV RT-RPA was quicker and much easier to handle in the field than real-time RT-PCR. Thus RT-RPA could be easily implemented to perform diagnostics at quarantine stations or farms for rapid spot-of-infection detection. PMID:23977101

A portable reverse transcription recombinase polymerase amplification assay for rapid detection of foot-and-mouth disease virus.

PubMed

Abd El Wahed, Ahmed; El-Deeb, Ayman; El-Tholoth, Mohamed; Abd El Kader, Hanaa; Ahmed, Abeer; Hassan, Sayed; Hoffmann, Bernd; Haas, Bernd; Shalaby, Mohamed A; Hufert, Frank T; Weidmann, Manfred

2013-01-01

Foot-and-mouth disease (FMD) is a trans-boundary viral disease of livestock, which causes huge economic losses and constitutes a serious infectious threat for livestock farming worldwide. Early diagnosis of FMD helps to diminish its impact by adequate outbreak management. In this study, we describe the development of a real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of FMD virus (FMDV). The FMDV RT-RPA design targeted the 3D gene of FMDV and a 260 nt molecular RNA standard was used for assay validation. The RT-RPA assay was fast (4-10 minutes) and the analytical sensitivity was determined at 1436 RNA molecules detected by probit regression analysis. The FMDV RT-RPA assay detected RNA prepared from all seven FMDV serotypes but did not detect classical swine fever virus or swine vesicular disease virus. The FMDV RT-RPA assay was used in the field during the recent FMD outbreak in Egypt. In clinical samples, reverse transcription polymerase chain reaction (RT-PCR) and RT-RPA showed a diagnostic sensitivity of 100% and 98%, respectively. In conclusion, FMDV RT-RPA was quicker and much easier to handle in the field than real-time RT-PCR. Thus RT-RPA could be easily implemented to perform diagnostics at quarantine stations or farms for rapid spot-of-infection detection.

Combination of longitudinal and circumferential three-dimensional esophageal dose distribution predicts acute esophagitis in hypofractionated reirradiation of patients with non-small-cell lung cancer treated in stereotactic body frame.

PubMed

Poltinnikov, Igor M; Fallon, Kevin; Xiao, Yian; Reiff, Jay E; Curran, Walter J; Werner-Wasik, Maria

2005-07-01

To evaluate dosimetric predictors of acute esophagitis (AE) and clinical outcome of patients with non-small-cell lung cancer (NSCLC) receiving reirradiation. Seventeen patients with NSCLC received reirradiation to the lung tumors/mediastinum, while immobilized in stereotactic body frame (SBF). CT simulation and hypofractionated three-dimensional radiotherapy were used. Two axial segments of esophagus contours merged together were defined as esophagus disc (ED). For each ED, the percentage (%) of the volume of esophageal circumference treated to % of prescribed dose (PD) was assessed. Number of EDs with 50% or any % of volume (V) of esophageal circumference receiving more than or equal to (>/=) 50%, 80%, and 100% of PD (50% V >/=50% PD; 50% V >/=80% PD; any % V >/=100% PD) were calculated. These dosimetric variables and the length of the esophagus within the radiation therapy (RT) port were correlated with AE using exact Wilcoxon test. A median RT dose was 32 Gy with a median fraction size of 4 Gy. Eleven of 13 patients presenting with pain and/or shortness of breath had complete or partial resolution of symptoms. Median survival time from the start of reirradiation in SBF until death was 5.5 months. AE was observed in 7 patients and resolved within 3 months of RT completion. No Grade 3 or higher events were noticed. The length of the esophagus within RT port did not predict for AE (p = 0.71). However, an increased number of EDs predicted for AE for the following dosimetric variables: 50% V >/=50% PD (p = 0.023), 50% V >/=80% PD (p = 0.047), and any % V >/=100% PD (p = 0.004). Patients with at least 2 EDs receiving >/=100% PD to any % V of circumference had AE compared to those with zero EDs. Reirradiation using hypofractionated three-dimensional radiotherapy and SBF immobilization is an effective strategy for palliation of symptoms in selected patients with recurrent NSCLC. The length of the esophagus in the RT field does not predict for AE. However, an increasing number of EDs displaying the combination of longitudinal and circumferential three-dimensional dose distribution along the esophagus is a valuable predictor for AE.

Cost-Effectiveness Analysis of Preoperative Versus Postoperative Radiation Therapy in Extremity Soft Tissue Sarcoma

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

Qu, Xuanlu M.; Louie, Alexander V.; Ashman, Jonathan

Purpose: Surgery combined with radiation therapy (RT) is the cornerstone of multidisciplinary management of extremity soft tissue sarcoma (STS). Although RT can be given in either the preoperative or the postoperative setting with similar local recurrence and survival outcomes, the side effect profiles, costs, and long-term functional outcomes are different. The aim of this study was to use decision analysis to determine optimal sequencing of RT with surgery in patients with extremity STS. Methods and Materials: A cost-effectiveness analysis was conducted using a state transition Markov model, with quality-adjusted life years (QALYs) as the primary outcome. A time horizon ofmore » 5 years, a cycle length of 3 months, and a willingness-to-pay threshold of $50,000/QALY was used. One-way deterministic sensitivity analyses were performed to determine the thresholds at which each strategy would be preferred. The robustness of the model was assessed by probabilistic sensitivity analysis. Results: Preoperative RT is a more cost-effective strategy ($26,633/3.00 QALYs) than postoperative RT ($28,028/2.86 QALYs) in our base case scenario. Preoperative RT is the superior strategy with either 3-dimensional conformal RT or intensity-modulated RT. One-way sensitivity analyses identified the relative risk of chronic adverse events as having the greatest influence on the preferred timing of RT. The likelihood of preoperative RT being the preferred strategy was 82% on probabilistic sensitivity analysis. Conclusions: Preoperative RT is more cost effective than postoperative RT in the management of resectable extremity STS, primarily because of the higher incidence of chronic adverse events with RT in the postoperative setting.« less

Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification.

PubMed

Hayasaka, Daisuke; Aoki, Kotaro; Morita, Kouichi

2013-03-04

Tick-borne encephalitis virus (TBEV) is a causative agent of acute central nervous system disease in humans. It has three subtypes, far eastern (FE), Siberian (Sib) and European (Eu) subtypes, which are distributed over a wide area of Europe and Asia. The objective of this study was to develop a simple and rapid assay for the detection of TBEV RNA by using reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) method that can differentiate the three subtypes of TBEV and can be used for clinical diagnosis and epidemiological study. Primers for TBEV-specific and subtype-specific RT-LAMP assay were designed to target the consensus sequence in NS1 of all subtypes and the consensus sequence in the E gene of each subtype, respectiveluy. In vitro transcribed RNA of Oshima strain that belongs to FE subtype was serially diluted and used to examine the sensitivity of the assay. Cross-reactivity of subtype-specific RT-LAMP assay was tested by using the RNA of Oshima and Sofjin (FE), IR-99 (Sib) and Hochosterwitz (Eu) strains. RNA extracted from the mixtures of TBEV and ticks, and of TBEV and human blood, and the mouse tissues infected with TBEV, were evaluated in the assay. Positive amplification was observed by real-time monitoring of turbidity and by visual detection of color change. The sensitivity of TBEV-specific RT-LAMP assay was 102 copies of target RNA per reaction volume. FE-specific RT-LAMP assay amplified viral genes of Oshima and Sofjin strains but not of IR-99 and Hochosterwitz strains, and of Japanese encephalitis virus. RT-LAMP assay for Sib and for Eu specifically amplified viral genes of IR-99 and Hochosterwitz strains, respectively. We also showed that tick or human blood extract did not inhibit the amplification of viral gene during the assay. Furthermore, we confirmed that the TBEV RT-LAMP could detect virus RNA from peripheral and central nervous system tissues of laboratory mice infected with TBEV. TBEV RT-LAMP assay offers a sensitive, specific, rapid and easy-to-handle method for the detection of TBEV RNA in tick samples and this may be applied in the clinical samples collected from TBE-suspected patients.

SU-E-T-50: Automatic Validation of Megavoltage Beams Modeled for Clinical Use in Radiation Therapy

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

Melchior, M; Salinas Aranda, F; 21st Century Oncology, Ft. Myers, FL

2014-06-01

Purpose: To automatically validate megavoltage beams modeled in XiO™ 4.50 (Elekta, Stockholm, Sweden) and Varian Eclipse™ Treatment Planning Systems (TPS) (Varian Associates, Palo Alto, CA, USA), reducing validation time before beam-on for clinical use. Methods: A software application that can automatically read and analyze DICOM RT Dose and W2CAD files was developed using MatLab integrated development environment.TPS calculated dose distributions, in DICOM RT Dose format, and dose values measured in different Varian Clinac beams, in W2CAD format, were compared. Experimental beam data used were those acquired for beam commissioning, collected on a water phantom with a 2D automatic beam scanningmore » system.Two methods were chosen to evaluate dose distributions fitting: gamma analysis and point tests described in Appendix E of IAEA TECDOC-1583. Depth dose curves and beam profiles were evaluated for both open and wedged beams. Tolerance parameters chosen for gamma analysis are 3% and 3 mm dose and distance, respectively.Absolute dose was measured independently at points proposed in Appendix E of TECDOC-1583 to validate software results. Results: TPS calculated depth dose distributions agree with measured beam data under fixed precision values at all depths analyzed. Measured beam dose profiles match TPS calculated doses with high accuracy in both open and wedged beams. Depth and profile dose distributions fitting analysis show gamma values < 1. Relative errors at points proposed in Appendix E of TECDOC-1583 meet therein recommended tolerances.Independent absolute dose measurements at points proposed in Appendix E of TECDOC-1583 confirm software results. Conclusion: Automatic validation of megavoltage beams modeled for their use in the clinic was accomplished. The software tool developed proved efficient, giving users a convenient and reliable environment to decide whether to accept or not a beam model for clinical use. Validation time before beam-on for clinical use was reduced to a few hours.« less

Retention assessment of magnetic nanoparticles in rat arteries with micro-computed tomography

NASA Astrophysics Data System (ADS)

Tu, Shu-Ju; Wu, Siao-Yun; Wang, Fu-Sheng; Ma, Yunn-Hwa

2014-03-01

Magnetic nanoparticles (MNPs) may serve as carriers for pharmacological agents to the target in a magnetic-force guiding system. It is essential to achieve effective retention of MNPs through the external magnet placement. However, it is difficult to estimate the retention efficiency of MNPs and validate the experimental strategies. Micro-CT was used to identify the spatial distribution of MNP retention and image analysis is then extended to evaluate the MNP delivery efficiency. Male Sprague Dawley rats were anesthetized to expose abdominal arteries with an NdFeB magnet of 4.9 kG placed by the left iliac artery. After a 20 min equilibrium period, arteries were ligated, removed and fixed in a paraformaldehyde solution. Experiments were performed with intravenous injection in our platform with two independent groups. MNPs were used in the first group, while chemical compounds of recombinant tissue plaminogen activator were attached to MNPs as rtPA (recombinant tissue plaminogen activator)-MNPs in the second group. Image analysis of micro-CT shows the average retention volume of MNPs and rtPA-MNPs in the left iliac arteries is 9.3 and 6.3 fold of that in the right. Large local aggregation of MNPs and rtPA-MNPs in the left iliac arteries is the consequence of external magnet placement, suggesting feasibility of magnetic targeting through the intravenous administration. We also determined that on average 0.57% and 0.064% of MNPs and rtPA-MNPs respectively were retained in the left iliac artery. It was estimated that the average rtPA concentration of 60.16 µg mL-1 may be achieved with rtPA-MNPs. With the micro-CT imaging approach, we accomplished visualization of the aggregation of retained particles; reconstructed 3D distribution of relative retention; estimated the average particle number of local retention; determined efficiency of targeted delivery. In particular, our quantitative image assessment suggests that intravenous administration of rtPA-MNPs may retain local concentration of rtPA high enough to induce thrombolysis.

Effects of reverberation time on the cognitive load in speech communication: theoretical considerations.

PubMed

Kjellberg, A

2004-01-01

The paper presents a theoretical analysis of possible effects of reverberation time on the cognitive load in speech communication. Speech comprehension requires not only phonological processing of the spoken words. Simultaneously, this information must be further processed and stored. All this processing takes place in the working memory, which has a limited processing capacity. The more resources that are allocated to word identification, the fewer resources are therefore left for the further processing and storing of the information. Reverberation conditions that allow the identification of almost all words may therefore still interfere with speech comprehension and memory storing. These problems are likely to be especially serious in situations where speech has to be followed continuously for a long time. An unfavourable reverberation time (RT) then could contribute to the development of cognitive fatigue, which means that working memory resources are gradually reduced. RT may also affect the cognitive load in two other ways: RT may change the distracting effects of a sound and a person's mood. Both effects could influence the cognitive load of a listener. It is argued that we need studies of RT effects in realistic long-lasting listening situations to better understand the effect of RT on speech communication. Furthermore, the effect of RT on distraction and mood need to be better understood.

Diagnosis of Cetacean morbillivirus: A sensitive one step real time RT fast-PCR method based on SYBR(®) Green.

PubMed

Sacristán, Carlos; Carballo, Matilde; Muñoz, María Jesús; Bellière, Edwige Nina; Neves, Elena; Nogal, Verónica; Esperón, Fernando

2015-12-15

Cetacean morbillivirus (CeMV) (family Paramyxoviridae, genus Morbillivirus) is considered the most pathogenic virus of cetaceans. It was first implicated in the bottlenose dolphin (Tursiops truncatus) mass stranding episode along the Northwestern Atlantic coast in the late 1980s, and in several more recent worldwide epizootics in different Odontoceti species. This study describes a new one step real-time reverse transcription fast polymerase chain reaction (real-time RT-fast PCR) method based on SYBR(®) Green to detect a fragment of the CeMV fusion protein gene. This primer set also works for conventional RT-PCR diagnosis. This method detected and identified all three well-characterized strains of CeMV: porpoise morbillivirus (PMV), dolphin morbillivirus (DMV) and pilot whale morbillivirus (PWMV). Relative sensitivity was measured by comparing the results obtained from 10-fold dilution series of PMV and DMV positive controls and a PWMV field sample, to those obtained by the previously described conventional phosphoprotein gene based RT-PCR method. Both the conventional and real-time RT-PCR methods involving the fusion protein gene were 100- to 1000-fold more sensitive than the previously described conventional RT-PCR method. Copyright © 2015 Elsevier B.V. All rights reserved.

Inactivation conditions for human Norovirus measured by an in situ capture-qRT-PCR Method

USDA-ARS?s Scientific Manuscript database

Human noroviruses (HuNoVs) are the major cause of epidemic non-bacterial gastroenteritis. Due to the inability to cultivate HuNoVs, it has been a challenge to determine their infectivity. Quantitative real-time RT-PCR (qRT-PCR) is widely used in detecting HuNoVs. However, qRT-PCR only detects the...

Performance Evaluation of Real-Time Precise Point Positioning Method

NASA Astrophysics Data System (ADS)

Alcay, Salih; Turgut, Muzeyyen

2017-12-01

Post-Processed Precise Point Positioning (PPP) is a well-known zero-difference positioning method which provides accurate and precise results. After the experimental tests, IGS Real Time Service (RTS) officially provided real time orbit and clock products for the GNSS community that allows real-time (RT) PPP applications. Different software packages can be used for RT-PPP. In this study, in order to evaluate the performance of RT-PPP, 3 IGS stations are used. Results, obtained by using BKG Ntrip Client (BNC) Software v2.12, are examined in terms of both accuracy and precision.

A real-time reverse transcription loop-mediated isothermal amplification assay for the rapid detection of yellow fever virus.

PubMed

Kwallah, Allan ole; Inoue, Shingo; Muigai, Anne W T; Kubo, Toru; Sang, Rosemary; Morita, Kouichi; Mwau, Matilu

2013-10-01

Yellow fever, a mosquito-borne disease, is an important viral hemorrhagic fever in Africa and South America where it is endemic. Detection of yellow fever virus (YFV) in Africa remains a challenge due to a lack of highly specific tests. The aim of this study was to develop and optimize a rapid detection reverse transcription loop-mediated isothermal amplification (RT-LAMP) for YFV. The RT-LAMP was done isothermally at 62 °C using a real-time turbidimeter that allowed detection within 1h. Specificity of the RT-LAMP was determined using RNA from flaviviruses and other related viruses where only YFV RNA was detected: West Nile virus, dengue viruses, Japanese encephalitis virus, Rift Valley fever virus, and chikungunya virus. In addition, equal sensitivity was also observed when the RT-LAMP and the real-time RT-PCR were compared using YFV-spiked human serum samples with a detection limit of 0.29 PFU/ml. Two Kenyan YFV wild strains showed an equal detection limit as the vaccine strain 17D in this study. The RT-LAMP reduced the time of reaction from 3h to 1h and increased sensitivity tenfold compared to RT-PCR. Therefore, this test offers a simple, rapid and reliable diagnostic tool for yellow fever when there are outbreaks of acute hemorrhagic fever in Kenya and other African countries. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India.

PubMed

Neeraja, M; Lakshmi, V; Lavanya, Vanjari; Priyanka, E N; Parida, M M; Dash, P K; Sharma, Shashi; Rao, P V Lakshmana; Reddy, Gopal

2015-01-01

Early and rapid detection of dengue virus (DENV) infection during the acute phase of illness is crucial for proper patient management and prevention of the spread of the infection. In the present study, the standardization and validation of a one step, four tube reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for rapid detection and serotyping of the DENV targeting NS1 gene using the Genie® II flourometer was carried out. The performance of the RT-LAMP was compared to RT-PCR, CDC 1-4 Real time PCR and the NS1 antigen ELISA, IgM and IgG anti DENV antibodies. Acute DENV infection was confirmed in 250/300 patients suspected clinically of DENV infection. RT- LAMP and CDC 1-4 Real time PCR assay was positive in 148/250 patients, while 92/250 patients were positive for anti- Dengue IgM and IgG antibodies. The RT-LAMP assay and the CDC real-time RT-PCR assay showed high concordance (k=1.0). The detection rate of acute DENV infection improved to 96% (240/250) when the results of RT-LAMP were combined with NS1 Ag, IgM and IgG ELISA. The RT-LAMP had a detection limit of 100 copies for DEN-1 and DEN-2, 10 copies for DEN-3 and DEN-4 compared to 1000 copies for DEN-1 and DEN-2, 100 copies for DEN-3 and DEN-4 by the conventional RT-PCR. The assay showed 100% specificity. The RT-LAMP assay developed in this study has potential use for early clinical diagnosis, serotyping and surveillance of DENV infection in endemic countries such as India. Copyright © 2014 Elsevier B.V. All rights reserved.

Rayleigh-Taylor mixing with time-dependent acceleration

NASA Astrophysics Data System (ADS)

Abarzhi, Snezhana

2016-10-01

We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a time-dependent acceleration. The acceleration is a power-law function of time, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical regimes of self-similar RT mixing-acceleration-driven Rayleigh-Taylor-type and dissipation-driven Richtymer-Meshkov-type with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with time-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.

Determining miRNA Expression Levels in Degraded RNA Samples Using Real-Time RT-qPCR and Microarray Technologies

PubMed Central

Tighe, S.; Holbrook, J.; Nadella, V.; Carmical, R.; Sol-Church, K.; Yueng, A.T.; Chittur, S.

2011-01-01

The Nucleic Acid Research Group (NARG) has previously conducted studies evaluating the impact of RNA integrity and priming strategies on cDNA synthesis and real-time RT-qPCR. The results of last year's field study as it relates to degraded RNA will be presented. In continuation of the RNA integrity theme, this year's study was designed to evaluate the impact of RNA integrity on the analysis of miRNA expression using real-time RT-qPCR. Target section was based on data obtained by the Microarray Research Group (MARG) and other published data from next gen sequencing. These 9 miRNAs represent three groups of miRNA that are expressed at low, medium or high levels in the First Choice human brain reference RNA sample. Two popular RT priming strategies tested in this study include the Megaplex miRNA TaqMan assay (ABI) and the RT2 miRNA qPCR assay (Qiagen/SA Biosciences). The basis for the ABI assay design is a target-specific stem-loop structure and reverse-transcription primer, while the Qiagen design combines poly(A) tailing and a universal reverse transcription in one cDNA synthesis reaction. For this study, the human brain reference RNA was subject to controlled degradation using RNase A to RIN (RNA Integrity Number) values of 7 (good), 4 (moderately degraded), and 2 (severely degraded).These templates were then used to assess both RT methods. In addition to this real-time RT-qPCR data, the same RNA templates were further analyzed using universal poly(A) tailing and hybridization to Affymetrix miRNA GeneChips. This talk will provide insights into RT priming strategies for miRNA and contrast the qPCR results obtained using different technologies.

On the additive effects of stimulus quality and word frequency in lexical decision: evidence for opposing interactive influences revealed by RT distributional analyses.

PubMed

Yap, Melvin J; Balota, David A; Tse, Chi-Shing; Besner, Derek

2008-05-01

The joint effects of stimulus quality and word frequency in lexical decision were examined in 4 experiments as a function of nonword type (legal nonwords, e.g., BRONE, vs. pseudohomophones, e.g., BRANE). When familiarity was a viable dimension for word-nonword discrimination, as when legal nonwords were used, additive effects of stimulus quality and word frequency were observed in both means and distributional characteristics of the response-time distributions. In contrast, when the utility of familiarity was undermined by using pseudohomophones, additivity was observed in the means but not in distributional characteristics. Specifically, opposing interactive effects in the underlying distribution were observed, producing apparent additivity in means. These findings are consistent with the suggestion that, when familiarity is deemphasized in lexical decision, cascaded processing between letter and word levels is in play, whereas, when familiarity is a viable dimension for word-nonword discrimination, processing is discrete.

New Breast Cancer Radiotherapy Technology Confers Higher Complications and Costs Before Effectiveness Proven: A Medicare Data Analysis

PubMed Central

Walter, Dawn; Tousimis, Eleni; Hayes, Mary Katherine

2018-01-01

A new breast cancer treatment, brachytherapy-based accelerated partial breast radiotherapy (RT), was adopted before long-term effectiveness evidence, potentially increasing morbidity and costs compared with whole breast RT. The aim of this study was to estimate complication rates and RT-specific and 1-year costs for a cohort of female Medicare beneficiaries diagnosed with breast cancer (N = 47 969). We analyzed 2005-2007 Medicare claims using multivariable logistic regression for complications and generalized linear models (log link, gamma distribution) for costs. Overall, 11% (n = 5296) underwent brachytherapy-based RT; 9.4% had complications. Odds of any complication were higher (odds ratio [OR]: 1.62; 95% confidence interval [CI]: 1.49-1.76) for brachytherapy versus whole breast RT, similarly to seroma (OR: 2.85; 95% CI: 1.97-4.13), wound complication/infection (OR: 1.72; 95% CI: 1.52-1.95), cellulitis (OR: 1.48; 95% CI: 1.27-1.73), and necrosis (OR: 2.07; 95% CI: 1.55-2.75). Mean RT-specific and 1-year total costs for whole breast RT were $6375, and $19 917, $4886, and $4803 lower than brachytherapy (P < .0001). Multivariable analyses indicated brachytherapy yielded 76% higher RT costs (risk ratio: 1.76; 95% CI: 1.74-1.78, P < .0001) compared with whole breast RT. Brachytherapy had higher complications and costs before long-term evidence proved its effectiveness. Policies should require treatment registries with reimbursement incentives to capture surveillance data for new technologies. PMID:29502466

Xerostomia and its predictors following parotid-sparing irradiation of head-and-neck cancer.

PubMed

Eisbruch, A; Kim, H M; Terrell, J E; Marsh, L H; Dawson, L A; Ship, J A

2001-07-01

To assess long-term xerostomia in patients receiving parotid-sparing radiation therapy (RT) for head-and-neck cancer, and to find the patient and therapy-related factors that affect its severity. From March 1994 through January 2000, 84 patients received comprehensive bilateral neck RT using conformal and multisegmental intensity-modulated RT (IMRT) aiming to spare the major salivary glands. Before RT and periodically through 2 years after the completion of RT, salivary flow rates from each of the major salivary glands were selectively measured. At the same time intervals, each patient completed an 8-item self-reported xerostomia-specific questionnaire (XQ). To gain a relative measure of the effect of RT on the minor salivary glands, whose output could not be measured, the surfaces of the oral cavity (extending to include the surface of the base of tongue) were outlined in the planning CT scans. The mean doses to the new organ ("oral cavity") were recorded. Forty-eight patients receiving unilateral neck RT were similarly studied and served as a benchmark for comparison. Factors predicting the XQ scores were analyzed using a random-effects model. The XQ was found to be reliable and valid in measuring patient-reported xerostomia. The spared salivary glands which had received moderate doses in the bilateral RT group recovered to their baseline salivary flow rates during the second year after RT, and the spared glands in the unilateral RT group, which had received very low doses, demonstrated increased salivary production beyond their pre-RT levels. The increase in the salivary flow rates during the second year after RT paralleled an improvement in xerostomia in both patient groups. The improvement in xerostomia was faster in the unilateral compared with the bilateral RT group, but the difference narrowed at 2 years. The major salivary gland flow rates had only a weak correlation with the xerostomia scores. Factors found to be independently associated with the xerostomia scores were the pre-RT baseline scores, the time since RT, and the mean doses to the major salivary glands (notably to the submandibular glands) and to the oral cavity. An improvement over time in xerostomia, occurring in tandem with rising salivary production from the spared major salivary glands, suggests a long-term clinical benefit from their sparing. The oral cavity mean dose, representing RT effect on the minor salivary glands, was found to be a significant, independent predictor of xerostomia. Thus, in addition to the major salivary glands, sparing the uninvolved oral cavity should be considered as a planning objective to further reduce xerostomia.

Bluetongue virus RNA detection by real-time rt-PCR in post-vaccination samples from cattle.

PubMed

De Leeuw, I; Garigliany, M; Bertels, G; Willems, T; Desmecht, D; De Clercq, K

2015-04-01

Bluetongue virus serotype 8 (BTV-8) was responsible for a large outbreak among European ruminant populations in 2006-2009. In spring 2008, a massive vaccination campaign was undertaken, leading to the progressive disappearance of the virus. During surveillance programmes in Western Europe in 2010-2011, a low but significant number of animals were found weakly positive using BTV-specific real-time RT-PCR, raising questions about a possible low level of virus circulation. An interference of the BTV-8 inactivated vaccine on the result of the real-time RT-PCR was also hypothesized. Several studies specifically addressed the potential association between a recent vaccination and BTV-8 RNA detection in the blood of sheep. Results were contradictory and cattles were not investigated. To enlighten this point, a large study was performed to determine the risks of detection of bluetongue vaccine-associated RNA in the blood and spleen of cattle using real-time RT-PCR. Overall, the results presented clearly demonstrate that vaccine viral RNA can reach the blood circulation in sufficient amounts to be detected by real-time RT-PCR in cattle. This BTV-8 vaccine RNA carriage appears as short lasting. © 2013 Blackwell Verlag GmbH.

Patterns of Recurrence Analysis in newly diagnosed GBM following 3D Conformal Radiation Therapy with respect to Pre-RT MR Spectroscopic Findings

PubMed Central

Park, Ilwoo; Tamai, Gregory; Lee, Michael C.; Chuang, Cynthia F.; Chang, Susan M.; Berger, Mitchel S.; Nelson, Sarah J.; Pirzkall, Andrea

2008-01-01

Purpose To determine whether the combined MRI and MR spectroscopy imaging (MRSI) prior to radiation therapy (RT) is valuable for RT target definition, and to evaluate the feasibility of replacing the current definition of uniform margins by custom shaped margins based on the information from MRI and MRSI. Methods and Materials Twenty three GBM patients underwent MRI and MRSI within 4 weeks after surgery but before the initiation of RT and at two month follow-up (FU) intervals thereafter. MRSI data were quantified on the basis of a Choline-to-NAA Index (CNI) as a measure of spectroscopic abnormality. A combined anatomic and metabolic ROI (MRI/S) consisting of T2-weighted hyperintensity, contrast enhancement (CE), resection cavity and CNI2 based on the pre-RT imaging was compared to CNI2 extent and RT dose distribution. The spatial relationship of the pre-RT MRI/S and the RT dose volume was compared to the extent of CE at each FU. Results Nine patients showed new or increased CE during FU, and 14 patients were either stable or had decreased CE. New or increased areas of CE occurred within CNI2 that was covered by 60 Gy in six patients and within the CNI2 that was not entirely covered by 60 Gy in three patients. New or increased CE resided within the pre-RT MRI/S lesion in 89 % (8/9) of the patients with new or increased CE. Conclusion These data indicate that the definition of RT target volumes according to the combined morphologic and metabolic abnormality may be sufficient for RT targeting. PMID:17513061

Image storage in radiation oncology: What did we learn from diagnostic radiology?

NASA Astrophysics Data System (ADS)

Blodgett, Kurt; Luick, Marc; Colonias, Athanasios; Gayou, Olivier; Karlovits, Stephen; Werts, E. Day

2009-02-01

The Digital Imaging and Communications in Medicine (DICOM) standard was developed by the National Electrical Manufacturers Association (NEMA) and the American College of Radiology (ACR) for medical image archiving and retrieval. An extension to this implemented a standard named DICOM-RT for use in Radiation Oncology. There are currently seven radiotherapy-specific DICOM objects which include: RT Structure Set, RT Plan, RT Dose, RT Image, RT Beams Treatment Record, RT Brachy Treatment Record, and RT Treatment Summary Record. The type of data associated with DICOM-RT includes (1) Radiation treatment planning datasets (CT, MRI, PET) with radiation treatment plans showing beam arrangements, isodose distributions, and dose volume histograms of targets/normal tissues and (2) Image-guided radiation modalities such as Siemens MVision mega-voltage cone beam CT (MV-CBCT). With the advent of such advancing technologies, there has been an exponential increase in image data collected for each patient, and the need for reliable and accessible image storage has become critical. A potential solution is a Radiation Oncology specific picture archiving and communication systems (PACS) that would allow data storage from multiple vendor devices and support the storage and retrieval needs not only of a single site but of a large, multi-facility network of radiation oncology clinics. This PACS system must be reliable, expandable, and cost-effective to operate while protecting sensitive patient image information in a Health Insurance Portability and Accountability Act (HIPAA) compliant environment. This paper emphasizes the expanding DICOM-RT storage requirements across our network of 8 radiation oncology clinics and the initiatives we undertook to address the increased volume of data by using the ImageGrid (CANDELiS Inc, Irvine CA) server and the IGViewer license (CANDELiS Inc, Irvine CA) to create a DICOM-RT compatible PACS system.

Distinct Thalamic Reticular Cell Types Differentially Modulate Normal and Pathological Cortical Rhythms.

PubMed

Clemente-Perez, Alexandra; Makinson, Stefanie Ritter; Higashikubo, Bryan; Brovarney, Scott; Cho, Frances S; Urry, Alexander; Holden, Stephanie S; Wimer, Matthew; Dávid, Csaba; Fenno, Lief E; Acsády, László; Deisseroth, Karl; Paz, Jeanne T

2017-06-06

Integrative brain functions depend on widely distributed, rhythmically coordinated computations. Through its long-ranging connections with cortex and most senses, the thalamus orchestrates the flow of cognitive and sensory information. Essential in this process, the nucleus reticularis thalami (nRT) gates different information streams through its extensive inhibition onto other thalamic nuclei, however, we lack an understanding of how different inhibitory neuron subpopulations in nRT function as gatekeepers. We dissociated the connectivity, physiology, and circuit functions of neurons within rodent nRT, based on parvalbumin (PV) and somatostatin (SOM) expression, and validated the existence of such populations in human nRT. We found that PV, but not SOM, cells are rhythmogenic, and that PV and SOM neurons are connected to and modulate distinct thalamocortical circuits. Notably, PV, but not SOM, neurons modulate somatosensory behavior and disrupt seizures. These results provide a conceptual framework for how nRT may gate incoming information to modulate brain-wide rhythms. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The effects of one-time inversion tillage on soil physical properties after long-term reduced tillage

NASA Astrophysics Data System (ADS)

Kuhwald, Michael; Augustin, Katja; Duttmann, Rainer

2017-04-01

The positive effects of reduced tillage on soil stability and on various soil functions such as infiltrability or saturated hydraulic conductivity are known in general. However, long-term employment of conservation tillage can increase weed pressure, damage by mice and soil compaction. Thus, the application of one-time inversion tillage (occasional or strategic tillage) is customarily used as a method for overcoming these drawbacks. Hitherto, the effects of one-time inversion tillage on soil physical properties have not been investigated. This study focuses on analysing whether the improved soil physical properties derived by long-term reduced tillage remain after one-time inversion tillage by mouldboard plough. The study was carried out in a 5.5 ha field in the southern part of Lower Saxony, Germany. Since 1996, this field has been subdivided into three plots, one managed conventionally by using a mouldboard plough (CT), while in the others a chisel plough (RT1) and a disk harrow (RT2) were employed. In October 2014, the entire field was ploughed by mouldboard plough to a depth of 30 cm. During the following year, four field studies were conducted to analyse the effects of this one-time inversion tillage on volumetric soil water content, bulk density, saturated hydraulic conductivity and infiltration rate. Additionally, penetration resistance measurements taken across the entire field were interpolated by kriging to analyse the spatial distribution of soil characteristics. The surveys of RT1 and RT2 were compared with CT and with analyses conducted before the one-time inversion tillage. This study shows that positive effects of long-term conservation tillage on several soil physical characteristics still remain after one-time mouldboard ploughing. Throughout the entire cropping season, the topsoil tilled under former conservation tillage practices revealed significantly higher (p < 0.05) values of saturated hydraulic conductivities and infiltration rates compared to the plot that experienced continuously conventional tillage. Moreover, field-wide measuring of penetration resistance indicated the removal of the compaction zone developed under conservation tillage in soil depths between 10 and 20 cm. After mouldboard ploughing, penetration resistance in the topsoil was significantly (p < 0.05) reduced in both plots, showing the same order of magnitude as measured in the conventionally managed plot. The results of this study suggest that one-time inversion tillage with a mouldboard plough offers a suitable management option for overcoming some of the main disadvantages associated with long-term conservation tillage, while conserving the improved soil physical properties and functions.

Variations in automatically recorded rumination time as explained by variations in intake of dietary fractions and milk production, and between-cow variation.

PubMed

Byskov, M V; Nadeau, E; Johansson, B E O; Nørgaard, P

2015-06-01

Individual recording of rumination time (RT) is now possible in commercial dairy herds, through development of a microphone-based sensor, which is able to record RT by the sound of rumination activity. The objectives of this study were to examine the relationship between daily RT and intakes of different dietary fractions, the relationship between RT in minutes per kilogram of dry matter intake (DMI) and milk production, and to examine the variation in RT within and between mid-lactating dairy cows. Data from 3 production trials were used in which a total of 27 different diets were fed. The data contained 761, 290, and 203 daily recordings of RT, milk yield, milk components, DMI, and intake of dietary fractions recorded on 29, 26, and 24 Holstein and Swedish Red cows from trials 1, 2, and 3, respectively. The dietary fractions included forage neutral detergent fiber (NDF), concentrate NDF, crude protein, sugar, starch, and the remaining fraction represented by organic matter--(forage NDF+concentrate NDF+crude protein+sugar+starch). The relationship between the dietary fractions and RT was analyzed in 2 steps. In step 1, the dietary fractions, which were significantly related to RT, were selected and simultaneously checked for multicollinearity between the dietary components; in step 2, a multivariate model, including the effect of repeated measurements, the main effect of the selected dietary fractions from step 1, random effects of cow(trial) and trial, and information on breed, days in milk, and parity was used to analyze the relationship between RT and the selected dietary fractions. Relationships between RT in minutes per kilogram of DMI and milk yield and milk components were analyzed, using the same multivariate model as in step 2. Approximately 32% of the variation in daily RT could be explained by variations in intakes of the dietary fractions, whereas 48% of the total variation in RT was accounted for by individual variations between cows. Intakes of forage NDF and starch were positively related to daily RT, whereas intakes of sugar and the remaining fraction were negatively related to daily RT. Rumination time in minutes per kilogram of DMI was negatively related to milk yield and protein percentage, but positively related to milk fat percentage. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Advanced ECCD based NTM control in closed-loop operation at ASDEX Upgrade (AUG)

NASA Astrophysics Data System (ADS)

Reich, Matthias; Barrera-Orte, Laura; Behler, Karl; Bock, Alexander; Giannone, Louis; Maraschek, Marc; Poli, Emanuele; Rapson, Chris; Stober, Jörg; Treutterer, Wolfgang

2012-10-01

In high performance plasmas, Neoclassical Tearing Modes (NTMs) are regularly observed at reactor-grade beta-values. They limit the achievable normalized beta, which is undesirable because fusion performance scales as beta squared. The method of choice for controlling and avoiding NTMs at AUG is the deposition of ECCD inside the magnetic island for stabilization in real-time (rt). Our approach to tackling such complex control problems using real-time diagnostics allows rigorous optimization of all subsystems. Recent progress in rt-equilibrium reconstruction (< 3.5 ms), rt-localization of NTMs (< 8 ms) and rt beam tracing (< 25 ms) allows closed-loop feedback operation using multiple movable mirrors as the ECCD deposition actuator. The rt-equilibrium uses function parametrization or a fast Grad-Shafranov solver with an option to include rt-MSE measurements. The island localization is based on a correlation of ECE and filtered Mirnov signals. The rt beam-tracing module provides deposition locations and their derivative versus actuator position of multiple gyrotrons. The ``MHD controller'' finally drives the actuators. Results utilizing closed-loop operation with multiple gyrotrons and their effect on NTMs are shown.

Timing of Radiotherapy and Outcome in Patients Receiving Adjuvant Endocrine Therapy

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

Karlsson, Per, E-mail: per.karlsson@oncology.gu.s; Cole, Bernard F.; International Breast Cancer Study Group Statistical Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA

2011-06-01

Purpose: To evaluate the association between the interval from breast-conserving surgery (BCS) to radiotherapy (RT) and the clinical outcome among patients treated with adjuvant endocrine therapy. Patients and Methods: Patient information was obtained from three International Breast Cancer Study Group trials. The analysis was restricted to 964 patients treated with BCS and adjuvant endocrine therapy. The patients were divided into two groups according to the median number of days between BCS and RT and into four groups according to the quartile of time between BCS and RT. The endpoints were the interval to local recurrence, disease-free survival, and overall survival.more » Proportional hazards regression analysis was used to perform comparisons after adjustment for baseline factors. Results: The median interval between BCS and RT was 77 days. RT timing was significantly associated with age, menopausal status, and estrogen receptor status. After adjustment for these factors, no significant effect of a RT delay {<=}20 weeks was found. The adjusted hazard ratio for RT within 77 days vs. after 77 days was 0.94 (95% confidence interval [CI], 0.47-1.87) for the interval to local recurrence, 1.05 (95% CI, 0.82-1.34) for disease-free survival, and 1.07 (95% CI, 0.77-1.49) for overall survival. For the interval to local recurrence the adjusted hazard ratio for {<=}48, 49-77, and 78-112 days was 0.90 (95% CI, 0.34-2.37), 0.86 (95% CI, 0.33-2.25), and 0.89 (95% CI, 0.33-2.41), respectively, relative to {>=}113 days. Conclusion: A RT delay of {<=}20 weeks was significantly associated with baseline factors such as age, menopausal status, and estrogen-receptor status. After adjustment for these factors, the timing of RT was not significantly associated with the interval to local recurrence, disease-free survival, or overall survival.« less

Development of efficient time-evolution method based on three-term recurrence relation

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

Akama, Tomoko, E-mail: a.tomo---s-b-l-r@suou.waseda.jp; Kobayashi, Osamu; Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp

The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrödinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function.more » Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost.« less

A response-time approach to comparing generalized rational and take-the-best models of decision making.

PubMed

Bergert, F Bryan; Nosofsky, Robert M

2007-01-01

The authors develop and test generalized versions of take-the-best (TTB) and rational (RAT) models of multiattribute paired-comparison inference. The generalized models make allowances for subjective attribute weighting, probabilistic orders of attribute inspection, and noisy decision making. A key new test involves a response-time (RT) approach. TTB predicts that RT is determined solely by the expected time required to locate the 1st discriminating attribute, whereas RAT predicts that RT is determined by the difference in summed evidence between the 2 alternatives. Critical test pairs are used that partially decouple these 2 factors. Under conditions in which ideal observer TTB and RAT strategies yield equivalent decisions, both the RT results and the estimated attribute weights suggest that the vast majority of subjects adopted the generalized TTB strategy. The RT approach is also validated in an experimental condition in which use of a RAT strategy is essentially forced upon subjects. (c) 2007 APA, all rights reserved.

Measurement of left ventricular dyssynchrony in patients with ischaemic cardiomyopathy: a comparison of real‐time three‐dimensional and tissue Doppler echocardiography

PubMed Central

Burgess, Malcolm I; Jenkins, Carly; Chan, Jonathan; Marwick, Thomas H

2007-01-01

Background Real‐time three‐dimensional echocardiography (RT3DE) is an alternative modality to tissue Doppler imaging (TDI) for assessment of intraventricular dyssynchrony but its role is yet to be defined. Objectives To (1) compare RT3DE and TDI for assessment of intraventricular dyssynchrony; (2) determine whether the two techniques agreed regarding the magnitude of dyssynchrony and identification of the site of maximal mechanical delay; and (3) investigate the reason for disagreement. Patients 100 patients with ischaemic cardiomyopathy. Setting Tertiary referral cardiac unit. Main outcome measures Dispersion in time interval from QRS onset to peak sustained systolic tissue velocity by TDI (SD‐TTV) and to minimal systolic volume by RT3DE (SD‐T3D) between 12 ventricular segments. Results RT3DE image quality was adequate for measurement of SD‐T3D in 77 (77%) patients. In the whole population, SD‐TTV was 40 (20) ms and SD‐T3D was 8.3% (3.4%). RT3DE identified a smaller proportion of patients as having significant dyssynchrony than TDI (49 (64%) patients vs 32 (42%) patients; p<0.01). The correlation between SD‐TTV and SD‐T3D was poor (r = 0.11, p = NS). There was concordance between TDI and RT3DE in identifying the site of maximal mechanical delay in 12 (16%) patients. Validating the two techniques with anatomical M‐mode (AMM) as a parameter of radial timing revealed better agreement with RT3DE than with TDI (χ2 = 11.8, p = 0.001). Conclusion In patients with ischaemic cardiomyopathy, TDI and RT3DE show poor agreement for evaluating the magnitude of intraventricular dyssynchrony and the site of maximal mechanical delay. This may partly relate to their respective assessment of longitudinal versus radial timing. PMID:17344326

Resistance training attenuates fat mass regain after weight loss in ovariectomized rats.

PubMed

Pighon, Abdolnaser; Paquette, Amélie; Barsalani, Razieh; Chapados, Natalie Ann; Rabasa-Lhoret, Rémi; Yasari, Siham; Prud'homme, Denis; Lavoie, Jean-Marc

2009-09-20

The aim of the present study was to investigate the effects of maintaining only one of the two components of a food restriction (FR)+resistance training (RT) regimen on the regain of body weight and fat mass (liver and adipocytes) in ovariectomized (Ovx) rats. Five week Ovx rats were submitted to a weight loss program consisting of a 26% FR combined with RT (OvxFR+RT) for 8 weeks. RT consisted of climbing a 1.5m vertical grid with a load attached to the tail, 20-40 times with progressively increasing loads 4 times/week. Following this weight loss intervention, OvxFR+RT rats were sub-divided into 3 groups for an additional 5 weeks: 2 groups went back to a normal ad libitum feeding with or without RT and the other group kept only FR. Combined FR+RT program in Ovx rats led to lower body mass gain, liver triacylglycerol (TAG) levels, and fat mass gain compared to sedentary normally fed Ovx rats (P<0.01). Stopping both FR and RT over a 5 week period resulted in the regain of body weight, intra-abdominal fat pad weight and liver TAG (P<0.01). When only FR was maintained, the regain of body and fat pad weight as well as liver and plasma TAG concentrations was completely prevented. However, when only RT was maintained, regain in the aforementioned parameters was attenuated but not prevented (P<0.05). It is concluded that following a FR+RT weight loss program, continuation of only RT constitutes an asset to attenuate body weight and fat mass regain in Ovx rats; although the impact is less than the maintaining FR alone. These results suggest that, in post-menopausal women, RT is a positive strategy to reduce body weight and fat mass relapse.

[Fluoroscopy dose reduction of computed tomography guided chest interventional radiology using real-time iterative reconstruction].

PubMed

Hasegawa, Hiroaki; Mihara, Yoshiyuki; Ino, Kenji; Sato, Jiro

2014-11-01

The purpose of this study was to evaluate the radiation dose reduction to patients and radiologists in computed tomography (CT) guided examinations for the thoracic region using CT fluoroscopy. Image quality evaluation of the real-time filtered back-projection (RT-FBP) images and the real-time adaptive iterative dose reduction (RT-AIDR) images was carried out on noise and artifacts that were considered to affect the CT fluoroscopy. The image standard deviation was improved in the fluoroscopy setting with less than 30 mA on 120 kV. With regard to the evaluation of artifact visibility and the amount generated by the needle attached to the chest phantom, there was no significant difference between the RT-FBP images with 120 kV, 20 mA and the RT-AIDR images with low-dose conditions (greater than 80 kV, 30 mA and less than 120 kV, 20 mA). The results suggest that it is possible to reduce the radiation dose by approximately 34% at the maximum using RT-AIDR while maintaining image quality equivalent to the RT-FBP images with 120 V, 20 mA.

Trends and advances in food analysis by real-time polymerase chain reaction.

PubMed

Salihah, Nur Thaqifah; Hossain, Mohammad Mosharraf; Lubis, Hamadah; Ahmed, Minhaz Uddin

2016-05-01

Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling.

A Qualitative Analysis of Real-Time Continuous Glucose Monitoring Data Sharing with Care Partners: To Share or Not to Share?

PubMed

Litchman, Michelle L; Allen, Nancy A; Colicchio, Vanessa D; Wawrzynski, Sarah E; Sparling, Kerri M; Hendricks, Krissa L; Berg, Cynthia A

2018-01-01

Little research exists regarding how real-time continuous glucose monitoring (RT-CGM) data sharing plays a role in the relationship between patients and their care partners. To (1) identify the benefits and challenges related to RT-CGM data sharing from the patient and care partner perspective and (2) to explore the number and type of individuals who share and follow RT-CGM data. This qualitative content analysis was conducted by examining publicly available blogs focused on RT-CGM and data sharing. A thematic analysis of blogs and associated comments was conducted. A systematic appraisal of personal blogs examined 39 blogs with 206 corresponding comments. The results of the study provided insight about the benefits and challenges related to individuals with diabetes sharing their RT-CGM data with a care partner(s). The analysis resulted in three themes: (1) RT-CGM data sharing enhances feelings of safety, (2) the need to communicate boundaries to avoid judgment, and (3) choice about sharing and following RT-CGM data. RT-CGM data sharing occurred within dyads (n = 46), triads (n = 15), and tetrads (n = 2). Adults and children with type 1 diabetes and their care partners are empowered by the ability to share and follow RT-CGM data. Our findings suggest that RT-CGM data sharing between an individual with diabetes and their care partner can complicate relationships. Healthcare providers need to engage patients and care partners in discussions about best practices related to RT-CGM sharing and following to avoid frustrations within the relationship.

Use of quantitative real-time RT-PCR to investigate the correlation between viremia and viral shedding of canine distemper virus, and infection outcomes in experimentally infected dogs.

PubMed

Sehata, Go; Sato, Hiroaki; Ito, Toshihiro; Imaizumi, Yoshitaka; Noro, Taichi; Oishi, Eiji

2015-07-01

We used real-time RT-PCR and virus titration to examine canine distemper virus (CDV) kinetics in peripheral blood and rectal and nasal secretions from 12 experimentally infected dogs. Real-time RT-PCR proved extremely sensitive, and the correlation between the two methods for rectal and nasal (r=0.78, 0.80) samples on the peak day of viral RNA was good. Although the dogs showed diverse symptoms, viral RNA kinetics were similar; the peak of viral RNA in the symptomatic dogs was consistent with the onset of symptoms. These results indicate that real-time RT-PCR is sufficiently sensitive to monitor CDV replication in experimentally infected dogs regardless of the degree of clinical manifestation and suggest that the peak of viral RNA reflects active CDV replication.

Use of quantitative real-time RT-PCR to investigate the correlation between viremia and viral shedding of canine distemper virus, and infection outcomes in experimentally infected dogs

PubMed Central

SEHATA, Go; SATO, Hiroaki; ITO, Toshihiro; IMAIZUMI, Yoshitaka; NORO, Taichi; OISHI, Eiji

2015-01-01

We used real-time RT-PCR and virus titration to examine canine distemper virus (CDV) kinetics in peripheral blood and rectal and nasal secretions from 12 experimentally infected dogs. Real-time RT-PCR proved extremely sensitive, and the correlation between the two methods for rectal and nasal (r=0.78, 0.80) samples on the peak day of viral RNA was good. Although the dogs showed diverse symptoms, viral RNA kinetics were similar; the peak of viral RNA in the symptomatic dogs was consistent with the onset of symptoms. These results indicate that real-time RT-PCR is sufficiently sensitive to monitor CDV replication in experimentally infected dogs regardless of the degree of clinical manifestation and suggest that the peak of viral RNA reflects active CDV replication. PMID:25728411

Comparison of reverse transcriptase PCR, reverse transcriptase loop-mediated isothermal amplification, and culture-based assays for Salmonella detection from pork processing environments.

PubMed

Techathuvanan, Chayapa; Draughon, Frances Ann; D'Souza, Doris Helen

2011-02-01

Novel rapid Salmonella detection assays without the need for sophisticated equipment or labor remain in high demand. Real-time reverse transcriptase PCR (RT-PCR) assays, though rapid and sensitive, require expensive thermocyclers, while a novel RT loop-mediated isothermal amplification (RT-LAMP) method requires only a simple water bath. Our objective was to compare the detection sensitivity of Salmonella Typhimurium from the pork processing environment by RT-LAMP, RT-PCR, and culture-based assays. Carcass and surface swabs and carcass rinses were obtained from a local processing plant. Autoclaved carcass rinses (500 ml) were spiked with Salmonella Typhimurium and filtered. Filters were placed in stomacher bags containing tetrathionate broth (TTB) and analyzed with or without 10-h enrichment at 37 °C. Natural swabs were stomached with buffered peptone water, and natural carcass rinses were filtered, preenriched, and further enriched in TTB. Serially-diluted enriched samples were enumerated by spread plating on xylose lysine Tergitol 4 agar. RNA was extracted from 5 ml of enriched TTB with TRIzol. RT-LAMP assay using previously described invA primers was conducted at 62 °C for 90 min in a water bath with visual detection and by gel electrophoresis. SYBR Green I-based-real-time RT-PCR was carried out with invA primers followed by melt temperature analysis. The results of RT-LAMP detection for spiked carcass rinses were comparable to those of RT-PCR and cultural plating, with detection limits of 1 log CFU/ml, although they were obtained significantly faster, within 24 h including preenrichment and enrichment. RT-LAMP showed 4 of 12 rinse samples positive, while RT-PCR showed 1 of 12 rinse samples positive. For swabs, 6 of 27 samples positive by RT-LAMP and 5 of 27 by RT-PCR were obtained. This 1-day RT-LAMP assay shows promise for routine Salmonella screening by the pork industry. Copyright ©, International Association for Food Protection

Consistency evaluation between EGSnrc and Geant4 charged particle transport in an equilibrium magnetic field.

PubMed

Yang, Y M; Bednarz, B

2013-02-21

Following the proposal by several groups to integrate magnetic resonance imaging (MRI) with radiation therapy, much attention has been afforded to examining the impact of strong (on the order of a Tesla) transverse magnetic fields on photon dose distributions. The effect of the magnetic field on dose distributions must be considered in order to take full advantage of the benefits of real-time intra-fraction imaging. In this investigation, we compared the handling of particle transport in magnetic fields between two Monte Carlo codes, EGSnrc and Geant4, to analyze various aspects of their electromagnetic transport algorithms; both codes are well-benchmarked for medical physics applications in the absence of magnetic fields. A water-air-water slab phantom and a water-lung-water slab phantom were used to highlight dose perturbations near high- and low-density interfaces. We have implemented a method of calculating the Lorentz force in EGSnrc based on theoretical models in literature, and show very good consistency between the two Monte Carlo codes. This investigation further demonstrates the importance of accurate dosimetry for MRI-guided radiation therapy (MRIgRT), and facilitates the integration of a ViewRay MRIgRT system in the University of Wisconsin-Madison's Radiation Oncology Department.

Consistency evaluation between EGSnrc and Geant4 charged particle transport in an equilibrium magnetic field

NASA Astrophysics Data System (ADS)

Yang, Y. M.; Bednarz, B.

2013-02-01

Following the proposal by several groups to integrate magnetic resonance imaging (MRI) with radiation therapy, much attention has been afforded to examining the impact of strong (on the order of a Tesla) transverse magnetic fields on photon dose distributions. The effect of the magnetic field on dose distributions must be considered in order to take full advantage of the benefits of real-time intra-fraction imaging. In this investigation, we compared the handling of particle transport in magnetic fields between two Monte Carlo codes, EGSnrc and Geant4, to analyze various aspects of their electromagnetic transport algorithms; both codes are well-benchmarked for medical physics applications in the absence of magnetic fields. A water-air-water slab phantom and a water-lung-water slab phantom were used to highlight dose perturbations near high- and low-density interfaces. We have implemented a method of calculating the Lorentz force in EGSnrc based on theoretical models in literature, and show very good consistency between the two Monte Carlo codes. This investigation further demonstrates the importance of accurate dosimetry for MRI-guided radiation therapy (MRIgRT), and facilitates the integration of a ViewRay MRIgRT system in the University of Wisconsin-Madison's Radiation Oncology Department.

The role of RT carry-over for congruence sequence effects in masked priming.

PubMed

Huber-Huber, Christoph; Ansorge, Ulrich

2017-05-01

The present study disentangles 2 sources of the congruence sequence effect with masked primes: congruence and response time of the previous trial (reaction time [RT] carry-over). Using arrows as primes and targets and a metacontrast masking procedure we found congruence as well as congruence sequence effects. In addition, congruence sequence effects decreased when RT carry-over was accounted for in a mixed model analysis, suggesting that RT carry-over contributes to congruence sequence effects in masked priming. Crucially, effects of previous trial congruence were not cancelled out completely indicating that RT carry-over and previous trial congruence are 2 sources feeding into the congruence sequence effect. A secondary task requiring response speed judgments demonstrated general awareness of response speed (Experiments 1), but removing this secondary task (Experiment 2) showed that RT carry-over effects were also present in single-task conditions. During (dual-task) prime-awareness test parts of both experiments, however, RT carry-over failed to modulate congruence effects, suggesting that some task sets of the participants can prevent the effect. The basic RT carry-over effects are consistent with the conflict adaptation account, with the adaptation to the statistics of the environment (ASE) model, and possibly with the temporal learning explanation. Additionally considering the task-dependence of RT carry-over, the results are most compatible with the conflict adaptation account. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Prospective evaluation of the prevalence and severity of fatigue in patients with prostate cancer undergoing radical external beam radiotherapy and neoadjuvant hormone therapy.

PubMed

Truong, Pauline T; Berthelet, Eric; Lee, Junella C; Petersen, Ross; Lim, Jan T W; Gaul, Catherine A; Pai, Howard; Blood, Paul; Ludgate, Charles M

2006-06-01

To prospectively evaluate the prevalence and severity of fatigue and its impact on quality of life (QOL) during and after radical external beam radiotherapy (RT) for prostate cancer. Twenty-eight men with prostate cancer undergoing RT over 6-8 consecutive weeks were prospectively accrued. The Brief Fatigue Inventory (BFI), a validated fatigue assessment tool, was administered at five time points: baseline (week 1), middle of RT (week 3-4), end of RT (last week of RT), and follow-up (median 6.5 weeks after RT). The BFI contained nine questions, each using 0-10 ratings to quantify fatigue severity and interference with six QOL domains. The prevalence of moderate-severe fatigue was plotted as a function of time. Mean sum and subscale scores at each time point were compared to baseline scores using Wilcoxon tests. Linear regression analyses were performed to assess associations between fatigue scores and age, tumor and treatment characteristics. The median age was 69 years (range 57-84), Gleason score 7 (range 6-10), and presenting PSA 9.0 ng/mL (range 2.5 ng/mL-103.0 ng/mL). Patients were treated once daily to a median dose of 74 Gy (range 60 Gy-78 Gy) over a median of 37 fractions (range 30-39). Hormone therapy was used in all patients (median duration 12.2 months). The prevalence of moderate-severe present fatigue increased from 7% at baseline to 8% at mid-RT and 32% at RT completion. Compared to baseline (mean score 11.5), fatigue increased significantly mid-RT (mean score 14.6, p = 0.03) and peaked at the end of RT (mean score 23.5, p = 0.001). Fatigue significantly interfered with walking ability, normal work, daily chores, and enjoyment of life only at the end of RT. After RT completion, fatigue improved but remained higher compared to baseline at 6.5 weeks of follow-up (mean score 15.0, p = 0.02). On linear regression analysis, age, Gleason score, PSA, T-stage, hormone therapy duration, RT dose and fractions were not significantly associated with mean fatigue scores. Patients undergoing 6-8 weeks of RT experienced significant fatigue adversely affecting QOL persisting after therapy completion. Since walking ability was not affected until the end of RT, a walking exercise intervention to combat fatigue is likely feasible and is being investigated.

Removing the effect of response time on brain activity reveals developmental differences in conflict processing in the posterior medial prefrontal cortex.

PubMed

Carp, Joshua; Fitzgerald, Kate Dimond; Taylor, Stephan F; Weissman, Daniel H

2012-01-02

In functional magnetic resonance imaging (fMRI) studies, researchers often attempt to ensure that group differences in brain activity are not confounded with group differences in mean reaction time (RT). However, even when groups are matched for performance, they may differ in terms of the RT-BOLD relationship: the degree to which brain activity varies with RT on a trial-by-trial basis. Group activation differences might therefore be influenced by group differences in the relationship between brain activity and time on task. Here, we investigated whether correcting for this potential confound alters group differences in brain activity. Specifically, we reanalyzed data from a functional MRI study of response conflict in children and adults, in which conventional analyses indicated that conflict-related activity did not differ between groups. We found that the RT-BOLD relationship was weaker in children than in adults. Consequently, after removing the effect of RT on brain activity, children exhibited greater conflict-related activity than adults in both the posterior medial prefrontal cortex and the right dorsolateral prefrontal cortex. These results identify the RT-BOLD relationship as an important potential confound in fMRI studies of group differences. They also suggest that the magnitude of the RT-BOLD relationship may be a useful biomarker of brain maturity. Copyright © 2011 Elsevier Inc. All rights reserved.

A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay.

PubMed

Amer, H M; Abd El Wahed, A; Shalaby, M A; Almajhdi, F N; Hufert, F T; Weidmann, M

2013-11-01

Bovine coronavirus (BCoV) is an economically significant cause of calf scours and winter dysentery of adult cattle, and may induce respiratory tract infections in cattle of all ages. Early diagnosis of BCoV helps to diminish its burden on the dairy and beef industry. Real-time RT-PCR assay for the detection of BCoV has been described, but it is relatively expensive, requires well-equipped laboratories and is not suitable for on-site screening. A novel assay, using reverse transcription recombinase polymerase amplification (RT-RPA), for the detection of BCoV is developed. The BCoV RT-RPA was rapid (10-20 min) and has an analytical sensitivity of 19 molecules. No cross-reactivity with other viruses causing bovine gastrointestinal and/or respiratory infections was observed. The assay performance on clinical samples was validated by testing 16 fecal and 14 nasal swab specimens and compared to real-time RT-PCR. Both assays provided comparable results. The RT-RPA assay was significantly more rapid than the real-time RT-PCR assay. The BCoV RT-RPA constitutes a suitable accurate, sensitive and rapid alternative to the common measures used for BCoV diagnosis. In addition, the use of a portable fluorescence reading device extends its application potential to use in the field and point-of-care diagnosis. Copyright © 2013 Elsevier B.V. All rights reserved.

A broadly reactive one-step real-time RT-PCR assay for rapid and sensitive detection of hepatitis E virus.

PubMed

Jothikumar, Narayanan; Cromeans, Theresa L; Robertson, Betty H; Meng, X J; Hill, Vincent R

2006-01-01

Hepatitis E virus (HEV) is transmitted by the fecal-oral route and causes sporadic and epidemic forms of acute hepatitis. Large waterborne HEV epidemics have been documented exclusively in developing countries. At least four major genotypes of HEV have been reported worldwide: genotype 1 (found primarily in Asian countries), genotype 2 (isolated from a single outbreak in Mexico), genotype 3 (identified in swine and humans in the United States and many other countries), and genotype 4 (identified in humans, swine and other animals in Asia). To better detect and quantitate different HEV strains that may be present in clinical and environmental samples, we developed a rapid and sensitive real-time RT-PCR assay for the detection of HEV RNA. Primers and probes for the real-time RT-PCR were selected based on the multiple sequence alignments of 27 sequences of the ORF3 region. Thirteen HEV isolates representing genotypes 1-4 were used to standardize the real-time RT-PCR assay. The TaqMan assay detected as few as four genome equivalent (GE) copies of HEV plasmid DNA and detected as low as 0.12 50% pig infectious dose (PID50) of swine HEV. Different concentrations of swine HEV (120-1.2PID50) spiked into a surface water concentrate were detected in the real-time RT-PCR assay. This is the first reporting of a broadly reactive TaqMan RT-PCR assay for the detection of HEV in clinical and environmental samples.

Choice reaction time to movement of eccentric visual targets during concurrent rotary acceleration

NASA Technical Reports Server (NTRS)

Hamerman, J. A.

1979-01-01

This study investigates the influence of concurrent rotary acceleration on choice reaction time (RT) to a small, accelerating visual cursor on a cathode-ray tube. Subjects sat in an enclosed rotating device at the center of rotation and observed a 3-mm dot accelerating at different rates across a cathode-ray tube. The dot was viewed at various eccentricities under conditions of visual stimulation alone and with concurrent rotary acceleration. Subjects responded to both vertical and horizontal dot movements. There was a significant inverse relationship between choice RT and level of dot acceleration (p less than .001), and a significant direct relationship between choice RT and eccentricity (p less than .001). There was no significant difference between choice RT to vertical or horizontal dot motion (p greater than .25), and choice RT was not significantly affected by concurrent rotary acceleration (p greater than .10). The results are discussed in terms of the effects of vestibular stimulation on choice RT to visual motion.

Real-time automatic hospital-wide surveillance of nosocomial infections and outbreaks in a large Chinese tertiary hospital

PubMed Central

2014-01-01

Background We aimed to develop a real-time nosocomial infection surveillance system (RT-NISS) to monitor all nosocomial infections (NIs) and outbreaks in a Chinese comprehensive hospital to better prevent and control NIs. Methods The screening algorithm used in RT-NISS included microbiological reports, antibiotic usage, serological and molecular testing, imaging reports, and fever history. The system could, in real-time, identify new NIs, record data, and produce time-series reports to align NI cases. Results Compared with a manual survey of NIs (the gold standard), the sensitivity and specificity of RT-NISS was 98.8% (84/85) and 93.0% (827/889), with time-saving efficiencies of about 200 times. RT-NISS obtained the highest hospital-wide monthly NI rate of 2.62%, while physician and medical record reviews reported rates of 1.52% and 2.35% respectively. It took about two hours for one infection control practitioner (ICP) to deal with 70 new suspicious NI cases; there were 3,500 inpatients each day in the study hospital. The system could also provide various updated data (i.e. the daily NI rate, surgical site infection (SSI) rate) for each ward, or the entire hospital. Within 3 years of implementing RT-NISS, the ICPs monitored and successfully controlled about 30 NI clusters and 4 outbreaks at the study hospital. Conclusions Just like the “ICPs’ eyes”, RT-NISS was an essential and efficient tool for the day-to-day monitoring of all NIs and outbreak within the hospital; a task that would not have been accomplished through manual process. PMID:24475790

A novel method of multiple nucleic acid detection: Real-time RT-PCR coupled with probe-melting curve analysis.

PubMed

Han, Yang; Hou, Shao-Yang; Ji, Shang-Zhi; Cheng, Juan; Zhang, Meng-Yue; He, Li-Juan; Ye, Xiang-Zhong; Li, Yi-Min; Zhang, Yi-Xuan

2017-11-15

A novel method, real-time reverse transcription PCR (real-time RT-PCR) coupled with probe-melting curve analysis, has been established to detect two kinds of samples within one fluorescence channel. Besides a conventional TaqMan probe, this method employs another specially designed melting-probe with a 5' terminus modification which meets the same label with the same fluorescent group. By using an asymmetric PCR method, the melting-probe is able to detect an extra sample in the melting stage effectively while it almost has little influence on the amplification detection. Thus, this method allows the availability of united employment of both amplification stage and melting stage for detecting samples in one reaction. The further demonstration by simultaneous detection of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) in one channel as a model system is presented in this essay. The sensitivity of detection by real-time RT-PCR coupled with probe-melting analysis was proved to be equal to that detected by conventional real-time RT-PCR. Because real-time RT-PCR coupled with probe-melting analysis can double the detection throughputs within one fluorescence channel, it is expected to be a good solution for the problem of low-throughput in current real-time PCR. Copyright © 2017 Elsevier Inc. All rights reserved.

Fast interactive real-time volume rendering of real-time three-dimensional echocardiography: an implementation for low-end computers

NASA Technical Reports Server (NTRS)

Saracino, G.; Greenberg, N. L.; Shiota, T.; Corsi, C.; Lamberti, C.; Thomas, J. D.

2002-01-01

Real-time three-dimensional echocardiography (RT3DE) is an innovative cardiac imaging modality. However, partly due to lack of user-friendly software, RT3DE has not been widely accepted as a clinical tool. The object of this study was to develop and implement a fast and interactive volume renderer of RT3DE datasets designed for a clinical environment where speed and simplicity are not secondary to accuracy. Thirty-six patients (20 regurgitation, 8 normal, 8 cardiomyopathy) were imaged using RT3DE. Using our newly developed software, all 3D data sets were rendered in real-time throughout the cardiac cycle and assessment of cardiac function and pathology was performed for each case. The real-time interactive volume visualization system is user friendly and instantly provides consistent and reliable 3D images without expensive workstations or dedicated hardware. We believe that this novel tool can be used clinically for dynamic visualization of cardiac anatomy.

Near Real-Time Applications of Earth Remote Sensing for Response to Meteorological Disasters

NASA Technical Reports Server (NTRS)

Molthan, Andrew L.; Burks, Jason E.; McGrath, Kevin M.; Bell, Jordan R.

2013-01-01

Numerous on-orbit satellites provide a wide range of spatial, spectral, and temporal resolutions supporting the use of their resulting imagery in assessments of disasters that are meteorological in nature. This presentation will provide an overview of recent use of Earth remote sensing by NASA's Short-term Prediction Research and Transition (SPoRT) Center in response to disaster activities in 2012 and 2013, along with case studies supporting ongoing research and development. The SPoRT Center, with support from NASA's Applied Sciences Program, has explored a variety of new applications of Earth-observing sensors to support disaster response. In May 2013, the SPoRT Center developed unique power outage composites representing the first clear sky view of damage inflicted upon Moore and Oklahoma City, Oklahoma following the devastating EF-5 tornado that occurred on May 20. Subsequent ASTER, MODIS, Landsat-7 and Landsat-8 imagery help to identify the damaged area. Higher resolution imagery of Moore, Oklahoma were provided by commercial satellites and the recently available International Space Station (ISS) SERVIR Environmental Research and Visualization System (ISERV) instrument. New techniques are being explored by the SPoRT team in order to better identify damage visible in high resolution imagery, and to monitor ongoing recovery for Moore, Oklahoma. Other applications are being developed to refine light source detections with the VIIRS day-night band and to map hail during the growing season through combination of available satellite and radar imagery. The aforementioned products and support are not useful unless they are distributed in a timely manner and within an appropriate decision support system. This presentation will provide an update on ongoing activities to support inclusion of these data sets within the NOAA National Weather Service Damage Assessment Toolkit, which allows meteorologists in the field to consult available satellite imagery while performing their damage assessment.

Near Real-­Time Applications of Earth Remote Sensing for Response to Meteorological Disasters

NASA Technical Reports Server (NTRS)

Molthan, Andrew L.; Burks, Jason E.; McGrath, Kevin M.; Bell, Jordan R.

2013-01-01

Numerous on-orbit satellites provide a wide range of spatial, spectral, and temporal resolutions supporting the use of their resulting imagery in assessments of disasters that are meteorological in nature. This presentation will provide an overview of recent use of Earth remote sensing by NASA's Short-term Prediction Research and Transition (SPoRT) Center in response to disaster activities in 2012 and 2013, along with case studies supporting ongoing research and development. The SPoRT Center, with support from NASA's Applied Sciences Program, has explored a variety of new applications of Earth-observing sensors to support disaster response. In May 2013, the SPoRT Center developed unique power outage composites representing the first clear sky view of damage inflicted upon Moore and Oklahoma City, Oklahoma following the devastating EF-5 tornado that occurred on May 20. Subsequent ASTER, MODIS, Landsat-7 and Landsat-8 imagery help to identify the damaged area. Higher resolution imagery of Moore, Oklahoma were provided by commercial satellites and the recently available International Space Station (ISS) SERVIR Environmental Research and Visualization System (ISERV) instrument. New techniques are being explored by the SPoRT team in order to better identify damage visible in high resolution imagery, and to monitor ongoing recovery for Moore, Oklahoma. Other applications are being developed to refine light source detections with the VIIRS day-night band and to map hail during the growing season through combination of available satellite and radar imagery. The aforementioned products and support are not useful unless they are distributed in a timely manner and within an appropriate decision support system. This presentation will provide an update on ongoing activities to support inclusion of these data sets within the NOAA National Weather Service Damage Assessment Toolkit, which allows meteorologists in the field to consult available satellite imagery while performing their damage assessment.

Evidence for a Cognitive Control Network for Goal-Directed Attention in Simple Sustained Attention

ERIC Educational Resources Information Center

Hilti, Caroline C.; Jann, Kay; Heinemann, Doerthe; Federspiel, Andrea; Dierks, Thomas; Seifritz, Erich; Cattapan-Ludewig, Katja

2013-01-01

The deterioration of performance over time is characteristic for sustained attention tasks. This so-called "performance decrement" is measured by the increase of reaction time (RT) over time. Some behavioural and neurobiological mechanisms of this phenomenon are not yet fully understood. Behaviourally, we examined the increase of RT over time and…

Differential Detection of Enterovirus and Herpes Simplex Virus in Cerebrospinal Fluid by Real-Time RT-PCR.

PubMed

Sarquiz-Martínez, Brenda; González-Bonilla, César R; Santacruz-Tinoco, Clara Esperanza; Muñoz-Medina, José E; Pardavé-Alejandre, Héctor D; Barbosa-Cabrera, Elizabeth; Ramírez-González, José Ernesto; Díaz-Quiñonez, José Alberto

2017-01-01

Enterovirus (EV) and herpes simplex virus 1 and 2 (HSV1 and HSV2) are the main etiologic agents of central nervous system infections. Early laboratory confirmation of these infections is performed by viral culture of the cerebrospinal fluid (CSF), or the detection of specific antibodies in serum (e.g., HSV). The sensitivity of viral culture ranges from 65 to 75%, with a recovery time varying from 3 to 10 days. Serological tests are faster and easy to carry out, but they exhibit cross-reactivity between HSV1 and HSV2. Although molecular techniques are more sensitive (sensitivity >95%), they are more expensive and highly susceptible to cross-contamination. A real-time RT-PCR for the detection of EV, HSV1, and HSV2 was compared with end-point nested PCR. We tested 87 CSF samples of patients with a clinical diagnosis of viral meningitis or encephalitis. Fourteen samples were found to be positive by RT-PCR, but only 8 were positive by end-point PCR. The RT-PCR showed a specificity range of 94-100%, the negative predictive value was 100%, and the positive predictive value was 62, 100, and 28% for HSV1, HSV2, and EV, respectively. Real-time RT-PCR detected EV, HSV1, and HSV2 with a higher sensitivity and specificity than end-point nested RT-PCR. © 2017 S. Karger AG, Basel.

Optimization of Catheter Based rtPA Thrombolysis in a Novel In Vitro Clot Model for Intracerebral Hemorrhage

PubMed Central

Masomi-Bornwasser, Julia; Müller-Werkmeister, Hendrik; Kantelhardt, Sven Rainer; König, Jochem; Kempski, Oliver; Giese, Alf

2017-01-01

Hematoma lysis with recombinant tissue plasminogen activator (rtPA) has emerged as an alternative therapy for spontaneous intracerebral hemorrhage (ICH). Optimal dose and schedule are still unclear. The aim of this study was to create a reliable in vitro blood clot model for investigation of optimal drug dose and timing. An in vitro clot model was established, using 25 mL and 50 mL of human blood. Catheters were placed into the clots and three groups, using intraclot application of rtPA, placebo, and catheter alone, were analyzed. Dose-response relationship, repetition, and duration of rtPA treatment and its effectiveness in aged clots were investigated. A significant relative end weight difference was found in rtPA treated clots compared to catheter alone (p = 0.002) and placebo treated clots (p < 0.001). Dose-response analysis revealed 95% effective dose around 1 mg rtPA in 25 and 50 mL clots. Approximately 80% of relative clot lysis could be achieved after 15 min incubation. Lysis of aged clots was less effective. A new clot model for in vitro investigation was established. Our data suggest that current protocols for rtPA based ICH therapy may be optimized by using less rtPA at shorter incubation times. PMID:28459065

Optimization of Catheter Based rtPA Thrombolysis in a Novel In Vitro Clot Model for Intracerebral Hemorrhage.

PubMed

Keric, Naureen; Masomi-Bornwasser, Julia; Müller-Werkmeister, Hendrik; Kantelhardt, Sven Rainer; König, Jochem; Kempski, Oliver; Giese, Alf

2017-01-01

Hematoma lysis with recombinant tissue plasminogen activator (rtPA) has emerged as an alternative therapy for spontaneous intracerebral hemorrhage (ICH). Optimal dose and schedule are still unclear. The aim of this study was to create a reliable in vitro blood clot model for investigation of optimal drug dose and timing. An in vitro clot model was established, using 25 mL and 50 mL of human blood. Catheters were placed into the clots and three groups, using intraclot application of rtPA, placebo, and catheter alone, were analyzed. Dose-response relationship, repetition, and duration of rtPA treatment and its effectiveness in aged clots were investigated. A significant relative end weight difference was found in rtPA treated clots compared to catheter alone ( p = 0.002) and placebo treated clots ( p < 0.001). Dose-response analysis revealed 95% effective dose around 1 mg rtPA in 25 and 50 mL clots. Approximately 80% of relative clot lysis could be achieved after 15 min incubation. Lysis of aged clots was less effective. A new clot model for in vitro investigation was established. Our data suggest that current protocols for rtPA based ICH therapy may be optimized by using less rtPA at shorter incubation times.

Evaluating the Impact of Atmospheric Infrared Sounder (AIRS) Data On Convective Forecasts

NASA Technical Reports Server (NTRS)

Kozlowski, Danielle; Zavodsky, Bradley

2011-01-01

The Short-term Prediction Research and Transition Center (SPoRT) is a collaborative partnership between NASA and operational forecasting partners, including a number of National Weather Service (NWS) offices. SPoRT provides real-time NASA products and capabilities to its partners to address specific operational forecast challenges. The mission of SPoRT is to transition observations and research capabilities into operations to help improve short-term weather forecasts on a regional scale. Two areas of focus are data assimilation and modeling, which can to help accomplish SPoRT's programmatic goals of transitioning NASA data to operational users. Forecasting convective weather is one challenge that faces operational forecasters. Current numerical weather prediction (NWP) models that operational forecasters use struggle to properly forecast location, timing, intensity and/or mode of convection. Given the proper atmospheric conditions, convection can lead to severe weather. SPoRT's partners in the National Oceanic and Atmospheric Administration (NOAA) have a mission to protect the life and property of American citizens. This mission has been tested as recently as this 2011 severe weather season, which has seen more than 300 fatalities and injuries and total damages exceeding $10 billion. In fact, during the three day period from 25-27 April, 1,265 storms reports (362 tornado reports) were collected making this three day period one of most active in American history. To address the forecast challenge of convective weather, SPoRT produces a real-time NWP model called the SPoRT Weather Research and Forecasting (SPoRT-WRF), which incorporates unique NASA data sets. One of the NASA assets used in this unique model configuration is retrieved profiles from the Atmospheric Infrared Sounder (AIRS).The goal of this project is to determine the impact that these AIRS profiles have on the SPoRT-WRF forecasts by comparing to a current operational model and a control SPoRT-WRF model that does not contain AIRS profiles.

Annual Research Review: Reaction time variability in ADHD and autism spectrum disorders: measurement and mechanisms of a proposed trans-diagnostic phenotype

PubMed Central

Karalunas, Sarah L.; Geurts, Hilde M.; Konrad, Kerstin; Bender, Stephan; Nigg, Joel T.

2014-01-01

Background Intraindividual variability in reaction time (RT) has received extensive discussion as an indicator of cognitive performance, a putative intermediate phenotype of many clinical disorders, and a possible trans-diagnostic phenotype that may elucidate shared risk factors for mechanisms of psychiatric illnesses. Scope and Methodology Using the examples of attention deficit hyperactivity disorder (ADHD) and autism spectrum disorders (ASD), we discuss RT variability. We first present a new meta-analysis of RT variability in ASD with and without comorbid ADHD. We then discuss potential mechanisms that may account for RT variability and statistical models that disentangle the cognitive processes affecting RTs. We then report a second meta-analysis comparing ADHD and non-ADHD children on diffusion model parameters. We consider how findings inform the search for neural correlates of RT variability. Findings Results suggest that RT variability is increased in ASD only when children with comorbid ADHD are included in the sample. Furthermore, RT variability in ADHD is explained by moderate to large increases (d = 0.63–0.99) in the ex-Gaussian parameter τ and the diffusion parameter drift rate, as well as by smaller differences (d = 0.32) in the diffusion parameter of nondecision time. The former may suggest problems in state regulation or arousal and difficulty detecting signal from noise, whereas the latter may reflect contributions from deficits in motor organization or output. The neuroimaging literature converges with this multicomponent interpretation and also highlights the role of top-down control circuits. Conclusion We underscore the importance of considering the interactions between top-down control, state regulation (e.g. arousal), and motor preparation when interpreting RT variability and conclude that decomposition of the RT signal provides superior interpretive power and suggests mechanisms convergent with those implicated using other cognitive paradigms. We conclude with specific recommendations for the field for next steps in the study of RT variability in neurodevelopmental disorders. PMID:24628425

Guanfacine potentiates the activation of prefrontal cortex evoked by warning signals.

PubMed

Clerkin, Suzanne M; Schulz, Kurt P; Halperin, Jeffrey M; Newcorn, Jeffrey H; Ivanov, Iliyan; Tang, Cheuk Y; Fan, Jin

2009-08-15

Warning signals evoke an alert state of readiness that prepares for a rapid response by priming a thalamo-frontal-striatal network that includes the dorsolateral prefrontal cortex (DLPFC). Animal models indicate that noradrenergic input is essential for this stimulus-driven activation of DLPFC, but the precise mechanisms involved have not been determined. We tested the role that postsynaptic alpha(2A) adrenoceptors play in the activation of DLPFC evoked by warning cues using a placebo-controlled challenge with the alpha(2A) agonist guanfacine. Sixteen healthy young adults were scanned twice with event-related functional magnetic resonance imaging (fMRI), while performing a simple cued reaction time (RT) task following administration of a single dose of oral guanfacine (1 mg) and placebo in counterbalanced order. The RT task temporally segregates the neural effects of warning cues and motor responses and minimizes mnemonic demands. Warning cues produced a marked reduction in RT accompanied by significant activation in a distributed thalamo-frontal-striatal network, including bilateral DLPFC. Guanfacine selectively increased the cue-evoked activation of the left DLPFC and right anterior cerebellum, although this increase was not accompanied by further reductions in RT. The effects of guanfacine on DLPFC activation were specifically associated with the warning cue and were not seen for visual- or target-related activation. Guanfacine produced marked increases in the cue-evoked activation of DLPFC that correspond to the well-described actions of postsynaptic alpha(2) adrenoceptor stimulation. The current procedures provide an opportunity to test postsynaptic alpha(2A) adrenoceptor function in the prefrontal cortex in the pathophysiology of several psychiatric disorders.

Effect of resistance training on C-reactive protein, blood glucose and lipid profile in older women with differing levels of RT experience.

PubMed

Ribeiro, Alex S; Tomeleri, Crisieli M; Souza, Mariana F; Pina, Fábio Luiz C; Schoenfeld, Brad J; Nascimento, Matheus A; Venturini, Danielle; Barbosa, Décio S; Cyrino, Edilson S

2015-12-01

The purpose of this study was to analyze the effects of a progressive resistance training (RT) program on C-reactive protein (CRP), blood glucose (GLU), and lipid profile in older women with differing levels of RT experience. Sixty-five older women (68.9 ± 6.1 years, 67.1 ± 13.1 kg) were separated according to RT experience: an advanced group composed by 35 participants who previously carried out 24 weeks of RT and a novice group composed by 30 participants without previous experience in RT (n = 30). Both groups performed a RT program comprised of eight exercises targeting all the major muscles. Training was carried out 3 days/week for 8 weeks. Serum triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), GLU, and CRP concentrations were determined pre- and post- intervention after 12 h fasting. A significant group by time interaction (P < 0.05) for the TC (novice = -1.9% vs. advanced = 1.0%), and CRP (novice = -22.9% vs. advanced = -54.5%) was observed. A main effect of time (P < 0.05) was identified for the GLU (novice = -2.6% vs. advanced = -6.6%), TG (novice = -12.9% vs. advanced = -5.7%), HDL-C (novice = +6.7% vs. advanced = +2.6%), and LDL-C (novice = -34.0% vs. advanced = -25.4%). These results suggest that RT improves the metabolic profile of older women and that training for a longer period of time seems to produce more pronounced reductions mainly on CRP.

A Comparison of Forecast Error Generators for Modeling Wind and Load Uncertainty

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

Lu, Ning; Diao, Ruisheng; Hafen, Ryan P.

2013-12-18

This paper presents four algorithms to generate random forecast error time series, including a truncated-normal distribution model, a state-space based Markov model, a seasonal autoregressive moving average (ARMA) model, and a stochastic-optimization based model. The error time series are used to create real-time (RT), hour-ahead (HA), and day-ahead (DA) wind and load forecast time series that statistically match historically observed forecasting data sets, used for variable generation integration studies. A comparison is made using historical DA load forecast and actual load values to generate new sets of DA forecasts with similar stoical forecast error characteristics. This paper discusses and comparesmore » the capabilities of each algorithm to preserve the characteristics of the historical forecast data sets.« less

Addressing BI Transactional Flows in the Real-Time Enterprise Using GoldenGate TDM

NASA Astrophysics Data System (ADS)

Pareek, Alok

It's time to visit low latency and reliable real-time (RT) infrastructures to support next generation BI applications instead of continually debating the need and notion of real-time. The last few years have illuminated some key paradigms affecting data management. The arguments put forth to move away from traditional DBMS architectures have proven persuasive - and specialized architectural data stores are being adopted in the industry [1]. The change from traditional database pull methods towards intelligent routing/push models is underway, causing applications to be redesigned, redeployed, and re-architected. One direct result of this is that despite original warnings about replication [2] - enterprises continue to deploy multiple replicas to support both performance, and high availability of RT applications, with an added complexity around manageability of heterogeneous computing systems. The enterprise is overflowing with data streams that require instantaneous processing and integration, to deliver faster visibility and invoke conjoined actions for RT decision making, resulting in deployment of advanced BI applications as can be seen by stream processing over RT feeds from operational systems for CEP [3]. Given these various paradigms, a multitude of new challenges and requirements have emerged, thereby necessitating different approaches to management of RT applications for BI. The purpose of this paper is to offer a viewpoint on how RT affects critical operational applications, evolves the weight of non-critical applications, and pressurizes availability/data-movement requirements in the underlying infrastructure. I will discuss how the GoldenGate TDM platform is being deployed within the RTE to manage some of these challenges particularly around RT dissemination of transactional data to reduce latency in data integration flows, to enable real-time reporting/DW, and to increase availability of underlying operational systems. Real world case studies will be used to support the various discussion points. The paper is an argument to augment traditional DI flows with a real-time technology (referred to as transactional data management) to support operational BI requirements.

ARCHER{sub RT} – A GPU-based and photon-electron coupled Monte Carlo dose computing engine for radiation therapy: Software development and application to helical tomotherapy

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

Su, Lin; Du, Xining; Liu, Tianyu

Purpose: Using the graphical processing units (GPU) hardware technology, an extremely fast Monte Carlo (MC) code ARCHER{sub RT} is developed for radiation dose calculations in radiation therapy. This paper describes the detailed software development and testing for three clinical TomoTherapy® cases: the prostate, lung, and head and neck. Methods: To obtain clinically relevant dose distributions, phase space files (PSFs) created from optimized radiation therapy treatment plan fluence maps were used as the input to ARCHER{sub RT}. Patient-specific phantoms were constructed from patient CT images. Batch simulations were employed to facilitate the time-consuming task of loading large PSFs, and to improvemore » the estimation of statistical uncertainty. Furthermore, two different Woodcock tracking algorithms were implemented and their relative performance was compared. The dose curves of an Elekta accelerator PSF incident on a homogeneous water phantom were benchmarked against DOSXYZnrc. For each of the treatment cases, dose volume histograms and isodose maps were produced from ARCHER{sub RT} and the general-purpose code, GEANT4. The gamma index analysis was performed to evaluate the similarity of voxel doses obtained from these two codes. The hardware accelerators used in this study are one NVIDIA K20 GPU, one NVIDIA K40 GPU, and six NVIDIA M2090 GPUs. In addition, to make a fairer comparison of the CPU and GPU performance, a multithreaded CPU code was developed using OpenMP and tested on an Intel E5-2620 CPU. Results: For the water phantom, the depth dose curve and dose profiles from ARCHER{sub RT} agree well with DOSXYZnrc. For clinical cases, results from ARCHER{sub RT} are compared with those from GEANT4 and good agreement is observed. Gamma index test is performed for voxels whose dose is greater than 10% of maximum dose. For 2%/2mm criteria, the passing rates for the prostate, lung case, and head and neck cases are 99.7%, 98.5%, and 97.2%, respectively. Due to specific architecture of GPU, modified Woodcock tracking algorithm performed inferior to the original one. ARCHER{sub RT} achieves a fast speed for PSF-based dose calculations. With a single M2090 card, the simulations cost about 60, 50, 80 s for three cases, respectively, with the 1% statistical error in the PTV. Using the latest K40 card, the simulations are 1.7–1.8 times faster. More impressively, six M2090 cards could finish the simulations in 8.9–13.4 s. For comparison, the same simulations on Intel E5-2620 (12 hyperthreading) cost about 500–800 s. Conclusions: ARCHER{sub RT} was developed successfully to perform fast and accurate MC dose calculation for radiotherapy using PSFs and patient CT phantoms.« less

Structural MRI research in patients with nasopharyngeal carcinoma following radiotherapy: A DTI and VBM study.

PubMed

Leng, Xi; Fang, Peng; Lin, Huan; An, Jie; Tan, Xin; Zhang, Chi; Wu, Donglin; Shen, Wen; Qiu, Shijun

2017-11-01

The aim of the present study was to investigate the microstructural characteristics of the brain lobes following radiotherapy (RT) for patients with nasopharyngeal carcinoma (NPC) at distinct times. Diffusion tensor imaging (DTI) and 3D-T1-weighted imaging was performed in 70 age- and sex-matched subjects, 24 of whom were pre-treatment patients. The patients were divided into three groups, according to the time following completion of RT. Fractional anisotropy (FA) and gray matter (GM) volume were determined. The DTI data were analyzed using tract-based spatial statistics and the GM volume was analyzed using voxel-based morphometry (VBM). Compared with the pre-RT group, the mean FA values in the left parietal lobe white matter (WM) and right cerebellum decreased significantly in the post-RT 0-6 month group (P<0.05). In addition, the mean FA values in the right parietal lobe WM decreased significantly in the post-RT 6-12 month group (P<0.05), compared with the pre-RT group. The FA level in the right temporal lobe remained significantly decreased, compared with that in the pre-RT group (P<0.05) for 1 year after RT. Furthermore, compared with pre-RT group, the GM volume in the bilateral frontal lobe, right occipital lobe, left parietal lobe, right temporal lobe and left cerebellum decreased significantly in the post-RT 0-6 month group (P<0.05), and in the bilateral temporal lobe, parietal lobe, right frontal lobe and left cerebellum, the GM volume decreased significantly in the post-RT 6-12 month group (P<0.05). The GM volume in the right temporal lobe, bilateral frontal lobe and bilateral cerebellum remained significantly decreased compared with that in the pre-RT group (P<0.05) for 1 year after RT. A combination of DTI and VBM may be used to determine radiation-induced brain injury in patients treated for NPC.

Brainstem dose is associated with patient-reported acute fatigue in head and neck cancer radiation therapy.

PubMed

Ferris, Matthew J; Zhong, Jim; Switchenko, Jeffrey M; Higgins, Kristin A; Cassidy, Richard J; McDonald, Mark W; Eaton, Bree R; Patel, Kirtesh R; Steuer, Conor E; Baddour, H Michael; Miller, Andrew H; Bruner, Deborah W; Xiao, Canhua; Beitler, Jonathan J

2018-01-01

Radiation (RT) dose to the central nervous system (CNS) has been implicated as a contributor to treatment-related fatigue in head and neck cancer (HNC) patients undergoing radiation therapy (RT). This study evaluates the association of RT dose to CNS structures with patient-reported (PRO) fatigue scores in a population of HNC patients. At pre-RT (baseline), 6th week of RT, and 1-month post-RT time points, Multidimensional Fatigue Inventory (MFI-20) scores were prospectively obtained from 124 patients undergoing definitive treatment for HNC. Medulla, pons, midbrain, total brainstem, cerebellum, posterior fossa, and pituitary dosimetry were evaluated using summary statistics and dose-volume histograms, and associations with MFI-20 scores were analyzed. Maximum dose (Dmax) to the brainstem and medulla was significantly associated with MFI-20 scores at 6th week of RT and 1-month post-RT time points, after controlling for baseline scores (p<0.05). Each 1Gy increase in medulla Dmax resulted in an increase in total MFI-20 score over baseline of 0.30 (p=0.026), and 0.25 (p=0.037), at the 6th week of RT and 1-month post-RT, respectively. Each 1Gy increase in brainstem Dmax resulted in an increase in total MFI-20 score over baseline of 0.30 (p=0.027), and 0.25 (p=0.037) at the 6th week of RT, 1-month post-RT, respectively. Statistically significant associations were not found between dosimetry for the other CNS structures and MFI-20 scores. In this analysis of PRO fatigue scores from a population of patients undergoing definitive RT for HNC, maximum dose to the brainstem and medulla was associated with a significantly increased risk of acute patient fatigue. Copyright © 2017 Elsevier B.V. All rights reserved.

OR.NET RT: how service-oriented medical device architecture meets real-time communication.

PubMed

Pfeiffer, Jonas H; Kasparick, Martin; Strathen, Benjamin; Dietz, Christian; Dingler, Max E; Lueth, Tim C; Timmermann, Dirk; Radermacher, Klaus; Golatowski, Frank

2018-02-23

Today's landscape of medical devices is dominated by stand-alone systems and proprietary interfaces lacking cross-vendor interoperability. This complicates or even impedes the innovation of novel, intelligent assistance systems relying on the collaboration of medical devices. Emerging approaches use the service-oriented architecture (SOA) paradigm based on Internet protocol (IP) to enable communication between medical devices. While this works well for scenarios with no or only soft timing constraints, the underlying best-effort communication scheme is insufficient for time critical data. Real-time (RT) networks are able to reliably guarantee fixed latency boundaries, for example, by using time division multiple access (TDMA) communication patterns. However, deterministic RT networks come with their own limitations such as tedious, inflexible configuration and a more restricted bandwidth allocation. In this contribution we overcome the drawbacks of both approaches by describing and implementing mechanisms that allow the two networks to interact. We introduce the first implementation of a medical device network that offers hard RT guarantees for control and sensor data and integrates into SOA networks. Based on two application examples we show how the flexibility of SOA networks and the reliability of RT networks can be combined to achieve an open network infrastructure for medical devices in the operating room (OR).

SU-G-JeP3-02: Comparison of Magnitude and Frequency of Patient Positioning Errors in Breast Irradiation Using AlignRT 3D Optical Surface Imaging and Skin Mark Techniques

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

Yao, R; Chisela, W; Dorbu, G

2016-06-15

Purpose: To evaluate clinical usefulness of AlignRT (Vision RT Ltd., London, UK) in reducing patient positioning errors in breast irradiation. Methods: 60 patients undergoing whole breast irradiation were selected for this study. Patients were treated to the left or right breast lying on Qfix Access breast board (Qfix, Avondale, PA) in supine position for 28 fractions using tangential fields. 30 patients were aligned using AlignRT by aligning a breast surface region of interest (ROI) to the same area from a reference surface image extracted from planning CT. When the patient’s surface image deviated from the reference by more than 3mmmore » on one or more translational and rotational directions, a new reference was acquired using AlignRT in-room cameras. The other 30 patients were aligned to the skin marks with room lasers. On-Board MV portal images of medial field were taken daily and matched to the DRRs. The magnitude and frequency of positioning errors were determined from measured translational shifts. Kolmogorov-Smirnov test was used to evaluate statistical differences of positional accuracy and precision between AlignRT and non-AlignRT patients. Results: The percentage of port images with no shift required was 46.5% and 27.0% in vertical, 49.8% and 25.8% in longitudinal, 47.6% and 28.5% in lateral for AlignRT and non-AlignRT patients, respectively. The percentage of port images requiring more than 3mm shifts was 18.1% and 35.1% in vertical, 28.6% and 50.8% in longitudinal, 11.3% and 24.2% in lateral for AlignRT and non-AlignRT patients, respectively. Kolmogorov-Smirnov test showed that there were significant differences between the frequency distributions of AlignRT and non-AlignRT in vertical, longitudinal, and lateral shifts. Conclusion: As confirmed by port images, AlignRT-assisted patient positioning can significantly reduce the frequency and magnitude of patient setup errors in breast irradiation compared to the use of lasers and skin marks.« less

Individual differences in the components of children's and adults' information processing for simple symbolic and non-symbolic numeric decisions.

PubMed

Thompson, Clarissa A; Ratcliff, Roger; McKoon, Gail

2016-10-01

How do speed and accuracy trade off, and what components of information processing develop as children and adults make simple numeric comparisons? Data from symbolic and non-symbolic number tasks were collected from 19 first graders (Mage=7.12 years), 26 second/third graders (Mage=8.20 years), 27 fourth/fifth graders (Mage=10.46 years), and 19 seventh/eighth graders (Mage=13.22 years). The non-symbolic task asked children to decide whether an array of asterisks had a larger or smaller number than 50, and the symbolic task asked whether a two-digit number was greater than or less than 50. We used a diffusion model analysis to estimate components of processing in tasks from accuracy, correct and error response times, and response time (RT) distributions. Participants who were accurate on one task were accurate on the other task, and participants who made fast decisions on one task made fast decisions on the other task. Older participants extracted a higher quality of information from the stimulus arrays, were more willing to make a decision, and were faster at encoding, transforming the stimulus representation, and executing their responses. Individual participants' accuracy and RTs were uncorrelated. Drift rate and boundary settings were significantly related across tasks, but they were unrelated to each other. Accuracy was mainly determined by drift rate, and RT was mainly determined by boundary separation. We concluded that RT and accuracy operate largely independently. Copyright © 2016 Elsevier Inc. All rights reserved.

Detection of rat hepatitis E virus in wild Norway rats (Rattus norvegicus) and Black rats (Rattus rattus) from 11 European countries.

PubMed

Ryll, René; Bernstein, Samuel; Heuser, Elisa; Schlegel, Mathias; Dremsek, Paul; Zumpe, Maxi; Wolf, Sandro; Pépin, Michel; Bajomi, Daniel; Müller, Gabi; Heiberg, Ann-Charlotte; Spahr, Carina; Lang, Johannes; Groschup, Martin H; Ansorge, Hermann; Freise, Jona; Guenther, Sebastian; Baert, Kristof; Ruiz-Fons, Francisco; Pikula, Jiri; Knap, Nataša; Tsakmakidis, Ιoannis; Dovas, Chrysostomos; Zanet, Stefania; Imholt, Christian; Heckel, Gerald; Johne, Reimar; Ulrich, Rainer G

2017-09-01

Rat hepatitis E virus (HEV) is genetically only distantly related to hepeviruses found in other mammalian reservoirs and in humans. It was initially detected in Norway rats (Rattus norvegicus) from Germany, and subsequently in rats from Vietnam, the USA, Indonesia, China, Denmark and France. Here, we report on a molecular survey of Norway rats and Black rats (Rattus rattus) from 12 European countries for ratHEV and human pathogenic hepeviruses. RatHEV-specific real-time and conventional RT-PCR investigations revealed the presence of ratHEV in 63 of 508 (12.4%) rats at the majority of sites in 11 of 12 countries. In contrast, a real-time RT-PCR specific for human pathogenic HEV genotypes 1-4 and a nested broad-spectrum (NBS) RT-PCR with subsequent sequence determination did not detect any infections with these genotypes. Only in a single Norway rat from Belgium a rabbit HEV-like genotype 3 sequence was detected. Phylogenetic analysis indicated a clustering of all other novel Norway and Black rat-derived sequences with ratHEV sequences from Europe, the USA and a Black rat-derived sequence from Indonesia within the proposed ratHEV genotype 1. No difference in infection status was detected related to age, sex, rat species or density of human settlements and zoological gardens. In conclusion, our investigation shows a broad geographical distribution of ratHEV in Norway and Black rats from Europe and its presence in all settlement types investigated. Copyright © 2017 Elsevier B.V. All rights reserved.

Development and evaluation of a simple and effective RT-qPCR inhibitory assay for detection of the efficacy of compounds towards HIV reverse transcriptase.

PubMed

Marino-Merlo, Francesca; Frezza, Caterina; Papaianni, Emanuela; Valletta, Elena; Mastino, Antonio; Macchi, Beatrice

2017-11-01

Assessing the actual efficacy of compounds to directly inhibit HIV reverse transcriptase (RT) activity is a main goal in preclinical antiretroviral studies. Our previous studies demonstrated that the effects of inhibitor compounds towards HIV-RT could be efficiently assessed through a simple cell-free assay based on conventional reverse transcription PCR. In the present study, we describe a modified variant of our assay, termed RT real-time quantitative PCR inhibitory assay (RT-qPCR-IA), in which the ability of compounds to restrict the complementary DNA (cDNA) generation by HIV-RT using a specific RNA template is performed by the real-time technique, in order to improve both accuracy and sensitivity of the method. As specific RNA template, RNA extracted from stable transfectants ectopically expressing the herpes simplex virus 1 glycoprotein D gene was utilized. HIV-RT, of both commercial or house-made viral lysate origin, was employed for the assay. To assess the reliability of RT-qPCR-IA, we performed a comparative, quantitative analysis of the dose-dependent effect exerted by known nucleotide and non-nucleotide reverse-transcriptase inhibitors, using the SYBR Green dye chemistry as detection system. The results obtained with RT-qPCR-IA were compared to that obtained using a one-step PicoGreen technology-based commercial kit. The outcome of our study indicates that the development of the novel RT-qPCR-IA will provide rapid and accurate evaluation of the inhibitory efficacy of compounds towards HIV-RT activity. This evaluation could be very useful for large-scale screening of potential new anti-HIV drugs.

Reference data on reaction time and aging using the Nintendo Wii Balance Board: A cross-sectional study of 354 subjects from 20 to 99 years of age.

PubMed

Blomkvist, Andreas W; Eika, Fredrik; Rahbek, Martin T; Eikhof, Karin D; Hansen, Mette D; Søndergaard, Malene; Ryg, Jesper; Andersen, Stig; Jørgensen, Martin G

2017-01-01

Falls among older adults is one of the major public health challenges facing the rapidly changing demography. The valid assessment of reaction time (RT) and other well-documented risk factors for falls are mainly restricted to specialized clinics due to the equipment needed. The Nintendo Wii Balance Board has the potential to be a multi-modal test and intervention instrument for these risk factors, however, reference data are lacking. To provide RT reference data and to characterize the age-related changes in RT measured by the Nintendo Wii Balance Board. Healthy participants were recruited at various locations and their RT in hands and feet were tested by six assessors using the Nintendo Wii Balance Board. Reference data were analysed and presented in age-groups, while the age-related change in RT was tested and characterized with linear regression models. 354 participants between 20 and 99 years of age were tested. For both hands and feet, mean RT and its variation increased with age. There was a statistically significant non-linear increase in RT with age. The averaged difference between male and female was significant, with males being faster than females for both hands and feet. The averaged difference between dominant and non-dominant side was non-significant. This study reported reference data with percentiles for a new promising method for reliably testing RT. The RT data were consistent with previously known effects of age and gender on RT.

Reference data on reaction time and aging using the Nintendo Wii Balance Board: A cross-sectional study of 354 subjects from 20 to 99 years of age

PubMed Central

Rahbek, Martin T.; Eikhof, Karin D.; Hansen, Mette D.; Søndergaard, Malene; Ryg, Jesper; Andersen, Stig; Jørgensen, Martin G.

2017-01-01

Background Falls among older adults is one of the major public health challenges facing the rapidly changing demography. The valid assessment of reaction time (RT) and other well-documented risk factors for falls are mainly restricted to specialized clinics due to the equipment needed. The Nintendo Wii Balance Board has the potential to be a multi-modal test and intervention instrument for these risk factors, however, reference data are lacking. Objective To provide RT reference data and to characterize the age-related changes in RT measured by the Nintendo Wii Balance Board. Method Healthy participants were recruited at various locations and their RT in hands and feet were tested by six assessors using the Nintendo Wii Balance Board. Reference data were analysed and presented in age-groups, while the age-related change in RT was tested and characterized with linear regression models. Results 354 participants between 20 and 99 years of age were tested. For both hands and feet, mean RT and its variation increased with age. There was a statistically significant non-linear increase in RT with age. The averaged difference between male and female was significant, with males being faster than females for both hands and feet. The averaged difference between dominant and non-dominant side was non-significant. Conclusion This study reported reference data with percentiles for a new promising method for reliably testing RT. The RT data were consistent with previously known effects of age and gender on RT. PMID:29287063

Reverberation time influences musical enjoyment with cochlear implants.

PubMed

Certo, Michael V; Kohlberg, Gavriel D; Chari, Divya A; Mancuso, Dean M; Lalwani, Anil K

2015-02-01

To identify factors that enhance the enjoyment of music in cochlear implant (CI) recipients. Specifically, we assessed the hypothesis that variations in reverberation time (RT60) may be linked to variations in the level of musical enjoyment in CI users. Prospective analysis of music enjoyment in normal-hearing individuals. Single tertiary academic medical center. Normal-hearing adults (N = 20) were asked to rate a novel 20-second melody on three enjoyment modalities: musicality, pleasantness, and naturalness. Subjective rating of music excerpts. Participants listened to seven different instruments play the melody, each with five levels (0.2, 1.6, 3.0, 5.0, 10.0 s) of RT60, both with and without CI simulation processing. Linear regression analysis with analysis of variance was used to assess the impact of RT60 on music enjoyment. Without CI simulation, music samples with RT60 = 3.0 seconds were ranked most pleasant and most musical, whereas those with RT60 = 1.6 seconds and RT60 = 3.0 seconds were ranked equally most natural (all p < 0.05). With CI simulation, music samples with RT60 = 0.2 seconds were ranked most pleasant, most musical, and most natural (all p < 0.05). Samples without CI simulation show a preference for middle-range RT60, whereas samples with CI simulation show a negative linear relationship between RT60 and musical enjoyment, with preference for minimal reverberation. Minimization of RT60 may be a useful strategy for increasing musical enjoyment under CI conditions, both in altering existing music as well as in composition of new music.

Improved serotype-specific dengue virus detection in Trinidad and Tobago using a multiplex, real-time RT-PCR.

PubMed

Waggoner, Jesse J; Sahadeo, Nikita S D; Brown, Arianne; Mohamed-Hadley, Alisha; Hadley, Dexter; Carrington, Leslie; Carrington, Christine V F; Pinsky, Benjamin A

2015-02-01

Dengue virus (DENV) transmission occurs throughout the Caribbean, though laboratory confirmation and epidemiologic surveillance are limited by the availability of serotype-specific molecular diagnostics. In this study, we show that a serotype-specific DENV multiplex, real-time reverse transcriptase-PCR (RT-PCR) detected DENV RNA in significantly more samples (82/182) than a reference hemi-nested RT-PCR (57/182; P=0.01). Copyright © 2015 Elsevier Inc. All rights reserved.

Serious games for elderly continuous monitoring.

PubMed

Lemus-Zúñiga, Lenin-G; Navarro-Pardo, Esperanza; Moret-Tatay, Carmen; Pocinho, Ricardo

2015-01-01

Information technology (IT) and serious games allow older population to remain independent for longer. Hence, when designing technology for this population, developmental changes, such as attention and/or perception, should be considered. For instance, a crucial developmental change has been related to cognitive speed in terms of reaction time (RT). However, this variable presents a skewed distribution that difficult data analysis. An alternative strategy is to characterize the data to an ex-Gaussian function. Furthermore, this procedure provides different parameters that have been related to underlying cognitive processes in the literature. Another issue to be considered is the optimal data recording, storing and processing. For that purpose mobile devices (smart phones and tablets) are a good option for targeting serious games where valuable information can be stored (time spent in the application, reaction time, frequency of use, and a long etcetera). The data stored inside the smartphones and tablets can be sent to a central computer (cloud storage) in order to store the data collected to not only fill the distribution of reaction times to mathematical functions, but also to estimate parameters which may reflect cognitive processes underlying language, aging, and decisional process.

Quantitative contrast-enhanced ultrasonography for the differential diagnosis of endometrial hyperplasia and endometrial neoplasms

PubMed Central

Liu, Ying; Xu, Yi; Cheng, Wen; Liu, Xinghan

2016-01-01

The present study aimed to investigate the feasibility of applying contrast-enhanced ultrasonography (CEUS) imaging technology for distinguishing between benign and malignant endometrial lesions, and to screen markers that could be correlated with the pathological results. In this study, endometrial diseases were diagnosed by biopsy under hysteroscopy and CEUS examinations. The intensity and time parameters of the time-intensity curve (TIC) were analyzed. The mean arrival time (AT), time-to-peak (TTP), rise time (RT), washout half-time and clearance half-time of malignant lesions were shorter than those of benign lesions (P<0.05), whereas the average peak intensity (PI) and enhancement intensity (EI) of malignant lesions were higher than those of benign lesions (P<0.05). The receiver operating characteristic curve showed the following cut-off values: PI, 29.2 dB; EI, 21.35 dB; AT, 12.75 sec; TTP, 26.75 sec; RT, 13.2 sec; clearance half-time, 89.3 sec; and washout half-time, 75.45 sec. The lesions with PI, an EI higher than that of the cut-off and lesions with an AT, TTP, RT, half clearing time and washout half-time shorter than the cut-off were considered malignant. The TTP, RT and half clearing time were negatively correlated with microvessel density (MVD), i.e., MVD was higher when the TTP, RT and half clearing time were shorter. Overall, changes in the enhancement and clearing of lesions could be quantitatively analyzed by CEUS TIC and further discriminate benign from malignant lesions. In the present study, CEUS appeared to indirectly reflect blood vessel changes inside the lesions and provided a pre-operative non-invasive fast imaging method for the diagnosis of endometrial disease. PMID:27895728

The effect of attention loading on the inhibition of choice reaction time to visual motion by concurrent rotary motion

NASA Technical Reports Server (NTRS)

Looper, M.

1976-01-01

This study investigates the influence of attention loading on the established intersensory effects of passive bodily rotation on choice reaction time (RT) to visual motion. Subjects sat at the center of rotation in an enclosed rotating chamber and observed an oscilloscope on which were, in the center, a tracking display and, 10 deg left of center, a RT line. Three tracking tasks and a no-tracking control condition were presented to all subjects in combination with the RT task, which occurred with and without concurrent cab rotations. Choice RT to line motions was inhibited (probability less than .001) both when there was simultaneous vestibular stimulation and when there was a tracking task; response latencies lengthened progressively with increased similarity between the RT and tracking tasks. However, the attention conditions did not affect the intersensory effect; the significance of this for the nature of the sensory interaction is discussed.

Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus.

PubMed

Zhang, Jianqiang; Tsai, Yun-Long; Lee, Pei-Yu Alison; Chen, Qi; Zhang, Yan; Chiang, Cheng-Jen; Shen, Yu-Han; Li, Fu-Chun; Chang, Hsiao-Fen Grace; Gauger, Phillip C; Harmon, Karen M; Wang, Hwa-Tang Thomas

2016-08-01

Recent outbreaks of porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) in multiple countries have caused significant economic losses and remain a serious challenge to the swine industry. Rapid diagnosis is critical for the implementation of efficient control strategies before and during PEDV and PDCoV outbreaks. Insulated isothermal PCR (iiPCR) on the portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, a singleplex PEDV RT-iiPCR, a singleplex PDCoV RT-iiPCR, and a duplex PEDV/PDCoV real-time RT-PCR (rRT-PCR) commercial reagents targeting the M gene were compared to an N gene-based PEDV rRT-PCR and an M gene-based PDCoV rRT-PCR that were previously published and used as reference PCRs. All PCR assays were highly specific and did not cross react with other porcine enteric pathogens. Analytical sensitivities of the PEDV RT-iiPCR, PDCoV RT-iiPCR and duplex PEDV/PDCoV rRT-PCR were determined using in vitro transcribed RNA as well as viral RNA extracted from ten-fold serial dilutions of PEDV and PDCoV cell culture isolates. Performance of each PCR assay was further evaluated using 170 clinical samples (86 fecal swabs, 24 feces, 19 intestines, and 41 oral fluids). Compared to the reference PEDV rRT-PCR, the sensitivity, specificity and accuracy of the PEDV RT-iiPCR were 97.73%, 98.78%, and 98.24%, respectively, and those of the duplex PEDV/PDCoV rRT-PCR were 98.86%, 96.34%, and 97.65%, respectively. Compared to the reference PDCoV rRT-PCR, the sensitivity, specificity and accuracy of the PDCoV RT-iiPCR were 100%, 100%, and 100%, respectively, and those of the PEDV/PDCoV duplex rRT-PCR were 96.34%, 100%, and 98.24%, respectively. Overall, all three new PCR assays were comparable to the reference rRT-PCRs for detection of PEDV and/or PDCoV. The PEDV and PDCoV RT-iiPCRs are potentially useful tools for on-site detection and the duplex PEDV/PDCoV rRT-PCR provides a convenient method to simultaneously detect the two viruses and differentiate PEDV from PDCoV. Copyright © 2016 Elsevier B.V. All rights reserved.

Reverse Transcription Recombinase Polymerase Amplification Assay for the Detection of Middle East Respiratory Syndrome Coronavirus

PubMed Central

Abd El Wahed, Ahmed; Patel, Pranav; Heidenreich, Doris; Hufert, Frank T.; Weidmann, Manfred

2013-01-01

The emergence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in the eastern Mediterranean and imported cases to Europe has alerted public health authorities. Currently, detection of MERS-CoV in patient samples is done by real-time RT-PCR. Samples collected from suspected cases are sent to highly-equipped centralized laboratories for screening. A rapid point-of-care test is needed to allow more widespread mobile detection of the virus directly from patient material. In this study, we describe the development of a reverse transcription isothermal Recombinase Polymerase Amplification (RT-RPA) assay for the identification of MERS-CoV. A partial nucleocapsid gene RNA molecular standard of MERS-coronavirus was used to determine the assay sensitivity. The isothermal (42°C) MERS-CoV RT-RPA was as sensitive as real-time RT-PCR (10 RNA molecules), rapid (3-7 minutes) and mobile (using tubescanner weighing 1kg). The MERS-CoV RT-RPA showed cross-detection neither of any of the RNAs of several coronaviruses and respiratory viruses affecting humans nor of the human genome. The developed isothermal real-time RT-RPA is ideal for rapid mobile molecular MERS-CoV monitoring in acute patients and may also facilitate the search for the animal reservoir of MERS-CoV. PMID:24459611

Real-time functional magnetic resonance imaging neurofeedback in motor neurorehabilitation.

PubMed

Linden, David E J; Turner, Duncan L

2016-08-01

Recent developments in functional magnetic resonance imaging (fMRI) have catalyzed a new field of translational neuroscience. Using fMRI to monitor the aspects of task-related changes in neural activation or brain connectivity, investigators can offer feedback of simple or complex neural signals/patterns back to the participant on a quasireal-time basis [real-time-fMRI-based neurofeedback (rt-fMRI-NF)]. Here, we introduce some background methodology of the new developments in this field and give a perspective on how they may be used in neurorehabilitation in the future. The development of rt-fMRI-NF has been used to promote self-regulation of activity in several brain regions and networks. In addition, and unlike other noninvasive techniques, rt-fMRI-NF can access specific subcortical regions and in principle any region that can be monitored using fMRI including the cerebellum, brainstem and spinal cord. In Parkinson's disease and stroke, rt-fMRI-NF has been demonstrated to alter neural activity after the self-regulation training was completed and to modify specific behaviours. Future exploitation of rt-fMRI-NF could be used to induce neuroplasticity in brain networks that are involved in certain neurological conditions. However, currently, the use of rt-fMRI-NF in randomized, controlled clinical trials is in its infancy.

Development of real-time RT-PCR for the detection of low concentrations of Rift Valley fever virus.

PubMed

Maquart, Marianne; Temmam, Sarah; Héraud, Jean-Michel; Leparc-Goffart, Isabelle; Cêtre-Sossah, Catherine; Dellagi, Koussay; Cardinale, Eric; Pascalis, Hervé

2014-01-01

In recent years, Madagascar and the Comoros archipelago have been affected by epidemics of Rift Valley fever (RVF), however detection of Rift Valley fever virus (RVFV) in zebu, sheep and goats during the post epidemic periods was frequently unsuccessful. Thus, a highly sensitive real-time RT-PCR assay was developed for the detection of RVFV at low viral loads. A new RVF SYBR Green RT-PCR targeting the M segment was tested on serum from different RVF seronegative ruminant species collected from May 2010 to August 2011 in Madagascar and the Comoros archipelago and compared with a RVF specific quantitative real time RT-PCR technique, which is considered as the reference technique. The specificity was tested on a wide range of arboviruses or other viruses giving RVF similar clinical signs. A total of 38 out of 2756 serum samples tested positive with the new RT-PCR, whereas the reference technique only detected 5 out of the 2756. The described RT-PCR is an efficient diagnostic tool for the investigation of enzootic circulation of the RVF virus. It allows the detection of low viral RNA loads adapted for the investigations of reservoirs or specific epidemiological situations such as inter-epizootic periods. Copyright © 2013 Elsevier B.V. All rights reserved.

Development and deployment of a rapid recombinase polymerase amplification Ebola virus detection assay in Guinea in 2015.

PubMed

Faye, Oumar; Faye, Ousmane; Soropogui, Barré; Patel, Pranav; El Wahed, Ahmed Abd; Loucoubar, Cheikh; Fall, Gamou; Kiory, Davy; Magassouba, N'Faly; Keita, Sakoba; Kondé, Mandy Kader; Diallo, Alpha Amadou; Koivogui, Lamine; Karlberg, Helen; Mirazimi, Ali; Nentwich, Oliver; Piepenburg, Olaf; Niedrig, Matthias; Weidmann, Manfred; Sall, Amadou Alpha

2015-01-01

In the absence of a vaccine or specific treatments for Ebola virus disease (EVD), early identification of cases is crucial for the control of EVD epidemics. We evaluated a new extraction kit (SpeedXtract (SE), Qiagen) on sera and swabs in combination with an improved diagnostic reverse transcription recombinase polymerase amplification assay for the detection of Ebola virus (EBOV-RT-RPA). The performance of combined extraction and detection was best for swabs. Sensitivity and specificity of the combined SE and EBOV-RT-RPA were tested in a mobile laboratory consisting of a mobile glovebox and a Diagnostics-in-a-Suitcase powered by a battery and solar panel, deployed to Matoto Conakry, Guinea as part of the reinforced surveillance strategy in April 2015 to reach the goal of zero cases. The EBOV-RT-RPA was evaluated in comparison to two real-time PCR assays. Of 928 post-mortem swabs, 120 tested positive, and the combined SE and EBOV-RT-RPA yielded a sensitivity and specificity of 100% in reference to one real-time RT-PCR assay. Another widely used real-time RT-PCR was much less sensitive than expected. Results were provided very fast within 30 to 60 min, and the field deployment of the mobile laboratory helped improve burial management and community engagement.

Estimating the Attack Ratio of Dengue Epidemics under Time-varying Force of Infection using Aggregated Notification Data

NASA Astrophysics Data System (ADS)

Coelho, Flavio Codeço; Carvalho, Luiz Max De

2015-12-01

Quantifying the attack ratio of disease is key to epidemiological inference and public health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation of the attack ratio of an epidemic and the initial fraction of susceptibles using aggregated incidence data. We derive the probability distribution of the effective reproductive number, Rt, and use MCMC to obtain posterior distributions of the parameters of a single-strain SIR transmission model with time-varying force of infection. Our method is showcased in a data set consisting of 18 years of dengue incidence in the city of Rio de Janeiro, Brazil. We demonstrate that it is possible to learn about the initial fraction of susceptibles and the attack ratio even in the absence of serotype specific data. On the other hand, the information provided by this approach is limited, stressing the need for detailed serological surveys to characterise the distribution of serotype-specific immunity in the population.

Performance of nested RT-PCR on CSF for tuberculous meningitis diagnosis in HIV-infected patients.

PubMed

Gualberto, F A S; Gonçalves, M G; Fukasawa, L O; Santos, A M Ramos Dos; Sacchi, C T; Harrison, L H; Boulware, D R; Vidal, J E

2017-10-01

Timely diagnosis of tuberculous meningitis (TBM) in patients with human immunodeficiency virus (HIV) infection remains a challenge. Despite the current scale-up of the Xpert® MTB/RIF assay, other molecular diagnostic tools are necessary, particularly in referral centres in low- and middle-income countries without Xpert testing. To determine the diagnostic performance of nested real-time polymerase chain reaction (nRT-PCR) in HIV-infected TBM patients categorised according to standardised clinical case definitions. Based on clinical, laboratory and imaging data, HIV-infected patients with suspected TBM were prospectively categorised as 'definite TBM', 'probable TBM', 'possible TBM' or 'not TBM'. We evaluated nRT-PCR sensitivity and specificity in diagnosing TBM among definite TBM cases, and among definite + probable TBM cases. Ninety-two participants were enrolled in the study. nRT-PCR sensitivity for definite TBM (n = 8) was 100% (95%CI 67-100) and 86% (95%CI 60-96) for both definite and probable TBM (n = 6). Assuming that 'not TBM' patients (n = 74) were true-negatives, nRT-PCR specificity was 100% (95%CI 95-100). The possible TBM group (n = 4) had no nRT-PCR positives. The nRT-PCR is a useful rule-in test for HIV-infected patients with TBM according to international consensus case definitions. As nRT-PCR cannot exclude TBM, studies comparing and combining nRT-PCR with other assays are necessary for a rule-out test.

Detection of Papaya leaf distortion mosaic virus by reverse-transcription loop-mediated isothermal amplification.

PubMed

Shen, Wentao; Tuo, Decai; Yan, Pu; Li, Xiaoying; Zhou, Peng

2014-01-01

Papaya leaf distortion mosaic virus (PLDMV) can infect transgenic papaya resistant to a related pathogen, Papaya ringspot virus (PRSV), posing a substantial threat to papaya production in China. Current detection methods, however, are unable to be used for rapid detection in the field. Here, a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of PLDMV, using a set of four RT-LAMP primers designed based on the conserved sequence of PLDMV CP. The RT-LAMP method detected specifically PLDMV and was highly sensitive, with a detection limit of 1.32×10(-6) μg of total RNA per reaction. Indeed, the reaction was 10 times more sensitive than one-step RT-PCR, while also requiring significantly less time and equipment. The effectiveness of RT-LAMP and one-step RT-PCR in detecting the virus were compared using 90 field samples of non-transgenic papaya and 90 field samples of commercialized PRSV-resistant transgenic papaya from Hainan Island. None of the non-transgenic papaya tested positive for PLDMV using either method. In contrast, 19 of the commercialized PRSV-resistant transgenic papaya samples tested positive by RT-LAMP assay, and 6 of those tested negative by RT-PCR. Therefore, the PLDMV-specific RT-LAMP is a simple, rapid, sensitive, and cost-effective tool in the field diagnosis and control of PLDMV. Copyright © 2013 Elsevier B.V. All rights reserved.

Rumination time as a potential predictor of common diseases in high-productive Holstein dairy cows.

PubMed

Moretti, Riccardo; Biffani, Stefano; Tiezzi, Francesco; Maltecca, Christian; Chessa, Stefania; Bozzi, Riccardo

2017-11-01

We examined the hypothesis that rumination time (RT) could serve as a useful predictor of various common diseases of high producing dairy cows and hence improve herd management and animal wellbeing. We measured the changes in rumination time (RT) in the days before the recording of diseases (specifically: mastitis, reproductive system diseases, locomotor system issues, and gastroenteric diseases). We built predictive models to assess the association between RT and these diseases, using the former as the outcome variable, and to study the effects of the latter on the former. The average Pseudo-R 2 of the fitted models was moderate to low, and this could be due to the fact that RT is influenced by other additional factors which have a greater effect than the predictors used here. Although remaining in a moderate-to-low range, the average Pseudo-R 2 of the models regarding locomotion issues and gastroenteric diseases was higher than the others, suggesting the greater effect of these diseases on RT. The results are encouraging, but further work is needed if these models are to become useful predictors.

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer.

PubMed

Chalabala, Jan; Uhlig, Frank; Slavíček, Petr

2018-03-29

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

Performance evaluation of latest integrated multi-satellite retrievals for Global Precipitation Measurement (IMERG) over the northern highlands of Pakistan

NASA Astrophysics Data System (ADS)

Anjum, Muhammad Naveed; Ding, Yongjian; Shangguan, Donghui; Ahmad, Ijaz; Ijaz, Muhammad Wajid; Farid, Hafiz Umar; Yagoub, Yousif Elnour; Zaman, Muhammad; Adnan, Muhammad

2018-06-01

Recently, the Global Precipitation Measurement (GPM) mission has released the Integrated Multi-satellite Retrievals for GPM (IMERG) at a fine spatial (0.1° × 0.1°) and temporal (half hourly) resolutions. A comprehensive evaluation of this newly launched precipitation product is very important for satellite-based precipitation data users as well as for algorithm developers. The objective of this study was to provide a preliminary and timely performance evaluation of the IMERG product over the northern high lands of Pakistan. For comparison reference, the real-time and post real-time Tropical Rainfall Measuring Mission (TRMM) Multisatellite Precipitation Analysis (TMPA) products were also evaluated parallel to the IMERG. All of the selected precipitation products were evaluated at annual, monthly, seasonal and daily time scales using reference gauges data from April 2014 to December 2016. The results showed that: (1) the precipitation estimates from IMERG, 3B42V7 and 3B42RT products correlated well with the reference gauges observations at monthly time scale (CC = 0.93, 0.91, 0.88, respectively), whereas moderately at the daily time scale (CC = 0.67, 0.61, and 0.58, respectively); (2) Compared to the 3B42V7 and 3B42RT, the precipitation estimates from IMERG were more reliable in all seasons particularly in the winter season with lowest relative bias (2.61%) and highest CC (0.87); (3) IMERG showed a clear superiority over 3B42V7 and 3B42RT products in order to capture spatial distribution of precipitation over the northern Pakistan; (4) Relative to the 3B42V7 and 3B42RT, daily precipitation estimates from IMEREG showed lowest relative bias (9.20% vs. 21.40% and 26.10%, respectively) and RMSE (2.05 mm/day vs. 2.49 mm/day and 2.88 mm/day, respectively); and (5) Light precipitation events (0-1 mm/day) were usually overestimated by all said satellite-based precipitation products. In contrast moderate (1-20 mm/day) to heavy (>20 mm/day) precipitation events were underestimated by both TMPA products while IMERG was found capable to detect moderate to heavy precipitation events more precisely. Overall, the performance of IMERG was better than that of TMPA products. This preliminary evaluation of new generation of satellite-based precipitation estimates might be a useful feedback for sensor and algorithm developers as well as data users.

Plume Tracker: A New Toolkit for the Mapping of Volcanic Plumes with Multispectral Thermal Infrared Remote Sensing

NASA Astrophysics Data System (ADS)

Realmuto, V. J.; Baxter, S.; Webley, P. W.

2011-12-01

Plume Tracker is the next generation of interactive plume mapping tools pioneered by MAP_SO2. First developed in 1995, MAP_SO2 has been used to study plumes at a number of volcanoes worldwide with data acquired by both airborne and space-borne instruments. The foundation of these tools is a radiative transfer (RT) model, based on MODTRAN, which we use as the forward model for our estimation of ground temperature and sulfur dioxide concentration. Plume Tracker retains the main functions of MAP_SO2, providing interactive tools to input radiance measurements and ancillary data, such as profiles of atmospheric temperature and humidity, to the retrieval procedure, generating the retrievals, and visualizing the resulting retrievals. Plume Tracker improves upon MAP_SO2 in the following areas: (1) an RT model based on an updated version of MODTRAN, (2) a retrieval procedure based on maximizing the vector projection of model spectra onto observed spectra, rather than minimizing the least-squares misfit between the model and observed spectra, (3) an ability to input ozone profiles to the RT model, (4) increased control over the vertical distribution of the atmospheric gas species used in the model, (5) a standard programmatic interface to the RT model code, based on the Component Object Model (COM) interface, which will provide access to any programming language that conforms to the COM standard, and (6) a new binning algorithm that decreases running time by exploiting spatial redundancy in the radiance data. Based on our initial testing, the binning algorithm can reduce running time by an order of magnitude. The Plume Tracker project is a collaborative effort between the Jet Propulsion Laboratory and Geophysical Institute (GI) of the University of Alaska-Fairbanks. Plume Tracker is integrated into the GI's operational plume dispersion modeling system and will ingest temperature and humidity profiles generated by the Weather Research and Forecasting model, together with plume height estimates from the Puff model. The access to timely forecasts of atmospheric conditions, together with the reductions in running time, will increase the utility of Plume Tracker in the Alaska Volcano Observatory's mission to mitigate volcanic hazards in Alaska and the Northern Pacific region.

Detection of spring viraemia of carp virus (SVCV) by loop-mediated isothermal amplification (LAMP) in koi carp, Cyprinus carpio L

USGS Publications Warehouse

Shivappa, R.B.; Savan, R.; Kono, T.; Sakai, M.; Emmenegger, E.; Kurath, G.; Levine, Jay F.

2008-01-01

Spring viraemia of carp virus (SVCV) is a rhabdovirus associated with systemic illness and mortality in cyprinids. Several diagnostic tests are available for detection of SVCV. However, most of these tests are time consuming and are not well adapted for field-based diagnostics. In this study, a diagnostic tool for SVCV detection based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been developed. Based on the nucleotide sequence of the glycoprotein (G) gene of SVCV North Carolina (NC) isolate, four sets (each set containing two outer and two inner) of primers were designed. Temperature and time conditions were optimized to 65 ??C and 60 min, respectively, for LAMP and RT-LAMP using one primer set. In vitro specificity was evaluated using four different strains of fish rhabdoviruses and RT-LAMP was found to be specific to SVCV. Serial dilutions of SVCV NC isolate was used to evaluate the in vitro sensitivity of RT-LAMP. Sensitivity of the assays was similar to RT-PCR and detected SVCV even at the lowest dilution of 10 1 TCID50 mL-1. The ability of RT-LAMP to detect SVCV from infected carp was also tested and the assay detected SVCV from all infected fish. The isothermal temperature requirements, high specificity and sensitivity, and short incubation time of the RT-LAMP assay make it an excellent choice as a field diagnostic test for SVCV. ?? 2008 The Authors.

National survey on the practice of radiation therapists in Australia.

PubMed

Sale, Charlotte; Halkett, Georgia; Cox, Jenny

2016-06-01

Radiation therapy (RT), like many allied health professions, has lacked professional practice clarity, which until 2008 had not been comprehensively investigated. This manuscript describes the first phase of a three-phase project investigating the current and future practices of radiation therapists (RTs) in Australia. The aim of phase 1 was to define the practice of RTs in Australia. A quantitative approach was used to gain an understanding of RT practice. A national survey was distributed to RTs in Australia. Descriptive statistics and content analysis were used to analyse the data. RT practice was analysed in relation to core and non-core roles, where non-core roles were further divided into basic and advanced practices. The data from the national survey were representative of the Australian RT population (n = 525). The current practice of RTs is presented in summary tables for each area of work (treatment, planning, simulation, mould room and general). This study provided clarification of RT practice and indicated there was a desire to relinquish administrative roles to focus on RT-specific practice. There was evidence that some advanced roles were currently practiced in Australia; however, there was no structure to support these roles and they were based only on local need. This study identified that the profession needs to consider how they will maintain core RT practice, while encouraging the development of new roles, and whether some roles need to be relinquished.

Molecular surveillance of Dengue in Sukabumi, West Java province, Indonesia.

PubMed

Nusa, Roy; Prasetyowati, Heni; Meutiawati, Febrina; Yohan, Benediktus; Trimarsanto, Hidayat; Setianingsih, Tri Yuli; Sasmono, R Tedjo

2014-06-11

Dengue is endemic and affects people in all Indonesian provinces. Increasing dengue cases have been observed every year in Sukabumi in West Java province. Despite the endemicity, limited data is available on the genetic of dengue viruses (DENV) circulating in the country. To understand the dynamics of dengue disease, we performed molecular and serological surveillance of dengue in Sukabumi. A total of 113 patients were recruited for this study. Serological data were obtained using anti-dengue IgM and IgG tests plus dengue NS1 antigen detection. Dengue detection and serotyping were performed using real-time RT-PCR. Viruses were isolated and the envelope genes were sequenced. Phylogenetic and evolutionary analyses were performed to determine the genotype of the viruses and their evolutionary rates. Real-time RT-PCR detected DENV in 25 (22%) of 113 samples. Serotyping revealed the predominance of DENV-2 (16 isolates, 64%), followed by DENV-1 (5 isolates, 20%), and DENV-4 (4 isolates, 16%). No DENV-3 was detected in the samples. Co-circulation of genotype I and IV of DENV-1 was observed. The DENV-2 isolates all belonged to the Cosmopolitan genotype, while DENV-4 isolates were grouped into genotype II. Overall, their evolutionary rates were similar to DENV from other countries. We revealed the distribution of DENV serotypes and genotypes in Sukabumi. Compared to data obtained from other cities in Indonesia, we observed the differing predominance of DENV serotypes but similar genotype distribution, where the infecting viruses were closely related with Indonesian endemic viruses isolated previously.

Application of radio frequency based digital thermometer for real-time monitoring of dairy cattle rectal temperature

PubMed Central

Debnath, Tridib; Bera, Santanu; Deb, Suman; Pal, Prasenjit; Debbarma, Nibash; Haldar, Avijit

2017-01-01

Aim: Dairy cattle health monitoring program becomes vital for detecting the febrile conditions to prevent the outbreak of the animal diseases as well as ensuring the fitness of the animals that are directly affecting the health of the consumers. The aim of this study was to validate real-time rectal temperature (RT) data of radio frequency based digital (RFD) thermometer with RT data of mercury bulb (MB) thermometer in dairy cattle. Materials and Methods: Two experiments were conducted. In experiment I, six female Jersey crossbred cattle with a mean (±standard error of the mean) body weight of 534.83±13.90 kg at the age of 12±0.52 years were used to record RT for 2 h on empty stomach and 2 h after feeding at 0, 30, 60, 90, and 120 min using a RFD thermometer as well as a MB thermometer. In experiment II, six female Jersey crossbred cattle were further used to record RT for 2 h before exercise and 2 h after exercise at 0, 30, 60, 90, and 120 min. Two-way repeated measures analysis of variance with post hoc comparisons by Bonferroni test was done. Results: Real-time RT data recorded by RFD thermometer as well as MB thermometer did not differ (p>0.05) before and after feeding/exercise. An increase (p<0.05) in RT after feeding/exercise in experimental crossbred cattle was recorded by both RFD thermometer and MB thermometer. Conclusion: The results obtained in the present study suggest that the body temperature recordings from RFD thermometer would be acceptable and thus RFD thermometer could work well for monitoring real-time RT in cattle. PMID:29062193

A Cross-Sectional Cohort Study of Cerebrovascular Disease and Late Effects After Radiation Therapy for Craniopharyngioma.

PubMed

Lo, Andrea C; Howard, A Fuchsia; Nichol, Alan; Hasan, Haroon; Martin, Monty; Heran, Manraj; Goddard, Karen

2016-05-01

The study objective was to describe radiation-induced vascular abnormalities, stroke prevalence, and stroke risk factors in survivors of childhood craniopharyngioma. Twenty survivors of childhood craniopharyngioma who received radiotherapy (RT) were included in the study. A clinical history, quality of life assessment, cognitive functioning assessment, magnetic resonance angiogram or computed tomography angiogram, fasting lipid profile, and fasting glucose or hemoglobin A1c test were obtained. Median age at diagnosis was 10.3 years and median age at time of study was 29.0 years. Vascular abnormalities were detected in six (32%) of 19 patients' angiograms (vascular stenosis, decreased artery size, aneurysm, cavernoma, and small vessel disease). Five (25%) of 20 patients experienced a stroke after RT. Median time since RT was 27.8 versus 9.1 years in patients with versus without vascular abnormalities (P = 0.02). A low level of high-density lipoproteiin (HDL) was present in 100% (5/5) of patients who had a post-RT stroke as compared with 13% (2/15) of patients who did not have any post-RT stroke (P = 0.02). Previous stroke had occurred in 0% (0/5) of patients receiving growth hormone (GH) replacement at the time of study, compared to 40% (6/15) of patients who were not receiving GH replacement (P = 0.09). Patients with craniopharyngioma treated with RT have a high prevalence of stroke and vascular abnormalities, particularly those with low HDL and longer duration of time since RT. There is a trend to suggest that continual GH replacement may reduce the risk of stroke. These patients should undergo careful monitoring and aggressive modification of stroke risk factors. © 2016 Wiley Periodicals, Inc.

REAL TIME MRI GUIDED RADIOFREQUENCY ATRIAL ABLATION AND VISUALIZATION OF LESION FORMATION AT 3-TESLA

PubMed Central

Vergara, Gaston R.; Vijayakumar, Sathya; Kholmovski, Eugene G.; Blauer, Joshua J.E.; Guttman, Mike A.; Gloschat, Christopher; Payne, Gene; Vij, Kamal; Akoum, Nazem W.; Daccarett, Marcos; McGann, Christopher J.; MacLeod, Rob S.; Marrouche, Nassir F.

2011-01-01

Background MRI allows visualization of location and extent of RF ablation lesion, myocardial scar formation, and real-time (RT) assessment of lesion formation. In this study, we report a novel 3-Tesla RT-MRI based porcine RF ablation model and visualization of lesion formation in the atrium during RF energy delivery. Objective To develop of a 3-Tesla RT-MRI based catheter ablation and lesion visualization system. Methods RF energy was delivered to six pigs under RT-MRI guidance. A novel MRI compatible mapping and ablation catheter was used. Under RT-MRI this catheter was safely guided and positioned within either the left or right atrium. Unipolar and bi-polar electrograms were recorded. The catheter tip-tissue interface was visualized with a T1-weighted gradient echo sequence. RF energy was then delivered in a power-controlled fashion. Myocardial changes and lesion formation were visualized with a T2-weighted (T2w) HASTE sequence during ablation. Results Real-time visualization of lesion formation was achieved in 30% of the ablations performed. In the other cases, either the lesion was formed outside the imaged region (25%) or lesion was not created (45%) presumably due to poor tissue-catheter tip contact. The presence of lesions was confirmed by late gadolinium enhancement (LGE) MRI and macroscopic tissue examination. Conclusion MRI compatible catheters can be navigated and RF energy safely delivered under 3-Tesla RT-MRI guidance. It is also feasible to record electrograms during RT imaging. Real-time visualization of lesion as it forms during delivery of RF energy is possible and was demonstrated using T2w HASTE imaging. PMID:21034854

Application of radio frequency based digital thermometer for real-time monitoring of dairy cattle rectal temperature.

PubMed

Debnath, Tridib; Bera, Santanu; Deb, Suman; Pal, Prasenjit; Debbarma, Nibash; Haldar, Avijit

2017-09-01

Dairy cattle health monitoring program becomes vital for detecting the febrile conditions to prevent the outbreak of the animal diseases as well as ensuring the fitness of the animals that are directly affecting the health of the consumers. The aim of this study was to validate real-time rectal temperature (RT) data of radio frequency based digital (RFD) thermometer with RT data of mercury bulb (MB) thermometer in dairy cattle. Two experiments were conducted. In experiment I, six female Jersey crossbred cattle with a mean (±standard error of the mean) body weight of 534.83±13.90 kg at the age of 12±0.52 years were used to record RT for 2 h on empty stomach and 2 h after feeding at 0, 30, 60, 90, and 120 min using a RFD thermometer as well as a MB thermometer. In experiment II, six female Jersey crossbred cattle were further used to record RT for 2 h before exercise and 2 h after exercise at 0, 30, 60, 90, and 120 min. Two-way repeated measures analysis of variance with post hoc comparisons by Bonferroni test was done. Real-time RT data recorded by RFD thermometer as well as MB thermometer did not differ (p>0.05) before and after feeding/exercise. An increase (p<0.05) in RT after feeding/exercise in experimental crossbred cattle was recorded by both RFD thermometer and MB thermometer. The results obtained in the present study suggest that the body temperature recordings from RFD thermometer would be acceptable and thus RFD thermometer could work well for monitoring real-time RT in cattle.

Increased Intrasubject Variability in Response Time in Youths with Bipolar Disorder and At-Risk Family Members

ERIC Educational Resources Information Center

Brotman, Melissa A.; Rooney, Melissa H.; Skup, Martha; Pine, Daniel S.; Leibenluft, Ellen

2009-01-01

Intrasubject variability in response time (ISV-RT) was higher in youths with bipolar disorder (BD) and those with first-degree relatives with BD compared to youths without BD. ISV-RT may be a risk marker for BD.

Is Reaction Time Variability in ADHD Mainly at Low Frequencies?

ERIC Educational Resources Information Center

Karalunas, Sarah L.; Huang-Pollock, Cynthia L.; Nigg, Joel T.

2013-01-01

Background: Intraindividual variability in reaction times (RT variability) has garnered increasing interest as an indicator of cognitive and neurobiological dysfunction in children with attention deficit hyperactivity disorder (ADHD). Recent theory and research has emphasized specific low-frequency patterns of RT variability. However, whether…

No significant effect of transcranial direct current stimulation (tDCS) found on simple motor reaction time comparing 15 different simulation protocols.

PubMed

Horvath, Jared Cooney; Carter, Olivia; Forte, Jason D

2016-10-01

Research exploring the behavioral impact of transcranial direct current stimulation (tDCS) over M1 has produced homogenous results. The most common explanations to address this homogeneity concerns the differential impact of varied tDCS parameters (such as stimulation intensity or electrode montage). To explore this, we systematically examined the effects of 15 different tDCS protocols on a well-elucidated neurobehavioral system: simple visual motor reaction time (smRT). For the initial phase of this study, 150 healthy participants were randomly assigned to one of 5 experimental groups (2mA anodal, 2mA cathodal, 1mA anodal, 1mA cathodal, or sham) across 3 different conditions (orbitofrontal, bilateral, or extracephalic reference electrode location). The active electrode was always placed over M1 and tDCS lasted for 20min. Starting ~5min prior to stimulation and running continuously for ~30min, participants were repeatedly presented with a visual cue centered on a computer monitor and asked to press a response button as quickly as possible at stimulus onset (stimuli number: 100 pre-, 400 during-, and 100-post stimulation - interstimulus interval: 1-3s). Ex-gaussian distribution curves, miss, and error rates were determined for each normalized batch of 100 RTs and compared using a two-way ANOVA. As the largest group differences were seen with 2mA anodal (compared to sham) stimulation using an orbitofrontal montage, an additional 60 healthy participants were recruited to further test for significance in this condition. No significant impact of tDCS was seen on any parameter of smRT distribution, error rate, or miss rate, regardless of polarity, stimulation intensity, electrode montage, or stimulation-to-task relationship. Our results suggest that tDCS over M1 might not have a predictable or reliable effect on short duration smRT. Our results raise interesting questions regarding the mechanisms by which tDCS might modulate more complex motor behaviors. Additional research utilizing multiple tDCS protocols as undertaken here will help address and clarify these concerns. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards real-time cardiovascular magnetic resonance guided transarterial CoreValve implantation: in vivo evaluation in swine

PubMed Central

2012-01-01

Background Real-time cardiovascular magnetic resonance (rtCMR) is considered attractive for guiding TAVI. Owing to an unlimited scan plane orientation and an unsurpassed soft-tissue contrast with simultaneous device visualization, rtCMR is presumed to allow safe device navigation and to offer optimal orientation for precise axial positioning. We sought to evaluate the preclinical feasibility of rtCMR-guided transarterial aortic valve implatation (TAVI) using the nitinol-based Medtronic CoreValve bioprosthesis. Methods rtCMR-guided transfemoral (n = 2) and transsubclavian (n = 6) TAVI was performed in 8 swine using the original CoreValve prosthesis and a modified, CMR-compatible delivery catheter without ferromagnetic components. Results rtCMR using TrueFISP sequences provided reliable imaging guidance during TAVI, which was successful in 6 swine. One transfemoral attempt failed due to unsuccessful aortic arch passage and one pericardial tamponade with subsequent death occurred as a result of ventricular perforation by the device tip due to an operating error, this complication being detected without delay by rtCMR. rtCMR allowed for a detailed, simultaneous visualization of the delivery system with the mounted stent-valve and the surrounding anatomy, resulting in improved visualization during navigation through the vasculature, passage of the aortic valve, and during placement and deployment of the stent-valve. Post-interventional success could be confirmed using ECG-triggered time-resolved cine-TrueFISP and flow-sensitive phase-contrast sequences. Intended valve position was confirmed by ex-vivo histology. Conclusions Our study shows that rtCMR-guided TAVI using the commercial CoreValve prosthesis in conjunction with a modified delivery system is feasible in swine, allowing improved procedural guidance including immediate detection of complications and direct functional assessment with reduction of radiation and omission of contrast media. PMID:22453050

Towards real-time cardiovascular magnetic resonance guided transarterial CoreValve implantation: in vivo evaluation in swine.

PubMed

Kahlert, Philipp; Parohl, Nina; Albert, Juliane; Schäfer, Lena; Reinhardt, Renate; Kaiser, Gernot M; McDougall, Ian; Decker, Brad; Plicht, Björn; Erbel, Raimund; Eggebrecht, Holger; Ladd, Mark E; Quick, Harald H

2012-03-27

Real-time cardiovascular magnetic resonance (rtCMR) is considered attractive for guiding TAVI. Owing to an unlimited scan plane orientation and an unsurpassed soft-tissue contrast with simultaneous device visualization, rtCMR is presumed to allow safe device navigation and to offer optimal orientation for precise axial positioning. We sought to evaluate the preclinical feasibility of rtCMR-guided transarterial aortic valve implatation (TAVI) using the nitinol-based Medtronic CoreValve bioprosthesis. rtCMR-guided transfemoral (n = 2) and transsubclavian (n = 6) TAVI was performed in 8 swine using the original CoreValve prosthesis and a modified, CMR-compatible delivery catheter without ferromagnetic components. rtCMR using TrueFISP sequences provided reliable imaging guidance during TAVI, which was successful in 6 swine. One transfemoral attempt failed due to unsuccessful aortic arch passage and one pericardial tamponade with subsequent death occurred as a result of ventricular perforation by the device tip due to an operating error, this complication being detected without delay by rtCMR. rtCMR allowed for a detailed, simultaneous visualization of the delivery system with the mounted stent-valve and the surrounding anatomy, resulting in improved visualization during navigation through the vasculature, passage of the aortic valve, and during placement and deployment of the stent-valve. Post-interventional success could be confirmed using ECG-triggered time-resolved cine-TrueFISP and flow-sensitive phase-contrast sequences. Intended valve position was confirmed by ex-vivo histology. Our study shows that rtCMR-guided TAVI using the commercial CoreValve prosthesis in conjunction with a modified delivery system is feasible in swine, allowing improved procedural guidance including immediate detection of complications and direct functional assessment with reduction of radiation and omission of contrast media.

Lab-scale demonstration of recuperative thickening technology for enhanced biogas production and dewaterability in anaerobic digestion processes.

PubMed

Cobbledick, Jeffrey; Aubry, Nicholas; Zhang, Victor; Rollings-Scattergood, Sasha; Latulippe, David R

2016-05-15

There is growing interest in the use of high performance anaerobic digestion (AD) processes for the production of biogas at wastewater treatment facilities to offset the energy demands associated with wastewater treatment. Recuperative thickening (RT) is a promising technique which involves recycling a portion of the digested solids back to the incoming feed. In general there exists a significant number of knowledge gaps in the field of RT because the studies that have been conducted to date have almost exclusively occurred in pilot plant or full scale trials; this approach greatly limits the amount of process optimization that can be done in a given trial. In this work, a detailed and comprehensive study of RT was conducted at the lab scale; two custom designed digesters (capacity = 1.5 L) were operated in parallel with one acting as a 'control' digester and the other operating under a semi-batch RT mode. There was no significant change in biogas methane composition for the two digesters, however the RT digester had an average biogas productivity over two times higher than the control one. It was found that the recycling of the polymer flocculant back into the RT digester resulted in a significant improvement in dewatering performance. At the highest polymer concentration tested, the capillary suction time (CST) values for flocculated samples for the RT digester were over 6 times lower than the corresponding values for the control digester. Thus, there exists an opportunity to decrease the overall consumption of polymer flocculants through judicious selection of the dose of polymer flocculant that is used both for the thickening and end-stage dewatering steps in RT processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

One-step cross-genogroup multiplex RT-qPCR with an internal control system for the detection of infectious pancreatic necrosis virus (IPNV).

PubMed

Hoferer, Marc; Braun, Anne; Skrypski, Julia; Bock, Sabine; Thalheim, Sabine; Sting, Reinhard

2017-09-01

Infectious pancreatic necrosis virus (IPNV) causes great losses in fish hatcheries world-wide. The detection of IPNV can be challenging in certain circumstances, particularly due to low viral load and the genetic variability of this RNA virus. For the first time, this project created a quantitative triplex real-time reverse transcription PCR (RT-qPCR), including an endogenous control system, for specific, sensitive and rapid detection of IPNV in routine diagnostics. Multiple sequence alignment of 46 nucleotide sequences of the segment A genome obtained from the NCBI database allowed the design of two RT-qPCR systems covering the IPNV genogroup 1 and genogroups 2-5, respectively. The completed triplex RT-qPCR including a salmonid-specific endogenous control showed high specificity and an analytical sensitivity of 20-40 oligonucleotide copies. Testing of dilution series of virus-loaded cell culture suspensions proved equality of the triplex RT-qPCR with virus detection in cell culture and a higher sensitivity than conventional RT-PCR in field samples. In comparative studies of a total of 77 field samples tested, 51 showed identical positive and 19 identical negative results in cell culture and the triplex RT-qPCR. However, seven other samples yielded positive results in the triplex RT-qPCR, but negative results in cell culture. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2010-01-01

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

Ring trial 2016 for Bluetongue virus detection by real-time RT-PCR in France.

PubMed

Sailleau, Corinne; Viarouge, Cyril; Breard, Emmanuel; Vitour, Damien; Zientara, Stephan

2017-05-01

Since the unexpected emergence of BTV-8 in Northern Europe and the incursion of BTV-8 and 1 in France in 2006-2007, molecular diagnosis has considerably evolved. Several real-time RT-PCR (rtRT-PCR) methods have been developed and published, and are currently being used in many countries across Europe for BTV detection and typing. In France, the national reference laboratory (NRL) for orbiviruses develops and validates 'ready-to-use' kits with private companies for viral RNA detection. The regional laboratories network that was set up to deal with a heavy demand for analyses has used these available kits. From 2007, ring tests were organized to monitor the performance of the French laboratories. This study presents the results of 63 regional laboratories in the ring trial organized in 2016. Blood samples were sent to the laboratories. Participants were asked to use the rtRT-PCR methods in place in their laboratory, for detection of all BTV serotypes and specifically BTV-8. The French regional laboratories are able to detect and genotype BTV in affected animals. Despite the use of several methods (i.e. RNA extraction and different commercial rtRT-PCRs), the network is homogeneous. The ring trial demonstrated that the French regional veterinary laboratories have reliable and robust BTV diagnostic tools for BTV genome detection.

Comparison of Radiation-Induced Normal Lung Tissue Density Changes for Patients From Multiple Institutions Receiving Conventional or Hypofractionated Treatments

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

Diot, Quentin, E-mail: quentin.diot@ucdenver.edu; Marks, Lawrence B.; Bentzen, Soren M.

Purpose: To quantitatively assess changes in computed tomography (CT)–defined normal lung tissue density after conventional and hypofractionated radiation therapy (RT). Methods and Materials: The pre-RT and post-RT CT scans from 118 and 111 patients receiving conventional and hypofractionated RT, respectively, at 3 institutions were registered to each other and to the 3-dimensional dose distribution to quantify dose-dependent changes in normal lung tissue density. Dose-response curves (DRC) for groups of patients receiving conventional and hypofractionated RT were generated for each institution, and the frequency of density changes >80 Hounsfield Units (HU) was modeled depending on the fractionation type using a Probitmore » model for different follow-up times. Results: For the pooled data from all institutions, there were significant differences in the DRC between the conventional and hypofractionated groups; the respective doses resulting in 50% complication risk (TD{sub 50}) were 62 Gy (95% confidence interval [CI] 57-67) versus 36 Gy (CI 33-39) at <6 months, 48 Gy (CI 46-51) versus 31 Gy (CI 28-33) at 6-12 months, and 47 Gy (CI 45-49) versus 35 Gy (32-37) at >12 months. The corresponding m values (slope of the DRC) were 0.52 (CI 0.46-0.59) versus 0.31 (CI 0.28-0.34) at <6 months, 0.46 (CI 0.42-0.51) versus 0.30 (CI 0.26-0.34) at 6-12 months, and 0.45 (CI 0.42-0.50) versus 0.31 (CI 0.27-0.35) at >12 months (P<.05 for all comparisons). Conclusion: Compared with conventional fractionation, hypofractionation has a lower TD{sub 50} and m value, both suggesting an increased degree of normal tissue density sensitivity with hypofractionation.« less

SlicerRT: radiation therapy research toolkit for 3D Slicer.

PubMed

Pinter, Csaba; Lasso, Andras; Wang, An; Jaffray, David; Fichtinger, Gabor

2012-10-01

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula)

USDA-ARS?s Scientific Manuscript database

Quantitative real-time polymerase chain reaction (qRT-PCR) is the most important tool in measuring levels of gene expression due to its accuracy, specificity, and sensitivity. However, the accuracy of qRT-PCR analysis strongly depends on transcript normalization using stably expressed reference gene...

Effect of glare on simple reaction time.

PubMed

Aguirre, Rolando C; Colombo, Elisa M; Barraza, José F

2008-07-01

We systematized the study of the effect of glare on reaction time (RT), for visual conditions similar to the ones found during night driving: Mesopic range of adaptation (0.14 cd/m2), glare levels of the order of those produced by car headlights (E(G)=15, 60 lx), suprathreshold luminance contrasts, and a variety of spatial frequencies covering the selected range of visibility (1, 2, 4, and 8 c/deg). We found that for the no-glare situation, RT increases with decreasing contrast and increasing spatial frequency, which agrees with previous findings. When data are plotted as a function of the inverse of contrast, RT varies linearly, with k--the RT-contrast factor of Pieron's law--representing the slope of the lines. The effect of glare on RT is an increase in the slope of these lines. This effect is different for each spatial frequency, which cannot be accounted for in the classic approach considering that glare can be replaced by a single veiling luminance. We show that the effect of glare on RT must be modeled by an equivalent glare luminance that depends on spatial frequency.

Historical trends in the use of radiation therapy for pediatric cancers: 1973-2008.

PubMed

Jairam, Vikram; Roberts, Kenneth B; Yu, James B

2013-03-01

This study was undertaken to assess historical trends in the use of radiation therapy (RT) for pediatric cancers over the past 4 decades. The National Cancer Institute's Surveillance, Epidemiology, and End Results database of the 9 original tumor registries (SEER-9) was queried to identify patients aged 0 to 19 years with acute lymphoblastic leukemia, acute myeloid leukemia, bone and joint cancer, cancer of the brain and nervous system, Hodgkin lymphoma, neuroblastoma, non-Hodgkin lymphoma, soft tissue cancer, Wilms tumor, or retinoblastoma from 1973 to 2008. Patients were grouped into 4-year time epochs. The number and percentage of patients who received RT as part of their initial treatment were calculated per epoch by each diagnosis group from 1973 to 2008. RT use for acute lymphoblastic leukemia, non-Hodgkin lymphoma, and retinoblastoma declined sharply from 57%, 57%, and 30% in 1973 to 1976 to 11%, 15%, and 2%, respectively, in 2005 to 2008. Similarly, smaller declines in RT use were also seen in brain cancer (70%-39%), bone cancer (41%-21%), Wilms tumor (75%-53%), and neuroblastoma (60%-25%). RT use curves for Wilms tumor and neuroblastoma were nonlinear with nadirs in 1993 to 1996 at 39% and 19%, respectively. There were minimal changes in RT use for Hodgkin lymphoma, soft tissue cancer, or acute myeloid leukemia, roughly stable at 72%, 40%, and 11%, respectively. Almost all patients treated with RT were given external beam RT exclusively. However, from 1985 to 2008, treatments involving brachytherapy, radioisotopes, or combination therapy increased in frequency, comprising 1.8%, 4.6%, and 11.9% of RT treatments in brain cancer, soft tissue cancer, and retinoblastoma, respectively. The use of RT is declining over time in 7 of 10 pediatric cancer categories. A limitation of this study is a potential under-ascertainment of RT use in the SEER-9 database including the delayed use of RT. Copyright © 2013 Elsevier Inc. All rights reserved.

Abilities of the mCP Agar Method and CRENAME Alpha Toxin-Specific Real-Time PCR Assay To Detect Clostridium perfringens Spores in Drinking Water

PubMed Central

Maheux, Andrée F.; Bérubé, Ève; Boudreau, Dominique K.; Villéger, Romain; Cantin, Philippe; Boissinot, Maurice; Bissonnette, Luc

2013-01-01

We first determined the analytical specificity and ubiquity (i.e., the ability to detect all or most strains) of a Clostridium perfringens-specific real-time PCR (rtPCR) assay based on the cpa gene (cpa rtPCR) by using a bacterial strain panel composed of C. perfringens and non-C. perfringens Clostridium strains. All non-C. perfringens Clostridium strains tested negative, whereas all C. perfringens strains tested positive with the cpa rtPCR, for an analytical specificity and ubiquity of 100%. The cpa rtPCR assay was then used to confirm the identity of 116 putative C. perfringens isolates recovered after filtration of water samples and culture on mCP agar. Colonies presenting discordant results between the phenotype on mCP agar and cpa rtPCR were identified by sequencing the 16S rRNA and cpa genes. Four mCP−/rtPCR+ colonies were identified as C. perfringens, whereas 3 mCP+/rtPCR− colonies were identified as non-C. perfringens. The cpa rtPCR was negative with all 51 non-C. perfringens strains and positive with 64 of 65 C. perfringens strains. Finally, we compared mCP agar and a CRENAME (concentration and recovery of microbial particles, extraction of nucleic acids, and molecular enrichment) procedure plus cpa rtPCR (CRENAME + cpa rtPCR) for their abilities to detect C. perfringens spores in drinking water. CRENAME + cpa rtPCR detected as few as one C. perfringens CFU per 100 ml of drinking water sample in less than 5 h, whereas mCP agar took at least 25 h to deliver results. CRENAME + cpa rtPCR also allows the simultaneous and sensitive detection of Escherichia coli and C. perfringens from the same potable water sample. In itself, it could be used to assess the public health risk posed by drinking water potentially contaminated with pathogens more resistant to disinfection. PMID:24077714

Historical Trends in the Use of Radiation Therapy for Pediatric Cancers: 1973-2008

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

Jairam, Vikram; Roberts, Kenneth B.; Yale Cancer Center, New Haven, Connecticut

Purpose: This study was undertaken to assess historical trends in the use of radiation therapy (RT) for pediatric cancers over the past 4 decades. Methods: The National Cancer Institute's Surveillance, Epidemiology, and End Results database of the 9 original tumor registries (SEER-9) was queried to identify patients aged 0 to 19 years with acute lymphoblastic leukemia, acute myeloid leukemia, bone and joint cancer, cancer of the brain and nervous system, Hodgkin lymphoma, neuroblastoma, non-Hodgkin lymphoma, soft tissue cancer, Wilms tumor, or retinoblastoma from 1973 to 2008. Patients were grouped into 4-year time epochs. The number and percentage of patients whomore » received RT as part of their initial treatment were calculated per epoch by each diagnosis group from 1973 to 2008. Results: RT use for acute lymphoblastic leukemia, non-Hodgkin lymphoma, and retinoblastoma declined sharply from 57%, 57%, and 30% in 1973 to 1976 to 11%, 15%, and 2%, respectively, in 2005 to 2008. Similarly, smaller declines in RT use were also seen in brain cancer (70%-39%), bone cancer (41%-21%), Wilms tumor (75%-53%), and neuroblastoma (60%-25%). RT use curves for Wilms tumor and neuroblastoma were nonlinear with nadirs in 1993 to 1996 at 39% and 19%, respectively. There were minimal changes in RT use for Hodgkin lymphoma, soft tissue cancer, or acute myeloid leukemia, roughly stable at 72%, 40%, and 11%, respectively. Almost all patients treated with RT were given external beam RT exclusively. However, from 1985 to 2008, treatments involving brachytherapy, radioisotopes, or combination therapy increased in frequency, comprising 1.8%, 4.6%, and 11.9% of RT treatments in brain cancer, soft tissue cancer, and retinoblastoma, respectively. Conclusions: The use of RT is declining over time in 7 of 10 pediatric cancer categories. A limitation of this study is a potential under-ascertainment of RT use in the SEER-9 database including the delayed use of RT.« less

The NASA Short-term Prediction and Research Transition (SPoRT) Center: A Research to Operations Test Bed

NASA Technical Reports Server (NTRS)

Jedlovec, Gary J.

2005-01-01

Over the last three years, NASA/MSFC scientists have embarked on an effort to transition unique NASA EOS data/products and research technology to selected NWSEOs in the southeast U.S. This activity, called the Short-term Prediction and - Research Transition (SPoRT) program, supports the NASA Science Mission Directorate and its Earth-Sun System Mission to develop a scientific understanding of the Earth System and its response to natural or human-induced changes that will enable improved prediction capability for climate, weather, and natural hazards. The overarching question related to weather prediction is "How well can weather forecasting duration and reliability be improved by new space-based observations, data assimilation, and modeling?" The transition activity has included the real-time delivery of MODIS data and products to several NWS Forecast Offices. Local NWS FOs have used the MODIS data to complement the coarse resolution GOES data for a number of applications. Specialized products have also been developed and made available to local and remote offices for their weather applications. Data from &e Lightning Mapping Array (LMA) network has been used in severe storm forecasts at several offices in the region. At the regional scale and forecast horizons from 0-1 day, the next generation of high-resolution mesoscale forecast and data assimilation models have been used to provide local offices with unique weather forecasts not otherwise available. The continued use of near red-time infusion of NASA science products into high-resolution mesoscale forecast and decision-making models can be expected to improve the model initialization as well as short-term forecasts. A current focus of SPoRT is to expand collaborations to include contributions from the assimilation of AMSR-E data in the ADASIARPS forecast system (OU), inclusion of MODIS SSTs and AIRS thermodynamic profiles in the WRF, and to extend the distribution of real-time MODIS and AMSR-E data and products to the Florida coastal WFOs. A SPoRT Test bed, together with input from other interagency and university partners, will provide a means and a process to effectively transition ESE observations and technology to NWS operations and decision makers at both the globdnational and regional scales. The transition of emerging experimental products into operations through the SPoRT infrastructure will allow NASA to foster and accelerate the progress of this Science Mission Directorate research strategy over the coming years.

In-flight demonstration of a Real-Time Flush Airdata Sensing (RT-FADS) system

NASA Technical Reports Server (NTRS)

Whitmore, Stephen A.; Davis, Roy J.; Fife, John Michael

1995-01-01

A prototype real-time flush airdata sensing (RT-FADS) system has been developed and flight tested at the NASA Dryden Flight Research Center. This system uses a matrix of pressure orifices on the vehicle nose to estimate airdata parameters in real time using nonlinear regression. The algorithm is robust to sensor failures and noise in the measured pressures. The RT-FADS system has been calibrated using inertial trajectory measurements that were bootstrapped for atmospheric conditions using meteorological data. Mach numbers as high as 1.6 and angles of attack greater than 45 deg have been tested. The system performance has been evaluated by comparing the RT-FADS to the ship system airdata computer measurements to give a quantitative evaluation relative to an accepted measurement standard. Nominal agreements of approximately 0.003 in Mach number and 0.20 deg in angle of attack and angle of sideslip have been achieved.

Rectal cancer delivery of radiotherapy in adequate time and with adequate dose is influenced by treatment center, treatment schedule, and gender and is prognostic parameter for local control: Results of study CAO/ARO/AIO-94

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

Fietkau, Rainer; Roedel, Claus; Hohenberger, Werner

2007-03-15

Purpose: The impact of the delivery of radiotherapy (RT) on treatment results in rectal cancer patients is unknown. Methods and Materials: The data from 788 patients with rectal cancer treated within the German CAO/AIO/ARO-94 phase III trial were analyzed concerning the impact of the delivery of RT (adequate RT: minimal radiation RT dose delivered, 4300 cGy for neoadjuvant RT or 4700 cGy for adjuvant RT; completion of RT in <44 days for neoadjuvant RT or <49 days for adjuvant RT) in different centers on the locoregional recurrence rate (LRR) and disease-free survival (DFS) at 5 years. The LRR, DFS, andmore » delivery of RT were analyzed as endpoints in multivariate analysis. Results: A significant difference was found between the centers and the delivery of RT. The overall delivery of RT was a prognostic factor for the LRR (no RT, 29.6% {+-} 7.8%; inadequate RT, 21.2% {+-} 5.6%; adequate RT, 6.8% {+-} 1.4%; p = 0.0001) and DFS (no RT, 55.1% {+-} 9.1%; inadequate RT, 57.4% {+-} 6.3%; adequate RT, 69.1% {+-} 2.3%; p = 0.02). Postoperatively, delivery of RT was a prognostic factor for LRR on multivariate analysis (together with pathologic stage) but not for DFS (independent parameters, pathologic stage and age). Preoperatively, on multivariate analysis, pathologic stage, but not delivery of RT, was an independent prognostic parameter for LRR and DFS (together with adequate chemotherapy). On multivariate analysis, the treatment center, treatment schedule (neoadjuvant vs. adjuvant RT), and gender were prognostic parameters for adequate RT. Conclusion: Delivery of RT should be regarded as a prognostic factor for LRR in rectal cancer and is influenced by the treatment center, treatment schedule, and patient gender.« less

Co-morbid conditions in use of recombinant tissue plasminogen activator (rt-PA) for the treatment of acute ischaemic stroke.

PubMed

Nathaniel, Thomas I; Cochran, Thomas; Chaves, Jose; Fulmer, Eric; Sosa, Crystal; Yi, Sara; Fredwall, Megan; Sternberg, Shannon; Blackhurst, Dawn; Nelson, Alfred; Leacock, Rodney

2016-01-01

The objective of this study was to characterize the comorbidities in a population of patients with an acute ischaemic stroke, comparing patients that received recombinant tissue plasminogen activator (rt-PA) to those that did not receive rt-PA. In a retrospective sample of 663 patients admitted for acute ischaemic stroke, this study analysed the effects of co-morbid conditions in the use of rt-PA. It determined non-cerebrovascular risk factors (comorbidities) that differentiate patients who received rt-PA from those who did not receive rt-PA. Patients with a history of carotid stenosis, CHF and previous strokes are significantly (p < 0.05) associated with high risk of not receiving rt-PA. A significant number of patients with a history of hypertension and smoking received rt-PA (p < 0.05). The findings indicate that certain risk factors including carotid stenosis, CHF and previous stroke history impact the treatment of patients with acute ischaemic stroke, specifically the decision to administer rt-PA. Treatment with rt-PA is dependent on stroke severity and onset to treatment time, but the findings suggest that rt-PA use may also depend on patient comorbidities.

Evaluating model parameterizations of submicron aerosol scattering and absorption with in situ data from ARCTAS 2008

NASA Astrophysics Data System (ADS)

Alvarado, Matthew J.; Lonsdale, Chantelle R.; Macintyre, Helen L.; Bian, Huisheng; Chin, Mian; Ridley, David A.; Heald, Colette L.; Thornhill, Kenneth L.; Anderson, Bruce E.; Cubison, Michael J.; Jimenez, Jose L.; Kondo, Yutaka; Sahu, Lokesh K.; Dibb, Jack E.; Wang, Chien

2016-07-01

Accurate modeling of the scattering and absorption of ultraviolet and visible radiation by aerosols is essential for accurate simulations of atmospheric chemistry and climate. Closure studies using in situ measurements of aerosol scattering and absorption can be used to evaluate and improve models of aerosol optical properties without interference from model errors in aerosol emissions, transport, chemistry, or deposition rates. Here we evaluate the ability of four externally mixed, fixed size distribution parameterizations used in global models to simulate submicron aerosol scattering and absorption at three wavelengths using in situ data gathered during the 2008 Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) campaign. The four models are the NASA Global Modeling Initiative (GMI) Combo model, GEOS-Chem v9-02, the baseline configuration of a version of GEOS-Chem with online radiative transfer calculations (called GC-RT), and the Optical Properties of Aerosol and Clouds (OPAC v3.1) package. We also use the ARCTAS data to perform the first evaluation of the ability of the Aerosol Simulation Program (ASP v2.1) to simulate submicron aerosol scattering and absorption when in situ data on the aerosol size distribution are used, and examine the impact of different mixing rules for black carbon (BC) on the results. We find that the GMI model tends to overestimate submicron scattering and absorption at shorter wavelengths by 10-23 %, and that GMI has smaller absolute mean biases for submicron absorption than OPAC v3.1, GEOS-Chem v9-02, or GC-RT. However, the changes to the density and refractive index of BC in GC-RT improve the simulation of submicron aerosol absorption at all wavelengths relative to GEOS-Chem v9-02. Adding a variable size distribution, as in ASP v2.1, improves model performance for scattering but not for absorption, likely due to the assumption in ASP v2.1 that BC is present at a constant mass fraction throughout the aerosol size distribution. Using a core-shell mixing rule in ASP overestimates aerosol absorption, especially for the fresh biomass burning aerosol measured in ARCTAS-B, suggesting the need for modeling the time-varying mixing states of aerosols in future versions of ASP.

Use of NASA Near Real-Time and Archived Satellite Data to Support Disaster Assessment

NASA Technical Reports Server (NTRS)

McGrath, Kevin M.; Molthan, Andrew L.; Burks, Jason E.

2014-01-01

NASA's Short-term Prediction Research and Transition (SPoRT) Center partners with the NWS to provide near realtime data in support of a variety of weather applications, including disasters. SPoRT supports NASA's Applied Sciences Program: Disasters focus area by developing techniques that will aid the disaster monitoring, response, and assessment communities. SPoRT has explored a variety of techniques for utilizing archived and near real-time NASA satellite data. An increasing number of end-users - such as the NWS Damage Assessment Toolkit (DAT) - access geospatial data via a Web Mapping Service (WMS). SPoRT has begun developing open-standard Geographic Information Systems (GIS) data sets via WMS to respond to end-user needs.

Verification of Dose Distribution in Carbon Ion Radiation Therapy for Stage I Lung Cancer

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

Irie, Daisuke; Saitoh, Jun-ichi, E-mail: junsaito@gunma-u.ac.jp; Shirai, Katsuyuki

Purpose: To evaluate robustness of dose distribution of carbon-ion radiation therapy (C-ion RT) in non-small cell lung cancer (NSCLC) and to identify factors affecting the dose distribution by simulated dose distribution. Methods and Materials: Eighty irradiation fields for delivery of C-ion RT were analyzed in 20 patients with stage I NSCLC. Computed tomography images were obtained twice before treatment initiation. Simulated dose distribution was reconstructed on computed tomography for confirmation under the same settings as actual treatment with respiratory gating and bony structure matching. Dose-volume histogram parameters, such as %D95 (percentage of D95 relative to the prescribed dose), were calculated.more » Patients with any field for which the %D95 of gross tumor volume (GTV) was below 90% were classified as unacceptable for treatment, and the optimal target margin for such cases was examined. Results: Five patients with a total of 8 fields (10% of total number of fields analyzed) were classified as unacceptable according to %D95 of GTV, although most patients showed no remarkable change in the dose-volume histogram parameters. Receiver operating characteristic curve analysis showed that tumor displacement and change in water-equivalent pathlength were significant predictive factors of unacceptable cases (P<.001 and P=.002, respectively). The main cause of degradation of the dose distribution was tumor displacement in 7 of the 8 unacceptable fields. A 6-mm planning target volume margin ensured a GTV %D95 of >90%, except in 1 extremely unacceptable field. Conclusions: According to this simulation analysis of C-ion RT for stage I NSCLC, a few fields were reported as unacceptable and required resetting of body position and reconfirmation. In addition, tumor displacement and change in water-equivalent pathlength (bone shift and/or chest wall thickness) were identified as factors influencing the robustness of dose distribution. Such uncertainties should be regarded in planning.« less

Economic consequence of local control with radiotherapy: Cost analysis of internal mammary and medial supraclavicular lymph node radiotherapy in breast cancer

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

Lievens, Yolande; Kesteloot, Katrien; Bogaert, Walter van den

2005-11-15

Purpose: To investigate the financial implications of radiotherapy (RT) to the internal mammary and medial supraclavicular lymph node chain (IM-MS) in postoperative breast cancer. Methods and Materials: A cost-effectiveness and cost-utility analysis were performed, using Markov models, comparing the early and delayed costs and effects of IM-MS during a 20-year time span from a societal viewpoint. The outcome estimates were based on Level I evidence from postoperative RT literature and the cost estimates on the standard practice of the Leuven University Hospitals, with the RT costs derived from an activity-based costing program developed in the department. Results: On the basismore » of the assumptions of the model and seen during a 20-year time span, primary treatment including IM-MS RT results in a cost savings (approximately EURO 10,000) compared with a strategy without RT. Because IM-MS RT also results in better clinical effectiveness and greater quality of life, the treatment with IM-MS dominates the approach without IM-MS. Sensitivity analyses confirmed the robustness of these results in all tested circumstances. Although threshold values were found for the cost of IM-MS, the cost at relapse, and the quality of life after treatment, these were substantially different from the baseline estimates, indicating that it is very unlikely that omitting IM-MS would become superior. Conclusion: This ex-ante cost evaluation of IM-MS RT showed that the upfront costs of locoregional RT are easily compensated for by avoiding the costs of treating locoregional and distant relapse at a later stage. The cost-sparing effect of RT should, however, be evaluated for a sufficiently long time span and is most specifically found in tumors with a rather slow natural history and a multitude of available systemic treatments at relapse, such as breast cancer.« less

SCAR Radiologic Technologist Survey: analysis of technologist workforce and staffing.

PubMed

Reiner, Bruce; Siegel, Eliot; Carrino, John A; McElveny, Ceela

2002-09-01

One of the greatest dilemmas facing medical imaging departments today is the worsening personnel crisis in the radiologic technologist (RT) workforce. As the volume and complexity of medical imaging studies continues to increase, an unprecedented imbalance exists between RT supply and demand. A number of etiologic factors have been postulated to contribute to this RT shortage including decreasing morale, perceived inadequacies in compensation, decreasing number of training programs, and limitations in the career ladder. Previous studies have cited improved technologist productivity as imaging departments successfully transition from film-based to filmless operation. This study was undertaken to address the impact of digital technologies (information systems, PACS, digital radiography) on technologist productivity, in an attempt to determine whether these technologies can be used to positively affect the existing RT workforce imbalance. A total of 112 facilities participated in this nationwide study, with representation of imaging providers that paralleled the demographic profile of the marketplace as a whole. Survey results indicate the existing RT staffing shortage is greatest within academic and rural-based hospitals and is most severe in the area of general radiography, which accounts for 65-70% of imaging department volumes. For general radiography alone, respondents report an average shortage of 2 RT full-time equivalents (FTE's) per institution, when comparing the number of budgeted RT FTE's versus the actual number of RT FTE's. Preliminary results indicate that at this time, RT staffing shortages are not affected by the presence or absence of digital information technologies. Additional research is planned through a five-year longitudinal data collection, to better delineate the complex relationship that exists between implementation of digital technologies and RT staffing.

A DICOM-RT radiation oncology ePR with decision support utilizing a quantified knowledge base from historical data

NASA Astrophysics Data System (ADS)

Documet, Jorge R.; Liu, Brent; Le, Anh; Law, Maria

2008-03-01

During the last 2 years we have been working on developing a DICOM-RT (Radiation Therapy) ePR (Electronic Patient Record) with decision support that will allow physicists and radiation oncologists during their decision-making process. This ePR allows offline treatment dose calculations and plan evaluation, while at the same time it compares and quantifies treatment planning algorithms using DICOM-RT objects. The ePR framework permits the addition of visualization, processing, and analysis tools, which combined with the core functionality of reporting, importing and exporting of medical studies, creates a very powerful application that can improve the efficiency while planning cancer treatments. Usually a Radiation Oncology department will have disparate and complex data generated by the RT modalities as well as data scattered in RT Information/Management systems, Record & Verify systems, and Treatment Planning Systems (TPS) which can compromise the efficiency of the clinical workflow since the data crucial for a clinical decision may be time-consuming to retrieve, temporarily missing, or even lost. To address these shortcomings, the ACR-NEMA Standards Committee extended its DICOM (Digital Imaging & Communications in Medicine) standard from Radiology to RT by ratifying seven DICOM RT objects starting in 1997 [1,2]. However, they are not broadly used yet by the RT community in daily clinical operations. In the past, the research focus of an RT department has primarily been developing new protocols and devices to improve treatment process and outcomes of cancer patients with minimal effort dedicated to integration of imaging and information systems. Our attempt is to show a proof-of-concept that a DICOM-RT ePR system can be developed as a foundation to perform medical imaging informatics research in developing decision-support tools and knowledge base for future data mining applications.

Experimental study of quantitative assessment of left ventricular mass with contrast enhanced real-time three-dimensional echocardiography.

PubMed

Zhuang, Lei; Wang, Xin-Fang; Xie, Ming-Xing; Chen, Li-Xin; Fei, Hong-Wen; Yang, Ying; Wang, Jing; Huang, Run-Qing; Chen, Ou-Di; Wang, Liang-Yu

2004-01-01

To evaluate the feasibility and accuracy of measurement of left ventricular mass with intravenous contrast enhanced real-time three-dimensional (RT3D) echocardiography in the experimental setting. RT3D echocardiography was performed in 13 open-chest mongrel dogs before and after intravenous infusion of a perfluorocarbon contrast agent. Left ventricular myocardium volume was measured according to the apical four-plane method provided by TomTec 4D cardio-View RT1.0 software, then the left ventricular mass was calculated as the myocardial volume multiplied by the relative density of myocardium. Correlative analysis and paired t-test were performed between left ventricular mass obtained from RT3D echocardiography and the anatomic measurements. Anatomic measurement of total left ventricular mass was 55.6 +/- 9.3 g, whereas RT3D echocardiographic calculation of left ventricular mass before and after intravenous perfluorocarbon contrast agent was 57.5 +/- 11.4 and 55.5 +/- 9.3 g, respectively. A significant correlation was observed between the RT3D echocardiographic estimates of total left ventricular mass and the corresponding anatomic measurements (r = 0.95). A strong correlation was found between RT3D echocardiographic estimates of left ventricular mass with perfluorocarbon contrast and the anatomic results (r = 0.99). Analysis of intraobserver and interobserver variability showed strong indexes of agreement in the measurement of left ventricular mass with pre and post-contrast RT3D echocardiography. Measurements of left ventricular mass derived from RT3D echocardiography with and without intravenous contrast showed a significant correlation with the anatomic results. Contrast enhanced RT3D echocardiography permitted better visualization of the endocardial border, which would provide a more accurate and reliable means of determining left ventricular myocardial mass in the experimental setting.

Enhanced control of dorsolateral prefrontal cortex neurophysiology with real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback training and working memory practice.

PubMed

Sherwood, Matthew S; Kane, Jessica H; Weisend, Michael P; Parker, Jason G

2016-01-01

Real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback can be used to train localized, conscious regulation of blood oxygen level-dependent (BOLD) signals. As a therapeutic technique, rt-fMRI neurofeedback reduces the symptoms of a variety of neurologic disorders. To date, few studies have investigated the use of self-regulation training using rt-fMRI neurofeedback to enhance cognitive performance. This work investigates the utility of rt-fMRI neurofeedback as a tool to enhance human cognition by training healthy individuals to consciously control activity in the left dorsolateral prefrontal cortex (DLPFC). A cohort of 18 healthy participants in the experimental group underwent rt-fMRI neurofeedback from the left DLPFC in five training sessions across two weeks while 7 participants in the control group underwent similar training outside the MRI and without rt-fMRI neurofeedback. Working memory (WM) performance was evaluated on two testing days separated by the five rt-fMRI neurofeedback sessions using two computerized tests. We investigated the ability to control the BOLD signal across training sessions and WM performance across the two testing days. The group with rt-fMRI neurofeedback demonstrated a significant increase in the ability to self-regulate the BOLD signal in the left DLPFC across sessions. WM performance showed differential improvement between testing days one and two across the groups with the highest increases observed in the rt-fMRI neurofeedback group. These results provide evidence that individuals can quickly gain the ability to consciously control the left DLPFC, and this training results in improvements of WM performance beyond that of training alone. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

The Cost-Effectiveness of Real-Time Continuous Glucose Monitoring (RT-CGM) in Type 2 Diabetes.

PubMed

Fonda, Stephanie J; Graham, Claudia; Munakata, Julie; Powers, Julia M; Price, David; Vigersky, Robert A

2016-07-01

This analysis models the cost-effectiveness of real-time continuous glucose monitoring (RT-CGM) using evidence from a randomized controlled trial (RCT) that demonstrated RT-CGM reduced A1C, for up to 9 months after using the technology, among patients with type 2 diabetes not on prandial insulin. RT-CGM was offered short-term and intermittently as a self-care tool to inform patients' behavior. The analyses projected lifetime clinical and economic outcomes for RT-CGM versus self-monitoring of blood glucose by fingerstick only. The base-case analysis was consistent with the RCT (RT-CGM for 2 weeks on/1 week off over 3 months). A scenario analysis simulated outcomes of an RT-CGM "refresher" after the active intervention of the RCT. Analyses used the IMS CORE Diabetes Model and were conducted from a US third-party payer perspective, including direct costs obtained from published sources and inflated to 2011 US dollars. Costs and health outcomes were discounted at 3% per annum. Life expectancy (LE) and quality-adjusted life expectancy (QALE) from RT-CGM were 0.10 and 0.07, with a cost of $653/patient over a lifetime. Incremental LE and QALE from a "refresher" were 0.14 and 0.10, with a cost of $1312/patient over a lifetime, and incremental cost-effectiveness ratios were $9319 and $13 030 per LY and QALY gained. RT-CGM, as a self-care tool, is a cost-effective disease management option in the US for people with type 2 diabetes not on prandial insulin. Repeated use of RT-CGM may result in additional cost-effectiveness. © 2016 Diabetes Technology Society.

Comparison of human immunodeficiency virus assays in window phase and elite controller samples: viral load distribution and implications for transmission risk

PubMed Central

Vermeulen, Marion; Coleman, Charl; Mitchel, Josephine; Reddy, Ravi; van Drimmelen, Harry; Fickett, Tracy; Busch, Michael; Lelie, Nico

2016-01-01

BACKGROUND After 3 years of individual-donation nucleic acid test (ID-NAT) screening by the South African National Blood Service (SANBS), a repository of 73 human immunodeficiency virus antibody (anti-HIV)-negative window period (WP)-yield samples and 28 anti-HIV–positive, HIV-RNA–negative elite controllers (ECs) became available for comparison of a p24 antigen (p24 Ag) assay (Innogenetics), two viral load assays (Siemens branch DNA [bDNA] 3.0 and Abbott real-time polymerase chain reaction [RT-PCR]), and three triplex NAT assays (Novartis Diagnostics Ultrio and Ultrio-Plus and Roche TaqScreen) by replicate testing of dilutions. STUDY DESIGN AND METHODS Viral loads were assessed by bDNA and RT-PCR assays and if below 100 copies (cps)/mL, by Ultrio limiting dilution probit analysis. The probability of virus transmission by WP and EC donations was estimated for different levels of the 50% minimum infectious dose (ID50) using Poisson distribution statistics. RESULTS The equal distribution of WP donations plotted by log HIV-RNA levels indicated a random appearance of donors in the ramp-up phase. The HIV p24 Ag assay detected 45% of WP samples and the cutoff crossing point was estimated at 8140 (bDNA)/ 22,710 (RT-PCR) cps/mL. On replicate retesting of 40 HIV p24 Ag–negative ID-NAT WP-yield samples Ultrio minipool (MP)8, Ultrio-Plus MP8, and TaqScreen MP6 detected 79, 81, and 78%, respectively. Modeling with an estimated ID50 of 31.6 virions/RBC indicated that 15% of p24 Ag–negative ID-NAT WP-yield donations would have transmitted HIV if MP6–8 NAT had been used. Only 2% of RBC transfusions from ECs are estimated to be infectious with a worst-case ID50 estimate of 316 virions. CONCLUSION Our analysis of viremia and infectivity of WP and EC donations enables comparison of the efficacy of NAT options in preventing HIV transmission risk. PMID:23445273

Comparison of human immunodeficiency virus assays in window phase and elite controller samples: viral load distribution and implications for transmission risk.

PubMed

Vermeulen, Marion; Coleman, Charl; Mitchel, Josephine; Reddy, Ravi; van Drimmelen, Harry; Fickett, Tracy; Busch, Michael; Lelie, Nico

2013-10-01

After 3 years of individual-donation nucleic acid test (ID-NAT) screening by the South African National Blood Service (SANBS), a repository of 73 human immunodeficiency virus antibody (anti-HIV)-negative window period (WP)-yield samples and 28 anti-HIV-positive, HIV-RNA-negative elite controllers (ECs) became available for comparison of a p24 antigen (p24 Ag) assay (Innogenetics), two viral load assays (Siemens branch DNA [bDNA] 3.0 and Abbott real-time polymerase chain reaction [RT-PCR]), and three triplex NAT assays (Novartis Diagnostics Ultrio and Ultrio-Plus and Roche TaqScreen) by replicate testing of dilutions. Viral loads were assessed by bDNA and RT-PCR assays and if below 100 copies (cps)/mL, by Ultrio limiting dilution probit analysis. The probability of virus transmission by WP and EC donations was estimated for different levels of the 50% minimum infectious dose (ID50 ) using Poisson distribution statistics. The equal distribution of WP donations plotted by log HIV-RNA levels indicated a random appearance of donors in the ramp-up phase. The HIV p24 Ag assay detected 45% of WP samples and the cutoff crossing point was estimated at 8140 (bDNA)/22,710 (RT-PCR) cps/mL. On replicate retesting of 40 HIV p24 Ag-negative ID-NAT WP-yield samples Ultrio minipool (MP)8, Ultrio-Plus MP8, and TaqScreen MP6 detected 79, 81, and 78%, respectively. Modeling with an estimated ID50 of 31.6 virions/RBC indicated that 15% of p24 Ag-negative ID-NAT WP-yield donations would have transmitted HIV if MP6-8 NAT had been used. Only 2% of RBC transfusions from ECs are estimated to be infectious with a worst-case ID50 estimate of 316 virions. Our analysis of viremia and infectivity of WP and EC donations enables comparison of the efficacy of NAT options in preventing HIV transmission risk. © 2013 American Association of Blood Banks.

RT-PCR for detection of all seven genotypes of Lyssavirus genus.

PubMed

Vázquez-Morón, S; Avellón, A; Echevarría, J E

2006-08-01

The Lyssavirus genus includes seven species or genotypes named 1-7. Rabies genotypes correlate with geographical distribution and specific hosts. Co-circulation of different lyssaviruses, imported cases, and the presence of unknown viruses, such as Aravan, Khujand, Irkut and West Caucasian Bat Virus, make it necessary to use generic methods able to detect all lyssaviruses. Primer sequences were chosen from conserved regions in all genotypes in order to optimise a generic RT-PCR. Serial dilutions of 12 RNA extracts from all seven Lyssavirus genotypes were examined to compare the sensitivity of the RT-PCR standardised in this study with a published RT-PCR optimised for EBLV1 detection and capable of amplifying RNA from all seven lyssaviruses. All seven genotypes were detected by both RT-PCRs, however, the sensitivity was higher with the new version of the test. Twenty samples submitted for rabies diagnosis were tested by the new RT-PCR. Eight out of 20 samples from six dogs, one horse and one bat were found positive, in agreement with immunofluorescence results. Seven samples from terrestrial mammals were genotype 1 and one from a bat was genotype 5. In conclusion, this method can be used to complement immunofluorescence for the diagnosis of rabies, enabling the detection of unexpected lyssaviruses during rabies surveillance.

Virus-like attachment sites as structural landmarks of plants retrotransposons.

PubMed

Ochoa Cruz, Edgar Andres; Cruz, Guilherme Marcello Queiroga; Vieira, Andréia Prata; Van Sluys, Marie-Anne

2016-01-01

The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process. Here we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. We used these patterns to generate a specific quick-response (QR) code for each genome that could be used as a barcode of identification of plants in the future. The universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. This is an important finding that expands the information about the structural similarity between LTR-RT and retroviruses. We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. All the structural vl-att site signatures are strong candidates for further functional studies. Moreover, this is the first identification of specific LTR-RT content and their amplification patterns in a large dataset of LTR-RT lineages and angiosperm genomes. These distribution patterns could be used in the future with biotechnological identification purposes.

Distribution of muscle fibre conduction velocity for representative samples of motor units in the full recruitment range of the tibialis anterior muscle.

PubMed

Del Vecchio, A; Negro, F; Felici, F; Farina, D

2018-02-01

Motor units are recruited in an orderly manner according to the size of motor neurones. Moreover, because larger motor neurones innervate fibres with larger diameters than smaller motor neurones, motor units should be recruited orderly according to their conduction velocity (MUCV). Because of technical limitations, these relations have been previously tested either indirectly or in small motor unit samples that revealed weak associations between motor unit recruitment threshold (RT) and MUCV. Here, we analyse the relation between MUCV and RT for large samples of motor units. Ten healthy volunteers completed a series of isometric ankle dorsiflexions at forces up to 70% of the maximum. Multi-channel surface electromyographic signals recorded from the tibialis anterior muscle were decomposed into single motor unit action potentials, from which the corresponding motor unit RT, MUCV and action potential amplitude were estimated. Established relations between muscle fibre diameter and CV were used to estimate the fibre size. Within individual subjects, the distributions of MUCV and fibre diameters were unimodal and did not show distinct populations. MUCV was strongly correlated with RT (mean (SD) R 2  = 0.7 (0.09), P < 0.001; 406 motor units), which supported the hypothesis that fibre diameter is associated with RT. The results provide further evidence for the relations between motor neurone and muscle fibre properties for large samples of motor units. The proposed methodology for motor unit analysis has also the potential to open new perspectives in the study of chronic and acute neuromuscular adaptations to ageing, training and pathology. © 2017 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd.

Rapid detection of Enterovirus and Coxsackievirus A10 by a TaqMan based duplex one-step real time RT-PCR assay.

PubMed

Chen, Jingfang; Zhang, Rusheng; Ou, Xinhua; Yao, Dong; Huang, Zheng; Li, Linzhi; Sun, Biancheng

2017-06-01

A TaqMan based duplex one-step real time RT-PCR (rRT-PCR) assay was developed for the rapid detection of Coxsackievirus A10 (CV-A10) and other enterovirus (EVs) in clinical samples. The assay was fully evaluated and found to be specific and sensitive. When applied in 115 clinical samples, a 100% diagnostic sensitivity in CV-A10 detection and 97.4% diagnostic sensitivity in other EVs were found. Copyright © 2017 Elsevier Ltd. All rights reserved.

Visual response time to colored stimuli in peripheral retina - Evidence for binocular summation

NASA Technical Reports Server (NTRS)

Haines, R. F.

1977-01-01

Simple onset response time (RT) experiments, previously shown to exhibit binocular summation effects for white stimuli along the horizontal meridian, were performed for red and green stimuli along 5 oblique meridians. Binocular RT was significantly shorter than monocular RT for a 45-min-diameter spot of red, green, or white light within eccentricities of about 50 deg from the fovea. Relatively large meridian differences were noted that appear to be due to the degree to which the images fall on corresponding retinal areas.

SPring-8 beamline control system.

PubMed

Ohata, T; Konishi, H; Kimura, H; Furukawa, Y; Tamasaku, K; Nakatani, T; Tanabe, T; Matsumoto, N; Ishii, M; Ishikawa, T

1998-05-01

The SPring-8 beamline control system is now taking part in the control of the insertion device (ID), front end, beam transportation channel and all interlock systems of the beamline: it will supply a highly standardized environment of apparatus control for collaborative researchers. In particular, ID operation is very important in a third-generation synchrotron light source facility. It is also very important to consider the security system because the ID is part of the storage ring and is therefore governed by the synchrotron ring control system. The progress of computer networking systems and the technology of security control require the development of a highly flexible control system. An interlock system that is independent of the control system has increased the reliability. For the beamline control system the so-called standard model concept has been adopted. VME-bus (VME) is used as the front-end control system and a UNIX workstation as the operator console. CPU boards of the VME-bus are RISC processor-based board computers operated by a LynxOS-based HP-RT real-time operating system. The workstation and the VME are linked to each other by a network, and form the distributed system. The HP 9000/700 series with HP-UX and the HP 9000/743rt series with HP-RT are used. All the controllable apparatus may be operated from any workstation.

Comparison of Four Precipitation Forcing Datasets in Land Information System Simulations over the Continental U.S.

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Kumar, Sujay V.; Kuliogwski, Robert J.; Langston, Carrie

2013-01-01

This paper and poster presented a description of the current real-time SPoRT-LIS run over the southeastern CONUS to provide high-resolution, land surface initialization grids for local numerical model forecasts at NWS forecast offices. The LIS hourly output also offers a supplemental dataset to aid in situational awareness for convective initiation forecasts, assessing flood potential, and monitoring drought at fine scales. It is a goal of SPoRT and several NWS forecast offices to expand the LIS to an entire CONUS domain, so that LIS output can be utilized by NWS Western Region offices, among others. To make this expansion cleanly so as to provide high-quality land surface output, SPoRT tested new precipitation datasets in LIS as an alternative forcing dataset to the current radar+gauge Stage IV product. Similar to the Stage IV product, the NMQ product showed comparable patterns of precipitation and soil moisture distribution, but suffered from radar gaps in the intermountain West, and incorrectly set values to zero instead of missing in the data-void regions of Mexico and Canada. The other dataset tested was the next-generation GOES-R QPE algorithm, which experienced a high bias in both coverage and intensity of accumulated precipitation relative to the control (NLDAS2), Stage IV, and NMQ simulations. The resulting root zone soil moisture was substantially higher in most areas.

Molecular cloning, characterization, and expression profiles of androgen receptors in spotted scat (Scatophagus argus).

PubMed

Chen, H P; Deng, S P; Dai, M L; Zhu, C H; Li, G L

2016-04-07

Androgen plays critical roles in vertebrate reproductive systems via androgen receptors (ARs). In the present study, the full-length spotted scat (Scatophagus argus) androgen receptor (sAR) cDNA sequence was cloned from testis. The sAR cDNA measured 2448 bp in length with an open-reading frame of 2289 bp, encoding 763 amino acids. Amino acid alignment analyses showed that the sARs exhibited highly evolutionary conserved functional domains. Phylogenetically, the sARs clustered within the ARβ common vertebrate group. Real-time polymerase chain reaction (RT-PCR) revealed that sAR expression varied in level and distribution throughout the tissues of both females and males. sAR expression was detected during testicular development by quantitative RT-PCR. The results showed that the highest transcription of sARs was observed in the mid-testicular stage, and remained at a high expression level until the late-testicular stage. In addition, the effects of 17α-methyltestosterone (MT) and estrogen (E2) on the expression of sARs in ovaries were determined using quantitative RT-PCR. sAR expression increased at 12 and 24 h post-MT treatment and decreased with E2 treatment. The present study provides preliminary evidence indicating gonadal plasticity of spotted scat under exogenous steroidal hormone treatments. It also provides a theoretical basis for sex reversal and production of artificial pseudo-males for female monosex breeding.

Development of Fluorescent Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) using Quenching Probes for the Detection of the Middle East Respiratory Syndrome Coronavirus.

PubMed

Shirato, Kazuya; Semba, Shohei; El-Kafrawy, Sherif A; Hassan, Ahmed M; Tolah, Ahmed M; Takayama, Ikuyo; Kageyama, Tsutomu; Notomi, Tsugunori; Kamitani, Wataru; Matsuyama, Shutoku; Azhar, Esam Ibraheem

2018-05-12

Clinical detection of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in patients is achieved using genetic diagnostic methods, such as real-time RT-PCR assay. Previously, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of MERS-CoV [Virol J. 2014. 11:139]. Generally, amplification of RT-LAMP is monitored by the turbidity induced by precipitation of magnesium pyrophosphate with newly synthesized DNA. However, this mechanism cannot completely exclude the possibility of unexpected reactions. Therefore, in this study, fluorescent RT-LAMP assays using quenching probes (QProbes) were developed specifically to monitor only primer-derived signals. Two primer sets (targeting nucleocapsid and ORF1a sequences) were constructed to confirm MERS cases by RT-LAMP assay only. Our data indicate that both primer sets were capable of detecting MERS-CoV RNA to the same level as existing genetic diagnostic methods, and that both were highly specific with no cross-reactivity observed with other respiratory viruses. These primer sets were highly efficient in amplifying target sequences derived from different MERS-CoV strains, including camel MERS-CoV. In addition, the detection efficacy of QProbe RT-LAMP was comparable to that of real-time RT-PCR assay using clinical specimens from patients in Saudi Arabia. Altogether, these results indicate that QProbe RT-LAMP assays described here can be used as powerful diagnostic tools for rapid detection and surveillance of MERS-CoV infections. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Patterns of Practice in Palliative Radiotherapy for Painful Bone Metastases: Impact of a Regional Rapid Access Clinic on Access to Care

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

Wu, Jackson S.Y., E-mail: jackson.wu@cancerboard.ab.c; Kerba, Marc; Wong, Rebecca K.S.

2010-10-01

Purpose: External beam radiotherapy (RT) is commonly indicated for the palliation of symptomatic bone metastases, but there is evidence of underutilization of this treatment modality in palliative care for cancer populations. This study was conducted to investigate factors that influenced the use of palliative RT services at a regional comprehensive cancer center. Methods and Materials: A cohort of patients with radiographically confirmed bone metastases and first-time users of palliative RT between 2003 and 2005 was retrospectively reviewed from the time of initial diagnosis of bone metastases to death or last follow-up. Type of radiation treatment service provider used (rapid accessmore » or routine access) and patient-, tumor-, and treatment-related factors were analyzed for their influences on the number of treatment courses given over the duration of disease. Results: A total of 887 patients received 1,354 courses of palliative RT for bone metastases at a median interval of 4.0 months between courses. Thirty-three percent of patients required more than one RT course. Increased age and travel distance reduced the likelihood and number of treatment courses, while service through a rapid access clinic was independently associated with an increase in subsequent use of palliative RT. Conclusions: A rapid access service model for palliative RT facilitated access to RT. Travel distance and other factors remained substantial barriers to use of palliative RT services. The pattern of practice suggests an unmet need for symptom control in patients with bone metastases.« less

Selection of reference genes for RT-qPCR analysis in the monarch butterfly, Danaus plexippus (L.), a migrating bio-indicator

USDA-ARS?s Scientific Manuscript database

Quantitative real-time PCR (qRT-PCR) is a reliable and reproducible technique for measuring and evaluating changes in gene expression. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. In this study, expres...

ADHD Preschoolers with and without ODD: Do They Act Differently Depending on Degree of Task Engagement/Reward?

ERIC Educational Resources Information Center

Gopin, Chaya B.; Berwid, Olga; Marks, David J.; Mlodnicka, Agnieska; Halperin, Jeffrey M.

2013-01-01

Objective: To examine the impact of reinforcement on reaction time (RT) and RT variability (RT standard deviation [RTSD]) in preschoolers with ADHD with and without oppositional defiant disorder (ODD), and a typically developing (TD) comparison group. Method: Participants were administered a computerized task consisting of two conditions: simple…

Corpus Callosum Size, Reaction Time Speed and Variability in Mild Cognitive Disorders and in a Normative Sample

ERIC Educational Resources Information Center

Anstey, Kaarin J.; Mack, Holly A.; Christensen, Helen; Li, Shu-Chen; Reglade-Meslin, Chantal; Maller, Jerome; Kumar, Rajeev; Dear, Keith; Easteal, Simon; Sachdev, Perminder

2007-01-01

Intra-individual variability in reaction time increases with age and with neurological disorders, but the neural correlates of this increased variability remain uncertain. We hypothesized that both faster mean reaction time (RT) and less intra-individual RT variability would be associated with larger corpus callosum (CC) size in older adults, and…

Building a new predictor for multiple linear regression technique-based corrective maintenance turnaround time.

PubMed

Cruz, Antonio M; Barr, Cameron; Puñales-Pozo, Elsa

2008-01-01

This research's main goals were to build a predictor for a turnaround time (TAT) indicator for estimating its values and use a numerical clustering technique for finding possible causes of undesirable TAT values. The following stages were used: domain understanding, data characterisation and sample reduction and insight characterisation. Building the TAT indicator multiple linear regression predictor and clustering techniques were used for improving corrective maintenance task efficiency in a clinical engineering department (CED). The indicator being studied was turnaround time (TAT). Multiple linear regression was used for building a predictive TAT value model. The variables contributing to such model were clinical engineering department response time (CE(rt), 0.415 positive coefficient), stock service response time (Stock(rt), 0.734 positive coefficient), priority level (0.21 positive coefficient) and service time (0.06 positive coefficient). The regression process showed heavy reliance on Stock(rt), CE(rt) and priority, in that order. Clustering techniques revealed the main causes of high TAT values. This examination has provided a means for analysing current technical service quality and effectiveness. In doing so, it has demonstrated a process for identifying areas and methods of improvement and a model against which to analyse these methods' effectiveness.

SimulatorToFMU v0.1

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

Nouidui, Thierry; Wetter, Michael

SimulatorToFMU is a software package written in Python which allows users to export a memoryless Python-driven simulation program or script as a Functional Mock-up Unit (FMU) for model exchange or co-simulation.In CyDER (Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smart Grids), SimulatorToFMU will allow exporting OPAL-RT as an FMU. This will enable OPAL-RT to be linked to CYMDIST and GridDyn FMUs through a standardized open source interface.

A non-discrete method for computation of residence time in fluid mechanics simulations.

PubMed

Esmaily-Moghadam, Mahdi; Hsia, Tain-Yen; Marsden, Alison L

2013-11-01

Cardiovascular simulations provide a promising means to predict risk of thrombosis in grafts, devices, and surgical anatomies in adult and pediatric patients. Although the pathways for platelet activation and clot formation are not yet fully understood, recent findings suggest that thrombosis risk is increased in regions of flow recirculation and high residence time (RT). Current approaches for calculating RT are typically based on releasing a finite number of Lagrangian particles into the flow field and calculating RT by tracking their positions. However, special care must be taken to achieve temporal and spatial convergence, often requiring repeated simulations. In this work, we introduce a non-discrete method in which RT is calculated in an Eulerian framework using the advection-diffusion equation. We first present the formulation for calculating residence time in a given region of interest using two alternate definitions. The physical significance and sensitivity of the two measures of RT are discussed and their mathematical relation is established. An extension to a point-wise value is also presented. The methods presented here are then applied in a 2D cavity and two representative clinical scenarios, involving shunt placement for single ventricle heart defects and Kawasaki disease. In the second case study, we explored the relationship between RT and wall shear stress, a parameter of particular importance in cardiovascular disease.

Revealing the Radial Effect on Orientation Discrimination by Manual Reaction Time

PubMed Central

Liang, Lixin; Zhou, Yang; Zhang, Mingsha; Pan, Yujun

2017-01-01

It has been shown that the sensitivity and accuracy of orientation perception in the periphery is significantly better when the orientations are radial with respect to the fixation point than when they are tangential. However, since perception and action may be dissociated, it is unclear whether the perceptual radial effect has a counterpart in reaction time (RT) of motor responses. Furthermore, it is unknown whether or how stimulus-response-compatibility (SRC) effect interacts with the radial effect to determine RT. To address these questions, we measured subjects' manual RT to grating stimuli that appeared across upper visual field (VF). We found that (1) RTs were significantly shorter when a grating was oriented closer to the radial direction than when it was oriented closer to the tangential direction even though the perceptual accuracies for the more radial and more tangential orientations were not significantly different under our experimental condition; (2) This RT version of the radial effect was larger in the left VF than in the right VF; (3) The radial effect and SRC effect interacted with each other to determine the overall RT. These results suggest that the RT radial effect reported here is not a passive reflection of the radial effect in perceptual accuracy, but instead, represents different processing time of radial and tangential orientations along the sensorimotor pathway. PMID:29225564

A Multiplex RT-PCR Assay for S. aureus, L. monocytogenes, and Salmonella spp. Detection in Raw Milk with Pre-enrichment.

PubMed

Ding, Tian; Suo, Yuanjie; Zhang, Zhaohuan; Liu, Donghong; Ye, Xingqian; Chen, Shiguo; Zhao, Yong

2017-01-01

This study firstly developed a multiplex real-time PCR (RT-PCR) technique combined with a pre-enrichment step to simultaneously detect Staphylococcus aureus ( S. aureus ), Listeria monocytogenes ( L. monocytogenes ) and Salmonella spp. in raw milk and the dairy farm environment (feces, soil, feed, water) in one reaction. Brain heart infusion (BHI) broth was selected for the enrichment step to increase the density of the target bacteria by using an incubation of 4 h before multiplex RT-PCR. The results showed that the detection limit of the multiplex real-time assay was approximately 10 2 CFU/mL for pure cultures and artificially contaminated milk without enrichment, while 12, 14, and 10 CFU/25 mL, respectively, for S. aureus, L. monocytogenes , and Salmonella spp. after pre-enrichment. The newly developed multiplex RT-PCR assay was applied to 46 dairy farm environmental samples and raw milk samples covering a wide variety of sample types. The results demonstrated that the multiplex RT-PCR assay coupled with the BHI enrichment broth was suitable for the simultaneous screening of S. aureus, L. monocytogenes , and Salmonella spp. in the pasture environment and in raw milk. The multiplex RT-PCR assay clearly and successfully shortened the total detection time and reduced labor compared to conventional culture-based methods for testing natural samples.

A non-discrete method for computation of residence time in fluid mechanics simulations

NASA Astrophysics Data System (ADS)

Esmaily-Moghadam, Mahdi; Hsia, Tain-Yen; Marsden, Alison L.

2013-11-01

Cardiovascular simulations provide a promising means to predict risk of thrombosis in grafts, devices, and surgical anatomies in adult and pediatric patients. Although the pathways for platelet activation and clot formation are not yet fully understood, recent findings suggest that thrombosis risk is increased in regions of flow recirculation and high residence time (RT). Current approaches for calculating RT are typically based on releasing a finite number of Lagrangian particles into the flow field and calculating RT by tracking their positions. However, special care must be taken to achieve temporal and spatial convergence, often requiring repeated simulations. In this work, we introduce a non-discrete method in which RT is calculated in an Eulerian framework using the advection-diffusion equation. We first present the formulation for calculating residence time in a given region of interest using two alternate definitions. The physical significance and sensitivity of the two measures of RT are discussed and their mathematical relation is established. An extension to a point-wise value is also presented. The methods presented here are then applied in a 2D cavity and two representative clinical scenarios, involving shunt placement for single ventricle heart defects and Kawasaki disease. In the second case study, we explored the relationship between RT and wall shear stress, a parameter of particular importance in cardiovascular disease.

A non-discrete method for computation of residence time in fluid mechanics simulations

PubMed Central

Esmaily-Moghadam, Mahdi; Hsia, Tain-Yen; Marsden, Alison L.

2013-01-01

Cardiovascular simulations provide a promising means to predict risk of thrombosis in grafts, devices, and surgical anatomies in adult and pediatric patients. Although the pathways for platelet activation and clot formation are not yet fully understood, recent findings suggest that thrombosis risk is increased in regions of flow recirculation and high residence time (RT). Current approaches for calculating RT are typically based on releasing a finite number of Lagrangian particles into the flow field and calculating RT by tracking their positions. However, special care must be taken to achieve temporal and spatial convergence, often requiring repeated simulations. In this work, we introduce a non-discrete method in which RT is calculated in an Eulerian framework using the advection-diffusion equation. We first present the formulation for calculating residence time in a given region of interest using two alternate definitions. The physical significance and sensitivity of the two measures of RT are discussed and their mathematical relation is established. An extension to a point-wise value is also presented. The methods presented here are then applied in a 2D cavity and two representative clinical scenarios, involving shunt placement for single ventricle heart defects and Kawasaki disease. In the second case study, we explored the relationship between RT and wall shear stress, a parameter of particular importance in cardiovascular disease. PMID:24046509

A Multiplex RT-PCR Assay for S. aureus, L. monocytogenes, and Salmonella spp. Detection in Raw Milk with Pre-enrichment

PubMed Central

Ding, Tian; Suo, Yuanjie; Zhang, Zhaohuan; Liu, Donghong; Ye, Xingqian; Chen, Shiguo; Zhao, Yong

2017-01-01

This study firstly developed a multiplex real-time PCR (RT-PCR) technique combined with a pre-enrichment step to simultaneously detect Staphylococcus aureus (S. aureus), Listeria monocytogenes (L. monocytogenes) and Salmonella spp. in raw milk and the dairy farm environment (feces, soil, feed, water) in one reaction. Brain heart infusion (BHI) broth was selected for the enrichment step to increase the density of the target bacteria by using an incubation of 4 h before multiplex RT-PCR. The results showed that the detection limit of the multiplex real-time assay was approximately 102 CFU/mL for pure cultures and artificially contaminated milk without enrichment, while 12, 14, and 10 CFU/25 mL, respectively, for S. aureus, L. monocytogenes, and Salmonella spp. after pre-enrichment. The newly developed multiplex RT-PCR assay was applied to 46 dairy farm environmental samples and raw milk samples covering a wide variety of sample types. The results demonstrated that the multiplex RT-PCR assay coupled with the BHI enrichment broth was suitable for the simultaneous screening of S. aureus, L. monocytogenes, and Salmonella spp. in the pasture environment and in raw milk. The multiplex RT-PCR assay clearly and successfully shortened the total detection time and reduced labor compared to conventional culture-based methods for testing natural samples. PMID:28620364

Conformal and intensity modulated irradiation of head and neck cancer: the potential for improved target irradiation, salivary gland function, and quality of life.

PubMed

Eisbruch, A; Dawson, L A; Kim, H M; Bradford, C R; Terrell, J E; Chepeha, D B; Teknos, T N; Anzai, Y; Marsh, L H; Martel, M K; Ten Haken, R K; Wolf, G T; Ship, J A

1999-01-01

To develop techniques which facilitate sparing of the major salivary glands while adequately treating the targets in patients requiring comprehensive bilateral neck irradiation (RT). Conformal and static, multisegmental intensity modulated (IMRT) techniques have been developed. The salivary flow rates before and periodically after RT have been measured selectively from each major salivary gland and the residual flows correlated with glands' dose volume histograms. Subjective xerostomia questionnaires have been developed and validated. The pattern of local-regional recurrences has been examined using CT scans at the time of recurrence, transferring the recurrence volumes to the planning CT scans and regenerating the dose distributions at the recurrence sites. Target coverage and dose homogeneity in IMRT treatment plans were found to be significantly better than standard RT plans. Significant parotid gland sparing was achieved. The relationships among dose, irradiated volume and saliva flow rates from the parotid glands were characterized by dose and volume thresholds. A mean dose of 26 Gy was found to be the threshold for stimulated saliva. Subjective xerostomia was significantly reduced in patients irradiated with parotid sparing techniques, compared to patients with similar tumors treated with standard RT. The large majority of recurrences occurred inside high-risk targets. Tangible gains in salivary gland sparing and target coverage are being achieved and an improvement in some measures of quality of life is suggested by our findings. A mean parotid gland dose of < or = 26 Gy should be a planning objective if significant parotid function preservation is desired. The pattern of recurrence suggests that careful escalation of the dose to targets judged to be at highest risk may improve tumor control.

Recent Upgrades to NASA SPoRT Initialization Datasets for the Environmental Modeling System

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; LaFontaine, Frank J.; Molthan, Andrew L.; Zavodsky, Bradley T.; Rozumalski, Robert A.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its National Weather Service (NWS) partners that can initialize specific fields for local model runs within the NOAA/NWS Science and Training Resource Center (STRC) Environmental Modeling System (EMS). In last year's NWA abstract on this topic, the suite of SPoRT products supported in the STRC EMS was presented, which includes a Sea Surface Temperature (SST) composite, a Great Lakes sea-ice extent, a Green Vegetation Fraction (GVF) composite, and NASA Land Information System (LIS) gridded output. This abstract and companion presentation describes recent upgrades made to the SST and GVF composites, as well as the real-time LIS runs. The Great Lakes sea-ice product is unchanged from 2011. The SPoRT SST composite product has been expanded geographically and as a result, the resolution has been coarsened from 1 km to 2 km to accommodate the larger domain. The expanded domain covers much of the northern hemisphere from eastern Asia to western Europe (0 N to 80 N latitude and 150 E to 10 E longitude). In addition, the NESDIS POES-GOES product was added to fill in gaps caused by the Moderate Resolution Imaging Spectroradiometer (MODIS) being unable to sense in cloudy regions, replacing the recently-lost Advanced Microwave Scanning Radiometer for EOS with negligible change to product fidelity. The SST product now runs twice per day for Terra and Aqua combined data collections from 0000 to 1200 UTC and from 1200 to 0000 UTC, with valid analysis times at 0600 and 1800 UTC. The twice-daily compositing technique reduces the overall latency of the previous version while still representing the diurnal cycle characteristics. The SST composites are available at approximately four hours after the end of each collection period (i.e. 1600 UTC for the nighttime analysis and 0400 UTC for the daytime analysis). The real-time MODIS GVF composite has only received minor updates in the past year. The domain was expanded slightly to extend further west, north, and east to improve coverage over parts of southern Canada. Minor adjustments were also made to the manner in which GVF is calculated from the distribution of maximum Normalized Difference Vegetation Index from MODIS. The presentation will highlight some examples of the substantial inter-annual change in GVF that occurred from 2010 to 2011 in the U.S. Southern Plains as a result of the summer 2011 drought, and the early vegetation green up across the eastern U.S. due to the very warm conditions in March 2012. Finally, the SPoRT LIS runs the operational Noah land surface model (LSM) in real time over much of the eastern half of the CONUS. The Noah LSM is continually cycled in real time, uncoupled to any model, and driven by operational atmospheric analyses over a long-term, multi-year integration. The LIS-Noah provides the STRC EMS with high-resolution (3 km) LSM initialization data that are in equilibrium with the operational analysis forcing. The Noah LSM within the SPoRT LIS has been upgraded from version 2.7.1 to version 3.2, which has improved look-up table attributes for several land surface quantities. The surface albedo field is now being adjusted based on the input real-time MODIS GVF, thereby improving the net radiation. Also, the LIS-Noah now uses the newer MODIS-based land use classification scheme (i.e. the International Biosphere-Geosphere Programme [IGBP]) that has a better depiction of urban corridors in areas where urban sprawl has occurred. STRC EMS users interested in initializing their LSM fields with high-resolution SPoRT LIS data should set up their model domain with the MODIS-IGBP 20-class land use database and select Noah as the LSM.

A Reactive Transport Model for the Distribution and Age of Carbon in Soils and Sediments Through Direct Simulation of the Stable and Radiogenic Isotopologues

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Lawrence, C. R.

2015-12-01

We present a reactive transport (RT) approach to link hydrologic transport, geochemical transformations and microbial activity influencing the magnitude and residence time of different carbon pools under variably saturated conditions. This model explicitly simulates the simultaneous transport, transformation, fractionation and decay of the three isotopes of carbon (12C, 13C and 14C) through a mechanistic framework. This is demonstrated with a modification of the CrunchTope multi-component RT software to extend the isotope-specific versions of both microbially-mediated and transition state theory (TST) rate laws to accommodate a three-isotope system. In addition both aqueous and solid phase decay of 14C are tracked, yielding in an implicit means of accounting for the 13C/12C correction in normalized radiocarbon ages. The capacity of this approach to quantify the storage and flux of carbon through subsurface compartments is demonstrated using two examples distinguished by timescale. The first considers a simplified flow path in which an influent containing labile organic carbon is distributed by biogenic reduction and mineralization into a suite of reaction products. The residence time of these pools and their characteristic stable isotope ratios are tracked through a variety of transient processes occurring at short timescales (e.g. months). These include a change in fluid flow rate, a limitation of ammonium supporting anabolic growth and an influx of oxygenated fluid. The second example considers the distribution of carbon over the timescale of soil development (e.g., millennia), using a dataset of stable isotope ratios and radiocarbon ages of organic and inorganic carbon present in both dissolved and solid phases from a soil chronosequence near Santa Cruz, CA. The results of these model simulations suggest the promise of this tool for improving our understanding of coupling between hydrologic transport and biogeochemical reactions in soils.

Rapid and Sensitive Salmonella Typhi Detection in Blood and Fecal Samples Using Reverse Transcription Loop-Mediated Isothermal Amplification.

PubMed

Fan, Fenxia; Yan, Meiying; Du, Pengcheng; Chen, Chen; Kan, Biao

2015-09-01

Typhoid fever caused by Salmonella enterica serovar Typhi remains a significant public health problem in developing countries. Although the main method for diagnosing typhoid fever is blood culture, the test is time consuming and not always able to detect infections. Thus, it is very difficult to distinguish typhoid from other infections in patients with nonspecific symptoms. A simple and sensitive laboratory detection method remains necessary. The purpose of this study is to establish and evaluate a rapid and sensitive reverse transcription-based loop-mediated isothermal amplification (RT-LAMP) method to detect Salmonella Typhi infection. In this study, a new specific gene marker, STY1607, was selected to develop a STY1607-RT-LAMP assay; this is the first report of specific RT-LAMP detection assay for typhoid. Human-simulated and clinical blood/stool samples were used to evaluate the performance of STY1607-RT-LAMP for RNA detection; this method was compared with STY1607-LAMP, reverse transcription real-time polymerase chain reaction (rRT-PCR), and bacterial culture methods for Salmonella Typhi detection. Using mRNA as the template, STY1607-RT-LAMP exhibited 50-fold greater sensitivity than STY1607-LAMP for DNA detection. The STY1607-RT-LAMP detection limit is 3 colony-forming units (CFU)/mL for both the pure Salmonella Typhi samples and Salmonella Typhi-simulated blood samples and was 30 CFU/g for the simulated stool samples, all of which were 10-fold more sensitive than the rRT-PCR method. RT-LAMP exhibited improved Salmonella Typhi detection sensitivity compared to culture methods and to rRT-PCR of clinical blood and stool specimens from suspected typhoid fever patients. Because it can be performed without sophisticated equipment or skilled personnel, RT-LAMP is a valuable tool for clinical laboratories in developing countries. This method can be applied in the clinical diagnosis and care of typhoid fever patients as well as for a quick public health response.

Development of a pan-Simbu real-time reverse transcriptase PCR for the detection of Simbu serogroup viruses and comparison with SBV diagnostic PCR systems.

PubMed

Fischer, Melina; Schirrmeier, Horst; Wernike, Kerstin; Wegelt, Anne; Beer, Martin; Hoffmann, Bernd

2013-11-05

Schmallenberg virus (SBV), a novel orthobunyavirus of the Simbu serogroup, was first identified in October 2011 in dairy cattle in Germany, where it caused fever, diarrhea and a drop in milk yield. Since then, SBV additionally has been detected in adult sheep and goats. Although symptoms of acute infection were not observed, infection during a vulnerable phase of pregnancy caused congenital malformations and stillbirths. In view of the current situation and the possible emergence of further Simbu serogroup members, a pan-Simbu real-time reverse transcriptase (RT) PCR system for the reliable detection of Simbu serogroup viruses should be developed. In this study a pan-Simbu real-time RT-PCR system was established and compared to several SBV real-time RT-PCR assays. All PCR-systems were tested using a panel of different Simbu serogroup viruses as well as several field samples from diseased cattle, sheep and goats originating from all over Germany. Several pan-Simbu real-time RT-PCR products were sequenced via Sanger sequencing. Furthermore, in silico analyses were performed to investigate suitability for the detection of further orthobunyaviruses. All tested members of the Simbu serogroup (n = 14) as well as most of the field samples were successfully detected by the pan-Simbu real-time RT-PCR system. The comparison of this intercalating dye assay with different TaqMan probe-based assays developed for SBV diagnostics confirmed the functionality of the pan-Simbu assay for screening purposes. However, the SBV-TaqMan-assay SBV-S3 delivered the highest analytical sensitivity of less than ten copies per reaction for duplex systems including an internal control. In addition, for confirmation of SBV-genome detection the highly specific SBV-M1 assay was established. The pan-Simbu real-time RT-PCR system was able to detect all tested members of the Simbu serogroup, most of the SBV field samples as well as three tested Bunyamwera serogroup viruses with a suitable sensitivity. According to in silico analyses, this system seems to be able to detect a broad orthobunyavirus spectrum. As an additional feature of the pan-Simbu real-time RT-PCR system, subsequent species classification via sequencing is feasible. Regarding SBV diagnostics, the performance of the S-segment targeting SBV-S3 assay was superior with respect to the analytical sensitivity.

Comparison of four molecular assays for the detection of Tembusu virus.

PubMed

Tang, Yi; Yeh, Yin-Ting; Chen, Hao; Yu, Chunmei; Gao, Xuhui; Diao, Youxiang

2015-10-01

Tembusu virus (TMUV) belongs to the genus Flavivirus that may cause severe egg drop in ducks. In order to evaluate the most efficient TMUV detection method, the performances of a conventional RT-PCR (C-RT-PCR), a semi-nested PCR (SN-RT-PCR), a reverse-transcriptase real-time quantitative PCR (Q-RT-PCR), and a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) targeting the TMUV virus-specific NS5 gene were examined. In order to compare the sensitivity of these four techniques, two templates were used: (1) plasmid DNA that contained a partial region of the NS5 gene and (2) genomic RNA from TMUV-positive cell culture supernatants. The sensitivities using plasmid DNA detection by C-RT-PCR, SN-RT-PCR, Q-RT-PCR, and RT-LAMP were 2 × 10(4) copies/μL, 20 copies/μL, 2 copies/μL, and 20 copies/μL, respectively. The sensitivities using genomic RNA for the C-RT-PCR, SN-RT-PCR, Q-RT-PCR, and RT-LAMP were 100 pg/tube, 100, 10, and 100 fg/tube, respectively. All evaluated assays were specific for TMUV detection. The TMUV-specific RNA was detected in cloacal swabs from experimentally infected ducks using these four methods with different rates (52-92%), but not in the control (non-inoculated) samples. The sensitivities of RT-PCR, SN-RT-PCR, Q-RT-PCR, and RT-LAMP performed with cloacal swabs collected from suspected TMUV infected ducks within 2 weeks of severe egg-drop were 38/69 (55.1%), 52/69 (75.4%), 57/69 (82.6%), and 55/69 (79.7%), respectively. In conclusion, both RT-LAMP and Q-RT-PCR can provide a rapid diagnosis of TMUV infection, but RT-LAMP is more useful in TMUV field situations or poorly equipped laboratories.

Effect of short-term room temperature storage on the microbial community in infant fecal samples.

PubMed

Guo, Yong; Li, Sheng-Hui; Kuang, Ya-Shu; He, Jian-Rong; Lu, Jin-Hua; Luo, Bei-Jun; Jiang, Feng-Ju; Liu, Yao-Zhong; Papasian, Christopher J; Xia, Hui-Min; Deng, Hong-Wen; Qiu, Xiu

2016-05-26

Sample storage conditions are important for unbiased analysis of microbial communities in metagenomic studies. Specifically, for infant gut microbiota studies, stool specimens are often exposed to room temperature (RT) conditions prior to analysis. This could lead to variations in structural and quantitative assessment of bacterial communities. To estimate such effects of RT storage, we collected feces from 29 healthy infants (0-3 months) and partitioned each sample into 5 portions to be stored for different lengths of time at RT before freezing at -80 °C. Alpha diversity did not differ between samples with storage time from 0 to 2 hours. The UniFrac distances and microbial composition analysis showed significant differences by testing among individuals, but not by testing between different time points at RT. Changes in the relative abundance of some specific (less common, minor) taxa were still found during storage at room temperature. Our results support previous studies in children and adults, and provided useful information for accurate characterization of infant gut microbiomes. In particular, our study furnished a solid foundation and justification for using fecal samples exposed to RT for less than 2 hours for comparative analyses between various medical conditions.

Smart Radiation Therapy Biomaterials.

PubMed

Ngwa, Wilfred; Boateng, Francis; Kumar, Rajiv; Irvine, Darrell J; Formenti, Silvia; Ngoma, Twalib; Herskind, Carsten; Veldwijk, Marlon R; Hildenbrand, Georg Lars; Hausmann, Michael; Wenz, Frederik; Hesser, Juergen

2017-03-01

Radiation therapy (RT) is a crucial component of cancer care, used in the treatment of over 50% of cancer patients. Patients undergoing image guided RT or brachytherapy routinely have inert RT biomaterials implanted into their tumors. The single function of these RT biomaterials is to ensure geometric accuracy during treatment. Recent studies have proposed that the inert biomaterials could be upgraded to "smart" RT biomaterials, designed to do more than 1 function. Such smart biomaterials include next-generation fiducial markers, brachytherapy spacers, and balloon applicators, designed to respond to stimuli and perform additional desirable functions like controlled delivery of therapy-enhancing payloads directly into the tumor subvolume while minimizing normal tissue toxicities. More broadly, smart RT biomaterials may include functionalized nanoparticles that can be activated to boost RT efficacy. This work reviews the rationale for smart RT biomaterials, the state of the art in this emerging cross-disciplinary research area, challenges and opportunities for further research and development, and a purview of potential clinical applications. Applications covered include using smart RT biomaterials for boosting cancer therapy with minimal side effects, combining RT with immunotherapy or chemotherapy, reducing treatment time or health care costs, and other incipient applications. Copyright © 2016 Elsevier Inc. All rights reserved.

One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples.

PubMed

Gautam, Rashi; Mijatovic-Rustempasic, Slavica; Esona, Mathew D; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D

2016-01-01

Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8-100% sensitivity, 99.7-100% specificity, 85-95% efficiency and a limit of detection of 4-60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81-92% efficiency and limit of detection of 150-600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8-100% sensitivity, 100% specificity, 86-89% efficiency and a limit of detection of 12-400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82-90% efficiency and limit of detection of 120-4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains.

One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples

PubMed Central

Mijatovic-Rustempasic, Slavica; Esona, Mathew D.; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D.

2016-01-01

Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8–100% sensitivity, 100% specificity, 86–89% efficiency and a limit of detection of 12–400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82–90% efficiency and limit of detection of 120–4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains. PMID:26839745

Comparing individual differences in inconsistency and plasticity as predictors of cognitive function in older adults.

PubMed

Grand, Jacob H G; Stawski, Robert S; MacDonald, Stuart W S

2016-01-01

Recent theorizing differentiates key constraints on cognition, including one's current range of processing efficiency (i.e., flexibility or inconsistency) as well as the capacity to expand flexibility over time (i.e., plasticity). The present study uses intensive assessment of response time data to examine the interplay between markers of intraindividual variability (inconsistency) and gains across biweekly retest sessions (plasticity) in relation to age-related cognitive function. Participants included 304 adults (aged 64 to 92 years: M = 74.02, SD = 5.95) from Project MIND, a longitudinal burst design study assessing performance across micro and macro intervals (response latency trials, weekly bursts, annual retests). For two reaction time (RT) measures (choice RT and one-back choice RT), baseline measures of RT inconsistency (intraindividual standard deviation, ISD, across trials at the first testing session) and plasticity (within-person performance gains in average RT across the 5 biweekly burst sessions) were computed and were then employed in linear mixed models as predictors of individual differences in cognitive function and longitudinal (6-year) rates of cognitive change. Independent of chronological age and years of education, higher RT inconsistency was associated uniformly with poorer cognitive function at baseline and with increased cognitive decline for measures of episodic memory and crystallized verbal ability. In contrast, predictive associations for plasticity were more modest for baseline cognitive function and were absent for 6-year cognitive change. These findings underscore the potential utility of response times for articulating inconsistency and plasticity as dynamic predictors of cognitive function in older adults.

Comparison of nested competitive RT-PCR and real-time RT-PCR for the detection and quantification of AML1/MTG8 fusion transcripts in t(8;21) positive acute myelogenous leukemia.

PubMed

Wattjes, M P; Krauter, J; Nagel, S; Heidenreich, O; Ganser, A; Heil, G

2000-02-01

The chromosomal translocation t(8;21)(q22;q22) is one of the most frequent karyotypic aberrations in acute myeloid leukemia (AML) and results in a chimeric fusion transcript AML1/MTG8. Since AML1/MTG8 fusion transcripts remain detectable by RT-PCR in t(8;21) AML patients in long-term hematological remission, quantitative assessment of AML1/MTG8 transcripts is necessary for the monitoring of minimal residual disease (MRD) in these patients. Competitive RT-PCR and recently real-time RT-PCR are increasingly used for detection and quantification of leukemia specific fusion transcripts. For the direct comparison of both methods we cloned a 42 bp DNA fragment into the original AML1/MTG8 sequence. The resulting molecule was used as an internal competitor for our novel competitive nested RT-PCR for AML1/MTG8 and as an external standard for the generation of AML1/MTG8 standard curves in a real-time PCR assay. Using this standard molecule for both PCR techniques, we compared their sensitivity, linearity and reproducibility. Both methods were comparable with regard to all parameters tested irrespective of analyzing serial dilutions of plasmids, cell lines or samples from t(8;21) positive AML patients at different stages of the disease. Therefore, both techniques can be recommended for the monitoring of MRD in these particular AML patients. However, the automatization of the real-time PCR technique offers some technical advantages.

Neoadjuvant long-course chemoradiation remains strongly favored over short-course radiotherapy by radiation oncologists in the United States.

PubMed

Mowery, Yvonne M; Salama, Joseph K; Zafar, S Yousuf; Moore, Harvey G; Willett, Christopher G; Czito, Brian G; Hopkins, M Benjamin; Palta, Manisha

2017-04-15

Short-course radiotherapy (SC-RT) and long-course chemoradiotherapy (LC-CRT) are accepted neoadjuvant treatments of rectal cancer. In the current study, the authors surveyed US radiation oncologists to assess practice patterns and attitudes regarding SC-RT and LC-CRT for patients with rectal cancer. The authors distributed a survey to 1701 radiation oncologists regarding treatment of neoadjuvant rectal cancer. Respondents were asked questions regarding the number of patients with rectal cancer treated, preference for SC-RT versus LC-CRT, and factors influencing regimen choice. Of 1659 contactable physicians, 182 responses (11%) were received. Approximately 83% treated at least 5 patients with rectal cancer annually. The majority of responding radiation oncologists (96%) preferred neoadjuvant LC-CRT for the treatment of patients with locally advanced rectal cancer and 44% never used SC-RT. Among radiation oncologists using SC-RT, respondents indicated they would not recommend this regimen for patients with low (74%) or bulky tumors (70%) and/or concern for a positive circumferential surgical resection margin (69%). The most frequent reasons for not offering SC-RT were insufficient downstaging for sphincter preservation (53%) and a desire for longer follow-up (45%). Many radiation oncologists indicated they would prescribe SC-RT for patients not receiving chemotherapy (62%) or patients with a geographic barrier to receiving LC-CRT (82%). Patient comorbidities appeared to influence regimen preferences for 79% of respondents. Approximately 20% of respondents indicated that altered oncology care reimbursement using capitated payment by diagnosis would impact their consideration of SC-RT. US radiation oncologists rarely use neoadjuvant SC-RT despite 3 randomized controlled trials demonstrating no significant differences in outcome compared with LC-CRT. Further research is necessary to determine whether longer follow-up coupled with the benefits of lower cost, increased patient convenience, and lower acute toxicity will increase the adoption of SC-RT by radiation oncologists in the United States. Cancer 2017;123:1434-1441. © 2016 American Cancer Society. © 2016 American Cancer Society.

Risk factors for severe hemorrhagic transformation in ischemic stroke patients treated with recombinant tissue plasminogen activator: a secondary analysis of the European-Australasian Acute Stroke Study (ECASS II).

PubMed

Larrue, V; von Kummer R, R; Müller, A; Bluhmki, E

2001-02-01

Intravenous thrombolysis with recombinant tissue plasminogen activator (rtPA) improves the outcome for ischemic stroke patients who can be treated within 3 hours of symptom onset. The efficacy of thrombolysis has been demonstrated despite an increased risk of severe hemorrhagic transformation (HT) in patients treated with rtPA. We performed an analysis of risk factors for severe HT in the second European-Australasian Acute Stroke Study (ECASS II). HTs were classified by using clinical and radiological criteria as follows: hemorrhagic infarction (HI), parenchymal hemorrhage (PH), and symptomatic intracranial hemorrhage (SICH). Potential risk factors for HT were tested by stepwise logistic regression analysis, including rtPA-by-variable interactions. In addition, the distribution of bad outcome (modified Rankin score 5 to 6) at day 90 was stratified according to each category of HT. PH and SICH but not HI were associated with rtPA. Also, PH and SICH but not HI were more severe in rtPA-treated patients than in those receiving placebo. Risk factors for PH were rtPA, extent of parenchymal hypoattenuation on baseline CT, congestive heart failure, increasing age, and baseline systolic blood pressure. The risk of PH on rtPA was increased in older patients and in those who were treated with aspirin before thrombolysis. Risk factors for SICH were rtPA, congestive heart failure, extent of parenchymal hypoattenuation, and increasing age. The risk of SICH on rtPA was increased in patients who were treated with aspirin before thrombolysis. This secondary analysis of ECASS II has confirmed the importance of the extent of hypoattenuation as a risk factor for severe HT. The findings also suggest that older patients and those who have used aspirin before stroke are at higher risk of a severe HT on rtPA.

Real-Time Reverse Transcription–Polymerase Chain Reaction Assay for SARS-associated Coronavirus

PubMed Central

Emery, Shannon L.; Bowen, Michael D.; Newton, Bruce R.; Winchell, Jonas M.; Meyer, Richard F.; Tong, Suxiang; Cook, Byron T.; Holloway, Brian P.; McCaustland, Karen A.; Rota, Paul A.; Bankamp, Bettina; Lowe, Luis E.; Ksiazek, Tom G.; Bellini, William J.; Anderson, Larry J.

2004-01-01

A real-time reverse transcription–polymerase chain reaction (RT-PCR) assay was developed to rapidly detect the severe acute respiratory syndrome–associated coronavirus (SARS-CoV). The assay, based on multiple primer and probe sets located in different regions of the SARS-CoV genome, could discriminate SARS-CoV from other human and animal coronaviruses with a potential detection limit of <10 genomic copies per reaction. The real-time RT-PCR assay was more sensitive than a conventional RT-PCR assay or culture isolation and proved suitable to detect SARS-CoV in clinical specimens. Application of this assay will aid in diagnosing SARS-CoV infection. PMID:15030703

Development of a GNSS-Enhanced Tsunami Early Warning System

NASA Astrophysics Data System (ADS)

Bawden, G. W.; Melbourne, T. I.; Bock, Y.; Song, Y. T.; Komjathy, A.

2015-12-01

The past decade has witnessed a terrible loss of life and economic disruption caused by large earthquakes and resultant tsunamis impacting coastal communities and infrastructure across the Indo-Pacific region. NASA has funded the early development of a prototype real-time Global Navigation Satellite System (RT-GNSS) based rapid earthquake and tsunami early warning (GNSS-TEW) system that may be used to enhance seismic tsunami early warning systems for large earthquakes. This prototype GNSS-TEW system geodetically estimates fault parameters (earthquake magnitude, location, strike, dip, and slip magnitude/direction on a gridded fault plane both along strike and at depth) and tsunami source parameters (seafloor displacement, tsunami energy scale, and 3D tsunami initials) within minutes after the mainshock based on dynamic numerical inversions/regressions of the real-time measured displacements within a spatially distributed real-time GNSS network(s) spanning the epicentral region. It is also possible to measure fluctuations in the ionosphere's total electron content (TEC) in the RT-GNSS data caused by the pressure wave from the tsunami. This TEC approach can detect if a tsunami has been triggered by an earthquake, track its waves as they propagate through the oceanic basins, and provide upwards of 45 minutes early warning. These combined real-time geodetic approaches will very quickly address a number of important questions in the immediate minutes following a major earthquake: How big was the earthquake and what are its fault parameters? Could the earthquake have produced a tsunami and was a tsunami generated?

Assessment of the Rate of Adherence to International Guidelines for Androgen Deprivation Therapy with External-beam Radiation Therapy: A Population-based Study.

PubMed

Dell'Oglio, Paolo; Abou-Haidar, Hiba; Leyh-Bannurah, Sami-Ramzi; Tian, Zhe; Larcher, Alessandro; Gandaglia, Giorgio; Fossati, Nicola; Shariat, Shahrokh F; Capitanio, Umberto; Briganti, Alberto; Montorsi, Francesco; Graefen, Markus; Saad, Fred; Karakiewicz, Pierre I

2016-09-01

The National Comprehensive Cancer Network and the European Association of Urology guidelines recommend using radiation therapy (RT) with androgen deprivation therapy (ADT) to treat high-risk and locally advanced prostate cancer patients. To evaluate the degree of adherence to these guidelines. Between 2003 and 2009, in the Surveillance Epidemiology and End Results (SEER)-Medicare database, 14 180 patients were diagnosed with high-risk (T1-T2 with World Health Organization histologic grade 3) or locally advanced (T3-T4 with any histologic grade) prostatic adenocarcinoma. Administration of RT-ADT versus RT alone. We assessed the rate of adherence to guidelines with respect to use of RT-ADT in the overall population and after stratification according to stage-grade groupings (T1-T2 G3 vs T3-T4 any grade), age (66-69, 70-74, 75-79, ≥80 yr), Charlson Comorbidity Index (CCI) (0, 1, ≥2), and preexisting baseline cardiovascular (CV) disease. We depicted the rate of RT-ADT administration graphically over the study period. Multivariable logistic regression analyses were performed to assess the predictors of RT-ADT use. RT-ADT rates and guideline adherence were 58-75%, with the highest rate (75%) in 2003 and the lowest (58%) in 2009. When stratified according to stage-grade groupings, age, CCI, and preexisting baseline CV disease, similar results were obtained. In multivariable analyses, year of diagnosis (p<0.001), patient age (p<0.001), stage-grade groupings (p<0.001), CCI (p=0.036), race (p<0.001), marital status (p<0.001), population density (p<0.001), and US regions (p<0.001) were independent predictors of RT-ADT use. The limitations of our study include age >65 yr and exclusive Medicare coverage. The rate of guideline adherence regarding the use of RT-ADT is suboptimal and decreases with time instead of increasing. This population-based study provides evidence of low adherence to international urologic guidelines regarding the combination of radiation therapy (RT) with androgen deprivation therapy (ADT) for high-risk and locally advanced prostate cancer (PCa) patients. Despite the increasing number of randomized controlled trials over time that showed a survival benefit for patients with high-risk and locally advanced PCa treated with RT-ADT compared with RT alone, the rate of adherence to guidelines decreased with time. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Species distribution and detection of Crimean Congo Hemorrhagic Fever Virus (CCHFV) in field-collected ticks in Ankara Province, Central Anatolia, Turkey.

PubMed

Hekimoglu, Olcay; Ozer, Nurdan; Ergunay, Koray; Ozkul, Aykut

2012-01-01

Ticks may act as vectors for a number of infectious diseases including Crimean Congo Hemorrhagic Fever (CCHF). The causative agent is Crimean Congo Hemorrhagic Fever Virus (CCHFV), a member of Bunyaviridae, causing extensive ecchymosis, visceral bleeding and hepatic dysfunction with a high fatality rate in the affected individuals. CCHF was initially recognized in Turkey in 2002 and the current number of reported cases exceeds 4,400. This study was conducted to confirm the presence of tick species established as potential CCHFV vectors and investigate CCHFV activity in ticks at Ankara province, Turkey's second most-densely populated province, where CCHF cases were demonstrated. A total of 1,196 adult ticks, collected from various animals and vegetation in 12 sites located in 5 counties of Ankara during April-July 2010 were identified to species level. Twenty-two tick pools from county K2 were also evaluated for the presence of CCHFV RNA via a one-step real-time RT-PCR assay and reactive results were further confirmed by an in house nested RT-PCR assay. Nine tick species were identified: Rhipicephalus bursa (44.9%), R. sanguineus (18.9%), R. turanicus (18.1%), Haemaphysalis parva (8.3%), Hyalomma marginatum marginatum (5.4%), H. aegyptium (1.4%), H. anatolicum excavatum (1.3%), Hae. punctata (0.3%) and Dermacentor marginatus (0.2%). A total of five tick pools (22.7%) were reactive in real-time and nested RT-PCR assays. The pools included R. bursa, H. m. marginatum and Hae. parva ticks, collected from mammal hosts from two villages in one county. This is the first documentation of CCHFV activity in ticks from Ankara province, which indicates requirement for detailed surveillance to predict high risk zones in the region.

Monitoring Elite Soccer Players' External Loads Using Real-Time Data.

PubMed

Barrett, Steve

2017-11-01

To assess the validity of measuring locomotor activities and PlayerLoad using real-time (RT) data collection during soccer training. Twenty-nine English soccer players participated. Each player wore the same MEMS device (Micromechanical Electrical Systems; S5, Optimeye; CatapultSports, Melbourne, Australia) during 21 training sessions (N = 331 data sets) in the 2015-16 and 2016-17 seasons. An RT receiver (TRX; Catapultsports, Melbourne, Australia) was used to collect the locomotor activities and PlayerLoad data in RT and compared with the postevent downloaded (PED) data. PlayerLoad and locomotor activities (total distance covered; total high-speed running distance covered, >5.5#x00A0;m/s; total sprinting distance covered, >7 m/s; maximum velocity) were analyzed. Correlations were near perfect for all variables analyzed (r = .98-1.00), with a varied level of noise between RT and PED also (0.3-9.7% coefficient of variation). Locomotor activities and PlayerLoad can use both RT and PED concurrently to quantify a player's physical output during a training session. Caution should be taken with higher-velocity-based locomotor activities during RT compared to PED.

1H-MR spectroscopy and diffusion tensor imaging of normal-appearing temporal white matter in patients with nasopharyngeal carcinoma after irradiation: initial experience.

PubMed

Xiong, Wei Feng; Qiu, Shi Jun; Wang, Hong Zhuo; Lv, Xiao Fei

2013-01-01

To detect radiation-induced changes of temporal lobe normal-appearing white mater (NAWM) following radiation therapy (RT) for nasopharyngeal carcinoma (NPC). Seventy-five H(1)-MR spectroscopy and diffusion-tensor imaging (DTI) examinations were performed in 55 patients before and after receiving fractionated radiation therapy (total dose; 66-75GY). We divided the dataset into six groups, a pre-RT control group and five other groups based on time after completion of RT. N-acetylaspartic acid (NAA)/choline (Cho), NAA/creatine (Cr), Cho/Cr, mean diffusibility (MD), functional anisotropy (FA), radial diffusibility (λ(⊥)), and axial diffusibility (λ(||)) were calculated. NAA/Cho and NAA/Cr decreased and λ(⊥) increased significantly within 1 year after RT compared with pre-RT. After 1 year, NAA/Cho, NAA/Cr, and λ(⊥) were not significantly different from pre-RT. In all post-RT groups, FA decreased significantly. λ(||) decreased within 9 months after RT compared with pre-RT, but was not significantly different from pre-RT more than 9 months after RT. DTI and H(1)-MR spectroscopy can be used to detect early radiation-induced changes of temporal lobe NAWM following radiation therapy for NPC. Metabolic alterations and water diffusion characteristics of temporal lobe NAWM in patients with NPC after RT were dynamic and transient. Copyright © 2012 Wiley Periodicals, Inc.

Tunneling nanotubes promote intercellular mitochondria transfer followed by increased invasiveness in bladder cancer cells

PubMed Central

Lu, Jinjin; Zheng, Xiufen; Li, Fan; Yu, Yang; Chen, Zhong; Liu, Zheng; Wang, Zhihua; Xu, Hua; Yang, Weimin

2017-01-01

Intercellular transfer of organelles via tunneling nanotubes (TNTs) is a novel means of cell-to-cell communication. Here we demonstrate the existence of TNTs between co-cultured RT4 and T24 bladder cancer cells using light microscopy, fluorescence imaging, and scanning electron microscopy (SEM). Spontaneous unidirectional transfer of mitochondria from T24 to RT4 cells was detected using fluorescence imaging and flow cytometry. The distribution of mitochondria migrated from T24 cells was in good agreement with the original mitochondria in RT4 cells, which may imply mitochondrial fusion. We detected cytoskeleton reconstruction in RT4-Mito-T24 cells by observing F-actin redistribution. Akt, mTOR, and their downstream mediators were activated and increased. The resultant increase in the invasiveness of bladder cancer cells was detected in vitro and in vivo. These data indicate that TNTs promote intercellular mitochondrial transfer between heterogeneous cells, followed by an increase in the invasiveness of bladder cancer cells. PMID:28107184

Real-time Simulation of Turboprop Engine Control System

NASA Astrophysics Data System (ADS)

Sheng, Hanlin; Zhang, Tianhong; Zhang, Yi

2017-05-01

On account of the complexity of turboprop engine control system, real-time simulation is the technology, under the prerequisite of maintaining real-time, to effectively reduce development cost, shorten development cycle and avert testing risks. The paper takes RT-LAB as a platform and studies the real-time digital simulation of turboprop engine control system. The architecture, work principles and external interfaces of RT-LAB real-time simulation platform are introduced firstly. Then based on a turboprop engine model, the control laws of propeller control loop and fuel control loop are studied. From that and on the basis of Matlab/Simulink, an integrated controller is designed which can realize the entire process control of the engine from start-up to maximum power till stop. At the end, on the basis of RT-LAB platform, the real-time digital simulation of the designed control system is studied, different regulating plans are tried and more ideal control effects have been obtained.

Physiological Evidence for Response Inhibition in Choice Reaction Time Tasks

ERIC Educational Resources Information Center

Burle, Boris; Vidal, Frank; Tandonnet, Christophe; Hasbroucq, Thierry

2004-01-01

Inhibition is a widely used notion proposed to account for data obtained in choice reaction time (RT) tasks. However, this concept is weakly supported by empirical facts. In this paper, we review a series of experiments using Hoffman reflex, transcranial magnetic stimulation and electroencephalography to study inhibition in choice RT tasks. We…

Salmonella detection from chicken rinsate with surface enhanced Raman spectroscopy and RT-PCR validation

USDA-ARS?s Scientific Manuscript database

Optical detection of bacteria has been approached in recent years as a bacteria detection method that can counter time restraints of traditional plating or the high reoccurring cost of real-time polymerase chain reaction (RT-PCR). The goal of optical detection is to identify bacteria with spectral s...

Serial Reaction Time Learning in Preschool- and School-Age Children.

ERIC Educational Resources Information Center

Thomas, Kathleen M.; Nelson, Charles A.

2001-01-01

Two experiments assessed visuomotor sequence learning in 4- to 10-year-olds using a serial reaction time (SRT) task with random and sequenced trials. Found that children demonstrated sequence-specific decreases in RT. Participants with explicit awareness of the sequence at the session's end showed larger sequence-specific RT decrements than…

Rapid Access Real-Time device and Rapid Access software: new tools in the armamentarium of capsule endoscopy.

PubMed

Spada, Cristiano; Riccioni, Maria Elena; Costamagna, Guido

2007-07-01

Small bowel capsule endoscopy represents a significant advance in the investigation of the small bowel, allowing direct visualization of this section of the gastrointestinal system. More recently, new video capsules have been released, specifically designed to investigate the esophagus and the colon. In June 2006, Given Imaging Ltd received marketing clearance from the US FDA for the Rapid Access Real-Time (RT) and Rapid Access software. The Rapid Access RT is a handheld device that enables real-time viewing during capsule endoscopy procedures. To date, the clinical benefits of this device are unknown as studies on the Rapid Access RT system have not yet been published. However, it appears that the Rapid Access RT system may reduce the examination and reading time, and may impact significantly in cases where it is important to know the precise localization of the capsule (during PillCam ESO ingestion procedures, PillCam Colon examinations or when delayed gastric transit is suspected) or in case of severe gastrointestinal bleeding (when a therapeutic procedure is required urgently).

Radiotherapy after radical prostatectomy: does transient androgen suppression improve outcomes?

PubMed

King, Christopher R; Presti, Joseph C; Gill, Harcharan; Brooks, James; Hancock, Steven L

2004-06-01

The long-term biochemical relapse-free survival and overall survival were compared for patients receiving either radiotherapy (RT) alone or radiotherapy combined with a short-course of total androgen suppression for failure after radical prostatectomy. Between 1985 and 2001, a total of 122 patients received RT after radical prostatectomy at our institution. Fifty-three of these patients received a short-course of total androgen suppression (TAS) 2 months before and 2 months concurrent with RT with a nonsteroidal antiandrogen and an luteinizing hormone-releasing hormone (LHRH) agonist (combined therapy group); the remaining 69 patients received RT alone. Treatment failure was defined after postoperative RT as a detectable PSA >0.05 ng/mL. Clinical and treatment variables examined included: presurgical PSA, clinical T stage, pathologic Gleason sum (pGS), seminal vesicle (SV) involvement, lymph node involvement, surgical margins, pre-RT PSA, prostate dose, pelvic irradiation, indication for postoperative RT (salvage or adjuvant), and time interval between surgery and RT. Minimum follow-up after postoperative RT was 1 year and median follow-up was 5.9 years (maximum, 14 years) for patients receiving RT alone, and 3.9 years (maximum, 11 years) for patients receiving RT with TAS (combined therapy group). Kaplan-Meier analysis was performed for PSA failure-free survival (bNED) and for overall survival (OS). Cox proportional hazards multivariable analysis examined the influence all clinical and treatment variables predicting for bNED and OS. The median time to PSA failure after postoperative RT was 1.34 years for the combined therapy group and 0.97 years for the RT alone group (p = 0.19), with no failures beyond 5 years. At 5 years, the actuarial bNED rates were 57% for the combined therapy group compared with 31% for the RT alone group (p = 0.0012). Overall survival rates at 5 years were 100% for the combined therapy group compared with 87% for the RT alone group (p = 0.0008). For pGS or=8 the 5-year bNED rates were 65% for combined therapy and 17% for RT alone (p = 0.075). The 5-year OS rates for pGS or=8 was 100% for combined therapy and 54% for RT alone (p = 0.04). On multivariable analysis, only SV involvement (p = 0.0145) and the addition of short-course TAS to postoperative RT (p = 0.0019) were significant covariates predicting for bNED and, similarly, approached significance for overall survival (p = 0.0594 and p = 0.0856, respectively). Radiotherapy combined with a short-course TAS after radical prostatectomy appears to confer a PSA relapse-free survival advantage and possibly an overall survival advantage when compared with RT alone. The hypothesis that a transient course of androgen suppression with salvage or adjuvant RT after prostatectomy improves outcomes will need to be tested in a randomized trial.

Viscous bursting of suspended films

NASA Astrophysics Data System (ADS)

Debrégeas, G.; Martin, P.; Brochard-Wyart, F.

1995-11-01

Soap films break up by an inertial process. We present here the first observations on freely suspended films of long-chain polymers, where viscous effects are dominant and no surfactant is present. A hole is nucleated at time 0 and grows up to a radius R(t) at time t. A surprising feature is that the liquid from the hole is not collected into a rim (as it is in soap films): The liquid spreads out without any significant change of the film thickness. The radius R(t) grows exponentially with time, R~exp(t/τ) [while in soap films R(t) is linear]. The rise time τ~ηe/2γ where η is viscosity, e is thickness (in the micron range), and γ is surface tension. A simple model is developed to explain this growth law.

Expansion of the Real-time Sport-land Information System for NOAA/National Weather Service Situational Awareness and Local Modeling Applications

NASA Technical Reports Server (NTRS)

Case, Jonathan L.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has been running a real-time version of the Land Information System (LIS) since summer 2010 (hereafter, SPoRTLIS). The real-time SPoRT-LIS runs the Noah land surface model (LSM) in an offline capacity apart from a numerical weather prediction model, using input atmospheric and precipitation analyses (i.e., "forcings") to drive the Noah LSM integration at 3-km resolution. Its objectives are to (1) produce local-scale information about the soil state for NOAA/National Weather Service (NWS) situational awareness applications such as drought monitoring and assessing flood potential, and (2) provide land surface initialization fields for local modeling initiatives. The current domain extent has been limited by the input atmospheric analyses that drive the Noah LSM integration within SPoRT-LIS, specifically the National Centers for Environmental Prediction (NCEP) Stage IV precipitation analyses. Due to the nature of the geographical edges of the Stage IV precipitation grid and its limitations in the western U.S., the SPoRT-LIS was originally confined to a domain fully nested within the Stage IV grid, over the southeastern half of the Conterminous United States (CONUS). In order to expand the real-time SPoRT-LIS to a full CONUS domain, alternative precipitation forcing datasets were explored in year-long, offline comparison runs of the Noah LSM. Based on results of these comparison simulations, we chose to implement the radar/gauge-based precipitation analyses from the National Severe Storms Laboratory as a replacement to the Stage IV product. The Multi-Radar Multi-Sensor (MRMS; formerly known as the National Mosaic and multi-sensor Quantitative precipitation estimate) product has full CONUS coverage at higher-resolution, thereby providing better coverage and greater detail than that of the Stage IV product. This paper will describe the expanded/upgraded SPoRT-LIS, present comparisons between the original and upgraded SPoRT-LIS, and discuss the path forward for future collaboration opportunities with SPoRT partners in the NWS.

Left-ventricle segmentation in real-time 3D echocardiography using a hybrid active shape model and optimal graph search approach

NASA Astrophysics Data System (ADS)

Zhang, Honghai; Abiose, Ademola K.; Campbell, Dwayne N.; Sonka, Milan; Martins, James B.; Wahle, Andreas

2010-03-01

Quantitative analysis of the left ventricular shape and motion patterns associated with left ventricular mechanical dyssynchrony (LVMD) is essential for diagnosis and treatment planning in congestive heart failure. Real-time 3D echocardiography (RT3DE) used for LVMD analysis is frequently limited by heavy speckle noise or partially incomplete data, thus a segmentation method utilizing learned global shape knowledge is beneficial. In this study, the endocardial surface of the left ventricle (LV) is segmented using a hybrid approach combining active shape model (ASM) with optimal graph search. The latter is used to achieve landmark refinement in the ASM framework. Optimal graph search translates the 3D segmentation into the detection of a minimum-cost closed set in a graph and can produce a globally optimal result. Various information-gradient, intensity distributions, and regional-property terms-are used to define the costs for the graph search. The developed method was tested on 44 RT3DE datasets acquired from 26 LVMD patients. The segmentation accuracy was assessed by surface positioning error and volume overlap measured for the whole LV as well as 16 standard LV regions. The segmentation produced very good results that were not achievable using ASM or graph search alone.

Contrast enhancement of mail piece images

NASA Astrophysics Data System (ADS)

Shin, Yong-Chul; Sridhar, Ramalingam; Demjanenko, Victor; Palumbo, Paul W.; Hull, Jonathan J.

1992-08-01

A New approach to contrast enhancement of mail piece images is presented. The contrast enhancement is used as a preprocessing step in the real-time address block location (RT-ABL) system. The RT-ABL system processes a stream of mail piece images and locates destination address blocks. Most of the mail pieces (classified into letters) show high contrast between background and foreground. As an extreme case, however, the seasonal greeting cards usually use colored envelopes which results in reduced contrast osured by an error rate by using a linear distributed associative memory (DAM). The DAM is trained to recognize the spectra of three classes of images: with high, medium, and low OCR error rates. The DAM is not forced to make a classification every time. It is allowed to reject as unknown a spectrum presented that does not closely resemble any that has been stored in the DAM. The DAM was fairly accurate with noisy images but conservative (i.e., rejected several text images as unknowns) when there was little ground and foreground degradations without affecting the nondegraded images. This approach provides local enhancement which adapts to local features. In order to simplify the computation of A and (sigma) , dynamic programming technique is used. Implementation details, performance, and the results on test images are presented in this paper.

Dual-Energy CT Imaging of Tumor Liposome Delivery After Gold Nanoparticle-Augmented Radiation Therapy

PubMed Central

Ashton, Jeffrey R.; Castle, Katherine D.; Qi, Yi; Kirsch, David G.; West, Jennifer L.; Badea, Cristian T.

2018-01-01

Gold nanoparticles (AuNPs) are emerging as promising agents for both cancer therapy and computed tomography (CT) imaging. AuNPs absorb x-rays and subsequently release low-energy, short-range photoelectrons during external beam radiation therapy (RT), increasing the local radiation dose. When AuNPs are near tumor vasculature, the additional radiation dose can lead to increased vascular permeability. This work focuses on understanding how tumor vascular permeability is influenced by AuNP-augmented RT, and how this effect can be used to improve the delivery of nanoparticle chemotherapeutics. Methods: Dual-energy CT was used to quantify the accumulation of both liposomal iodine and AuNPs in tumors following AuNP-augmented RT in a mouse model of primary soft tissue sarcoma. Mice were injected with non-targeted AuNPs, RGD-functionalized AuNPs (vascular targeting), or no AuNPs, after which they were treated with varying doses of RT. The mice were injected with either liposomal iodine (for the imaging study) or liposomal doxorubicin (for the treatment study) 24 hours after RT. Increased tumor liposome accumulation was assessed by dual-energy CT (iodine) or by tracking tumor treatment response (doxorubicin). Results: A significant increase in vascular permeability was observed for all groups after 20 Gy RT, for the targeted and non-targeted AuNP groups after 10 Gy RT, and for the vascular-targeted AuNP group after 5 Gy RT. Combining targeted AuNPs with 5 Gy RT and liposomal doxorubicin led to a significant tumor growth delay (tumor doubling time ~ 8 days) compared to AuNP-augmented RT or chemotherapy alone (tumor doubling time ~3-4 days). Conclusions: The addition of vascular-targeted AuNPs significantly improved the treatment effect of liposomal doxorubicin after RT, consistent with the increased liposome accumulation observed in tumors in the imaging study. Using this approach with a liposomal drug delivery system can increase specific tumor delivery of chemotherapeutics, which has the potential to significantly improve tumor response and reduce the side effects of both RT and chemotherapy. PMID:29556356

Improved Survival With Radiation Therapy in Stage I-II Primary Mediastinal B Cell Lymphoma: A Surveillance, Epidemiology, and End Results Database Analysis

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

Jackson, Matthew W., E-mail: matthew.jackson@ucdenver.edu; Rusthoven, Chad G.; Jones, Bernard L.

Background: Primary mediastinal B cell lymphoma (PMBCL) is an uncommon lymphoma for which trials are few with small patient numbers. The role of radiation therapy (RT) after standard immunochemotherapy for early-stage disease has never been studied prospectively. We used the Surveillance, Epidemiology, and End Results (SEER) database to evaluate PMBCL and the impact of RT on outcomes. Methods and Materials: We queried the SEER database for patients with stage I-II PMBCL diagnosed from 2001 to 2011. Retrievable data included age, gender, race (white/nonwhite), stage, extranodal disease, year of diagnosis, and use of RT as a component of definitive therapy. Kaplan-Meier overallmore » survival (OS) estimates, univariate (UVA) log-rank and multivariate (MVA) Cox proportional hazards regression analyses were performed. Results: Two hundred fifty patients with stage I-II disease were identified, with a median follow-up time of 39 months (range, 3-125 months). The median age was 36 years (range, 18-89 years); 61% were female; 76% were white; 45% had stage I disease, 60% had extranodal disease, and 55% were given RT. The 5-year OS for the entire cohort was 86%. On UVA, OS was improved with RT (hazard ratio [HR] 0.446, P=.029) and decreased in association with nonwhite race (HR 2.70, P=.006). The 5-year OS was 79% (no RT) and 90% (RT). On MVA, white race and RT remained significantly associated with improved OS (P=.007 and .018, respectively). The use of RT decreased over time: 61% for the 67 patients whose disease was diagnosed from 2001 to 2005 and 53% in the 138 patients treated from 2006 to 2010. Conclusion: This retrospective population-based analysis is the largest PMBCL dataset to date and demonstrates a significant survival benefit associated with RT. Nearly half of patients treated in the United States do not receive RT, and its use appears to be declining. In the absence of phase 3 data, the use of RT should be strongly considered for its survival benefit in early-stage disease.« less

Avoiding Severe Toxicity From Combined BRAF Inhibitor and Radiation Treatment: Consensus Guidelines from the Eastern Cooperative Oncology Group (ECOG)

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

Anker, Christopher J., E-mail: chris.anker@UVMHealth.org; Grossmann, Kenneth F.; Atkins, Michael B.

2016-06-01

BRAF kinase gene V600 point mutations drive approximately 40% to 50% of all melanomas, and BRAF inhibitors (BRAFi) have been found to significantly improve survival outcomes. Although radiation therapy (RT) provides effective symptom palliation, there is a lack of toxicity and efficacy data when RT is combined with BRAFi, including vemurafenib and dabrafenib. This literature review provides a detailed analysis of potential increased dermatologic, pulmonary, neurologic, hepatic, esophageal, and bowel toxicity from the combination of BRAFi and RT for melanoma patients described in 27 publications. Despite 7 publications noting potential intracranial neurotoxicity, the rates of radionecrosis and hemorrhage from wholemore » brain RT (WBRT), stereotactic radiosurgery (SRS), or both do not appear increased with concurrent or sequential administration of BRAFis. Almost all grade 3 dermatitis reactions occurred when RT and BRAFi were administered concurrently. Painful, disfiguring nondermatitis cutaneous reactions have been described from concurrent or sequential RT and BRAFi administration, which improved with topical steroids and time. Visceral toxicity has been reported with RT and BRAFi, with deaths possibly related to bowel perforation and liver hemorrhage. Increased severity of radiation pneumonitis with BRAFi is rare, but more concerning was a potentially related fatal pulmonary hemorrhage. Conversely, encouraging reports have described patients with leptomeningeal spread and unresectable lymphadenopathy rendered disease free from combined RT and BRAFi. Based on our review, the authors recommend holding RT ≥3 days before and after fractionated RT and ≥1 day before and after SRS. No fatal reactions have been described with a dose <4 Gy per fraction, and time off systemic treatment should be minimized. Future prospective data will serve to refine these recommendations.« less

Validation of real-time three-dimensional echocardiography for quantifying left ventricular volumes in the presence of a left ventricular aneurysm: in vitro and in vivo studies

NASA Technical Reports Server (NTRS)

Qin, J. X.; Jones, M.; Shiota, T.; Greenberg, N. L.; Tsujino, H.; Firstenberg, M. S.; Gupta, P. C.; Zetts, A. D.; Xu, Y.; Ping Sun, J.;

Avoiding Severe Toxicity From Combined BRAF Inhibitor and Radiation Treatment: Consensus Guidelines from the Eastern Cooperative Oncology Group (ECOG)

PubMed Central

Anker, Christopher J.; Grossmann, Kenneth F.; Atkins, Michael B.; Suneja, Gita; Tarhini, Ahmad A.; Kirkwood, John M.

2016-01-01

BRAF kinase gene V600 point mutations drive approximately 40% to 50% of all melanomas, and BRAF inhibitors (BRAFi) have been found to significantly improve survival outcomes. Although radiation therapy (RT) provides effective symptom palliation, there is a lack of toxicity and efficacy data when RT is combined with BRAFi, including vemurafenib and dabrafenib. This literature review provides a detailed analysis of potential increased dermatologic, pulmonary, neurologic, hepatic, esophageal, and bowel toxicity from the combination of BRAFi and RT for melanoma patients described in 27 publications. Despite 7 publications noting potential intracranial neurotoxicity, the rates of radionecrosis and hemorrhage from whole brain RT (WBRT), stereotactic radiosurgery (SRS), or both do not appear increased with concurrent or sequential administration of BRAFis. Almost all grade 3 dermatitis reactions occurred when RT and BRAFi were administered concurrently. Painful, disfiguring nondermatitis cutaneous reactions have been described from concurrent or sequential RT and BRAFi administration, which improved with topical steroids and time. Visceral toxicity has been reported with RT and BRAFi, with deaths possibly related to bowel perforation and liver hemorrhage. Increased severity of radiation pneumonitis with BRAFi is rare, but more concerning was a potentially related fatal pulmonary hemorrhage. Conversely, encouraging reports have described patients with leptomeningeal spread and unresectable lymphadenopathy rendered disease free from combined RT and BRAFi. Based on our review, the authors recommend holding BRAFi and/or MEK inhibitors ≥3 days before and after fractionated RT and ≥1 day before and after SRS. No fatal reactions have been described with a dose <4 Gy per fraction, and time off systemic treatment should be minimized. Future prospective data will serve to refine these recommendations. PMID:27131079

Real-time magnetic resonance imaging-guided radiofrequency atrial ablation and visualization of lesion formation at 3 Tesla.

PubMed

Vergara, Gaston R; Vijayakumar, Sathya; Kholmovski, Eugene G; Blauer, Joshua J E; Guttman, Mike A; Gloschat, Christopher; Payne, Gene; Vij, Kamal; Akoum, Nazem W; Daccarett, Marcos; McGann, Christopher J; Macleod, Rob S; Marrouche, Nassir F

2011-02-01

Magnetic resonance imaging (MRI) allows visualization of location and extent of radiofrequency (RF) ablation lesion, myocardial scar formation, and real-time (RT) assessment of lesion formation. In this study, we report a novel 3-Tesla RT -RI based porcine RF ablation model and visualization of lesion formation in the atrium during RF energy delivery. The purpose of this study was to develop a 3-Tesla RT MRI-based catheter ablation and lesion visualization system. RF energy was delivered to six pigs under RT MRI guidance. A novel MRI-compatible mapping and ablation catheter was used. Under RT MRI, this catheter was safely guided and positioned within either the left or right atrium. Unipolar and bipolar electrograms were recorded. The catheter tip-tissue interface was visualized with a T1-weighted gradient echo sequence. RF energy was then delivered in a power-controlled fashion. Myocardial changes and lesion formation were visualized with a T2-weighted (T2W) half Fourier acquisition with single-shot turbo spin echo (HASTE) sequence during ablation. RT visualization of lesion formation was achieved in 30% of the ablations performed. In the other cases, either the lesion was formed outside the imaged region (25%) or the lesion was not created (45%) presumably due to poor tissue-catheter tip contact. The presence of lesions was confirmed by late gadolinium enhancement MRI and macroscopic tissue examination. MRI-compatible catheters can be navigated and RF energy safely delivered under 3-Tesla RT MRI guidance. Recording electrograms during RT imaging also is feasible. RT visualization of lesion as it forms during RF energy delivery is possible and was demonstrated using T2W HASTE imaging. Copyright © 2011 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Response time intra-subject variability: commonalities between children with autism spectrum disorders and children with ADHD

PubMed Central

Adamo, Nicoletta; Huo, Lan; Adelsberg, Samantha; Petkova, Eva; Castellanos, F. Xavier

2013-01-01

Despite the common co-occurrence of symptoms of attention deficit hyperactivity disorder (ADHD) in individuals with autism spectrum disorders (ASD), the underlying mechanisms are under-explored. A potential candidate for investigation is response time intra-subject variability (RT-ISV), a hypothesized marker of attentional lapses. Direct comparisons of RT-ISV in ASD versus ADHD are limited and contradictory. We aimed to examine whether distinct fluctuations in RT-ISV characterize children with ASD and with ADHD relative to typically developing children (TDC). We applied both a priori-based and data-driven strategies to RT performance of 46 children with ASD, 46 with ADHD, and 36 TDC (aged 7–11.9 years). Specifically, we contrasted groups relative to the amplitude of four preselected frequency bands as well as to 400 frequency bins from 0.006 to 0.345 Hz. In secondary analyses, we divided the ASD group into children with and without substantial ADHD symptoms (ASD+ and ASD−, respectively). Regardless of the strategy employed, RT-ISV fluctuations at frequencies between 0.20 and 0.345 Hz distinguished children with ADHD, but not children with ASD, from TDC. Children with ASD+ and those with ADHD shared elevated amplitudes of RT-ISV fluctuations in frequencies between 0.18 and 0.345 Hz relative to TDC. In contrast, the ASD− subgroup did not differ from TDC in RT-ISV frequency fluctuations. RT-ISV fluctuations in frequencies 0.18–0.345 Hz (i.e., periods between 3 and 5 s) are associated with ADHD symptoms regardless of categorical diagnosis and may represent a biomarker. These results suggest that children with ADHD and those with ASD+ share common underlying pathophysiological mechanisms of RT-ISV. PMID:23716135

Evaluation of RIDA®GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis.

PubMed

Kanwar, N; Hassan, F; Barclay, L; Langley, C; Vinjé, J; Bryant, P W; George, K St; Mosher, L; Matthews-Greer, J M; Rocha, M A; Beenhouwer, D O; Harrison, C J; Moffatt, M; Shastri, N; Selvarangan, R

2018-04-10

Norovirus is the leading cause of epidemic and sporadic acute gastroenteritis (AGE) in the United States. Widespread prevalence necessitates implementation of accurate norovirus detection assays in clinical diagnostic laboratories. To evaluate RIDA ® GENE norovirus GI/GII real-time RT-PCR assay (RGN RT-PCR) using stool samples from patients with sporadic AGE. Patients between 14 days to 101 years of age with symptoms of AGE were enrolled prospectively at four sites across the United States during 2014-2015. Stool specimens were screened for the presence of norovirus RNA by the RGN RT-PCR assay. Results were compared with a reference method that included conventional RT-PCR and sequencing of a partial region of the 5'end of the norovirus ORF2 gene. A total of 259 (36.0%) of 719 specimens tested positive for norovirus by the reference method. The RGN RT-PCR assay detected norovirus in 244 (94%) of these 259 norovirus positive specimens. The sensitivity and specificity (95% confidence interval) of the RGN RT-PCR assay for detecting norovirus genogroup (G) I was 82.8% (63.5-93.5) and 99.1% (98.0-99.6) and for GII was 94.8% (90.8-97.2) and 98.6% (96.9-99.4), respectively. Seven specimens tested positive by the RGN-RT PCR that were negative by the reference method. The fifteen false negative samples were typed as GII.4 Sydney, GII.13, GI.3, GI.5, GI.2, GII.1, and GII.3 in the reference method. The RGN RT-PCR assay had a high sensitivity and specificity for the detection of norovirus in stool specimens from patients with sporadic AGE. Copyright © 2018. Published by Elsevier B.V.

Larger Stimuli Require Longer Processing Time for Perception.

PubMed

Kanai, Ryota; Dalmaijer, Edwin S; Sherman, Maxine T; Kawakita, Genji; Paffen, Chris L E

2017-05-01

The time it takes for a stimulus to reach awareness is often assessed by measuring reaction times (RTs) or by a temporal order judgement (TOJ) task in which perceived timing is compared against a reference stimulus. Dissociations of RT and TOJ have been reported earlier in which increases in stimulus intensity such as luminance intensity results in a decrease of RT, whereas perceived perceptual latency in a TOJ task is affected to a lesser degree. Here, we report that a simple manipulation of stimulus size has stronger effects on perceptual latency measured by TOJ than on motor latency measured by RT tasks. When participants were asked to respond to the appearance of a simple stimulus such as a luminance blob, the perceptual latency measured against a standard reference stimulus was up to 40 ms longer for a larger stimulus. In other words, the smaller stimulus was perceived to occur earlier than the larger one. RT on the other hand was hardly affected by size. The TOJ results were further replicated in a simultaneity judgement task, suggesting that the effects of size are not due to TOJ-specific response biases but more likely reflect an effect on perceived timing.

Timing of cortical excitability changes during the reaction time of movements superimposed on tonic motor activity.

PubMed

Schneider, Cyril; Lavoie, Brigitte A; Barbeau, Hugues; Capaday, Charles

2004-12-01

Seated subjects were instructed to react to an auditory cue by simultaneously contracting the tibialis anterior (TA) muscle of each ankle isometrically. Focal transcranial magnetic stimulation of the leg area of the motor cortex (MCx) was used to determine the time course of changes in motor-evoked potential amplitude (MEP) during the reaction time (RT). In one condition the voluntary contraction was superimposed on tonic EMG activity maintained at 10% of maximal voluntary contraction. In the other condition the voluntary contraction was made starting from rest. MEPs in the TA contralateral to the stimulation coil were evoked at various times during the RT in each condition. These were compared to the control MEPs evoked during tonic voluntary activity or with the subject at rest. The RT was measured trial by trial from the EMG activity of the TA ipsilateral to the magnetic stimulus, taking into account the nearly constant time difference between the two sides. The MEPs became far greater than control MEPs during the RT (mean = 332%, SD = 44 %, of control MEPs, P < 0.001) without any measurable change in the background level of EMG activity. The onset of this facilitation occurred on average 12.80 ms (SD = 7.55 ms) before the RT. There was no difference in the onset of facilitation between the two conditions. Because MEPs were facilitated without a change in the background EMG activity, it is concluded that this facilitation is specifically due to an increase of MCx excitability just before voluntary muscle activation. This conclusion is further reinforced by the observation that MEPs evoked by near-threshold anodal stimuli to the MCx were not facilitated during the RT, in contrast to those evoked by near-threshold transcranial magnetic stimulation. However, several observations in the present and previous studies indicate that MEP amplitude may be more sensitive to alpha-motoneuron activity than to motor cortical neuron activity, an idea that has important methodological implications.

Applications of NASA and NOAA Satellite Observations by NASA's Short-term Prediction Research and Transition (SPoRT) Center in Response to Natural Disasters

NASA Technical Reports Server (NTRS)

Molthan, Andrew L.; Burks, Jason E.; McGrath, Kevin M.; Jedlovec, Gary J.

2012-01-01

NASA s Short-term Prediction Research and Transition (SPoRT) Center supports the transition of unique NASA and NOAA research activities to the operational weather forecasting community. SPoRT emphasizes real-time analysis and prediction out to 48 hours. SPoRT partners with NOAA s National Weather Service (NWS) Weather Forecast Offices (WFOs) and National Centers to improve current products, demonstrate future satellite capabilities and explore new data assimilation techniques. Recently, the SPoRT Center has been involved in several activities related to disaster response, in collaboration with NOAA s National Weather Service, NASA s Applied Sciences Disasters Program, and other partners.

Comparative lytic efficacy of rt-PA and ultrasound in porcine versus human clots.

PubMed

Huang, Shenwen; Shekhar, Himanshu; Holland, Christy K

2017-01-01

Porcine thrombi are employed routinely in preclinical models of ischemic stroke. In this study, we examined the differential lytic susceptibility of porcine and human whole blood clots with and without the use of microbubbles and ultrasound (US) as an adjuvant. An in vitro system equipped with time-lapse microscopy was used to evaluate recombinant tissue-plasminogen activator (rt-PA) lysis of porcine and human clots in the same species or cross species plasma. Human and porcine whole blood clots were treated with rt-PA and an echo contrast agent, Definity®, and exposed to intermittent 120 kHz US. The rt-PA lytic efficacy observed for porcine clots in porcine plasma was 22 times lower than for human clots in human plasma reported previously. Further, porcine clots did not exhibit increased lysis with adjuvant Definity® and US exposure. However, the rt-PA lytic susceptibility of the porcine clots in human plasma was similar to that of human clots in human plasma. Human clots perfused with porcine plasma did not respond to rt-PA, but adjuvant use of Definity® and US enhanced lysis. These results reveal considerable differences in lytic susceptibility of porcine clots and human clots to rt-PA. The use of porcine clot models to test new human thrombolytic therapies may necessitate modulation of coagulation and thrombolytic factors to reflect human hemostasis accurately.

Comparison of ELISA and dual stage real time RT-PCR to differentiate Sabin like and non-Sabin like poliovirus isolates.

PubMed

Kaundal, Nirmal; Sarkate, Purva; Prakash, Charu; Rishi, Narayan

2017-06-01

Environmental surveillance of polioviruses has been used as an important tool in monitoring circulation of wild polioviruses and/or Vaccine derived polioviruses in sewage samples. It is important to distinguish Sabin like isolates from non-Sabin like; ELISA & dual stage real time RT-PCR have been used for the same. Current study was carried out on sewage isolates to compare ELISA & RT-PCR with sequencing to distinguish Sabin like from non-Sabin like. Out of 468 sewage specimens, 91 (19.44%) were non-polio enteroviruses positive and 377 (80.56%) were polio positive by virus isolation method. A total of 488 polio virus isolates were detected by L20B and RD route which were further subjected to ELISA and RT-PCR. The results were compared with sequencing. On comparison, the specificity of ELISA was only 66.67% in spite of very low sensitivity (3.43%). The sensitivity of RT-PCR was 97.71% which makes it a good primary screening test for detection of non-Sabin like viruses. However, the specificity was only 33.33%. RT-PCR appears to be a sensitive tool for detecting non-Sabin like viruses however; the isolates which are non-Sabin like by RT-PCR may not necessarily be mutated viruses. ELISA cannot be used for differentiation of Sabin likes from non-Sabin likes due to low sensitivity.

Laboratory validation of two real-time RT-PCR methods with 5'-tailed primers for an enhanced detection of foot-and-mouth disease virus.

PubMed

Vandenbussche, Frank; Lefebvre, David J; De Leeuw, Ilse; Van Borm, Steven; De Clercq, Kris

2017-08-01

The 3D and 5UTR real-time RT-PCR assays (RT-qPCR) from Callahan et al. (2002) and Reid et al. (2002) are commonly used reference methods for the detection of foot-and-mouth disease virus (FMDV). For an optimal detection of FMDV in clinical samples, it is advised to use both assays simultaneously (King et al., 2006). Recently, Vandenbussche et al. (2016) showed that the addition of 5'-tails to the FMDV-specific primers enhances the detection of FMDV in both the 3D and the 5UTR RT-qPCR assay. To validate the 3D and 5UTR RT-qPCR assays with 5'-tailed primers for diagnostic purposes, both assays were run in parallel in a triplex one-step RT-qPCR protocol with beta-actin as an internal control and synthetic RNA as an external control. We obtained low limits of detection and high linearity's, high repeatability and reproducibility, near 100% analytical specificity and >99% diagnostic accuracy for both assays. It was concluded that the 3D and 5UTR RT-qPCR assays with 5'-tailed primers are particularly suited for the detection of FMDV as well as to exclude the presence of FMDV. Copyright © 2017 Elsevier B.V. All rights reserved.

Reduced Toxicity With Intensity Modulated Radiation Therapy (IMRT) for Desmoplastic Small Round Cell Tumor (DSRCT): An Update on the Whole Abdominopelvic Radiation Therapy (WAP-RT) Experience

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

Desai, Neil B.; Stein, Nicholas F.; LaQuaglia, Michael P.

2013-01-01

Purpose: Desmoplastic small round cell tumor (DSRCT) is a rare malignancy typically involving the peritoneum in young men. Whole abdominopelvic radiation therapy (WAP-RT) using conventional 2-dimensional (2D) radiation therapy (RT) is used to address local recurrence but has been limited by toxicity. Our objectives were to assess the benefit of intensity modulated radiation therapy (IMRT) on toxicity and to update the largest series on radiation for DSRCT. Methods and Materials: The records of 31 patients with DSRCT treated with WAP-RT (22 with 2D-RT and 9 with IMRT) between 1992 and 2011 were retrospectively reviewed. All received multi-agent chemotherapy and maximalmore » surgical debulking followed by 30 Gy of WAP-RT. A further focal boost of 12 to 24 Gy was used in 12 cases. Boost RT and autologous stem cell transplantation were nearly exclusive to patients treated with 2D-RT. Toxicities were assessed with the Common Terminology Criteria for Adverse Events. Dosimetric analysis compared IMRT and simulated 2D-RT dose distributions. Results: Of 31 patients, 30 completed WAP-RT, with a median follow-up after RT of 19 months. Acute toxicity was reduced with IMRT versus 2D-RT: P=.04 for gastrointestinal toxicity of grade 2 or higher (33% vs 77%); P=.02 for grade 4 hematologic toxicity (33% vs 86%); P=.01 for rates of granulocyte colony-stimulating factor; and P=.04 for rates of platelet transfusion. Post treatment red blood cell and platelet transfusion rates were also reduced (P=.01). IMRT improved target homogeneity ([D05-D95]/D05 of 21% vs 46%) and resulted in a 21% mean bone dose reduction. Small bowel obstruction was the most common late toxicity (23% overall). Updated 3-year overall survival and progression-free survival rates were 50% and 24%, respectively. Overall survival was associated with distant metastasis at diagnosis on multivariate analysis. Most failures remained intraperitoneal (88%). Conclusions: IMRT for consolidative WAP-RT in DSRCT improves hematologic toxicity in particular. Although the long-term efficacy of current treatment options remains disappointing, the improved therapeutic index of IMRT may aid in generalizing its use and allowing the addition of novel approaches such as intraperitoneal immunotherapy.« less

Managing Contention and Timing Constraints in a Real-Time Database System

DTIC Science & Technology

1995-01-01

In order to realize many of these goals, StarBase is constructed on top of RT-Mach, a real - time operating system developed at Carnegie Mellon...University [ll]. StarBase differs from previous RT-DBMS work [l, 2, 31 in that a) it relies on a real - time operating system which provides priority...CPU and resource scheduling pro- vided by tlhe underlying real - time operating system . Issues of data contention are dealt with by use of a priority

Calculation of upper esophageal sphincter restitution time from high resolution manometry data using machine learning.

PubMed

Jungheim, Michael; Busche, Andre; Miller, Simone; Schilling, Nicolas; Schmidt-Thieme, Lars; Ptok, Martin

2016-10-15

After swallowing, the upper esophageal sphincter (UES) needs a certain amount of time to return from maximum pressure to the resting condition. Disturbances of sphincter function not only during the swallowing process but also in this phase of pressure restitution may lead to globus sensation or dysphagia. Since UES pressures do not decrease in a linear or asymptotic manner, it is difficult to determine the exact time when the resting pressure is reached, even when using high resolution manometry (HRM). To overcome this problem a Machine Learning model was established to objectively determine the UES restitution time (RT) and moreover to collect physiological data on sphincter function after swallowing. HRM-data of 15 healthy participants performing 10 swallows each were included. After manual annotation of the RT interval by two swallowing experts, data were transferred to the Machine Learning model, which applied a sequence labeling modeling approach based on logistic regression to learn and objectivize the characteristics of all swallows. Individually computed RT values were then compared with the annotated values. Estimates of the RT were generated by the Machine Learning model for all 150 swallows. When annotated by swallowing experts mean RT of 11.16s±5.7 (SD) and 10.04s±5.74 were determined respectively, compared to model-generated values from 8.91s±3.71 to 10.87s±4.68 depending on model selection. The correlation score for the annotated RT of both examiners was 0.76 and 0.63 to 0.68 for comparison of model predicted values. Restitution time represents an important physiologic swallowing parameter not previously considered in HRM-studies of the UES, especially since disturbances of UES restitution may increase the risk of aspiration. The data presented here show that it takes approximately 9 to 11s for the UES to come to rest after swallowing. Based on maximal RT values, we demonstrate that an interval of 25-30s in between swallows is necessary until the next swallow is initiated. This should be considered in any further HRM-studies designed to evaluate the characteristics of individual swallows. The calculation model enables a quick and reproducible determination of the time it takes for the UES to come to rest after swallowing (RT). The results of the calculation are partially independent of the input of the investigator. Adding more swallows and integrating additional parameters will improve the Machine Leaning model in the future. By applying similar models to other swallowing parameters of the pharynx and UES, such as the relaxation time of the UES or the activity time during swallowing, a complete automatic evaluation of HRM-data of a swallow should be possible. Copyright © 2016 Elsevier Inc. All rights reserved.

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

Vern-Gross, Tamara Z.; Shivnani, Anand T., E-mail: Anand.Shivnani@usoncology.com; Chen, Ke

Purpose: The benefit of adjuvant radiotherapy (RT) after surgical resection for extrahepatic cholangiocarcinoma has not been clearly established. We analyzed survival outcomes of patients with resected extrahepatic cholangiocarcinoma and examined the effect of adjuvant RT. Methods and Materials: Data were obtained from the Surveillance, Epidemiology, and End Results (SEER) program between 1973 and 2003. The primary endpoint was the overall survival time. Cox regression analysis was used to perform univariate and multivariate analyses of the following clinical variables: age, year of diagnosis, histologic grade, localized (Stage T1-T2) vs. regional (Stage T3 or greater and/or node positive) stage, gender, race, andmore » the use of adjuvant RT after surgical resection. Results: The records for 2,332 patients were obtained. Patients with previous malignancy, distant disease, incomplete or conflicting records, atypical histologic features, and those treated with preoperative/intraoperative RT were excluded. Of the remaining 1,491 patients eligible for analysis, 473 (32%) had undergone adjuvant RT. After a median follow-up of 27 months (among surviving patients), the median overall survival time for the entire cohort was 20 months. Patients with localized and regional disease had a median survival time of 33 and 18 months, respectively (p < .001). The addition of adjuvant RT was not associated with an improvement in overall or cause-specific survival for patients with local or regional disease. Conclusion: Patients with localized disease had significantly better overall survival than those with regional disease. Adjuvant RT was not associated with an improvement in long-term overall survival in patients with resected extrahepatic bile duct cancer. Key data, including margin status and the use of combined chemotherapy, was not available through the SEER database.« less

Outcomes of malignant tumors of the lacrimal apparatus: the University of Texas MD Anderson Cancer Center experience.

PubMed

Skinner, Heath D; Garden, Adam S; Rosenthal, David I; Ang, K Kian; Morrison, William H; Esmaeli, Bita; Pinnix, Chelsea C; Frank, Steven J

2011-06-15

Malignant epithelial neoplasms of the lacrimal apparatus are rare and are typically treated with surgery and occasionally adjuvant radiation therapy (RT). The purpose of this study was to assess treatment outcomes by type of surgery (orbital exenteration vs eye-sparing surgery) and clarify the role of adjuvant RT for this rare disease. Forty-six patients with malignant epithelial neoplasms of the lacrimal apparatus were treated at a single institution from 1945 through 2008. Twenty-seven patients (59%) were treated with orbital exenteration and 19 (41%) with eye-sparing surgery; 64% of the orbital exenteration group and 83% of the eye-sparing surgery group also received adjuvant RT (median dose, 60 grays). Median follow-up time for all patients was 38 months (range, 3-460 months). For the orbital exenteration and eye-sparing surgery groups, the 5-year overall survival (OS) rates were 59% and 62%, and the 5-year disease-free survival (DFS) rates were 49% and 39%, respectively (P = .56, P = .35). Tumor status (T1-2 vs T3-4) was associated with OS (P = .02), and tumor size (<3.5 vs >3.5 cm) with DFS (P = .015). Median time to locoregional recurrence was 85 months for orbital exenteration, and 123 months for eye-sparing surgery. All patients who did not receive RT experienced local recurrence, and RT extended time to locoregional recurrence (median 460 vs 30 months, P = .009). Seven grade ≥3 complications were experienced after adjuvant RT. For appropriately selected patients, an eye-sparing surgery for lacrimal apparatus tumors can achieve similar survival outcomes to those in patients treated with an orbital exenteration. Adjuvant RT should be considered for all patients presenting with these rare tumors. Copyright © 2011 American Cancer Society.

Atomoxetine could improve intra-individual variability in drug-naïve adults with attention-deficit/hyperactivity disorder comparably with methylphenidate: A head-to-head randomized clinical trial.

PubMed

Ni, Hsing-Chang; Hwang Gu, Shoou-Lian; Lin, Hsiang-Yuan; Lin, Yu-Ju; Yang, Li-Kuang; Huang, Hui-Chun; Gau, Susan Shur-Fen

2016-05-01

Intra-individual variability in reaction time (IIV-RT) is common in individuals with attention-deficit/hyperactivity disorder (ADHD). It can be improved by stimulants. However, the effects of atomoxetine on IIV-RT are inconclusive. We aimed to investigate the effects of atomoxetine on IIV-RT, and directly compared its efficacy with methylphenidate in adults with ADHD. An 8-10 week, open-label, head-to-head, randomized clinical trial was conducted in 52 drug-naïve adults with ADHD, who were randomly assigned to two treatment groups: immediate-release methylphenidate (n=26) thrice daily (10-20 mg per dose) and atomoxetine once daily (n=26) (0.5-1.2 mg/kg/day). IIV-RT, derived from the Conners' continuous performance test (CCPT), was represented by the Gaussian (reaction time standard error, RTSE) and ex-Gaussian models (sigma and tau). Other neuropsychological functions, including response errors and mean of reaction time, were also measured. Participants received CCPT assessments at baseline and week 8-10 (60.4±6.3 days). We found comparable improvements in performances of CCPT between the immediate-release methylphenidate- and atomoxetine-treated groups. Both medications significantly improved IIV-RT in terms of reducing tau values with comparable efficacy. In addition, both medications significantly improved inhibitory control by reducing commission errors. Our results provide evidence to support that atomoxetine could improve IIV-RT and inhibitory control, of comparable efficacy with immediate-release methylphenidate, in drug-naïve adults with ADHD. Shared and unique mechanisms underpinning these medication effects on IIV-RT awaits further investigation. © The Author(s) 2016.

Evaluation of Two Lyophilized Molecular Assays to Rapidly Detect Foot-and-Mouth Disease Virus Directly from Clinical Samples in Field Settings.

PubMed

Howson, E L A; Armson, B; Madi, M; Kasanga, C J; Kandusi, S; Sallu, R; Chepkwony, E; Siddle, A; Martin, P; Wood, J; Mioulet, V; King, D P; Lembo, T; Cleaveland, S; Fowler, V L

2017-06-01

Accurate, timely diagnosis is essential for the control, monitoring and eradication of foot-and-mouth disease (FMD). Clinical samples from suspect cases are normally tested at reference laboratories. However, transport of samples to these centralized facilities can be a lengthy process that can impose delays on critical decision making. These concerns have motivated work to evaluate simple-to-use technologies, including molecular-based diagnostic platforms, that can be deployed closer to suspect cases of FMD. In this context, FMD virus (FMDV)-specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) and real-time RT-PCR (rRT-PCR) assays, compatible with simple sample preparation methods and in situ visualization, have been developed which share equivalent analytical sensitivity with laboratory-based rRT-PCR. However, the lack of robust 'ready-to-use kits' that utilize stabilized reagents limits the deployment of these tests into field settings. To address this gap, this study describes the performance of lyophilized rRT-PCR and RT-LAMP assays to detect FMDV. Both of these assays are compatible with the use of fluorescence to monitor amplification in real-time, and for the RT-LAMP assays end point detection could also be achieved using molecular lateral flow devices. Lyophilization of reagents did not adversely affect the performance of the assays. Importantly, when these assays were deployed into challenging laboratory and field settings within East Africa they proved to be reliable in their ability to detect FMDV in a range of clinical samples from acutely infected as well as convalescent cattle. These data support the use of highly sensitive molecular assays into field settings for simple and rapid detection of FMDV. © 2015 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Characterization of the collagen component of cartilage repair tissue of the talus with quantitative MRI: comparison of T2 relaxation time measurements with a diffusion-weighted double-echo steady-state sequence (dwDESS).

PubMed

Kretzschmar, M; Bieri, O; Miska, M; Wiewiorski, M; Hainc, N; Valderrabano, V; Studler, U

2015-04-01

The purpose of this study was to characterize the collagen component of repair tissue (RT) of the talus after autologous matrix-induced chondrogenesis (AMIC) using quantitative T2 and diffusion-weighted imaging. Mean T2 values and diffusion coefficients of AMIC-RT and normal cartilage of the talus of 25 patients with posttraumatic osteochondral lesions and AMIC repair were compared in a cross-sectional design using partially spoiled steady-state free precession (pSSFP) for T2 quantification, and diffusion-weighted double-echo steady-state (dwDESS) for diffusion measurement. RT and cartilage were graded with modified Noyes and MOCART scores on morphological sequences. An association between follow-up interval and quantitative MRI measures was assessed using multivariate regression, after stratifying the cohort according to time interval between surgery and MRI. Mean T2 of the AMIC-RT and cartilage were 43.1 ms and 39.1 ms, respectively (p = 0.26). Mean diffusivity of the RT (1.76 μm(2)/ms) was significantly higher compared to normal cartilage (1.46 μm(2)/ms) (p = 0.0092). No correlation was found between morphological and quantitative parameters. RT diffusivity was lowest in the subgroup with follow-up >28 months (p = 0.027). Compared to T2-mapping, dwDESS demonstrated greater sensitivity in detecting differences in the collagen matrix between AMIC-RT and cartilage. Decreased diffusivity in patients with longer follow-up times may indicate an increased matrix organization of RT. • MRI is used to assess morphology of the repair tissue during follow-up. • Quantitative MRI allows an estimation of biochemical properties of the repair tissue. • Differences between repair tissue and cartilage were more significant with dwDESS than T2 mapping.

Combined Effects of Lignosus rhinocerotis Supplementation and Resistance Training on Isokinetic Muscular Strength and Power, Anaerobic and Aerobic Fitness Level, and Immune Parameters in Young Males.

PubMed

Chen, Chee Keong; Hamdan, Nor Faeiza; Ooi, Foong Kiew; Wan Abd Hamid, Wan Zuraida

2016-01-01

This study investigated the effects of Lignosus rhinocerotis (LRS) supplementation and resistance training (RT) on isokinetic muscular strength and power, anaerobic and aerobic fitness, and immune parameters in young males. Participants were randomly assigned to four groups: Control (C), LRS, RT, and combined RT-LRS (RT-LRS). Participants in the LRS and RT-LRS groups consumed 500 mg of LRS daily for 8 weeks. RT was conducted 3 times/week for 8 weeks for participants in the RT and RT-LRS groups. The following parameters were measured before and after the intervention period: Anthropometric data, isokinetic muscular strength and power, and anaerobic and aerobic fitness. Blood samples were also collected to determine immune parameters. Isokinetic muscular strength and power were increased ( P < 0.05) in participants of both RT and RT-LRS groups. RT-LRS group had shown increases ( P < 0.05) in shoulder extension peak torque, shoulder flexion and extension average power, knee flexion peak torque, and knee flexion and extension average power. There were also increases ( P < 0.05) in anaerobic power and capacity and aerobic fitness in this group. Similarly, RT group had increases ( P < 0.05) in shoulder flexion average power, knee flexion and extension peak torque, and knee flexion and extension average power. In addition, increases ( P < 0.05) in anaerobic power and capacity, aerobic fitness, T lymphocytes (CD3 and CD4), and B lymphocytes (CD19) counts were observed in the RT group. RT elicited increased isokinetic muscular strength and power, anaerobic and aerobic fitness, and immune parameters among young males. However, supplementation with LRS during RT did not provide additive benefits.

Combined Effects of Lignosus rhinocerotis Supplementation and Resistance Training on Isokinetic Muscular Strength and Power, Anaerobic and Aerobic Fitness Level, and Immune Parameters in Young Males

PubMed Central

Chen, Chee Keong; Hamdan, Nor Faeiza; Ooi, Foong Kiew; Wan Abd Hamid, Wan Zuraida

2016-01-01

Background: This study investigated the effects of Lignosus rhinocerotis (LRS) supplementation and resistance training (RT) on isokinetic muscular strength and power, anaerobic and aerobic fitness, and immune parameters in young males. Methods: Participants were randomly assigned to four groups: Control (C), LRS, RT, and combined RT-LRS (RT-LRS). Participants in the LRS and RT-LRS groups consumed 500 mg of LRS daily for 8 weeks. RT was conducted 3 times/week for 8 weeks for participants in the RT and RT-LRS groups. The following parameters were measured before and after the intervention period: Anthropometric data, isokinetic muscular strength and power, and anaerobic and aerobic fitness. Blood samples were also collected to determine immune parameters. Results: Isokinetic muscular strength and power were increased (P < 0.05) in participants of both RT and RT-LRS groups. RT-LRS group had shown increases (P < 0.05) in shoulder extension peak torque, shoulder flexion and extension average power, knee flexion peak torque, and knee flexion and extension average power. There were also increases (P < 0.05) in anaerobic power and capacity and aerobic fitness in this group. Similarly, RT group had increases (P < 0.05) in shoulder flexion average power, knee flexion and extension peak torque, and knee flexion and extension average power. In addition, increases (P < 0.05) in anaerobic power and capacity, aerobic fitness, T lymphocytes (CD3 and CD4), and B lymphocytes (CD19) counts were observed in the RT group. Conclusions: RT elicited increased isokinetic muscular strength and power, anaerobic and aerobic fitness, and immune parameters among young males. However, supplementation with LRS during RT did not provide additive benefits. PMID:27833721

Breaking Continuous Flash Suppression: A New Measure of Unconscious Processing during Interocular Suppression?

PubMed Central

Stein, Timo; Hebart, Martin N.; Sterzer, Philipp

2011-01-01

Until recently, it has been thought that under interocular suppression high-level visual processing is strongly inhibited if not abolished. With the development of continuous flash suppression (CFS), a variant of binocular rivalry, this notion has now been challenged by a number of reports showing that even high-level aspects of visual stimuli, such as familiarity, affect the time stimuli need to overcome CFS and emerge into awareness. In this “breaking continuous flash suppression” (b-CFS) paradigm, differential unconscious processing during suppression is inferred when (a) speeded detection responses to initially invisible stimuli differ, and (b) no comparable differences are found in non-rivalrous control conditions supposed to measure non-specific threshold differences between stimuli. The aim of the present study was to critically evaluate these assumptions. In six experiments we compared the detection of upright and inverted faces. We found that not only under CFS, but also in control conditions upright faces were detected faster and more accurately than inverted faces, although the effect was larger during CFS. However, reaction time (RT) distributions indicated critical differences between the CFS and the control condition. When RT distributions were matched, similar effect sizes were obtained in both conditions. Moreover, subjective ratings revealed that CFS and control conditions are not perceptually comparable. These findings cast doubt on the usefulness of non-rivalrous control conditions to rule out non-specific threshold differences as a cause of shorter detection latencies during CFS. Thus, at least in its present form, the b-CFS paradigm cannot provide unequivocal evidence for unconscious processing under interocular suppression. Nevertheless, our findings also demonstrate that the b-CFS paradigm can be fruitfully applied as a highly sensitive device to probe differences between stimuli in their potency to gain access to awareness. PMID:22194718

Immunolocalization and distribution of functional temperature-sensitive TRP channels in salivary glands.

PubMed

Sobhan, Ubaidus; Sato, Masaki; Shinomiya, Takashi; Okubo, Migiwa; Tsumura, Maki; Muramatsu, Takashi; Kawaguchi, Mitsuru; Tazaki, Masakazu; Shibukawa, Yoshiyuki

2013-11-01

Transient receptor potential (TRP) cation channels are unique cellular sensors involved in multiple cellular functions. Their role in salivary secretion remains to be elucidated. The expression and localization of temperature-sensitive TRP channels in salivary (submandibular, sublingual and parotid) glands were analyzed by immunohistochemistry and quantitative real-time reverse transcription plus the polymerase chain reaction (RT-PCR). The effects of various TRP channel agonists on carbachol (CCh)-induced salivary secretion in the submandibular gland and on the intracellular Ca(2+) concentration ([Ca(2+)]i) in a submandibular epithelial cell line were also investigated. Immunohistochemistry revealed the expression of TRP-melastatin subfamily member 8 (TRPM8) and TRP-ankyrin subfamily member 1 (TRPA1) in myoepithelial, acinar and ductal cells in the sublingual, submandibular and parotid glands. In addition, TRP-vanilloid subfamily member 1 (TRPV1), TRPV3 and TRPV4 were also expressed in myoepithelial, acinar and ductal cells in all three types of gland. Quantitative real-time RT-PCR results demonstrated the mRNA expression of TRPV1, TRPV3, TRPV4, TRPM8 and TRPA1 in acinar and ductal cells in these salivary glands. Perfusion of the entire submandibular gland with the TRPV1 agonist capsaicin (1 μM) via the submandibular artery significantly increased CCh-induced salivation, whereas perfusion with TRPM8 and TRPA1 agonists (0.5 μM WS12 and 100 μM allyl isothiocyanate) decreased it. Application of agonists for each of the thermosensitive TRP channels increased [Ca(2+)]i in a submandibular epithelial cell line. These results indicate that temperature-sensitive TRP channels are localized and distributed in acinar, ductal and myoepithelial cells in salivary glands and that they play a functional role in the regulation and/or modulation of salivary secretion.

Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot.

PubMed

Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen; Ma, Yan; Fang, Qun; Yao, Bo

2015-04-01

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis.

Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot

PubMed Central

Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen; Ma, Yan; Fang, Qun; Yao, Bo

2015-01-01

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis. PMID:25828383

Individual Differences in Visual Word Recognition: Insights from the English Lexicon Project

PubMed Central

Yap, Melvin J.; Balota, David A.; Sibley, Daragh E.; Ratcliff, Roger

2011-01-01

Empirical work and models of visual word recognition have traditionally focused on group-level performance. Despite the emphasis on the prototypical reader, there is clear evidence that variation in reading skill modulates word recognition performance. In the present study, we examined differences between individuals who contributed to the English Lexicon Project (http://elexicon.wustl.edu), an online behavioral database containing nearly four million word recognition (speeded pronunciation and lexical decision) trials from over 1,200 participants. We observed considerable within- and between-session reliability across distinct sets of items, in terms of overall mean response time (RT), RT distributional characteristics, diffusion model parameters (Ratcliff, Gomez, & McKoon, 2004), and sensitivity to underlying lexical dimensions. This indicates reliably detectable individual differences in word recognition performance. In addition, higher vocabulary knowledge was associated with faster, more accurate word recognition performance, attenuated sensitivity to stimuli characteristics, and more efficient accumulation of information. Finally, in contrast to suggestions in the literature, we did not find evidence that individuals were trading-off in their utilization of lexical and nonlexical information. PMID:21728459

Second cancers in patients with Chronic Lymphocytic Leukemia who received frontline FCR therapy – Distribution and clinical outcomes

PubMed Central

Benjamini, Ohad; Jain, Preetesh; Trinh, Long; Qiao, Wei; Strom, Sara S.; Lerner, Susan; Wang, Xuemei; Burger, Jan; Ferrajoli, Alessandra; Kantarjian, Hagop; O’Brien, Susan; Wierda, William; Estrov, Zeev; Keating, Michael

2015-01-01

Patients with Chronic Lymphocytic Leukemia (CLL) are known to have an increased incidence of second cancers, but the contribution of commonly used frontline therapies to the incidence of second cancers is unclear. We report on the characteristics, incidence, outcomes and factors associated with second cancers in 234 patients receiving Fludarabine, Cyclophosphamide, and Rituximab (FCR) based regimens in the frontline setting. The risk of second cancers was 2.38 times higher than the expected risk in the general population. Ninety three patients (40%) had other cancers before and 66 patients (28%) after FCR. The rates of t-AML/MDS (5.1%) and Richter’s transformation (RT) (9%) were high while solid tumors were not increased. Overall survival of patients with second cancers after frontline FCR was shorter (median of 4.5 years) compared to patients with and without prior cancers. Second cancer risk after frontline FCR is mainly due to high rates of t-AML/MDS and RT and as speculated the survival of affected patients is shorter. PMID:25308294

Time interval between primary radiotherapy and salvage laryngectomy: a predictor of pharyngocutaneous fistula formation.

PubMed

Scotton, William J; Nixon, I J; Pezier, T F; Cobb, R; Joshi, A; Urbano, T Guerrero; Oakley, R; Jeannon, J P; Simo, R S

2014-08-01

Salvage laryngectomy (SL) is associated with high levels of morbidity. Rates of pharyngocutaneous fistulae (PCF) are as high as 35 % in some series. Patients at highest risk of such complications may be candidates for altered surgical management in terms of additional tissue transfer, or delayed tracheoesophageal puncture. This study investigates the relationship between the time from primary radiotherapy (RT) to salvage surgery and the development of PCF. 26 consecutive patients who underwent SL between 2000 and 2010 were identified from our institutional database. Demographic, staging, treatment and complication data were collected. Subgroup analysis was performed using the Student's t test or Mann-Whitney U test for continuous variables and either Chi-squared test or Fisher's Exact test for categorical variables. 26 patients underwent SL between October 2003 and July 2010. Of these, 15 (58 %) developed a PCF. On analysis of the time between pre-operative RT and surgery, a significant difference was seen, with a mean time of 19.5 months in those who developed a PCF versus 47.0 months in those who did not (p = 0.02). Patient characteristics, treatment, and pathology results were comparable between the two groups. There was no significant difference in distribution of the other covariates between the PCF and non-PCF groups. We reported a high rate of PCF and identified an association between PCF and a short time from primary treatment to salvage surgery. Identifying factors associated with higher rates of post-operative morbidity allows surgeons to adapt surgical planning in an attempt to minimize rates of PCF.

Real time hardware implementation of power converters for grid integration of distributed generation and STATCOM systems

NASA Astrophysics Data System (ADS)

Jaithwa, Ishan

Deployment of smart grid technologies is accelerating. Smart grid enables bidirectional flows of energy and energy-related communications. The future electricity grid will look very different from today's power system. Large variable renewable energy sources will provide a greater portion of electricity, small DERs and energy storage systems will become more common, and utilities will operate many different kinds of energy efficiency. All of these changes will add complexity to the grid and require operators to be able to respond to fast dynamic changes to maintain system stability and security. This thesis investigates advanced control technology for grid integration of renewable energy sources and STATCOM systems by verifying them on real time hardware experiments using two different systems: d SPACE and OPAL RT. Three controls: conventional, direct vector control and the intelligent Neural network control were first simulated using Matlab to check the stability and safety of the system and were then implemented on real time hardware using the d SPACE and OPAL RT systems. The thesis then shows how dynamic-programming (DP) methods employed to train the neural networks are better than any other controllers where, an optimal control strategy is developed to ensure effective power delivery and to improve system stability. Through real time hardware implementation it is proved that the neural vector control approach produces the fastest response time, low overshoot, and, the best performance compared to the conventional standard vector control method and DCC vector control technique. Finally the entrepreneurial approach taken to drive the technologies from the lab to market via ORANGE ELECTRIC is discussed in brief.

Individual differences in attention influence perceptual decision making.

PubMed

Nunez, Michael D; Srinivasan, Ramesh; Vandekerckhove, Joachim

2015-01-01

Sequential sampling decision-making models have been successful in accounting for reaction time (RT) and accuracy data in two-alternative forced choice tasks. These models have been used to describe the behavior of populations of participants, and explanatory structures have been proposed to account for between individual variability in model parameters. In this study we show that individual differences in behavior from a novel perceptual decision making task can be attributed to (1) differences in evidence accumulation rates, (2) differences in variability of evidence accumulation within trials, and (3) differences in non-decision times across individuals. Using electroencephalography (EEG), we demonstrate that these differences in cognitive variables, in turn, can be explained by attentional differences as measured by phase-locking of steady-state visual evoked potential (SSVEP) responses to the signal and noise components of the visual stimulus. Parameters of a cognitive model (a diffusion model) were obtained from accuracy and RT distributions and related to phase-locking indices (PLIs) of SSVEPs with a single step in a hierarchical Bayesian framework. Participants who were able to suppress the SSVEP response to visual noise in high frequency bands were able to accumulate correct evidence faster and had shorter non-decision times (preprocessing or motor response times), leading to more accurate responses and faster response times. We show that the combination of cognitive modeling and neural data in a hierarchical Bayesian framework relates physiological processes to the cognitive processes of participants, and that a model with a new (out-of-sample) participant's neural data can predict that participant's behavior more accurately than models without physiological data.

Direct sequencing of hepatitis A virus and norovirus RT-PCR products from environmentally contaminated oyster using M13-tailed primers.

PubMed

Williams-Woods, Jacquelina; González-Escalona, Narjol; Burkhardt, William

2011-12-01

Human norovirus (HuNoV) and hepatitis A (HAV) are recognized as leading causes of non-bacterial foodborne associated illnesses in the United States. DNA sequencing is generally considered the standard for accurate viral genotyping in support of epidemiological investigations. Due to the genetic diversity of noroviruses (NoV), degenerate primer sets are often used in conventional reverse transcription (RT) PCR and real-time RT-quantitative PCR (RT-qPCR) for the detection of these viruses and cDNA fragments are generally cloned prior to sequencing. HAV detection methods that are sensitive and specific for real-time RT-qPCR yields small fragments sizes of 89-150bp, which can be difficult to sequence. In order to overcome these obstacles, norovirus and HAV primers were tailed with M13 forward and reverse primers. This modification increases the sequenced product size and allows for direct sequencing of the amplicons utilizing complementary M13 primers. HuNoV and HAV cDNA products from environmentally contaminated oysters were analyzed using this method. Alignments of the sequenced samples revealed ≥95% nucleotide identities. Tailing NoV and HAV primers with M13 sequence increases the cDNA product size, offers an alternative to cloning, and allows for rapid, accurate and direct sequencing of cDNA products produced by conventional or real time RT-qPCR assays. Published by Elsevier B.V.

Evaluation of NK Cell Function by Flowcytometric Measurement and Impedance Based Assay Using Real-Time Cell Electronic Sensing System

PubMed Central

Park, Ki-Hyun; Park, Hyesun; Kim, Myungshin; Kim, Yonggoo; Han, Kyungja; Oh, Eun-Jee

2013-01-01

Although real-time cell electronic sensing (RT-CES) system-based natural killer (NK) cytotoxicity has been introduced, it has not been evaluated using human blood samples. In present study, we measured flowcytometry based assay (FCA) and RT-CES based NK cytotoxicity and analyzed degranulation activity (CD107a) and cytokine production. In 98 healthy individuals, FCA with peripheral blood mononuclear cells (PBMCs) at effector to target (E/T) ratio of 32 revealed 46.5 ± 2.6% cytolysis of K562 cells, and 23.5 ± 1.1% of NK cells showed increased degranulation. In RT-CES system, adherent NIH3T3 target cells were resistant to basal killing by PBMC or NK cells. NK cell activation by adding IL-2 demonstrated real-time dynamic killing activity, and lymphokine-activated PBMC (E/T ratio of 32) from 15 individuals showed 59.1 ± 6.2% cytotoxicity results after 4 hours incubation in RT-CES system. However, there was no significant correlation between FCA and RT-CES cytotoxicity. After K562 target cell stimulation, PBMC produced profound proinflammatory and immunoregulatory cytokines/chemokines including IL-2, IL-8, IL-10, MIP-1α β, IFN-γ, and TNF-α, and cytokine/chemokine secretion was related to flowcytometry-based NK cytotoxicity. These data suggest that RT-CES and FCA differ in sensitivity, applicability and providing information, and further investigations are necessary in variable clinical conditions. PMID:24236291

Evaluation of NK cell function by flowcytometric measurement and impedance based assay using real-time cell electronic sensing system.

PubMed

Park, Ki-Hyun; Park, Hyesun; Kim, Myungshin; Kim, Yonggoo; Han, Kyungja; Oh, Eun-Jee

2013-01-01

Although real-time cell electronic sensing (RT-CES) system-based natural killer (NK) cytotoxicity has been introduced, it has not been evaluated using human blood samples. In present study, we measured flowcytometry based assay (FCA) and RT-CES based NK cytotoxicity and analyzed degranulation activity (CD107a) and cytokine production. In 98 healthy individuals, FCA with peripheral blood mononuclear cells (PBMCs) at effector to target (E/T) ratio of 32 revealed 46.5 ± 2.6% cytolysis of K562 cells, and 23.5 ± 1.1% of NK cells showed increased degranulation. In RT-CES system, adherent NIH3T3 target cells were resistant to basal killing by PBMC or NK cells. NK cell activation by adding IL-2 demonstrated real-time dynamic killing activity, and lymphokine-activated PBMC (E/T ratio of 32) from 15 individuals showed 59.1 ± 6.2% cytotoxicity results after 4 hours incubation in RT-CES system. However, there was no significant correlation between FCA and RT-CES cytotoxicity. After K562 target cell stimulation, PBMC produced profound proinflammatory and immunoregulatory cytokines/chemokines including IL-2, IL-8, IL-10, MIP-1 α β , IFN- γ , and TNF- α , and cytokine/chemokine secretion was related to flowcytometry-based NK cytotoxicity. These data suggest that RT-CES and FCA differ in sensitivity, applicability and providing information, and further investigations are necessary in variable clinical conditions.

Expression of gibberellin 3 beta-hydroxylase gene in a gravi-response mutant, weeping Japanese flowering cherry

NASA Technical Reports Server (NTRS)

Sugano, Mami; Nakagawa, Yuriko; Nyunoya, Hiroshi; Nakamura, Teruko

2004-01-01

Expressions of the gibberellin biosynthesis gene were investigated in a normal upright type and a gravi-response mutant, a weeping type of Japanese flowering cherry (Prunus spachiana), that is unable to support its own weight and elongates downward. A segment of the gibberellin 3 beta-hydroxylase cDNA of Prunus spachiana (Ps3ox), which is responsible for active gibberellin synthesis, was amplified by using real-time RT-PCR. The content of Ps3ox mRNA in the weeping type was much greater than that in the upright type, while the endogenous gibberellin level was much higher in the elongating zone of the weeping type. These results suggest that the amount and distribution of synthesized gibberellin regulate secondary xylem formation, and the unbalanced distribution of gibberellin affects the gravi-response of the Prunus tree.

Time-extended local rtPA infiltration for acutely thrombosed hemodialysis fistulas.

PubMed

Regus, Susanne; Lang, Werner; Heinz, Marco; Rother, Ulrich; Meyer, Alexander; Almási-Sperling, Veronika; Uder, Michael; Schmid, Axel

2018-01-01

This study describes results of a modified local thrombolysis technique for acutely thrombosed hemodialysis (HD) arteriovenous fistulas (AVF), which is characterized by prolonged recombinant tissue plasminogen activator (rtPA) local exposure times. Contrary to the standard lyse- and- wait (L&W) technique with local reaction times of 20-40 minutes, the modified protocol allows timing of challenging angioplasty maneuvers to the next regular working day. From February 2009 to April 2014, 84 patients on HD presented with 152 acutely thrombosed AVF. They proceeded to local thrombolysis including a single shot infiltration of rtPA, local reaction time up to 40 hours and finally percutaneous stenosis angioplasty. Success rates, major adverse events and need for temporary catheter placements (TCP) were retrospectively analyzed. The local thrombolysis time after single shot infiltration was 18.6 ± 6.2 (range 2-40) hours. Mean rtPA- dosage was 2.7 mg ± 1.2. The overall success rate was 89.5% and the major complication rate was 3.3%, whereas TCP was necessary in 12.5%. The PP/SP at 1, 3, 6, 12, 18, and 24 month were 86% ± 3%/95% ± 2%, 68% ± 4%/92% ± 2%, 43% ± 4%/90% ± 2%, 28% ± 4%/82% ± 3%, 12% ± 3%/82% ± 3%, 7% ± 2%/63% ± 4%, respectively. The modified L&W technique with prolonged local rtPA reaction times is a safe and effective declotting procedure. The need for TCP was not increased and therefore comparable to the standard technique. © 2017 International Society for Hemodialysis.

A New Zenith Tropospheric Delay Grid Product for Real-Time PPP Applications over China.

PubMed

Lou, Yidong; Huang, Jinfang; Zhang, Weixing; Liang, Hong; Zheng, Fu; Liu, Jingnan

2017-12-27

Tropospheric delay is one of the major factors affecting the accuracy of electromagnetic distance measurements. To provide wide-area real-time high precision zenith tropospheric delay (ZTD), the temporal and spatial variations of ZTD with altitude were analyzed on the bases of the latest meteorological reanalysis product (ERA-Interim) provided by the European Center for Medium-Range Weather Forecasts (ECMWF). An inverse scale height model at given locations taking latitude, longitude and day of year as inputs was then developed and used to convert real-time ZTD at GPS stations in Crustal Movement Observation Network of China (CMONOC) from station height to mean sea level (MSL). The real-time ZTD grid product (RtZTD) over China was then generated with a time interval of 5 min. Compared with ZTD estimated in post-processing mode, the bias and error RMS of ZTD at test GPS stations derived from RtZTD are 0.39 and 1.56 cm, which is significantly more accurate than commonly used empirical models. In addition, simulated real-time kinematic Precise Point Positioning (PPP) tests show that using RtZTD could accelerate the BDS-PPP convergence time by up to 32% and 65% in the horizontal and vertical components (set coordinate error thresholds to 0.4 m), respectively. For GPS-PPP, the convergence time using RtZTD can be accelerated by up to 29% in the vertical component (0.2 m).

Age-related slowing: perceptuomotor, decision, or attention decline?

PubMed

Godefroy, Olivier; Roussel, Martine; Despretz, Pascal; Quaglino, Véronique; Boucart, Muriel

2010-04-01

Age-related slowing is well documented but its origin remains unclear. A first validation study (Study 1) performed in 46 participants examined the effect of attention allocation (manipulated through a dual task) on various portions of individual simple reaction time (SRT) distribution (minimum, centile 5, centile 50, and centile 95 RTs). It showed that attention 'deprivation' due to a secondary task is not uniform throughout the distribution but impaired mainly the ability to produce a large number of fast responses. Study 2 investigated in 88 healthy participants age-related slowing of perceptual, motor, decision, and attentional processes using SRT and choice reaction time (CRT), finger tapping, and visual inspection time tests. It showed that the majority of SRT slowing after the age of 40 is due to lengthening of centile 5 RT, suggesting perceptuomotor slowing, an interpretation supported by longer visual inspection time and lower tapping frequency. After 60 years, SRT lengthening was due to a further lengthening of the centile 5-centile 50 SRT index, suggesting the participation of attentional decline. These findings support the hypothesis that age-related slowing in simple repetitive tasks is mainly related to slowing at the stage of perceptuomotor processes, and after 60 years, to additional decline of attention.

Effect of Combined Sensorimotor-Resistance Training on Strength, Balance, and Jumping Performance of Soccer Players.

PubMed

Manolopoulos, Konstantinos; Gissis, Ioannis; Galazoulas, Christos; Manolopoulos, Evaggelos; Patikas, Dimitrios; Gollhofer, Albert; Kotzamanidis, Christos

2016-01-01

The purpose of the study was to investigate the effects of resistance training (RT) and sensorimotor training combined with RT (SM-RT) on balance, 1 repetition maximum (RM), rate of force development (RFD), and squat jump (SJ) height. Twenty amateur soccer players were equally divided into 2 groups assigned as SM-RT group (age: 22 ± 1.7 years, body mass: 79.9 ± 6.3 kg, body height: 1.81 ± 0.06 m) and RT group (age: 21.3 ± 1.3 years, body mass: 77.4 ± 9.3 kg, body height: 1.78 ± 0.04 m). Both groups were trained over a 6-week period with 2 session units per week. SM-RT group performed sensorimotor training (balance on balance board) followed by a high-intensity RT at 8-5RM leg press. The RT group performed the resistance program only. Both groups showed significantly increased 1RM leg press strength, RFD, SJ height, and balance abilities (p ≤ 0.05), whereas no significant between-group differences were observed in any of the outcome variables (p > 0.05). It was concluded that SM-RT was not superior compared with RT for both balance and strength enhancement. These findings have implications in time management during training for soccer players.

Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus

USGS Publications Warehouse

Purcell, Maureen K.; Hart, S. Alexandra; Kurath, Gael; Winton, James R.

2006-01-01

The fish rhabdovirus, Infectious hematopoietic necrosis virus (IHNV), is an important pathogen of salmonids. Cell culture assays have traditionally been used to quantify levels of IHNV in samples; however, real-time or quantitative RT-PCR assays have been proposed as a rapid alternative. For viruses having a single-stranded, negative-sense RNA genome, standard qRT-PCR assays do not distinguish between the negative-sense genome and positive-sense RNA species including mRNA and anti-genome. Thus, these methods do not determine viral genome copy number. This study reports development of strand-specific, qRT-PCR assays that use tagged primers for enhancing strand specificity during cDNA synthesis and quantitative PCR. Protocols were developed for positive-strand specific (pss-qRT-PCR) and negative-strand specific (nss-qRT-PCR) assays for IHNV glycoprotein (G) gene sequences. Validation with synthetic RNA transcripts demonstrated the assays could discriminate the correct strand with greater than 1000-fold fidelity. The number of genome copies in livers of IHNV-infected fish determined by nss-qRT-PCR was, on average, 8000-fold greater than the number of infectious units as determined by plaque assay. We also compared the number of genome copies with the quantity of positive-sense RNA and determined that the ratio of positive-sense molecules to negative-sense genome copies was, on average, 2.7:1. Potential future applications of these IHNV strand-specific qRT-PCR assays are discussed.

Ursolic Acid-Induced Elevation of Serum Irisin Augments Muscle Strength During Resistance Training in Men

PubMed Central

Bang, Hyun Seok; Seo, Dae Yun; Chung, Yong Min; Oh, Kyoung-Mo; Park, Jung Jun; Arturo, Figueroa; Jeong, Seung-Hun; Kim, Nari

2014-01-01

Ursolic acid (UA), a type of pentacyclic triterpenoid carboxylic acid purified from natural plants, can promote skeletal muscle development. We measured the effect of resistance training (RT) with/without UA on skeletal muscle development and related factors in men. Sixteen healthy male participants (age, 29.37±5.14 years; body mass index=27.13±2.16 kg/m2) were randomly assigned to RT (n=7) or RT with UA (RT+UA, n=9) groups. Both groups completed 8 weeks of intervention consisting of 5 sets of 26 exercises, with 10~15 repetitions at 60~80% of 1 repetition maximum and a 60~90-s rest interval between sets, performed 6 times/week. UA or placebo was orally ingested as 1 capsule 3 times/day for 8 weeks. The following factors were measured pre-and post-intervention: body composition, insulin, insulin-like growth factor-1 (IGF-1), irisin, and skeletal muscle strength. Body fat percentage was significantly decreased (p<0.001) in the RT+UA group, despite body weight, body mass index, lean body mass, glucose, and insulin levels remaining unchanged. IGF-1 and irisin were significantly increased compared with baseline levels in the RT+UA group (p<0.05). Maximal right and left extension (p<0.01), right flexion (p<0.05), and left flexion (p<0.001) were significantly increased compared with baseline levels in the RT+UA group. These findings suggest that UA-induced elevation of serum irisin may be useful as an agent for the enhancement of skeletal muscle strength during RT. PMID:25352765

Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Method for Rapid Detection of Severe Acute Respiratory Syndrome Coronavirus

PubMed Central

Thai, Hong Thi Cam; Le, Mai Quynh; Vuong, Cuong Duc; Parida, Manmohan; Minekawa, Harumi; Notomi, Tsugunori; Hasebe, Futoshi; Morita, Kouichi

2004-01-01

The development and evaluation of a one-step single-tube accelerated real-time quantitative reverse transcription (RT) loop-mediated isothermal amplification (LAMP) assay is reported for rapid detection of the severe acute respiratory syndrome coronavirus (SARS-CoV) replicase gene. A total of 49 samples (15 throat washes, 13 throat swabs, and 21 combined throat and nasal swabs) collected from patients admitted to the Hanoi-French and Ninhbinh hospitals in Vietnam during the SARS epidemic were evaluated and compared to conventional RT-PCR. The RT-LAMP assay demonstrated 100-fold-greater sensitivity, with a detection limit of 0.01 PFU. The sensitivity and specificity of RT-LAMP assay for detecting viral RNA in clinical specimens with regard to RT-PCR were 100 and 87%, respectively. The specificity of the RT-LAMP assay was further validated by restriction analysis as well as nucleotide sequencing of the amplified product. The concentration of virus in most of the clinical samples was 0.1 PFU (0.1 to 102 PFU), as determined from the standard curve of SARS RT-LAMP and based on the time of positivity. The assay procedure is quite simple, wherein the amplification is carried out in a single tube under isothermal conditions at 63°C, and the result can be obtained in less than 1 h (as early as 11 min). Thus, the RT-LAMP assay reported here has the advantages of rapid amplification, simple operation, and easy detection and will be useful for rapid and reliable clinical diagnosis of SARS-CoV in developing countries. PMID:15131154

Accuracy evaluation of a new real-time continuous glucose monitoring algorithm in hypoglycemia.

PubMed

Mahmoudi, Zeinab; Jensen, Morten Hasselstrøm; Dencker Johansen, Mette; Christensen, Toke Folke; Tarnow, Lise; Christiansen, Jens Sandahl; Hejlesen, Ole

2014-10-01

The purpose of this study was to evaluate the performance of a new continuous glucose monitoring (CGM) calibration algorithm and to compare it with the Guardian(®) REAL-Time (RT) (Medtronic Diabetes, Northridge, CA) calibration algorithm in hypoglycemia. CGM data were obtained from 10 type 1 diabetes patients undergoing insulin-induced hypoglycemia. Data were obtained in two separate sessions using the Guardian RT CGM device. Data from the same CGM sensor were calibrated by two different algorithms: the Guardian RT algorithm and a new calibration algorithm. The accuracy of the two algorithms was compared using four performance metrics. The median (mean) of absolute relative deviation in the whole range of plasma glucose was 20.2% (32.1%) for the Guardian RT calibration and 17.4% (25.9%) for the new calibration algorithm. The mean (SD) sample-based sensitivity for the hypoglycemic threshold of 70 mg/dL was 31% (33%) for the Guardian RT algorithm and 70% (33%) for the new algorithm. The mean (SD) sample-based specificity at the same hypoglycemic threshold was 95% (8%) for the Guardian RT algorithm and 90% (16%) for the new calibration algorithm. The sensitivity of the event-based hypoglycemia detection for the hypoglycemic threshold of 70 mg/dL was 61% for the Guardian RT calibration and 89% for the new calibration algorithm. Application of the new calibration caused one false-positive instance for the event-based hypoglycemia detection, whereas the Guardian RT caused no false-positive instances. The overestimation of plasma glucose by CGM was corrected from 33.2 mg/dL in the Guardian RT algorithm to 21.9 mg/dL in the new calibration algorithm. The results suggest that the new algorithm may reduce the inaccuracy of Guardian RT CGM system within the hypoglycemic range; however, data from a larger number of patients are required to compare the clinical reliability of the two algorithms.

Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress

USDA-ARS?s Scientific Manuscript database

Lolium temulentum is a valuable model grass species for the study of stress in forage and turf grasses. Gene expression analysis by quantitative real time RT-PCR relies on the use of proper internal standards. The aim of this study was to identify and evaluate reference genes for use in real-time q...

Age and Sex Differences in Intra-Individual Variability in a Simple Reaction Time Task

ERIC Educational Resources Information Center

Ghisletta, Paolo; Renaud, Olivier; Fagot, Delphine; Lecerf, Thierry; de Ribaupierre, Anik

2018-01-01

While age effects in reaction time (RT) tasks across the lifespan are well established for level of performance, analogous findings have started appearing also for indicators of intra-individual variability (IIV). Children are not only slower, but also display more variability than younger adults in RT. Yet, little is known about potential…

The Role of RT Carry-Over for Congruence Sequence Effects in Masked Priming

ERIC Educational Resources Information Center

Huber-Huber, Christoph; Ansorge, Ulrich

2017-01-01

The present study disentangles 2 sources of the congruence sequence effect with masked primes: congruence and response time of the previous trial (reaction time [RT] carry-over). Using arrows as primes and targets and a metacontrast masking procedure we found congruence as well as congruence sequence effects. In addition, congruence sequence…

A Ballistic Model of Choice Response Time

ERIC Educational Resources Information Center

Brown, Scott; Heathcote, Andrew

2005-01-01

Almost all models of response time (RT) use a stochastic accumulation process. To account for the benchmark RT phenomena, researchers have found it necessary to include between-trial variability in the starting point and/or the rate of accumulation, both in linear (R. Ratcliff & J. N. Rouder, 1998) and nonlinear (M. Usher & J. L. McClelland, 2001)…

Psy Toolkit: A Novel Web-Based Method for Running Online Questionnaires and Reaction-Time Experiments

ERIC Educational Resources Information Center

Stoet, Gijsbert

2017-01-01

This article reviews PsyToolkit, a free web-based service designed for setting up, running, and analyzing online questionnaires and reaction-time (RT) experiments. It comes with extensive documentation, videos, lessons, and libraries of free-to-use psychological scales and RT experiments. It provides an elaborate interactive environment to use (or…