A technique to detect periodic and non-periodic ultra-rapid flux time variations with standard radio-astronomical data

NASA Astrophysics Data System (ADS)

Borra, Ermanno F.; Romney, Jonathan D.; Trottier, Eric

2018-06-01

We demonstrate that extremely rapid and weak periodic and non-periodic signals can easily be detected by using the autocorrelation of intensity as a function of time. We use standard radio-astronomical observations that have artificial periodic and non-periodic signals generated by the electronics of terrestrial origin. The autocorrelation detects weak signals that have small amplitudes because it averages over long integration times. Another advantage is that it allows a direct visualization of the shape of the signals, while it is difficult to see the shape with a Fourier transform. Although Fourier transforms can also detect periodic signals, a novelty of this work is that we demonstrate another major advantage of the autocorrelation, that it can detect non-periodic signals while the Fourier transform cannot. Another major novelty of our work is that we use electric fields taken in a standard format with standard instrumentation at a radio observatory and therefore no specialized instrumentation is needed. Because the electric fields are sampled every 15.625 ns, they therefore allow detection of very rapid time variations. Notwithstanding the long integration times, the autocorrelation detects very rapid intensity variations as a function of time. The autocorrelation could also detect messages from Extraterrestrial Intelligence as non-periodic signals.

Illumination Invariant Change Detection (iicd): from Earth to Mars

NASA Astrophysics Data System (ADS)

Wan, X.; Liu, J.; Qin, M.; Li, S. Y.

2018-04-01

Multi-temporal Earth Observation and Mars orbital imagery data with frequent repeat coverage provide great capability for planetary surface change detection. When comparing two images taken at different times of day or in different seasons for change detection, the variation of topographic shades and shadows caused by the change of sunlight angle can be so significant that it overwhelms the real object and environmental changes, making automatic detection unreliable. An effective change detection algorithm therefore has to be robust to the illumination variation. This paper presents our research on developing and testing an Illumination Invariant Change Detection (IICD) method based on the robustness of phase correlation (PC) to the variation of solar illumination for image matching. The IICD is based on two key functions: i) initial change detection based on a saliency map derived from pixel-wise dense PC matching and ii) change quantization which combines change type identification, motion estimation and precise appearance change identification. Experiment using multi-temporal Landsat 7 ETM+ satellite images, Rapid eye satellite images and Mars HiRiSE images demonstrate that our frequency based image matching method can reach sub-pixel accuracy and thus the proposed IICD method can effectively detect and precisely segment large scale change such as landslide as well as small object change such as Mars rover, under daily and seasonal sunlight changes.

The Role of Inheritance in Behavior.

ERIC Educational Resources Information Center

Plomin, Robert

1990-01-01

Discussed are some of the strategies required to try to detect and explain DNA markers that account for small amounts of behavioral variation. Situations in both animal and human behavior are described. The link between molecular biology and behavior is highlighted. (CW)

Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC

PubMed Central

Walter, Vonn; Patel, Nirali M.; Eberhard, David A.; Hayward, Michele C.; Salazar, Ashley H.; Jo, Heejoon; Soloway, Matthew G.; Wilkerson, Matthew D.; Parker, Joel S.; Yin, Xiaoying; Zhang, Guosheng; Siegel, Marni B.; Rosson, Gary B.; Earp, H. Shelton; Sharpless, Norman E.; Gulley, Margaret L.; Weck, Karen E.

2015-01-01

The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS) panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV) as well as small insertions and deletions (indel). In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV), similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07–0120 tissue cohort) and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11–1115 tissue cohort) and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion. PMID:26076459

Fetal head detection and measurement in ultrasound images by an iterative randomized Hough transform

NASA Astrophysics Data System (ADS)

Lu, Wei; Tan, Jinglu; Floyd, Randall C.

2004-05-01

This paper describes an automatic method for measuring the biparietal diameter (BPD) and head circumference (HC) in ultrasound fetal images. A total of 217 ultrasound images were segmented by using a K-Mean classifier, and the head skull was detected in 214 of the 217 cases by an iterative randomized Hough transform developed for detection of incomplete curves in images with strong noise without user intervention. The automatic measurements were compared with conventional manual measurements by sonographers and a trained panel. The inter-run variations and differences between the automatic and conventional measurements were small compared with published inter-observer variations. The results showed that the automated measurements were as reliable as the expert measurements and more consistent. This method has great potential in clinical applications.

The 57Fe hyperfine interactions in iron storage proteins in liver and spleen tissues from normal human and two patients with mantle cell lymphoma and acute myeloid leukemia: a Mössbauer effect study

NASA Astrophysics Data System (ADS)

Oshtrakh, M. I.; Alenkina, I. V.; Vinogradov, A. V.; Konstantinova, T. S.; Semionkin, V. A.

2015-04-01

Study of human spleen and liver tissues from healthy persons and two patients with mantle cell lymphoma and acute myeloid leukemia was carried out using Mössbauer spectroscopy with a high velocity resolution. Small variations in the 57Fe hyperfine parameters for normal and patient's tissues were detected and related to small variations in the 57Fe local microenvironment in ferrihydrite cores. The differences in the relative parts of more crystalline and more amorphous core regions were also supposed for iron storage proteins in normal and patients' spleen and liver tissues.

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance.

PubMed

Bashir, Ali; Bansal, Vikas; Bafna, Vineet

2010-06-18

Massively parallel DNA sequencing technologies have enabled the sequencing of several individual human genomes. These technologies are also being used in novel ways for mRNA expression profiling, genome-wide discovery of transcription-factor binding sites, small RNA discovery, etc. The multitude of sequencing platforms, each with their unique characteristics, pose a number of design challenges, regarding the technology to be used and the depth of sequencing required for a particular sequencing application. Here we describe a number of analytical and empirical results to address design questions for two applications: detection of structural variations from paired-end sequencing and estimating mRNA transcript abundance. For structural variation, our results provide explicit trade-offs between the detection and resolution of rearrangement breakpoints, and the optimal mix of paired-read insert lengths. Specifically, we prove that optimal detection and resolution of breakpoints is achieved using a mix of exactly two insert library lengths. Furthermore, we derive explicit formulae to determine these insert length combinations, enabling a 15% improvement in breakpoint detection at the same experimental cost. On empirical short read data, these predictions show good concordance with Illumina 200 bp and 2 Kbp insert length libraries. For transcriptome sequencing, we determine the sequencing depth needed to detect rare transcripts from a small pilot study. With only 1 Million reads, we derive corrections that enable almost perfect prediction of the underlying expression probability distribution, and use this to predict the sequencing depth required to detect low expressed genes with greater than 95% probability. Together, our results form a generic framework for many design considerations related to high-throughput sequencing. We provide software tools http://bix.ucsd.edu/projects/NGS-DesignTools to derive platform independent guidelines for designing sequencing experiments (amount of sequencing, choice of insert length, mix of libraries) for novel applications of next generation sequencing.

Comparison of Genetic Structure of Epixylic Liverwort Crossocalyx hellerianus between Central European and Fennoscandian Populations.

PubMed

Holá, Eva; Košnar, Jiří; Kučera, Jan

2015-01-01

Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei's gene diversity in large populations reached high values and ranged between 4.41-4.97, 3.13-4.45, and 0.94-0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00-4.42, 1.00-2.73, and 0.00-0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances (20-80 m), suggesting effective dispersal of asexual propagules.

Comparison of Genetic Structure of Epixylic Liverwort Crossocalyx hellerianus between Central European and Fennoscandian Populations

PubMed Central

Holá, Eva; Košnar, Jiří; Kučera, Jan

2015-01-01

Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei’s gene diversity in large populations reached high values and ranged between 4.41–4.97, 3.13–4.45, and 0.94–0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00–4.42, 1.00–2.73, and 0.00–0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances (20–80 m), suggesting effective dispersal of asexual propagules. PMID:26186214

Colony membership is reflected by variations in cuticular hydrocarbon profile in a Neotropical paper wasp, Polistes satan (Hymenoptera, Vespidae).

PubMed

Tannure-Nascimento, I C; Nascimento, F S; Turatti, I C; Lopes, N P; Trigo, J R; Zucchi, R

2007-06-27

Nestmate recognition is one the most important features in social insect colonies. Although epicuticular lipids or cuticular hydrocarbons have both structural and defensive functions in insects, they also seem to be involved in several aspects of communication in wasps, bees and ants. We analyzed and described for the first time the cuticular hydrocarbons of a Neotropical paper wasp, Polistes satan, and found that variation in hydrocarbon profile was sufficiently strong to discriminate individuals according to their colony membership. Therefore, it seems that small differences in the proportion of these compounds can be detected and used as a chemical-based cue by nestmates to detect invaders and avoid usurpation.

Fetal head detection and measurement in ultrasound images by a direct inverse randomized Hough transform

NASA Astrophysics Data System (ADS)

Lu, Wei; Tan, Jinglu; Floyd, Randall C.

2005-04-01

Object detection in ultrasound fetal images is a challenging task for the relatively low resolution and low signal-to-noise ratio. A direct inverse randomized Hough transform (DIRHT) is developed for filtering and detecting incomplete curves in images with strong noise. The DIRHT combines the advantages of both the inverse and the randomized Hough transforms. In the reverse image, curves are highlighted while a large number of unrelated pixels are removed, demonstrating a "curve-pass filtering" effect. Curves are detected by iteratively applying the DIRHT to the filtered image. The DIRHT was applied to head detection and measurement of the biparietal diameter (BPD) and head circumference (HC). No user input or geometric properties of the head were required for the detection. The detection and measurement took 2 seconds for each image on a PC. The inter-run variations and the differences between the automatic measurements and sonographers" manual measurements were small compared with published inter-observer variations. The results demonstrated that the automatic measurements were consistent and accurate. This method provides a valuable tool for fetal examinations.

A detection method of subrecent to recent tectonic activity in the anticlinal system of the northern Negev, Israel

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

Zilberman, E.; Wachs, D.

Geomorphological and geophysical methods combined with borehole information were employed to search for possible subrecent small-scale vertical movement along the anticlinal fold belt of the central Negev, Israel. Such tectonic deformation might indicate displacement on the buried reverse faults underneath the anticlines. Variations in the thickness of the alluvial fill in the study area, which are in accordance with the fold structures, could be an indication of recent folding activity along the anticlinal system. In order to detect these thickness variations in the alluvial fill, seismic refraction and electrical resistivity measurements were carries out along the valley of Nahal Besor,more » which crosses the anticlinal belt. The thickness variations of the alluvial fill along the valley were not found to indicate any significant tectonic movement along the anticlines during the Pleistocene. The thickest alluvium was found overlying a karst bedrock, hence karst relief is suggested to be responsible for these variations.« less

Reliable detection of fluence anomalies in EPID-based IMRT pretreatment quality assurance using pixel intensity deviations

PubMed Central

Gordon, J. J.; Gardner, J. K.; Wang, S.; Siebers, J. V.

2012-01-01

Purpose: This work uses repeat images of intensity modulated radiation therapy (IMRT) fields to quantify fluence anomalies (i.e., delivery errors) that can be reliably detected in electronic portal images used for IMRT pretreatment quality assurance. Methods: Repeat images of 11 clinical IMRT fields are acquired on a Varian Trilogy linear accelerator at energies of 6 MV and 18 MV. Acquired images are corrected for output variations and registered to minimize the impact of linear accelerator and electronic portal imaging device (EPID) positioning deviations. Detection studies are performed in which rectangular anomalies of various sizes are inserted into the images. The performance of detection strategies based on pixel intensity deviations (PIDs) and gamma indices is evaluated using receiver operating characteristic analysis. Results: Residual differences between registered images are due to interfraction positional deviations of jaws and multileaf collimator leaves, plus imager noise. Positional deviations produce large intensity differences that degrade anomaly detection. Gradient effects are suppressed in PIDs using gradient scaling. Background noise is suppressed using median filtering. In the majority of images, PID-based detection strategies can reliably detect fluence anomalies of ≥5% in ∼1 mm2 areas and ≥2% in ∼20 mm2 areas. Conclusions: The ability to detect small dose differences (≤2%) depends strongly on the level of background noise. This in turn depends on the accuracy of image registration, the quality of the reference image, and field properties. The longer term aim of this work is to develop accurate and reliable methods of detecting IMRT delivery errors and variations. The ability to resolve small anomalies will allow the accuracy of advanced treatment techniques, such as image guided, adaptive, and arc therapies, to be quantified. PMID:22894421

Global Biomass Variation and its Geodynamic Effects, 1982-1998

NASA Technical Reports Server (NTRS)

Rodell, M.; Chao, B. F.; Au, A. Y.; Kimball, J. S.; McDonald, K. C.

2005-01-01

Redistribution of mass near Earth's surface alters its rotation, gravity field, and geocenter location. Advanced techniques for measuring these geodetic variations now exist, but the ability to attribute the observed modes to individual Earth system processes has been hampered by a shortage of reliable global data on such processes, especially hydrospheric processes. To address one aspect of this deficiency, 17 yrs of monthly, global maps of vegetation biomass were produced by applying field-based relationships to satellite-derived vegetation type and leaf area index. The seasonal variability of biomass was estimated to be as large as 5 kg m(exp -2). Of this amount, approximately 4 kg m(exp -2) is due to vegetation water storage variations. The time series of maps was used to compute geodetic anomalies, which were then compared with existing geodetic observations as well as the estimated measurement sensitivity of the Gravity Recovery and Climate Experiment (GRACE). For gravity, the seasonal amplitude of biomass variations may be just within GRACE'S limits of detectability, but it is still an order of magnitude smaller than current observation uncertainty using the satellite-laser-ranging technique. The contribution of total biomass variations to seasonal polar motion amplitude is detectable in today's measurement, but it is obscured by contributions from various other sources, some of which are two orders of magnitude larger. The influence on the length of day is below current limits of detectability. Although the nonseasonal geodynamic signals show clear interannual variability, they are too small to be detected.

Detecting drift bias and exposure errors in solar and photosynthetically active radiation data

USDA-ARS?s Scientific Manuscript database

All-black thermopile pyranometers are commonly used to measure solar radiation. Ensuring that the sensors are stable and free of drift is critical to accurately measure small variations in global solar irradiance (K'), which is a potential driver of changes in surface temperature. We demonstrate tha...

Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat.

PubMed

Hess, Moritz; Wildhagen, Henning; Junker, Laura Verena; Ensminger, Ingo

2016-08-26

Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction. The majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.

Quantitative Detection of Cracks in Steel Using Eddy Current Pulsed Thermography.

PubMed

Shi, Zhanqun; Xu, Xiaoyu; Ma, Jiaojiao; Zhen, Dong; Zhang, Hao

2018-04-02

Small cracks are common defects in steel and often lead to catastrophic accidents in industrial applications. Various nondestructive testing methods have been investigated for crack detection; however, most current methods focus on qualitative crack identification and image processing. In this study, eddy current pulsed thermography (ECPT) was applied for quantitative crack detection based on derivative analysis of temperature variation. The effects of the incentive parameters on the temperature variation were analyzed in the simulation study. The crack profile and position are identified in the thermal image based on the Canny edge detection algorithm. Then, one or more trajectories are determined through the crack profile in order to determine the crack boundary through its temperature distribution. The slope curve along the trajectory is obtained. Finally, quantitative analysis of the crack sizes was performed by analyzing the features of the slope curves. The experimental verification showed that the crack sizes could be quantitatively detected with errors of less than 1%. Therefore, the proposed ECPT method was demonstrated to be a feasible and effective nondestructive approach for quantitative crack detection.

Toward predicting clay landslide with ambient seismic noise

NASA Astrophysics Data System (ADS)

Larose, E. F.; Mainsant, G.; Carriere, S.; Chambon, G.; Michoud, C.; Jongmans, D.; Jaboyedoff, M.

2013-12-01

Clay-rich pose critical problems in risk management worldwide. The most widely proposed mechanism leading to such flow-like movements is the increase in water pore pressure in the sliding mass, generating partial or complete liquefaction. This solid-to-liquid transition results in a dramatic reduction of mechanical rigidity, which could be detected by monitoring shear wave velocity variations, The ambient seismic noise correlation technique has been applied to measure the variation in the seismic surface wave velocity in the Pont Bourquin landslide (Swiss Alps). This small but active composite earthslide-earthflow was equipped with continuously recording seismic sensors during spring and summer 2010, and then again from fall 2011 on. An earthslide of a few thousand cubic meters was triggered in mid-August 2010, after a rainy period. This article shows that the seismic velocity of the sliding material, measured from daily noise correlograms, decreased continuously and rapidly for several days prior to the catastrophic event. From a spectral analysis of the velocity decrease, it was possible to determine the location of the change at the base of the sliding layer. These results are confirmed by analogous small-scale experiments in the laboratory. These results demonstrate that ambient seismic noise can be used to detect rigidity variations before failure and could potentially be used to predict landslides.

Tropical anurans mature early and die young: Evidence from eight Afromontane Hyperolius species and a meta-analysis

PubMed Central

2017-01-01

Age- and size-related life-history traits of anuran amphibians are thought to vary systematically with latitude and altitude. Because the available data base is strongly biased towards temperate-zone species, we provide new estimates on eight afrotropical Reed Frog species. A meta-analysis of the demographic traits in 44 tropical anuran species aims to test for the predicted clinal variation and to contrast results with variation detected in temperate-zone species. The small-sized reed frogs reach sexual maturity during the first or second year of life, but longevity does not exceed three to four years. Latitudinal effects on demographic life-history traits are not detectable in tropical anurans, and altitudinal effects are limited to a slight size reduction at higher elevations. Common features of anuran life-history in the tropics are early sexual maturation at small size and low longevity resulting in low lifetime fecundity. This pattern contrasts with that found in temperate-zone anurans which mature later at larger size and grow considerably older yielding greater lifetime fecundity than in the tropics. Latitudinal and altitudinal contraction of the yearly activity period shape the evolution of life-history traits in the temperate region, while trait variation in the tropics seems to be driven by distinct, not yet identified selective forces. PMID:28182738

Improvement on Exoplanet Detection Methods and Analysis via Gaussian Process Fitting Techniques

NASA Astrophysics Data System (ADS)

Van Ross, Bryce; Teske, Johanna

2018-01-01

Planetary signals in radial velocity (RV) data are often accompanied by signals coming solely from stellar photo- or chromospheric variation. Such variation can reduce the precision of planet detection and mass measurements, and cause misidentification of planetary signals. Recently, several authors have demonstrated the utility of Gaussian Process (GP) regression for disentangling planetary signals in RV observations (Aigrain et al. 2012; Angus et al. 2017; Czekala et al. 2017; Faria et al. 2016; Gregory 2015; Haywood et al. 2014; Rajpaul et al. 2015; Foreman-Mackey et al. 2017). GP models the covariance of multivariate data to make predictions about likely underlying trends in the data, which can be applied to regions where there are no existing observations. The potency of GP has been used to infer stellar rotation periods; to model and disentangle time series spectra; and to determine physical aspects, populations, and detection of exoplanets, among other astrophysical applications. Here, we implement similar analysis techniques to times series of the Ca-2 H and K activity indicator measured simultaneously with RVs in a small sample of stars from the large Keck/HIRES RV planet search program. Our goal is to characterize the pattern(s) of non-planetary variation to be able to know what is/ is not a planetary signal. We investigated ten different GP kernels and their respective hyperparameters to determine the optimal combination (e.g., the lowest Bayesian Information Criterion value) in each stellar data set. To assess the hyperparameters’ error, we sampled their posterior distributions using Markov chain Monte Carlo (MCMC) analysis on the optimized kernels. Our results demonstrate how GP analysis of stellar activity indicators alone can contribute to exoplanet detection in RV data, and highlight the challenges in applying GP analysis to relatively small, irregularly sampled time series.

Multi-approaches analysis reveals local adaptation in the emmer wheat (Triticum dicoccoides) at macro- but not micro-geographical scale.

PubMed

Volis, Sergei; Ormanbekova, Danara; Yermekbayev, Kanat; Song, Minshu; Shulgina, Irina

2015-01-01

Detecting local adaptation and its spatial scale is one of the most important questions of evolutionary biology. However, recognition of the effect of local selection can be challenging when there is considerable environmental variation across the distance at the whole species range. We analyzed patterns of local adaptation in emmer wheat, Triticum dicoccoides, at two spatial scales, small (inter-population distance less than one km) and large (inter-population distance more than 50 km) using several approaches. Plants originating from four distinct habitats at two geographic scales (cold edge, arid edge and two topographically dissimilar core locations) were reciprocally transplanted and their success over time was measured as 1) lifetime fitness in a year of planting, and 2) population growth four years after planting. In addition, we analyzed molecular (SSR) and quantitative trait variation and calculated the QST/FST ratio. No home advantage was detected at the small spatial scale. At the large spatial scale, home advantage was detected for the core population and the cold edge population in the year of introduction via measuring life-time plant performance. However, superior performance of the arid edge population in its own environment was evident only after several generations via measuring experimental population growth rate through genotyping with SSRs allowing counting the number of plants and seeds per introduced genotype per site. These results highlight the importance of multi-generation surveys of population growth rate in local adaptation testing. Despite predominant self-fertilization of T. dicoccoides and the associated high degree of structuring of genetic variation, the results of the QST - FST comparison were in general agreement with the pattern of local adaptation at the two spatial scales detected by reciprocal transplanting.

Assessing the complex architecture of polygenic traits in diverged yeast populations.

PubMed

Cubillos, Francisco A; Billi, Eleonora; Zörgö, Enikö; Parts, Leopold; Fargier, Patrick; Omholt, Stig; Blomberg, Anders; Warringer, Jonas; Louis, Edward J; Liti, Gianni

2011-04-01

Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is to identify the causative variants driving phenotypic variation. Recently, the baker's yeast, Saccharomyces cerevisiae has emerged as a powerful model for dissecting complex traits. However, past studies using a laboratory strain were unable to reveal the complete architecture of polygenic traits. Here, we present a linkage study using 576 recombinant strains obtained from crosses of isolates representative of the major lineages. The meiotic recombinational landscape appears largely conserved between populations; however, strain-specific hotspots were also detected. Quantitative measurements of growth in 23 distinct ecologically relevant environments show that our recombinant population recapitulates most of the standing phenotypic variation described in the species. Linkage analysis detected an average of 6.3 distinct QTLs for each condition tested in all crosses, explaining on average 39% of the phenotypic variation. The QTLs detected are not constrained to a small number of loci, and the majority are specific to a single cross-combination and to a specific environment. Moreover, crosses between strains of similar phenotypes generate greater variation in the offspring, suggesting the presence of many antagonistic alleles and epistatic interactions. We found that subtelomeric regions play a key role in defining individual quantitative variation, emphasizing the importance of the adaptive nature of these regions in natural populations. This set of recombinant strains is a powerful tool for investigating the complex architecture of polygenic traits. © 2011 Blackwell Publishing Ltd.

General practice performance in referral for suspected cancer: influence of number of cases and case-mix on publicly reported data.

PubMed

Murchie, P; Chowdhury, A; Smith, S; Campbell, N C; Lee, A J; Linden, D; Burton, C D

2015-05-26

Publicly available data show variation in GPs' use of urgent suspected cancer (USC) referral pathways. We investigated whether this could be due to small numbers of cancer cases and random case-mix, rather than due to true variation in performance. We analysed individual GP practice USC referral detection rates (proportion of the practice's cancer cases that are detected via USC) and conversion rates (proportion of the practice's USC referrals that prove to be cancer) in routinely collected data from GP practices in all of England (over 4 years) and northeast Scotland (over 7 years). We explored the effect of pooling data. We then modelled the effects of adding random case-mix to practice variation. Correlations between practice detection rate and conversion rate became less positive when data were aggregated over several years. Adding random case-mix to between-practice variation indicated that the median proportion of poorly performing practices correctly identified after 25 cancer cases were examined was 20% (IQR 17 to 24) and after 100 cases was 44% (IQR 40 to 47). Much apparent variation in GPs' use of suspected cancer referral pathways can be attributed to random case-mix. The methods currently used to assess the quality of GP-suspected cancer referral performance, and to compare individual practices, are misleading. These should no longer be used, and more appropriate and robust methods should be developed.

Discovery of interstellar circular polarization in the direction of the Crab Nebula.

NASA Technical Reports Server (NTRS)

Martin, P. G.; Illing, R.; Angel, J. R. P.

1972-01-01

A search in many small regions of the Crab Nebula has resulted in the detection of a small component of circular polarization. The variation of the sign and magnitude with position in the Nebula indicates that the polarization is of interstellar origin. On the basis of the polarity, strength, and colour dependence, it is concluded that the composition of the aligned grains causing this polarization is dielectric. Metallic particles are clearly ruled out. Some stars have also been observed with negative results.

Association of parameter, software, and hardware variation with large-scale behavior across 57,000 climate models

PubMed Central

Knight, Christopher G.; Knight, Sylvia H. E.; Massey, Neil; Aina, Tolu; Christensen, Carl; Frame, Dave J.; Kettleborough, Jamie A.; Martin, Andrew; Pascoe, Stephen; Sanderson, Ben; Stainforth, David A.; Allen, Myles R.

2007-01-01

In complex spatial models, as used to predict the climate response to greenhouse gas emissions, parameter variation within plausible bounds has major effects on model behavior of interest. Here, we present an unprecedentedly large ensemble of >57,000 climate model runs in which 10 parameters, initial conditions, hardware, and software used to run the model all have been varied. We relate information about the model runs to large-scale model behavior (equilibrium sensitivity of global mean temperature to a doubling of carbon dioxide). We demonstrate that effects of parameter, hardware, and software variation are detectable, complex, and interacting. However, we find most of the effects of parameter variation are caused by a small subset of parameters. Notably, the entrainment coefficient in clouds is associated with 30% of the variation seen in climate sensitivity, although both low and high values can give high climate sensitivity. We demonstrate that the effect of hardware and software is small relative to the effect of parameter variation and, over the wide range of systems tested, may be treated as equivalent to that caused by changes in initial conditions. We discuss the significance of these results in relation to the design and interpretation of climate modeling experiments and large-scale modeling more generally. PMID:17640921

A new single crystal diamond dosimeter for small beam: comparison with different commercial active detectors.

PubMed

Marsolat, F; Tromson, D; Tranchant, N; Pomorski, M; Le Roy, M; Donois, M; Moignau, F; Ostrowsky, A; De Carlan, L; Bassinet, C; Huet, C; Derreumaux, S; Chea, M; Cristina, K; Boisserie, G; Bergonzo, P

2013-11-07

Recent developments of new therapy techniques using small photon beams, such as stereotactic radiotherapy, require suitable detectors to determine the delivered dose with a high accuracy. The dosimeter has to be as close as possible to tissue equivalence and to exhibit a small detection volume compared to the size of the irradiation field, because of the lack of lateral electronic equilibrium in small beam. Characteristics of single crystal diamond (tissue equivalent material Z = 6, high density) make it an ideal candidate to fulfil most of small beam dosimetry requirements. A commercially available Element Six electronic grade synthetic diamond was used to develop a single crystal diamond dosimeter (SCDDo) with a small detection volume (0.165 mm(3)). Long term stability was studied by irradiating the SCDDo in a (60)Co beam over 14 h. A good stability (deviation less than ± 0.1%) was observed. Repeatability, dose linearity, dose rate dependence and energy dependence were studied in a 10 × 10 cm(2) beam produced by a Varian Clinac 2100 C linear accelerator. SCDDo lateral dose profile, depth dose curve and output factor (OF) measurements were performed for small photon beams with a micro multileaf collimator m3 (BrainLab) attached to the linac. This study is focused on the comparison of SCDDo measurements to those obtained with different commercially available active detectors: an unshielded silicon diode (PTW 60017), a shielded silicon diode (Sun Nuclear EDGE), a PinPoint ionization chamber (PTW 31014) and two natural diamond detectors (PTW 60003). SCDDo presents an excellent spatial resolution for dose profile measurements, due to its small detection volume. Low energy dependence (variation of 1.2% between 6 and 18 MV photon beam) and low dose rate dependence of the SCDDo (variation of 1% between 0.53 and 2.64 Gy min(-1)) are obtained, explaining the good agreement between the SCDDo and the efficient unshielded diode (PTW 60017) in depth dose curve measurements. For field sizes ranging from 0.6 × 0.6 to 10 × 10 cm(2), OFs obtained with the SCDDo are between the OFs measured with the PinPoint ionization chamber and the Sun Nuclear EDGE diode that are known to respectively underestimate and overestimate OF values in small beam, due to the large detection volume of the chamber and the non-water equivalence of both detectors.

Detection of Road Markings Recorded in In-Vehicle Camera Images by Using Position-Dependent Classifiers

NASA Astrophysics Data System (ADS)

Noda, Masafumi; Takahashi, Tomokazu; Deguchi, Daisuke; Ide, Ichiro; Murase, Hiroshi; Kojima, Yoshiko; Naito, Takashi

In this study, we propose a method for detecting road markings recorded in an image captured by an in-vehicle camera by using a position-dependent classifier. Road markings are symbols painted on the road surface that help in preventing traffic accidents and in ensuring traffic smooth. Therefore, driver support systems for detecting road markings, such as a system that provides warning in the case when traffic signs are overlooked, and supporting the stopping of a vehicle are required. It is difficult to detect road markings because their appearance changes with the actual traffic conditions, e. g. the shape and resolution change. The variation in these appearances depend on the positional relation between the vehicle and the road markings, and on the vehicle posture. Although these variations are quite large in an entire image, they are relatively small in a local area of the image. Therefore, we try to improve the detection performance by taking into account the local variations in these appearances. We propose a method in which a position-dependent classifier is used to detect road markings recorded in images captured by an in-vehicle camera. Further, to train the classifier efficiently, we propose a generative learning method that takes into consideration the positional relation between the vehicle and road markings, and also the vehicle posture. Experimental results showed that the detection performance when the proposed method was used was better than when a method involving a single classifier was used.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

PubMed Central

Schadt, Eric E.; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H.; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A.; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

PubMed

Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.

Sub-micron elastic property characterization of materials using a near-field scanning optical microscope

NASA Astrophysics Data System (ADS)

Blodgett, David W.; Spicer, James B.

2001-12-01

The ability to characterize the sub-surface mechanical properties of a bulk or thin film material at the sub-micron level has applications in the microelectronics and thin film industries. In the microelectronics industry, with the decrease of line widths and the increase of component densities, sub-surface voids have become increasingly detrimental. Any voids along an integrated circuit (IC) line can lead to improper electrical connections between components and can cause failure of the device. In the thin film industry, the detection of impurities is also important. Any impurities can detract from the film's desired optical, electrical, or mechanical properties. Just as important as the detection of voids and impurities, is the measurement of the elastic properties of a material on the nanometer scale. These elastic measurements provide insight into the microstructural properties of the material. We have been investigating a technique that couples the high-resolution surface imaging capabilities of the apertureless near-field scanning optical microscope (ANSOM) with the sub-surface characterization strengths of high-frequency ultrasound. As an ultrasonic wave propagates, the amplitude decreases due to geometrical spreading, attenuation from absorption, and scattering from discontinuities. Measurement of wave speeds and attenuation provides the information needed to quantify the bulk or surface properties of a material. The arrival of an ultrasonic wave at or along the surface of a material is accompanied with a small surface displacement. Conventional methods for the ultrasound detection rely on either a contact transducer or optical technique (interferometric, beam deflection, etc.). However, each of these methods is limited by the spatial resolution dictated by the detection footprint. As the footprint size increases, variations across the ultrasonic wavefront are effectively averaged, masking the presence of any nanometer-scale sub-surface or surface mechanical property variations. The use of an ANSOM for sensing ultrasonic wave arrivals reduces the detection footprint allowing any nanometer scale variations in the microstructure of a material to be detected. In an ANSOM, the ultrasonic displacement is manifested as perturbations on the near-field signal due to the small variations in the tip-sample caused by the wave arrival. Due to the linear dependence of the near-field signal on tip-sample separation, these perturbations can be interpreted using methods identical to those for conventional ultrasonic techniques. In this paper, we report results using both contact transducer (5 MHz) and laser-generated ultrasound.

ULTRAVIOLET EXTINCTION AT HIGH GALACTIC LATITUDES

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

Peek, J. E. G.; Schiminovich, David, E-mail: jegpeek@gmail.com

In order to study the properties and effects of high Galactic latitude dust, we present an analysis of 373,303 galaxies selected from the Galaxy Evolution Explorer All-Sky Survey and Wide-field Infrared Explorer All-Sky Data Release. By examining the variation in aggregate ultraviolet colors and number density of these galaxies, we measure the extinction curve at high latitude. We additionally consider a population of spectroscopically selected galaxies from the Sloan Digital Sky Survey to measure extinction in the optical. We find that dust at high latitude is neither quantitatively nor qualitatively consistent with standard reddening laws. Extinction in the FUV andmore » NUV is {approx}10% and {approx}35% higher than expected, with significant variation across the sky. We find that no single R{sub V} parameter fits both the optical and ultraviolet extinction at high latitude, and that while both show detectable variation across the sky, these variations are not related. We propose that the overall trends we detect likely stem from an increase in very small silicate grains in the interstellar medium.« less

Topology of Plant - Flower-Visitor Networks in a Tropical Mountain Forest: Insights on the Role of Altitudinal and Temporal Variation.

PubMed

Cuartas-Hernández, Sandra; Medel, Rodrigo

2015-01-01

Understanding the factors determining the spatial and temporal variation of ecological networks is fundamental to the knowledge of their dynamics and functioning. In this study, we evaluate the effect of elevation and time on the structure of plant-flower-visitor networks in a Colombian mountain forest. We examine the level of generalization of plant and animal species and the identity of interactions in 44 bipartite matrices obtained from eight altitudinal levels, from 2200 to 2900 m during eight consecutive months. The contribution of altitude and time to the overall variation in the number of plant (P) and pollinator (A) species, network size (M), number of interactions (I), connectance (C), and nestedness was evaluated. In general, networks were small, showed high connectance values and non-nested patterns of organization. Variation in P, M, I and C was better accounted by time than elevation, seemingly related to temporal variation in precipitation. Most plant and insect species were specialists and the identity of links showed a high turnover over months and at every 100 m elevation. The partition of the whole system into smaller network units allowed us to detect small-scale patterns of interaction that contrasted with patterns commonly described in cumulative networks. The specialized but erratic pattern of network organization observed in this tropical mountain suggests that high connectance coupled with opportunistic attachment may confer robustness to plant-flower-visitor networks occurring at small spatial and temporal units.

Quantitative Trait Loci Differentiating the Outbreeding Mimulus Guttatus from the Inbreeding M. Platycalyx

PubMed Central

Lin, J. Z.; Ritland, K.

1997-01-01

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6-28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect. PMID:9215912

Age-specific infectious period shapes dynamics of pneumonia in bighorn sheep.

PubMed

Plowright, Raina K; Manlove, Kezia R; Besser, Thomas E; Páez, David J; Andrews, Kimberly R; Matthews, Patrick E; Waits, Lisette P; Hudson, Peter J; Cassirer, E Frances

2017-10-01

Superspreading, the phenomenon where a small proportion of individuals contribute disproportionately to new infections, has profound effects on disease dynamics. Superspreading can arise through variation in contacts, infectiousness or infectious periods. The latter has received little attention, yet it drives the dynamics of many diseases of critical public health, livestock health and conservation concern. Here, we present rare evidence of variation in infectious periods underlying a superspreading phenomenon in a free-ranging wildlife system. We detected persistent infections of Mycoplasma ovipneumoniae, the primary causative agent of pneumonia in bighorn sheep (Ovis canadensis), in a small number of older individuals that were homozygous at an immunologically relevant genetic locus. Interactions among age-structure, genetic composition and infectious periods may drive feedbacks in disease dynamics that determine the magnitude of population response to infection. Accordingly, variation in initial conditions may explain divergent population responses to infection that range from recovery to catastrophic decline and extirpation. © 2017 John Wiley & Sons Ltd/CNRS.

The sidereal anisotropy of cosmic rays around 3 x 10 (15) eV observed at a middle north latitude

NASA Technical Reports Server (NTRS)

Murakami, K.; Kifune, T.; Hayashida, N.

1985-01-01

The sidereal time variation of cosmic rays (median primary energy : 3 10 to the 15th power eV) is investigated with air shower observations at Akeno, Japan (900 m a.s.l.) which started in September 1981. Air showers are detected by a coincidence requirement on several muon detectors. The result obtained for three years is suggestive of a big semi-diurnal variation (0.37 % in amplitude). On the other hand, the diurnal variation is rather small than the semi-diurnal one. The feature of the sidereal anisotropy supposed from the present result looks quite different from that below 10 to the 14th power eV.

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales).

PubMed

Boopathi, Thangavelu; Faria, Daphne Georgina; Cheon, Ju-Yong; Youn, Seok Hyun; Ki, Jang-Seu

2015-01-01

The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

CNV-RF Is a Random Forest-Based Copy Number Variation Detection Method Using Next-Generation Sequencing.

PubMed

Onsongo, Getiria; Baughn, Linda B; Bower, Matthew; Henzler, Christine; Schomaker, Matthew; Silverstein, Kevin A T; Thyagarajan, Bharat

2016-11-01

Simultaneous detection of small copy number variations (CNVs) (<0.5 kb) and single-nucleotide variants in clinically significant genes is of great interest for clinical laboratories. The analytical variability in next-generation sequencing (NGS) and artifacts in coverage data because of issues with mappability along with lack of robust bioinformatics tools for CNV detection have limited the utility of targeted NGS data to identify CNVs. We describe the development and implementation of a bioinformatics algorithm, copy number variation-random forest (CNV-RF), that incorporates a machine learning component to identify CNVs from targeted NGS data. Using CNV-RF, we identified 12 of 13 deletions in samples with known CNVs, two cases with duplications, and identified novel deletions in 22 additional cases. Furthermore, no CNVs were identified among 60 genes in 14 cases with normal copy number and no CNVs were identified in another 104 patients with clinical suspicion of CNVs. All positive deletions and duplications were confirmed using a quantitative PCR method. CNV-RF also detected heterozygous deletions and duplications with a specificity of 50% across 4813 genes. The ability of CNV-RF to detect clinically relevant CNVs with a high degree of sensitivity along with confirmation using a low-cost quantitative PCR method provides a framework for providing comprehensive NGS-based CNV/single-nucleotide variant detection in a clinical molecular diagnostics laboratory. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Infrasonic Monitoring,

DTIC Science & Technology

1995-08-14

seismic network. At large range, infrasound signals are oscillatory acoustic signals detected as small pressure variations about the ambient value... Infrasound Review and Background Infrasound signals are regular acoustic signals in that they are longitudinal pressure waves albeit at rather low frequency...energy is concentrated at higher frequency than that for higher yield sources. Infrasound can be generated by natural and manmade processes; moreover

Detection of copy number variations in epilepsy using exome data.

PubMed

Tsuchida, N; Nakashima, M; Kato, M; Heyman, E; Inui, T; Haginoya, K; Watanabe, S; Chiyonobu, T; Morimoto, M; Ohta, M; Kumakura, A; Kubota, M; Kumagai, Y; Hamano, S-I; Lourenco, C M; Yahaya, N A; Ch'ng, G-S; Ngu, L-H; Fattal-Valevski, A; Weisz Hubshman, M; Orenstein, N; Marom, D; Cohen, L; Goldberg-Stern, H; Uchiyama, Y; Imagawa, E; Mizuguchi, T; Takata, A; Miyake, N; Nakajima, H; Saitsu, H; Miyatake, S; Matsumoto, N

2018-03-01

Epilepsies are common neurological disorders and genetic factors contribute to their pathogenesis. Copy number variations (CNVs) are increasingly recognized as an important etiology of many human diseases including epilepsy. Whole-exome sequencing (WES) is becoming a standard tool for detecting pathogenic mutations and has recently been applied to detecting CNVs. Here, we analyzed 294 families with epilepsy using WES, and focused on 168 families with no causative single nucleotide variants in known epilepsy-associated genes to further validate CNVs using 2 different CNV detection tools using WES data. We confirmed 18 pathogenic CNVs, and 2 deletions and 2 duplications at chr15q11.2 of clinically unknown significance. Of note, we were able to identify small CNVs less than 10 kb in size, which might be difficult to detect by conventional microarray. We revealed 2 cases with pathogenic CNVs that one of the 2 CNV detection tools failed to find, suggesting that using different CNV tools is recommended to increase diagnostic yield. Considering a relatively high discovery rate of CNVs (18 out of 168 families, 10.7%) and successful detection of CNV with <10 kb in size, CNV detection by WES may be able to surrogate, or at least complement, conventional microarray analysis. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus).

PubMed

Marsden, Clare D; Woodroffe, Rosie; Mills, Michael G L; McNutt, J Weldon; Creel, Scott; Groom, Rosemary; Emmanuel, Masenga; Cleaveland, Sarah; Kat, Pieter; Rasmussen, Gregory S A; Ginsberg, Joshua; Lines, Robin; André, Jean-Marc; Begg, Colleen; Wayne, Robert K; Mable, Barbara K

2012-03-01

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e)  < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift. © 2012 Blackwell Publishing Ltd.

Detection of protruding lesion in wireless capsule endoscopy videos of small intestine

NASA Astrophysics Data System (ADS)

Wang, Chengliang; Luo, Zhuo; Liu, Xiaoqi; Bai, Jianying; Liao, Guobin

2018-02-01

Wireless capsule endoscopy (WCE) is a developed revolutionary technology with important clinical benefits. But the huge image data brings a heavy burden to the doctors for locating and diagnosing the lesion images. In this paper, a novel and efficient approach is proposed to help clinicians to detect protruding lesion images in small intestine. First, since there are many possible disturbances such as air bubbles and so on in WCE video frames, which add the difficulty of efficient feature extraction, the color-saliency region detection (CSD) method is developed for extracting the potentially saliency region of interest (SROI). Second, a novel color channels modelling of local binary pattern operator (CCLBP) is proposed to describe WCE images, which combines grayscale and color angle. The CCLBP feature is more robust to variation of illumination and more discriminative for classification. Moreover, support vector machine (SVM) classifier with CCLBP feature is utilized to detect protruding lesion images. Experimental results on real WCE images demonstrate that proposed method has higher accuracy on protruding lesion detection than some art-of-state methods.

Variations in Global Precipitation: Climate-scale to Floods

NASA Technical Reports Server (NTRS)

Adler, Robert

2006-01-01

Variations in global precipitation from climate-scale to small scale are examined using satellite-based analyses of the Global Precipitation Climatology Project (GPCP) and information from the Tropical Rainfall Measuring Mission (TRMM). Global and large regional rainfall variations and possible long-term changes are examined using the 27- year (1979-2005) monthly dataset from the GPCP. In addition to global patterns associated with phenomena such as ENSO, the data set is explored for evidence of longterm change. Although the global change of precipitation in the data set is near zero, the data set does indicate a small upward trend in the Tropics (25S-25N), especially over ocean. Techniques are derived to isolate and eliminate variations due to ENS0 and major volcanic eruptions and the significance of the trend is examined. The status of TRMM estimates is examined in terms of evaluating and improving the long-term global data set. To look at rainfall variations on a much smaller scale TRMM data is used in combination with observations from other satellites to produce a 3-hr resolution, eight-year data set for examination of weather events and for practical applications such as detecting floods. Characteristics of the data set are presented and examples of recent flood events are examined.

Development and Characterization of a High Speed Mid-IR Tunable Diode Laser Absorption Spectrometer for CO and CO2 Detection in Detonation Events

DTIC Science & Technology

2014-03-27

through a four step process. First, the I0 data was adjusted in the vertical direction. Because there were small effects due to the luminescence of...for a calibrated diffusion burner, the data showed that at 5 mm above the flame front the reaction was nearly complete. The small variation in...of collecting data at a 10 kHz repetition rate near 4.5 µm, was developed. This system was made feasible in recent years due to the development of

Orbital period variations of two W UMa-type binaries: UY UMa and EF Boo

NASA Astrophysics Data System (ADS)

Yu, Yun-Xia; Zhang, Xu-Dong; Hu, Ke; Xiang, Fu-Yuan

2017-08-01

The orbital period variations of two W UMa-type contact binaries, UY UMa and EF Boo, are analyzed by using all available times of light minimum. It is detected that the general trends of their (O - C) curves show an upward parabolic variation, which reveals their continuous period increases at the rates of dP / dt = 2.545 ×10-7 days yr-1 and dP / dt = 2.623 ×10-7 days yr-1 , respectively. Meanwhile, UY UMa also shows a cyclic period variation with a small amplitude of A = 0.0026 days superposed on the long-term increase. Due to their contact configurations, the secular period increases are interpreted as a result of mass transfer from the less massive component to the more massive one. The cyclic period variation of UY UMa may be interpreted in terms of either the magnetic activity or the light time effect.

Wavelet Analyses of Oil Prices, USD Variations and Impact on Logistics

NASA Astrophysics Data System (ADS)

Melek, M.; Tokgozlu, A.; Aslan, Z.

2009-07-01

This paper is related with temporal variations of historical oil prices and Dollar and Euro in Turkey. Daily data based on OECD and Central Bank of Turkey records beginning from 1946 has been considered. 1D-continuous wavelets and wavelet packets analysis techniques have been applied on data. Wavelet techniques help to detect abrupt changing's, increasing and decreasing trends of data. Estimation of variables has been presented by using linear regression estimation techniques. The results of this study have been compared with the small and large scale effects. Transportation costs of track show a similar variation with fuel prices. The second part of the paper is related with estimation of imports, exports, costs, total number of vehicles and annual variations by considering temporal variation of oil prices and Dollar currency in Turkey. Wavelet techniques offer a user friendly methodology to interpret some local effects on increasing trend of imports and exports data.

Spatial heterogeneity and temporal variations in Echinococcus multilocularis infections in wild hosts in a North American urban setting.

PubMed

Liccioli, Stefano; Kutz, Susan J; Ruckstuhl, Kathreen E; Massolo, Alessandro

2014-06-01

Echinococcus multilocularis, the causative agent of human alveolar echinococcosis, has the potential to circulate in urban areas where wild host populations and humans coexist. The spatial and temporal distribution of infection in wild hosts locally affects the risk of transmission to humans. We investigated the spatial and temporal patterns of E. multilocularis infection in coyotes and rodent intermediate hosts within the city of Calgary, Canada, and the association between spatial variations in coyote infection and the relative composition of small mammal assemblages. Infection by E. multilocularis was examined in small mammals and coyote faeces collected monthly in five city parks from June 2012 to June 2013. Coyote faeces were analysed using a ZnCl(2) centrifugation and sedimentation protocol. Infection in intermediate hosts was assessed through lethal trapping and post-mortem analysis. Parasite eggs and metacestodes were morphologically identified and molecularly confirmed through species-specific PCR assays. Of 982 small mammals captured, infection was detected in 2/305 (0.66%) deer mice (Peromyscus maniculatus), 2/267 (0.75%) meadow voles (Microtus pennsylvanicus), and 1/71 (1.41%) southern red backed voles (Myodes gapperi). Overall faecal prevalence in coyotes was 21.42% (n = 385) and varied across sites, ranging from 5.34% to 61.48%. Differences in coyote faecal prevalence across sites were consistent with local variations in the relative abundance of intermediate hosts within the small mammal assemblages. Infections peaked in intermediate hosts during autumn (0.68%) and winter (3.33%), and in coyotes during spring (43.47%). Peaks of infections in coyote faeces up to 83.8% in autumn were detected in a hyper-endemic area. To the best of our knowledge, our findings represent the first evidence of a sylvatic life-cycle of E. multilocularis in a North American urban setting, and provide new insights into the complexity of the parasite transmission ecology. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Quantification of intensity variations in functional MR images using rotated principal components

NASA Astrophysics Data System (ADS)

Backfrieder, W.; Baumgartner, R.; Sámal, M.; Moser, E.; Bergmann, H.

1996-08-01

In functional MRI (fMRI), the changes in cerebral haemodynamics related to stimulated neural brain activity are measured using standard clinical MR equipment. Small intensity variations in fMRI data have to be detected and distinguished from non-neural effects by careful image analysis. Based on multivariate statistics we describe an algorithm involving oblique rotation of the most significant principal components for an estimation of the temporal and spatial distribution of the stimulated neural activity over the whole image matrix. This algorithm takes advantage of strong local signal variations. A mathematical phantom was designed to generate simulated data for the evaluation of the method. In simulation experiments, the potential of the method to quantify small intensity changes, especially when processing data sets containing multiple sources of signal variations, was demonstrated. In vivo fMRI data collected in both visual and motor stimulation experiments were analysed, showing a proper location of the activated cortical regions within well known neural centres and an accurate extraction of the activation time profile. The suggested method yields accurate absolute quantification of in vivo brain activity without the need of extensive prior knowledge and user interaction.

Can natural variation in grain P concentrations be exploited in rice breeding to lower fertilizer requirements?

PubMed

Wang, Fanmiao; King, James Douglas Morrison; Rose, Terry; Kretzschmar, Tobias; Wissuwa, Matthias

2017-01-01

Agricultural usage of phosphorus (P) is largely driven by the amount of P removed from fields in harvested plant matter as offtake needs to be balanced by P fertilizer application. Reducing P concentration in grains is a way to decrease P offtake and reduce P fertilizer requirements or soil P mining where insufficient P is applied. Our objective was to assesses the genotypic variation for grain P concentration present within the rice gene pool and resolve to what extent it is affected by environment (P supply) or associated with genetic factors. About 2-fold variation in grain P concentrations were detected in two rice diversity panels, however, environmental effects were stronger than genotype effects. Genome wide association studies identified several putative loci associated with grain P concentrations. In most cases this was caused by minor haplotype associations with high grain P concentrations while associations with reduced P concentrations were identified on chromosomes 1, 6, 8, 11 and 12. Only the latter type of locus is of interest in breeding for reduced P concentrations and the most promising locus was at 20.7 Mb on chromosome 8, where a rare haplotype that was absent from all modern varieties studied reduced grain P concentration by 9.3%. This and all other loci were not consistently detected across environments or association panels, confirming that genetic effects were small compared to effects of environment. We conclude that the genetic effects detected were not sufficiently large or consistent to be of utility in plant breeding. Instead breeding efforts may have to rely on small to medium effect mutants already identified and attempt to achieve a more pronounced reduction in grain P concentration through the introgression of these mutants into a single genetic background.

Can natural variation in grain P concentrations be exploited in rice breeding to lower fertilizer requirements?

PubMed Central

Wang, Fanmiao; King, James Douglas Morrison; Rose, Terry; Kretzschmar, Tobias

2017-01-01

Agricultural usage of phosphorus (P) is largely driven by the amount of P removed from fields in harvested plant matter as offtake needs to be balanced by P fertilizer application. Reducing P concentration in grains is a way to decrease P offtake and reduce P fertilizer requirements or soil P mining where insufficient P is applied. Our objective was to assesses the genotypic variation for grain P concentration present within the rice gene pool and resolve to what extent it is affected by environment (P supply) or associated with genetic factors. About 2-fold variation in grain P concentrations were detected in two rice diversity panels, however, environmental effects were stronger than genotype effects. Genome wide association studies identified several putative loci associated with grain P concentrations. In most cases this was caused by minor haplotype associations with high grain P concentrations while associations with reduced P concentrations were identified on chromosomes 1, 6, 8, 11 and 12. Only the latter type of locus is of interest in breeding for reduced P concentrations and the most promising locus was at 20.7 Mb on chromosome 8, where a rare haplotype that was absent from all modern varieties studied reduced grain P concentration by 9.3%. This and all other loci were not consistently detected across environments or association panels, confirming that genetic effects were small compared to effects of environment. We conclude that the genetic effects detected were not sufficiently large or consistent to be of utility in plant breeding. Instead breeding efforts may have to rely on small to medium effect mutants already identified and attempt to achieve a more pronounced reduction in grain P concentration through the introgression of these mutants into a single genetic background. PMID:28651022

Non-radioactive detection of trinucleotide repeat size variability.

PubMed

Tomé, Stéphanie; Nicole, Annie; Gomes-Pereira, Mario; Gourdon, Genevieve

2014-03-06

Many human diseases are associated with the abnormal expansion of unstable trinucleotide repeat sequences. The mechanisms of trinucleotide repeat size mutation have not been fully dissected, and their understanding must be grounded on the detailed analysis of repeat size distributions in human tissues and animal models. Small-pool PCR (SP-PCR) is a robust, highly sensitive and efficient PCR-based approach to assess the levels of repeat size variation, providing both quantitative and qualitative data. The method relies on the amplification of a very low number of DNA molecules, through sucessive dilution of a stock genomic DNA solution. Radioactive Southern blot hybridization is sensitive enough to detect SP-PCR products derived from single template molecules, separated by agarose gel electrophoresis and transferred onto DNA membranes. We describe a variation of the detection method that uses digoxigenin-labelled locked nucleic acid probes. This protocol keeps the sensitivity of the original method, while eliminating the health risks associated with the manipulation of radiolabelled probes, and the burden associated with their regulation, manipulation and waste disposal.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.

PubMed

Castle, John; Garrett-Engele, Phil; Armour, Christopher D; Duenwald, Sven J; Loerch, Patrick M; Meyer, Michael R; Schadt, Eric E; Stoughton, Roland; Parrish, Mark L; Shoemaker, Daniel D; Johnson, Jason M

2003-01-01

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing

PubMed Central

Castle, John; Garrett-Engele, Phil; Armour, Christopher D; Duenwald, Sven J; Loerch, Patrick M; Meyer, Michael R; Schadt, Eric E; Stoughton, Roland; Parrish, Mark L; Shoemaker, Daniel D; Johnson, Jason M

2003-01-01

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing. PMID:14519201

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing.

PubMed

Vinner, Lasse; Mourier, Tobias; Friis-Nielsen, Jens; Gniadecki, Robert; Dybkaer, Karen; Rosenberg, Jacob; Langhoff, Jill Levin; Cruz, David Flores Santa; Fonager, Jannik; Izarzugaza, Jose M G; Gupta, Ramneek; Sicheritz-Ponten, Thomas; Brunak, Søren; Willerslev, Eske; Nielsen, Lars Peter; Hansen, Anders Johannes

2015-08-19

Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.

In-line verification of linewidth uniformity for 0.18 and below: design rule reticles

NASA Astrophysics Data System (ADS)

Tan, TaiSheng; Kuo, Shen C.; Wu, Clare; Falah, Reuven; Hemar, Shirley; Sade, Amikam; Gottlib, Gidon

2000-07-01

Mask making process development and control is addressed using a reticle inspection tool equipped with the new revolutionized application called LBM-Linewidth Bias Monitoring. In order to use the LBM for mask-making process control, procedures and corresponding test plates are a developed, such that routine monitoring of the manufacturing process discloses process variation and machine variation. At the same time systematic variation are studied and either taken care of or taken into consideration to allow successful production line work. In this paper the contribution of the LBM for mask quality monitoring is studied with respect to dense layers, e.g. DRAM. Another aspect of this application - the detection of very small CD mis-uniformity areas is discussed.

A framework to evaluate the effects of small area variations in healthcare infrastructure on diagnostics and patient outcomes of rare diseases based on administrative data.

PubMed

Stargardt, Tom; Schreyögg, Jonas

2012-05-01

Small area variations in healthcare infrastructure may result in differences in early detection and outcomes for patients with rare diseases. It is our aim to provide a framework for evaluating small area variations in healthcare infrastructure on the diagnostics and health outcomes of rare diseases. We focus on administrative data as it allows (a) for relatively large sample sizes even though the prevalence of rare diseases is very low, and (b) makes it possible to link information on healthcare infrastructure to morbidity, mortality, and utilization. For identifying patients with a rare disease in a database, a combination of different classification systems has to be used due to usually multiple diseases sharing one ICD code. Outcomes should be chosen that are (a) appropriate for the disease, (b) identifiable and reliably coded in the administrative database, and (c) observable during the limited time period of the follow-up. Risk adjustment using summary scores of disease-specific or comprehensive risk adjustment instruments might be preferable over empirical weights because of the lower number of variables needed. The proposed framework will help to identify differences in time to diagnosis and treatment outcomes across areas in the context of rare diseases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Detecting deviations from metronomic timing in music: effects of perceptual structure on the mental timekeeper.

PubMed

Repp, B H

1999-04-01

The detectability of a deviation from metronomic timing--of a small local increment in interonset interval (IOI) duration--in a musical excerpt is subject to positional biases, or "timing expectations," that are closely related to the expressive timing (sequence of IOI durations) typically produced by musicians in performance (Repp, 1992b, 1998c, 1998d). Experiment 1 replicated this finding with some changes in procedure and showed that the perception-performance correlation is not the result of formal musical training or availability of a musical score. Experiments 2 and 3 used a synchronization task to examine the hypothesis that participants' perceptual timing expectations are due to systematic modulations in the period of a mental timekeeper that also controls perceptual-motor coordination. Indeed, there was systematic variation in the asynchronies between taps and metronomically timed musical event onsets, and this variation was correlated both with the variations in IOI increment detectability (Experiment 1) and with the typical expressive timing pattern in performance. When the music contained local IOI increments (Experiment 2), they were almost perfectly compensated for on the next tap, regardless of their detectability in Experiment 1, which suggests a perceptual-motor feedback mechanism that is sensitive to subthreshold timing deviations. Overall, the results suggest that aspects of perceived musical structure influence the predictions of mental timekeeping mechanisms, thereby creating a subliminal warping of experienced time.

Characteristics of speaking style and implications for speech recognition.

PubMed

Shinozaki, Takahiro; Ostendorf, Mari; Atlas, Les

2009-09-01

Differences in speaking style are associated with more or less spectral variability, as well as different modulation characteristics. The greater variation in some styles (e.g., spontaneous speech and infant-directed speech) poses challenges for recognition but possibly also opportunities for learning more robust models, as evidenced by prior work and motivated by child language acquisition studies. In order to investigate this possibility, this work proposes a new method for characterizing speaking style (the modulation spectrum), examines spontaneous, read, adult-directed, and infant-directed styles in this space, and conducts pilot experiments in style detection and sampling for improved speech recognizer training. Speaking style classification is improved by using the modulation spectrum in combination with standard pitch and energy variation. Speech recognition experiments on a small vocabulary conversational speech recognition task show that sampling methods for training with a small amount of data benefit from the new features.

High-throughput infrared spectrometer for standoff chemical detection

NASA Astrophysics Data System (ADS)

Chadha, Suneet; Stevenson, Chuck; Curtiss, Lawrence E.

1999-01-01

Advanced autonomous detection of chemical warfare agents and other organic materials has long been a major military concern. While significant advances have recently been accomplished in remote spectral sensing using rugged FTIRs with point detectors, efforts towards spatial chemical discrimination have been lacking. Foster-Miller, Inc. has developed a radically different mid-IR and long wave IR spectrometer for standoff detection of chemical warfare agents and other molecular species.This no moving parts device will eliminate the cost, complexity, reliability and bandwidth/resolution problems associated with either Fabry Perot or Michelson Interferometer based approaches currently under consideration. Given the small size and performance insensitivity to on-board vibration, high EMI, thermal variations, the proposed optic would easily adapt cryocooling and field deployable requirements for low radiance detection.

Water quality of Lake Austin and Town Lake, Austin, Texas

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

Andrews, F.L.; Wells, F.C.; Shelby, W.J.

1988-01-01

Lake Austin and Town Lake are impoundments on the Colorado River in Travis County, central Texas, and are a source of water for municipal industrial water supplies, electrical-power generation, and recreation for more than 500,000 people in the Austin metropolitan area. Small vertical temperature variations in both lakes were attributed to shallow depths in the lakes and short retention times of water in the lakes during the summer months. The largest areal variations in dissolved oxygen generally occur in Lake Austin during the summer as a result of releases of water from below the thermocline in Lake Travis. Except formore » iron, manganese, and mercury, dissolved concentrations of trace elements in water collected from Lake Austin and Town Lake did not exceed the primary or secondary drinking water standards set by the US Environmental Protection Agency. Little or no effect of stormwater runoff on temperature, dissolved oxygen, or minor elements could be detected in either Lake Austin or Town Lake. Little seasonal or areal variation was noted in nitrogen concentrations in Lake Austin or Town lake. Total phosphorus concentrations generally were small in both lakes. Increased concentrations of nitrogen and phosphorus were detected after storm runoff inflow in Town Lake, but not in Lake Austin; densities of fecal-coliform bacteria increased in Lake Austin and Town Lake, but were substantially greater in Town Lake than in Lake Austin. 18 refs., 38 figs., 59 tabs.« less

High-sensitivity density fluctuation detector

NASA Technical Reports Server (NTRS)

Azzazy, M.; Modarress, D.; Hoeft, T.

1987-01-01

A high-sensitivity differential interferometer has been developed to detect small density fluctuations over an optical path length of the order of the boundary layer thickness near transition. Two experimental configurations have been used to evaluate the performance of the interferometer: an open shear-layer configuration and a wind-tunnel turbulent spot configuration. In each experiment small temperature fluctuations were introduced as the signal source. Simultaneous cold-wire measurements have been compared with the interferometer data. The comparison shows that the interferometer is sensitive to very weak phase variations of the order of 0.001 of the laser wavelength.

[Development of a continuous blood pressure monitoring and recording system].

PubMed

Zhang, Yang; Li, Yong; Gao, Shumei; Song, Yilin

2012-09-01

A small experimental system is constructed with working principle of continuous blood pressure monitoring based on the volume compensation method. The preliminary experimental results show that the system can collect blood pressure signals at the radial artery effectively. The digital PID algorithm can track the variation of blood pressure. And the accuracy of continuous blood pressure detecting achieve the level of same kind of product.

Characterization of naturally developing small intestinal bacterial overgrowth in 16 German shepherd dogs.

PubMed

Willard, M D; Simpson, R B; Fossum, T W; Cohen, N D; Delles, E K; Kolp, D L; Carey, D P; Reinhart, G A

1994-04-15

Sixteen German Shepherd Dogs were found, via quantitative microbial culture of intestinal fluid samples, to have small intestinal bacterial overgrowth (IBO) over an 11-month period. All dogs were deficient in serum IgA. Consistent clinical signs suggestive of an alimentary tract disorder were not observed. Serum cobalamin determinations were not helpful in detecting IBO. Serum folate concentrations had variable sensitivity and specificity for detecting dogs from which we could culture > or = 1 x 10(5) bacterial/ml from intestinal fluid samples in the nonfed state. Histologic and intestinal mucosal cytologic examinations were not useful in detecting IBO. Substantial within-dog and between-dog variation was found in the numbers and species of bacteria in the intestines. The difficulty in diagnosing IBO, the variability in organisms found in individual dogs on repeated sampling, the likelihood that intestinal fluid microbial cultures failed to diagnose IBO in some dogs, and the potential of IBO to be clinically inapparent were the most important findings in this study.

PROTON MICROPROBE ANALYSIS OF TRACE-ELEMENT VARIATIONS IN VITRINITES IN THE SAME AND DIFFERENT COAL BEDS.

USGS Publications Warehouse

Minkin, J.A.; Chao, E.C.T.; Blank, Herma; Dulong, F.T.

1987-01-01

The PIXE (proton-induced X-ray emission) microprobe can be used for nondestructive, in-situ analyses of areas as small as those analyzed by the electron microprobe, and has a sensitivity of detection as much as two orders of magnitude better than the electron microprobe. Preliminary studies demonstrated that PIXE provides a capability for quantitative determination of elemental concentrations in individual coal maceral grains with a detection limit of 1-10 ppm for most elements analyzed. Encouraged by the earlier results, we carried out the analyses reported below to examine trace element variations laterally (over a km range) as well as vertically (cm to m) in the I and J coal beds in the Upper Cretaceous Ferron Sandstone Member of the Mancos Shale in central Utah, and to compare the data with the data from two samples of eastern coals of Pennsylvanian age.

Novel applications of array comparative genomic hybridization in molecular diagnostics.

PubMed

Cheung, Sau W; Bi, Weimin

2018-05-31

In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

Automated mask and wafer defect classification using a novel method for generalized CD variation measurements

NASA Astrophysics Data System (ADS)

Verechagin, V.; Kris, R.; Schwarzband, I.; Milstein, A.; Cohen, B.; Shkalim, A.; Levy, S.; Price, D.; Bal, E.

2018-03-01

Over the years, mask and wafers defects dispositioning has become an increasingly challenging and time consuming task. With design rules getting smaller, OPC getting complex and scanner illumination taking on free-form shapes - the probability of a user to perform accurate and repeatable classification of defects detected by mask inspection tools into pass/fail bins is reducing. The critical challenging of mask defect metrology for small nodes ( < 30 nm) was reviewed in [1]. While Critical Dimension (CD) variation measurement is still the method of choice for determining a mask defect future impact on wafer, the high complexity of OPCs combined with high variability in pattern shapes poses a challenge for any automated CD variation measurement method. In this study, a novel approach for measurement generalization is presented. CD variation assessment performance is evaluated on multiple different complex shape patterns, and is benchmarked against an existing qualified measurement methodology.

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

PubMed Central

Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

2015-01-01

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

Effects of the magnetic field variation on the spin wave interference in a magnetic cross junction

NASA Astrophysics Data System (ADS)

Balynskiy, M.; Chiang, H.; Kozhevnikov, A.; Dudko, G.; Filimonov, Y.; Balandin, A. A.; Khitun, A.

2018-05-01

This article reports results of the investigation of the effect of the external magnetic field variation on the spin wave interference in a magnetic cross junction. The experiments were performed using a micrometer scale Y3Fe5O12 cross structure with a set of micro-antennas fabricated on the edges of the cross arms. Two of the antennas were used for the spin wave excitation while a third antenna was used for detecting the inductive voltage produced by the interfering spin waves. It was found that a small variation of the bias magnetic field may result in a significant change of the output inductive voltage. The effect is most prominent under the destructive interference condition. The maximum response exceeds 30 dB per 0.1 Oe at room temperature. It takes a relatively small bias magnetic field variation of about 1 Oe to drive the system from the destructive to the constructive interference conditions. The switching is accompanied by a significant, up to 50 dB, change in the output voltage. The obtained results demonstrate a feasibility of the efficient spin wave interference control by an external magnetic field, which may be utilized for engineering novel type of magnetometers and magnonic logic devices.

A comparison of EBSD based strain indicators for the study of Fe-3Si steel subjected to cyclic loading

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

Schayes, Claire; Valeo Engine Electrical Systems, 2 Rue André Boulle, 94046 Créteil; Bouquerel, Jérémie, E-mail: jeremie.bouquerel@univ-lille1.fr

The current work aims at proposing an EBSD-based indicator for fatigue damage of a Fe-3Si steel. At the same time direct observation of dislocation structures is provided by electron channelling contrast imaging (ECCI). The investigation consisted in processing the EBSD data from patterns collected on specimen subjected to low cycle fatigue. It revealed two different regimes depending on the applied total strain variation which is explained by the identification of the dislocations structures and their evolution. At low strain variation, strain accommodation occurs by planar glide of dislocations uniformly distributed throughout the grains. No misorientation evolution is observed. At highermore » strain variation, the vein-channel structure is observed within the grain and the wall-channel structure in the vicinity of grain boundaries. The misorientation between these two dislocation structures is evaluated at about 0.7° which is detected by the EBSD analyses and explains the increase of the different misorientation based criteria. The EBSD study enables also the prediction of crack initiation mode. Finally, this study points out the limits of the EBSD technique as no misorientation evolution is detected at small strain variation. Indeed, the lattice distortion is too weak to be detected by conventional EBSD. - Highlights: • Microstructure investigation of the fatigue behaviour of an iron-silicon steel • Use of cECCI to investigate the fatigue dislocations structures • Characterisation of local plastic accommodation through EBSD misorientation criteria.« less

Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes.

PubMed

Beghain, Johann; Langlois, Anne-Claire; Legrand, Eric; Grange, Laura; Khim, Nimol; Witkowski, Benoit; Duru, Valentine; Ma, Laurence; Bouchier, Christiane; Ménard, Didier; Paul, Richard E; Ariey, Frédéric

2016-04-12

In eukaryotic genomes, deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation. In Plasmodium falciparum, relatively few transcription factors have been identified, and the regulation of transcription is seemingly largely influenced by gene amplification events. Thus copy number variation (CNV) is a major mechanism enabling parasite genomes to adapt to new environmental changes. Currently, the detection of CNVs is based on quantitative PCR (qPCR), which is significantly limited by the relatively small number of genes that can be analysed at any one time. Technological advances that facilitate whole-genome sequencing, such as next generation sequencing (NGS) enable deeper analyses of the genomic variation to be performed. Because the characteristics of Plasmodium CNVs need special consideration in algorithms and strategies for which classical CNV detection programs are not suited a dedicated algorithm to detect CNVs across the entire exome of P. falciparum was developed. This algorithm is based on a custom read depth strategy through NGS data and called PlasmoCNVScan. The analysis of CNV identification on three genes known to have different levels of amplification and which are located either in the nuclear, apicoplast or mitochondrial genomes is presented. The results are correlated with the qPCR experiments, usually used for identification of locus specific amplification/deletion. This tool will facilitate the study of P. falciparum genomic adaptation in response to ecological changes: drug pressure, decreased transmission, reduction of the parasite population size (transition to pre-elimination endemic area).

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

Kataria, T.; Showman, A. P.; Fortney, J. J.

We present three-dimensional atmospheric circulation models of GJ 1214b, a 2.7 Earth-radius, 6.5 Earth-mass super Earth detected by the MEarth survey. Here we explore the planet's circulation as a function of atmospheric metallicity and atmospheric composition, modeling atmospheres with a low mean molecular weight (MMW; i.e., H{sub 2}-dominated) and a high MMW (i.e., water- and CO{sub 2}-dominated). We find that atmospheres with a low MMW have strong day-night temperature variations at pressures above the infrared photosphere that lead to equatorial superrotation. For these atmospheres, the enhancement of atmospheric opacities with increasing metallicity lead to shallower atmospheric heating, larger day-night temperaturemore » variations, and hence stronger superrotation. In comparison, atmospheres with a high MMW have larger day-night and equator-to-pole temperature variations than low MMW atmospheres, but differences in opacity structure and energy budget lead to differences in jet structure. The circulation of a water-dominated atmosphere is dominated by equatorial superrotation, while the circulation of a CO{sub 2}-dominated atmosphere is instead dominated by high-latitude jets. By comparing emergent flux spectra and light curves for 50× solar and water-dominated compositions, we show that observations in emission can break the degeneracy in determining the atmospheric composition of GJ 1214b. The variation in opacity with wavelength for the water-dominated atmosphere leads to large phase variations within water bands and small phase variations outside of water bands. The 50× solar atmosphere, however, yields small variations within water bands and large phase variations at other characteristic wavelengths. These observations would be much less sensitive to clouds, condensates, and hazes than transit observations.« less

Two-Way Gold Nanoparticle Label-Free Sensing of Specific Sequence and Small Molecule Targets Using Switchable Concatemers.

PubMed

Zhu, Longjiao; Shao, Xiangli; Luo, Yunbo; Huang, Kunlung; Xu, Wentao

2017-05-19

A two-way colorimetric biosensor based on unmodified gold nanoparticles (GNPs) and a switchable double-stranded DNA (dsDNA) concatemer have been demonstrated. Two hairpin probes (H1 and H2) were first designed that provided the fuels to assemble the dsDNA concatemers via hybridization chain reaction (HCR). A functional hairpin (FH) was rationally designed to recognize the target sequences. All the hairpins contained a single-stranded DNA (ssDNA) loop and sticky end to prevent GNPs from salt-induced aggregation. In the presence of target sequence, the capture probe blocked in the FH recognizes the target to form a duplex DNA, which causes the release of the initiator probe by FH conformational change. This process then starts the alternate-opening of H1 and H2 through HCR, and dsDNA concatemers grow from the target sequence. As a result, unmodified GNPs undergo salt-induced aggregation because the formed dsDNA concatemers are stiffer and provide less stabilization. A light purple-to-blue color variation was observed in the bulk solution, termed the light-off sensing way. Furthermore, H1 ingeniously inserted an aptamer sequence to generate dsDNA concatemers with multiple small molecule binding sites. In the presence of small molecule targets, concatemers can be disassembled into mixtures with ssDNA sticky ends. A blue-to-purple reverse color variation was observed due to the regeneration of the ssDNA, termed the light-on way. The two-way biosensor can detect both nucleic acids and small molecule targets with one sensing device. This switchable sensing element is label-free, enzyme-free, and sophisticated-instrumentation-free. The detection limits of both targets were below nanomolar.

Biases in the OSSOS Detection of Large Semimajor Axis Trans-Neptunian Objects

NASA Astrophysics Data System (ADS)

Gladman, Brett; Shankman, Cory; OSSOS Collaboration

2017-10-01

The accumulating but small set of large semimajor axis trans-Neptunian objects (TNOs) shows an apparent clustering in the orientations of their orbits. This clustering must either be representative of the intrinsic distribution of these TNOs, or else have arisen as a result of observation biases and/or statistically expected variations for such a small set of detected objects. The clustered TNOs were detected across different and independent surveys, which has led to claims that the detections are therefore free of observational bias. This apparent clustering has led to the so-called “Planet 9” hypothesis that a super-Earth currently resides in the distant solar system and causes this clustering. The Outer Solar System Origins Survey (OSSOS) is a large program that ran on the Canada-France-Hawaii Telescope from 2013 to 2017, discovering more than 800 new TNOs. One of the primary design goals of OSSOS was the careful determination of observational biases that would manifest within the detected sample. We demonstrate the striking and non-intuitive biases that exist for the detection of TNOs with large semimajor axes. The eight large semimajor axis OSSOS detections are an independent data set, of comparable size to the conglomerate samples used in previous studies. We conclude that the orbital distribution of the OSSOS sample is consistent with being detected from a uniform underlying angular distribution.

OSSOS. VI. Striking Biases in the Detection of Large Semimajor Axis Trans-Neptunian Objects

NASA Astrophysics Data System (ADS)

Shankman, Cory; Kavelaars, J. J.; Bannister, Michele T.; Gladman, Brett J.; Lawler, Samantha M.; Chen, Ying-Tung; Jakubik, Marian; Kaib, Nathan; Alexandersen, Mike; Gwyn, Stephen D. J.; Petit, Jean-Marc; Volk, Kathryn

2017-08-01

The accumulating but small set of large semimajor axis trans-Neptunian objects (TNOs) shows an apparent clustering in the orientations of their orbits. This clustering must either be representative of the intrinsic distribution of these TNOs, or else have arisen as a result of observation biases and/or statistically expected variations for such a small set of detected objects. The clustered TNOs were detected across different and independent surveys, which has led to claims that the detections are therefore free of observational bias. This apparent clustering has led to the so-called “Planet 9” hypothesis that a super-Earth currently resides in the distant solar system and causes this clustering. The Outer Solar System Origins Survey (OSSOS) is a large program that ran on the Canada–France–Hawaii Telescope from 2013 to 2017, discovering more than 800 new TNOs. One of the primary design goals of OSSOS was the careful determination of observational biases that would manifest within the detected sample. We demonstrate the striking and non-intuitive biases that exist for the detection of TNOs with large semimajor axes. The eight large semimajor axis OSSOS detections are an independent data set, of comparable size to the conglomerate samples used in previous studies. We conclude that the orbital distribution of the OSSOS sample is consistent with being detected from a uniform underlying angular distribution.

Lateral variations of the Guerrero-Oaxaca subduction zone (Mexico) derived from weak seismicity (Mb3.5+) detected on a single array at teleseismic distance

NASA Astrophysics Data System (ADS)

Letort, Jean; Retailleau, Lise; Boué, Pierre; Radiguet, Mathilde; Gardonio, Blandine; Cotton, Fabrice; Campillo, Michel

2018-05-01

Detections of pP and sP phase arrivals (the so-called depth phases) at teleseismic distance provide one of the best ways to estimate earthquake focal depth, as the P-pP and the P-sP delays are strongly dependent on the depth. Based on a new processing workflow and using a single seismic array at teleseismic distance, we can estimate the depth of clusters of small events down to magnitude Mb 3.5. Our method provides a direct view of the relative variations of the seismicity depth from an active area. This study focuses on the application of this new methodology to study the lateral variations of the Guerrero subduction zone (Mexico) using the Eielson seismic array in Alaska (USA). After denoising the signals, 1232 Mb 3.5 + events were detected, with clear P, pP, sP and PcP arrivals. A high-resolution view of the lateral variations of the depth of the seismicity of the Guerero-Oaxaca area is thus obtained. The seismicity is shown to be mainly clustered along the interface, coherently following the geometry of the plate as constrained by the receiver-function analysis along the Meso America Subduction Experiment profile. From this study, the hypothesis of tears on the western part of Guerrero and the eastern part of Oaxaca are strongly confirmed by dramatic lateral changes in the depth of the earthquake clusters. The presence of these two tears might explain the observed lateral variations in seismicity, which is correlated with the boundaries of the slow slip events.

Qualitative and quantitative determination of extractives in heartwood of Scots pine (Pinus sylvestris L.) by gas chromatography.

PubMed

Ekeberg, Dag; Flaete, Per-Otto; Eikenes, Morten; Fongen, Monica; Naess-Andresen, Carl Fredrik

2006-03-24

A method for quantitative determination of extractives from heartwood of Scots pine (Pinus sylvestris L.) using gas chromatography (GC) with flame ionization detection (FID) was developed. The limit of detection (LOD) was 0.03 mg/g wood and the linear range (r = 0.9994) was up to 10 mg/g with accuracy within +/- 10% and precision of 18% relative standard deviation. The identification of the extractives was performed using gas chromatography combined with mass spectrometry (GC-MS). The yields of extraction by Soxhlet were tested for solid wood, small particles and fine powder. Small particles were chosen for further analysis. This treatment gave good yields of the most important extractives: pinosylvin, pinosylvin monomethyl ether, resin acids and free fatty acids. The method is used to demonstrate the variation of these extractives across stems and differences in north-south direction.

Are There Long-Run Effects of the Minimum Wage?

PubMed Central

Sorkin, Isaac

2014-01-01

An empirical consensus suggests that there are small employment effects of minimum wage increases. This paper argues that these are short-run elasticities. Long-run elasticities, which may differ from short-run elasticities, are policy relevant. This paper develops a dynamic industry equilibrium model of labor demand. The model makes two points. First, long-run regressions have been misinterpreted because even if the short- and long-run employment elasticities differ, standard methods would not detect a difference using US variation. Second, the model offers a reconciliation of the small estimated short-run employment effects with the commonly found pass-through of minimum wage increases to product prices. PMID:25937790

Are There Long-Run Effects of the Minimum Wage?

PubMed

Sorkin, Isaac

2015-04-01

An empirical consensus suggests that there are small employment effects of minimum wage increases. This paper argues that these are short-run elasticities. Long-run elasticities, which may differ from short-run elasticities, are policy relevant. This paper develops a dynamic industry equilibrium model of labor demand. The model makes two points. First, long-run regressions have been misinterpreted because even if the short- and long-run employment elasticities differ, standard methods would not detect a difference using US variation. Second, the model offers a reconciliation of the small estimated short-run employment effects with the commonly found pass-through of minimum wage increases to product prices.

Temporal variation of tectonic tremor activity in southern Taiwan around the 2010 ML6.4 Jiashian earthquake

NASA Astrophysics Data System (ADS)

Chao, Kevin; Peng, Zhigang; Hsu, Ya-Ju; Obara, Kazushige; Wu, Chunquan; Ching, Kuo-En; van der Lee, Suzan; Pu, Hsin-Chieh; Leu, Peih-Lin; Wech, Aaron

2017-07-01

Deep tectonic tremor, which is extremely sensitive to small stress variations, could be used to monitor fault zone processes during large earthquake cycles and aseismic processes before large earthquakes. In this study, we develop an algorithm for the automatic detection and location of tectonic tremor beneath the southern Central Range of Taiwan and examine the spatiotemporal relationship between tremor and the 4 March 2010 ML6.4 Jiashian earthquake, located about 20 km from active tremor sources. We find that tremor in this region has a relatively short duration, short recurrence time, and no consistent correlation with surface GPS data. We find a short-term increase in the tremor rate 19 days before the Jiashian main shock, and around the time when the tremor rate began to rise one GPS station recorded a flip in its direction of motion. We hypothesize that tremor is driven by a slow-slip event that preceded the occurrence of the shallower Jiashian main shock, even though the inferred slip is too small to be observed by all GPS stations. Our study shows that tectonic tremor may reflect stress variation during the prenucleation process of a nearby earthquake.

High-Speed Incoming Infrared Target Detection by Fusion of Spatial and Temporal Detectors

PubMed Central

Kim, Sungho

2015-01-01

This paper presents a method for detecting high-speed incoming targets by the fusion of spatial and temporal detectors to achieve a high detection rate for an active protection system (APS). The incoming targets have different image velocities according to the target-camera geometry. Therefore, single-target detector-based approaches, such as a 1D temporal filter, 2D spatial filter and 3D matched filter, cannot provide a high detection rate with moderate false alarms. The target speed variation was analyzed according to the incoming angle and target velocity. The speed of the distant target at the firing time is almost stationary and increases slowly. The speed varying targets are detected stably by fusing the spatial and temporal filters. The stationary target detector is activated by an almost zero temporal contrast filter (TCF) and identifies targets using a spatial filter called the modified mean subtraction filter (M-MSF). A small motion (sub-pixel velocity) target detector is activated by a small TCF value and finds targets using the same spatial filter. A large motion (pixel-velocity) target detector works when the TCF value is high. The final target detection is terminated by fusing the three detectors based on the threat priority. The experimental results of the various target sequences show that the proposed fusion-based target detector produces the highest detection rate with an acceptable false alarm rate. PMID:25815448

Mass-induced sea level variations in the Red Sea from GRACE, steric-corrected altimetry, in situ bottom pressure records, and hydrographic observations

NASA Astrophysics Data System (ADS)

Feng, W.; Lemoine, J.-M.; Zhong, M.; Hsu, H. T.

2014-08-01

An annual amplitude of ∼18 cm mass-induced sea level variations (SLV) in the Red Sea is detected from the Gravity Recovery and Climate Experiment (GRACE) satellites and steric-corrected altimetry from 2003 to 2011. The annual mass variations in the region dominate the mean SLV, and generally reach maximum in late January/early February. The annual steric component of the mean SLV is relatively small (<3 cm) and out of phase of the mass-induced SLV. In situ bottom pressure records at the eastern coast of the Red Sea validate the high mass variability observed by steric-corrected altimetry and GRACE. In addition, the horizontal water mass flux of the Red Sea estimated from GRACE and steric-corrected altimetry is validated by hydrographic observations.

Comparative sequencing in the genus Lycopersicon. Implications for the evolution of fruit size in the domestication of cultivated tomatoes.

PubMed Central

Nesbitt, T Clint; Tanksley, Steven D

2002-01-01

Sequence variation was sampled in cultivated and related wild forms of tomato at fw2.2--a fruit weight QTL key to the evolution of domesticated tomatoes. Variation at fw2.2 was contrasted with variation at four other loci not involved in fruit weight determination. Several conclusions could be reached: (1) Fruit weight variation attributable to fw2.2 is not caused by variation in the FW2.2 protein sequence; more likely, it is due to transcriptional variation associated with one or more of eight nucleotide changes unique to the promoter of large-fruit alleles; (2) fw2.2 and loci not involved in fruit weight have not evolved at distinguishably different rates in cultivated and wild tomatoes, despite the fact that fw2.2 was likely a target of selection during domestication; (3) molecular-clock-based estimates suggest that the large-fruit allele of fw2.2, now fixed in most cultivated tomatoes, arose in tomato germplasm long before domestication; (4) extant accessions of L. esculentum var. cerasiforme, the subspecies thought to be the most likely wild ancestor of domesticated tomatoes, appear to be an admixture of wild and cultivated tomatoes rather than a transitional step from wild to domesticated tomatoes; and (5) despite the fact that cerasiforme accessions are polymorphic for large- and small-fruit alleles at fw2.2, no significant association was detected between fruit size and fw2.2 genotypes in the subspecies--as tested by association genetic studies in the relatively small sample studied--suggesting the role of other fruit weight QTL in fruit weight variation in cerasiforme. PMID:12242247

Hawk Eyes I: Diurnal Raptors Differ in Visual Fields and Degree of Eye Movement

PubMed Central

O'Rourke, Colleen T.; Hall, Margaret I.; Pitlik, Todd; Fernández-Juricic, Esteban

2010-01-01

Background Different strategies to search and detect prey may place specific demands on sensory modalities. We studied visual field configuration, degree of eye movement, and orbit orientation in three diurnal raptors belonging to the Accipitridae and Falconidae families. Methodology/Principal Findings We used an ophthalmoscopic reflex technique and an integrated 3D digitizer system. We found inter-specific variation in visual field configuration and degree of eye movement, but not in orbit orientation. Red-tailed Hawks have relatively small binocular areas (∼33°) and wide blind areas (∼82°), but intermediate degree of eye movement (∼5°), which underscores the importance of lateral vision rather than binocular vision to scan for distant prey in open areas. Cooper's Hawks' have relatively wide binocular fields (∼36°), small blind areas (∼60°), and high degree of eye movement (∼8°), which may increase visual coverage and enhance prey detection in closed habitats. Additionally, we found that Cooper's Hawks can visually inspect the items held in the tip of the bill, which may facilitate food handling. American Kestrels have intermediate-sized binocular and lateral areas that may be used in prey detection at different distances through stereopsis and motion parallax; whereas the low degree eye movement (∼1°) may help stabilize the image when hovering above prey before an attack. Conclusions We conclude that: (a) there are between-species differences in visual field configuration in these diurnal raptors; (b) these differences are consistent with prey searching strategies and degree of visual obstruction in the environment (e.g., open and closed habitats); (c) variations in the degree of eye movement between species appear associated with foraging strategies; and (d) the size of the binocular and blind areas in hawks can vary substantially due to eye movements. Inter-specific variation in visual fields and eye movements can influence behavioral strategies to visually search for and track prey while perching. PMID:20877645

Hawk eyes I: diurnal raptors differ in visual fields and degree of eye movement.

PubMed

O'Rourke, Colleen T; Hall, Margaret I; Pitlik, Todd; Fernández-Juricic, Esteban

2010-09-22

Different strategies to search and detect prey may place specific demands on sensory modalities. We studied visual field configuration, degree of eye movement, and orbit orientation in three diurnal raptors belonging to the Accipitridae and Falconidae families. We used an ophthalmoscopic reflex technique and an integrated 3D digitizer system. We found inter-specific variation in visual field configuration and degree of eye movement, but not in orbit orientation. Red-tailed Hawks have relatively small binocular areas (∼33°) and wide blind areas (∼82°), but intermediate degree of eye movement (∼5°), which underscores the importance of lateral vision rather than binocular vision to scan for distant prey in open areas. Cooper's Hawks' have relatively wide binocular fields (∼36°), small blind areas (∼60°), and high degree of eye movement (∼8°), which may increase visual coverage and enhance prey detection in closed habitats. Additionally, we found that Cooper's Hawks can visually inspect the items held in the tip of the bill, which may facilitate food handling. American Kestrels have intermediate-sized binocular and lateral areas that may be used in prey detection at different distances through stereopsis and motion parallax; whereas the low degree eye movement (∼1°) may help stabilize the image when hovering above prey before an attack. We conclude that: (a) there are between-species differences in visual field configuration in these diurnal raptors; (b) these differences are consistent with prey searching strategies and degree of visual obstruction in the environment (e.g., open and closed habitats); (c) variations in the degree of eye movement between species appear associated with foraging strategies; and (d) the size of the binocular and blind areas in hawks can vary substantially due to eye movements. Inter-specific variation in visual fields and eye movements can influence behavioral strategies to visually search for and track prey while perching.

Interannual variability of sorted bedforms in the coastal German Bight (SE North Sea)

NASA Astrophysics Data System (ADS)

Mielck, F.; Holler, P.; Bürk, D.; Hass, H. C.

2015-12-01

Sorted bedforms are ubiquitous on the inner continental shelves worldwide. They are described as spatially-grain-size-sorted features consisting of small rippled medium-to-coarse sand and can remain stable for decades. However, the knowledge about their genesis and development is still fragmentary. For this study, a representative investigation area (water depth<15 m) located on the shelf west of the island of Sylt (SE North Sea, Germany) was periodically surveyed with hydroacoustic means (i.e. sidescan sonar, multibeam echo sounder, and sub-bottom profiler) during 2010-2014. Since this area is influenced by tidal and wind-driven currents, the aim was to detect and examine interannual variabilities in the characteristics of the prevailing sorted bedforms. Our measurements reveal sinuous stripes of rippled medium sand which are embedded in shallow symmetrical depressions. These domains are surrounded by relatively smooth fine-sand areas. These sorted bedforms were identified as flow-transverse features that are maintained by ebb and flood currents of almost equal strengths that flow in opposite directions. This bidirectional flow field generates sharp boundaries between the medium- and fine-sand domains in both current directions. Further to the north, where flood currents are dominant, asymmetric sorted bedforms were detected which show sharp boundaries only in flood-current direction. Comparisons between the measurements of the different years show no significant variations in morphology and distribution of the sorted bedforms. However, variations of the boundaries between the medium and the fine-sand domains were observed. Additionally, new minor sorted bedforms and rippled excavation marks as well as new fine-sand areas developed and disappeared occasionally. It can be supposed that such sediment winnowing and focusing processes take place during periodically recurring storm surges, which change the shapes of the features. Moreover, variations in alignments and sizes of the small ripple formations were detected. They seem to indicate the directions and intensities of previous storm events.

Variation in functional ascospore parts in the ascomycetous yeast Dipodascopsis uninucleata.

PubMed

Bareetseng, A S; Kock, J L F; Pohl, C H; Pretorius, E E; Van Wyk, P W J

2004-04-01

A variation in functional ascospore morphology was detected using electron microscopy (EM) in two varieties of the yeast Dipodascopsis uninucleata, i.e., D. uninucleata var. uninucleata and D. uninucleata var. wickerhamii. It was found that the latter produces ascospores characterized by the absence of small surface hooks which have been implicated in the release and re-assembly of ascospores in D. uninucleata var. uninucleata. These varieties are closely related on the basis of their mode of sexual reproduction, ascospore morphology as observed under the light microscope, physiological characteristics as well as the extent of divergence in the variable D1/D2 domain of the large subunit 26S ribosomal DNA.

Sequence Variation in the Small-Subunit rRNA Gene of Plasmodium malariae and Prevalence of Isolates with the Variant Sequence in Sichuan, China

PubMed Central

Liu, Qing; Zhu, Shenghua; Mizuno, Sahoko; Kimura, Masatsugu; Liu, Peina; Isomura, Shin; Wang, Xingzhen; Kawamoto, Fumihiko

1998-01-01

By two PCR-based diagnostic methods, Plasmodium malariae infections have been rediscovered at two foci in the Sichuan province of China, a region where no cases of P. malariae have been officially reported for the last 2 decades. In addition, a variant form of P. malariae which has a deletion of 19 bp and seven substitutions of base pairs in the target sequence of the small-subunit (SSU) rRNA gene was detected with high frequency. Alignment analysis of Plasmodium sp. SSU rRNA gene sequences revealed that the 5′ region of the variant sequence is identical to that of P. vivax or P. knowlesi and its 3′ region is identical to that of P. malariae. The same sequence variations were also found in P. malariae isolates collected along the Thai-Myanmar border, suggesting a wide distribution of this variant form from southern China to Southeast Asia. PMID:9774600

Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

PubMed Central

Goldsmith, Dawn B.; Parsons, Rachel J.; Beyene, Damitu; Salamon, Peter

2015-01-01

Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years. PMID:26157645

Multi-ampoule Bridgman growth of halide scintillator crystals using the self-seeding method

NASA Astrophysics Data System (ADS)

Lindsey, Adam C.; Wu, Yuntao; Zhuravleva, Mariya; Loyd, Matthew; Koschan, Merry; Melcher, Charles L.

2017-07-01

We investigate the multi-ampoule growth at 25 mm diameter of ternary iodide single crystal scintillator KCaI3:Eu using the randomly oriented self-seeded Bridgman method. We compare scintillation performance between cubic inch scale crystals containing small variations of low nominal europium concentrations previously shown to balance light yield with self-absorption in the host crystal. Growth conditions were optimized in the developmental furnace and four 2 in3 KCaI3:Eu crystals were grown simultaneously producing a total of six 25 mm × 25 mm cylinders. Small variations in activator concentration did not result in significant performance differences among the six measured crystals. A range of energy resolutions of 3.5-4.7% at 662 keV was achieved, surpassing that of NaI:Tl crystals commonly used in spectroscopic detection applications. The function and basic design of the multi-ampoule furnace as well as the process of growing single crystals of KCaI3 is included here.

Usual normalization strategies for gene expression studies impair the detection and analysis of circadian patterns.

PubMed

Figueredo, Diego de Siqueira; Barbosa, Mayara Rodrigues; Coimbra, Daniel Gomes; Dos Santos, José Luiz Araújo; Costa, Ellyda Fernanda Lopes; Koike, Bruna Del Vechio; Alexandre Moreira, Magna Suzana; de Andrade, Tiago Gomes

2018-03-01

Recent studies have shown that transcriptomes from different tissues present circadian oscillations. Therefore, the endogenous variation of total RNA should be considered as a potential bias in circadian studies of gene expression. However, normalization strategies generally include the equalization of total RNA concentration between samples prior to cDNA synthesis. Moreover, endogenous housekeeping genes (HKGs) frequently used for data normalization may exhibit circadian variation and distort experimental results if not detected or considered. In this study, we controlled experimental conditions from the amount of initial brain tissue samples through extraction steps, cDNA synthesis, and quantitative real time PCR (qPCR) to demonstrate a circadian oscillation of total RNA concentration. We also identified that the normalization of the RNA's yield affected the rhythmic profiles of different genes, including Per1-2 and Bmal1. Five widely used HKGs (Actb, Eif2a, Gapdh, Hprt1, and B2m) also presented rhythmic variations not detected by geNorm algorithm. In addition, the analysis of exogenous microRNAs (Cel-miR-54 and Cel-miR-39) spiked during RNA extraction suggests that the yield was affected by total RNA concentration, which may impact circadian studies of small RNAs. The results indicate that the approach of tissue normalization without total RNA equalization prior to cDNA synthesis can avoid bias from endogenous broad variations in transcript levels. Also, the circadian analysis of 2 -Cycle threshold (Ct) data, without HKGs, may be an alternative for chronobiological studies under controlled experimental conditions.

Topological Analysis and Gaussian Decision Tree: Effective Representation and Classification of Biosignals of Small Sample Size.

PubMed

Zhang, Zhifei; Song, Yang; Cui, Haochen; Wu, Jayne; Schwartz, Fernando; Qi, Hairong

2017-09-01

Bucking the trend of big data, in microdevice engineering, small sample size is common, especially when the device is still at the proof-of-concept stage. The small sample size, small interclass variation, and large intraclass variation, have brought biosignal analysis new challenges. Novel representation and classification approaches need to be developed to effectively recognize targets of interests with the absence of a large training set. Moving away from the traditional signal analysis in the spatiotemporal domain, we exploit the biosignal representation in the topological domain that would reveal the intrinsic structure of point clouds generated from the biosignal. Additionally, we propose a Gaussian-based decision tree (GDT), which can efficiently classify the biosignals even when the sample size is extremely small. This study is motivated by the application of mastitis detection using low-voltage alternating current electrokinetics (ACEK) where five categories of bisignals need to be recognized with only two samples in each class. Experimental results demonstrate the robustness of the topological features as well as the advantage of GDT over some conventional classifiers in handling small dataset. Our method reduces the voltage of ACEK to a safe level and still yields high-fidelity results with a short assay time. This paper makes two distinctive contributions to the field of biosignal analysis, including performing signal processing in the topological domain and handling extremely small dataset. Currently, there have been no related works that can efficiently tackle the dilemma between avoiding electrochemical reaction and accelerating assay process using ACEK.

Formulation of image quality prediction criteria for the Viking lander camera

NASA Technical Reports Server (NTRS)

Huck, F. O.; Jobson, D. J.; Taylor, E. J.; Wall, S. D.

1973-01-01

Image quality criteria are defined and mathematically formulated for the prediction computer program which is to be developed for the Viking lander imaging experiment. The general objective of broad-band (black and white) imagery to resolve small spatial details and slopes is formulated as the detectability of a right-circular cone with surface properties of the surrounding terrain. The general objective of narrow-band (color and near-infrared) imagery to observe spectral characteristics if formulated as the minimum detectable albedo variation. The general goal to encompass, but not exceed, the range of the scene radiance distribution within single, commandable, camera dynamic range setting is also considered.

Dispersion Measure Variation of Repeating Fast Radio Burst Sources

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

Yang, Yuan-Pei; Zhang, Bing, E-mail: yypspore@gmail.com, E-mail: zhang@physics.unlv.edu

The repeating fast radio burst (FRB) 121102 was recently localized in a dwarf galaxy at a cosmological distance. The dispersion measure (DM) derived for each burst from FRB 121102 so far has not shown significant evolution, even though an apparent increase was recently seen with newly detected VLA bursts. It is expected that more repeating FRB sources may be detected in the future. In this work, we investigate a list of possible astrophysical processes that might cause DM variation of a particular FRB source. The processes include (1) cosmological scale effects such as Hubble expansion and large-scale structure fluctuations; (2)more » FRB local effects such as gas density fluctuation, expansion of a supernova remnant (SNR), a pulsar wind nebula, and an H ii region; and (3) the propagation effect due to plasma lensing. We find that the DM variations contributed by the large-scale structure are extremely small, and any observable DM variation is likely caused by the plasma local to the FRB source. In addition to mechanisms that decrease DM over time, we suggest that an FRB source in an expanding SNR around a nearly neutral ambient medium during the deceleration (Sedov–Taylor and snowplow) phases or in a growing H ii region can increase DM. Some effects (e.g., an FRB source moving in an H ii region or plasma lensing) can produce either positive or negative DM variations. Future observations of DM variations of FRB 121102 and other repeating FRB sources can provide important clues regarding the physical origin of these sources.« less

Effects of CD36 Genotype on Oral Perception of Oleic Acid Supplemented Safflower Oil Emulsions in Two Ethnic Groups: A Preliminary Study.

PubMed

Burgess, Brenda; Melis, Melania; Scoular, Katelyn; Driver, Michael; Schaich, Karen M; Keller, Kathleen L; Tomassini Barbarossa, Iole; Tepper, Beverly J

2018-05-01

Previous studies demonstrate humans can detect fatty acids via specialized sensors on the tongue, such as the CD36 receptor. Genetic variation at the common single nucleotide polymorphism rs1761667 of CD36 has been shown to differentially impact the perception of fatty acids, but comparative data among different ethnic groups are lacking. In a small cohort of Caucasian and East Asian young adults, we investigated if: (1) participants could detect oleic acid (C18:1) added to safflower oil emulsions at a constant ratio of 3% (w/v); (2) supplementation of oleic acid to safflower oil emulsions enhanced perception of fattiness and creaminess; and (3) variation at rs1761667 influenced oleic acid detection and fat taste perception. In a 3-alternate forced choice test, 62% of participants detected 2.9 ± 0.7 mM oleic acid (or 0.08% w/v) in a 2.8% safflower oil emulsion. Supplementation of oleic acid did not enhance fattiness and creaminess perception for the cohort as a whole, though East Asians carrying the GG genotype perceived more overall fattiness and creaminess than their AA genotype counterparts (P < 0.001). No differences were observed for the Caucasians. These preliminary findings indicate that free oleic acid can be detected in an oil-in-water emulsion at concentrations found in commercial oils, but it does not increase fattiness or creaminess perception. Additionally, variation at rs1761667 may have ethnic-specific effects on fat taste perception. © 2018 The Authors Journal of Food Science published by Wiley Periodicals, Inc. on behalf of Institute of Food Technologists.

ESTIMATING WELFARE IN INSURANCE MARKETS USING VARIATION IN PRICES*

PubMed Central

Einav, Liran; Finkelstein, Amy; Cullen, Mark R.

2009-01-01

We provide a graphical illustration of how standard consumer and producer theory can be used to quantify the welfare loss associated with inefficient pricing in insurance markets with selection. We then show how this welfare loss can be estimated empirically using identifying variation in the price of insurance. Such variation, together with quantity data, allows us to estimate the demand for insurance. The same variation, together with cost data, allows us to estimate how insurer’s costs vary as market participants endogenously respond to price. The slope of this estimated cost curve provides a direct test for both the existence and nature of selection, and the combination of demand and cost curves can be used to estimate welfare. We illustrate our approach by applying it to data on employer-provided health insurance from one specific company. We detect adverse selection but estimate that the quantitative welfare implications associated with inefficient pricing in our particular application are small, in both absolute and relative terms. PMID:21218182

Consecutive analysis of mutation spectrum in the dystrophin gene of 507 Korean boys with Duchenne/Becker muscular dystrophy in a single center.

PubMed

Cho, Anna; Seong, Moon-Woo; Lim, Byung Chan; Lee, Hwa Jeen; Byeon, Jung Hye; Kim, Seung Soo; Kim, Soo Yeon; Choi, Sun Ah; Wong, Ai-Lynn; Lee, Jeongho; Kim, Jon Soo; Ryu, Hye Won; Lee, Jin Sook; Kim, Hunmin; Hwang, Hee; Choi, Ji Eun; Kim, Ki Joong; Hwang, Young Seung; Hong, Ki Ho; Park, Seungman; Cho, Sung Im; Lee, Seung Jun; Park, Hyunwoong; Seo, Soo Hyun; Park, Sung Sup; Chae, Jong Hee

2017-05-01

Duchenne and Becker muscular dystrophies (DMD and BMD) are allelic X-linked recessive muscle diseases caused by mutations in the large and complex dystrophin gene. We analyzed the dystrophin gene in 507 Korean DMD/BMD patients by multiple ligation-dependent probe amplification and direct sequencing. Overall, 117 different deletions, 48 duplications, and 90 pathogenic sequence variations, including 30 novel variations, were identified. Deletions and duplications accounted for 65.4% and 13.3% of Korean dystrophinopathy, respectively, suggesting that the incidence of large rearrangements in dystrophin is similar among different ethnic groups. We also detected sequence variations in >100 probands. The small variations were dispersed across the whole gene, and 12.3% were nonsense mutations. Precise genetic characterization in patients with DMD/BMD is timely and important for implementing nationwide registration systems and future molecular therapeutic trials in Korea and globally. Muscle Nerve 55: 727-734, 2017. © 2016 Wiley Periodicals, Inc.

High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations.

PubMed

Zhang, Pei; Huang, Kang; Zhang, Bingyi; Dunn, Derek W; Chen, Dan; Li, Fan; Qi, Xiaoguang; Guo, Songtao; Li, Baoguo

2018-03-13

Maintaining variation in immune genes, such as those of the major histocompatibility complex (MHC), is important for individuals in small, isolated populations to resist pathogens and parasites. The golden snub-nosed monkey (Rhinopithecus roxellana), an endangered primate endemic to China, has experienced a rapid reduction in numbers and severe population fragmentation over recent years. For this study, we measured the DRB diversity among 122 monkeys from three populations in the Qinling Mountains, and estimated the relative importance of different agents of selection in maintaining variation of DRB genes. We identified a total of 19 DRB sequences, in which five alleles were novel. We found high DRB variation in R. roxellana and three branches of evidence suggesting that balancing selection has contributed to maintaining MHC polymorphism over the long term in this species: i) different patterns of both genetic diversity and population differentiation were detected at MHC and neutral markers; ii) an excess of non-synonymous substitutions compared to synonymous substitutions at antigen binding sites, and maximum-likelihood-based random-site models, showed significant positive selection; and iii) phylogenetic analyses revealed a pattern of trans-species evolution for DRB genes. High levels of DRB diversity in these R. roxellana populations may reflect strong selection pressure in this species. Patterns of genetic diversity and population differentiation, positive selection, as well as trans-species evolution, suggest that pathogen-mediated balancing selection has contributed to maintaining MHC polymorphism in R. roxellana over the long term. This study furthers our understanding of the role pathogen-mediated balancing selection has in maintaining variation in MHC genes in small and fragmented populations of free-ranging vertebrates.

Dual-excitation wavelength resonance Raman explosives detector

NASA Astrophysics Data System (ADS)

Yellampalle, Balakishore; Sluch, Mikhail; Wu, Hai-Shan; Martin, Robert; McCormick, William; Ice, Robert; Lemoff, Brian E.

2013-05-01

Deep-ultraviolet resonance Raman spectroscopy (DUVRRS) is a promising approach to stand-off detection of explosive traces due to: 1) resonant enhancement of Raman cross-section, 2) λ-4-cross-section enhancement, and 3) fluorescence and solar background free signatures. For trace detection, these signal enhancements more than offset the small penetration depth due to DUV absorption. A key challenge for stand-off sensors is to distinguish explosives, with high confidence, from a myriad of unknown background materials that may have interfering spectral peaks. To address this, we are developing a stand-off explosive sensor using DUVRRS with two simultaneous DUV excitation wavelengths. Due to complex interplay of resonant enhancement, self-absorption and laser penetration depth, significant amplitude variation is observed between corresponding Raman bands with different excitation wavelengths. These variations with excitation wavelength provide an orthogonal signature that complements the traditional Raman signature to improve specificity relative to single-excitation-wavelength techniques. As part of this effort, we are developing two novel CW DUV lasers, which have potential to be compact, and a compact dual-band high throughput DUV spectrometer, capable of simultaneous detection of Raman spectra in two spectral windows. We have also developed a highly sensitive algorithm for the detection of explosives under low signal-to-noise situations.

Adverse surgical outcomes in screen-detected ductal carcinoma in situ of the breast.

PubMed

Thomas, Jeremy; Hanby, Andrew; Pinder, Sarah E; Ball, Graham; Lawrence, Gill; Maxwell, Anthony; Wallis, Matthew; Evans, Andrew; Dobson, Hilary; Clements, Karen; Thompson, Alastair

2014-07-01

The Sloane Project is the largest prospective audit of ductal carcinoma in situ (DCIS) worldwide, with over 12,000 patients registered between 2003 and 2012, accounting for 50% of screen-detected DCIS diagnosed in the United Kingdom (UK) over the period of accrual. Complete multidisciplinary data from 8313 patients with screen-detected DCIS were analysed for surgical outcome in relation to key radiological and pathological parameters for the cohort and also by hospital of treatment. Adverse surgical outcomes were defined as either failed breast conservation surgery (BCS) or mastectomy for small lesions (<20mm) (MFSL). Inter-hospital variation was analysed by grouping hospitals into high, medium and low frequency subgroups for these two adverse outcomes. Patients with failed BCS or MFSL together accounted for 49% of all mastectomies. Of 6633 patients embarking on BCS, 799 (12.0%) required mastectomy. MFSL accounted for 510 (21%) of 2479 mastectomy patients. Failed BCS was associated with significant radiological under-estimation of disease extent and MFSL significant radiological over-estimation of disease extent. There was considerable and significant inter-hospital variation in failed BCS (range 3-32%) and MFSL (0-60%) of a hospital's BCS/mastectomy workload respectively. Conversely, there were no differences between the key radiological and pathological parameters in high, medium and low frequency adverse-outcome hospitals. This evidence suggests significant practice variation, not patient factors, is responsible for these adverse surgical outcomes in screen-detected DCIS. The Sloane Project provides an evidence base for future practice benchmarking. Copyright © 2014 Elsevier Ltd. All rights reserved.

Living on the edge: reconstructing the genetic history of the Finnish wolf population

PubMed Central

2014-01-01

Background Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference. Results Our analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of Ne were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected. Conclusions Our genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong. PMID:24678616

Diode‐based transmission detector for IMRT delivery monitoring: a validation study

PubMed Central

Li, Taoran; Wu, Q. Jackie; Matzen, Thomas; Yin, Fang‐Fang

2016-01-01

The purpose of this work was to evaluate the potential of a new transmission detector for real‐time quality assurance of dynamic‐MLC‐based radiotherapy. The accuracy of detecting dose variation and static/dynamic MLC position deviations was measured, as well as the impact of the device on the radiation field (surface dose, transmission). Measured dose variations agreed with the known variations within 0.3%. The measurement of static and dynamic MLC position deviations matched the known deviations with high accuracy (0.7–1.2 mm). The absorption of the device was minimal (∼ 1%). The increased surface dose was small (1%–9%) but, when added to existing collimator scatter effects could become significant at large field sizes (≥30×30 cm2). Overall the accuracy and speed of the device show good potential for real‐time quality assurance. PACS number(s): 87.55.Qr PMID:27685115

Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing

PubMed Central

Ku, Ti-Hsuan; Zhang, Tiantian; Luo, Hua; Yen, Tony M.; Chen, Ping-Wei; Han, Yuanyuan; Lo, Yu-Hwa

2015-01-01

Detection of small molecules or proteins of living cells provides an exceptional opportunity to study genetic variations and functions, cellular behaviors, and various diseases including cancer and microbial infections. Our aim in this review is to give an overview of selected research activities related to nucleic acid-based aptamer techniques that have been reported in the past two decades. Limitations of aptamers and possible approaches to overcome these limitations are also discussed. PMID:26153774

Portable IR dye laser optofluidic microresonator as a temperature and chemical sensor.

PubMed

Lahoz, F; Martín, I R; Gil-Rostra, J; Oliva-Ramirez, M; Yubero, F; Gonzalez-Elipe, A R

2016-06-27

A compact and portable optofluidic microresonator has been fabricated and characterized. It is based on a Fabry-Perot microcavity consisting essentially of two tailored dichroic Bragg mirrors prepared by reactive magnetron sputtering deposition. The microresonator has been filled with an ethanol solution of Nile-Blue dye. Infrared laser emission has been measured with a pump threshold as low as 0.12 MW/cm² and an external energy conversion efficiency of 41%. The application of the device as a temperature and a chemical sensor is demonstrated. Small temperature variations as well as small amount of water concentrations in the liquid laser medium are detected as a shift of the resonant laser modes.

On the Detection of Non-transiting Hot Jupiters in Multiple-planet Systems

NASA Astrophysics Data System (ADS)

Millholland, Sarah; Wang, Songhu; Laughlin, Gregory

2016-05-01

We outline a photometric method for detecting the presence of a non-transiting short-period giant planet in a planetary system harboring one or more longer-period transiting planets. Within a prospective system of the type that we consider, a hot Jupiter on an interior orbit inclined to the line of sight signals its presence through approximately sinusoidal full-phase photometric variations in the stellar light curve, correlated with astrometrically induced transit timing variations for exterior transiting planets. Systems containing a hot Jupiter along with a low-mass outer planet or planets on inclined orbits are a predicted hallmark of in situ accretion for hot Jupiters, and their presence can thus be used to test planetary formation theories. We outline the prospects for detecting non-transiting hot Jupiters using photometric data from typical Kepler objects of interest (KOIs). As a demonstration of the technique, we perform a brief assessment of Kepler candidates and identify a potential non-transiting hot Jupiter in the KOI-1822 system. Candidate non-transiting hot Jupiters can be readily confirmed with a small number of Doppler velocity observations, even for stars with V ≳ 14.

Predicting above-ground density and distribution of small mammal prey species at large spatial scales

PubMed Central

2017-01-01

Grassland and shrub-steppe ecosystems are increasingly threatened by anthropogenic activities. Loss of native habitats may negatively impact important small mammal prey species. Little information, however, is available on the impact of habitat variability on density of small mammal prey species at broad spatial scales. We examined the relationship between small mammal density and remotely-sensed environmental covariates in shrub-steppe and grassland ecosystems in Wyoming, USA. We sampled four sciurid and leporid species groups using line transect methods, and used hierarchical distance-sampling to model density in response to variation in vegetation, climate, topographic, and anthropogenic variables, while accounting for variation in detection probability. We created spatial predictions of each species’ density and distribution. Sciurid and leporid species exhibited mixed responses to vegetation, such that changes to native habitat will likely affect prey species differently. Density of white-tailed prairie dogs (Cynomys leucurus), Wyoming ground squirrels (Urocitellus elegans), and leporids correlated negatively with proportion of shrub or sagebrush cover and positively with herbaceous cover or bare ground, whereas least chipmunks showed a positive correlation with shrub cover and a negative correlation with herbaceous cover. Spatial predictions from our models provide a landscape-scale metric of above-ground prey density, which will facilitate the development of conservation plans for these taxa and their predators at spatial scales relevant to management. PMID:28520757

Identification of temporal variations in mental workload using locally-linear-embedding-based EEG feature reduction and support-vector-machine-based clustering and classification techniques.

PubMed

Yin, Zhong; Zhang, Jianhua

2014-07-01

Identifying the abnormal changes of mental workload (MWL) over time is quite crucial for preventing the accidents due to cognitive overload and inattention of human operators in safety-critical human-machine systems. It is known that various neuroimaging technologies can be used to identify the MWL variations. In order to classify MWL into a few discrete levels using representative MWL indicators and small-sized training samples, a novel EEG-based approach by combining locally linear embedding (LLE), support vector clustering (SVC) and support vector data description (SVDD) techniques is proposed and evaluated by using the experimentally measured data. The MWL indicators from different cortical regions are first elicited by using the LLE technique. Then, the SVC approach is used to find the clusters of these MWL indicators and thereby to detect MWL variations. It is shown that the clusters can be interpreted as the binary class MWL. Furthermore, a trained binary SVDD classifier is shown to be capable of detecting slight variations of those indicators. By combining the two schemes, a SVC-SVDD framework is proposed, where the clear-cut (smaller) cluster is detected by SVC first and then a subsequent SVDD model is utilized to divide the overlapped (larger) cluster into two classes. Finally, three-class MWL levels (low, normal and high) can be identified automatically. The experimental data analysis results are compared with those of several existing methods. It has been demonstrated that the proposed framework can lead to acceptable computational accuracy and has the advantages of both unsupervised and supervised training strategies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Genetic diversity among pandemic 2009 influenza viruses isolated from a transmission chain

PubMed Central

2013-01-01

Background Influenza viruses such as swine-origin influenza A(H1N1) virus (A(H1N1)pdm09) generate genetic diversity due to the high error rate of their RNA polymerase, often resulting in mixed genotype populations (intra-host variants) within a single infection. This variation helps influenza to rapidly respond to selection pressures, such as those imposed by the immunological host response and antiviral therapy. We have applied deep sequencing to characterize influenza intra-host variation in a transmission chain consisting of three cases due to oseltamivir-sensitive viruses, and one derived oseltamivir-resistant case. Methods Following detection of the A(H1N1)pdm09 infections, we deep-sequenced the complete NA gene from two of the oseltamivir-sensitive virus-infected cases, and all eight gene segments of the viruses causing the remaining two cases. Results No evidence for the resistance-causing mutation (resulting in NA H275Y substitution) was observed in the oseltamivir-sensitive cases. Furthermore, deep sequencing revealed a subpopulation of oseltamivir-sensitive viruses in the case carrying resistant viruses. We detected higher levels of intra-host variation in the case carrying oseltamivir-resistant viruses than in those infected with oseltamivir-sensitive viruses. Conclusions Oseltamivir-resistance was only detected after prophylaxis with oseltamivir, suggesting that the mutation was selected for as a result of antiviral intervention. The persisting oseltamivir-sensitive virus population in the case carrying resistant viruses suggests either that a small proportion survive the treatment, or that the oseltamivir-sensitive virus rapidly re-establishes itself in the virus population after the bottleneck. Moreover, the increased intra-host variation in the oseltamivir-resistant case is consistent with the hypothesis that the population diversity of a RNA virus can increase rapidly following a population bottleneck. PMID:23587185

Semi-automated image analysis for the assessment of megafaunal densities at the Arctic deep-sea observatory HAUSGARTEN.

PubMed

Schoening, Timm; Bergmann, Melanie; Ontrup, Jörg; Taylor, James; Dannheim, Jennifer; Gutt, Julian; Purser, Autun; Nattkemper, Tim W

2012-01-01

Megafauna play an important role in benthic ecosystem function and are sensitive indicators of environmental change. Non-invasive monitoring of benthic communities can be accomplished by seafloor imaging. However, manual quantification of megafauna in images is labor-intensive and therefore, this organism size class is often neglected in ecosystem studies. Automated image analysis has been proposed as a possible approach to such analysis, but the heterogeneity of megafaunal communities poses a non-trivial challenge for such automated techniques. Here, the potential of a generalized object detection architecture, referred to as iSIS (intelligent Screening of underwater Image Sequences), for the quantification of a heterogenous group of megafauna taxa is investigated. The iSIS system is tuned for a particular image sequence (i.e. a transect) using a small subset of the images, in which megafauna taxa positions were previously marked by an expert. To investigate the potential of iSIS and compare its results with those obtained from human experts, a group of eight different taxa from one camera transect of seafloor images taken at the Arctic deep-sea observatory HAUSGARTEN is used. The results show that inter- and intra-observer agreements of human experts exhibit considerable variation between the species, with a similar degree of variation apparent in the automatically derived results obtained by iSIS. Whilst some taxa (e. g. Bathycrinus stalks, Kolga hyalina, small white sea anemone) were well detected by iSIS (i. e. overall Sensitivity: 87%, overall Positive Predictive Value: 67%), some taxa such as the small sea cucumber Elpidia heckeri remain challenging, for both human observers and iSIS.

Semi-Automated Image Analysis for the Assessment of Megafaunal Densities at the Arctic Deep-Sea Observatory HAUSGARTEN

PubMed Central

Schoening, Timm; Bergmann, Melanie; Ontrup, Jörg; Taylor, James; Dannheim, Jennifer; Gutt, Julian; Purser, Autun; Nattkemper, Tim W.

2012-01-01

Megafauna play an important role in benthic ecosystem function and are sensitive indicators of environmental change. Non-invasive monitoring of benthic communities can be accomplished by seafloor imaging. However, manual quantification of megafauna in images is labor-intensive and therefore, this organism size class is often neglected in ecosystem studies. Automated image analysis has been proposed as a possible approach to such analysis, but the heterogeneity of megafaunal communities poses a non-trivial challenge for such automated techniques. Here, the potential of a generalized object detection architecture, referred to as iSIS (intelligent Screening of underwater Image Sequences), for the quantification of a heterogenous group of megafauna taxa is investigated. The iSIS system is tuned for a particular image sequence (i.e. a transect) using a small subset of the images, in which megafauna taxa positions were previously marked by an expert. To investigate the potential of iSIS and compare its results with those obtained from human experts, a group of eight different taxa from one camera transect of seafloor images taken at the Arctic deep-sea observatory HAUSGARTEN is used. The results show that inter- and intra-observer agreements of human experts exhibit considerable variation between the species, with a similar degree of variation apparent in the automatically derived results obtained by iSIS. Whilst some taxa (e. g. Bathycrinus stalks, Kolga hyalina, small white sea anemone) were well detected by iSIS (i. e. overall Sensitivity: 87%, overall Positive Predictive Value: 67%), some taxa such as the small sea cucumber Elpidia heckeri remain challenging, for both human observers and iSIS. PMID:22719868

Differential expression of the eight genes of the petunia ribulose bisphosphate carboxylase small subunit multi-gene family

PubMed Central

Dean, Caroline; Elzen, Peter van den; Tamaki, Stanley; Dunsmuir, Pamela; Bedbrook, John

1985-01-01

Of the eight nuclear genes in the plant multi-gene family which encodes the small subunit (rbcS) of Petunia (Mitchell) ribulose bisphosphate carboxylase, one rbcS gene accounts for 47% of the total rbcS gene expression in petunia leaf tissue. Expression of each of five other rbcS genes is detected at levels between 2 and 23% of the total rbcS expression in leaf tissue, while expression of the remaining two rbcS genes is not detected. There is considerable variation (500-fold) in the levels of total rbcS mRNA in six organs of petunia (leaves, sepals, petals, stems, roots and stigmas/anthers). One gene, SSU301, showed the highest levels of steady-state mRNA in each of the organs examined. We discuss the differences in the steady-state mRNA levels of the individual rbcS genes in relation to their gene structure, nucleotide sequence and genomic linkage. ImagesFig. 2.Fig. 3. PMID:16453647

Meteoroid head echo polarization features studied by numerical electromagnetics modeling

NASA Astrophysics Data System (ADS)

Vertatschitsch, L. E.; Sahr, J. D.; Colestock, P.; Close, S.

2011-12-01

Meteoroid head echoes are radar returns associated with scatter from the dense plasma surrounding meteoroids striking the Earth's atmosphere. Such echoes are detected by high power, large aperture (HPLA) radars. Frequently such detections show large variations in signal strength that suggest constructive and destructive interference. Using the ARPA Long-Range Tracking and Instrumentation Radar (ALTAIR) we can also observe the polarization of the returns. Usually, scatter from head echoes resembles scatter from a small sphere; when transmitting right circular polarization (RC), the received signal consists entirely of left circular polarization (LC). For some detections, power is also received in the RC channel, which indicates the presence of a more complicated scattering process. Radar returns of a fragmenting meteoroid are simulated using a hard-sphere scattering model numerically evaluated in the resonant region of Mie scatter. The cross- and co-polar scattering cross-sections are computed for pairs of spheres lying within a few wavelengths, simulating the earliest stages of fragmentation upon atmospheric impact. The likelihood of detecting this sort of idealized fragmentation event is small, but this demonstrates the measurements that would result from such an event would display RC power comparable to LC power, matching the anomalous data. The resulting computations show that fragmentation is a consistent interpretation for these head echo radar returns.

Methods to maximise recovery of environmental DNA from water samples.

PubMed

Hinlo, Rheyda; Gleeson, Dianne; Lintermans, Mark; Furlan, Elise

2017-01-01

The environmental DNA (eDNA) method is a detection technique that is rapidly gaining credibility as a sensitive tool useful in the surveillance and monitoring of invasive and threatened species. Because eDNA analysis often deals with small quantities of short and degraded DNA fragments, methods that maximize eDNA recovery are required to increase detectability. In this study, we performed experiments at different stages of the eDNA analysis to show which combinations of methods give the best recovery rate for eDNA. Using Oriental weatherloach (Misgurnus anguillicaudatus) as a study species, we show that various combinations of DNA capture, preservation and extraction methods can significantly affect DNA yield. Filtration using cellulose nitrate filter paper preserved in ethanol or stored in a -20°C freezer and extracted with the Qiagen DNeasy kit outperformed other combinations in terms of cost and efficiency of DNA recovery. Our results support the recommendation to filter water samples within 24hours but if this is not possible, our results suggest that refrigeration may be a better option than freezing for short-term storage (i.e., 3-5 days). This information is useful in designing eDNA detection of low-density invasive or threatened species, where small variations in DNA recovery can signify the difference between detection success or failure.

Wire-inhomogeneity detector

DOEpatents

Gibson, G.H.; Smits, R.G.; Eberhard, P.H.

1982-08-31

A device for uncovering imperfections in electrical conducting wire, particularly superconducting wire, by detecting variations in eddy currents. Eddy currents effect the magnetic field in a gap of an inductor, contained in a modified commercial ferrite core, through which the wire being tested is passed. A small increase or decrease in the amount of conductive material, such as copper, in a fixed cross section of wire will unbalance a bridge used to measure the impedance of the inductor, tripping a detector and sounding an alarm.

WD 0158-160, a new pulsating DB white dwarf

NASA Astrophysics Data System (ADS)

Kilkenny, D.

2016-03-01

The DB star, WD 0158-160 (=EC 01585-1600) is shown to be a variable white dwarf with a rich pulsation spectrum, dominated by a strong variation with a frequency near 1637 μHz (amplitude ˜0.024 mag, period 598 s), though at least 10 frequencies are detected between about 1285 and 5747 μHz (780-173 s) in a relatively small data set. At ˜14.5 mag, the star is one of the brightest known DBV stars.

Detection of Subclinical Mastitis in Small Ruminants on Six Farms in Northern Tanzania

DTIC Science & Technology

2005-10-18

cause a 53% and 30% reduction in milk yield in sheep and goats respectively (Gonzalo et al., 1994, Leitner et all, 2004). This decrease in milk ...Factors influencing variations of test-day milk yield, somatic-cell count, fat and protein in dairy sheep . J. Dairy Sci. 77:1537-1542 7 Leitner,G., U...the pastoral life of the Maasai people of northern Tanzania. Although the Maasai culture centers on cattle, East African goats and Fat-tailed sheep are

Spatial heterogeneity in statistical power to detect changes in lake area in Alaskan National Wildlife Refuges

USGS Publications Warehouse

Nicol, Samuel; Roach, Jennifer K.; Griffith, Brad

2013-01-01

Over the past 50 years, the number and size of high-latitude lakes have decreased throughout many regions; however, individual lake trends have been variable in direction and magnitude. This spatial heterogeneity in lake change makes statistical detection of temporal trends challenging, particularly in small analysis areas where weak trends are difficult to separate from inter- and intra-annual variability. Factors affecting trend detection include inherent variability, trend magnitude, and sample size. In this paper, we investigated how the statistical power to detect average linear trends in lake size of 0.5, 1.0 and 2.0 %/year was affected by the size of the analysis area and the number of years of monitoring in National Wildlife Refuges in Alaska. We estimated power for large (930–4,560 sq km) study areas within refuges and for 2.6, 12.9, and 25.9 sq km cells nested within study areas over temporal extents of 4–50 years. We found that: (1) trends in study areas could be detected within 5–15 years, (2) trends smaller than 2.0 %/year would take >50 years to detect in cells within study areas, and (3) there was substantial spatial variation in the time required to detect change among cells. Power was particularly low in the smallest cells which typically had the fewest lakes. Because small but ecologically meaningful trends may take decades to detect, early establishment of long-term monitoring will enhance power to detect change. Our results have broad applicability and our method is useful for any study involving change detection among variable spatial and temporal extents.

Cryptic intragenic deletion of the SHOX gene in a family with Léri-Weill dyschondrosteosis detected by Multiplex Ligation-Dependent Probe Amplification (MLPA).

PubMed

Funari, Mariana F A; Jorge, Alexander A L; Pinto, Emilia M; Arnhold, Ivo J P; Mendonca, Berenice B; Nishi, Mirian Y

2008-11-01

LWD is associated to SHOX haploinsufficiency, in most cases, due to gene deletion. Generally FISH and microsatellite analysis are used to identify SHOX deletion. MLPA is a new method of detecting gene copy variation, allowing simultaneous analysis of several regions. Here we describe the presence of a SHOX intragenic deletion in a family with LWD, analyzed through different methodologies. Genomic DNA of 11 subjects from one family were studied by microsatellite analysis, direct sequencing and MLPA. FISH was performed in two affected individuals. Microsatellite analysis showed that all affected members shared the same haplotype suggesting the involvement of SHOX. MLPA detected an intragenic deletion involving exons IV-VIa, which was not detected by FISH and microsatellite analysis. In conclusion, the MLPA technique was proved to be the best solution on detecting this small deletion, it has the advantage of being less laborious also allowing the analysis of several regions simultaneously.

Use of a capillary electrophoresis instrument with laser-induced fluorescence detection for DNA quantitation. Comparison of YO-PRO-1 and PicoGreen assays.

PubMed

Guillo, Christelle; Ferrance, Jerome P; Landers, James P

2006-04-28

Highly selective and sensitive assays are required for detection and quantitation of the small masses of DNA typically encountered in clinical and forensic settings. High detection sensitivity is achieved using fluorescent labeling dyes and detection techniques such as spectrofluorometers, microplate readers and cytometers. This work describes the use of a laser-induced fluorescence (LIF) detector in conjunction with a commercial capillary electrophoresis instrument for DNA quantitation. PicoGreen and YO-PRO-1, two fluorescent DNA labeling dyes, were used to assess the potential of the system for routine DNA analysis. Linearity, reproducibility, sensitivity, limits of detection and quantitation, and sample stability were examined for the two assays. The LIF detector response was found to be linear (R2 > 0.999) and reproducible (RSD < 9%) in both cases. The PicoGreen assay displayed lower limits of detection and quantitation (20 pg and 60 pg, respectively) than the YO-PRO-1 assay (60 pg and 260 pg, respectively). Although a small variation in fluorescence was observed for the DNA/dye complexes over time, quantitation was not significantly affected and the solutions were found to be relatively stable for 80 min. The advantages of the technique include a 4- to 40-fold reduction in the volume of sample required compared to traditional assays, a 2- to 20-fold reduction in the volume of reagents consumed, fast and automated analysis, and low cost (no specific instrumentation required).

Sources of variation in detection of wading birds from aerial surveys in the Florida Everglades

USGS Publications Warehouse

Conroy, M.J.; Peterson, J.T.; Bass, O.L.; Fonnesbeck, C.J.; Howell, J.E.; Moore, C.T.; Runge, J.P.

2008-01-01

We conducted dual-observer trials to estimate detection probabilities (probability that a group that is present and available is detected) for fixed-wing aerial surveys of wading birds in the Everglades system, Florida. Detection probability ranged from <0.2 to similar to 0.75 and varied according to species, group size, observer, and the observer's position in the aircraft (front or rear seat). Aerial-survey simulations indicated that incomplete detection can have a substantial effect oil assessment of population trends, particularly river relatively short intervals (<= 3 years) and small annual changes in population size (<= 3%). We conclude that detection bias is an important consideration for interpreting observations from aerial surveys of wading birds, potentially limiting the use of these data for comparative purposes and trend analyses. We recommend that workers conducting aerial surveys for wading birds endeavor to reduce observer and other controllable sources of detection bias and account for uncontrollable sources through incorporation of dual-observer or other calibratior methods as part of survey design (e.g., using double sampling).

Flexible feature-space-construction architecture and its VLSI implementation for multi-scale object detection

NASA Astrophysics Data System (ADS)

Luo, Aiwen; An, Fengwei; Zhang, Xiangyu; Chen, Lei; Huang, Zunkai; Jürgen Mattausch, Hans

2018-04-01

Feature extraction techniques are a cornerstone of object detection in computer-vision-based applications. The detection performance of vison-based detection systems is often degraded by, e.g., changes in the illumination intensity of the light source, foreground-background contrast variations or automatic gain control from the camera. In order to avoid such degradation effects, we present a block-based L1-norm-circuit architecture which is configurable for different image-cell sizes, cell-based feature descriptors and image resolutions according to customization parameters from the circuit input. The incorporated flexibility in both the image resolution and the cell size for multi-scale image pyramids leads to lower computational complexity and power consumption. Additionally, an object-detection prototype for performance evaluation in 65 nm CMOS implements the proposed L1-norm circuit together with a histogram of oriented gradients (HOG) descriptor and a support vector machine (SVM) classifier. The proposed parallel architecture with high hardware efficiency enables real-time processing, high detection robustness, small chip-core area as well as low power consumption for multi-scale object detection.

Detectability index of differential phase contrast CT compared with conventional CT: a preliminary channelized Hotelling observer study

NASA Astrophysics Data System (ADS)

Tang, Xiangyang; Yang, Yi; Tang, Shaojie

2013-03-01

Under the framework of model observer with signal and background exactly known (SKE/BKE), we investigate the detectability of differential phase contrast CT compared with that of the conventional attenuation-based CT. Using the channelized Hotelling observer and the radially symmetric difference-of-Gaussians channel template , we investigate the detectability index and its variation over the dimension of object and detector cells. The preliminary data show that the differential phase contrast CT outperforms the conventional attenuation-based CT significantly in the detectability index while both the object to be detected and the cell of detector used for data acquisition are relatively small. However, the differential phase contrast CT's dominance in the detectability index diminishes with increasing dimension of either object or detector cell, and virtually disappears while the dimension of object or detector cell approaches a threshold, respectively. It is hoped that the preliminary data reported in this paper may provide insightful understanding of the differential phase contrast CT's characteristic in the detectability index and its comparison with that of the conventional attenuation-based CT.

Skin Cancer, Irradiation, and Sunspots: The Solar Cycle Effect

PubMed Central

Zurbenko, Igor

2014-01-01

Skin cancer is diagnosed in more than 2 million individuals annually in the United States. It is strongly associated with ultraviolet exposure, with melanoma risk doubling after five or more sunburns. Solar activity, characterized by features such as irradiance and sunspots, undergoes an 11-year solar cycle. This fingerprint frequency accounts for relatively small variation on Earth when compared to other uncorrelated time scales such as daily and seasonal cycles. Kolmogorov-Zurbenko filters, applied to the solar cycle and skin cancer data, separate the components of different time scales to detect weaker long term signals and investigate the relationships between long term trends. Analyses of crosscorrelations reveal epidemiologically consistent latencies between variables which can then be used for regression analysis to calculate a coefficient of influence. This method reveals that strong numerical associations, with correlations >0.5, exist between these small but distinct long term trends in the solar cycle and skin cancer. This improves modeling skin cancer trends on long time scales despite the stronger variation in other time scales and the destructive presence of noise. PMID:25126567

Collapse of a pollination web in small conservation areas.

PubMed

Pauw, Anton

2007-07-01

A suspected global decline in pollinators has heightened interest in their ecological significance. In a worst-case scenario, the decline of generalist pollinators is predicted to trigger cascades of linked declines among the multiple specialist plant species to which they are linked, but this has not been documented. I studied a portion of a pollination web involving a generalist pollinator, the oil-collecting bee Rediviva peringueyi, and a community of oil-secreting plants. Across 27 established conservation areas located in the Cape Floral Region, I found substantial variation in the bees' occurrence in relation to soil type and the successional stage of the vegetation. Anthropogenic declines were detectable against this background of naturally occurring variation: R. peringueyi was absent from small conservation areas (< 385 ha) in an urban matrix. In the absence of the bee, seed set failed in six specialist plant species that are pollinated only by R. peringueyi but remained high in a pollination generalist, which had replacement pollinators. The findings are consistent with theoretical predictions of the importance of generalist pollinators in maintaining the structure of pollination webs.

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

Sandhaus, Phoebe H.; Debes, John H.; Ely, Justin

The search for transiting habitable exoplanets has broadened to include several types of stars that are smaller than the Sun in an attempt to increase the observed transit depth and hence the atmospheric signal of the planet. Of all spectral types, white dwarfs (WDs) are the most favorable for this type of investigation. The fraction of WDs that possess close-in rocky planets is unknown, but several large angle stellar surveys have the photometric precision and cadence to discover at least one if they are common. Ultraviolet observations of WDs may allow for detection of molecular oxygen or ozone in themore » atmosphere of a terrestrial planet. We use archival Hubble Space Telescope data from the Cosmic Origins Spectrograph to search for transiting rocky planets around UV-bright WDs. In the process, we discovered unusual variability in the pulsating WD GD 133, which shows slow sinusoidal variations in the UV. While we detect no planets around our small sample of targets, we do place stringent limits on the possibility of transiting planets, down to sub-lunar radii. We also point out that non-transiting small planets in thermal equilibrium are detectable around hotter WDs through infrared excesses, and identify two candidates.« less

Real-Time Polymerase Chain Reaction for Detection of Schistosoma DNA in Small-Volume Urine Samples Reflects Focal Distribution of Urogenital Schistosomiasis in Primary School Girls in KwaZulu Natal, South Africa

PubMed Central

Pillay, Pavitra; Taylor, Myra; Zulu, Siphosenkosi G.; Gundersen, Svein G.; Verweij, Jaco J.; Hoekstra, Pytsje; Brienen, Eric A. T.; Kleppa, Elisabeth; Kjetland, Eyrun F.; van Lieshout, Lisette

2014-01-01

Schistosoma haematobium eggs and Schistosoma DNA levels were measured in urine samples from 708 girls recruited from 18 randomly sampled primary schools in South Africa. Microscopic analysis of two 10-mL urine subsamples collected on three consecutive days confirmed high day-to-day variation; 103 (14.5%) girls had positive results at all six examinations, and at least one positive sample was seen in 225 (31.8%) girls. Schistosoma-specific DNA, which was measured in a 200-μL urine subsample by using real-time polymerase chain reaction, was detected in 180 (25.4%) cases, and levels of DNA corresponded significantly with average urine egg excretion. In concordance with microscopic results, polymerase chain reaction results were significantly associated with history of gynecologic symptoms and confirmed highly focal distribution of urogenital schistosomiasis. Parasite-specific DNA detection has a sensitivity comparable to single urine microscopy and could be used as a standardized high-throughput procedure to assess distribution of urogenital schistosomiasis in relatively large study populations by using small sample volumes. PMID:24470560

Neutral particle beam sensing and steering

DOEpatents

Maier, II, William B.; Cobb, Donald D.; Robiscoe, Richard T.

1991-01-01

The direction of a neutral particle beam (NPB) is determined by detecting Ly.alpha. radiation emitted during motional quenching of excited H(2S) atoms in the beam during movement of the atoms through a magnetic field. At least one detector is placed adjacent the beam exit to define an optical axis that intercepts the beam at a viewing angle to include a volume generating a selected number of photons for detection. The detection system includes a lens having an area that is small relative to the NPB area and a pixel array located in the focal plane of the lens. The lens viewing angle and area pixel array are selected to optimize the beam tilt sensitivity. In one embodiment, two detectors are placed coplanar with the beam axis to generate a difference signal that is insensitive to beam variations other than beam tilt.

Coupled analysis of high and low frequency resonant ultrasound spectroscopy: Application to the detection of defects in ceramic balls

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

Deneuville, Francois; Duquennoy, Marc; Ouaftouh, Mohammadi

2009-05-15

A coupled analysis of high and low frequency resonant ultrasound spectroscopy of spheroidal modes is presented in this paper. Experimentally, by using an ultrasonic probe for the excitation (piezoelectric transducer) and a heterodyne optic probe for the receiver (interferometer), it was possible to take spectroscopic measurements of spheroidal vibrations over a large frequency range of 100 kHz-45 MHz in a continuous regime. This wide analysis range enabled variations in velocity due to the presence of defects to be differentiated from the inherent characteristics of the balls and consequently, it offers the possibility of detecting cracks independently of production variations. Thismore » kind of defect is difficult to detect because the C-shaped surface crack is very small and narrow (500x5 {mu}m{sup 2}), and its depth does not exceed 50 {mu}m. The proposed methodology can excite spheroidal vibrations in the ceramic balls and detect such vibrations over a large frequency range. On the one hand, low frequency resonances are used in order to estimate the elastic coefficients of the balls according to various inspection depths. This method has the advantage of providing highly accurate evaluations of the elastic coefficients over a wide frequency range. On the other hand, high frequency vibrations are considered because they are similar to the surface waves propagating in the surface zone of the ceramic balls and consequently can be used to detect C-crack defects.« less

Detection of CO2 leakage by the surface-soil CO2-concentration monitoring (SCM) system in a small scale CO2 release test

NASA Astrophysics Data System (ADS)

Chae, Gitak; Yu, Soonyoung; Sung, Ki-Sung; Choi, Byoung-Young; Park, Jinyoung; Han, Raehee; Kim, Jeong-Chan; Park, Kwon Gyu

2015-04-01

Monitoring of CO2 release through the ground surface is essential to testify the safety of CO2 storage projects. We conducted a feasibility study of the multi-channel surface-soil CO2-concentration monitoring (SCM) system as a soil CO2 monitoring tool with a small scale injection. In the system, chambers are attached onto the ground surface, and NDIR sensors installed in each chamber detect CO2 in soil gas released through the soil surface. Before injection, the background CO2 concentrations were measured. They showed the distinct diurnal variation, and were positively related with relative humidity, but negatively with temperature. The negative relation of CO2 measurements with temperature and the low CO2 concentrations during the day imply that CO2 depends on respiration. The daily variation of CO2 concentrations was damped with precipitation, which can be explained by dissolution of CO2 and gas release out of pores through the ground surface with recharge. For the injection test, 4.2 kg of CO2 was injected 1 m below the ground for about 30 minutes. In result, CO2 concentrations increased in all five chambers, which were located less than 2.5 m of distance from an injection point. The Chamber 1, which is closest to the injection point, showed the largest increase of CO2 concentrations; while Chamber 2, 3, and 4 showed the peak which is 2 times higher than the average of background CO2. The CO2 concentrations increased back after decreasing from the peak around 4 hours after the injection ended in Chamber 2, 4, and 5, which indicated that CO2 concentrations seem to be recovered to the background around 4 hours after the injection ended. To determine the leakage, the data in Chamber 2 and 5, which had low increase rates in the CO2 injection test, were used for statistical analysis. The result shows that the coefficient of variation (CV) of CO2 measurements for 30 minutes is efficient to determine a leakage signal, with reflecting the abnormal change in CO2 concentrations. The CV of CO2 measurements for 30 minutes exceeded 5% about 5 minutes before the maximum CO2 concentration was detected. The contributions of this work are as follows: (1) SCM is an efficient monitoring tool to detect the CO2 release through the ground surface. (2) The statistical analysis method to determine the leakage and a monitoring frequency are provided, with analyzing background concentrations and CO2 increases in a small-scale injection test. (3) The 5% CV of CO2 measurements for 30 minutes can be used for the early warning in CO2 storage sites.

Autonomous physics-based color learning under daylight

NASA Astrophysics Data System (ADS)

Berube Lauziere, Yves; Gingras, Denis J.; Ferrie, Frank P.

1999-09-01

An autonomous approach for learning the colors of specific objects assumed to have known body spectral reflectances is developed for daylight illumination conditions. The main issue is to be able to find these objects autonomously in a set of training images captured under a wide variety of daylight illumination conditions, and to extract their colors to determine color space regions that are representative of the objects' colors and their variations. The work begins by modeling color formation under daylight using the color formation equations and the semi-empirical model of Judd, MacAdam and Wyszecki (CIE daylight model) for representing the typical spectral distributions of daylight. This results in color space regions that serve as prior information in the initial phase of learning which consists in detecting small reliable clusters of pixels having the appropriate colors. These clusters are then expanded by a region growing technique using broader color space regions than those predicted by the model. This is to detect objects in a way that is able to account for color variations which the model cannot due to its limitations. Validation on the detected objects is performed to filter out those that are not of interest and to eliminate unreliable pixel color values extracted from the remaining ones. Detection results using the color space regions determined from color values obtained by this procedure are discussed.

Defect detection of castings in radiography images using a robust statistical feature.

PubMed

Zhao, Xinyue; He, Zaixing; Zhang, Shuyou

2014-01-01

One of the most commonly used optical methods for defect detection is radiographic inspection. Compared with methods that extract defects directly from the radiography image, model-based methods deal with the case of an object with complex structure well. However, detection of small low-contrast defects in nonuniformly illuminated images is still a major challenge for them. In this paper, we present a new method based on the grayscale arranging pairs (GAP) feature to detect casting defects in radiography images automatically. First, a model is built using pixel pairs with a stable intensity relationship based on the GAP feature from previously acquired images. Second, defects can be extracted by comparing the difference of intensity-difference signs between the input image and the model statistically. The robustness of the proposed method to noise and illumination variations has been verified on casting radioscopic images with defects. The experimental results showed that the average computation time of the proposed method in the testing stage is 28 ms per image on a computer with a Pentium Core 2 Duo 3.00 GHz processor. For the comparison, we also evaluated the performance of the proposed method as well as that of the mixture-of-Gaussian-based and crossing line profile methods. The proposed method achieved 2.7% and 2.0% false negative rates in the noise and illumination variation experiments, respectively.

Compact terahertz passive spectrometer with wideband superconductor-insulator-superconductor mixer.

PubMed

Kikuchi, K; Kohjiro, S; Yamada, T; Shimizu, N; Wakatsuki, A

2012-02-01

We developed a compact terahertz (THz) spectrometer with a superconductor-insulator-superconductor (SIS) mixer, aiming to realize a portable and highly sensitive spectrometer to detect dangerous gases at disaster sites. The receiver cryostat which incorporates the SIS mixer and a small cryocooler except for a helium compressor has a weight of 27 kg and dimensions of 200 mm × 270 mm × 690 mm. In spite of the small cooling capacity of the cryocooler, the SIS mixer is successfully cooled lower than 4 K, and the temperature variation is suppressed for the sensitive measurement. By adopting a frequency sweeping system using photonic local oscillator, we demonstrated a spectroscopic measurement of CH(3)CN gas in 0.2-0.5 THz range.

Two-Dimensional Photonic Crystals for Sensitive Microscale Chemical and Biochemical Sensing

PubMed Central

Miller, Benjamin L.

2015-01-01

Photonic crystals – optical devices able to respond to changes in the refractive index of a small volume of space – are an emerging class of label-free chemical-and bio-sensors. This review focuses on one class of photonic crystal, in which light is confined to a patterned planar material layer of sub-wavelength thickness. These devices are small (on the order of tens to 100s of microns square), suitable for incorporation into lab-on-a-chip systems, and in theory can provide exceptional sensitivity. We introduce the defining characteristics and basic operation of two-dimensional photonic crystal sensors, describe variations of their basic design geometry, and summarize reported detection results from chemical and biological sensing experiments. PMID:25563402

A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging

PubMed Central

Logsdon, Benjamin A.; Carty, Cara L.; Reiner, Alexander P.; Dai, James Y.; Kooperberg, Charles

2012-01-01

Motivation: For many complex traits, including height, the majority of variants identified by genome-wide association studies (GWAS) have small effects, leaving a significant proportion of the heritable variation unexplained. Although many penalized multiple regression methodologies have been proposed to increase the power to detect associations for complex genetic architectures, they generally lack mechanisms for false-positive control and diagnostics for model over-fitting. Our methodology is the first penalized multiple regression approach that explicitly controls Type I error rates and provide model over-fitting diagnostics through a novel normally distributed statistic defined for every marker within the GWAS, based on results from a variational Bayes spike regression algorithm. Results: We compare the performance of our method to the lasso and single marker analysis on simulated data and demonstrate that our approach has superior performance in terms of power and Type I error control. In addition, using the Women's Health Initiative (WHI) SNP Health Association Resource (SHARe) GWAS of African-Americans, we show that our method has power to detect additional novel associations with body height. These findings replicate by reaching a stringent cutoff of marginal association in a larger cohort. Availability: An R-package, including an implementation of our variational Bayes spike regression (vBsr) algorithm, is available at http://kooperberg.fhcrc.org/soft.html. Contact: blogsdon@fhcrc.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22563072

Mass-induced sea level variations in the Red Sea from steric-corrected altimetry, GRACE, in-situ bottom pressure records, and hydrographic observations

NASA Astrophysics Data System (ADS)

Feng, Wei; Lemoine, Jean-Michel; Zhong, Min; Xu, Houze

2014-05-01

An annual amplitude of ~18 cm mass-induced sea level variations (SLV) in the Red Sea is detected from steric-corrected altimetry and the Gravity Recovery and Climate Experiment (GRACE) satellites from 2003 to 2011, which dominates the mean sea level in the region. Seawater mass variations here generally reach maximum in late January/early February. The steric component of SLV calculated from oceanographic temperature and salinity data is relatively small and peaks about seven months later than mass variations. The phase difference between the steric SLV and the mass-induced SLV indicates that when the Red Sea gains the mass from inflow water in winter, the steric SLV fall, and vice versa in summer. In-situ bottom pressure records in the eastern coast of the Red Sea validate the high mass variability observed by steric-corrected altimetry and GRACE. Furthermore, we compare the horizontal water mass flux in the Red Sea from steric-corrected altimetry and GRACE with that estimated from hydrographic observations.

Global trends

NASA Technical Reports Server (NTRS)

Megie, G.; Chanin, M.-L.; Ehhalt, D.; Fraser, P.; Frederick, J. F.; Gille, J. C.; Mccormick, M. P.; Schoebert, M.; Bishop, L.; Bojkov, R. D.

1990-01-01

Measuring trends in ozone, and most other geophysical variables, requires that a small systematic change with time be determined from signals that have large periodic and aperiodic variations. Their time scales range from the day-to-day changes due to atmospheric motions through seasonal and annual variations to 11 year cycles resulting from changes in the sun UV output. Because of the magnitude of all of these variations is not well known and highly variable, it is necessary to measure over more than one period of the variations to remove their effects. This means that at least 2 or more times the 11 year sunspot cycle. Thus, the first requirement is for a long term data record. The second related requirement is that the record be consistent. A third requirement is for reasonable global sampling, to ensure that the effects are representative of the entire Earth. The various observational methods relevant to trend detection are reviewed to characterize their quality and time and space coverage. Available data are then examined for long term trends or recent changes in ozone total content and vertical distribution, as well as related parameters such as stratospheric temperature, source gases and aerosols.

Line profile variations in M giants - Clues to mass-loss and chromospheric heating mechanisms

NASA Technical Reports Server (NTRS)

Judge, P. G.; Luttermoser, D. G.; Neff, D. H.; Cuntz, M.; Stencel, R. E.

1993-01-01

Analysis is presented of time-series, high dispersion spectra of the Mg II, k, Ca II H, and K lines of the semiregular giants Rho Per (M4 II-III, periodicity of about 50 days), R Lyr (M5 III, period of about 46 days), and g Her (M6 III, period of about 90 days). The fine error sensor on the IUE satellite and ground based UBV photometry was used to relate line profile variations to photospheric variations. The above mentioned stars were selected to study the relative importance of convective motions and global stellar pulsations in determining the structure of the outer atmospheres. Small amplitude changes, but substantial changes in the profiles of Mg II and Ca II lines were detected. It is contended that the observed variability is due to changes in chromospheric conditions and not variations within the circumstellar shell. The picture of a steady state chromosphere, which is modulated on long time scales, is corroborated by these observations. Localized heating is found in g Her.

An Analysis of Periodic Components in BL Lac Object S5 0716 +714 with MUSIC Method

NASA Astrophysics Data System (ADS)

Tang, J.

2012-01-01

Multiple signal classification (MUSIC) algorithms are introduced to the estimation of the period of variation of BL Lac objects.The principle of MUSIC spectral analysis method and theoretical analysis of the resolution of frequency spectrum using analog signals are included. From a lot of literatures, we have collected a lot of effective observation data of BL Lac object S5 0716 + 714 in V, R, I bands from 1994 to 2008. The light variation periods of S5 0716 +714 are obtained by means of the MUSIC spectral analysis method and periodogram spectral analysis method. There exist two major periods: (3.33±0.08) years and (1.24±0.01) years for all bands. The estimation of the period of variation of the algorithm based on the MUSIC spectral analysis method is compared with that of the algorithm based on the periodogram spectral analysis method. It is a super-resolution algorithm with small data length, and could be used to detect the period of variation of weak signals.

Uncovering Spatial Variation in Acoustic Environments Using Sound Mapping.

PubMed

Job, Jacob R; Myers, Kyle; Naghshineh, Koorosh; Gill, Sharon A

2016-01-01

Animals select and use habitats based on environmental features relevant to their ecology and behavior. For animals that use acoustic communication, the sound environment itself may be a critical feature, yet acoustic characteristics are not commonly measured when describing habitats and as a result, how habitats vary acoustically over space and time is poorly known. Such considerations are timely, given worldwide increases in anthropogenic noise combined with rapidly accumulating evidence that noise hampers the ability of animals to detect and interpret natural sounds. Here, we used microphone arrays to record the sound environment in three terrestrial habitats (forest, prairie, and urban) under ambient conditions and during experimental noise introductions. We mapped sound pressure levels (SPLs) over spatial scales relevant to diverse taxa to explore spatial variation in acoustic habitats and to evaluate the number of microphones needed within arrays to capture this variation under both ambient and noisy conditions. Even at small spatial scales and over relatively short time spans, SPLs varied considerably, especially in forest and urban habitats, suggesting that quantifying and mapping acoustic features could improve habitat descriptions. Subset maps based on input from 4, 8, 12 and 16 microphones differed slightly (< 2 dBA/pixel) from those based on full arrays of 24 microphones under ambient conditions across habitats. Map differences were more pronounced with noise introductions, particularly in forests; maps made from only 4-microphones differed more (> 4 dBA/pixel) from full maps than the remaining subset maps, but maps with input from eight microphones resulted in smaller differences. Thus, acoustic environments varied over small spatial scales and variation could be mapped with input from 4-8 microphones. Mapping sound in different environments will improve understanding of acoustic environments and allow us to explore the influence of spatial variation in sound on animal ecology and behavior.

Elevational Gradients in β-Diversity Reflect Variation in the Strength of Local Community Assembly Mechanisms across Spatial Scales

PubMed Central

Tello, J. Sebastián; Myers, Jonathan A.; Macía, Manuel J.; Fuentes, Alfredo F.; Cayola, Leslie; Arellano, Gabriel; Loza, M. Isabel; Torrez, Vania; Cornejo, Maritza; Miranda, Tatiana B.; Jørgensen, Peter M.

2015-01-01

Despite long-standing interest in elevational-diversity gradients, little is known about the processes that cause changes in the compositional variation of communities (β-diversity) across elevations. Recent studies have suggested that β-diversity gradients are driven by variation in species pools, rather than by variation in the strength of local community assembly mechanisms such as dispersal limitation, environmental filtering, or local biotic interactions. However, tests of this hypothesis have been limited to very small spatial scales that limit inferences about how the relative importance of assembly mechanisms may change across spatial scales. Here, we test the hypothesis that scale-dependent community assembly mechanisms shape biogeographic β-diversity gradients using one of the most well-characterized elevational gradients of tropical plant diversity. Using an extensive dataset on woody plant distributions along a 4,000-m elevational gradient in the Bolivian Andes, we compared observed patterns of β-diversity to null-model expectations. β-deviations (standardized differences from null values) were used to measure the relative effects of local community assembly mechanisms after removing sampling effects caused by variation in species pools. To test for scale-dependency, we compared elevational gradients at two contrasting spatial scales that differed in the size of local assemblages and regions by at least an order of magnitude. Elevational gradients in β-diversity persisted after accounting for regional variation in species pools. Moreover, the elevational gradient in β-deviations changed with spatial scale. At small scales, local assembly mechanisms were detectable, but variation in species pools accounted for most of the elevational gradient in β-diversity. At large spatial scales, in contrast, local assembly mechanisms were a dominant force driving changes in β-diversity. In contrast to the hypothesis that variation in species pools alone drives β-diversity gradients, we show that local community assembly mechanisms contribute strongly to systematic changes in β-diversity across elevations. We conclude that scale-dependent variation in community assembly mechanisms underlies these iconic gradients in global biodiversity. PMID:25803846

Diversity of human copy number variation and multicopy genes.

PubMed

Sudmant, Peter H; Kitzman, Jacob O; Antonacci, Francesca; Alkan, Can; Malig, Maika; Tsalenko, Anya; Sampas, Nick; Bruhn, Laurakay; Shendure, Jay; Eichler, Evan E

2010-10-29

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

An Analysis of Water Line Profiles in Star Formation Regions Observed by SWAS

NASA Technical Reports Server (NTRS)

Ashby, Matthew L. N.; Bergin, Edwin A.; Plume, Rene; Carpenter, John M.; Neufeld, David A.; Chin, Gordon; Erickson, Neal R.; Goldsmith, Paul F.; Harwit, Martin; Howe, J. E.

2000-01-01

We present spectral line profiles for the 557 GHz 1(sub 1,0) yields 1(sub 0,1) ground-state rotational transition of ortho-H2(16)O for 18 galactic star formation regions observed by SWAS. 2 Water is unambiguously detected in every source. The line profiles exhibit a wide variety of shapes, including single-peaked spectra and self-reversed profiles. We interpret these profiles using a Monte Carlo code to model the radiative transport. The observed variations in the line profiles can be explained by variations in the relative strengths of the bulk flow and small-scale turbulent motions within the clouds. Bulk flow (infall, outflow) must be present in some cloud cores, and in certain cases this bulk flow dominates the turbulent motions.

Temporal genetic change in the last remaining population of woolly mammoth

PubMed Central

Nyström, Veronica; Dalén, Love; Vartanyan, Sergey; Lidén, Kerstin; Ryman, Nils; Angerbjörn, Anders

2010-01-01

During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population. PMID:20356891

Characteristics of Drug Resistant Tuberculosis in Sanatoria of North Korea

PubMed Central

2017-01-01

Although several reports about drug-resistant tuberculosis (TB) in North Korea have been published, a nationwide surveillance on this disease remains to be performed. This study aims to analyze the drug resistance patterns of Mycobacterium tuberculosis among the patients in the sanatoria of North Korea, especially during the period when second-line drugs (SLDs) had not yet been officially supplied to this country. The Eugene Bell Foundation (EBF) transferred 947 sputum specimens obtained from 667 patients from 2007 to 2009 to the Clinical Research Center, Masan National Tuberculosis Hospital (MNTH), South Korea. Four hundred ninety-two patients were culture positive for TB (73.8%). Drug susceptibility test (DST) was performed for the bacilli isolated from 489 patients. Over 3 quarters of the cases (76.9%) were multidrug-resistant (MDR)-TB. Additionally, 2 patients had extremely drug-resistant (XDR)-TB. Very high resistance to first-line drugs and low resistance to fluoroquinolones (FQs) and injectable drugs (IDs) except for streptomycin (S) were detected. A small but significant regional variation in resistance pattern was observed. Big city regions had higher rate of MDR-TB, higher resistance to FQs and IDs than relatively isolated regions. In conclusion, significant number of drug-resistant TB was detected in North Korean sanatoria, and small but significant regional variations in resistance pattern were noticeable. However, the data in this study do not represent the nationwide drug resistance pattern in North Korea. Further large-scale evaluations are necessary to estimate the resistance pattern of TB in North Korea. PMID:28581266

Design of a model observer to evaluate calcification detectability in breast tomosynthesis and application to smoothing prior optimization.

PubMed

Michielsen, Koen; Nuyts, Johan; Cockmartin, Lesley; Marshall, Nicholas; Bosmans, Hilde

2016-12-01

In this work, the authors design and validate a model observer that can detect groups of microcalcifications in a four-alternative forced choice experiment and use it to optimize a smoothing prior for detectability of microcalcifications. A channelized Hotelling observer (CHO) with eight Laguerre-Gauss channels was designed to detect groups of five microcalcifications in a background of acrylic spheres by adding the CHO log-likelihood ratios calculated at the expected locations of the five calcifications. This model observer is then applied to optimize the detectability of the microcalcifications as a function of the smoothing prior. The authors examine the quadratic and total variation (TV) priors, and a combination of both. A selection of these reconstructions was then evaluated by human observers to validate the correct working of the model observer. The authors found a clear maximum for the detectability of microcalcification when using the total variation prior with weight β TV = 35. Detectability only varied over a small range for the quadratic and combined quadratic-TV priors when weight β Q of the quadratic prior was changed by two orders of magnitude. Spearman correlation with human observers was good except for the highest value of β for the quadratic and TV priors. Excluding those, the authors found ρ = 0.93 when comparing detection fractions, and ρ = 0.86 for the fitted detection threshold diameter. The authors successfully designed a model observer that was able to predict human performance over a large range of settings of the smoothing prior, except for the highest values of β which were outside the useful range for good image quality. Since detectability only depends weakly on the strength of the combined prior, it is not possible to pick an optimal smoothness based only on this criterion. On the other hand, such choice can now be made based on other criteria without worrying about calcification detectability.

Automated surface-scanning detection of pathogenic bacteria on fresh produce

NASA Astrophysics Data System (ADS)

Horikawa, Shin; Du, Songtao; Liu, Yuzhe; Chen, I.-Hsuan; Xi, Jianguo; Crumpler, Michael S.; Sirois, Donald L.; Best, Steve R.; Wikle, Howard C.; Chin, Bryan A.

2017-05-01

This paper investigates the effects of surface-scanning detector position on the resonant frequency and signal amplitude of a wireless magnetoelastic (ME) biosensor for direct pathogen detection on solid surfaces. The experiments were conducted on the surface of a flat polyethylene (PE) plate as a model study. An ME biosensor (1 mm × 0.2 mm × 30 μm) was placed on the PE surface, and a surface-scanning detector was brought close and aligned to the sensor for wireless resonant frequency measurement. The position of the detector was accurately controlled by using a motorized three-axis translation system (i.e., controlled X, Y, and Z positions). The results showed that the resonant frequency variations of the sensor were -125 to +150 Hz for X and Y detector displacements of +/-600 μm and Z displacements of +100 to +500 μm. These resonant frequency variations were small compared to the sensor's initial resonant frequency (< 0.007% of 2.2 MHz initial resonant frequency) measured at the detector home position, indicating high accuracy of the measurement. In addition, the signal amplitude was, as anticipated, found to decrease exponentially with increasing detection distance (i.e., Z distance). Finally, additional experiments were conducted on the surface of cucumbers. Similar results were obtained.

Creation of Mice Bearing a Partial Duplication of HPRT Gene Marked with a GFP Gene and Detection of Revertant Cells In Situ as GFP-Positive Somatic Cells.

PubMed

Noda, Asao; Suemori, Hirofumi; Hirai, Yuko; Hamasaki, Kanya; Kodama, Yoshiaki; Mitani, Hiroshi; Landes, Reid D; Nakamura, Nori

2015-01-01

It is becoming clear that apparently normal somatic cells accumulate mutations. Such accumulations or propagations of mutant cells are thought to be related to certain diseases such as cancer. To better understand the nature of somatic mutations, we developed a mouse model that enables in vivo detection of rare genetically altered cells via GFP positive cells. The mouse model carries a partial duplication of 3' portion of X-chromosomal HPRT gene and a GFP gene at the end of the last exon. In addition, although HPRT gene expression was thought ubiquitous, the expression level was found insufficient in vivo to make the revertant cells detectable by GFP positivity. To overcome the problem, we replaced the natural HPRT-gene promoter with a CAG promoter. In such animals, termed HPRT-dup-GFP mouse, losing one duplicated segment by crossover between the two sister chromatids or within a single molecule of DNA reactivates gene function, producing hybrid HPRT-GFP proteins which, in turn, cause the revertant cells to be detected as GFP-positive cells in various tissues. Frequencies of green mutant cells were measured using fixed and frozen sections (liver and pancreas), fixed whole mount (small intestine), or by means of flow cytometry (unfixed splenocytes). The results showed that the frequencies varied extensively among individuals as well as among tissues. X-ray exposure (3 Gy) increased the frequency moderately (~2 times) in the liver and small intestine. Further, in two animals out of 278 examined, some solid tissues showed too many GFP-positive cells to score (termed extreme jackpot mutation). Present results illustrated a complex nature of somatic mutations occurring in vivo. While the HPRT-dup-GFP mouse may have a potential for detecting tissue-specific environmental mutagens, large inter-individual variations of mutant cell frequency cause the results unstable and hence have to be reduced. This future challenge will likely involve lowering the background mutation frequency, thus reducing inter-individual variation.

Characterization of Raman Scattering in Solid Samples with Different Particle Sizes and Elucidation on the Trends of Particle Size-Dependent Intensity Variations in Relation to Changes in the Sizes of Laser Illumination and Detection Area.

PubMed

Duy, Pham K; Chun, Seulah; Chung, Hoeil

2017-11-21

We have systematically characterized Raman scatterings in solid samples with different particle sizes and investigated subsequent trends of particle size-induced intensity variations. For this purpose, both lactose powders and pellets composed of five different particle sizes were prepared. Uniquely in this study, three spectral acquisition schemes with different sizes of laser illuminations and detection windows were employed for the evaluation, since it was expected that the experimental configuration would be another factor potentially influencing the intensity of the lactose peak, along with the particle size itself. In both samples, the distribution of Raman photons became broader with the increase in particle size, as the mean free path of laser photons, the average photon travel distance between consecutive scattering locations, became longer under this situation. When the particle size was the same, the Raman photon distribution was narrower in the pellets since the individual particles were more densely packed in a given volume (the shorter mean free path). When the size of the detection window was small, the number of photons reaching the detector decreased as the photon distribution was larger. Meanwhile, a large-window detector was able to collect the widely distributed Raman photons more effectively; therefore, the trends of intensity change with the variation in particle size were dissimilar depending on the employed spectral acquisition schemes. Overall, the Monte Carlo simulation was effective at probing the photon distribution inside the samples and helped to support the experimental observations.

Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort.

PubMed

Moon, Sanghoon; Kim, Young Jin; Hong, Chang Bum; Kim, Dong-Joon; Lee, Jong-Young; Kim, Bong-Jo

2011-11-01

To date, hundreds of thousands of copy-number variation (CNV) data have been reported using various platforms. The proportion of Asians in these data is, however, relatively small as compared with that of other ethnic groups, such as Caucasians and Yorubas. Because of limitations in platform resolution and the high noise level in signal intensity, in most CNV studies (particularly those using single nucleotide polymorphism arrays), the average number of CNVs in an individual is less than the number of known CNVs. In this study, we ascertained reliable, common CNV regions (CNVRs) and identified actual frequency rates in the Korean population to provide more CNV information. We performed two-stage analyses for detecting structural variations with two platforms. We discovered 576 common CNVRs (88 CNV segments on average in an individual), and 87% (501 of 576) of these CNVRs overlapped by ≥1 bp with previously validated CNV events. Interestingly, from the frequency analysis of CNV profiles, 52 of 576 CNVRs had a frequency rate of <1% in the 8842 individuals. Compared with other common CNV studies, this study found six common CNVRs that were not reported in previous CNV studies. In conclusion, we propose the data-driven detection approach to discover common CNVRs including those of unreported in the previous Korean CNV study while minimizing false positives. Through our approach, we successfully discovered more common CNVRs than previous Korean CNV study and conducted frequency analysis. These results will be a valuable resource for the effective level of CNVs in the Korean population.

Major Variations in HIV-1 Capsid Assembly Morphologies Involve Minor Variations in Molecular Structures of Structurally Ordered Protein Segments*

PubMed Central

Lu, Jun-Xia; Bayro, Marvin J.; Tycko, Robert

2016-01-01

We present the results of solid state nuclear magnetic resonance (NMR) experiments on HIV-1 capsid protein (CA) assemblies with three different morphologies, namely wild-type CA (WT-CA) tubes with 35–60 nm diameters, planar sheets formed by the Arg18-Leu mutant (R18L-CA), and R18L-CA spheres with 20–100 nm diameters. The experiments are intended to elucidate molecular structural variations that underlie these variations in CA assembly morphology. We find that multidimensional solid state NMR spectra of 15N,13C-labeled CA assemblies are remarkably similar for the three morphologies, with only small differences in 15N and 13C chemical shifts, no significant differences in NMR line widths, and few differences in the number of detectable NMR cross-peaks. Thus, the pronounced differences in morphology do not involve major differences in the conformations and identities of structurally ordered protein segments. Instead, morphological variations are attributable to variations in conformational distributions within disordered segments, which do not contribute to the solid state NMR spectra. Variations in solid state NMR signals from certain amino acid side chains are also observed, suggesting differences in the intermolecular dimerization interface between curved and planar CA lattices, as well as possible differences in intramolecular helix-helix packing. PMID:27129282

Detection of retinal capillary nonperfusion in fundus fluorescein angiogram of diabetic retinopathy.

PubMed

Rasta, Seyed Hossein; Nikfarjam, Shima; Javadzadeh, Alireza

2015-01-01

Retinal capillary nonperfusion (CNP) is one of the retinal vascular diseases in diabetic retinopathy (DR) patients. As there is no comprehensive detection technique to recognize CNP areas, we proposed a different method for computing detection of ischemic retina, non-perfused (NP) regions, in fundus fluorescein angiogram (FFA) images. Whilst major vessels appear as ridges, non-perfused areas are usually observed as ponds that are surrounded by healthy capillaries in FFA images. A new technique using homomorphic filtering to correct light illumination and detect the ponds surrounded in healthy capillaries on FFA images was designed and applied on DR fundus images. These images were acquired from the diabetic patients who had referred to the Nikookari hospital and were diagnosed for diabetic retinopathy during one year. Our strategy was screening the whole image with a fixed window size, which is small enough to enclose areas with identified topographic characteristics. To discard false nominees, we also performed a thresholding operation on the screen and marked images. To validate its performance we applied our detection algorithm on 41 FFA diabetic retinopathy fundus images in which the CNP areas were manually delineated by three clinical experts. Lesions were found as smooth regions with very high uniformity, low entropy, and small intensity variations in FFA images. The results of automated detection method were compared with manually marked CNP areas so achieved sensitivity of 81%, specificity of 78%, and accuracy of 91%.The result was present as a Receiver operating character (ROC) curve, which has an area under the curve (AUC) of 0.796 with 95% confidence intervals. This technique introduced a new automated detection algorithm to recognize non-perfusion lesions on FFA. This has potential to assist detecting and managing of ischemic retina and may be incorporated into automated grading diabetic retinopathy structures.

A multi-wavelength search for photometric variability in L dwarfs

NASA Astrophysics Data System (ADS)

Gelino, Christopher Ryan

Previous studies investigating L-dwarf variability have been conducted in the optical I filter. These studies have shown that some, but not all L dwarfs are variable in this filter. In this dissertation I increase the number of L dwarfs observed for variations in the I filter from 10 to 25, with another three from the original ten reexamined here. I find that at least 7 and possibly as many as 12 are variable. One of these variable objects has a puzzling saw-tooth pattern in part of its light curve and another displays a feature that could indicate the creation and dissipation of a large storm. There is no evidence for significant differences between the variable and non- variable objects in their colors, Hα emission, or Li I absorption. I argue that the lack of a correlation between Hα and variability, coupled with low magnetic Reynolds number and ionization fraction in the upper atmosphere, suggests a non-magnetic origin for the variations and favors non-uniform condensate coverage. Furthermore, the absence of significant periodicity in these objects could indicate that these clouds evolve rapidly on timescales of hours to days. In addition to the optical survey, I also present the first multi-wavelength near-infrared search for photometric variations in L dwarfs. I was unable to detect any definite variability in these eleven targets. The upper limits for the amplitude of possible variations suggest that L dwarfs display smaller variations in K than in J and H . The small number of objects on which this conclusion is based and the lack of variability detections underscores the importance of more work in this wavelength regime.

The effect of small variations in profile of airfoils

NASA Technical Reports Server (NTRS)

Ward, Kenneth E

1931-01-01

This report deals with the effect of small variations in ordinates specified by different laboratories for the airfoil section. This study was made in connection with a more general investigation of the effect of small irregularities of the airfoil surface on the aerodynamic characteristics of an airfoil. These tests show that small changes in airfoil contours, resulting from variations in the specified ordinates, have a sufficiently large effect upon the airfoil characteristics to justify the taking of great care in the specification of ordinates for the construction of models.

Clinical application of 2.7M Cytogenetics array for CNV detection in subjects with idiopathic autism and/or intellectual disability.

PubMed

Qiao, Y; Tyson, C; Hrynchak, M; Lopez-Rangel, E; Hildebrand, J; Martell, S; Fawcett, C; Kasmara, L; Calli, K; Harvard, C; Liu, X; Holden, J J A; Lewis, S M E; Rajcan-Separovic, E

2013-02-01

Higher resolution whole-genome arrays facilitate the identification of smaller copy number variations (CNVs) and their integral genes contributing to autism and/or intellectual disability (ASD/ID). Our study describes the use of one of the highest resolution arrays, the Affymetrix(®) Cytogenetics 2.7M array, coupled with quantitative multiplex polymerase chain reaction (PCR) of short fluorescent fragments (QMPSF) for detection and validation of small CNVs. We studied 82 subjects with ASD and ID in total (30 in the validation and 52 in the application cohort) and detected putatively pathogenic CNVs in 6/52 cases from the application cohort. This included a 130-kb maternal duplication spanning exons 64-79 of the DMD gene which was found in a 3-year-old boy manifesting autism and mild neuromotor delays. Other pathogenic CNVs involved 4p14, 12q24.31, 14q32.31, 15q13.2-13.3, and 17p13.3. We established the optimal experimental conditions which, when applied to select small CNVs for QMPSF confirmation, reduced the false positive rate from 60% to 25%. Our work suggests that selection of small CNVs based on the function of integral genes, followed by review of array experimental parameters resulting in highest confirmation rate using multiplex PCR, may enhance the usefulness of higher resolution platforms for ASD and ID gene discovery. © 2012 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.

Computational Prediction of miRNA Genes from Small RNA Sequencing Data

PubMed Central

Kang, Wenjing; Friedländer, Marc R.

2015-01-01

Next-generation sequencing now for the first time allows researchers to gage the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in cells at single copies, more advanced computational tools are needed to accurately annotate and profile them. microRNAs (miRNAs) are 22 nucleotide small RNAs (sRNAs) that post-transcriptionally reduce the output of protein coding genes. They have established roles in numerous biological processes, including cancers and other diseases. During miRNA biogenesis, the sRNAs are sequentially cleaved from precursor molecules that have a characteristic hairpin RNA structure. The vast majority of new miRNA genes that are discovered are mined from small RNA sequencing (sRNA-seq), which can detect more than a billion RNAs in a single run. However, given that many of the detected RNAs are degradation products from all types of transcripts, the accurate identification of miRNAs remain a non-trivial computational problem. Here, we review the tools available to predict animal miRNAs from sRNA sequencing data. We present tools for generalist and specialist use cases, including prediction from massively pooled data or in species without reference genome. We also present wet-lab methods used to validate predicted miRNAs, and approaches to computationally benchmark prediction accuracy. For each tool, we reference validation experiments and benchmarking efforts. Last, we discuss the future of the field. PMID:25674563

Quality control and quality assurance in genotypic data for genome-wide association studies

PubMed Central

Laurie, Cathy C.; Doheny, Kimberly F.; Mirel, Daniel B.; Pugh, Elizabeth W.; Bierut, Laura J.; Bhangale, Tushar; Boehm, Frederick; Caporaso, Neil E.; Cornelis, Marilyn C.; Edenberg, Howard J.; Gabriel, Stacy B.; Harris, Emily L.; Hu, Frank B.; Jacobs, Kevin; Kraft, Peter; Landi, Maria Teresa; Lumley, Thomas; Manolio, Teri A.; McHugh, Caitlin; Painter, Ian; Paschall, Justin; Rice, John P.; Rice, Kenneth M.; Zheng, Xiuwen; Weir, Bruce S.

2011-01-01

Genome-wide scans of nucleotide variation in human subjects are providing an increasing number of replicated associations with complex disease traits. Most of the variants detected have small effects and, collectively, they account for a small fraction of the total genetic variance. Very large sample sizes are required to identify and validate findings. In this situation, even small sources of systematic or random error can cause spurious results or obscure real effects. The need for careful attention to data quality has been appreciated for some time in this field, and a number of strategies for quality control and quality assurance (QC/QA) have been developed. Here we extend these methods and describe a system of QC/QA for genotypic data in genome-wide association studies. This system includes some new approaches that (1) combine analysis of allelic probe intensities and called genotypes to distinguish gender misidentification from sex chromosome aberrations, (2) detect autosomal chromosome aberrations that may affect genotype calling accuracy, (3) infer DNA sample quality from relatedness and allelic intensities, (4) use duplicate concordance to infer SNP quality, (5) detect genotyping artifacts from dependence of Hardy-Weinberg equilibrium (HWE) test p-values on allelic frequency, and (6) demonstrate sensitivity of principal components analysis (PCA) to SNP selection. The methods are illustrated with examples from the ‘Gene Environment Association Studies’ (GENEVA) program. The results suggest several recommendations for QC/QA in the design and execution of genome-wide association studies. PMID:20718045

Improved flaw detection and characterization with difference thermography

NASA Astrophysics Data System (ADS)

Winfree, William P.; Zalameda, Joseph N.; Howell, Patricia A.

2011-05-01

Flaw detection and characterization with thermographic techniques in graphite polymer composites is often limited by localized variations in the thermographic response. Variations in properties such as acceptable porosity, variations in fiber volume content and surface polymer thickness result in variations in the thermal response that in general cause significant variations in the initial thermal response. These variations result in a noise floor that increases the difficulty of detecting and characterizing deeper flaws. The paper investigates comparing thermographic responses taken before and after a change in state in a composite to improve the detection of subsurface flaws. A method is presented for registration of the responses before finding the difference. A significant improvement in the detectability is achieved by comparing the differences in response. Examples of changes in state due to application of a load and impact are presented.

Improved Flaw Detection and Characterization with Difference Thermography

NASA Technical Reports Server (NTRS)

Winfree, William P.; Zalameda, Joseph N.; Howell, Patricia A.

2011-01-01

Flaw detection and characterization with thermographic techniques in graphite polymer composites is often limited by localized variations in the thermographic response. Variations in properties such as acceptable porosity, variations in fiber volume content and surface polymer thickness result in variations in the thermal response that in general cause significant variations in the initial thermal response. These variations result in a noise floor that increases the difficulty of detecting and characterizing deeper flaws. The paper investigates comparing thermographic responses taken before and after a change in state in a composite to improve the detection of subsurface flaws. A method is presented for registration of the responses before finding the difference. A significant improvement in the detectability is achieved by comparing the differences in response. Examples of changes in state due to application of a load and impact are presented.

Impact of basic angle variations on the parallax zero point for a scanning astrometric satellite

NASA Astrophysics Data System (ADS)

Butkevich, Alexey G.; Klioner, Sergei A.; Lindegren, Lennart; Hobbs, David; van Leeuwen, Floor

2017-07-01

Context. Determination of absolute parallaxes by means of a scanning astrometric satellite such as Hipparcos or Gaia relies on the short-term stability of the so-called basic angle between the two viewing directions. Uncalibrated variations of the basic angle may produce systematic errors in the computed parallaxes. Aims: We examine the coupling between a global parallax shift and specific variations of the basic angle, namely those related to the satellite attitude with respect to the Sun. Methods: The changes in observables produced by small perturbations of the basic angle, attitude, and parallaxes were calculated analytically. We then looked for a combination of perturbations that had no net effect on the observables. Results: In the approximation of infinitely small fields of view, it is shown that certain perturbations of the basic angle are observationally indistinguishable from a global shift of the parallaxes. If these kinds of perturbations exist, they cannot be calibrated from the astrometric observations but will produce a global parallax bias. Numerical simulations of the astrometric solution, using both direct and iterative methods, confirm this theoretical result. For a given amplitude of the basic angle perturbation, the parallax bias is smaller for a larger basic angle and a larger solar aspect angle. In both these respects Gaia has a more favourable geometry than Hipparcos. In the case of Gaia, internal metrology is used to monitor basic angle variations. Additionally, Gaia has the advantage of detecting numerous quasars, which can be used to verify the parallax zero point.

Acousto-optical assessment of skin viscoelasticity

NASA Astrophysics Data System (ADS)

Kirkpatrick, Sean J.; Duncan, Donald D.

2003-07-01

A multiphysics approach, combining acoustics, optics, and mechanics can be used to detect regions of skin with distinct mechanical behavior that may indicate a pathology, such as a cancerous skin lesion. Herein, an acousto-optical approach to evaluating the viscoelastic behavior of superficial skin layers will be presented. The method relies upon inducing low frequency guided surface waves in the skin and detecting these waves by monitoring the shift in the backscattered laser speckle pattern created by illuminating a small region of the skin with coherent light. Artificial lesions in the form of chemical cross-linking and chemical softening were induced in superficial porcine skin layers and detected based upon variations in local mechanical behavior. The lesions affect not only the time-of-flight of the guided surface waves, but also change the relative phase of the acoustic waves as determined optically. The method may be applicable in the study and diagnosis of superficial skin lesions.

Optical assessment of tissue mechanics: acousto-optical elastography of skin

NASA Astrophysics Data System (ADS)

Kirkpatrick, Sean J.

2003-10-01

A multiphysics approach, combining acoustics, optics, and mechanics can be used to detect regions of skin with distinct mechanical behavior that may indicate a pathology, such as a cancerous skin lesion. Herein, an acousto - optical approach to evaluating the viscoelastic behavior of superficial skin layers will be presented. The method relies upon inducing low frequency guided surface waves in the skin and detecting these waves by monitoring the shift in the backscattered laser speckle pattern created by illuminating a small region of the skin with coherent light. Artificial lesions in the form of chemical cross-linking and chemical softening were induced in superficial porcine skin layers and detected based upon variations in local mechanical behavior. The lesions affect not only the time-of-flight of the guided surface waves, but also change the relative phase of the acoustic waves as determined optically. The method may be applicable in the study and diagnosis of superficial skin lesions.

Error detection and response adjustment in youth with mild spastic cerebral palsy: an event-related brain potential study.

PubMed

Hakkarainen, Elina; Pirilä, Silja; Kaartinen, Jukka; van der Meere, Jaap J

2013-06-01

This study evaluated the brain activation state during error making in youth with mild spastic cerebral palsy and a peer control group while carrying out a stimulus recognition task. The key question was whether patients were detecting their own errors and subsequently improving their performance in a future trial. Findings indicated that error responses of the group with cerebral palsy were associated with weak motor preparation, as indexed by the amplitude of the late contingent negative variation. However, patients were detecting their errors as indexed by the amplitude of the response-locked negativity and thus improved their performance in a future trial. Findings suggest that the consequence of error making on future performance is intact in a sample of youth with mild spastic cerebral palsy. Because the study group is small, the present findings need replication using a larger sample.

Bubble-on-fiber (BoF): a built-in tunable broadband acousto-optic sensor for liquid-immersible in situ measurements.

PubMed

Xu, Hongsong; Wang, Guanyu; Ma, Jun; Jin, Long; Oh, Kyunghwan; Guan, Bai-Ou

2018-04-30

A new type of tunable broadband fiber-optic acousto-optic sensor was experimentally demonstrated by utilizing a bubble-on-fiber (BoF) interferometer. A single micro-bubble was generated by injecting a heating laser at λ = 980 nm on the metalized facet of an optical fiber. The BoF formed a spherical micro-cavity in water whose acoustic deformation was precisely detected by using a narrowband DFB laser at 1550 nm. The heating light and the interrogating light were fed into a single fiber probe by wavelength division multiplexing (WDM) realizing a small footprint all-fiber configuration. The diameter of the BoF was stabilized with a variation less than 0.5 nm by fast servo-control of the heating laser power. The stabilized BoF served as a Fabry-Pérot cavity that can be deformed by acoustic perturbation, and a minimum detectable pressure level of as low as ~1 mPa/Hz 1/2 was achieved in a frequency range of over 60 kHz in water at room temperature. Our proposed BoF technology can provide a tunable, flexible and all-fiber solution to detect minute acoustically driven perturbations combining high-precision interferometry. Due to the very small form-factor, the technique can find applications of liquid-immersible in situ measurements in bio-molecular/cell detection and biochemical phenomena study.

Fibre optic sensor for the detection of adulterant traces in coconut oil

NASA Astrophysics Data System (ADS)

Sheeba, M.; Rajesh, M.; Vallabhan, C. P. G.; Nampoori, V. P. N.; Radhakrishnan, P.

2005-11-01

The design and development of a fibre optic evanescent wave refractometer for the detection of trace amounts of paraffin oil and palm oil in coconut oil is presented. This sensor is based on a side-polished plastic optical fibre. At the sensing region, the cladding and a small portion of the core are removed and the fibre nicely polished. The sensing region is fabricated in such a manner that it sits perfectly within a bent mould. This bending of the sensing region enhances its sensitivity. The oil mixture of different mix ratios is introduced into the sensing region and we observed a sharp decrease in the output intensity. The observed variation in the intensity is found to be linear and the detection limit is 2% (by volume) paraffin oil/palm oil in coconut oil. The resolution of this refractometric sensor is of the order of 10-3. Since coconut oil is consumed in large volumes as edible oil in south India, this fibre optic sensor finds great relevance for the detection of adulterants such as paraffin oil or palm oil which are readily miscible in coconut oil. The advantage of this type of sensor is that it is inexpensive and easy to set up. Another attraction of the side-polished fibre is that only a very small amount of analyte is needed and its response time is only 7 s.

A new laser pain threshold model detects a faster onset of action from a liquid formulation of 1 g paracetamol than an equivalent tablet formulation

PubMed Central

Sutton, J A; Gillin, W P; Grattan, T J; Clarke, G D; Kilminster, S G

2002-01-01

Aims To discover whether a new infra-red laser method could detect a change in pain threshold after as mild an analgesic as paracetamol and whether an effervescent liquid formulation produced a faster onset of action than tablets. Methods This double-blind, placebo controlled randomized study used a portable, infra-red laser to measure ‘first pain’ thresholds on the nondominant forearm in 12 normal volunteers before and after 1 g of paracetamol or placebo. The mean of six recordings was determined three times before dosing, the first being used as a familiarization procedure, and 14 times after dosing. Results We detected a small (2%), statistically significant difference in pain threshold between a liquid formulation of paracetamol and placebo at 30 and 60 min (P = 0.004 and P = 0.001), but not between tablets and placebo. Liquid also increased the threshold significantly compared with tablets at 60 min (P = 0.01). Conclusions To detect such a small increase in pain threshold requires a highly consistent measure and the coefficient of variation was 2% for the study overall, surprisingly low for a subjective phenomenon. The reasons for this include minimizing reflectance by blacking the skin, using a nonhairy site, averaging six data points at each sample time and controlling closely the ambient conditions and the subjects’ preparation for studies. PMID:11849194

Estimation of completeness magnitude with a Bayesian modeling of daily and weekly variations in earthquake detectability

NASA Astrophysics Data System (ADS)

Iwata, T.

2014-12-01

In the analysis of seismic activity, assessment of earthquake detectability of a seismic network is a fundamental issue. For this assessment, the completeness magnitude Mc, the minimum magnitude above which all earthquakes are recorded, is frequently estimated. In most cases, Mc is estimated for an earthquake catalog of duration longer than several weeks. However, owing to human activity, noise level in seismic data is higher on weekdays than on weekends, so that earthquake detectability has a weekly variation [e.g., Atef et al., 2009, BSSA]; the consideration of such a variation makes a significant contribution to the precise assessment of earthquake detectability and Mc. For a quantitative evaluation of the weekly variation, we introduced the statistical model of a magnitude-frequency distribution of earthquakes covering an entire magnitude range [Ogata & Katsura, 1993, GJI]. The frequency distribution is represented as the product of the Gutenberg-Richter law and a detection rate function. Then, the weekly variation in one of the model parameters, which corresponds to the magnitude where the detection rate of earthquakes is 50%, was estimated. Because earthquake detectability also have a daily variation [e.g., Iwata, 2013, GJI], and the weekly and daily variations were estimated simultaneously by adopting a modification of a Bayesian smoothing spline method for temporal change in earthquake detectability developed in Iwata [2014, Aust. N. Z. J. Stat.]. Based on the estimated variations in the parameter, the value of Mc was estimated. In this study, the Japan Meteorological Agency catalog from 2006 to 2010 was analyzed; this dataset is the same as analyzed in Iwata [2013] where only the daily variation in earthquake detectability was considered in the estimation of Mc. A rectangular grid with 0.1° intervals covering in and around Japan was deployed, and the value of Mc was estimated for each gridpoint. Consequently, a clear weekly variation was revealed; the detectability is better on Sundays than on the other days. The estimated spatial variation in Mc was compared with that estimated in Iwata [2013]; the maximum difference between Mc values with and without considering the weekly variation approximately equals to 0.2, suggesting the importance of accounting for the weekly variation in the estimation of Mc.

Reconstruction-free sensitive wavefront sensor based on continuous position sensitive detectors.

PubMed

Godin, Thomas; Fromager, Michael; Cagniot, Emmanuel; Brunel, Marc; Aït-Ameur, Kamel

2013-12-01

We propose a new device that is able to perform highly sensitive wavefront measurements based on the use of continuous position sensitive detectors and without resorting to any reconstruction process. We demonstrate experimentally its ability to measure small wavefront distortions through the characterization of pump-induced refractive index changes in laser material. In addition, it is shown using computer-generated holograms that this device can detect phase discontinuities as well as improve the quality of sharp phase variations measurements. Results are compared to reference Shack-Hartmann measurements, and dramatic enhancements are obtained.

Wire inhomogeneity detector having a core with opposing pole pieces and guide pieces adjacent the opposing pole pieces

DOEpatents

Gibson, George H.; Smits, Robert G.; Eberhard, Philippe H.

1989-01-01

A device for uncovering imperfections in electrical conducting wire, particularly superconducting wire, by detecting variations in eddy currents. Eddy currents effect the magnetic field in a gap of an inductor, contained in a modified commercial ferrite core, through which the wire being tested is passed. A small increase or decrease in the amount of conductive material, such as copper, in a fixed cross section of wire will unbalance a bridge used to measure the impedance of the inductor, tripping a detector and sounding an alarm.

The reliability of running economy expressed as oxygen cost and energy cost in trained distance runners.

PubMed

Shaw, Andrew J; Ingham, Stephen A; Fudge, Barry W; Folland, Jonathan P

2013-12-01

This study assessed the between-test reliability of oxygen cost (OC) and energy cost (EC) in distance runners, and contrasted it with the smallest worthwhile change (SWC) of these measures. OC and EC displayed similar levels of within-subject variation (typical error < 3.85%). However, the typical error (2.75% vs 2.74%) was greater than the SWC (1.38% vs 1.71%) for both OC and EC, respectively, indicating insufficient sensitivity to confidently detect small, but meaningful, changes in OC and EC.

Phylogenetic relationships among anuran trypanosomes as revealed by riboprinting.

PubMed

Clark, C G; Martin, D S; Diamond, L S

1995-01-01

Twenty trypanosome isolates from Anura (frogs and toads) assigned to several species were characterized by riboprinting-restriction enzyme digestion of polymerase chain reaction amplified small subunit ribosomal RNA genes. Restriction site polymorphisms allowed distinction of all the recognized species and no intraspecific variation in riboprint patterns was detected. Phylogenetic reconstruction using parsimony and distance estimates based on restriction fragment comigration showed Trypanosoma chattoni to be only distantly related to the other species, while T. ranarum and T. fallisi appear to be sister taxa despite showing non-overlapping host specificities.

The first eclipsing binary catalogue from the MOA-II data base

NASA Astrophysics Data System (ADS)

Li, M. C. A.; Rattenbury, N. J.; Bond, I. A.; Sumi, T.; Bennett, D. P.; Koshimoto, N.; Abe, F.; Asakura, Y.; Barry, R.; Bhattacharya, A.; Donachie, M.; Evans, P.; Freeman, M.; Fukui, A.; Hirao, Y.; Itow, Y.; Ling, C. H.; Masuda, K.; Matsubara, Y.; Muraki, Y.; Nagakane, M.; Ohnishi, K.; Saito, To.; Sharan, A.; Sullivan, D. J.; Suzuki, D.; Tristram, P. J.; Yonehara, A.

2017-09-01

We present the first catalogue of eclipsing binaries in two MOA (Microlensing Observations in Astrophysics) fields towards the Galactic bulge, in which over 8000 candidates, mostly contact and semidetached binaries of periods <1 d, were identified. In this paper, the light curves of a small number of interesting candidates, including eccentric binaries, binaries with noteworthy phase modulations and eclipsing RS Canum Venaticorum type stars, are shown as examples. In addition, we identified three triple object candidates by detecting the light-travel-time effect in their eclipse time variation curves.

MULTICHANNEL PULSE-HEIGHT ANALYZER

DOEpatents

Russell, J.T.; Lefevre, H.W.

1958-01-21

This patent deals with electronic computing circuits and more particularly to pulse-height analyzers used for classifying variable amplitude pulses into groups of different amplitudes. The device accomplishes this pulse allocation by by converting the pulses into frequencies corresponding to the amplitudes of the pulses, which frequencies are filtered in channels individually pretuned to a particular frequency and then detected and recorded in the responsive channel. This circuit substantially overcomes the disadvantages of prior annlyzers incorporating discriminators pre-set to respond to certain voltage levels, since small variation in component values is not as critical to satisfactory circuit operation.

Nuclear Power Plant Thermocouple Sensor-Fault Detection and Classification Using Deep Learning and Generalized Likelihood Ratio Test

NASA Astrophysics Data System (ADS)

Mandal, Shyamapada; Santhi, B.; Sridhar, S.; Vinolia, K.; Swaminathan, P.

2017-06-01

In this paper, an online fault detection and classification method is proposed for thermocouples used in nuclear power plants. In the proposed method, the fault data are detected by the classification method, which classifies the fault data from the normal data. Deep belief network (DBN), a technique for deep learning, is applied to classify the fault data. The DBN has a multilayer feature extraction scheme, which is highly sensitive to a small variation of data. Since the classification method is unable to detect the faulty sensor; therefore, a technique is proposed to identify the faulty sensor from the fault data. Finally, the composite statistical hypothesis test, namely generalized likelihood ratio test, is applied to compute the fault pattern of the faulty sensor signal based on the magnitude of the fault. The performance of the proposed method is validated by field data obtained from thermocouple sensors of the fast breeder test reactor.

Simple detection method of amyloid-beta peptide using p-FET with optical filtering layer and magnetic particle

NASA Astrophysics Data System (ADS)

Kim, Kwan-Soo; Kim, Chang-Beom; Song, Ki-Bong

2013-05-01

This article describes a novel method for detection of amyloid-β (Aβ) peptide that utilizes a photo-sensitive field-effect transistor (p-FET). According to a recent study, Aβ protein is known to play a central role in the pathogenesis of Alzheimer's disease (AD). Accordingly, we investigated the variation of photo current of the p-FET generated by the magnetic beads conjugated with Aβ peptides which are placed on the p-FET sensing areas. Additionally, in order to amplify the output signal, we used the lock-in amplifier (LIA) and confirmed the generating the photo current by a small incident light power under 100 μW. It means that it is possible to simply detect a certain protein using magnetic beads conjugated with Aβ peptide and fluorescent label located on the p-FET device. Therefore, in this paper, we suggest that our method could detect tiny amounts of Aβ peptide for early diagnosis of AD using the p-FET devices.

High-Throughput Genetic Analysis and Combinatorial Chiral Separations Based on Capillary Electrophoresis

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

Zhong, Wenwan

2003-01-01

Capillary electrophoresis (CE) offers many advantages over conventional analytical methods, such as speed, simplicity, high resolution, low cost, and small sample consumption, especially for the separation of enantiomers. However, chiral method developments still can be time consuming and tedious. They designed a comprehensive enantioseparation protocol employing neutral and sulfated cyclodextrins as chiral selectors for common basic, neutral, and acidic compounds with a 96-capillary array system. By using only four judiciously chosen separation buffers, successful enantioseparations were achieved for 49 out of 54 test compounds spanning a large variety of pKs and structures. Therefore, unknown compounds can be screened in thismore » manner to identify optimal enantioselective conditions in just one rn. In addition to superior separation efficiency for small molecules, CE is also the most powerful technique for DNA separations. Using the same multiplexed capillary system with UV absorption detection, the sequence of a short DNA template can be acquired without any dye-labels. Two internal standards were utilized to adjust the migration time variations among capillaries, so that the four electropherograms for the A, T, C, G Sanger reactions can be aligned and base calling can be completed with a high level of confidence. the CE separation of DNA can be applied to study differential gene expression as well. Combined with pattern recognition techniques, small variations among electropherograms obtained by the separation of cDNA fragments produced from the total RNA samples of different human tissues can be revealed. These variations reflect the differences in total RNA expression among tissues. Thus, this Ce-based approach can serve as an alternative to the DNA array techniques in gene expression analysis.« less

Spatial scale and sampling resolution affect measures of gap disturbance in a lowland tropical forest: implications for understanding forest regeneration and carbon storage.

PubMed

Lobo, Elena; Dalling, James W

2014-03-07

Treefall gaps play an important role in tropical forest dynamics and in determining above-ground biomass (AGB). However, our understanding of gap disturbance regimes is largely based either on surveys of forest plots that are small relative to spatial variation in gap disturbance, or on satellite imagery, which cannot accurately detect small gaps. We used high-resolution light detection and ranging data from a 1500 ha forest in Panama to: (i) determine how gap disturbance parameters are influenced by study area size, and the criteria used to define gaps; and (ii) to evaluate how accurately previous ground-based canopy height sampling can determine the size and location of gaps. We found that plot-scale disturbance parameters frequently differed significantly from those measured at the landscape-level, and that canopy height thresholds used to define gaps strongly influenced the gap-size distribution, an important metric influencing AGB. Furthermore, simulated ground surveys of canopy height frequently misrepresented the true location of gaps, which may affect conclusions about how relatively small canopy gaps affect successional processes and contribute to the maintenance of diversity. Across site comparisons need to consider how gap definition, scale and spatial resolution affect characterizations of gap disturbance, and its inferred importance for carbon storage and community composition.

Ambient seismic noise monitoring of a clay landslide: Toward failure prediction

NASA Astrophysics Data System (ADS)

Mainsant, Guénolé; Larose, Eric; Brönnimann, Cornelia; Jongmans, Denis; Michoud, Clément; Jaboyedoff, Michel

2012-03-01

Given that clay-rich landslides may become mobilized, leading to rapid mass movements (earthflows and debris flows), they pose critical problems in risk management worldwide. The most widely proposed mechanism leading to such flow-like movements is the increase in water pore pressure in the sliding mass, generating partial or complete liquefaction. This solid-to-liquid transition results in a dramatic reduction of mechanical rigidity in the liquefied zones, which could be detected by monitoring shear wave velocity variations. With this purpose in mind, the ambient seismic noise correlation technique has been applied to measure the variation in the seismic surface wave velocity in the Pont Bourquin landslide (Swiss Alps). This small but active composite earthslide-earthflow was equipped with continuously recording seismic sensors during spring and summer 2010. An earthslide of a few thousand cubic meters was triggered in mid-August 2010, after a rainy period. This article shows that the seismic velocity of the sliding material, measured from daily noise correlograms, decreased continuously and rapidly for several days prior to the catastrophic event. From a spectral analysis of the velocity decrease, it was possible to determine the location of the change at the base of the sliding layer. These results demonstrate that ambient seismic noise can be used to detect rigidity variations before failure and could potentially be used to predict landslides.

Predicting ecological effects of pollutants: A role for marine mesocosms

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

Ward, T.J.

1994-12-31

The major uncertainty in predicting the ecological effects of a pollutant is the relationship between dose and the ecological response. Mesocosms may be used to simulate population-level biological processes and to estimate the nature and shape of dose-related responses to pollutants, for use in predictive evaluations of pollutant impacts. To ensure that responses observed in mesocosm tests are representative it is necessary to confirm that the simulated processes operate at rates similar to those found in the field. Pilot experiments were conducted in small marine mesocosms simulating major processes in two local habitat types: unvegetated sand and sand colonized bymore » the brown macroalga Sargassum. The results showed that for a range of variates (such as the % of egg-bearing harpacticoid copepods, or the chlorophyll a concentration in surface sediments) the mean values for measurements in the tanks over a 9 week period did not consistently converge or diverge from those in the field. Also, for a number of the variates, a modelled decrease of more than about 60% in the mean could be detected with greater than 80% statistical power. This indicates that the effects of a pollutant could be detected with acceptable power. Use of a combination of such variates based on different functional or taxonomic groups for pollutant effects testing could greatly decrease uncertainty about the predicted effects of pollutants discharged to these habitats.« less

Water-quality assessment of the Rio Grande Valley, Colorado, New Mexico, and Texas : shallow ground-water quality and land use in the Albuquerque area, central New Mexico, 1993

USGS Publications Warehouse

Anderholm, Scott K.

1997-01-01

This report describes the quality of shallow ground water and the relations between land use and the quality of that shallow ground water in an urban area in and adjacent to Albuquerque, New Mexico. Water samples were collected from 24 shallow wells. Samples were analyzed for selected common constituents, nutrients, trace elements, radionuclides, volatile organic compounds, and pesticides. The study area, which is in the Albuquerque Basin in central New Mexico, was limited to the Rio Grande flood plain; depth to water in this area generally is less than 25 feet. The amount and composition of recharge to the shallow ground-water system are important factors that affect shallow ground-water composition in this area. Important sources of recharge that affect shallow ground-water quality in the area include infiltration of surface water, which is used in agricultural land-use areas to irrigate crops, and infiltration of septic-system effluent in residential areas. Agricultural land use represents about 28 percent of the area, and residential land use represents about 35 percent of the total study area. In most of the study area, agricultural land use is interspersed with residential land use and neither is the dominant land use in the area. Land use in the study area historically has been changing from agricultural to urban. The composition of shallow ground water in the study area varies considerably. The dissolved solids concentration in shallow ground water in the study area ranges from 272 to 1,650 milligrams per liter, although the relative percentages of selected cations and anions do not vary substantially. Calcium generally is the dominant cation and bicarbonate generally is the dominant anion. Concentrations of nutrients generally were less than 1 milligram per liter. The concentration of many trace elements in shallow ground water was below or slightly above 1 microgram per liter and there was little variation in the concentrations. Barium, iron, manganese, molybdenum, and uranium were the only trace elements analyzed for that had median concentrations greater than 5 micrograms per liter. Volatile organic compounds were detected in 5 of 24 samples. Cis-1,2-dichloroethene and 1,1-dichloroethane were the most commonly detected volatile organic compounds (detected in two samples each). Pesticides were detected in 8 of 24 samples. Prometon was the most commonly detected pesticide (detected in 5 of 24 samples). Concentrations of volatile organic compounds and pesticides detected were much smaller than any U.S. Environmental Protection Agency standards that have been established. Infiltration of surface water and the evaporation or transpiration of this water, which partially is the result of past and present agricultural land use, seem to affect the concentrations of common constituents in shallow ground water in the study area. The small excess chloride in shallow ground water relative to surface water that has been affected by evaporation or transpiration could be due to mixing of shallow ground water with small amounts of precipitation/bulk deposition or septic-system effluent. Infiltration of septic-system effluent (residential land use) has affected the shallow ground-water composition in parts of the study area on the basis of the small dissolved oxygen concentrations, large dissolved organic carbon concentrations, and excess chloride. Despite the loading of nitrogen to the shallow ground-water system as the result of infiltration of septic-system effluent, the small nitrogen concentrations in shallow ground water probably are due to the small dissolved oxygen concentrations and relatively large dissolved organic carbon concentrations. The small concentrations and lack of variation of most trace elements indicate that land use has not substantially affected the concentration

Cluster signal-to-noise analysis for evaluation of the information content in an image.

PubMed

Weerawanich, Warangkana; Shimizu, Mayumi; Takeshita, Yohei; Okamura, Kazutoshi; Yoshida, Shoko; Yoshiura, Kazunori

2018-01-01

(1) To develop an observer-free method of analysing image quality related to the observer performance in the detection task and (2) to analyse observer behaviour patterns in the detection of small mass changes in cone-beam CT images. 13 observers detected holes in a Teflon phantom in cone-beam CT images. Using the same images, we developed a new method, cluster signal-to-noise analysis, to detect the holes by applying various cut-off values using ImageJ and reconstructing cluster signal-to-noise curves. We then evaluated the correlation between cluster signal-to-noise analysis and the observer performance test. We measured the background noise in each image to evaluate the relationship with false positive rates (FPRs) of the observers. Correlations between mean FPRs and intra- and interobserver variations were also evaluated. Moreover, we calculated true positive rates (TPRs) and accuracies from background noise and evaluated their correlations with TPRs from observers. Cluster signal-to-noise curves were derived in cluster signal-to-noise analysis. They yield the detection of signals (true holes) related to noise (false holes). This method correlated highly with the observer performance test (R 2 = 0.9296). In noisy images, increasing background noise resulted in higher FPRs and larger intra- and interobserver variations. TPRs and accuracies calculated from background noise had high correlation with actual TPRs from observers; R 2 was 0.9244 and 0.9338, respectively. Cluster signal-to-noise analysis can simulate the detection performance of observers and thus replace the observer performance test in the evaluation of image quality. Erroneous decision-making increased with increasing background noise.

QTLs for heading date and plant height under multiple environments in rice.

PubMed

Han, Zhongmin; Hu, Wei; Tan, Cong; Xing, Yongzhong

2017-02-01

Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions. Among them, major QTLs qHd7.1, qHd7.2 and qHd8 for heading date, and qPh1 and qPh7.1 for plant height were commonly detected. qHd7.1 and qHd7.2 were mapped to small regions of less than 1 cM. Genome position comparison of previously cloned genes with QTLs detected in this study revealed that qHd5 and qPh3.1 were two novel QTLs. The alleles of these QTLs increasing trait values were dispersed in both parents, which well explained the transgressive segregation observed in this population. In addition, the interaction between qHd7.1 and qHd8 was detected under all LD conditions. Multiple-QTL model analysis revealed that all QTLs and their interactions explained over 80% of heading date variation and 50% of plant height variation. Two heading date QTLs were detected under SD condition. Of them, qHd10 were commonly identified under LD condition. The difference in QTL detection between LD and SD conditions indicated most heading date QTLs are sensitive to photoperiod. These findings will benefit breeding design for heading date and plant height in rice.

Ionospheric effects of thunderstorms and lightning

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

Lay, Erin H.

2014-02-03

Tropospheric thunderstorms have been reported to disturb the lower ionosphere (~65-90 km) by convective atmospheric gravity waves and by electromagnetic field changes produced by lightning discharges. However, due to the low electron density in the lower ionosphere, active probing of its electron distribution is difficult, and the various perturbative effects are poorly understood. Recently, we have demonstrated that by using remotely-detected ?me waveforms of lightning radio signals it is possible to probe the lower ionosphere and its fluctuations in a spatially and temporally-resolved manner. Here we report evidence of gravity wave effects on the lower ionosphere originating from the thunderstorm.more » We also report variations in the nighttime ionosphere atop a small thunderstorm and associate the variations with the storm’s electrical activity. Finally, we present a data analysis technique to map ionospheric acoustic waves near thunderstorms.« less

Using Volcanic Lightning Measurements to Discern Variations in Explosive Volcanic Activity

NASA Astrophysics Data System (ADS)

Behnke, S. A.; Thomas, R. J.; McNutt, S. R.; Edens, H. E.; Krehbiel, P. R.; Rison, W.

2013-12-01

VHF observations of volcanic lightning have been made during the recent eruptions of Augustine Volcano (2006, Alaska, USA), Redoubt Volcano (2009, Alaska, USA), and Eyjafjallajökull (2010, Iceland). These show that electrical activity occurs both on small scales at the vent of the volcano, concurrent with an eruptive event and on large scales throughout the eruption column during and subsequent to an eruptive event. The small-scale discharges at the vent of the volcano are often referred to as 'vent discharges' and are on the order of 10-100 meters in length and occur at rates on the order of 1000 per second. The high rate of vent discharges produces a distinct VHF signature that is sometimes referred to as 'continuous RF' radiation. VHF radiation from vent discharges has been observed at sensors placed as far as 100 km from the volcano. VHF and infrasound measurements have shown that vent discharges occur simultaneously with the onset of eruption, making their detection an unambiguous indicator of explosive volcanic activity. The fact that vent discharges are observed concurrent with explosive volcanic activity indicates that volcanic ejecta are charged upon eruption. VHF observations have shown that the intensity of vent discharges varies between eruptive events, suggesting that fluctuations in eruptive processes affect the electrification processes giving rise to vent discharges. These fluctuations may be variations in eruptive vigor or variations in the type of eruption; however, the data obtained so far do not show a clear relationship between eruption parameters and the intensity or occurrence of vent discharges. Further study is needed to clarify the link between vent discharges and eruptive behavior, such as more detailed lightning observations concurrent with tephra measurements and other measures of eruptive strength. Observations of vent discharges, and volcanic lightning observations in general, are a valuable tool for volcano monitoring, providing a method for rapid detection of volcanic activity in real-time.

The impact of temperature and precipitation on blacklegged tick activity and Lyme disease incidence in endemic and emerging regions.

PubMed

Burtis, James C; Sullivan, Patrick; Levi, Taal; Oggenfuss, Kelly; Fahey, Timothy J; Ostfeld, Richard S

2016-11-25

The incidence of Lyme disease shows high degrees of inter-annual variation in the northeastern United States, but the factors driving this variation are not well understood. Complicating matters, it is also possible that these driving factors may vary in regions with differing histories of Lyme disease endemism. We evaluated the effect of the number of hot (T > 25 °C), dry (precipitation = 0) days during the questing periods of the two immature Ixodes scapularis life stages (larval and nymphal) on inter-annual variation in Lyme disease incidence between 2000 and 2011 in long-term endemic versus recently endemic areas. We also evaluated the effect of summer weather on tick questing activity and the number of ticks found on small mammals between 1994 and 2012 on six sites in Millbrook, NY. The number of hot, dry days during the larval period of the previous year did not affect the human incidence of Lyme disease or the density of questing nymphs the following season. However, dry summer weather during the nymphal questing period had a significant negative effect on the incidence of Lyme disease in the long-term endemic areas, and on the density of questing nymphs. Summer weather conditions had a more pronounced effect on actively questing I. scapularis collected via dragging than on the number of ticks found feeding on small mammals. In recently endemic areas Lyme disease incidence increased significantly over time, but no trend was detected between disease incidence and dry summer weather. Recently endemic regions showed an increase in Lyme disease incidence over time, while incidence in long-term endemic regions appears to have stabilized. Only within the stabilized areas were we able to detect reduced Lyme disease incidence in years with hot, dry summer weather. These patterns were reflected in our field data, which showed that questing activity of nymphal I. scapularis was reduced by hot, dry summer weather.

Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders

PubMed Central

Pfundt, Rolph; del Rosario, Marisol; Vissers, Lisenka E.L.M.; Kwint, Michael P.; Janssen, Irene M.; de Leeuw, Nicole; Yntema, Helger G.; Nelen, Marcel R.; Lugtenberg, Dorien; Kamsteeg, Erik-Jan; Wieskamp, Nienke; Stegmann, Alexander P.A.; Stevens, Servi J.C.; Rodenburg, Richard J.T.; Simons, Annet; Mensenkamp, Arjen R.; Rinne, Tuula; Gilissen, Christian; Scheffer, Hans; Veltman, Joris A.; Hehir-Kwa, Jayne Y.

2017-01-01

Purpose: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10–20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. Methods: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. Results: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to –5.8% per disorder). Conclusions: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics. Genet Med advance online publication 27 October 2016 PMID:28574513

Ground-based detectability of terrestrial and Jovian extrasolar planets: observations of CM Draconis at Lick Observatory.

PubMed

Doyle, L R; Dunham, E T; Deeg, H J; Blue, J E; Jenkins, J M

1996-06-25

The detection of terrestrial-sized extrasolar planets from the ground has been thought to be virtually impossible due to atmospheric scintillation limits. However, we show that this is not the case especially selected (but nevertheless main sequence) stars, namely small eclipsing binaries. For the smallest of these systems, CM Draconis, several months to a few years of photometric observations with 1-m-class telescopes will be sufficient to detect the transits of any short-period planets of sizes > or = 1.5 Earth radii (RE), using cross-correlation analysis with moderately good photometry. Somewhat larger telescopes will be needed to extend this detectability to terrestrial planets in larger eclipsing binary systems. (We arbitrarily define "terrestrial planets" herein as those whose disc areas are closer to that of Earth's than Neptune's i.e., less than about 2.78 RE.) As a "spin-off" of such observations, we will also be able to detect the presence of Jovian-mass planets without transits using the timing of the eclipse minima. Eclipse minima will drift in time as the binary system is offset by a sufficiently massive planet (i.e., one Jupiter mass) about the binary/giant-planet barycenter, causing a periodic variation in the light travel time to the observer. We present here an outline of present observations taking place at the University of California Lick Observatory using the Crossley 0.9-m telescope in collaboration with other observatories (in South Korea, Crete, France, Canary Islands, and New York) to detect or constrain the existence of terrestrial planets around main sequence eclipsing binary star systems, starting with CM Draconis. We demonstrate the applicability of photometric data to the general detection of gas giant planets via eclipse minima timings in many other small-mass eclipsing binary systems as well.

Ground-based detectability of terrestrial and Jovian extrasolar planets: observations of CM Draconis at Lick Observatory

NASA Technical Reports Server (NTRS)

Doyle, L. R.; Dunham, E. T.; Deeg, H. J.; Blue, J. E.; Jenkins, J. M.

1996-01-01

The detection of terrestrial-sized extrasolar planets from the ground has been thought to be virtually impossible due to atmospheric scintillation limits. However, we show that this is not the case especially selected (but nevertheless main sequence) stars, namely small eclipsing binaries. For the smallest of these systems, CM Draconis, several months to a few years of photometric observations with 1-m-class telescopes will be sufficient to detect the transits of any short-period planets of sizes > or = 1.5 Earth radii (RE), using cross-correlation analysis with moderately good photometry. Somewhat larger telescopes will be needed to extend this detectability to terrestrial planets in larger eclipsing binary systems. (We arbitrarily define "terrestrial planets" herein as those whose disc areas are closer to that of Earth's than Neptune's i.e., less than about 2.78 RE.) As a "spin-off" of such observations, we will also be able to detect the presence of Jovian-mass planets without transits using the timing of the eclipse minima. Eclipse minima will drift in time as the binary system is offset by a sufficiently massive planet (i.e., one Jupiter mass) about the binary/giant-planet barycenter, causing a periodic variation in the light travel time to the observer. We present here an outline of present observations taking place at the University of California Lick Observatory using the Crossley 0.9-m telescope in collaboration with other observatories (in South Korea, Crete, France, Canary Islands, and New York) to detect or constrain the existence of terrestrial planets around main sequence eclipsing binary star systems, starting with CM Draconis. We demonstrate the applicability of photometric data to the general detection of gas giant planets via eclipse minima timings in many other small-mass eclipsing binary systems as well.

An Automated Flying-Insect-Detection System

NASA Technical Reports Server (NTRS)

Vann, Timi; Andrews, Jane C.; Howell, Dane; Ryan, Robert

2005-01-01

An automated flying-insect-detection system (AFIDS) was developed as a proof-of-concept instrument for real-time detection and identification of flying insects. This type of system has use in public health and homeland security decision support, agriculture and military pest management, and/or entomological research. Insects are first lured into the AFIDS integrated sphere by insect attractants. Once inside the sphere, the insect's wing beats cause alterations in light intensity that is detected by a photoelectric sensor. Following detection, the insects are encouraged (with the use of a small fan) to move out of the sphere and into a designated insect trap where they are held for taxonomic identification or serological testing. The acquired electronic wing beat signatures are preprocessed (Fourier transformed) in real-time to display a periodic signal. These signals are sent to the end user where they are graphically displayed. All AFIDS data are pre-processed in the field with the use of a laptop computer equipped with LABVIEW. The AFIDS software can be programmed to run continuously or at specific time intervals when insects are prevalent. A special DC-restored transimpedance amplifier reduces the contributions of low-frequency background light signals, and affords approximately two orders of magnitude greater AC gain than conventional amplifiers. This greatly increases the signal-to-noise ratio and enables the detection of small changes in light intensity. The AFIDS light source consists of high-intensity Al GaInP light-emitting diodes (LEDs). The AFIDS circuitry minimizes brightness fluctuations in the LEDs and when integrated with an integrating sphere, creates a diffuse uniform light field. The insect wing beats isotropically scatter the diffuse light in the sphere and create wing beat signatures that are detected by the sensor. This configuration minimizes variations in signal associated with insect flight orientation.

[Variations in the diagnostic confirmation process between breast cancer mass screening units].

PubMed

Natal, Carmen; Fernández-Somoano, Ana; Torá-Rocamora, Isabel; Tardón, Adonina; Castells, Xavier

2016-01-01

To analyse variations in the diagnostic confirmation process between screening units, variations in the outcome of each episode and the relationship between the use of the different diagnostic confirmation tests and the lesion detection rate. Observational study of variability of the standardised use of diagnostic and lesion detection tests in 34 breast cancer mass screening units participating in early-detection programmes in three Spanish regions from 2002-2011. The diagnostic test variation ratio in percentiles 25-75 ranged from 1.68 (further appointments) to 3.39 (fine-needle aspiration). The variation ratio in detection rates of benign lesions, ductal carcinoma in situ and invasive cancer were 2.79, 1.99 and 1.36, respectively. A positive relationship between rates of testing and detection rates was found with fine-needle aspiration-benign lesions (R(2): 0.53), fine-needle aspiration-invasive carcinoma (R(2): 0 28), core biopsy-benign lesions (R(2): 0.64), core biopsy-ductal carcinoma in situ (R(2): 0.61) and core biopsy-invasive carcinoma (R(2): 0.48). Variation in the use of invasive tests between the breast cancer screening units participating in early-detection programmes was found to be significantly higher than variations in lesion detection. Units which conducted more fine-needle aspiration tests had higher benign lesion detection rates, while units that conducted more core biopsies detected more benign lesions and cancer. Copyright © 2016 SESPAS. Published by Elsevier Espana. All rights reserved.

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

Liu Huigen; Zhang Hui; Zhou Jilin, E-mail: huigen@nju.edu.cn

Six P-type planets have been found thus far around five binary systems, i.e., Kepler-16b, 34b, 35b, 38b, and 47b and c, which are all Neptune- or Jupiter-like planets. The stability of planets and the habitable zones are influenced by the gravitational and radiative perturbations of binary companions. In this Letter, we check the stability of an additional habitable Earth-mass planet in each system. Based on our simulations in 10 Myr, a habitable ''Earth'' is hardly stable in Kepler-16, while a stable ''Earth'' in Kepler-47 close to the boundaries of the habitable zone is possible. In contrast, Kepler-34, 35, and 38more » seem to have high probabilities of being able to tolerante a stable ''Earth'' in their habitable zones. The affects of transit time variations are quite small due to the small mass of an undetected ''Earth,'' except that of Kepler-16b. With a time precision of 10{sup -3} day ({approx}88 s), an ''Earth'' in the corotational resonance with Kepler-16b can be detected in three years, while habitable ''Earths'' in the Kepler-34 and 38 systems can be detected in 10 yr. Habitable ''Earths'' in Kepler-35 and 47 are not likely to be detected in 10 yr under this precision.« less

DYZ1 copy number variation, Y chromosome polymorphism and early recurrent spontaneous abortion/early embryo growth arrest.

PubMed

Yan, Junhao; Fan, Lingling; Zhao, Yueran; You, Li; Wang, Laicheng; Zhao, Han; Li, Yuan; Chen, Zi-Jiang

2011-12-01

To find the association between recurrent spontaneous abortion (RSA)/early embryo growth arrest and Y chromosome polymorphism. Peripheral blood samples of the male patients of big Y chromosome, small Y chromosome and other male patients whose partners suffered from unexplained RSA/early embryo growth arrest were collected. PCR and real-time fluorescent quantitative PCR were used to test the deletion and the copy number variation of DYZ1 region in Y chromosome of the patients. A total of 79 big Y chromosome patients (48 of whose partners suffered from RSA or early embryo growth arrest), 7 small Y chromosome patients, 106 other male patients whose partners had suffered from unexplained RSA or early embryo growth arrest, and 100 normal male controls were enrolled. There was no fraction deletion of DYZ1 detected both in big Y patients and in normal men. Of RSA patients, 1 case showed deletion of 266bp from the gene locus 25-290bp, and 2 cases showed deletion of 773bp from 1347 to 2119bp. Of only 7 small Y chromosome patients, 2 cases showed deletion of 266bp from 25 to 290bp, and 4 cases showed deletion of 773bp from 1347 to 2119bp and 275bp from 3128 to 3420bp. The mean of DYZ1 copies was 3900 in normal control men; the mean in big Y patients was 5571, in RSA patients was 2655, and in small Y patients was 1059. All of the others were significantly different (P<0.01) compared with normal control men, which meant that DYZ1 copy number in normal control men was less than that of big Y chromosome patients, and was more than that of unexplained early RSA patients and small Y patients. The integrity and copy number variation of DYZ1 are closely related to the Y chromosome length under microscope. The cause of RSA/early embryo growth arrest in some couples may be the increase (big Y patients) or decrease of DYZ1 copy number in the husbands' Y chromosome. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Small-scale density variations in the lunar crust revealed by GRAIL

NASA Astrophysics Data System (ADS)

Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W.; Milbury, C.; Kiefer, W. S.; Soderblom, J. M.; Zuber, M. T.

2017-07-01

Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that ∼98% of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2% of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10‧s of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by ± 10% over scales ranging from centimeters to 100‧s of kilometers.

Small-Scale Density Variations in the Lunar Crust Revealed by GRAIL

NASA Technical Reports Server (NTRS)

Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W., III; Milbury, C.;

TU-F-CAMPUS-T-04: Variations in Nominally Identical Small Fields From Photon Jaw Reproducibility and Associated Effects On Small Field Dosimetric Parameters

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

Muir, B R; McEwen, M R

2015-06-15

Purpose: To investigate uncertainties in small field output factors and detector specific correction factors from variations in field size for nominally identical fields using measurements and Monte Carlo simulations. Methods: Repeated measurements of small field output factors are made with the Exradin W1 (plastic scintillation detector) and the PTW microDiamond (synthetic diamond detector) in beams from the Elekta Precise linear accelerator. We investigate corrections for a 0.6x0.6 cm{sup 2} nominal field size shaped with secondary photon jaws at 100 cm source to surface distance (SSD). Measurements of small field profiles are made in a water phantom at 10 cm depthmore » using both detectors and are subsequently used for accurate detector positioning. Supplementary Monte Carlo simulations with EGSnrc are used to calculate the absorbed dose to the detector and absorbed dose to water under the same conditions when varying field size. The jaws in the BEAMnrc model of the accelerator are varied by a reasonable amount to investigate the same situation without the influence of measurements uncertainties (such as detector positioning or variation in beam output). Results: For both detectors, small field output factor measurements differ by up to 11 % when repeated measurements are made in nominally identical 0.6x0.6 cm{sup 2} fields. Variations in the FWHM of measured profiles are consistent with field size variations reported by the accelerator. Monte Carlo simulations of the dose to detector vary by up to 16 % under worst case variations in field size. These variations are also present in calculations of absorbed dose to water. However, calculated detector specific correction factors are within 1 % when varying field size because of cancellation of effects. Conclusion: Clinical physicists should be aware of potentially significant uncertainties in measured output factors required for dosimetry of small fields due to field size variations for nominally identical fields.« less

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

PubMed

Saunders, Christopher T; Wong, Wendy S W; Swamy, Sajani; Becq, Jennifer; Murray, Lisa J; Cheetham, R Keira

2012-07-15

Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. csaunders@illumina.com

Management of stones in childhood.

PubMed

Thomas, Ben G

2010-03-01

The purpose of this review was to report on the latest world literature relating to paediatric stone disease. Inevitably, because of the small numbers, the literature is limited and consists mainly of case series from individual centres. There is also a wide variation in criteria and techniques, making direct comparison limited. Changes in the incidence of stone disease are becoming more apparent particularly in female patients. Metabolic abnormalities can be identified in the majority of children with stones, and even in the absence of obvious physical stone, if detected warrant further follow-up. Data supporting the safety and efficacy of treatments for stones in children is improving constantly, but choosing the best option may be difficult on current evidence. Better long-term follow-up is still needed regarding adverse effects of treatment. A high index of suspicion is required for the diagnosis of stone disease in children, especially in the very young. After exclusion of anatomical abnormalities, metabolic evaluation is important in management and prevention of recurrence. Modalities for treatment are expanding all the time, but due to overall small numbers, and variations in the availability of technology, consensus views about treatment are difficult to agree.

On the possibility of detecting local refractive index changes in optically transparent objects by means of a point nanoantenna attached to a fibre microaxicon

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

Kulchin, Yu N; Vitrik, O B; Kuchmizhak, A A

2014-10-31

It is shown theoretically that the use of the spectral registration of the dipole local plasmon resonance (DLPR) displacement in a single spherical gold nanoantenna, placed near the surface of a homogeneous dielectric medium, allows the mapping of extremely small variations (to 5 × 10{sup -4}) of the refractive index (RI) of this medium. Using the quasi-static approximation, we have developed an analytic model that allows evaluation of the spectral displacement of the nanoantenna DLPR depending on the variation in the medium refractive index. The point probe based on a fibre microaxicon with a gold spherical nanoantenna attached to itsmore » top is proposed that allows practical implementation of the developed RI scanning method. Numerical calculations of the probe characteristics using the time-domain finite-difference method are presented, and it is shown that for the case of a gold spherical nanoantenna of small size, comparable with the skin layer thickness in gold, the relative spectral shift value is in good agreement with the results obtained by using the developed analytic model. (laser applications and other topics in quantum electronics)« less

Rigid shape matching by segmentation averaging.

PubMed

Wang, Hongzhi; Oliensis, John

2010-04-01

We use segmentations to match images by shape. The new matching technique does not require point-to-point edge correspondence and is robust to small shape variations and spatial shifts. To address the unreliability of segmentations computed bottom-up, we give a closed form approximation to an average over all segmentations. Our method has many extensions, yielding new algorithms for tracking, object detection, segmentation, and edge-preserving smoothing. For segmentation, instead of a maximum a posteriori approach, we compute the "central" segmentation minimizing the average distance to all segmentations of an image. For smoothing, instead of smoothing images based on local structures, we smooth based on the global optimal image structures. Our methods for segmentation, smoothing, and object detection perform competitively, and we also show promising results in shape-based tracking.

Tropical small streams are a consistent source of methane

NASA Astrophysics Data System (ADS)

Vihermaa, Leena; Waldron, Susan

2013-04-01

To date only a few studies have quantified diffusive methane emissions from headwater streams therefore the magnitude and seasonal variation of these emissions remain poorly understood. Here we present results from two Western Amazonian small streams (first and second order) in Tambopata National Reserve, Peru. Towards the end of wet season, April-May 2012, the streams were sampled using a static floating chamber to accumulate methane. Samples were drawn from the headspace twice daily over period of four days on three separate occasions. The methane concentrations were analysed using a gas chromatograph and the linear part of concentration increase used to calculate the flux rates. The streams were consistently outgassing methane. The seasonally active first order stream outgassed 6 ±2.4 nmol CH4-C m-2 s-1 and the second order stream 20 ±4.0 nmol CH4-C m-2 s-1. The latter flux rate is comparable to fluxes measured from seasonally flooded Amazonian forest in previous studies. The range measured in our streams is comparable to previous results in temperate streams and the lower end of fluxes observed in some peatland streams. The only other study on Amazonian small streams detected methane fluxes that were 100 times greater than those measured here. Depending on the density of small streams in Amazonian basin and the prevalent flux rate, the fluvial methane fluxes may constitute a significant global warming potential. Upscaling to the Amazon basin, assuming small stream density of 0.2 %, as was found at our field site, and the flux rates detected, yields an annual global warming potential equal to approximately 1.5 Mt of CO2 which is of minor importance compared to aquatic CO2-C flux of 500 Mt yr-1 from the basin. However, if the higher fluxes detected in the previous study were prevalent, the basin wide methane flux could become significant. Further studies are needed to establish the stream density in the Amazon basin and typical methane flux rates.

The Needs of Students with Intersex Variations

ERIC Educational Resources Information Center

Jones, Tiffany

2016-01-01

To date, people with intersex variations have been mainly studied via small-scale clinical research, with only a small amount of reflective commentary contributed by sociocultural scholars. This paper reports on findings from a 2015 online Australian survey of 272 people with intersex variations, which aimed to redress the gap in research on this…

Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders.

PubMed

Carpenter, Danielle; Walker, Susan; Prescott, Natalie; Schalkwijk, Joost; Armour, John Al

2011-08-18

Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn's disease, rheumatoid arthritis and psoriasis clinical cohorts. We evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn's disease, rheumatoid arthritis or psoriasis. Differential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion.

Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders

PubMed Central

2011-01-01

Background Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn's disease, rheumatoid arthritis and psoriasis clinical cohorts. Results We evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn's disease, rheumatoid arthritis or psoriasis. Conclusions Differential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion. PMID:21851606

Detection of Small Stress Relaxation in Tightened Metallic Structures by Ultrasounds

NASA Astrophysics Data System (ADS)

Augereau, F.; Portal, A.

Experimental data are presented here to highlight the performances of ultrasounds for the control or the better understanding of the quality of the mechanical contact between tightened plates. Thus, variations of the mechanical load as small as those induced by creep or stress relaxation are potentially detectable by simply monitoring the amplitude of the reflected acoustic plane wave reflected at this interface. To illustrate this, two 3 cm thick aluminium plates are firstly tightened with a given torque and next, the amplitude of the acoustic wave is monitored for several days. All long this test, the temperature of the sample is controlled as well as the compression load applied to the plates using a thermocouple and a bolt gauge sensor. The reflected amplitude decreases quickly during first hours and then stabilises after a week approximately. The total variation reaches -28% of the initial value of the reflected amplitude. During this test, temperature is remained almost constant and its fluctuation around the ambient temperature is not correlated with the reflected amplitude. As expected from classic stress relaxation tests, the compression load has slowly decreased by an amount of only -1% but this should have logically increased the reflected amplitude. Further investigations have shown that instrumentation drift were negligible. Consequently, this large decrease of the reflected amplitude has been interpreted as the indication of the increase of the contact area between the two tightened plates. This test attests the high sensitivity of ultrasonic reflection measurement to investigate quality of mechanical contacts for non destructive testing.

Characteristics of Drug Resistant Tuberculosis in Sanatoria of North Korea.

PubMed

Jung, Jihee; Jegal, Yangjin; Ki, Moran; Shin, Young Jeon; Kim, Cheon Tae; Shim, Tae Sun; Sung, Nackmoon

2017-07-01

Although several reports about drug-resistant tuberculosis (TB) in North Korea have been published, a nationwide surveillance on this disease remains to be performed. This study aims to analyze the drug resistance patterns of Mycobacterium tuberculosis among the patients in the sanatoria of North Korea, especially during the period when second-line drugs (SLDs) had not yet been officially supplied to this country. The Eugene Bell Foundation (EBF) transferred 947 sputum specimens obtained from 667 patients from 2007 to 2009 to the Clinical Research Center, Masan National Tuberculosis Hospital (MNTH), South Korea. Four hundred ninety-two patients were culture positive for TB (73.8%). Drug susceptibility test (DST) was performed for the bacilli isolated from 489 patients. Over 3 quarters of the cases (76.9%) were multidrug-resistant (MDR)-TB. Additionally, 2 patients had extremely drug-resistant (XDR)-TB. Very high resistance to first-line drugs and low resistance to fluoroquinolones (FQs) and injectable drugs (IDs) except for streptomycin (S) were detected. A small but significant regional variation in resistance pattern was observed. Big city regions had higher rate of MDR-TB, higher resistance to FQs and IDs than relatively isolated regions. In conclusion, significant number of drug-resistant TB was detected in North Korean sanatoria, and small but significant regional variations in resistance pattern were noticeable. However, the data in this study do not represent the nationwide drug resistance pattern in North Korea. Further large-scale evaluations are necessary to estimate the resistance pattern of TB in North Korea. © 2017 The Korean Academy of Medical Sciences.

Using genomics to characterize evolutionary potential for conservation of wild populations

PubMed Central

Harrisson, Katherine A; Pavlova, Alexandra; Telonis-Scott, Marina; Sunnucks, Paul

2014-01-01

Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework. PMID:25553064

Genetic Variation and Geographic Differentiation Among Populations of the Nonmigratory Agricultural Pest Oedaleus infernalis (Orthoptera: Acridoidea) in China

PubMed Central

Sun, Wei; Dong, Hui; Gao, Yue-Bo; Su, Qian-Fu; Qian, Hai-Tao; Bai, Hong-Yan; Zhang, Zhu-Ting; Cong, Bin

2015-01-01

The nonmigratory grasshopper Oedaleus infernalis Saussure (Orthoptera : Acridoidea) is an agricultural pest to crops and forage grasses over a wide natural geographical distribution in China. The genetic diversity and genetic variation among 10 geographically separated populations of O. infernalis was assessed using polymerase chain reaction-based molecular markers, including the intersimple sequence repeat and mitochondrial cytochrome oxidase sequences. A high level of genetic diversity was detected among these populations from the intersimple sequence repeat (H: 0.2628, I: 0.4129, Hs: 0.2130) and cytochrome oxidase analyses (Hd: 0.653). There was no obvious geographical structure based on an unweighted pair group method analysis and median-joining network. The values of FST, θII, and Gst estimated in this study are low, and the gene flow is high (Nm > 4). Analysis of the molecular variance suggested that most of the genetic variation occurs within populations, whereas only a small variation takes place between populations. No significant correlation was found between the genetic distance and geographical distance. Overall, our results suggest that the geographical distance plays an unimpeded role in the gene flow among O. infernalis populations. PMID:26496789

Common polymorphic variation in the genetically diverse African insulin gene and its association with size at birth.

PubMed

Petry, Clive J; Rayco-Solon, Pura; Fulford, Anthony J C; Stead, John D H; Wingate, Dianne L; Ong, Ken K; Sirugo, Giorgio; Prentice, Andrew M; Dunger, David B

2009-09-01

The insulin variable number of tandem repeats (INS VNTR) has been variably associated with size at birth in non-African populations. Small size at birth is a major determinant of neonatal mortality, so the INS VNTR may influence survival. We tested the hypothesis, therefore, that genetic variation around the INS VNTR in a rural Gambian population, who experience seasonal variation in nutrition and subsequently birth weight, may be associated with foetal and early growth. Six polymorphisms flanking the INS VNTR were genotyped in over 2,500 people. Significant associations were detected between the maternally inherited SNP 27 (rs689) allele and birth length [effect size 17.5 (5.2-29.8) mm; P = 0.004; n = 361]. Significant associations were also found between the maternally inherited African-specific SNP 28 (rs5506) allele and post-natal weight gain [effect size 0.19 (0.05-0.32) z score points/year; P = 0.005; n = 728). These results suggest that in the Gambian population studied there are associations between polymorphic variation in the genetically diverse INS gene and foetal and early growth characteristics, which contribute to overall polygenic associations with these traits.

Molecular technology and antigenic variation among intraerythrocytic hemoparasites: do we see reality?

PubMed

Allred, D R

2001-11-22

Antigenic variation is one mechanism of immune evasion utilized by many microorganisms--encompassing such broad evolutionary groups as viruses, bacteria, and protozoa--to survive the onslaught of a specifically activated host immune system. Because of its importance to the survival of many infectious agents there is considerable interest in understanding this phenomenon. With knowledge of the molecular mechanisms by which these microbes deliberately manipulate their genomes, it may be possible to disrupt the molecular machinery of the responsible genetic mechanisms. Among intraerythrocytic parasites, genetic mechanisms that have been observed or postulated to control antigenic variation include segmental gene conversion, epigenetically controlled in situ transcriptional switching, alterations of chromosomal structure associated with transcriptional control, and recombination during sexual reproduction. Likely, more than one type of mechanism is used by all organisms that undergo antigenic variation. In this paper, both the observed mechanisms and some of the molecular technology used to detect these mechanisms are discussed. While often seemingly straightforward from a technical standpoint, sometimes subtle differences in the methods used to study this process may affect what is observed. Some examples of this phenomenon are discussed in the context of a small selection of intraerythrocytic parasites.

Kernel parameter variation-based selective ensemble support vector data description for oil spill detection on the ocean via hyperspectral imaging

NASA Astrophysics Data System (ADS)

Uslu, Faruk Sukru

2017-07-01

Oil spills on the ocean surface cause serious environmental, political, and economic problems. Therefore, these catastrophic threats to marine ecosystems require detection and monitoring. Hyperspectral sensors are powerful optical sensors used for oil spill detection with the help of detailed spectral information of materials. However, huge amounts of data in hyperspectral imaging (HSI) require fast and accurate computation methods for detection problems. Support vector data description (SVDD) is one of the most suitable methods for detection, especially for large data sets. Nevertheless, the selection of kernel parameters is one of the main problems in SVDD. This paper presents a method, inspired by ensemble learning, for improving performance of SVDD without tuning its kernel parameters. Additionally, a classifier selection technique is proposed to get more gain. The proposed approach also aims to solve the small sample size problem, which is very important for processing high-dimensional data in HSI. The algorithm is applied to two HSI data sets for detection problems. In the first HSI data set, various targets are detected; in the second HSI data set, oil spill detection in situ is realized. The experimental results demonstrate the feasibility and performance improvement of the proposed algorithm for oil spill detection problems.

VarDetect: a nucleotide sequence variation exploratory tool

PubMed Central

Ngamphiw, Chumpol; Kulawonganunchai, Supasak; Assawamakin, Anunchai; Jenwitheesuk, Ekachai; Tongsima, Sissades

2008-01-01

Background Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides. Results We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency. Availability VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at . PMID:19091032

Organic geochemistry in Pennsylvanian tidally influenced sediments from SW Indiana

USGS Publications Warehouse

Mastalerz, Maria; Kvale, E.P.; Stankiewicz, B.A.; Portle, K.

1999-01-01

Tidal rhythmites are vertically stacked small-scale sedimentary structures that record daily variations in tidal current energy and are known to overlie some low-sulfur coals in the Illinois Basin. Tidal rhythmites from the Pennsylvanian Brazil Formation in Indiana have been analyzed sedimentologically, petrographically, and geochemically in order to understand the character and distribution of organic matter (OM) preserved in an environment of daily interactions between marine and fresh waters. The concentration of organic matter (TOC) ranges from traces to 6.9% and sulfur rarely exceeds 0.1% in individual laminae. Angular vitrinite is the major organic matter type, accounting for 50-90% of total OM. The C/S ratio decreases as the verfical distance from the underlying coal increases. A decreasing C/S ratio coupled with decreases in Pr/Ph, Pr/n-C17, Ph/n-C18 ratios and a shift of carbon isotopic composition towards less negative values suggest an increase in salinity from freshwater in the mudflat tidal rhythmite facies close to the coal to brackish/marine in the sandflat tidal rhythmite facies further above from the coal. Within an interval spanning one year of deposition, TOC and S values show monthly variability. On a daily scale, TOC and S oscillations are still detectable but they are of lower magnitude than on a monthly scale. These small-scale variations are believed to reflect oscillations in water salinity related to tidal cycles.Tidal rhythmites are vertically stacked small-scale sedimentary structures that record daily variations in tidal current energy and are known to overlie some low-sulfur coals in the Illinois Basin. Tidal rhythmites from the Pennsylvanian Brazil Formation in Indiana have been analyzed sedimentologically, petrographically, and geochemically in order to understand the character and distribution of organic matter (OM) preserved in an environment of daily interactions between marine and fresh waters. The concentration of organic matter (TOC) ranges from traces to 6.9% and sulfur rarely exceeds 0.1% in individual laminae. Angular vitrinite is the major organic matter type, accounting for 50-90% of total OM. The C/S ratio decreases as the vertical distance from the underlying coal increases. A decreasing C/S ratio coupled with decreases in Pr/Ph, Pr/n-C17, Ph/n-C18 ratios and a shift of carbon isotopic composition towards less negative values suggest an increase in salinity from freshwater in the mudflat tidal rhythmite facies close to the coal to brackish/marine in the sandflat tidal rhythmite facies further above from the coal. Within an interval spanning one year of deposition, TOC and S values show monthly variability. On a daily scale, TOC and S oscillations are still detectable but they are of lower magnitude than on a monthly scale. These small-scale variations are believed to reflect oscillations in water salinity related to tidal cycles.

Modified electrical survey for effective leakage detection at concrete hydraulic facilities

NASA Astrophysics Data System (ADS)

Lee, Bomi; Oh, Seokhoon

2018-02-01

Three original electrode arrays for the effective leakage detection of concrete hydraulic facilities through electrical resistivity surveys are proposed: 'cross-potential', 'direct-potential' and modified tomography-like arrays. The main differences with respect to the commonly used arrays are that the current line-sources are separated from potential pole lines and floated upon the water. The potential pole lines are located directly next to the facility in order to obtain intuitive data and useful interpretations of the internal conditions of the hydraulic facility. This modified configuration of the array clearly displays the horizontal variation of the electrical field around the damaged zones of the concrete hydraulic facility, and any anomalous regions that might be found between potential poles placed across the facilities. In order to facilitate the interpretation of these modified electrical surveys, a new and creative way of presenting the measurements is also proposed and an inversion approach is provided for the modified tomography-like array. A numerical modeling and two field tests were performed to verify these new arrays and interpretation methods. The cross and direct potential array implied an ability to detect small variations of the potential field near the measurement poles. The proposed array showed the overall potential distribution across the hydraulic facility which may be used to assist in the search of trouble zones within the structure, in combination with the traditional electrical resistivity array.

Designing better methane mitigation policies: the challenge of distributed small sources in the natural gas sector

NASA Astrophysics Data System (ADS)

Ravikumar, Arvind P.; Brandt, Adam R.

2017-04-01

Methane—a short-lived and potent greenhouse gas—presents a unique challenge: it is emitted from a large number of highly distributed and diffuse sources. In this regard, the United States’ Environmental Protection Agency (EPA) has recommended periodic leak detection and repair surveys at oil and gas facilities using optical gas imaging technology. This regulation requires an operator to fix all detected leaks within a set time period. Whether such ‘find-all-fix-all’ policies are effective depends on significant uncertainties in the character of emissions. In this work, we systematically analyze the effect of facility-related and mitigation-related uncertainties on regulation effectiveness. Drawing from multiple publicly-available datasets, we find that: (1) highly-skewed leak-size distributions strongly influence emissions reduction potential; (2) variations in emissions estimates across facilities leads to large variability in mitigation effectiveness; (3) emissions reductions from optical gas imaging-based leak detection programs can range from 15% to over 70%; and (4) while implementation costs are uniformly lower than EPA estimates, benefits from saved gas are highly variable. Combining empirical evidence with model results, we propose four policy options for effective methane mitigation: performance-oriented targets for accelerated emission reductions, flexible policy mechanisms to account for regional variation, technology-agnostic regulations to encourage adoption of the most cost-effective measures, and coordination with other greenhouse gas mitigation policies to reduce unintended spillover effects.

Screening the low molecular weight fraction of human serum using ATR-IR spectroscopy.

PubMed

Bonnier, Franck; Brachet, Guillaume; Duong, Romain; Sojinrin, Tobiloba; Respaud, Renaud; Aubrey, Nicolas; Baker, Matthew J; Byrne, Hugh J; Chourpa, Igor

2016-10-01

Vibrational spectroscopic techniques can detect small variations in molecular content, linked with disease, showing promise for screening and early diagnosis. Biological fluids, particularly blood serum, are potentially valuable for diagnosis purposes. The so-called Low Molecular Weight Fraction (LMWF) contains the associated peptidome and metabolome and has been identified as potentially the most relevant molecular population for disease-associated biomarker research. Although vibrational spectroscopy can deliver a specific chemical fingerprint of the samples, the High Molecular Weight Fraction (HMWF), composed of the most abundant serum proteins, strongly dominates the response and ultimately makes the detection of minor spectral variations a challenging task. Spectroscopic detection of potential serum biomarkers present at relatively low concentrations can be improved using pre-analytical depletion of the HMWF. In the present study, human serum fractionation by centrifugal filtration was used prior to analysis by Attenuated Total Reflection infrared spectroscopy. Using a model sample based on glycine spiked serum, it is demonstrated that the screening of the LMWF can be applied to quantify blinded concentrations up to 50 times lower. Moreover, the approach is easily transferable to different bodily fluids which would support the development of more efficient and suitable clinical protocols exploring vibrational spectroscopy based ex-vivo diagnostic tools. Revealing serum LMWF for spectral serological diagnostic applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Damage sensitivity investigations of EMI technique on different materials through coupled field analysis

NASA Astrophysics Data System (ADS)

Joshi, Bhrigu; Adhikari, Sailesh; Bhalla, Suresh

2016-04-01

This paper presents a comparative study through the piezoelectric coupled field analysis mode of finite element method (FEM) on detection of damages of varying magnitude, encompassing three different types of structural materials, using piezo impedance transducers. An aluminum block, a concrete block and a steel block of dimensions 48×48×10 mm were modelled in finite element software ANSYS. A PZT patch of 10×10×0.3 mm was also included in the model as surface bonded on the block. Coupled field analysis (CFA) was performed to obtain the admittance signatures of the piezo sensor in the frequency range of 0-250 kHz. The root mean square deviation (RMSD) index was employed to quantify the degree of variation of the signatures. It was found that concrete exhibited deviation in the signatures only with the change of damping values. However, the other two materials showed variation in the signatures even with changes in density and elasticity values in a small portion of the specimen. The comparative study shows that the PZT patches are more sensitive to damage detection in materials with low damping and the sensitivity typically decreases with increase in the damping.

Recent advances in rapid pathogen detection method based on biosensors.

PubMed

Chen, Ying; Wang, Zhenzhen; Liu, Yingxun; Wang, Xin; Li, Ying; Ma, Ping; Gu, Bing; Li, Hongchun

2018-06-01

As strain variation and drug resistance become more pervasive, the prevention and control of infection have been a serious problem in recent years. The detection of pathogen is one of the most important parts of the process of diagnosis. Having a series of advantages, such as rapid response, high sensitivity, ease of use, and low cost, biosensors have received much attention and been studied deeply. Moreover, relying on its characteristics of small size, real time, and multiple analyses, biosensors have developed rapidly and used widely and are expected to be applied for microbiological detection in order to meet higher accuracy required by clinical diagnosis. The main goal of this contribution is not to simply collect and list all papers related to pathogen detection based on biosensors published recently, but to discuss critically the development and application of many kinds of biosensors such as electrochemical (amperometric, impedimetric, potentiometric, and conductometric), optical (fluorescent, fibre optic and surface plasmon resonance), and piezoelectric (quartz crystal microbalances and atomic force microscopy) biosensors in pathogen detection as well as the comparisons with the existing clinical detection methods (traditional culture, enzyme-linked immunosorbent assay, polymerase chain reaction, and mass spectrometry).

Validation of a method to detect cocaine and its metabolites in nails by gas chromatography-mass spectrometry.

PubMed

Valente-Campos, Simone; Yonamine, Mauricio; de Moraes Moreau, Regina Lucia; Silva, Ovandir Alves

2006-06-02

The objective of the present work was to compare previously published methods and provide validation data to detect simultaneously cocaine (COC), benzoylecgonine (BE) and norcocaine (NCOC) in nail. Finger and toenail samples (5mg) were cut in very small pieces and submitted to an initial procedure for external decontamination. Methanol (3 ml) was used to release analytes from the matrix. A cleanup step was performed simultaneously by solid-phase extraction (SPE) and the residue was derivatized with pentafluoropropionic anhydride/pentafluoropropanol (PFPA/PFP). Gas chromatography-mass spectrometry (GC-MS) was used to detect the analytes in selected ion monitoring mode (SIM). Confidence parameters of validation of the method were: recovery, intra- and inter-assay precision, as well as limit of detection (LOD) of the analytes. The limits of detection were: 3.5 ng/mg for NCOC and 3.0 ng/mg for COC and BE. Good intra-assay precision was observed for all detected substances (coefficient of variation (CV)<11%). The inter-assay precision for norcocaine and benzoylecgonine were <4%. For intra- and inter-assay precision deuterated internal standards were used. Toenail and fingernail samples from eight declared cocaine users were submitted to the validated method.

Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation

NASA Astrophysics Data System (ADS)

Zhang, Miao; Schmidt, Torsten; Jemt, Anders; Sahlén, Pelin; Sychugov, Ilya; Lundeberg, Joakim; Linnros, Jan

2015-08-01

Optical nanopore sensing offers great potential in single-molecule detection, genotyping, or DNA sequencing for high-throughput applications. However, one of the bottle-necks for fluorophore-based biomolecule sensing is the lack of an optically optimized membrane with a large array of nanopores, which has large pore-to-pore distance, small variation in pore size and low background photoluminescence (PL). Here, we demonstrate parallel detection of single-fluorophore-labeled DNA strands (450 bps) translocating through an array of silicon nanopores that fulfills the above-mentioned requirements for optical sensing. The nanopore array was fabricated using electron beam lithography and anisotropic etching followed by electrochemical etching resulting in pore diameters down to ∼7 nm. The DNA translocation measurements were performed in a conventional wide-field microscope tailored for effective background PL control. The individual nanopore diameter was found to have a substantial effect on the translocation velocity, where smaller openings slow the translocation enough for the event to be clearly detectable in the fluorescence. Our results demonstrate that a uniform silicon nanopore array combined with wide-field optical detection is a promising alternative with which to realize massively-parallel single-molecule detection.

Variation of haemoglobin extinction coefficients can cause errors in the determination of haemoglobin concentration measured by near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Kim, J. G.; Liu, H.

2007-10-01

Near-infrared spectroscopy or imaging has been extensively applied to various biomedical applications since it can detect the concentrations of oxyhaemoglobin (HbO2), deoxyhaemoglobin (Hb) and total haemoglobin (Hbtotal) from deep tissues. To quantify concentrations of these haemoglobin derivatives, the extinction coefficient values of HbO2 and Hb have to be employed. However, it was not well recognized among researchers that small differences in extinction coefficients could cause significant errors in quantifying the concentrations of haemoglobin derivatives. In this study, we derived equations to estimate errors of haemoglobin derivatives caused by the variation of haemoglobin extinction coefficients. To prove our error analysis, we performed experiments using liquid-tissue phantoms containing 1% Intralipid in a phosphate-buffered saline solution. The gas intervention of pure oxygen was given in the solution to examine the oxygenation changes in the phantom, and 3 mL of human blood was added twice to show the changes in [Hbtotal]. The error calculation has shown that even a small variation (0.01 cm-1 mM-1) in extinction coefficients can produce appreciable relative errors in quantification of Δ[HbO2], Δ[Hb] and Δ[Hbtotal]. We have also observed that the error of Δ[Hbtotal] is not always larger than those of Δ[HbO2] and Δ[Hb]. This study concludes that we need to be aware of any variation in haemoglobin extinction coefficients, which could result from changes in temperature, and to utilize corresponding animal's haemoglobin extinction coefficients for the animal experiments, in order to obtain more accurate values of Δ[HbO2], Δ[Hb] and Δ[Hbtotal] from in vivo tissue measurements.

Zinc pharmacokinetic parameters in the determination of body zinc status in children.

PubMed

Vale, S H L; Leite, L D; Alves, C X; Dantas, M M G; Costa, J B S; Marchini, J S; França, M C; Brandão-Neto, J

2014-02-01

Serum or tissue zinc concentrations are often used to assess body zinc status. However, all of these methods are relatively inaccurate. Thus, we investigated three different kinetic methods for the determination of zinc clearance to establish which of these could detect small changes in the body zinc status of children. Forty apparently healthy children were studied. Renal handling of zinc was investigated during intravenous zinc administration (0.06537 mg Zn/kg of body weight), both before and after oral zinc supplementation (5 mg Zn/day for 3 months). Three kinetic methods were used to determine zinc clearance: CZn-Formula A and CZn-Formula B were both used to calculate systemic clearance; the first is a general formula and the second is used for the specific analysis of a single-compartment model; CZn-Formula C is widely used in medical practices to analyze kinetic routine. Basal serum zinc values, which were within the reference range for healthy children, increased significantly after oral zinc supplementation. The three formulas used gave different results for zinc clearance both before and after oral zinc supplementation. CZn-Formula B showed a positive correlation with basal serum zinc concentration after oral supplementation (R2=0.1172, P=0.0306). In addition, CZn-Formula B (P=0.0002) was more effective than CZn-Formula A (P=0.6028) and CZn-Formula C (P=0.0732) in detecting small variations in body zinc status. All three of the formulas used are suitable for studying zinc kinetics; however, CZn-Formula B is particularly effective at detecting small changes in body zinc status in healthy children.

Microclimatic Variation Within Sleeve Cages Used in Ecological Studies

PubMed Central

Nelson, Lori A.; Rieske, Lynne K.

2014-01-01

Abstract Sleeve cages for enclosing or excluding arthropods are essential components of field studies evaluating trophic interactions. Microclimatic variation in sleeve cages was evaluated to characterize its potential effects on subsequent long-term experiments. Two sleeve cage materials, polyester and nylon, and two cage sizes, 400 and 6000 cm 2 , were tested on eastern hemlock, Tsuga canadensis (L.) Carrière. Temperature and relative humidity inside and outside cages, and the cost and durability of the cage materials, were compared. Long-term effects of the sleeve cages were observed by measuring new growth on T. canadensis branches. The ultimate goal was to identify a material that minimizes bag-induced microclimatic variation. Bagged branches whose microclimates mimic those of surrounding unbagged branches should have minimal effects on plant growth and may prove ideal venues for assessing herbivore and predator behavior under natural conditions. No differences were found in temperature or humidity between caging materials. Small cages had higher average temperatures than large cages, especially in the winter, but this difference was confounded by the fact that small cages were positioned higher in trees than large cages. Differences in plant growth were detected. Eastern hemlock branches enclosed within polyester cages produced fewer new growth tips than uncaged controls. Both polyester and nylon cages reduced the length of new shoot growth relative to uncaged branches. In spite of higher costs, nylon cages were superior to polyester with respect to durability and ease of handling. PMID:25368083

Spatial variation in selection on corolla shape in a generalist plant is promoted by the preference patterns of its local pollinators.

PubMed

Gómez, José M; Bosch, Jordi; Perfectti, Francisco; Fernández, J D; Abdelaziz, Mohamed; Camacho, J P M

2008-10-07

An adaptive role of corolla shape has been often asserted without an empirical demonstration of how natural selection acts on this trait. In generalist plants, in which flowers are visited by diverse pollinator fauna that commonly vary spatially, detecting pollinator-mediated selection on corolla shape is even more difficult. In this study, we explore the mechanisms promoting selection on corolla shape in the generalist crucifer Erysimum mediohispanicum Polatschek (Brassicaceae). We found that the main pollinators of E. mediohispanicum (large bees, small bees and bee flies) discriminate between different corolla shapes when offered artificial flowers without reward. Importantly, different pollinators prefer different shapes: bees prefer flowers with narrow petals, whereas bee flies prefer flowers with rounded overlapping petals. We also found that flowers with narrow petals (those preferred by bees) produce both more pollen and nectar than those with rounded petals. Finally, different plant populations were visited by different faunas. As a result, we found spatial variation in the selection acting on corolla shape. Selection favoured flowers with narrow petals in the populations where large or small bees are the most abundant pollinator groups. Our study suggests that pollinators, by preferring flowers with high reward, exert strong selection on the E. mediohispanicum corolla shape. The geographical variation in the pollinator-mediated selection on E. mediohispanicum corolla shape suggests that phenotypic evolution and diversification can occur in this complex floral trait even without specialization.

Detection of IL28B SNP DNA from Buccal Epithelial Cells, Small Amounts of Serum, and Dried Blood Spots

PubMed Central

Halfon, Philippe; Ouzan, Denis; Khiri, Hacène; Pénaranda, Guillaume; Castellani, Paul; Oulès, Valerie; Kahloun, Asma; Amrani, Nolwenn; Fanteria, Lise; Martineau, Agnès; Naldi, Lou; Bourlière, Marc

2012-01-01

Background & Aims Point mutations in the coding region of the interleukin 28 gene (rs12979860) have recently been identified for predicting the outcome of treatment of hepatitis C virus infection. This polymorphism detection was based on whole blood DNA extraction. Alternatively, DNA for genetic diagnosis has been derived from buccal epithelial cells (BEC), dried blood spots (DBS), and genomic DNA from serum. The aim of the study was to investigate the reliability and accuracy of alternative routes of testing for single nucleotide polymorphism allele rs12979860CC. Methods Blood, plasma, and sera samples from 200 patients were extracted (400 µL). Buccal smears were tested using an FTA card. To simulate postal delay, we tested the influence of storage at ambient temperature on the different sources of DNA at five time points (baseline, 48 h, 6 days, 9 days, and 12 days) Results There was 100% concordance between blood, plasma, sera, and BEC, validating the use of DNA extracted from BEC collected on cytology brushes for genetic testing. Genetic variations in HPTR1 gene were detected using smear technique in blood smear (3620 copies) as well as in buccal smears (5870 copies). These results are similar to those for whole blood diluted at 1/10. A minimum of 0.04 µL, 4 µL, and 40 µL was necessary to obtain exploitable results respectively for whole blood, sera, and plasma. No significant variation between each time point was observed for the different sources of DNA. IL28B SNPs analysis at these different time points showed the same results using the four sources of DNA. Conclusion We demonstrated that genomic DNA extraction from buccal cells, small amounts of serum, and dried blood spots is an alternative to DNA extracted from peripheral blood cells and is helpful in retrospective and prospective studies for multiple genetic markers, specifically in hard-to-reach individuals. PMID:22412970

Detection of Thermal Erosion Gullies from High-Resolution Images Using Deep Learning

NASA Astrophysics Data System (ADS)

Huang, L.; Liu, L.; Jiang, L.; Zhang, T.; Sun, Y.

2017-12-01

Thermal erosion gullies, one type of thermokarst landforms, develop due to thawing of ice-rich permafrost. Mapping the location and extent of thermal erosion gullies can help understand the spatial distribution of thermokarst landforms and their temporal evolution. Remote sensing images provide an effective way for mapping thermokarst landforms, especially thermokarst lakes. However, thermal erosion gullies are challenging to map from remote sensing images due to their small sizes and significant variations in geometric/radiometric properties. It is feasible to manually identify these features, as a few previous studies have carried out. However manual methods are labor-intensive, therefore, cannot be used for a large study area. In this work, we conduct automatic mapping of thermal erosion gullies from high-resolution images by using Deep Learning. Our study area is located in Eboling Mountain (Qinghai, China). Within a 6 km2 peatland area underlain by ice-rich permafrost, at least 20 thermal erosional gullies are well developed. The image used is a 15-cm-resolution Digital Orthophoto Map (DOM) generated in July 2016. First, we extracted 14 gully patches and ten non-gully patches as training data. And we performed image augmentation. Next, we fine-tuned the pre-trained model of DeepLab, a deep-learning algorithm for semantic image segmentation based on Deep Convolutional Neural Networks. Then, we performed inference on the whole DOM and obtained intermediate results in forms of polygons for all identified gullies. At last, we removed misidentified polygons based on a few pre-set criteria on the size and shape of each polygon. Our final results include 42 polygons. Validated against field measurements using GPS, most of the gullies are detected correctly. There are 20 false detections due to the small number and low quality of training images. We also found three new gullies that missed in the field observations. This study shows that (1) despite a challenging mapping task, DeepLab can detect small, irregular-shaped thermal erosion gullies with high accuracy. (2) Automatic detection is critical for mapping thermal erosion gully since manual mapping or field work may miss some targets even in a relatively small region. (3) The quantity and quality of training data are crucial for detection accuracy.

Monitoring Structure and Regional-Level Displacements for Lisbon Using Mltitemporal InSAR Techniques

NASA Astrophysics Data System (ADS)

Roque, Dora; Perissin, Daniele Falcao, Ana Paula; Fonseca, Ana Maria; Henriques, Maria Joao

2015-05-01

The city of Lisbon is the capital of Portugal and has been devastated by catastrophic events in the past, such as earthquakes and tsunamis. This study provides a regional analysis of displacements for the city and its neighbourhoods, between 2008 and 2010, through the application of mutitemporal InSAR techniques on Envisat ASAR images. Smaller areas with identified problems were subjected to a more refined processing. Besides, the behaviour of some key infrastructures, such as important buildings or railways, was carefully analysed in order to evaluate their safety. Subsidence was detected at the regional and small areas, in which the highest subsidence rates were verified on industrial parks or on landfills close to the river. Seasonal trends were found for the small areas, mainly related with structure thermal expansion or variations in underground water.

Small-scale variability of zooplankton pyruvate kinase activity in the Gironde Estuary plume (Atlantic French Coast): A case study under unusually low freshwater discharge

NASA Astrophysics Data System (ADS)

Bergeron, Jean-Pierre

2006-09-01

Pyruvate kinase (PK) activity measurements are used to assess the role of carbohydrates in global feeding of mesozooplankton communities inhabiting an estuary plume. As a consequence of a remarkably low freshwater discharge rate, the sea surface layers of the area under estuarine influence showed a very moderate salinity fall and a nearly total depletion in nitrates, whereas higher levels of these nutrients were found in deeper, more saline, layers. Small-scale PK activity variations in mesozooplankton appear to be closely correlated to nitrate integration values within the water column. The results were analysed in comparison with literature reports. The study produced a coherent overall interpretation, which strongly supports the reliability of this new biochemical tool in detecting assimilation of trace carbohydrates in the diet of mesozooplankton.

Impact of a century of climate change on small-mammal communities in Yosemite National Park, USA.

PubMed

Moritz, Craig; Patton, James L; Conroy, Chris J; Parra, Juan L; White, Gary C; Beissinger, Steven R

2008-10-10

We provide a century-scale view of small-mammal responses to global warming, without confounding effects of land-use change, by repeating Grinnell's early-20th century survey across a 3000-meter-elevation gradient that spans Yosemite National Park, California, USA. Using occupancy modeling to control for variation in detectability, we show substantial ( approximately 500 meters on average) upward changes in elevational limits for half of 28 species monitored, consistent with the observed approximately 3 degrees C increase in minimum temperatures. Formerly low-elevation species expanded their ranges and high-elevation species contracted theirs, leading to changed community composition at mid- and high elevations. Elevational replacement among congeners changed because species' responses were idiosyncratic. Though some high-elevation species are threatened, protection of elevation gradients allows other species to respond via migration.

Nanoparticle Enhancement Cascade for Sensitive Multiplex Measurements of Biomarkers in Complex Fluids with Surface Plasmon Resonance Imaging.

PubMed

Hendriks, Jan; Stojanovic, Ivan; Schasfoort, Richard B M; Saris, Daniël B F; Karperien, Marcel

2018-06-05

There is a large unmet need for reliable biomarker measurement systems for clinical application. Such systems should meet challenging requirements for large scale use, including a large dynamic detection range, multiplexing capacity, and both high specificity and sensitivity. More importantly, these requirements need to apply to complex biological samples, which require extensive quality control. In this paper, we present the development of an enhancement detection cascade for surface plasmon resonance imaging (SPRi). The cascade applies an antibody sandwich assay, followed by neutravidin and a gold nanoparticle enhancement for quantitative biomarker measurements in small volumes of complex fluids. We present a feasibility study both in simple buffers and in spiked equine synovial fluid with four cytokines, IL-1β, IL-6, IFN-γ, and TNF-α. Our enhancement cascade leads to an antibody dependent improvement in sensitivity up to 40 000 times, resulting in a limit of detection as low as 50 fg/mL and a dynamic detection range of more than 7 logs. Additionally, measurements at these low concentrations are highly reliable with intra- and interassay CVs between 2% and 20%. We subsequently showed this assay is suitable for multiplex measurements with good specificity and limited cross-reactivity. Moreover, we demonstrated robust detection of IL-6 and IL-1β in spiked undiluted equine synovial fluid with small variation compared to buffer controls. In addition, the availability of real time measurements provides extensive quality control opportunities, essential for clinical applications. Therefore, we consider this method is suitable for broad application in SPRi for multiplex biomarker detection in both research and clinical settings.

Detection limit of intragenic deletions with targeted array comparative genomic hybridization

PubMed Central

2013-01-01

Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

Multi-scale occupancy estimation and modelling using multiple detection methods

USGS Publications Warehouse

Nichols, James D.; Bailey, Larissa L.; O'Connell, Allan F.; Talancy, Neil W.; Grant, Evan H. Campbell; Gilbert, Andrew T.; Annand, Elizabeth M.; Husband, Thomas P.; Hines, James E.

2008-01-01

Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method.We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site.We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species.Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock's robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.

Lower stratosphere measurements of variation with latitude of CF2Cl2, CFCl3, CCl4, and N2O profiles in the northern hemisphere

NASA Technical Reports Server (NTRS)

Vedder, J. F.; Tyson, B. J.; Brewer, R. B.; Inn, E. C. Y.; Boitnott, C. A.

1978-01-01

Measurements were made from a U-2 aircraft of profiles of CF2Cl2, CFCl3, CCl4 and N2O in the lower stratosphere in a meridional survey at a longitude of 159 deg W during the period October 1 to November 14, 1976. The latitude distributions obtained show a marked decrease in mixing ratio with increasing latitude from about 7 deg N in the Intertropical Convergence Zone to about 79 deg N. The results suggest the importance of meridional transport and mixing in the stratosphere in accounting, at least in part, for the observed profile variation with latitude. The contaminants C2F4Cl2, C2F3Cl3, CHCCl3 and SF6 were also detected but their mixing ratios were small and no accurate standards were prepared for them.

Population Genetics of Trypanosoma evansi from Camel in the Sudan

PubMed Central

Salim, Bashir; de Meeûs, Thierry; Bakheit, Mohammed A.; Kamau, Joseph; Nakamura, Ichiro; Sugimoto, Chihiro

2011-01-01

Genetic variation of microsatellite loci is a widely used method for the analysis of population genetic structure of microorganisms. We have investigated genetic variation at 15 microsatellite loci of T. evansi isolated from camels in Sudan and Kenya to evaluate the genetic information partitioned within and between individuals and between sites. We detected a strong signal of isolation by distance across the area sampled. The results also indicate that either, and as expected, T. evansi is purely clonal and structured in small units at very local scales and that there are numerous allelic dropouts in the data, or that this species often sexually recombines without the need of the “normal” definitive host, the tsetse fly or as the recurrent immigration from sexually recombined T. brucei brucei. Though the first hypothesis is the most likely, discriminating between these two incompatible hypotheses will require further studies at much localized scales. PMID:21666799

Applications of thermal remote sensing to detailed ground water studies

NASA Technical Reports Server (NTRS)

Souto-Maior, J.

1973-01-01

Three possible applications of thermal (8-14 microns) remote sensing to detailed hydrogeologic studies are discussed in this paper: (1) the direct detection of seeps and springs, (2) the indirect evaluation of shallow ground water flow through its thermal effects on the land surface, and (3) the indirect location of small volumes of ground water inflow into surface water bodies. An investigation carried out with this purpose in an area containing a complex shallow ground water flow system indicates that the interpretation of the thermal imageries is complicated by many factors, among which the most important are: (1) altitude, angle of view, and thermal-spatial resolution of the sensor; (2) vegetation type, density, and vigor; (3) topography; (4) climatological and micrometeorological effects; (5) variation in soil type and soil moisture; (6) variation in volume and temperature of ground water inflow; (7) the hydraulic characteristics of the receiving water body, and (8) the presence of decaying organic material.

Multiscale 3D Shape Analysis using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2013-01-01

Shape priors attempt to represent biological variations within a population. When variations are global, Principal Component Analysis (PCA) can be used to learn major modes of variation, even from a limited training set. However, when significant local variations exist, PCA typically cannot represent such variations from a small training set. To address this issue, we present a novel algorithm that learns shape variations from data at multiple scales and locations using spherical wavelets and spectral graph partitioning. Our results show that when the training set is small, our algorithm significantly improves the approximation of shapes in a testing set over PCA, which tends to oversmooth data. PMID:16685992

Multiscale 3D shape analysis using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen R

2005-01-01

Shape priors attempt to represent biological variations within a population. When variations are global, Principal Component Analysis (PCA) can be used to learn major modes of variation, even from a limited training set. However, when significant local variations exist, PCA typically cannot represent such variations from a small training set. To address this issue, we present a novel algorithm that learns shape variations from data at multiple scales and locations using spherical wavelets and spectral graph partitioning. Our results show that when the training set is small, our algorithm significantly improves the approximation of shapes in a testing set over PCA, which tends to oversmooth data.

An audit of Cryptosporidium and Giardia detection in Scottish National Health Service Diagnostic Microbiology Laboratories.

PubMed

Alexander, C L; Currie, S; Pollock, K; Smith-Palmer, A; Jones, B L

2017-06-01

Giardia duodenalis and Cryptosporidium species are protozoan parasites capable of causing gastrointestinal disease in humans and animals through the ingestion of infective faeces. Whereas Cryptosporidium species can be acquired locally or through foreign travel, there is the mis-conception that giardiasis is considered to be largely travel-associated, which results in differences in laboratory testing algorithms. In order to determine the level of variation in testing criteria and detection methods between diagnostic laboratories for both pathogens across Scotland, an audit was performed. Twenty Scottish diagnostic microbiology laboratories were invited to participate with questions on sample acceptance criteria, testing methods, testing rates and future plans for pathogen detection. Reponses were received from 19 of the 20 laboratories representing each of the 14 territorial Health Boards. Detection methods varied between laboratories with the majority performing microscopy, one using a lateral flow immunochromatographic antigen assay, another using a manually washed plate-based enzyme immunoassay (EIA) and one laboratory trialling a plate-based EIA automated with an EIA plate washer. Whereas all laboratories except one screened every stool for Cryptosporidium species, an important finding was that significant variation in the testing algorithm for detecting Giardia was noted with only four laboratories testing all diagnostic stools. The most common criteria were 'travel history' (11 laboratories) and/or 'when requested' (14 laboratories). Despite only a small proportion of stools being examined in 15 laboratories for Giardia (2%-18% of the total number of stools submitted), of interest is the finding that a higher positivity rate was observed for Giardia than Cryptosporidium in 10 of these 15 laboratories. These findings highlight that the underreporting of Giardia in Scotland is likely based on current selection and testing algorithms.

Spatio-temporal Variations in Slow Earthquakes along the Mexican Subduction Zone

NASA Astrophysics Data System (ADS)

Ide, S.; Maury, J.; Cruz-Atienza, V. M.; Kostoglodov, V.

2017-12-01

Slow earthquakes in Mexico have been investigated independently in different areas. Here, we review differences in tremor behavior and slow slip events along the entire subduction zone to improve our understanding of its segmentation. Some similarities are observed between the Guerrero and Oaxaca areas. By combining our improved tremor detection capabilities with previous results, we suggest that there is no gap in tremor between Guerrero and Oaxaca. However some differences between Michoacan and Guerrero are seen (e.g., SSE magnitude, tremor zone width, tremor rate), suggesting that these two areas behave differently. Tremor initiation shows clear tidal sensitivity along the entire subduction zone. Tremor in Guerrero is sensitive to small tidal normal stress as well as shear stress suggesting the subduction plane may include local variations in dip. Estimation of the energy rate shows similar values along the subduction zone interface. The scaled tremor energy estimates are similar to those calculated in Nankai and Cascadia, suggesting a common mechanism. Along-strike differences in slow deformation may be related to variations in the subduction interface that yield different geometrical and temperature profiles.

Fundamental Physics from Observations of White Dwarf Stars

NASA Astrophysics Data System (ADS)

Bainbridge, M. B.; Barstow, M. A.; Reindl, N.; Barrow, J. D.; Webb, J. K.; Hu, J.; Preval, S. P.; Holberg, J. B.; Nave, G.; Tchang-Brillet, L.; Ayres, T. R.

2017-03-01

Variation in fundamental constants provide an important test of theories of grand unification. Potentially, white dwarf spectra allow us to directly observe variation in fundamental constants at locations of high gravitational potential. We study hot, metal polluted white dwarf stars, combining far-UV spectroscopic observations, atomic physics, atmospheric modelling and fundamental physics, in the search for variation in the fine structure constant. This registers as small but measurable shifts in the observed wavelengths of highly ionized Fe and Ni lines when compared to laboratory wavelengths. Measurements of these shifts were performed by Berengut et al (2013) using high-resolution STIS spectra of G191-B2B, demonstrating the validity of the method. We have extended this work by; (a) using new (high precision) laboratory wavelengths, (b) refining the analysis methodology (incorporating robust techniques from previous studies towards quasars), and (c) enlarging the sample of white dwarf spectra. A successful detection would be the first direct measurement of a gravitational field effect on a bare constant of nature. We describe our approach and present preliminary results.

Natural flow and vertical heterogeneities in a sedimentary geothermal reservoir (Paris Basin, France): Geochemical investigations

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

Criaud, Annie, Fouassier, Philippe; Fouillac, Christian; Brach, Michel

1988-01-01

Three geothermal wells tapping the Dogger aquifer were studied in detail for their variations in chemical composition with time or conditions of exploitation. Analytical improvements for the determination of Cl, SO{sub 4}, Ca, Mg, Na and K make it possible to detect variations respectively of 0.15, 0.8, 0.6, 1.8, 1.8 and 1.4 %. Despite the fact that the natural flow may be important in some parts of the basin aquifer, we conclude that this factor is not responsible for the small variations noticed in mineralization within the one year survey period. The results concerning reactive and nonreactive species are bestmore » explained if a vertical heterogeneity of the chemistry of the fluid is assumed. A number of calcareous sub-layers, already demonstrated by geological studies, contribute to varying degrees to the production of the hot water. The changes in pumping rates, which are fixed according to external requirements, play a major role in the hydrodynamic and chemical disequilibrium of the wells. The consequences for the geothermal exploitations are emphasized.« less

Spatiotemporal Variations in Slow Earthquakes Along the Mexican Subduction Zone

NASA Astrophysics Data System (ADS)

Maury, J.; Ide, S.; Cruz-Atienza, V. M.; Kostoglodov, V.

2018-02-01

Slow earthquakes in Mexico have been investigated independently in different areas. Here we review differences in tremor behavior and slow slip events along the entire subduction zone to improve our understanding of its segmentation. Some similarities are observed between the Guerrero and Oaxaca areas. By combining our improved tremor detection capabilities with previous results, we suggest that there is no gap in tremor between Guerrero and Oaxaca. However, some differences between Michoacan and Guerrero are seen (e.g., SSE magnitude, tremor zone width, and tremor rate), suggesting that these two areas behave differently. Tremor initiation shows clear tidal sensitivity along the entire subduction zone. Tremor in Guerrero is sensitive to small tidal normal stress as well as shear stress, suggesting that the subduction plane may include local variations in dip. Estimation of the energy rate shows similar values along the subduction zone interface. The scaled tremor energy estimates are similar to those calculated in Nankai and Cascadia, suggesting a common mechanism. Along-strike differences in slow deformation may be related to variations in the subduction interface that yield different geometrical and temperature profiles.

Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors

PubMed Central

Weng, Jian; Dong, Shanshan; He, Hongjian; Chen, Feiyan; Peng, Xiaogang

2015-01-01

Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group. PMID:26207985

Differential Cued-Stroop Performance in Cognitively Asymptomatic Older Adults with Biomarker-Identified Risk for Alzheimer's Disease: A Pilot Study.

PubMed

Patten, Ryan Van; Fagan, Anne M; Kaufman, David A S

2018-04-04

There exists a need for more sensitive measures, capable of detecting subtle cognitive decline due to Alzheimer's disease. To advance the literature in Alzheimer's disease by demonstrating that performance on a cued-Stroop task is impacted by preclinical Alzheimer's disease neuropathology. Twenty-nine cognitively asymptomatic older adults completed a computerized, cued-Stroop task in which accuracy rates and intraindividual variability in reaction times were the outcomes of interest. Cerebrospinal fluid biomarkers of Aβ42 and tau were measured and participants were then grouped according to a published p-tau/Aβ42 cutoff reflecting risk for Alzheimer's disease (preclinical Alzheimer's disease = 14; control = 15). ANOVAs indicated that accuracy rates did not differ between the groups but 4-second delay incongruent color-naming Stroop coefficient of variation reaction times were higher in the preclinical Alzheimer's disease group compared to the control group, reflecting increased within-person variability. Moreover, partial correlations showed no relationships between cerebrospinal fluid biomarkers and accuracy rates. However, increases in coefficient of variation reaction times correlated with decreased Aβ42 and increases in p-tau and the p-tau/Aβ42 ratio. Results supported the ability of the computerized, cued-Stroop task to detect subtle Alzheimer's disease neuropathology using a small cohort of cognitively asymptomatic older adults. The ongoing measurement of cued-Stroop coefficient of variation reaction times has both scientific and clinical utility in preclinical Alzheimer's disease. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Spatial scale and sampling resolution affect measures of gap disturbance in a lowland tropical forest: implications for understanding forest regeneration and carbon storage

PubMed Central

Lobo, Elena; Dalling, James W.

2014-01-01

Treefall gaps play an important role in tropical forest dynamics and in determining above-ground biomass (AGB). However, our understanding of gap disturbance regimes is largely based either on surveys of forest plots that are small relative to spatial variation in gap disturbance, or on satellite imagery, which cannot accurately detect small gaps. We used high-resolution light detection and ranging data from a 1500 ha forest in Panama to: (i) determine how gap disturbance parameters are influenced by study area size, and the criteria used to define gaps; and (ii) to evaluate how accurately previous ground-based canopy height sampling can determine the size and location of gaps. We found that plot-scale disturbance parameters frequently differed significantly from those measured at the landscape-level, and that canopy height thresholds used to define gaps strongly influenced the gap-size distribution, an important metric influencing AGB. Furthermore, simulated ground surveys of canopy height frequently misrepresented the true location of gaps, which may affect conclusions about how relatively small canopy gaps affect successional processes and contribute to the maintenance of diversity. Across site comparisons need to consider how gap definition, scale and spatial resolution affect characterizations of gap disturbance, and its inferred importance for carbon storage and community composition. PMID:24452032

Surface morphology of vacuum-evaporated pentacene film on Si substrate studied by in situ grazing-incidence small-angle X-ray scattering: I. The initial stage of formation of pentacene film

NASA Astrophysics Data System (ADS)

Hirosawa, Ichiro; Watanabe, Takeshi; Koganezawa, Tomoyuki; Kikuchi, Mamoru; Yoshimoto, Noriyuki

2018-03-01

The progress of the surface morphology of a growing sub-monolayered pentacene film on a Si substrate was studied by in situ grazing-incidence small angle X-ray scattering (GISAXS). The observed GISAXS profiles did not show sizes of pentacene islands but mainly protuberances on the boundaries around pentacene film. Scattering of X-ray by residual pits in the pentacene film was also detected in the GISAXS profiles of an almost fully covered film. The average radius of pentacene protuberances increased from 13 to 24 nm as the coverage increased to 0.83 monolayer, and the most frequent radius was almost constant at approximately 9 nm. This result suggests that the population of larger protuberances increase with increasing lengths of boundaries of the pentacene film. It can also be considered that the detected protuberances were crystallites of pentacene, since the average size of protuberances was nearly equal to crystallite sizes of pentacene films. The almost constant characteristic distance of 610 nm and amplitudes of pair correlation functions at low coverages suggest that the growth of pentacene films obeyed the diffusion-limited aggregation (DLA) model, as previously reported. It is also considered that the sites of islands show a triangular distribution for small variations of estimated correlation distances.

Genetic variation of growth dynamics in maize (Zea mays L.) revealed through automated non-invasive phenotyping.

PubMed

Muraya, Moses M; Chu, Jianting; Zhao, Yusheng; Junker, Astrid; Klukas, Christian; Reif, Jochen C; Altmann, Thomas

2017-01-01

Hitherto, most quantitative trait loci of maize growth and biomass yield have been identified for a single time point, usually the final harvest stage. Through this approach cumulative effects are detected, without considering genetic factors causing phase-specific differences in growth rates. To assess the genetics of growth dynamics, we employed automated non-invasive phenotyping to monitor the plant sizes of 252 diverse maize inbred lines at 11 different developmental time points; 50 k SNP array genotype data were used for genome-wide association mapping and genomic selection. The heritability of biomass was estimated to be over 71%, and the average prediction accuracy amounted to 0.39. Using the individual time point data, 12 main effect marker-trait associations (MTAs) and six pairs of epistatic interactions were detected that displayed different patterns of expression at various developmental time points. A subset of them also showed significant effects on relative growth rates in different intervals. The detected MTAs jointly explained up to 12% of the total phenotypic variation, decreasing with developmental progression. Using non-parametric functional mapping and multivariate mapping approaches, four additional marker loci affecting growth dynamics were detected. Our results demonstrate that plant biomass accumulation is a complex trait governed by many small effect loci, most of which act at certain restricted developmental phases. This highlights the need for investigation of stage-specific growth affecting genes to elucidate important processes operating at different developmental phases. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Semiconductor sensors

NASA Technical Reports Server (NTRS)

Gatos, Harry C. (Inventor); Lagowski, Jacek (Inventor)

1977-01-01

A semiconductor sensor adapted to detect with a high degree of sensitivity small magnitudes of a mechanical force, presence of traces of a gas or light. The sensor includes a high energy gap (i.e., .about. 1.0 electron volts) semiconductor wafer. Mechanical force is measured by employing a non-centrosymmetric material for the semiconductor. Distortion of the semiconductor by the force creates a contact potential difference (cpd) at the semiconductor surface, and this cpd is determined to give a measure of the force. When such a semiconductor is subjected to illumination with an energy less than the energy gap of the semiconductors, such illumination also creates a cpd at the surface. Detection of this cpd is employed to sense the illumination itself or, in a variation of the system, to detect a gas. When either a gas or light is to be detected and a crystal of a non-centrosymmetric material is employed, the presence of gas or light, in appropriate circumstances, results in a strain within the crystal which distorts the same and the distortion provides a mechanism for qualitative and quantitative evaluation of the gas or the light, as the case may be.

Quantum mechanical systems interacting with different polarizations of gravitational waves in noncommutative phase space

NASA Astrophysics Data System (ADS)

Saha, Anirban; Gangopadhyay, Sunandan; Saha, Swarup

2018-02-01

Owing to the extreme smallness of any noncommutative scale that may exist in nature, both in the spatial and momentum sector of the quantum phase space, a credible possibility of their detection lies in the gravitational wave (GW) detection scenario, where one effectively probes the relative length-scale variations ˜O [10-20-10-23] . With this motivation, we have theoretically constructed how a free particle and a harmonic oscillator will respond to linearly and circularly polarized gravitational waves if their quantum mechanical phase space has a noncommutative structure. We critically analyze the formal solutions which show resonance behavior in the responses of both free particle and HO systems to GW with both kind of polarizations. We discuss the possible implications of these solutions in detecting noncommutativity in a GW detection experiment. We use the currently available upper-bound estimates on various noncommutative parameters to anticipate the relative importance of various terms in the solutions. We also argue how the quantum harmonic oscillator system we considered here can be very relevant in the context of the resonant bar detectors of GW which are already operational.

Composition Pulse Time-Of-Flight Mass Flow Sensor

DOEpatents

Mosier, Bruce P.; Crocker, Robert W.; Harnett, Cindy K. l

2004-01-13

A device for measuring fluid flow rates over a wide range of flow rates (<1 nL/min to >10 .mu.L/min) and at pressures at least as great as 10,000 psi. The invention is particularly adapted for use in microfluidic systems. The device operates by producing compositional variations in the fluid, or pulses, that are subsequently detected downstream from the point of creation to derive a flow rate. Each pulse, comprising a small fluid volume, whose composition is different from the mean composition of the fluid, can be created by electrochemical means, such as by electrolysis of a solvent, electrolysis of a dissolved species, or electrodialysis of a dissolved ionic species. Measurements of the conductivity of the fluid can be used to detect the arrival time of the pulses, from which the fluid flow rate can be determined

Extended Malus law with terahertz metallic metamaterials for sensitive detection with giant tunable quality factor

NASA Astrophysics Data System (ADS)

Romain, Xavier; Baida, Fadi; Boyer, Philippe

2016-07-01

We study a polarizer-analyzer mounting for the terahertz regime with perfectly conducting metallic polarizers made of a periodic subwavelength pattern. With a renewed Jones formalism, we analytically investigate the influence of the multiple reflections, which occur between the polarizer and the analyzer, on the transmission response. We demonstrate that this interaction leads to a modified transmission response: the extended Malus law. In addition, we show that the transmission response can be controlled by the distance between the polarizer and the analyzer. For particular setups, the mounting exhibits extremely sensitive transmission responses. This interesting feature can be employed for high-precision sensing and characterization applications. We specifically propose a general design for measuring the electro-optical response of materials in the terahertz domain allowing detection of refractive index variations as small as 10-5.

A 64-pixel NbTiN superconducting nanowire single-photon detector array for spatially resolved photon detection.

PubMed

Miki, Shigehito; Yamashita, Taro; Wang, Zhen; Terai, Hirotaka

2014-04-07

We present the characterization of two-dimensionally arranged 64-pixel NbTiN superconducting nanowire single-photon detector (SSPD) array for spatially resolved photon detection. NbTiN films deposited on thermally oxidized Si substrates enabled the high-yield production of high-quality SSPD pixels, and all 64 SSPD pixels showed uniform superconducting characteristics within the small range of 7.19-7.23 K of superconducting transition temperature and 15.8-17.8 μA of superconducting switching current. Furthermore, all of the pixels showed single-photon sensitivity, and 60 of the 64 pixels showed a pulse generation probability higher than 90% after photon absorption. As a result of light irradiation from the single-mode optical fiber at different distances between the fiber tip and the active area, the variations of system detection efficiency (SDE) in each pixel showed reasonable Gaussian distribution to represent the spatial distributions of photon flux intensity.

Early melanoma diagnosis with mobile imaging.

PubMed

Do, Thanh-Toan; Zhou, Yiren; Zheng, Haitian; Cheung, Ngai-Man; Koh, Dawn

2014-01-01

We research a mobile imaging system for early diagnosis of melanoma. Different from previous work, we focus on smartphone-captured images, and propose a detection system that runs entirely on the smartphone. Smartphone-captured images taken under loosely-controlled conditions introduce new challenges for melanoma detection, while processing performed on the smartphone is subject to computation and memory constraints. To address these challenges, we propose to localize the skin lesion by combining fast skin detection and fusion of two fast segmentation results. We propose new features to capture color variation and border irregularity which are useful for smartphone-captured images. We also propose a new feature selection criterion to select a small set of good features used in the final lightweight system. Our evaluation confirms the effectiveness of proposed algorithms and features. In addition, we present our system prototype which computes selected visual features from a user-captured skin lesion image, and analyzes them to estimate the likelihood of malignance, all on an off-the-shelf smartphone.

Detecting single-electron events in TEM using low-cost electronics and a silicon strip sensor.

PubMed

Gontard, Lionel C; Moldovan, Grigore; Carmona-Galán, Ricardo; Lin, Chao; Kirkland, Angus I

2014-04-01

There is great interest in developing novel position-sensitive direct detectors for transmission electron microscopy (TEM) that do not rely in the conversion of electrons into photons. Direct imaging improves contrast and efficiency and allows the operation of the microscope at lower energies and at lower doses without loss in resolution, which is especially important for studying soft materials and biological samples. We investigate the feasibility of employing a silicon strip detector as an imaging detector for TEM. This device, routinely used in high-energy particle physics, can detect small variations in electric current associated with the impact of a single charged particle. The main advantages of using this type of sensor for direct imaging in TEM are its intrinsic radiation hardness and large detection area. Here, we detail design, simulation, fabrication and tests in a TEM of the front-end electronics developed using low-cost discrete components and discuss the limitations and applications of this technology for TEM.

Inferring Models of Bacterial Dynamics toward Point Sources

PubMed Central

Jashnsaz, Hossein; Nguyen, Tyler; Petrache, Horia I.; Pressé, Steve

2015-01-01

Experiments have shown that bacteria can be sensitive to small variations in chemoattractant (CA) concentrations. Motivated by these findings, our focus here is on a regime rarely studied in experiments: bacteria tracking point CA sources (such as food patches or even prey). In tracking point sources, the CA detected by bacteria may show very large spatiotemporal fluctuations which vary with distance from the source. We present a general statistical model to describe how bacteria locate point sources of food on the basis of stochastic event detection, rather than CA gradient information. We show how all model parameters can be directly inferred from single cell tracking data even in the limit of high detection noise. Once parameterized, our model recapitulates bacterial behavior around point sources such as the “volcano effect”. In addition, while the search by bacteria for point sources such as prey may appear random, our model identifies key statistical signatures of a targeted search for a point source given any arbitrary source configuration. PMID:26466373

Brain correlates of automatic visual change detection.

PubMed

Cléry, H; Andersson, F; Fonlupt, P; Gomot, M

2013-07-15

A number of studies support the presence of visual automatic detection of change, but little is known about the brain generators involved in such processing and about the modulation of brain activity according to the salience of the stimulus. The study presented here was designed to locate the brain activity elicited by unattended visual deviant and novel stimuli using fMRI. Seventeen adult participants were presented with a passive visual oddball sequence while performing a concurrent visual task. Variations in BOLD signal were observed in the modality-specific sensory cortex, but also in non-specific areas involved in preattentional processing of changing events. A degree-of-deviance effect was observed, since novel stimuli elicited more activity in the sensory occipital regions and at the medial frontal site than small changes. These findings could be compared to those obtained in the auditory modality and might suggest a "general" change detection process operating in several sensory modalities. Copyright © 2013 Elsevier Inc. All rights reserved.

Slope instability caused by small variations in hydraulic conductivity

USGS Publications Warehouse

Reid, M.E.

1997-01-01

Variations in hydraulic conductivity can greatly modify hillslope ground-water flow fields, effective-stress fields, and slope stability. In materials with uniform texture, hydraulic conductivities can vary over one to two orders of magnitude, yet small variations can be difficult to determine. The destabilizing effects caused by small (one order of magnitude or less) hydraulic conductivity variations using ground-water flow modeling, finite-element deformation analysis, and limit-equilibrium analysis are examined here. Low hydraulic conductivity materials that impede downslope ground-water flow can create unstable areas with locally elevated pore-water pressures. The destabilizing effects of small hydraulic heterogeneities can be as great as those induced by typical variations in the frictional strength (approximately 4??-8??) of texturally similar materials. Common "worst-case" assumptions about ground-water flow, such as a completely saturated "hydrostatic" pore-pressure distribution, do not account for locally elevated pore-water pressures and may not provide a conservative slope stability analysis. In site characterization, special attention should be paid to any materials that might impede downslope ground-water flow and create unstable regions.

Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption.

PubMed

Hsu, Jeremy L; Crawford, Jeremy Chase; Tammone, Mauro N; Ramakrishnan, Uma; Lacey, Eileen A; Hadly, Elizabeth A

2017-11-24

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected increase in variation in C. sociabilis. To explore this outcome further, we used targeted gene capture to sequence over 2,000 putatively neutral regions for both species. Our data revealed that, contrary to the microsatellite analyses, the eruption was associated with a small but significant decrease in genetic variation in both species. We suggest that genome-level analyses provide greater power than traditional molecular markers to detect the genetic consequences of population size changes, particularly changes that are recent, short-term, or modest in size. Consequently, genomic analyses promise to generate important new insights into the effects of specific environmental events on demography and genetic variation.

Regional-scale drivers of forest structure and function in northwestern Amazonia.

PubMed

Higgins, Mark A; Asner, Gregory P; Anderson, Christopher B; Martin, Roberta E; Knapp, David E; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest.

MAINTENANCE OF ECOLOGICALLY SIGNIFICANT GENETIC VARIATION IN THE TIGER SWALLOWTAIL BUTTERFLY THROUGH DIFFERENTIAL SELECTION AND GENE FLOW.

PubMed

Bossart, J L; Scriber, J M

1995-12-01

Differential selection in a heterogeneous environment is thought to promote the maintenance of ecologically significant genetic variation. Variation is maintained when selection is counterbalanced by the homogenizing effects of gene flow and random mating. In this study, we examine the relative importance of differential selection and gene flow in maintaining genetic variation in Papilio glaucus. Differential selection on traits contributing to successful use of host plants (oviposition preference and larval performance) was assessed by comparing the responses of southern Ohio, north central Georgia, and southern Florida populations of P. glaucus to three hosts: Liriodendron tulipifera, Magnolia virginiana, and Prunus serotina. Gene flow among populations was estimated using allozyme frequencies from nine polymorphic loci. Significant genetic differentiation was observed among populations for both oviposition preference and larval performance. This differentiation was interpreted to be the result of selection acting on Florida P. glaucus for enhanced use of Magnolia, the prevalent host in Florida. In contrast, no evidence of population differentiation was revealed by allozyme frequencies. F ST -values were very small and Nm, an estimate of the relative strengths of gene flow and genetic drift, was large, indicating that genetic exchange among P. glaucus populations is relatively unrestricted. The contrasting patterns of spatial differentiation for host-use traits and lack of differentiation for electrophoretically detectable variation implies that differential selection among populations will be counterbalanced by gene flow, thereby maintaining genetic variation for host-use traits. © 1995 The Society for the Study of Evolution.

Climatic and geographic predictors of life history variation in Eastern Massasauga (Sistrurus catenatus): A range-wide synthesis.

PubMed

Hileman, Eric T; King, Richard B; Adamski, John M; Anton, Thomas G; Bailey, Robyn L; Baker, Sarah J; Bieser, Nickolas D; Bell, Thomas A; Bissell, Kristin M; Bradke, Danielle R; Campa, Henry; Casper, Gary S; Cedar, Karen; Cross, Matthew D; DeGregorio, Brett A; Dreslik, Michael J; Faust, Lisa J; Harvey, Daniel S; Hay, Robert W; Jellen, Benjamin C; Johnson, Brent D; Johnson, Glenn; Kiel, Brooke D; Kingsbury, Bruce A; Kowalski, Matthew J; Lee, Yu Man; Lentini, Andrew M; Marshall, John C; Mauger, David; Moore, Jennifer A; Paloski, Rori A; Phillips, Christopher A; Pratt, Paul D; Preney, Thomas; Prior, Kent A; Promaine, Andrew; Redmer, Michael; Reinert, Howard K; Rouse, Jeremy D; Shoemaker, Kevin T; Sutton, Scott; VanDeWalle, Terry J; Weatherhead, Patrick J; Wynn, Doug; Yagi, Anne

2017-01-01

Elucidating how life history traits vary geographically is important to understanding variation in population dynamics. Because many aspects of ectotherm life history are climate-dependent, geographic variation in climate is expected to have a large impact on population dynamics through effects on annual survival, body size, growth rate, age at first reproduction, size-fecundity relationship, and reproductive frequency. The Eastern Massasauga (Sistrurus catenatus) is a small, imperiled North American rattlesnake with a distribution centered on the Great Lakes region, where lake effects strongly influence local conditions. To address Eastern Massasauga life history data gaps, we compiled data from 47 study sites representing 38 counties across the range. We used multimodel inference and general linear models with geographic coordinates and annual climate normals as explanatory variables to clarify patterns of variation in life history traits. We found strong evidence for geographic variation in six of nine life history variables. Adult female snout-vent length and neonate mass increased with increasing mean annual precipitation. Litter size decreased with increasing mean temperature, and the size-fecundity relationship and growth prior to first hibernation both increased with increasing latitude. The proportion of gravid females also increased with increasing latitude, but this relationship may be the result of geographically varying detection bias. Our results provide insights into ectotherm life history variation and fill critical data gaps, which will inform Eastern Massasauga conservation efforts by improving biological realism for models of population viability and climate change.

Climatic and geographic predictors of life history variation in Eastern Massasauga (Sistrurus catenatus): A range-wide synthesis

PubMed Central

King, Richard B.; Adamski, John M.; Anton, Thomas G.; Bailey, Robyn L.; Baker, Sarah J.; Bieser, Nickolas D.; Bell, Thomas A.; Bissell, Kristin M.; Bradke, Danielle R.; Campa, Henry; Casper, Gary S.; Cedar, Karen; Cross, Matthew D.; DeGregorio, Brett A.; Dreslik, Michael J.; Faust, Lisa J.; Harvey, Daniel S.; Hay, Robert W.; Jellen, Benjamin C.; Johnson, Brent D.; Johnson, Glenn; Kiel, Brooke D.; Kingsbury, Bruce A.; Kowalski, Matthew J.; Lee, Yu Man; Lentini, Andrew M.; Marshall, John C.; Mauger, David; Moore, Jennifer A.; Paloski, Rori A.; Phillips, Christopher A.; Pratt, Paul D.; Preney, Thomas; Prior, Kent A.; Promaine, Andrew; Redmer, Michael; Reinert, Howard K.; Rouse, Jeremy D.; Shoemaker, Kevin T.; Sutton, Scott; VanDeWalle, Terry J.; Weatherhead, Patrick J.; Wynn, Doug; Yagi, Anne

2017-01-01

Elucidating how life history traits vary geographically is important to understanding variation in population dynamics. Because many aspects of ectotherm life history are climate-dependent, geographic variation in climate is expected to have a large impact on population dynamics through effects on annual survival, body size, growth rate, age at first reproduction, size–fecundity relationship, and reproductive frequency. The Eastern Massasauga (Sistrurus catenatus) is a small, imperiled North American rattlesnake with a distribution centered on the Great Lakes region, where lake effects strongly influence local conditions. To address Eastern Massasauga life history data gaps, we compiled data from 47 study sites representing 38 counties across the range. We used multimodel inference and general linear models with geographic coordinates and annual climate normals as explanatory variables to clarify patterns of variation in life history traits. We found strong evidence for geographic variation in six of nine life history variables. Adult female snout-vent length and neonate mass increased with increasing mean annual precipitation. Litter size decreased with increasing mean temperature, and the size–fecundity relationship and growth prior to first hibernation both increased with increasing latitude. The proportion of gravid females also increased with increasing latitude, but this relationship may be the result of geographically varying detection bias. Our results provide insights into ectotherm life history variation and fill critical data gaps, which will inform Eastern Massasauga conservation efforts by improving biological realism for models of population viability and climate change. PMID:28196149

Global and disease-associated genetic variation in the human Fanconi anemia gene family

PubMed Central

Rogers, Kai J.; Fu, Wenqing; Akey, Joshua M.; Monnat, Raymond J.

2014-01-01

Fanconi anemia (FA) is a human recessive genetic disease resulting from inactivating mutations in any of 16 FANC (Fanconi) genes. Individuals with FA are at high risk of developmental abnormalities, early bone marrow failure and leukemia. These are followed in the second and subsequent decades by a very high risk of carcinomas of the head and neck and anogenital region, and a small continuing risk of leukemia. In order to characterize base pair-level disease-associated (DA) and population genetic variation in FANC genes and the segregation of this variation in the human population, we identified 2948 unique FANC gene variants including 493 FA DA variants across 57 240 potential base pair variation sites in the 16 FANC genes. We then analyzed the segregation of this variation in the 7578 subjects included in the Exome Sequencing Project (ESP) and the 1000 Genomes Project (1KGP). There was a remarkably high frequency of FA DA variants in ESP/1KGP subjects: at least 1 FA DA variant was identified in 78.5% (5950 of 7578) individuals included in these two studies. Six widely used functional prediction algorithms correctly identified only a third of the known, DA FANC missense variants. We also identified FA DA variants that may be good candidates for different types of mutation-specific therapies. Our results demonstrate the power of direct DNA sequencing to detect, estimate the frequency of and follow the segregation of deleterious genetic variation in human populations. PMID:25104853

Integration of geotechnical and geophysical techniques for the characterization of a small earth-filled canal dyke and the localization of water leakage

NASA Astrophysics Data System (ADS)

Bièvre, Grégory; Lacroix, Pascal; Oxarango, Laurent; Goutaland, David; Monnot, Guy; Fargier, Yannick

2017-04-01

This paper investigates the combined use of extensive geotechnical, hydrogeological and geophysical techniques to assess a small earth dyke with a permanent hydraulic head, namely a canal embankment. The experimental site was chosen because of known issues regarding internal erosion and piping phenomena. Two leakages were visually located following the emptying of the canal prior to remediation works. The results showed a good agreement between the geophysical imaging techniques (Electrical Resistivity Tomography, P- and SH-waves Tomography) and the geotechnical data to detect the depth to the bedrock and its lateral variations. It appeared that surface waves might not be fully adapted for dyke investigation because of the particular geometry of the studied dyke, non-respectful of the 1D assumption, and which induced depth and velocity discrepancies retrieved from Rayleigh and Love waves inversion. The use of these classical prospecting techniques however did not allow to directly locate the two leakages within the studied earth dyke. The analysis of ambient vibration time series with a modified beam-forming algorithm allowed to localize the most energetic water flow prior to remediation works. It was not possible to detect the leakage after remediation works, suggesting that they efficiently contributed to significantly reduce the water flow. The second leakage was not detected probably because of a non-turbulent water flow, generating few energetic vibrations.

Immune Response to Giardia duodenalis

PubMed Central

Faubert, Gaétan

2000-01-01

The intestinal protozoan Giardia duodenalis is a widespread opportunistic parasite of humans and animals. This parasite inhabits the upper part of the small intestine and has a direct life cycle. After ingestion of cysts, which are the infective stage, the trophozoites emerge from the cysts in the duodenum and attach to the small intestinal mucosa of the host. Since the migration of trophozoites from the lumen of the intestine into surrounding tissues is an unusual occurrence, the immune response to Giardia remains localized. The identification of antigens that play a role in acquired immunity has been difficult because of the occurrence of antigenic variation and because, Giardia being an ubiquituous organism, it is possible that the antigenic profiles of isolates from different geographic areas will vary. Innate-immunity mechanisms play a role in the control and/or severity of the infection. Both humoral and cell-mediated immune responses play a role in acquired immunity, but the mechanisms involved are unknown. A variety of serological assays have been used to detect circulating antibodies in serum. Because of the biological characteristics of the parasite and the lack of suitable antigens, the sensitivity of serological assays remains poor. On the other hand, detection of antigens in feces of infected patients has met with success. Commercial kits are available, and they are reported to be more sensitive than microscopic examination for the detection of giardiasis on a single specimen. PMID:10627490

Variation in detection of ductal carcinoma in situ (DCIS) during screening mammography A survey within the International Cancer Screening Network (ICSN)

PubMed Central

Lynge, Elsebeth; Ponti, Antonio; James, Ted; Májek, Ondřej; von Euler-Chelpin, My; Anttila, Ahti; Fitzpatrick, Patricia; Frigerio, Alfonso; Kawai, Masaaki; Scharpantgen, Astrid; Broeders, Mireille; Hofvind, Solveig; Vidal, Carmen; Ederra, Maria; Salas, Dolores; Bulliard, Jean-Luc; Tomatis, Mariano; Kerlikowske, Karla; Taplin, Stephen

2013-01-01

Background There is concern about detection of Ductal Carcinoma in Situ (DCIS) in screening mammography. DCIS accounts for a substantial proportion of screen detected lesions but its effect on breast cancer mortality is debated. The International Cancer Screening Network conducted a comparative analysis to determine variation in DCIS detection. Patients and Methods Data were collected during 2004–2008 on number of screening examinations, detected breast cancers, DCIS cases, and Globocan 2008 breast cancer incidence rates derived from national or regional cancer registers. We calculated screen-detection rates for breast cancers and DCIS. Results Data were obtained from 15 screening settings in 12 countries; 7,176,050 screening examinations; 29,605 breast cancers; and 5,324 DCIS cases. The ratio between highest and lowest breast cancer incidence was 2.88 (95% confidence interval (CI) 2.76–3.00); 2.97 (95% CI 2.51–3.51) for detection of breast cancer; and 3.49 (95% CI 2.70–4.51) for detection of DCIS. Conclusions Considerable international variation was found in DCIS detection. This variation could not be fully explained by variation in incidence nor in breast cancer detection rates. It suggests the potential for wide discrepancies in management of DCIS resulting in overtreatment of indolent DCIS or undertreatment of potentially curable disease. Comprehensive cancer registration is needed to monitor DCIS detection. Efforts to understand discrepancies and standardize management may improve care. PMID:24041876

The underlying processes of a soil mite metacommunity on a small scale.

PubMed

Dong, Chengxu; Gao, Meixiang; Guo, Chuanwei; Lin, Lin; Wu, Donghui; Zhang, Limin

2017-01-01

Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m) in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran's eigenvector maps (MEMs) were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables) and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA) were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend), indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important in the observed structure of the soil mite metacommunity at the studied small scale.

The underlying processes of a soil mite metacommunity on a small scale

PubMed Central

Guo, Chuanwei; Lin, Lin; Wu, Donghui; Zhang, Limin

2017-01-01

Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m) in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran’s eigenvector maps (MEMs) were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables) and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA) were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend), indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important in the observed structure of the soil mite metacommunity at the studied small scale. PMID:28481906

Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers.

PubMed

Ahmed Mohamed, Nadjim; Yu, Qian; Chanfi, Mohamed Ibrahim; Li, Yangping; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

2016-01-01

Small giant clam, Tridacna maxima , widely distributed from French Polynesia to East Africa, has faced population declines due to over-exploitation. Comoros islands are an important biogeographic region due to potential richness of marine species, but no relevant information is available. In order to facilitate devising effective conservation management plan for T. maxima , nine microsatellite markers were used to survey genetic diversity and population differentiation of 72 specimens collected from three Comoros islands, Grande Comore, Moheli and Anjouan. A total of 51 alleles were detected ranged from 2 to 8 per locus. Observed and expected heterozygosity varied from 0.260 to 0.790 and from 0.542 to 0.830, respectively. All populations have high genetic diversity, especially the population in Moheli, a protected area, has higher genetic diversity than the others. Significant heterozygote deficiencies were recorded, and null alleles were probably the main factor leading to these deficits. F ST value indicated medium genetic differentiation among the populations. Although significant, AMOVA revealed 48.9 % of genetic variation within individuals and only a small variation of 8.9 % was found between populations. Gene flow was high ( Nm  = 12.40) between Grande Comore and Moheli, while lower ( Nm  = 1.80) between Grande Comore and Anjouan, explaining geographic barriers to genetic exchanges might exist in these two islands. Global gene flow analysis ( Nm  = 5.50) showed that larval dispersal is enough to move between the islands. The high genetic diversity and medium population differentiation revealed in the present study offer useful information on genetic conservation of small giant clams.

Cable tunnel fire experiment study based on linear optical fiber fire detectors

NASA Astrophysics Data System (ADS)

Fan, Dian; Ding, Hongjun

2013-09-01

Aiming at exiting linear temperature fire detection technology including temperature sensing cable, fiber Raman scattering, fiber Bragg grating, this paper establish an experimental platform in cable tunnel, set two different experimental scenes of the fire and record temperature variation and fire detector response time in the processing of fire simulation. Since a small amount of thermal radiation and no flame for the beginning of the small-scale fire, only directly contacting heat detectors can make alarm response and the rest of other non- contact detectors are unable to respond. In large-scale fire, the alarm response time of the fiber Raman temperature sensing fire detector and fiber Bragg grating temperature sensing fire detector is about 30 seconds, and depending on the thermocouples' record the temperature over the fire is less than 35° in first 60 seconds of large-scale fire, while the temperature rising is more than 5°/min within the range of +/- 3m. According to the technical characteristics of the three detectors, the engineering suitability of the typical linear heat detectors in cable tunnels early fire detection is analyzed, which provide technical support for the preparation of norms.

Analysis of normalized radar cross section (sigma-O) signature of Amazon rain forest using SEASAT scatterometer data

NASA Technical Reports Server (NTRS)

Bracalente, E. M.; Sweet, J. L.

1984-01-01

The normalized radar cross section (NRCS) signature of the Amazon rain forest was SEASAT scatterometer data. Statistics of the measured (NRCS) values were determined from multiple orbit passes for three local time periods. Plots of mean normalized radar cross section, dB against incidence angle as a function of beam and polarization show that less than 0.3 dB relative bias exists between all beams over a range of incidence angle from 30 deg to 53 deg. The backscattered measurements analyzed show the Amazon rain forest to be relatively homogeneous, azimuthally isotropic and insensitive to polarization. The return from the rain forest target appears relatively consistent and stable, except for the small diurnal variation (0.75 dB) that occurs at sunrise. Because of the relative stability of the rain forest target and the scatterometer instrument, the response of versus incidence angle was able to detect errors in the estimated yaw altitude angle. Also, small instrument gain biases in some of the processing channels were detected. This led to the development of an improved NRCS algorithm, which uses a more accurate method for estimating the system noise power.

Strontium isotope systematics of mixing groundwater and oil-field brine at Goose Lake in northeastern Montana, USA

USGS Publications Warehouse

Peterman, Zell E.; Thamke, Joanna N.; Futa, Kiyoto; Preston, Todd

2012-01-01

Groundwater, surface water, and soil in the Goose Lake oil field in northeastern Montana have been affected by Cl−-rich oil-field brines during long-term petroleum production. Ongoing multidisciplinary geochemical and geophysical studies have identified the degree and local extent of interaction between brine and groundwater. Fourteen samples representing groundwater, surface water, and brine were collected for Sr isotope analyses to evaluate the usefulness of 87Sr/86Sr in detecting small amounts of brine. Differences in Sr concentrations and 87Sr/86Sr are optimal at this site for the experiment. Strontium concentrations range from 0.13 to 36.9 mg/L, and corresponding 87Sr/86Sr values range from 0.71097 to 0.70828. The local brine has 168 mg/L Sr and a 87Sr/86Sr value of 0.70802. Mixing relationships are evident in the data set and illustrate the sensitivity of Sr in detecting small amounts of brine in groundwater. The location of data points on a Sr isotope-concentration plot is readily explained by an evaporation-mixing model. The model is supported by the variation in concentrations of most of the other solutes.

Principles and Applications of the qPlus Sensor

NASA Astrophysics Data System (ADS)

Giessibl, Franz J.

The concept of the atomic force microscope (AFM) is a very simple one: map the surface of a sample by a sharp probe that scans over the surface similar to the finger of a blind person that reads Braille characters. In AFM, the role of that finger is taken by the probe tip that senses the presence of the sample surface by detecting the force between the tip of the probe and a sample. The qPlus sensor is a self sensing cantilever based on a quartz tuning fork that supplements the traditional microfabricated cantilevers made of silicon. Quartz tuning forks are used in the watch industry in quantities of billions annually, with the positive effects on quality and perfection. Three properties of these quartz-based sensors simplify the AFM significantly: (1) the piezoelectricity of quartz allows simple self sensing, (2) the mechanical properties of quartz show very small variations with temperature, and (3) the given stiffness of many quartz tuning forks is close to the ideal stiffness of cantilevers. The key properties of the qPlus sensor are a large stiffness that allows small amplitude operation, the large size that allows to mount single-crystal probe tips, and the self-sensing piezoelectric detection mechanism.

Detection limit for rate fluctuations in inhomogeneous Poisson processes

NASA Astrophysics Data System (ADS)

Shintani, Toshiaki; Shinomoto, Shigeru

2012-04-01

Estimations of an underlying rate from data points are inevitably disturbed by the irregular occurrence of events. Proper estimation methods are designed to avoid overfitting by discounting the irregular occurrence of data, and to determine a constant rate from irregular data derived from a constant probability distribution. However, it can occur that rapid or small fluctuations in the underlying density are undetectable when the data are sparse. For an estimation method, the maximum degree of undetectable rate fluctuations is uniquely determined as a phase transition, when considering an infinitely long series of events drawn from a fluctuating density. In this study, we analytically examine an optimized histogram and a Bayesian rate estimator with respect to their detectability of rate fluctuation, and determine whether their detectable-undetectable phase transition points are given by an identical formula defining a degree of fluctuation in an underlying rate. In addition, we numerically examine the variational Bayes hidden Markov model in its detectability of rate fluctuation, and determine whether the numerically obtained transition point is comparable to those of the other two methods. Such consistency among these three principled methods suggests the presence of a theoretical limit for detecting rate fluctuations.

Detection limit for rate fluctuations in inhomogeneous Poisson processes.

PubMed

Shintani, Toshiaki; Shinomoto, Shigeru

2012-04-01

Estimations of an underlying rate from data points are inevitably disturbed by the irregular occurrence of events. Proper estimation methods are designed to avoid overfitting by discounting the irregular occurrence of data, and to determine a constant rate from irregular data derived from a constant probability distribution. However, it can occur that rapid or small fluctuations in the underlying density are undetectable when the data are sparse. For an estimation method, the maximum degree of undetectable rate fluctuations is uniquely determined as a phase transition, when considering an infinitely long series of events drawn from a fluctuating density. In this study, we analytically examine an optimized histogram and a Bayesian rate estimator with respect to their detectability of rate fluctuation, and determine whether their detectable-undetectable phase transition points are given by an identical formula defining a degree of fluctuation in an underlying rate. In addition, we numerically examine the variational Bayes hidden Markov model in its detectability of rate fluctuation, and determine whether the numerically obtained transition point is comparable to those of the other two methods. Such consistency among these three principled methods suggests the presence of a theoretical limit for detecting rate fluctuations.

Decoherence as a way to measure extremely soft collisions with dark matter

NASA Astrophysics Data System (ADS)

Riedel, C. Jess; Yavin, Itay

2017-07-01

A new frontier in the search for dark matter (DM) is based on the idea of detecting the decoherence caused by DM scattering against a mesoscopic superposition of normal matter. Such superpositions are uniquely sensitive to very small momentum transfers from new particles and forces, especially DM with a mass below 100 MeV. Here we investigate what sorts of dark sectors are inaccessible with existing methods but would induce noticeable decoherence in the next generation of matter interferometers. We show that very soft but medium range (0.1 nm - 1 μ m ) elastic interactions between nuclei and DM are particularly suitable. We construct toy models for such interactions, discuss existing constraints, and delineate the expected sensitivity of forthcoming experiments. The first hints of DM in these devices would appear as small variations in the anomalous decoherence rate with a period of one sidereal day. This is a generic signature of interstellar sources of decoherence, clearly distinguishing it from terrestrial backgrounds. The OTIMA experiment under development in Vienna will begin to probe Earth-thermalizing DM once sidereal variations in the background decoherence rate are pushed below one part in a hundred for superposed 5-nm gold nanoparticles. The proposals by Bateman et al. and Geraci et al. could be similarly sensitive although they would require at least a month of data taking. DM that is absorbed or elastically reflected by the Earth, and so avoids a greenhouse density enhancement, would not be detectable by those three experiments. On the other hand, the aggressive proposals of the MAQRO collaboration and Pino et al. would immediately open up many orders of magnitude in DM mass, interaction range, and coupling strength, regardless of how DM behaves in bulk matter.

SDSS J211852.96-073227.5: a new γ-ray flaring narrow-line Seyfert 1 galaxy

NASA Astrophysics Data System (ADS)

Yang, Hui; Yuan, Weimin; Yao, Su; Li, Ye; Zhang, Jin; Zhou, Hongyan; Komossa, S.; Liu, He-Yang; Jin, Chichuan

2018-07-01

We report on the identification of a new γ-ray-emitting narrow-line Seyfert 1 (NLS1) galaxy, SDSS J211852.96-073227.5 (hereinafter J2118-0732). The galaxy, at a redshift of 0.26, is associated with a radio source of flat/inverted spectrum at high radio frequencies. The analysis of its optical spectrum obtained in the Sloan Digital Sky Survey (SDSS) revealed a small linewidth of the broad component of the Hβ line (full width at half-maximum = 1585 km s-1), making it a radio-loud NLS1 galaxy - an intriguing class of active galactic nuclei with exceptional multiwavelength properties. A new γ-ray source centred at J2118-0732 was sporadically detected during 2009-2013 in form of flares by the Fermi-LAT. Our XMM-Newton observations revealed a flat X-ray spectrum described by a simple power law, and a flux variation by a factor of ˜2.5 in five months. The source also shows intraday variability in the infrared band. Its broad-band spectral energy distribution can be modelled by emission from a simple one-zone leptonic jet model, and the flux drop from infrared to X-rays in five months can be explained by changes of the jet parameters, though the exact values may be subject to relatively large uncertainties. With the NLS1-blazar composite nucleus, the clear detection of the host galaxy, and the synchronous variations in the multiwavelength fluxes, J2118-0732 provides a new perspective on the formation and evolution of relativistic jets under the regime of relatively small black hole masses and high accretion rates.

Fiber-Optic Pressure Sensor With Dynamic Demodulation Developed

NASA Technical Reports Server (NTRS)

Lekki, John D.

2002-01-01

Researchers at the NASA Glenn Research Center developed in-house a method to detect pressure fluctuations using a fiber-optic sensor and dynamic signal processing. This work was in support of the Intelligent Systems Controls and Operations project under NASA's Information Technology Base Research Program. We constructed an optical pressure sensor by attaching a fiber-optic Bragg grating to a flexible membrane and then adhering the membrane to one end of a small cylinder. The other end of the cylinder was left open and exposed to pressure variations from a pulsed air jet. These pressure variations flexed the membrane, inducing a strain in the fiber-optic grating. This strain was read out optically with a dynamic spectrometer to record changes in the wavelength of light reflected from the grating. The dynamic spectrometer was built in-house to detect very small wavelength shifts induced by the pressure fluctuations. The spectrometer is an unbalanced interferometer specifically designed for maximum sensitivity to wavelength shifts. An optimum pathlength difference, which was determined empirically, resulted in a 14-percent sensitivity improvement over theoretically predicted path-length differences. This difference is suspected to be from uncertainty about the spectral power difference of the signal reflected from the Bragg grating. The figure shows the output of the dynamic spectrometer as the sensor was exposed to a nominally 2-kPa peak-to-peak square-wave pressure fluctuation. Good tracking, sensitivity, and signal-to-noise ratios are evident even though the sensor was constructed as a proof-of-concept and was not optimized in any way. Therefore the fiber-optic Bragg grating, which is normally considered a good candidate as a strain or temperature sensor, also has been shown to be a good candidate for a dynamic pressure sensor.

Planetary science and exploration in the deep subsurface: results from the MINAR Program, Boulby Mine, UK

NASA Astrophysics Data System (ADS)

Payler, Samuel J.; Biddle, Jennifer F.; Coates, Andrew J.; Cousins, Claire R.; Cross, Rachel E.; Cullen, David C.; Downs, Michael T.; Direito, Susana O. L.; Edwards, Thomas; Gray, Amber L.; Genis, Jac; Gunn, Matthew; Hansford, Graeme M.; Harkness, Patrick; Holt, John; Josset, Jean-Luc; Li, Xuan; Lees, David S.; Lim, Darlene S. S.; McHugh, Melissa; McLuckie, David; Meehan, Emma; Paling, Sean M.; Souchon, Audrey; Yeoman, Louise; Cockell, Charles S.

2017-04-01

The subsurface exploration of other planetary bodies can be used to unravel their geological history and assess their habitability. On Mars in particular, present-day habitable conditions may be restricted to the subsurface. Using a deep subsurface mine, we carried out a program of extraterrestrial analog research - MINe Analog Research (MINAR). MINAR aims to carry out the scientific study of the deep subsurface and test instrumentation designed for planetary surface exploration by investigating deep subsurface geology, whilst establishing the potential this technology has to be transferred into the mining industry. An integrated multi-instrument suite was used to investigate samples of representative evaporite minerals from a subsurface Permian evaporite sequence, in particular to assess mineral and elemental variations which provide small-scale regions of enhanced habitability. The instruments used were the Panoramic Camera emulator, Close-Up Imager, Raman spectrometer, Small Planetary Linear Impulse Tool, Ultrasonic drill and handheld X-ray diffraction (XRD). We present science results from the analog research and show that these instruments can be used to investigate in situ the geological context and mineralogical variations of a deep subsurface environment, and thus habitability, from millimetre to metre scales. We also show that these instruments are complementary. For example, the identification of primary evaporite minerals such as NaCl and KCl, which are difficult to detect by portable Raman spectrometers, can be accomplished with XRD. By contrast, Raman is highly effective at locating and detecting mineral inclusions in primary evaporite minerals. MINAR demonstrates the effective use of a deep subsurface environment for planetary instrument development, understanding the habitability of extreme deep subsurface environments on Earth and other planetary bodies, and advancing the use of space technology in economic mining.

SDSS J211852.96-073227.5: a new γ-ray flaring narrow-line Seyfert 1 galaxy

NASA Astrophysics Data System (ADS)

Yang, Hui; Yuan, Weimin; Yao, Su; Li, Ye; Zhang, Jin; Zhou, Hongyan; Komossa, S.; Liu, He-Yang; Jin, Chichuan

2018-04-01

We report on the identification of a new γ-ray-emitting narrow-line Seyfert 1 (NLS1) galaxy, SDSS J211852.96-073227.5 (hereafter J2118-0732). The galaxy, at a redshift of 0.26, is associated with a radio source of flat/inverted spectrum at high radio frequencies. The analysis of its optical spectrum obtained in the Sloan Digital Sky Survey revealed a small linewidth of the broad component of the Hβ line (FWHM = 1585 km s-1), making it a radio-loud NLS1 galaxy - an intriguing class of active galactic nuclei with exceptional multi-wavelength properties. A new γ-ray source centred at J2118-0732 was sporadically detected during 2009-2013 in form of flares by the Fermi-LAT. Our XMM-Newton observations revealed a flat X-ray spectrum described by a simple power law, and a flux variation by a factor of ˜2.5 in 5 months. The source also shows intraday variability in the infrared band. Its broad-band spectral energy distribution can be modelled by emission from a simple one-zone leptonic jet model, and the flux drop from infrared to X-rays in five months can be explained by changes of the jet parameters, though the exact values may be subject to relatively large uncertainties. With the NLS1-blazar composite nucleus, the clear detection of the host galaxy and the synchronous variations in the multi-wavelength fluxes, J2118-0732 provides a new perspective on the formation and evolution of relativistic jets under the regime of relatively small black hole masses and high accretion rates.

The functional spectrum of low-frequency coding variation.

PubMed

Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard

2011-09-14

Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

Mapping groundwater level and aquifer storage variations from InSAR measurements in the Madrid aquifer, Central Spain

NASA Astrophysics Data System (ADS)

Béjar-Pizarro, Marta; Ezquerro, Pablo; Herrera, Gerardo; Tomás, Roberto; Guardiola-Albert, Carolina; Ruiz Hernández, José M.; Fernández Merodo, José A.; Marchamalo, Miguel; Martínez, Rubén

2017-04-01

Groundwater resources are under stress in many regions of the world and the future water supply for many populations, particularly in the driest places on Earth, is threatened. Future climatic conditions and population growth are expected to intensify the problem. Understanding the factors that control groundwater storage variation is crucial to mitigate its adverse consequences. In this work, we apply satellite-based measurements of ground deformation over the Tertiary detritic aquifer of Madrid (TDAM), Central Spain, to infer the spatio-temporal evolution of water levels and estimate groundwater storage variations. Specifically, we use Persistent Scatterer Interferometry (PSI) data during the period 1992-2010 and piezometric time series on 19 well sites covering the period 1997-2010 to build groundwater level maps and quantify groundwater storage variations. Our results reveal that groundwater storage loss occurred in two different periods, 1992-1999 and 2005-2010 and was mainly concentrated in a region of ∼200 km2. The presence of more compressible materials in that region combined with a long continuous water extraction can explain this volumetric deficit. This study illustrates how the combination of PSI and piezometric data can be used to detect small aquifers affected by groundwater storage loss helping to improve their sustainable management.

Influence of gravel mining and other factors on detection probabilities of Coastal Plain fishes in the Mobile River Basin, Alabama

USGS Publications Warehouse

Hayer, C.-A.; Irwin, E.R.

2008-01-01

We used an information-theoretic approach to examine the variation in detection probabilities for 87 Piedmont and Coastal Plain fishes in relation to instream gravel mining in four Alabama streams of the Mobile River drainage. Biotic and abiotic variables were also included in candidate models. Detection probabilities were heterogeneous across species and varied with habitat type, stream, season, and water quality. Instream gravel mining influenced the variation in detection probabilities for 38% of the species collected, probably because it led to habitat loss and increased sedimentation. Higher detection probabilities were apparent at unmined sites than at mined sites for 78% of the species for which gravel mining was shown to influence detection probabilities, indicating potential negative impacts to these species. Physical and chemical attributes also explained the variation in detection probabilities for many species. These results indicate that anthropogenic impacts can affect detection probabilities for fishes, and such variation should be considered when developing monitoring programs or routine sampling protocols. ?? Copyright by the American Fisheries Society 2008.

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

PubMed

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

2013-07-01

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

Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes

PubMed Central

Johnstone, Daniel M.; Riveros, Carlos; Heidari, Moones; Graham, Ross M.; Trinder, Debbie; Berretta, Regina; Olynyk, John K.; Scott, Rodney J.; Moscato, Pablo; Milward, Elizabeth A.

2013-01-01

While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes. PMID:27605185

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

PubMed Central

2013-01-01

Background The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations – changes specific to a tumor and not within an individual’s germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific. Results We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity. Conclusion We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic. PMID:23642077

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.

PubMed

Christoforides, Alexis; Carpten, John D; Weiss, Glen J; Demeure, Michael J; Von Hoff, Daniel D; Craig, David W

2013-05-04

The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations--changes specific to a tumor and not within an individual's germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific. We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity. We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic.

Compensating temperature-induced ultrasonic phase and amplitude changes

NASA Astrophysics Data System (ADS)

Gong, Peng; Hay, Thomas R.; Greve, David W.; Junker, Warren R.; Oppenheim, Irving J.

2016-04-01

In ultrasonic structural health monitoring (SHM), environmental and operational conditions, especially temperature, can significantly affect the propagation of ultrasonic waves and thus degrade damage detection. Typically, temperature effects are compensated using optimal baseline selection (OBS) or optimal signal stretch (OSS). The OSS method achieves compensation by adjusting phase shifts caused by temperature, but it does not fully compensate phase shifts and it does not compensate for accompanying signal amplitude changes. In this paper, we develop a new temperature compensation strategy to address both phase shifts and amplitude changes. In this strategy, OSS is first used to compensate some of the phase shifts and to quantify the temperature effects by stretching factors. Based on stretching factors, empirical adjusting factors for a damage indicator are then applied to compensate for the temperature induced remaining phase shifts and amplitude changes. The empirical adjusting factors can be trained from baseline data with temperature variations in the absence of incremental damage. We applied this temperature compensation approach to detect volume loss in a thick wall aluminum tube with multiple damage levels and temperature variations. Our specimen is a thick-walled short tube, with dimensions closely comparable to the outlet region of a frac iron elbow where flow-induced erosion produces the volume loss that governs the service life of that component, and our experimental sequence simulates the erosion process by removing material in small damage steps. Our results show that damage detection is greatly improved when this new temperature compensation strategy, termed modified-OSS, is implemented.

A comparison of small-area hospitalisation rates, estimated morbidity and hospital access.

PubMed

Shulman, H; Birkin, M; Clarke, G P

2015-11-01

Published data on hospitalisation rates tend to reveal marked spatial variations within a city or region. Such variations may simply reflect corresponding variations in need at the small-area level. However, they might also be a consequence of poorer accessibility to medical facilities for certain communities within the region. To help answer this question it is important to compare these variable hospitalisation rates with small-area estimates of need. This paper first maps hospitalisation rates at the small-area level across the region of Yorkshire in the UK to show the spatial variations present. Then the Health Survey of England is used to explore the characteristics of persons with heart disease, using chi-square and logistic regression analysis. Using the most significant variables from this analysis the authors build a spatial microsimulation model of morbidity for heart disease for the Yorkshire region. We then compare these estimates of need with the patterns of hospitalisation rates seen across the region. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Combined hostile fire and optics detection

NASA Astrophysics Data System (ADS)

Brännlund, Carl; Tidström, Jonas; Henriksson, Markus; Sjöqvist, Lars

2013-10-01

Snipers and other optically guided weapon systems are serious threats in military operations. We have studied a SWIR (Short Wave Infrared) camera-based system with capability to detect and locate snipers both before and after shot over a large field-of-view. The high frame rate SWIR-camera allows resolution of the temporal profile of muzzle flashes which is the infrared signature associated with the ejection of the bullet from the rifle. The capability to detect and discriminate sniper muzzle flashes with this system has been verified by FOI in earlier studies. In this work we have extended the system by adding a laser channel for optics detection. A laser diode with slit-shaped beam profile is scanned over the camera field-of-view to detect retro reflection from optical sights. The optics detection system has been tested at various distances up to 1.15 km showing the feasibility to detect rifle scopes in full daylight. The high speed camera gives the possibility to discriminate false alarms by analyzing the temporal data. The intensity variation, caused by atmospheric turbulence, enables discrimination of small sights from larger reflectors due to aperture averaging, although the targets only cover a single pixel. It is shown that optics detection can be integrated in combination with muzzle flash detection by adding a scanning rectangular laser slit. The overall optics detection capability by continuous surveillance of a relatively large field-of-view looks promising. This type of multifunctional system may become an important tool to detect snipers before and after shot.

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

PubMed

Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

2017-09-01

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population differentiation highlight the conservation value of large populations throughout the species' range, particularly in light of climate change and direct human threats.

Automatic telangiectasia analysis in dermoscopy images using adaptive critic design.

PubMed

Cheng, B; Stanley, R J; Stoecker, W V; Hinton, K

2012-11-01

Telangiectasia, tiny skin vessels, are important dermoscopy structures used to discriminate basal cell carcinoma (BCC) from benign skin lesions. This research builds off of previously developed image analysis techniques to identify vessels automatically to discriminate benign lesions from BCCs. A biologically inspired reinforcement learning approach is investigated in an adaptive critic design framework to apply action-dependent heuristic dynamic programming (ADHDP) for discrimination based on computed features using different skin lesion contrast variations to promote the discrimination process. Lesion discrimination results for ADHDP are compared with multilayer perception backpropagation artificial neural networks. This study uses a data set of 498 dermoscopy skin lesion images of 263 BCCs and 226 competitive benign images as the input sets. This data set is extended from previous research [Cheng et al., Skin Research and Technology, 2011, 17: 278]. Experimental results yielded a diagnostic accuracy as high as 84.6% using the ADHDP approach, providing an 8.03% improvement over a standard multilayer perception method. We have chosen BCC detection rather than vessel detection as the endpoint. Although vessel detection is inherently easier, BCC detection has potential direct clinical applications. Small BCCs are detectable early by dermoscopy and potentially detectable by the automated methods described in this research. © 2011 John Wiley & Sons A/S.

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities. PMID:21346791

A universal reference sample derived from clone vector for improved detection of differential gene expression

PubMed Central

Khan, Rishi L; Gonye, Gregory E; Gao, Guang; Schwaber, James S

2006-01-01

Background Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing signals to be undetectable. In addition, undetectable spots represent a large problem for two-color microarray designs and most arrays contain at least 40% undetectable spots even when labeled with reference samples such as Stratagene's Universal Reference RNAs™. Results We introduce a novel universal reference sample that produces strong signal for all spots on the array, increasing the average fraction of detectable spots to 97%. Maximizing detectable spots on the reference image channel also decreases the variability of microarray data allowing for reliable detection of smaller differential gene expression changes. The reference sample is derived from sequence contained in the parental EST clone vector pT7T3D-Pac and is called vector RNA (vRNA). We show that vRNA can also be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This reference sample can be made inexpensively in large quantities as a renewable resource that is consistent across experiments. Conclusion Results of this study show that vRNA provides a useful universal reference that yields high signal for almost all spots on a microarray, reduces variation and allows for comparisons between experiments and laboratories. Further, it can be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This type of reference allows for detection of small changes in differential expression while reference designs in general allow for large-scale multivariate experimental designs. vRNA in combination with reference designs enable systems biology microarray experiments of small physiologically relevant changes. PMID:16677381

Time-varying sodium absorption in the Type Ia supernova 2013gh

DOE PAGES

Ferretti, Raphael; Amanullah, R.; Goobar, A.; ...

2016-07-18

Context. Temporal variability of narrow absorption lines in high-resolution spectra of Type Ia supernovae (SNe Ia) is studied to search for circumstellar matter. Time series which resolve the profiles of absorption lines such as Na I D or Ca II H&K are expected to reveal variations due to photoionisation and subsequent recombination of the gases. The presence, composition, and geometry of circumstellar matter may hint at the elusive progenitor system of SNe Ia and could also affect the observed reddening law. Aims. To date, there are few known cases of time-varying Na I D absorption in SNe Ia, all ofmore » which occurred during relatively late phases of the supernova (SN) evolution. Photoionisation, however, is predicted to occur during the early phases of SNe Ia, when the supernovae peak in the ultraviolet. We attempt, therefore, to observe early-time absorption-line variations by obtaining high-resolution spectra of SNe before maximum light. Methods. In this paper, we have obtained photometry and high-resolution spectroscopy of SNe Ia 2013gh and iPTF 13dge, to search for absorption-line variations. Furthermore, we study interstellar absorption features in relation to the observed photometric colours of the SNe. Results. Both SNe display deep Na I D and Ca II H&K absorption features. Furthermore, small but significant variations are detected in a feature of the Na I D profile of SN 2013gh. The variations are consistent with either geometric effects of rapidly moving or patchy gas clouds or photoionisation of Na I gas at R ≈ 10 19 cm from the explosion. Conclusions. Our analysis indicates that it is necessary to focus on early phases to detect photoionisation effects of gases in the circumstellar medium of SNe Ia. Different absorbers such as Na I and Ca II can be used to probe for matter at different distances from the SNe. Finally, the nondetection of variations during early phases makes it possible to put limits on the abundance of the species at those distances.« less

Seasonal and spatial variations of source and drinking water quality in small municipal systems of two Canadian regions.

PubMed

Scheili, A; Rodriguez, M J; Sadiq, R

2015-03-01

A one-year sampling program covering twenty-five small municipal systems was carried out in two Canadian regions to improve our understanding of the variability of water quality in small systems from water source to the end of the distribution system (DS). The database obtained was used to develop a global portrait of physical, chemical and microbiological water quality parameters. More precisely, the temporal and the spatial variability of these parameters were investigated. We observed that the levels of natural organic matter (NOM) were variable during different seasons, with maxima in the fall for both provinces. In the regions under study, the highest trihalomethane (THM) and haloacetic acid (HAA) levels were achieved in warmer seasons (summer, fall), as observed in previous studies involving large systems. Observed THM and HAA levels were three times higher in systems in the province of Newfoundland & Labrador than in the province of Quebec. Taste and odor indicators were detected during the summer and fall, and higher heterotrophic plate count (HPC) levels were associated with lower free chlorine levels. To determine spatial variations, stepwise statistical analysis was used to identify parameters and locations in the DS that act as indicators of drinking water quality. As observed for medium and large systems, free chlorine consumption, THM and HAA levels were dependent on their location in the DS. We also observed that the degradation of HAAs is more important in small systems than in medium or large DS reported in the literature, and this degradation can occur from the beginning of the DS. The results of this research may contribute to providing precious information on drinking water quality to small system operators and pave the way for several opportunities to improve water quality management. Copyright © 2014 Elsevier B.V. All rights reserved.

Geographic Variation in Diagnostic Ability and Quality of Care Metrics: A Case Study of Ankylosing Spondylitis and Low Back Pain

PubMed Central

Shafrin, Jason; Griffith, Jenny; Shim, Jin Joo; Huber, Caroline; Ganguli, Arijit; Aubry, Wade

2017-01-01

Studies examining geographic variation in care for low back pain often focus on process and outcome measures conditional on patient diagnosis but generally do not take into account a physician’s ability to diagnose the root cause of low back pain. In our case study, we used increased detection of ankylosing spondylitis—a relatively rare inflammatory back disease—as a proxy for diagnostic ability and measured the relationship between ankylosing spondylitis detection, potentially inappropriate low back pain care, and cost. Using 5 years of health insurance claims data, we found significant variation in ankylosing spondylitis detection across metropolitan statistical areas (MSAs), with 8.1% of the variation in detection explained by a region’s racial composition. Furthermore, low back pain patients in MSAs with higher ankylosing spondylitis detection had 7.9% lower use of corticosteroids, 9.0% lower use of opioids, and 8.2% lower pharmacy cost, compared with patients living in low-detection MSAs. PMID:28548005

Epigenetic changes detected in micropropagated hop plants.

PubMed

Peredo, Elena L; Arroyo-García, Rosa; Revilla, M Angeles

2009-07-01

Micropropagation is a widely used technique in hops (Humulus lupulus L.). However, to the best of our knowledge, the genetic and epigenetic stability of the microplants has never been tested before. In the present study, two hop accessions were established in vitro and micropropagated for 2 years. The genetic and epigenetic stability of the in vitro plants was analyzed with several molecular techniques: random amplified DNA polymorphism (RAPD), retrotransposon microsatellite amplified polymorphism (REMAP), and methylation-sensitive amplification polymorphism (MSAP). No genetic variation among control and treated plants was found, even after 12 cycles of micropropagation. Epigenetic variation was detected, first, when field and in vitro samples were compared. Nearly a 30% of the detected fragments presented the same pattern of alterations in all the vitroplants. Second, lower levels of epigenetic variation were detected among plants from the different subcultures. Part of this detected variation seemed to be accumulated along the 12 sequential subcultures tested.

Quantitative impedance characterization of sub-10 nm scale capacitors and tunnel junctions with an interferometric scanning microwave microscope.

PubMed

Wang, Fei; Clément, Nicolas; Ducatteau, Damien; Troadec, David; Tanbakuchi, Hassan; Legrand, Bernard; Dambrine, Gilles; Théron, Didier

2014-10-10

We present a method to characterize sub-10 nm capacitors and tunnel junctions by interferometric scanning microwave microscopy (iSMM) at 7.8 GHz. At such device scaling, the small water meniscus surrounding the iSMM tip should be reduced by proper tip tuning. Quantitative impedance characterization of attofarad range capacitors is achieved using an 'on-chip' calibration kit facing thousands of nanodevices. Nanoscale capacitors and tunnel barriers were detected through variations in the amplitude and phase of the reflected microwave signal, respectively. This study promises quantitative impedance characterization of a wide range of emerging functional nanoscale devices.

Seismic migration for SAR focusing: Interferometrical applications

NASA Astrophysics Data System (ADS)

Prati, C.; Montiguarnieri, A.; Damonti, E.; Rocca, F.

SAR (Synthetic Aperture Radar) data focusing is analyzed from a theoretical point of view. Two applications of a SAR data processing algorithm are presented, where the phases of the returns are used for the recovery of interesting parameters of the observed scenes. Migration techniques, similar to those used in seismic signal processing for oil prospecting, were implemented for the determination of the terrain altitude map from a satellite and the evaluation of the sensor attitude for an airplane. A satisfying precision was achieved, since it was shown how an interferometric system is able to detect variations of the airplane roll angle of a small fraction of a degree.

Analysing harmonic motions with an iPhone’s magnetometer

NASA Astrophysics Data System (ADS)

Yavuz, Ahmet; Kağan Temiz, Burak

2016-05-01

In this paper, we propose an experiment for analysing harmonic motion using an iPhone’s (or iPad’s) magnetometer. This experiment consists of the detection of magnetic field variations obtained from an iPhone’s magnetometer sensor. A graph of harmonic motion is directly displayed on the iPhone’s screen using the Sensor Kinetics application. Data from this application was analysed with Eureqa software to establish the equation of the harmonic motion. Analyses show that the use of an iPhone’s magnetometer to analyse harmonic motion is a practical and effective method for small oscillations and frequencies less than 15-20 Hz.

Plant genotyping using fluorescently tagged inter-simple sequence repeats (ISSRs): basic principles and methodology.

PubMed

Prince, Linda M

2015-01-01

Inter-simple sequence repeat PCR (ISSR-PCR) is a fast, inexpensive genotyping technique based on length variation in the regions between microsatellites. The method requires no species-specific prior knowledge of microsatellite location or composition. Very small amounts of DNA are required, making this method ideal for organisms of conservation concern, or where the quantity of DNA is extremely limited due to organism size. ISSR-PCR can be highly reproducible but requires careful attention to detail. Optimization of DNA extraction, fragment amplification, and normalization of fragment peak heights during fluorescent detection are critical steps to minimizing the downstream time spent verifying and scoring the data.

On the nature of the dwarf carbon star G77-61

NASA Technical Reports Server (NTRS)

Dearborn, D. S. P.; Liebert, J.; Aaronson, M.; Dahn, C. C.; Harrington, R.

1986-01-01

In the present study of astrometric, photometric, and spectrophotometric data for the low luminosity carbon star G77-61, radial velocity variations are detected which have a binary period of 245 days. The unseen companion is probably a cool white dwarf of much higher mass than the visible object. The most straightforward evolutionary hypothesis is that this star has an extremely metal-poor composition, and that it accreted a small amount of carbon-rich material when the now-unseen primary was at maximum radius. This may have inverted the C/O abundance of the secondary without achieving common envelope evolution and a sorter period.

Fabrication and evaluation of evanescent wave absorption based polyaniline-cladding modified fiber optic urea biosensor

NASA Astrophysics Data System (ADS)

Botewad, S. N.; Pahurkar, V. G.; Muley, G. G.

2018-01-01

The fabrication and study of cladding modified intrinsic fiber optic urea biosensor has been reported in the present investigation. A simple cladding modification technique was used to construct the sensor by uncladding the small portion from optical fiber. Further bare core was decorated by supportive porous, chemically and optically sensitive matrix material polyaniline (PANI) as an active cladding for enzyme residency. Enzyme-urease (Urs) was cross-linked on the active cladding region via glutaraldehyde solution. Confirmation of the prepared PANI in proper form determined by ultraviolet-visible and Fourier transform infrared spectroscopic techniques. X-ray diffraction technique was employed for nature and compatibility examination of PANI. Sensor parameters such as sensitivity, selectivity, stability and lower detection limit have been analyzed by absorption variation study in evanescent wave field. The response of prepared sensor was studied towards urea in the wide concentration range 100 nM-100 mM and confirmed its lowest detection limit as 100 nM. The stability of sensor was found 28 days with little variation in response. The fabricated sensor has not shown any response towards interference species like glucose, ascorbic acid, L-alanine, L-arginine and their combination with urea solution and hence found selective for urea solution only.

Secular trends, race, and geographic disparity of early-stage breast cancer incidence: 25 years of surveillance in Connecticut.

PubMed

Crabbe, J Christopher F; Gregorio, David I; Samociuk, Holly; Swede, Helen

2015-07-01

We considered changes in the geographic distribution of early stage breast cancer among White and non-White women while secular trends in lifestyle and health care were under way. We aggregated tumor registry and census data by age, race, place of residence, and year of diagnosis to evaluate rate variation across Connecticut census tracts between 1985 and 2009. Global and local cluster detection tests were completed. Age-adjusted incidence rates increased by 2.71% and 0.44% per year for White and non-White women, respectively. Significant global clustering was identified during surveillance of these populations, but the elements of clustering differed between groups. Among White women, fewer local clusters were detected after 1985 to 1989, whereas clustering increased over time among non-White women. Small-area variation of breast cancer incidence rates across time periods proved to be dynamic and race-specific. Incidence rates might have been affected by secular trends in lifestyle or health care. Single cross-sectional analyses might have confused our understanding of disease occurrence by not accounting for the social context in which patient preferences or provider capacity influence the numbers and locations of diagnosed cases. Serial analyses are recommended to identify "hot spots" where persistent geographic disparities in incidence occur.

Genetic dissection of adaptive form and function in rapidly speciating cichlid fishes.

PubMed

Henning, Frederico; Machado-Schiaffino, Gonzalo; Baumgarten, Lukas; Meyer, Axel

2017-05-01

Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses, and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick-lipped) and Pundamilia nyererei (thin-lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small-to-moderate and mainly additive effects were detected. Phenotypic variation in lip and head morphology was largely independent. Although several QTL overlapped for lip and head morphology traits, they were often of opposite effects. The distribution of effect signs suggests strong selection on lips. The fitness implications of several detected loci were demonstrated using a laboratory assay testing for the association between genotype and variation in foraging performance. The persistence of low fitness alleles in head morphology appears to be maintained through antagonistic pleiotropy/close linkage with positive-effect lip morphology alleles. Rather than being based on few major loci with strong positive genetic correlations, our results indicate that the evolution of the Lake Victoria thick-lipped ecomorph is the result of selection on numerous loci distributed throughout the genome. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Use of extremely short Förster resonance energy transfer probes in real-time polymerase chain reaction

PubMed Central

Kutyavin, Igor V.

2013-01-01

Described in the article is a new approach for the sequence-specific detection of nucleic acids in real-time polymerase chain reaction (PCR) using fluorescently labeled oligonucleotide probes. The method is based on the production of PCR amplicons, which fold into dumbbell-like secondary structures carrying a specially designed ‘probe-luring’ sequence at their 5′ ends. Hybridization of this sequence to a complementary ‘anchoring’ tail introduced at the 3′ end of a fluorescent probe enables the probe to bind to its target during PCR, and the subsequent probe cleavage results in the florescence signal. As it has been shown in the study, this amplicon-endorsed and guided formation of the probe-target duplex allows the use of extremely short oligonucleotide probes, up to tetranucleotides in length. In particular, the short length of the fluorescent probes makes possible the development of a ‘universal’ probe inventory that is relatively small in size but represents all possible sequence variations. The unparalleled cost-effectiveness of the inventory approach is discussed. Despite the short length of the probes, this new method, named Angler real-time PCR, remains highly sequence specific, and the results of the study indicate that it can be effectively used for quantitative PCR and the detection of polymorphic variations. PMID:24013564

Long-term Photometric Variability in Kepler Full-frame Images: Magnetic Cycles of Sun–like Stars

NASA Astrophysics Data System (ADS)

Montet, Benjamin T.; Tovar, Guadalupe; Foreman-Mackey, Daniel

2017-12-01

Photometry from the Kepler mission is optimized to detect small, short-duration signals like planet transits at the expense of long-term trends. This long-term variability can be recovered in photometry from the full-frame images (FFIs), a set of calibration data collected approximately monthly during the Kepler mission. Here we present f3, an open-source package to perform photometry on the Kepler FFIs in order to detect changes in the brightness of stars in the Kepler field of view over long time baselines. We apply this package to a sample of 4000 Sun–like stars with measured rotation periods. We find that ≈10% of these targets have long-term variability in their observed flux. For the majority of targets, we find that the luminosity variations are either correlated or anticorrelated with the short-term variability due to starspots on the stellar surface. We find a transition between anticorrelated (starspot-dominated) variability and correlated (facula-dominated) variability between rotation periods of 15 and 25 days, suggesting the transition between the two modes is complete for stars at the age of the Sun. We also identify a sample of stars with apparently complete cycles, as well as a collection of short-period binaries with extreme photometric variation over the Kepler mission.

DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato).

PubMed Central

Kado, Tomoyuki; Yoshimaru, Hiroshi; Tsumura, Yoshihiko; Tachida, Hidenori

2003-01-01

We investigated the nucleotide variation of a conifer, Cryptomeria japonica, and the divergence between this species and its closest relative, Taxodium distichum, at seven nuclear loci (Acl5, Chi1, Ferr, GapC, HemA, Lcyb, and Pat). Samples of C. japonica were collected from three areas, Kantou-Toukai, Hokuriku, and Iwate. No apparent geographic differentiation was found among these samples. However, the frequency spectrum of the nucleotide polymorphism revealed excesses of intermediate-frequency variants, which suggests that the population was not panmictic and a constant size in the past. The average nucleotide diversity, pi, for silent sites was 0.00383. However, values of pi for silent sites vary among loci. Comparisons of polymorphism to divergence among loci (the HKA test) showed that the polymorphism at the Acl5 locus was significantly lower. We also observed a nearly significant excess of replacement polymorphisms at the Lcyb locus. These results suggested possibilities of natural selection acting at some of the loci. Intragenic recombination was detected only once at the Chi1 locus and was not detected at the other loci. The low level of population recombination rate, 4Nr, seemed to be due to both low level of recombination, r, and small population size, N. PMID:12930759

Group benefit associated with polymorphic trichromacy in a Malagasy primate (Propithecus verreauxi)

PubMed Central

Veilleux, Carrie C.; Scarry, Clara J.; Di Fiore, Anthony; Kirk, E. Christopher; Bolnick, Deborah A.; Lewis, Rebecca J.

2016-01-01

In some primate lineages, polymorphisms in the X-linked M/LWS opsin gene have produced intraspecific variation in color vision. In these species, heterozygous females exhibit trichromacy, while males and homozygous females exhibit dichromacy. The evolutionary persistence of these polymorphisms suggests that balancing selection maintains color vision variation, possibly through a ‘trichromat advantage’ in detecting yellow/orange/red foods against foliage. We identified genetic evidence of polymorphic trichromacy in a population of Verreaux’s sifaka (Propithecus verreauxi) at Kirindy Mitea National Park in Madagascar, and explored effects of color vision on reproductive success and feeding behavior using nine years of morphological, demographic, and feeding data. We found that trichromats and dichromats residing in social groups with trichromats exhibit higher body mass indices than individuals in dichromat-only groups. Additionally, individuals in a trichromat social group devoted significantly more time to fruit feeding and had longer fruit feeding bouts than individuals in dichromat-only groups. We hypothesize that, due to small, cohesive sifaka social groups, a trichromat advantage in detecting productive fruit patches during the energetically stressful dry season also benefits dichromats in a trichromat’s group. Our results offer the first support for the ‘mutual benefit of association’ hypothesis regarding the maintenance of polymorphic trichromacy in primates. PMID:27910919

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

2015-09-01

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Somatic Genetic Variation in Solid Pseudopapillary Tumor of the Pancreas by Whole Exome Sequencing

PubMed Central

Guo, Meng; Luo, Guopei; Jin, Kaizhou; Long, Jiang; Cheng, He; Lu, Yu; Wang, Zhengshi; Yang, Chao; Xu, Jin; Ni, Quanxing; Yu, Xianjun; Liu, Chen

2017-01-01

Solid pseudopapillary tumor of the pancreas (SPT) is a rare pancreatic disease with a unique clinical manifestation. Although CTNNB1 gene mutations had been universally reported, genetic variation profiles of SPT are largely unidentified. We conducted whole exome sequencing in nine SPT patients to probe the SPT-specific insertions and deletions (indels) and single nucleotide polymorphisms (SNPs). In total, 54 SNPs and 41 indels of prominent variations were demonstrated through parallel exome sequencing. We detected that CTNNB1 mutations presented throughout all patients studied (100%), and a higher count of SNPs was particularly detected in patients with older age, larger tumor, and metastatic disease. By aggregating 95 detected variation events and viewing the interconnections among each of the genes with variations, CTNNB1 was identified as the core portion in the network, which might collaborate with other events such as variations of USP9X, EP400, HTT, MED12, and PKD1 to regulate tumorigenesis. Pathway analysis showed that the events involved in other cancers had the potential to influence the progression of the SNPs count. Our study revealed an insight into the variation of the gene encoding region underlying solid-pseudopapillary neoplasm tumorigenesis. The detection of these variations might partly reflect the potential molecular mechanism. PMID:28054945

Respiration rate detection based on intensity modulation using plastic optical fiber

NASA Astrophysics Data System (ADS)

Anwar, Zawawi Mohd; Ziran Nurul Sufia, Nor; Hadi, Manap

2017-11-01

This paper presents the implementation of respiration rate measurement via a simple intensity-based optical fiber sensor using optical fiber technology. The breathing rate is measured based on the light intensity variation due to the longitudinal gap changes between two separated fibers. In order to monitor the breathing rate continuously, the output from the photodetector conditioning circuit is connected to a low-cost Arduino kit. At the sensing point, two optical fiber cables are positioned in series with a small gap and fitted inside a transparent plastic tube. To ensure smooth movement of the fiber during inhale and exhale processes as well as to maintain the gap of the fiber during idle condition, the fiber is attached firmly to a stretchable bandage. This study shows that this simple fiber arrangement can be applied to detect respiration activity which might be critical for patient monitoring.

Establishing a baseline: the amphibians of Lower Suwannee National Wildlife Refuge, Dixie and Levy counties, Florida

USGS Publications Warehouse

Dodd, C. Kenneth; Barichivich, William J.; Johnson, Steve A.; Gunzburger Aresco, Margaret; Staiger, Jennifer S.

2018-01-01

recorded 23 amphibian species, 19 frogs and 4 salamanders. Species richness was lower than in other areas of the coastal Big Bend region to the north, perhaps due to a combination of proximity to the limits of species’ ranges, sampling techniques, times of year when sampling occurred, and variation in detection probabilities among years and regions. Amphibians occupied a wide variety of habitats and appeared tolerant of the generally acidic conditions of many of the wetlands. Small streams and the Suwannee River were less acidic and had greater conductivities and mineral concentrations than isolated ponds; concentrations of heavy metals varied and mercury was not detected. Although additional species may yet be found in LSNWR, this survey provides a historic baseline for assessing future status and trends of amphibian populations as areas adjacent to the refuge are disturbed and as restoration and multi-use management continue within its boundaries.

X-ray time lags in PG 1211+143

NASA Astrophysics Data System (ADS)

Lobban, A. P.; Vaughan, S.; Pounds, K.; Reeves, J. N.

2018-05-01

We investigate the X-ray time lags of a recent ˜630 ks XMM-Newton observation of PG 1211+143. We find well-correlated variations across the XMM-Newton EPIC bandpass, with the first detection of a hard lag in this source with a mean time delay of up to ˜3 ks at the lowest frequencies. We find that the energy-dependence of the low-frequency hard lag scales approximately linearly with log(E) when averaged over all orbits, consistent with the propagating fluctuations model. However, we find that the low-frequency lag behaviour becomes more complex on time-scales longer than a single orbit, suggestive of additional modes of variability. We also detect a high-frequency soft lag at ˜10-4 Hz with the magnitude of the delay peaking at ≲ 0.8 ks, consistent with previous observations, which we discuss in terms of small-scale reverberation.

The spatial variations of lightning during small Florida thunderstorms

NASA Technical Reports Server (NTRS)

Oram, Timothy D.; Krider, E. Philip

1991-01-01

Networks of field mills (FM's) and lightning direction finders (LDF's) were used to locate lightning over the NASA KSC on three storm days. Over 90 percent of all cloud-to-ground (CG) flashes that were detected by the LDF's in the study area were also detected by the LDF's. About 17 percent of the FM CG events could be fitted to either a monopole or a dipole charge model. These projected FM charge locations are compared to LDF locations, i.e., the ground strike points. It was found that 95 percent of the LDF points are within 12 km of the FM charge, 75 percent are within 8 km, and 50 percent are within 4 km. For a storm on 22 Jul. 1988, there was a systematic 5.6 km shift between the FM charge centers and the LDF strike points that might have been caused by the meteorological structure of the storm.

Mass flows and removal of antibiotics in two municipal wastewater treatment plants.

PubMed

Li, Bing; Zhang, Tong

2011-05-01

The mass flows and removal of 20 antibiotics of seven classes in two wastewater treatment plants (WWTPs) of Hong Kong were investigated in different seasons of a whole year, using bihourly 24h flow proportional composite samples. Antibiotics were detected at concentrations of 3.2-1718, 1.3-1176 and 1.1-233ngL(-1) in influents, secondary and disinfection effluents. Total daily discharges of all the detected antibiotics from effluents of Shatin and Stanley WWTPs were 470-710 and 3.0-5.2gd(-1), respectively. Ampicillin, cefalexin, sulfamethoxazole, sulfadiazine, sulfamethazine, chlortetracycline and vancomycin were effectively (52-100%) eliminated by activated sludge process while ampicillin and cefalexin were effectively (91-99%) eliminated by disinfection. Bihourly variation analysis showed that concentrations of the major antibiotics in influents varied more significantly in Stanley WWTP which served small communities. Copyright © 2011 Elsevier Ltd. All rights reserved.

Using pattern analysis methods to do fast detection of manufacturing pattern failures

NASA Astrophysics Data System (ADS)

Zhao, Evan; Wang, Jessie; Sun, Mason; Wang, Jeff; Zhang, Yifan; Sweis, Jason; Lai, Ya-Chieh; Ding, Hua

2016-03-01

At the advanced technology node, logic design has become extremely complex and is getting more challenging as the pattern geometry size decreases. The small sizes of layout patterns are becoming very sensitive to process variations. Meanwhile, the high pressure of yield ramp is always there due to time-to-market competition. The company that achieves patterning maturity earlier than others will have a great advantage and a better chance to realize maximum profit margins. For debugging silicon failures, DFT diagnostics can identify which nets or cells caused the yield loss. But normally, a long time period is needed with many resources to identify which failures are due to one common layout pattern or structure. This paper will present a new yield diagnostic flow, based on preliminary EFA results, to show how pattern analysis can more efficiently detect pattern related systematic defects. Increased visibility on design pattern related failures also allows more precise yield loss estimation.

Homeostatic enhancement of active mechanotransduction

NASA Astrophysics Data System (ADS)

Milewski, Andrew; O'Maoiléidigh, Dáibhid; Hudspeth, A. J.

2018-05-01

Our sense of hearing boasts exquisite sensitivity to periodic signals. Experiments and modeling imply, however, that the auditory system achieves this performance for only a narrow range of parameter values. As a result, small changes in these values could compromise the ability of the mechanosensory hair cells to detect stimuli. We propose that, rather than exerting tight control over parameters, the auditory system employs a homeostatic mechanism that ensures the robustness of its operation to variation in parameter values. Through analytical techniques and computer simulations we investigate whether a homeostatic mechanism renders the hair bundle's signal-detection ability more robust to alterations in experimentally accessible parameters. When homeostasis is enforced, the range of values for which the bundle's sensitivity exceeds a threshold can increase by more than an order of magnitude. The robustness of cochlear function based on somatic motility or hair bundle motility may be achieved by employing the approach we describe here.

Detection of drug active ingredients by chemometric processing of solid-state NMR spectrometry data -- the case of acetaminophen.

PubMed

Paradowska, Katarzyna; Jamróz, Marta Katarzyna; Kobyłka, Mariola; Gowin, Ewelina; Maczka, Paulina; Skibiński, Robert; Komsta, Łukasz

2012-01-01

This paper presents a preliminary study in building discriminant models from solid-state NMR spectrometry data to detect the presence of acetaminophen in over-the-counter pharmaceutical formulations. The dataset, containing 11 spectra of pure substances and 21 spectra of various formulations, was processed by partial least squares discriminant analysis (PLS-DA). The model found coped with the discrimination, and its quality parameters were acceptable. It was found that standard normal variate preprocessing had almost no influence on unsupervised investigation of the dataset. The influence of variable selection with the uninformative variable elimination by PLS method was studied, reducing the dataset from 7601 variables to around 300 informative variables, but not improving the model performance. The results showed the possibility to construct well-working PLS-DA models from such small datasets without a full experimental design.

An adaptive tracking observer for failure-detection systems

NASA Technical Reports Server (NTRS)

Sidar, M.

1982-01-01

The design problem of adaptive observers applied to linear, constant and variable parameters, multi-input, multi-output systems, is considered. It is shown that, in order to keep the observer's (or Kalman filter) false-alarm rate (FAR) under a certain specified value, it is necessary to have an acceptable proper matching between the observer (or KF) model and the system parameters. An adaptive observer algorithm is introduced in order to maintain desired system-observer model matching, despite initial mismatching and/or system parameter variations. Only a properly designed adaptive observer is able to detect abrupt changes in the system (actuator, sensor failures, etc.) with adequate reliability and FAR. Conditions for convergence for the adaptive process were obtained, leading to a simple adaptive law (algorithm) with the possibility of an a priori choice of fixed adaptive gains. Simulation results show good tracking performance with small observer output errors and accurate and fast parameter identification, in both deterministic and stochastic cases.

ROC analysis of diagnostic performance in liver scintigraphy.

PubMed

Fritz, S L; Preston, D F; Gallagher, J H

1981-02-01

Studies on the accuracy of liver scintigraphy for the detection of metastases were assembled from 38 sources in the medical literature. An ROC curve was fitted to the observed values of sensitivity and specificity using an algorithm developed by Ogilvie and Creelman. This ROC curve fitted the data better than average sensitivity and specificity values in each of four subsets of the data. For the subset dealing with Tc-99m sulfur colloid scintigraphy, performed for detection of suspected metastases and containing data on 2800 scans from 17 independent series, it was not possible to reject the hypothesis that interobserver variation was entirely due to the use of different decision thresholds by the reporting clinicians. Thus the ROC curve obtained is a reasonable baseline estimate of the performance potentially achievable in today's clinical setting. Comparison of new reports with these data is possible, but is limited by the small sample sizes in most reported series.

Molecular characterization and phylogenetic analysis of the causative agent of hemoplasma infection in small Indian Mongoose (Herpestes Javanicus).

PubMed

Sharifiyazdi, Hassan; Nazifi, Saeed; Shirzad Aski, Hesamaddin; Shayegh, Hossein

2014-09-01

Hemoplasmas are the trivial name for a group of erythrocyte-parasitizing bacteria of the genus Mycoplasma. This study is the first report of hemoplasma infection in Small Indian Mongoose (Herpestes Javanicus) based on molecular analysis of 16S rDNA. Whole blood samples were collected by sterile methods, from 14 live captured mongooses, in the south of Iran. Candidatus Mycoplasma turicensis (CMt)-like hemoplasma was detected in blood samples from one animal tested. BLAST search and phylogenetic analysis of partial 16S rDNA sequence (933bp) of the hemoplasma from Small Indian mongoose (KJ530704) revealed only 96-97% identity to the previously described CMt followed by 95% and 91% similarity with Mycoplasma coccoides and Mycoplasma haemomuris, respectively. Accordingly, the Iranian mongoose CMt isolate showed a high intra-specific genetic variation compared to all previously reported CMt strains in GenBank. Further molecular studies using multiple phylogenetic markers are required to characterize the exact species of Mongoose-derived hemoplasma. Copyright © 2014 Elsevier Ltd. All rights reserved.

Small sensitivity to temperature variations of Si-photonic Mach-Zehnder interferometer using Si and SiN waveguides

NASA Astrophysics Data System (ADS)

Hiraki, Tatsurou; Fukuda, Hiroshi; Yamada, Koji; Yamamoto, Tsuyoshi

2015-03-01

We demonstrated a small sensitivity to temperature variations of delay-line Mach-Zehnder interferometer (DL MZI) on a Si photonics platform. The key technique is to balance a thermo-optic effect in the two arms by using waveguide made of different materials. With silicon and silicon nitride waveguides, the fabricated DL MZI with a free-spectrum range of ~40 GHz showed a wavelength shift of -2.8 pm/K with temperature variations, which is 24 times smaller than that of the conventional Si-waveguide DL MZI. We also demonstrated the decoding of the 40-Gbit/s differential phase-shift keying signals to on-off keying signals with various temperatures. The tolerable temperature variation for the acceptable power penalty was significantly improved due to the small wavelength shifts.

Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

DOEpatents

McCutchen-Maloney, Sandra L.

2002-01-01

DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

Primer Vector Optimization: Survey of Theory, New Analysis and Applications

NASA Technical Reports Server (NTRS)

Guzman, J. J.; Mailhe, L. M.; Schiff, C.; Hughes, S. P.; Folta, D. C.

2002-01-01

In this paper, a summary of primer vector theory is presented. The applicability of primer vector theory is examined in an effort to understand when and why the theory can fail. For example, since the Calculus of Variations is based on "small" variations, singularities in the linearized (variational) equations of motion along the arcs must be taken into account. These singularities are a recurring problem in analyse that employ small variations. Two examples, the initialization of an orbit and a line of apsides rotation, are presented. Recommendations, future work, and the possible addition of other optimization techniques are also discussed.

Small-scale variation in ecosystem CO2 fluxes in an alpine meadow depends on plant biomass and species richness.

PubMed

Hirota, Mitsuru; Zhang, Pengcheng; Gu, Song; Shen, Haihua; Kuriyama, Takeo; Li, Yingnian; Tang, Yanhong

2010-07-01

Characterizing the spatial variation in the CO2 flux at both large and small scales is essential for precise estimation of an ecosystem's CO2 sink strength. However, little is known about small-scale CO2 flux variations in an ecosystem. We explored these variations in a Kobresia meadow ecosystem on the Qinghai-Tibetan plateau in relation to spatial variability in species composition and biomass. We established 14 points and measured net ecosystem production (NEP), gross primary production (GPP), and ecosystem respiration (Re) in relation to vegetation biomass, species richness, and environmental variables at each point, using an automated chamber system during the 2005 growing season. Mean light-saturated NEP and GPP were 30.3 and 40.5 micromol CO2 m(-2) s(-1) [coefficient of variation (CV), 42.7 and 29.4], respectively. Mean Re at 20 degrees C soil temperature, Re(20), was -10.9 micromol CO2 m(-2) s(-1) (CV, 27.3). Re(20) was positively correlated with vegetation biomass. GPP(max) was positively correlated with species richness, but 2 of the 14 points were outliers. Vegetation biomass was the main determinant of spatial variation of Re, whereas species richness mainly affected that of GPP, probably reflecting the complexity of canopy structure and light partitioning in this small grassland patch.

Saturn's very axisymmetric magnetic field: No detectable secular variation or tilt

NASA Astrophysics Data System (ADS)

Cao, Hao; Russell, Christopher T.; Christensen, Ulrich R.; Dougherty, Michele K.; Burton, Marcia E.

2011-04-01

Saturn is the only planet in the solar system whose observed magnetic field is highly axisymmetric. At least a small deviation from perfect symmetry is required for a dynamo-generated magnetic field. Analyzing more than six years of magnetometer data obtained by Cassini close to the planet, we show that Saturn's observed field is much more axisymmetric than previously thought. We invert the magnetometer observations that were obtained in the "current-free" inner magnetosphere for an internal model, varying the assumed unknown rotation rate of Saturn's deep interior. No unambiguous non-axially symmetric magnetic moment is detected, with a new upper bound on the dipole tilt of 0.06°. An axisymmetric internal model with Schmidt-normalized spherical harmonic coefficients g10 = 21,191 ± 24 nT, g20 = 1586 ± 7 nT. g30 = 2374 ± 47 nT is derived from these measurements, the upper bounds on the axial degree 4 and 5 terms are 720 nT and 3200 nT respectively. The secular variation for the last 30 years is within the probable error of each term from degree 1 to 3, and the upper bounds are an order of magnitude smaller than in similar terrestrial terms for degrees 1 and 2. Differentially rotating conducting stable layers above Saturn's dynamo region have been proposed to symmetrize the magnetic field (Stevenson, 1982). The new upper bound on the dipole tilt implies that this stable layer must have a thickness L >= 4000 km, and this thickness is consistent with our weak secular variation observations.

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.

PubMed

Cavanagh, Colin R; Chao, Shiaoman; Wang, Shichen; Huang, Bevan Emma; Stephen, Stuart; Kiani, Seifollah; Forrest, Kerrie; Saintenac, Cyrille; Brown-Guedira, Gina L; Akhunova, Alina; See, Deven; Bai, Guihua; Pumphrey, Michael; Tomar, Luxmi; Wong, Debbie; Kong, Stephan; Reynolds, Matthew; da Silva, Marta Lopez; Bockelman, Harold; Talbert, Luther; Anderson, James A; Dreisigacker, Susanne; Baenziger, Stephen; Carter, Arron; Korzun, Viktor; Morrell, Peter Laurent; Dubcovsky, Jorge; Morell, Matthew K; Sorrells, Mark E; Hayden, Matthew J; Akhunov, Eduard

2013-05-14

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

PubMed Central

Cavanagh, Colin R.; Chao, Shiaoman; Wang, Shichen; Huang, Bevan Emma; Stephen, Stuart; Kiani, Seifollah; Forrest, Kerrie; Saintenac, Cyrille; Brown-Guedira, Gina L.; Akhunova, Alina; See, Deven; Bai, Guihua; Pumphrey, Michael; Tomar, Luxmi; Wong, Debbie; Kong, Stephan; Reynolds, Matthew; da Silva, Marta Lopez; Bockelman, Harold; Talbert, Luther; Anderson, James A.; Dreisigacker, Susanne; Baenziger, Stephen; Carter, Arron; Korzun, Viktor; Morrell, Peter Laurent; Dubcovsky, Jorge; Morell, Matthew K.; Sorrells, Mark E.; Hayden, Matthew J.; Akhunov, Eduard

2013-01-01

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat. PMID:23630259

Genetic and epigenetic diversity and structure of Phragmites australis from local habitats of the Songnen Prairie using amplified fragment length polymorphism markers.

PubMed

Qiu, T; Jiang, L L; Yang, Y F

2016-08-19

The genetic and epigenetic diversity and structure of naturally occurring Phragmites australis populations occupying two different habitats on a small spatial scale in the Songnen Prairie in northeastern China were investigated by assessing amplified fragment length polymorphisms (AFLPs) and methylation-sensitive amplified polymorphisms (MSAPs) through fluorescent capillary detection. The two groups of P. australis were located in a seasonal waterlogged low-lying and alkalized meadow with a pH of 8-8.5 and in an alkaline patch without accumulated rainwater and with a pH greater than 10. These groups showed high levels of genetic diversity at the habitat level based on the percentage of polymorphic bands (90.32, 82.56%), Nei's gene diversity index (0.262, 0.248), and the Shannon diversity index (0.407, 0.383). Although little is known about the between-habitat genetic differentiation of P. australis on a small spatial scale, our results implied significant genetic differentiation between habitats. Extensive epigenetic diversity within habitats, along with clear differentiation, was found. Specifically, the former habitat (Habitat 1, designated H1) harbored higher levels of genetic and epigenetic diversity than the latter (Habitat 2, designated H2), and population-level diversity was also high. This study represents one of few attempts to predict habitat-based genetic differentiation of reeds on a small scale. These assessments of genetic and epigenetic variation are integral aspects of molecular ecological studies on P. australis. Possible causes for within- and between-habitat genetic and epigenetic variations are discussed.

Application of non-traditional stable isotopes in analytical ecogeochemistry assessed by MC ICP-MS--A critical review.

PubMed

Irrgeher, Johanna; Prohaska, Thomas

2016-01-01

Analytical ecogeochemistry is an evolving scientific field dedicated to the development of analytical methods and tools and their application to ecological questions. Traditional stable isotopic systems have been widely explored and have undergone continuous development during the last century. The variations of the isotopic composition of light elements (H, O, N, C, and S) have provided the foundation of stable isotope analysis followed by the analysis of traditional geochemical isotope tracers (e.g., Pb, Sr, Nd, Hf). Questions in a considerable diversity of scientific fields have been addressed, many of which can be assigned to the field of ecogeochemistry. Over the past 15 years, other stable isotopes (e.g., Li, Zn, Cu, Cl) have emerged gradually as novel tools for the investigation of scientific topics that arise in ecosystem research and have enabled novel discoveries and explorations. These systems are often referred to as non-traditional isotopes. The small isotopic differences of interest that are increasingly being addressed for a growing number of isotopic systems represent a challenge to the analytical scientist and push the limits of today's instruments constantly. This underlines the importance of a metrologically sound concept of analytical protocols and procedures and a solid foundation of data processing strategies and uncertainty considerations before these small isotopic variations can be interpreted in the context of applied ecosystem research. This review focuses on the development of isotope research in ecogeochemistry, the requirements for successful detection of small isotopic shifts, and highlights the most recent and innovative applications in the field.

Source characterization of a small earthquake cluster at Edmond, Oklahoma using a very dense array

NASA Astrophysics Data System (ADS)

Ng, R.; Nakata, N.

2017-12-01

Recent seismicity in Oklahoma has caught the attention of the public in the last few years since seismicity is commonly related to loss in urban areas. To account for the increase in public interest, improve the understanding of damaging ground motions produced in earthquakes and develop better seismic hazard assessment, we must characterize the seismicity in Oklahoma and its associated structure and source parameters. Regional changes in subsurface stresses have increased seismic activities due to reactivation of faults in places such as central Oklahoma. It is imperative for seismic investigation and modeling to characterize subsurface structural features that may influence the damaging effects of ground motion. We analyze the full-waveform data collected from a temporary dense array of 72 portable seismometers with a 110 meter spacing that were active for a one-month period from May to June 2017, deployed at Edmond, Oklahoma. The data from this one-month duration array captured over 10,000 events and enabled us to make measurements of small-scale lateral variations of earthquake wavefields. We examine the waveform for events using advanced methods of detection, location and determine the source mechanism. We compare our results with selected events listed in the Oklahoma Geological Survey (OGS) and United States Geological Survey (USGS) catalogue. Based on the detection and located small events, we will discuss the causative fault structure at the area and present the results of the investigation.

DNA methylation Landscape of body size variation in sheep.

PubMed

Cao, Jiaxue; Wei, Caihong; Liu, Dongming; Wang, Huihua; Wu, Mingming; Xie, Zhiyuan; Capellini, Terence D; Zhang, Li; Zhao, Fuping; Li, Li; Zhong, Tao; Wang, Linjie; Lu, Jian; Liu, Ruizao; Zhang, Shifang; Du, Yongfei; Zhang, Hongping; Du, Lixin

2015-10-16

Sub-populations of Chinese Mongolian sheep exhibit significant variance in body mass. In the present study, we sequenced the whole genome DNA methylation in these breeds to detect whether DNA methylation plays a role in determining the body mass of sheep by Methylated DNA immunoprecipitation - sequencing method. A high quality methylation map of Chinese Mongolian sheep was obtained in this study. We identified 399 different methylated regions located in 93 human orthologs, which were previously reported as body size related genes in human genome-wide association studies. We tested three regions in LTBP1, and DNA methylation of two CpG sites showed significant correlation with its RNA expression. Additionally, a particular set of differentially methylated windows enriched in the "development process" (GO: 0032502) was identified as potential candidates for association with body mass variation. Next, we validated small part of these windows in 5 genes; DNA methylation of SMAD1, TSC1 and AKT1 showed significant difference across breeds, and six CpG were significantly correlated with RNA expression. Interestingly, two CpG sites showed significant correlation with TSC1 protein expression. This study provides a thorough understanding of body size variation in sheep from an epigenetic perspective.

On radon emanation as a possible indicator of crustal deformation

USGS Publications Warehouse

King, C.-Y.

1979-01-01

Radon emanation has been monitored in shallow capped holes by a Tracketch method along several active faults and in the vicinity of some volcanoes and underground nuclear explosions. The measured emanation shows large temporal variations that appear to be partly related to crustal strain changes. This paper proposes a model that may explain the observed tectonic variations in radon emanation, and explores the possibility of using radon emanation as an indicator of crustal deformation. In this model the emanation variation is assumed to be due to the perturbation of near-surface profile of radon concentration in the soil gas caused by a change in the vertical flow rate of the soil gas which, in turn, is caused by the crustal deformation. It is shown that, for a typical soil, a small change in the flow rate (3 ?? 10-4 cm sec-1) can effect a significant change (a factor of 2) in radon emanation detected at a fixed shallow depth (0.7 m). The radon concentration profile has been monitored at several depths at a selected site to test the model. The results appear to be in satisfactory agreement. ?? 1979.

Variation in Strategy Use Across Measures of Verbal Working Memory

PubMed Central

Morrison, Alexandra B; Rosenbaum, Gail M.; Fair, Damien; Chein, Jason M.

2016-01-01

The working memory (WM) literature contains a number of tasks that vary on dimensions such as when or how memory items are reported. In addition to the ways in which WM tasks are designed to differ, tasks may also diverge according to the strategies participants use during task performance. The present study included seven tasks from the WM literature, each requiring short-term retention of verbal items. Following completion of a small number of trials from each task, individuals completed a self-report questionnaire to identify their primary strategy. Results indicated substantial variation across individuals for a given task, and within the same individual across tasks. Moreover, while direct comparisons between tasks showed that some tasks evinced similar patterns of strategy use despite differing task demands, others showed markedly different patterns of self-reported strategy use. A community detection algorithm aimed at identifying groups of individuals based on their profile of strategic choices revealed unique communities of individuals who are dependent on specific strategies under varying demands. Together, the findings suggest that researchers using common working memory paradigms should very carefully consider the implications of variation in strategy use when interpreting their findings. PMID:27038310

Genomic signatures of positive selection in humans and the limits of outlier approaches.

PubMed

Kelley, Joanna L; Madeoy, Jennifer; Calhoun, John C; Swanson, Willie; Akey, Joshua M

2006-08-01

Identifying regions of the human genome that have been targets of positive selection will provide important insights into recent human evolutionary history and may facilitate the search for complex disease genes. However, the confounding effects of population demographic history and selection on patterns of genetic variation complicate inferences of selection when a small number of loci are studied. To this end, identifying outlier loci from empirical genome-wide distributions of genetic variation is a promising strategy to detect targets of selection. Here, we evaluate the power and efficiency of a simple outlier approach and describe a genome-wide scan for positive selection using a dense catalog of 1.58 million SNPs that were genotyped in three human populations. In total, we analyzed 14,589 genes, 385 of which possess patterns of genetic variation consistent with the hypothesis of positive selection. Furthermore, several extended genomic regions were found, spanning >500 kb, that contained multiple contiguous candidate selection genes. More generally, these data provide important practical insights into the limits of outlier approaches in genome-wide scans for selection, provide strong candidate selection genes to study in greater detail, and may have important implications for disease related research.

Model-based diagnosis of large diesel engines based on angular speed variations of the crankshaft

NASA Astrophysics Data System (ADS)

Desbazeille, M.; Randall, R. B.; Guillet, F.; El Badaoui, M.; Hoisnard, C.

2010-07-01

This work aims at monitoring large diesel engines by analyzing the crankshaft angular speed variations. It focuses on a powerful 20-cylinder diesel engine with crankshaft natural frequencies within the operating speed range. First, the angular speed variations are modeled at the crankshaft free end. This includes modeling both the crankshaft dynamical behavior and the excitation torques. As the engine is very large, the first crankshaft torsional modes are in the low frequency range. A model with the assumption of a flexible crankshaft is required. The excitation torques depend on the in-cylinder pressure curve. The latter is modeled with a phenomenological model. Mechanical and combustion parameters of the model are optimized with the help of actual data. Then, an automated diagnosis based on an artificially intelligent system is proposed. Neural networks are used for pattern recognition of the angular speed waveforms in normal and faulty conditions. Reference patterns required in the training phase are computed with the model, calibrated using a small number of actual measurements. Promising results are obtained. An experimental fuel leakage fault is successfully diagnosed, including detection and localization of the faulty cylinder, as well as the approximation of the fault severity.

Conservation priorities for endangered Indian tigers through a genomic lens.

PubMed

Natesh, Meghana; Atla, Goutham; Nigam, Parag; Jhala, Yadvendradev V; Zachariah, Arun; Borthakur, Udayan; Ramakrishnan, Uma

2017-08-29

Tigers have lost 93% of their historical range worldwide. India plays a vital role in the conservation of tigers since nearly 60% of all wild tigers are currently found here. However, as protected areas are small (<300 km 2 on average), with only a few individuals in each, many of them may not be independently viable. It is thus important to identify and conserve genetically connected populations, as well as to maintain connectivity within them. We collected samples from wild tigers (Panthera tigris tigris) across India and used genome-wide SNPs to infer genetic connectivity. We genotyped 10,184 SNPs from 38 individuals across 17 protected areas and identified three genetically distinct clusters (corresponding to northwest, southern and central India). The northwest cluster was isolated with low variation and high relatedness. The geographically large central cluster included tigers from central, northeastern and northern India, and had the highest variation. Most genetic diversity (62%) was shared among clusters, while unique variation was highest in the central cluster (8.5%) and lowest in the northwestern one (2%). We did not detect signatures of differential selection or local adaptation. We highlight that the northwest population requires conservation attention to ensure persistence of these tigers.

Visibility vs. biomass in flowers: exploring corolla allocation in Mediterranean entomophilous plants.

PubMed

Herrera, Javier

2009-05-01

While pollinators may in general select for large, morphologically uniform floral phenotypes, drought stress has been proposed as a destabilizing force that may favour small flowers and/or promote floral variation within species. The general validity of this concept was checked by surveying a taxonomically diverse array of 38 insect-pollinated Mediterranean species. The interplay between fresh biomass investment, linear size and percentage corolla allocation was studied. Allometric relationships between traits were investigated by reduced major-axis regression, and qualitative correlates of floral variation explored using general linear-model MANOVA. Across species, flowers were perfectly isometrical with regard to corolla allocation (i.e. larger flowers were just scaled-up versions of smaller ones and vice versa). In contrast, linear size and biomass varied allometrically (i.e. there were shape variations, in addition to variations in size). Most floral variables correlated positively and significantly across species, except corolla allocation, which was largely determined by family membership and floral symmetry. On average, species with bilateral flowers allocated more to the corolla than those with radial flowers. Plant life-form was immaterial to all of the studied traits. Flower linear size variation was in general low among conspecifics (coefficients of variation around 10 %), whereas biomass was in general less uniform (e.g. 200-400 mg in Cistus salvifolius). Significant among-population differences were detected for all major quantitative floral traits. Flower miniaturization can allow an improved use of reproductive resources under prevailingly stressful conditions. The hypothesis that flower size reflects a compromise between pollinator attraction, water requirements and allometric constraints among floral parts is discussed.

Repeatability of Doppler ultrasound measurements of hindlimb blood flow in halothane anaesthetised horses.

PubMed

Raisis, A L; Young, L E; Meire, H; Walsh, K; Taylor, P M; Lekeux, P

2000-05-01

The purpose of this study was to determine the repeatability of femoral blood flow recorded using Doppler ultrasound in anaesthetised horses. Doppler ultrasound of the femoral artery and vein was performed in 6 horses anaesthetised with halothane and positioned in left lateral recumbency. Velocity spectra, recorded using low pulse repetition frequency, were used to calculate time-averaged mean velocity (TAV), velocity of component a (TaVa), velocity of component b (TaVb), volumetric flow, early diastolic deceleration slope (EDDS) and pulsatility index (PI). Within-patient variability was determined for sequential Doppler measurements recorded during a single standardised anaesthetic episode. Within-patient variability was also determined for Doppler and cardiovascular measurements recorded during 4 separate standardised anaesthetic episodes performed at intervals of at least one month. Within-patient variation during a single anaesthetic episode was small. Coefficients of variation (cv) were <12.5% for arterial measurements and <17% for venous measurements. Intraclass correlation coefficient was >0.75 for all measurements. No significant change was observed in measurements of cardiovascular function suggesting that within-patient variation observed during a single anaesthetic episode was due to measurement error. In contrast, within-patient variation during 4 separate anaesthetic episodes was marked (cv>17%) for most Doppler measurements obtained from arteries and veins. Variation in measurements of cardiovascular function were marked (cv>20%), suggesting that there is marked biological variation in central and peripheral observed. Further studies are warranted to determine the ability of this technique to detect differences in blood flow during administration of different anaesthetic agents.

Global and disease-associated genetic variation in the human Fanconi anemia gene family.

PubMed

Rogers, Kai J; Fu, Wenqing; Akey, Joshua M; Monnat, Raymond J

2014-12-20

Fanconi anemia (FA) is a human recessive genetic disease resulting from inactivating mutations in any of 16 FANC (Fanconi) genes. Individuals with FA are at high risk of developmental abnormalities, early bone marrow failure and leukemia. These are followed in the second and subsequent decades by a very high risk of carcinomas of the head and neck and anogenital region, and a small continuing risk of leukemia. In order to characterize base pair-level disease-associated (DA) and population genetic variation in FANC genes and the segregation of this variation in the human population, we identified 2948 unique FANC gene variants including 493 FA DA variants across 57,240 potential base pair variation sites in the 16 FANC genes. We then analyzed the segregation of this variation in the 7578 subjects included in the Exome Sequencing Project (ESP) and the 1000 Genomes Project (1KGP). There was a remarkably high frequency of FA DA variants in ESP/1KGP subjects: at least 1 FA DA variant was identified in 78.5% (5950 of 7578) individuals included in these two studies. Six widely used functional prediction algorithms correctly identified only a third of the known, DA FANC missense variants. We also identified FA DA variants that may be good candidates for different types of mutation-specific therapies. Our results demonstrate the power of direct DNA sequencing to detect, estimate the frequency of and follow the segregation of deleterious genetic variation in human populations. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Regional-Scale Drivers of Forest Structure and Function in Northwestern Amazonia

PubMed Central

Higgins, Mark A.; Asner, Gregory P.; Anderson, Christopher B.; Martin, Roberta E.; Knapp, David E.; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest. PMID:25793602

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

PubMed

Mak, Angel C Y; Lai, Yvonne Y Y; Lam, Ernest T; Kwok, Tsz-Piu; Leung, Alden K Y; Poon, Annie; Mostovoy, Yulia; Hastie, Alex R; Stedman, William; Anantharaman, Thomas; Andrews, Warren; Zhou, Xiang; Pang, Andy W C; Dai, Heng; Chu, Catherine; Lin, Chin; Wu, Jacob J K; Li, Catherine M L; Li, Jing-Woei; Yim, Aldrin K Y; Chan, Saki; Sibert, Justin; Džakula, Željko; Cao, Han; Yiu, Siu-Ming; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan

2016-01-01

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation. Copyright © 2016 by the Genetics Society of America.

Advanced Multilayer Composite Heavy-Oxide Scintillator Detectors for High Efficiency Fast Neutron Detection

NASA Astrophysics Data System (ADS)

Ryzhikov, Vladimir D.; Naydenov, Sergei V.; Pochet, Thierry; Onyshchenko, Gennadiy M.; Piven, Leonid A.; Smith, Craig F.

2018-01-01

We have developed and evaluated a new approach to fast neutron and neutron-gamma detection based on large-area multilayer composite heterogeneous detection media consisting of dispersed granules of small-crystalline scintillators contained in a transparent organic (plastic) matrix. Layers of the composite material are alternated with layers of transparent plastic scintillator material serving as light guides. The resulting detection medium - designated as ZEBRA - serves as both an active neutron converter and a detection scintillator which is designed to detect both neutrons and gamma-quanta. The composite layers of the ZEBRA detector consist of small heavy-oxide scintillators in the form of granules of crystalline BGO, GSO, ZWO, PWO and other materials. We have produced and tested the ZEBRA detector of sizes 100x100x41 mm and greater, and determined that they have very high efficiency of fast neutron detection (up to 49% or greater), comparable to that which can be achieved by large sized heavy-oxide single crystals of about Ø40x80 cm3 volume. We have also studied the sensitivity variation to fast neutron detection by using different types of multilayer ZEBRA detectors of 100 cm2 surface area and 41 mm thickness (with a detector weight of about 1 kg) and found it to be comparable to the sensitivity of a 3He-detector representing a total cross-section of about 2000 cm2 (with a weight of detector, including its plastic moderator, of about 120 kg). The measured count rate in response to a fast neutron source of 252Cf at 2 m for the ZEBRA-GSO detector of size 100x100x41 mm3 was 2.84 cps/ng, and this count rate can be doubled by increasing the detector height (and area) up to 200x100 mm2. In summary, the ZEBRA detectors represent a new type of high efficiency and low cost solid-state neutron detector that can be used for stationary neutron/gamma portals. They may represent an interesting alternative to expensive, bulky gas counters based on 3He or 10B neutron detection technologies.

Vascular Variations Associated with Intracranial Aneurysms.

PubMed

Orakdogen, Metin; Emon, Selin Tural; Somay, Hakan; Engin, Taner; Is, Merih; Hakan, Tayfun

2017-01-01

To investigate the vascular variations in patients with intracranial aneurysm in circle of Willis. We used the data on 128 consecutive intracranial aneurysm cases. Cerebral angiography images were analyzed retrospectively. Arteries were grouped as anterior cerebral arterial system (ACS), posterior cerebral arterial system (PCS) and middle cerebral arterial system (MCS) for grouping vascular variations. Lateralization, being single/multiple, gender; and also any connection with accompanying aneurysms" number, localization, dimension, whether bleeding/incidental aneurysm has been inspected. Variations were demonstrated in 57.8% of the cases. The most common variation was A1 variation (34.4%). The rate of variations was 36.7%, 24.2% and 10.2% respectively in ACS, PCS and MCS. MCS variations were significantly higher in males. Anterior communicating artery (ACoA) aneurysm observance rates were significantly higher and posterior communicating artery (PCoA) aneurysm and middle cerebral artery (MCA) aneurysm observance rates were significantly lower when compared to "no ACS variation detected" cases. In "PCS variation detected" cases, PCoA aneurysm observance rates and coexistence of multiple variations were significantly higher. The rate of vascular variations in patients with aneurysms was 57.8%. Arterial hypoplasia and aplasia were the most common variations. ACS was the most common region that variations were located in; they were mostly detected on the right side. Coexistence of ACoA aneurysm was higher than PCoA and MCA aneurysms. In the PCS variations group, PCoA aneurysms were the most common aneurysms that accompanying the variation and multiple variations were more common than in the other two groups. The variations in MCS were most common in males.

The frequency of Th17 cells in the small intestine exhibits a day-night variation dependent on circadian clock activity.

PubMed

Thu Le, Ha Pham; Nakamura, Yuki; Oh-Oka, Kyoko; Ishimaru, Kayoko; Nakajima, Shotaro; Nakao, Atsuhito

2017-08-19

Interleukin-17-producing CD4 + T helper (Th17) cells are a key immune lineage that protects against bacterial and fungal infections at mucosal surfaces. At steady state, Th17 cells are abundant in the small intestinal mucosa of mice. There are several mechanisms for regulating the population of Th17 cells in the small intestine, reflecting the importance of maintaining their numbers in the correct balance. Here we demonstrate the existence of a time-of-day-dependent variation in the frequency of Th17 cells in the lamina propria of the small intestine in wild-type mice, which was not observed in mice with a loss-of-function mutation of the core circadian gene Clock or in mice housed under aberrant light/dark conditions. Consistent with this, expression of CCL20, a chemokine that regulates homeostatic trafficking of Th17 cells to the small intestine, exhibited circadian rhythms in the small intestine of wild-type, but not Clock-mutated, mice. In support of these observations, the magnitude of ovalbumin (OVA)-specific antibody and T-cell responses in mice sensitized with OVA plus cholera toxin, a mucosal Th17 cell-dependent adjuvant, was correlated with daily variations in the proportion of Th17 cells in the small intestine. These results suggest that the proportion of Th17 cells in the small intestine exhibits a day-night variation in association with CCL20 expression, which depends on circadian clock activity. The findings provide novel insight into the regulation of the Th17 cell population in the small intestine at steady state, which may have translational potential for mucosal vaccination strategies. Copyright © 2017 Elsevier Inc. All rights reserved.

Herbicide and nitrate distribution in central Iowa rainfall

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

Hatfield, J.L.; Prueger, J.H.; Pfeiffer, R.L.

Herbicides are detected in rainfall; however, these are a small fraction of the total applied. This study was designed to evaluate monthly and annual variation in atrazine (6-chloro-N-ethyl-N{prime}-(1-methylethyl)-1,3,5-triazine-2,4-diamine), alachlor (2-chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl)acetamide), metolachlor (2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-1-methylethyl)acetamide), and NO{sub 3}-N concentrations in rainfall over Walnut Creek watershed south of Ames, IA. The study began in 1991 and continued through 1994. Within the watershed, two wet/dry precipitation samplers were positioned 4 km apart. Detections varied during the year with >90% of the herbicide detections occurring in April through early July. Concentrations varied among events from nondetectable amounts to concentrations of 154 {mu}g L{sup {minus}1}, which occurredmore » when atrazine was applied during an extremely humid day immediately followed by rainfall of <10 mm that washed spray drift from the atmosphere. This was a local scale phenomenon, because the other collector had a more typical concentration of 1.7 {mu}g L{sup {minus}1} with an 8-mm rainfall. VAriation between the two collectors suggests that local scale meteorological processes affect herbicide movement. Yearly atrazine deposition totals were >100 {mu}g m{sup {minus}2} representing <0.1% of the amount applied. Nitrate-N concentrations in precipitation were uniformly distributed throughout the year and without annual variation in the concentrations. Deposition rates of NO{sub 3}-N were about 1.2 g m{sup {minus}2}. Annual loading onto the watershed was about 25% of the amount applied from all forms of N fertilizers. Movement and rates of deposition provide an understanding of the processes and magnitude of the impact of agriculture on the environment. 7 refs., 5 figs., 3 tabs.« less

An Instantaneous Low-Cost Point-of-Care Anemia Detection Device

PubMed Central

Punter-Villagrasa, Jaime; Cid, Joan; Páez-Avilés, Cristina; Rodríguez-Villarreal, Ivón; Juanola-Feliu, Esteve; Colomer-Farrarons, Jordi; Miribel-Català, Pere Ll.

2015-01-01

We present a small, compact and portable device for point-of-care instantaneous early detection of anemia. The method used is based on direct hematocrit measurement from whole blood samples by means of impedance analysis. This device consists of a custom electronic instrumentation and a plug-and-play disposable sensor. The designed electronics rely on straightforward standards for low power consumption, resulting in a robust and low consumption device making it completely mobile with a long battery life. Another approach could be powering the system based on other solutions like indoor solar cells, or applying energy-harvesting solutions in order to remove the batteries. The sensing system is based on a disposable low-cost label-free three gold electrode commercial sensor for 50 μL blood samples. The device capability for anemia detection has been validated through 24 blood samples, obtained from four hospitalized patients at Hospital Clínic. As a result, the response, effectiveness and robustness of the portable point-of-care device to detect anemia has been proved with an accuracy error of 2.83% and a mean coefficient of variation of 2.57% without any particular case above 5%. PMID:25690552

A novel method for detecting neutralizing antibodies against therapeutic proteins by measuring gene expression.

PubMed

Yu, Yanbin; Piddington, Christopher; Fitzpatrick, Dan; Twomey, Brian; Xu, Ren; Swanson, Steven J; Jing, Shuqian

2006-10-20

The presence of neutralizing antibodies against protein therapeutics is a concern in the biomedical field. Such antibodies not only reduce the efficacy of protein therapeutics, but also impose potential dangers to the patients receiving them. To date, a small number of in vitro cell-based bioassays for detecting neutralizing antibodies against therapeutic proteins have been developed. Most of the existing assays, however, either involve the use of radioactive materials or have limited sensitivities and/or poor specificities. With advances in mRNA profiling and detection techniques, we have established a novel and non-radioactive bioassay system using branched DNA (bDNA) technology for detecting protein-therapeutic neutralizing antibodies in patient serum. Our assay measures the variations of target gene expression that reflect the biologic effect of the therapeutic agent and the capability of the antibodies, if present, to neutralize the therapeutics. Compared with most existing assays, the new assay is more sensitive and specific, and completely eliminates the use of radioactive materials. Application of the new assay system can be widely expanded if new target genes and responding cell lines for other therapeutics are identified or engineered.

Development and validation of a real-time PCR assay for the detection of Toxoplasma gondii DNA in animal and meat samples.

PubMed

Marino, Anna Maria Fausta; Percipalle, Maurizio; Giunta, Renato Paolo; Salvaggio, Antonio; Caracappa, Giulia; Alfonzetti, Tiziana; Aparo, Alessandra; Reale, Stefano

2017-03-01

We report a rapid and reliable method for the detection of Toxoplasma gondii in meat and animal tissues based on real-time polymerase chain reaction (PCR). Samples were collected from cattle, small ruminants, horses, and pigs raised or imported into Sicily, Italy. All DNA preparations were assayed by real-time PCR tests targeted to a 98-bp long fragment in the AF 529-bp repeat element and to the B1 gene using specific primers. Diagnostic sensitivity (100%), diagnostic specificity (100%), limit of detection (0.01 pg), efficiency (92-109%), and precision (mean coefficient of variation = 0.60%), repeatability (100%), reproducibility (100%), and robustness were evaluated using 240 DNA extracted samples (120 positives and 120 negative as per the OIE nested PCR method) from different matrices. Positive results were confirmed by the repetition of both real-time and nested PCR assays. Our study demonstrates the viability of a reliable, rapid, and specific real-time PCR on a large scale to monitor contamination with Toxoplasma cysts in meat and animal specimens. This validated method can be used for postmortem detection in domestic and wild animals and for food safety purposes.

The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation

PubMed Central

Valsesia, Armand; Macé, Aurélien; Jacquemont, Sébastien; Beckmann, Jacques S.; Kutalik, Zoltán

2013-01-01

Differences between genomes can be due to single nucleotide variants, translocations, inversions, and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 500 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease. Hence there is a need for better-tailored and more robust tools for the detection and genome-wide analyses of CNVs. While a link between a given CNV and a disease may have often been established, the relative CNV contribution to disease progression and impact on drug response is not necessarily understood. In this review we discuss the progress, challenges, and limitations that occur at different stages of CNV analysis from the detection (using DNA microarrays and next-generation sequencing) and identification of recurrent CNVs to the association with phenotypes. We emphasize the importance of germline CNVs and propose strategies to aid clinicians to better interpret structural variations and assess their clinical implications. PMID:23750167

Colour based fire detection method with temporal intensity variation filtration

NASA Astrophysics Data System (ADS)

Trambitckii, K.; Anding, K.; Musalimov, V.; Linß, G.

2015-02-01

Development of video, computing technologies and computer vision gives a possibility of automatic fire detection on video information. Under that project different algorithms was implemented to find more efficient way of fire detection. In that article colour based fire detection algorithm is described. But it is not enough to use only colour information to detect fire properly. The main reason of this is that in the shooting conditions may be a lot of things having colour similar to fire. A temporary intensity variation of pixels is used to separate them from the fire. These variations are averaged over the series of several frames. This algorithm shows robust work and was realised as a computer program by using of the OpenCV library.

Transit Timing Observations from Kepler. IX. Catalog of the Full Long-cadence Data Set

NASA Astrophysics Data System (ADS)

Holczer, Tomer; Mazeh, Tsevi; Nachmani, Gil; Jontof-Hutter, Daniel; Ford, Eric B.; Fabrycky, Daniel; Ragozzine, Darin; Kane, Mackenzie; Steffen, Jason H.

2016-07-01

We present a new transit timing catalog of 2599 Kepler Objects of Interest (KOIs), using the PDC-MAP long-cadence light curves that include the full 17 quarters of the mission (ftp://wise-ftp.tau.ac.il/pub/tauttv/TTV/ver_112). The goal is to produce an easy-to-use catalog that can stimulate further analyses of interesting systems. For 779 KOIs with high enough S/N, we derived the timing, duration, and depth of 69,914 transits. For 1820 KOIs with lower SNR, we derived only the timing of 225,273 transits. After removal of outlier timings, we derived various statistics for each KOI that were used to indicate significant variations. Including systems found by previous works, we have detected 260 KOIs that showed significant TTVs with long-term variations (>100 days), and another 14 KOIs with periodic modulations shorter than 100 days and small amplitudes. For five of those, the periodicity is probably due to the crossing of rotating stellar spots by the transiting planets.

Hydrolyzable Tannins, Flavonol Glycosides, and Phenolic Acids Show Seasonal and Ontogenic Variation in Geranium sylvaticum.

PubMed

Tuominen, Anu; Salminen, Juha-Pekka

2017-08-09

The seasonal variation of polyphenols in the aboveground organs and roots of Geranium sylvaticum in four populations was studied using UPLC-DAD-ESI-QqQ-MS/MS. The content of the main compound, geraniin, was highest (16% of dry weight) in the basal leaves after the flowering period but stayed rather constant throughout the growing season. Compound-specific mass spectrometric methods revealed the different seasonal patterns in minor polyphenols. Maximum contents of galloylglucoses and flavonol glycosides were detected in the small leaves in May, whereas the contents of further modified ellagitannins, such as ascorgeraniin and chebulagic acid, increased during the growing season. In flower organs, the polyphenol contents differed significantly between ontogenic phases so that maximum amounts were typically found in the bud phase, except in pistils the amount of gallotannins increased significantly in the fruit phase. These results can be used in evaluating the role of polyphenols in plant-herbivore interactions or in planning the best collection times of G. sylvaticum for compound isolation purposes.

Nondestructive ultrasonic measurement of bolt preload using the pulsed-phase locked-loop interferometer

NASA Technical Reports Server (NTRS)

Allison, S. G.; Heyman, J. S.

1985-01-01

Achieving accurate preload in threaded fasteners is an important and often critical problem which is encountered in nearly all sectors of government and industry. Conventional tensioning methods which rely on torque carry with them the disadvantage of requiring constant friction in the fastener in order to accurately correlate torque to preload. Since most of the applied torque typically overcomes friction rather than tensioning the fastener, small variations in friction can cause large variations in preload. An instrument called a pulsed phase locked loop interferometer, which was recently developed at NASA Langley, has found widespread use for measurement of stress as well as material properties. When used to measure bolt preload, this system detects changes in the fastener length and sound velocity which are independent of friction. The system is therefore capable of accurately establishing the correct change in bolt tension. This high resolution instrument has been used for precision measurement of preload in critical fasteners for numerous applications such as the space shuttle landing gear and helicopter main rotors.

Solar Cycle Fine Structure and Surface Rotation from Ca II K-Line Time Series Data

NASA Technical Reports Server (NTRS)

Scargle, Jeff; Keil, Steve; Worden, Pete

2011-01-01

Analysis of three and a half decades of data from the NSO/AFRL/Sac Peak K-line monitoring program yields evidence for four components to the variation: (a) the solar cycle, with considerable fine structure and a quasi-periodicity of 122.4 days; (b) a stochastic process, faster than (a) and largely independent of it, (c) a quasi-periodic signal due to rotational modulation, and of course (d) observational errors (shown to be quite small). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these chromospheric parameters. Time-frequency analysis is especially useful for extracting information about differential rotation, and in particular elucidates the connection between its behavior and fine structure of the solar cycle on approximately one-year time scales. These results further suggest that similar analyses will be useful at detecting and characterizing differential rotation in stars from stellar light-curves such as those being produced at NASA's Kepler observatory.

Pesticide transport in the San Joaquin River Basin

USGS Publications Warehouse

Dubrovsky, N.M.; Kratzer, C.R.; Panshin, S.Y.; Gronberg, J.A.M.; Kuivila, K.M.

2000-01-01

Pesticide occurrence and concentrations were evaluated in the San Joaquin River Basin to determine potential sources and mode of transport. Land use in the basin is mainly agricultural. Spatial variations in pesticide occurrence were evaluated in relation to pesticide application and cropping patterns in three contrasting subbasins and at the mouth of the basin. Temporal variability in pesticide occurrence was evaluated by fixed interval sampling and by sampling across the Hydrograph during winter storms. Four herbicides (simazine, metolachlor, dacthal, and EPTC) and two insecticides (diazinon and chlorpyrifos) were detected in more than 50 percent of the samples. Temporal, and to a lesser extent spatial, variation in pesticide occurrence is usually consistent with pesticide application and cropping patterns. Diazinon concentrations changed rapidly during winter storms, and both eastern and western tributaries contributed diazinon to the San Joaquin River at concentrations toxic to the water flea Ceriodaphnia dubia at different times during the hydrograph. During these storms, toxic concentrations resulted from the transport of only a very small portion of the applied diazinon.

Detection of Subtle Hydromechanical Medium Changes Caused By a Small-Magnitude Earthquake Swarm in NE Brazil

NASA Astrophysics Data System (ADS)

D'Hour, V.; Schimmel, M.; Do Nascimento, A. F.; Ferreira, J. M.; Lima Neto, H. C.

2016-04-01

Ambient noise correlation analyses are largely used in seismology to map heterogeneities and to monitor the temporal evolution of seismic velocity changes associated mostly with stress field variations and/or fluid movements. Here we analyse a small earthquake swarm related to a main mR 3.7 intraplate earthquake in North-East of Brazil to study the corresponding post-seismic effects on the medium. So far, post-seismic effects have been observed mainly for large magnitude events. In our study, we show that we were able to detect localized structural changes even for a small earthquake swarm in an intraplate setting. Different correlation strategies are presented and their performances are also shown. We compare the classical auto-correlation with and without pre-processing, including 1-bit normalization and spectral whitening, and the phase auto-correlation. The worst results were obtained for the pre-processed data due to the loss of waveform details. The best results were achieved with the phase cross-correlation which is amplitude unbiased and sensitive to small amplitude changes as long as there exist waveform coherence superior to other unrelated signals and noise. The analysis of 6 months of data using phase auto-correlation and cross-correlation resulted in the observation of a progressive medium change after the major recorded event. The progressive medium change is likely related to the swarm activity through opening new path ways for pore fluid diffusion. We further observed for the auto-correlations a lag time frequency-dependent change which likely indicates that the medium change is localized in depth. As expected, the main change is observed along the fault.

Multimodal MRI in cerebral small vessel disease: its relationship with cognition and sensitivity to change over time.

PubMed

Nitkunan, Arani; Barrick, Tom R; Charlton, Rebecca A; Clark, Chris A; Markus, Hugh S

2008-07-01

Cerebral small vessel disease is the most common cause of vascular dementia. Interest in using MRI parameters as surrogate markers of disease to assess therapies is increasing. In patients with symptomatic sporadic small vessel disease, we determined which MRI parameters best correlated with cognitive function on cross-sectional analysis and which changed over a period of 1 year. Thirty-five patients with lacunar stroke and leukoaraiosis were recruited. They underwent multimodal MRI (brain volume, fluid-attenuated inversion recovery lesion load, lacunar infarct number, fractional anisotropy, and mean diffusivity from diffusion tensor imaging) and neuropsychological testing. Twenty-seven agreed to reattend for repeat MRI and neuropsychology at 1 year. An executive function score correlated most strongly with diffusion tensor imaging (fractional anisotropy histogram, r=-0.640, P=0.004) and brain volume (r=0.501, P=0.034). Associations with diffusion tensor imaging were stronger than with all other MRI parameters. On multiple regression of all imaging parameters, a model that contained brain volume and fractional anisotropy, together with age, gender, and premorbid IQ, explained 74% of the variance of the executive function score (P=0.0001). Changes in mean diffusivity and fractional anisotropy were detectable over the 1-year follow-up; in contrast, no change in other MRI parameters was detectable over this time period. A multimodal MRI model explains a large proportion of the variation in executive function in cerebral small vessel disease. In particular, diffusion tensor imaging correlates best with executive function and is the most sensitive to change. This supports the use of MRI, in particular diffusion tensor imaging, as a surrogate marker in treatment trials.

Female fecundity variation affects reproducibility of experiments on host plant preference and acceptance in a phytophagous insect

PubMed Central

Schäpers, Alexander; Petrén, Hampus; Wheat, Christopher W.; Wiklund, Christer

2017-01-01

Reproducibility is a scientific cornerstone. Many recent studies, however, describe a reproducibility crisis and call for assessments of reproducibility across scientific domains. Here, we explore the reproducibility of a classic ecological experiment—that of assessing female host plant preference and acceptance in phytophagous insects, a group in which host specialization is a key driver of diversification. We exposed multiple cohorts of Pieris napi butterflies from the same population to traditional host acceptance and preference tests on three Brassicaceae host species. Whereas the host plant rank order was highly reproducible, the propensity to oviposit on low-ranked hosts varied significantly even among cohorts exposed to similar conditions. Much variation could be attributed to among-cohort variation in female fecundity, a trait strongly correlated both to female size and to the size of the nuptial gift a female receives during mating. Small males provide small spermatophores, and in our experiment small females that mated with small males had a disproportionally low propensity to oviposit on low-ranked hosts. Hence, our results provide empirical support to the theoretical prediction that female host utilization is strongly affected by non-genetic, environmental variation, and that such variation can affect the reproducibility of ecological experiments even under seemingly identical conditions. PMID:28202813

Further analysis of clinical feasibility of OCT-based glaucoma diagnosis with Pigment epithelium central limit- Inner limit of the retina Minimal Distance (PIMD)

NASA Astrophysics Data System (ADS)

Söderberg, Per G.; Malmberg, Filip; Sandberg-Melin, Camilla

2017-02-01

The present study aimed to elucidate if comparison of angular segments of Pigment epithelium central limit- Inner limit of the retina Minimal Distance, measured over 2π radians in the frontal plane (PIMD-2π) between visits of a patient, renders sufficient precision for detection of loss of nerve fibers in the optic nerve head. An optic nerve head raster scanned cube was captured with a TOPCON 3D OCT 2000 (Topcon, Japan) device in one early to moderate stage glaucoma eye of each of 13 patients. All eyes were recorded at two visits less than 1 month apart. At each visit, 3 volumes were captured. Each volume was extracted from the OCT device for analysis. Then, angular PIMD was segmented three times over 2π radians in the frontal plane, resolved with a semi-automatic algorithm in 500 equally separated steps, PIMD-2π. It was found that individual segmentations within volumes, within visits, within subjects can be phase adjusted to each other in the frontal plane using cross-correlation. Cross correlation was also used to phase adjust volumes within visits within subjects and visits to each other within subjects. Then, PIMD-2π for each subject was split into 250 bundles of 2 adjacent PIMDs. Finally, the sources of variation for estimates of segments of PIMD-2π were derived with analysis of variance assuming a mixed model. The variation among adjacent PIMDS was found very small in relation to the variation among segmentations. The variation among visits was found insignificant in relation to the variation among volumes and the variance for segmentations was found to be on the order of 20 % of that for volumes. The estimated variances imply that, if 3 segmentations are averaged within a volume and at least 10 volumes are averaged within a visit, it is possible to estimate around a 10 % reduction of a PIMD-2π segment from baseline to a subsequent visit as significant. Considering a loss rate for a PIMD-2π segment of 23 μm/yr., 4 visits per year, and averaging 3 segmentations per volume and 3 volumes per visit, a significant reduction from baseline can be detected with a power of 80 % in about 18 months. At higher loss rate for a PIMD-2π segment, a significant difference from baseline can be detected earlier. Averaging over more volumes per visit considerably decreases the time for detection of a significant reduction of a segment of PIMD-2π. Increasing the number of segmentations averaged per visit only slightly reduces the time for detection of a significant reduction. It is concluded that phase adjustment in the frontal plane with cross correlation allows high precision estimates of a segment of PIMD-2π that imply substantially shorter followup time for detection of a significant change than mean deviation (MD) in a visual field estimated with the Humphrey perimeter or neural rim area (NRA) estimated with the Heidelberg retinal tomograph.

Estimating abundance while accounting for rarity, correlated behavior, and other sources of variation in counts

USGS Publications Warehouse

Dorazio, Robert M.; Martin, Juulien; Edwards, Holly H.

2013-01-01

The class of N-mixture models allows abundance to be estimated from repeated, point count surveys while adjusting for imperfect detection of individuals. We developed an extension of N-mixture models to account for two commonly observed phenomena in point count surveys: rarity and lack of independence induced by unmeasurable sources of variation in the detectability of individuals. Rarity increases the number of locations with zero detections in excess of those expected under simple models of abundance (e.g., Poisson or negative binomial). Correlated behavior of individuals and other phenomena, though difficult to measure, increases the variation in detection probabilities among surveys. Our extension of N-mixture models includes a hurdle model of abundance and a beta-binomial model of detectability that accounts for additional (extra-binomial) sources of variation in detections among surveys. As an illustration, we fit this model to repeated point counts of the West Indian manatee, which was observed in a pilot study using aerial surveys. Our extension of N-mixture models provides increased flexibility. The effects of different sets of covariates may be estimated for the probability of occurrence of a species, for its mean abundance at occupied locations, and for its detectability.

Estimating abundance while accounting for rarity, correlated behavior, and other sources of variation in counts.

PubMed

Dorazio, Robert M; Martin, Julien; Edwards, Holly H

2013-07-01

The class of N-mixture models allows abundance to be estimated from repeated, point count surveys while adjusting for imperfect detection of individuals. We developed an extension of N-mixture models to account for two commonly observed phenomena in point count surveys: rarity and lack of independence induced by unmeasurable sources of variation in the detectability of individuals. Rarity increases the number of locations with zero detections in excess of those expected under simple models of abundance (e.g., Poisson or negative binomial). Correlated behavior of individuals and other phenomena, though difficult to measure, increases the variation in detection probabilities among surveys. Our extension of N-mixture models includes a hurdle model of abundance and a beta-binomial model of detectability that accounts for additional (extra-binomial) sources of variation in detections among surveys. As an illustration, we fit this model to repeated point counts of the West Indian manatee, which was observed in a pilot study using aerial surveys. Our extension of N-mixture models provides increased flexibility. The effects of different sets of covariates may be estimated for the probability of occurrence of a species, for its mean abundance at occupied locations, and for its detectability.

Use of next-generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia[S

PubMed Central

Iacocca, Michael A.; Wang, Jian; Dron, Jacqueline S.; Robinson, John F.; McIntyre, Adam D.; Cao, Henian

2017-01-01

Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene (LDLR). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories. PMID:28874442

Vibration-based damage detection in a concrete beam under temperature variations using AR models and state-space approaches

NASA Astrophysics Data System (ADS)

Clément, A.; Laurens, S.

2011-07-01

The Structural Health Monitoring of civil structures subjected to ambient vibrations is very challenging. Indeed, the variations of environmental conditions and the difficulty to characterize the excitation make the damage detection a hard task. Auto-regressive (AR) models coefficients are often used as damage sensitive feature. The presented work proposes a comparison of the AR approach with a state-space feature formed by the Jacobian matrix of the dynamical process. Since the detection of damage can be formulated as a novelty detection problem, Mahalanobis distance is applied to track new points from an undamaged reference collection of feature vectors. Data from a concrete beam subjected to temperature variations and damaged by several static loading are analyzed. It is observed that the damage sensitive features are effectively sensitive to temperature variations. However, the use of the Mahalanobis distance makes possible the detection of cracking with both of them. Early damage (before cracking) is only revealed by the AR coefficients with a good sensibility.

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

PubMed

Xie, Chao; Tammi, Martti T

2009-03-06

DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Simulation of various sequencing methods with coverage between 0.1x to 8x show overall specificity between 91.7 - 99.9%, and sensitivity between 72.2 - 96.5%. We also show the results for assessment of CNV between two individual human genomes.

Temporal variation of phytoplankton in a small tropical crater lake, Costa Rica.

PubMed

Umaña-Villalobos, Gerardo

2010-12-01

The temporal variation in lake's phytoplankton is important to understand its general biodiversity. For tropical lakes, it has been hypothesized that they follow a similar pattern as temperate ones, on a much accelerated pace; nevertheless, few case studies have tried to elucidate this. Most studies in Costa Rica have used a monthly sampling scheme and failed in showing the expected changes. In this study, the phytoplankton of the small Barvas's crater lake was followed for more than three years, first with monthly and later with weekly samplings, that covered almost two years. Additional information on temperature and oxygen vertical profiles was obtained on a monthly basis, and surface temperature was measured during weekly samplings around noon. Results showed that in spite of its shallow condition (max. depth: 7m) and low surface temperature (11 to 19 degrees C), the lake stratifies at least for brief periods. The phytoplankton showed both, rapid change periods, and prolonged ones of relative stasis. The plankton composition fluctuated between three main phases, one characterized by the abundance of small sized desmids (Staurastrum paradoxum, Cosmarium asphaerosporum), a second phase dominated by equally small cryptomonads (Chryptochrysis minor, Chroomonas sp.) and a third phase dominated by the green alga Eutetramorus tetrasporus. Although data evidenced that monthly sampling could miss short term events, the temporal variation did not follow the typical dry and rainy seasons of the region, or any particular annual pattern. Year to year variation was high. As this small lake is located at the summit of Barva Volcano and receives the influence from both the Caribbean and the Pacific weather, seasonality at the lake is not clearly defined as in the rest of the country and short term variations in the local weather might have a stronger effect than broad seasonal trends. The occurrence of this short term changes in the phytoplankton of small tropical lakes in response to weather variations needs to be further explored in other lakes.

A parallel spatiotemporal saliency and discriminative online learning method for visual target tracking in aerial videos.

PubMed

Aghamohammadi, Amirhossein; Ang, Mei Choo; A Sundararajan, Elankovan; Weng, Ng Kok; Mogharrebi, Marzieh; Banihashem, Seyed Yashar

2018-01-01

Visual tracking in aerial videos is a challenging task in computer vision and remote sensing technologies due to appearance variation difficulties. Appearance variations are caused by camera and target motion, low resolution noisy images, scale changes, and pose variations. Various approaches have been proposed to deal with appearance variation difficulties in aerial videos, and amongst these methods, the spatiotemporal saliency detection approach reported promising results in the context of moving target detection. However, it is not accurate for moving target detection when visual tracking is performed under appearance variations. In this study, a visual tracking method is proposed based on spatiotemporal saliency and discriminative online learning methods to deal with appearance variations difficulties. Temporal saliency is used to represent moving target regions, and it was extracted based on the frame difference with Sauvola local adaptive thresholding algorithms. The spatial saliency is used to represent the target appearance details in candidate moving regions. SLIC superpixel segmentation, color, and moment features can be used to compute feature uniqueness and spatial compactness of saliency measurements to detect spatial saliency. It is a time consuming process, which prompted the development of a parallel algorithm to optimize and distribute the saliency detection processes that are loaded into the multi-processors. Spatiotemporal saliency is then obtained by combining the temporal and spatial saliencies to represent moving targets. Finally, a discriminative online learning algorithm was applied to generate a sample model based on spatiotemporal saliency. This sample model is then incrementally updated to detect the target in appearance variation conditions. Experiments conducted on the VIVID dataset demonstrated that the proposed visual tracking method is effective and is computationally efficient compared to state-of-the-art methods.

A parallel spatiotemporal saliency and discriminative online learning method for visual target tracking in aerial videos

PubMed Central

2018-01-01

Visual tracking in aerial videos is a challenging task in computer vision and remote sensing technologies due to appearance variation difficulties. Appearance variations are caused by camera and target motion, low resolution noisy images, scale changes, and pose variations. Various approaches have been proposed to deal with appearance variation difficulties in aerial videos, and amongst these methods, the spatiotemporal saliency detection approach reported promising results in the context of moving target detection. However, it is not accurate for moving target detection when visual tracking is performed under appearance variations. In this study, a visual tracking method is proposed based on spatiotemporal saliency and discriminative online learning methods to deal with appearance variations difficulties. Temporal saliency is used to represent moving target regions, and it was extracted based on the frame difference with Sauvola local adaptive thresholding algorithms. The spatial saliency is used to represent the target appearance details in candidate moving regions. SLIC superpixel segmentation, color, and moment features can be used to compute feature uniqueness and spatial compactness of saliency measurements to detect spatial saliency. It is a time consuming process, which prompted the development of a parallel algorithm to optimize and distribute the saliency detection processes that are loaded into the multi-processors. Spatiotemporal saliency is then obtained by combining the temporal and spatial saliencies to represent moving targets. Finally, a discriminative online learning algorithm was applied to generate a sample model based on spatiotemporal saliency. This sample model is then incrementally updated to detect the target in appearance variation conditions. Experiments conducted on the VIVID dataset demonstrated that the proposed visual tracking method is effective and is computationally efficient compared to state-of-the-art methods. PMID:29438421

The 2006-2007 Observing Campaign On VX Hydrae

NASA Astrophysics Data System (ADS)

Templeton, Matthew R.; Samolyk, G.; Dvorak, S.; Poklar, R.; Butterworth, N.; Gerner, H. S.

2009-12-01

We present the results of the 2006-2007 observing campaign on the double-mode delta Scuti star VX Hydrae. Nearly 8800 V-band CCD observations were obtained during the two observing seasons. Although the data were taken with small telescopes (0.3-m or less, using consumer-grade CCD cameras), the data quality is very high, enabling the detection of variability at the millimagnitude level at some frequencies. Analysis of the data yields only two primary pulsation frequencies: f(0) = 4.4765 c/d, and f(1) = 5.7899 c/d. The two modes have comparable amplitude, although the amplitude of f(1) appears to have increased slightly from 2006 to 2007 by 0.01 mag. Only two pulsation modes are detected, but at least 18 additional linear combination frequencies are also clearly detected, some having amplitudes as low as 1 mmag, resulting in an incredibly rich Fourier spectrum. We discuss the evidence for amplitude variation in VX Hydrae, along with prospects for future study of this and other similar delta Scuti stars by AAVSO observers.

Metastatic Blue Nevus-Like Melanoma Detected by Liquid-Based Catheterized Urine Cytology.

PubMed

Kim, Sue Kyung; Yang, Ji Young; Han, Jae Ho; Kwon, Ji Eun

2018-06-01

Primary or metastatic malignant melanoma can mimic benign blue nevus in rare cases, making the diagnosis challenging. Herein, we report an exceptionally rare case of blue nevus-like melanoma and its blue nevus-like metastasis which was detected by catheterized urine cytology. The patient presented with blue-colored papuloplaques on his temple which were diagnosed as blue nevus-like melanoma on punch biopsies. While he was admitted for administration of chemotherapy, hematuria was detected. Catheterized urine cytology revealed singly scattered oval to spindle-shaped pigmented cells with a moderate degree of variation in shape and size. Many of them had small nuclei with indiscernible to inconspicuous nucleoli while only a few cells showed nuclear enlargement and nuclear hyperchromasia, which could be diagnostic pitfalls. Most of the cells on the smear were positive for HMB45 immunostaining, which confirmed the diagnosis of metastatic blue nevus-like melanoma. To the best of our knowledge, the present case is the first report describing cytomorphologic findings of blue nevus-like metastasis of melanoma in the urine specimen.

Detection of concealed explosives at stand-off distances using wide band swept millimetre waves

NASA Astrophysics Data System (ADS)

Andrews, David A.; Rezgui, Nacer D.; Smith, Sarah E.; Bowring, Nicholas; Southgate, Matthew; Baker, John G.

2008-10-01

Millimetre waves in the range 20 to 110 GHz have been used to detect the presence and thickness of dielectric materials, such as explosives, by measuring the frequency response of the return signal. Interference between the reflected signals from the front and back surfaces of the dielectric provides a characteristic frequency variation in the return signal, which may be processed to yield its optical depth [Bowring et al, Meas. Sci. Technol. 19, 024004 (2008)]. The depth resolution depends on the sweep bandwidth, which is typically 10 to 30 GHz. By using super-heterodyne detection the range of the object can also be determined, which enables a signal from a target, such as a suicide bomber to be extracted from background clutter. Using millimetre wave optics only a small area of the target is illuminated at a time, thus reducing interference from different parts of a human target. Results are presented for simulated explosive materials with water or human backing at stand-off distances. A method of data analysis that involves pattern recognition enables effective differentiation of target types.

Variation of a Lightning NOx Indicator for National Climate Assessment

NASA Technical Reports Server (NTRS)

Koshak, W. J.; Vant-Hull, B.; McCaul, E. W.; Peterson, H. S.

2014-01-01

In support of the National Climate Assessment (NCA) program, satellite Lightning Imaging Sensor (LIS) data is used to estimate lightning nitrogen oxides (LNOx) production over the southern portion of the conterminous US. The total energy of each flash is estimated by analyzing the LIS optical event data associated with each flash (i.e., event radiance, event footprint area, and derivable event range). The LIS detects an extremely small fraction of the total flash energy; this fraction is assumed to be constant apart from the variability associated with the flash optical energy detected across the narrow (0.909 nm) LIS band. The estimate of total energy from each flash is converted to moles of LNOx production by assuming a chemical yield of 10(17) molecules Joule(-1). The LIS-inferred variable LNOx production from each flash is summed to obtain total LNOx production, and then appropriately enhanced to account for LIS detection efficiency and LIS view time. Annual geographical plots and time series of LNOx production are provided for a 16 year period (1998-2013).

Capacitive Pressure Sensor with High Sensitivity and Fast Response to Dynamic Interaction Based on Graphene and Porous Nylon Networks.

PubMed

He, Zhongfu; Chen, Wenjun; Liang, Binghao; Liu, Changyong; Yang, Leilei; Lu, Dongwei; Mo, Zichao; Zhu, Hai; Tang, Zikang; Gui, Xuchun

2018-04-18

Flexible pressure sensors are of great importance to be applied in artificial intelligence and wearable electronics. However, assembling a simple structure, high-performance capacitive pressure sensor, especially for monitoring the flow of liquids, is still a big challenge. Here, on the basis of a sandwich-like structure, we propose a facile capacitive pressure sensor optimized by a flexible, low-cost nylon netting, showing many merits including a high response sensitivity (0.33 kPa -1 ) in a low-pressure regime (<1 kPa), an ultralow detection limit as 3.3 Pa, excellent working stability after more than 1000 cycles, and synchronous monitoring for human pulses and clicks. More important, this sensor exhibits an ultrafast response speed (<20 ms), which enables its detection for the fast variations of a small applied pressure from the morphological changing processes of a droplet falling onto the sensor. Furthermore, a capacitive pressure sensor array is fabricated for demonstrating the ability to spatial pressure distribution. Our developed pressure sensors show great prospects in practical applications such as health monitoring, flexible tactile devices, and motion detection.

Geographical Variation in Diabetes Prevalence and Detection in China: Multilevel Spatial Analysis of 98,058 Adults

PubMed Central

Zhou, Maigeng; Astell-Burt, Thomas; Bi, Yufang; Feng, Xiaoqi; Jiang, Yong; Li, Yichong; Page, Andrew; Wang, Limin; Xu, Yu

2015-01-01

OBJECTIVE To investigate the geographic variation in diabetes prevalence and detection in China. RESEARCH DESIGN AND METHODS Self-report and biomedical data were collected from 98,058 adults aged ≥18 years (90.5% response) from 162 areas spanning mainland China. Diabetes status was assessed using American Diabetes Association criteria. Among those with diabetes, detection was defined by prior diagnosis. Choropleth maps were used to visually assess geographical variation in each outcome at the provincial level. The odds of each outcome were assessed using multilevel logistic regression, with adjustment for person- and area-level characteristics. RESULTS Geographic visualization at the provincial level indicated widespread variation in diabetes prevalence and detection across China. Regional prevalence adjusted for age, sex, and urban/rural socioeconomic circumstances (SECs) ranged from 8.3% (95% CI 7.2%, 9.7%) in the northeast to 12.7% (11.1%, 14.6%) in the north. A clear negative gradient in diabetes prevalence was observed from 13.1% (12.0%, 14.4%) in the urban high-SEC to 8.7% (7.8%, 9.6%) in rural low-SEC counties/districts. Adjusting for health literacy and other person-level characteristics only partially attenuated these geographic variations. Only one-third of participants living with diabetes had been previously diagnosed, but this also varied substantively by geography. Regional detection adjusted for age, sex, and urban/rural SEC, for example, spanned from 40.4% (34.9%, 46.3%) in the north to 15.6% (11.7%, 20.5%) in the southwest. Compared with detection of 40.8% (37.3%, 44.4%) in urban high-SEC counties, detection was poorest among rural low-SEC counties at just 20.5% (17.7%, 23.7%). Person-level characteristics did not fully account for these geographic variations in diabetes detection. CONCLUSIONS Strategies for addressing diabetes risk and improving detection require geographical targeting. PMID:25352654

Seasonal gravity change at Yellowstone caldera

NASA Astrophysics Data System (ADS)

Poland, M. P.; de Zeeuw-van Dalfsen, E.

2017-12-01

The driving forces behind Yellowstone's dynamic deformation, vigorous hydrothermal system, and abundant seismicity are usually ascribed to "magmatic fluids," which could refer to magma, water, volatiles, or some combination. Deformation data alone cannot distinguish the relative importance of these fluids. Gravity measurements, however, provide an indication of mass change over time and, when combined with surface displacements, can constrain the density of subsurface fluids. Unfortunately, several decades of gravity surveys at Yellowstone have yielded ambiguous results. We suspect that the difficulty in interpreting Yellowstone gravity data is due to seasonal variations in environmental conditions—especially surface and ground water. Yellowstone gravity surveys are usually carried out at the same time of year (generally late summer) to minimize the impact of seasonality. Nevertheless, surface and subsurface water levels are not likely to be constant from year to year, given annual differences in precipitation. To assess the overall magnitude of seasonal gravity changes, we conducted gravity surveys of benchmarks in and around Yellowstone caldera in May, July, August, and October 2017. Our goal was to characterize seasonal variations due to snow melt/accumulation, changes in river and lake levels, changes in groundwater levels, and changes in hydrothermal activity. We also hope to identify sites that show little variation in gravity over the course of the 2017 surveys, as these locations may be less prone to seasonal changes and more likely to detect small variations due to magmatic processes. Preliminary examination of data collected in May and July 2017 emphasizes the importance of site location relative to sources of water. For example, a site on the banks of the Yellowstone River showed a gravity increase of several hundred microgals associated with a 50 cm increase in the river level. A high-altitude site far from rivers and lakes, in contrast, showed a relatively small gravity increase ( 25 microgals) over the same time period, despite the presence of 1 m of snow during the first survey and none during the second. Reinterpretation of past data collected at sites such as this one, where seasonal variations may be minor, could provide a clearer indication of mass changes in Yellowstone's magmatic system.

Multi-instrument Observations of Transient Luminous Events Associated with a Small-scale Winter Thunderstorm

NASA Astrophysics Data System (ADS)

Kolmasova, I.; Santolik, O.; Spurny, P.; Borovicka, J.; Mlynarczyk, J.; Popek, M.; Lan, R.; Uhlir, L.; Diendorfer, G.; Slosiar, R.

2017-12-01

We present observations of transient luminous events (TLEs) produced by a small-scale winter thunderstorm which occurred on 2 April 2017 in the southwest of Czechia. Elves, sprites and associated positive lightning strokes have been simultaneously recorded by different observational techniques. Optical data include video recordings of TLEs from Nydek (Czechia) and data recorded by high time-resolution photometers at several stations of the Czech fireball network which measured the all-sky brightness originating from lightning return strokes. Electromagnetic data sets include 3-component VLF measurements conducted in Rustrel (France), 2-component ELF measurements recorded at the Hylaty station (Poland) and signal intensity variations of a VLF transmitter (DHO38, Rhauderfehn, Germany) recorded in Bojnice (Slovakia). Optical and electromagnetic data are completed by positions and peak currents of all strokes recorded during the observed thunderstorm by the EUCLID lightning detection network. We focus our analysis on positive lightning discharges with high peak currents and we compare properties of those which produced TLE with properties of discharges for which TLE was not detected. The current moment waveforms and charge moment changes associated with the TLE events are reconstructed from the ELF electromagnetic signals. Obtained current moment waveforms show excellent agreement with high time-resolution optical data.

Solar Cycle Fine Structure and Surface Rotation from Ca II K-Line Time Series Data

NASA Astrophysics Data System (ADS)

Scargle, Jeff; Keil, Steve; Worden, Pete

2011-10-01

Analysis of three and a half decades of data from the NSO/AFRL/Sac Peak K-line monitoring program yields evidence for four components to the variation: (a) the solar cycle, with considerable fine structure and a quasi-periodicity of 122.4 days; (b) a stochastic process, faster than (a) and largely independent of it, (c) a quasi-periodic signal due to rotational modulation, and of course (d) observational errors (shown to be quite small). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these chromospheric parameters. Time-frequency analysis is especially useful for extracting information about differential rotation, and in particular elucidates the connection between its behavior and fine structure of the solar cycle on approximately one-year time scales. These results further suggest that similar analyses will be useful at detecting and characterizing differential rotation in stars from stellar light-curves such as those being produced by NASA's Kepler observatory. Component (b) consists of variations over a range of timescales, in the manner of a "1/f" random process. A time-dependent Wilson-Bappu effect appears to be present in the solar cycle variations (a), but not in the stochastic process (b). The data can be found at the National Solar Observatory web site http://nsosp.nso.edu/data/cak_mon.html, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.

Variations in the abundance of iron on Mercury's surface from MESSENGER X-Ray Spectrometer observations

NASA Astrophysics Data System (ADS)

Weider, Shoshana Z.; Nittler, Larry R.; Starr, Richard D.; McCoy, Timothy J.; Solomon, Sean C.

2014-06-01

We present measurements of Mercury's surface composition from the analysis of MESSENGER X-Ray Spectrometer data acquired during 55 large solar flares, which each provide a statistically significant detection of Fe X-ray fluorescence. The Fe/Si data display a clear dependence on phase angle, for which the results are empirically corrected. Mercury's surface has a low total abundance of Fe, with a mean Fe/Si ratio of ˜0.06 (equivalent to ˜1.5 wt% Fe). The absolute Fe/Si values are subject to a number of systematic uncertainties, including the phase-angle correction and possible mineral mixing effects. Individual Fe/Si measurements have an intrinsic error of ˜10%. Observed Fe/Si values display small variations (significant at two standard deviations) from the planetary average value across large regions in Mercury's southern hemisphere. Larger differences are observed between measured Fe/Si values from more spatially resolved footprints on volcanic smooth plains deposits in the northern hemisphere and from those in surrounding terrains. Fe is most likely contained as a minor component in sulfide phases (e.g., troilite, niningerite, daubréelite) and as Fe metal, rather than within mafic silicates. Variations in surface reflectance (i.e., differences in overall reflectance and spectral slope) across Mercury are unlikely to be caused by variations in the abundance of Fe.

Abnormal Circulation Changes in the Winter Stratosphere, Detected Through Variations of D Region Ionospheric Absorption

NASA Technical Reports Server (NTRS)

Delamorena, B. A.

1984-01-01

A method to detect stratospheric warmings using ionospheric absorption records obtained by an Absorption Meter (method A3) is introduced. The activity of the stratospheric circulation and the D region ionospheric absorption as well as other atmospheric parameters during the winter anomaly experience an abnormal variation. A simultaneity was found in the beginning of abnormal variation in the mentioned parameters, using the absorption records for detecting the initiation of the stratospheric warming. Results of this scientific experience of forecasting in the El Arenosillo Range, are presented.

A further contribution to the seasonal variation of weighted mean temperature

NASA Astrophysics Data System (ADS)

Ding, Maohua; Hu, Wusheng

2017-12-01

The weighted mean temperature Tm is a variable parameter in the Global Navigation Satellite System (GNSS) meteorology and the Askne-Nordius zenith wet delay (ZWD) model. Some parameters about the Tm seasonal variation (e.g. the annual mean value, the annual range, the annual and semi-annual amplitudes, and the long-term trend) were discussed before. In this study, some additional results about the Tm seasonal variation on a global scale were found by using the Tm time series at 309 global radiosonde sites. Periodic signals of the annual and semi-annual variations were detected in these Tm time series by using the Lomb-Scargle periodogram. The annual variation is the main component of the periodic Tm in non-tropical regions, while the annual variation or the semiannual variation can be the main component of the periodic Tm in tropics. The mean annual Tm almost keeps constant with the increasing latitude in tropics, while it decreases with the increasing latitude in non-tropical regions. From a global perspective, Tm has an increasing trend of 0.22 K/decade on average, which may be caused by the global warming effects. The annual phase is almost found in about January for the non-tropical regions of the Southern Hemisphere and in about July for the non-tropical regions of the Northern Hemisphere, but it has no clear symmetry in tropics. Unlike the annual phase, the geographical distributions of semi-annual phase do not follow obvious rules. In non-tropical regions, the maximum and minimum Tm of the seasonal model are usually found in respective summer and winter days while the maximum and minimum Tm are distributed over a whole year but not in any fixed seasons for tropical regions. The seasonal model errors increase with the increasing value of annual amplitude. A primary reason for the irregular seasonal variation in tropics is that Tm has rather small variations in this region.

A modified multiplex ligation-dependent probe amplification method for the detection of 22q11.2 copy number variations in patients with congenital heart disease.

PubMed

Zhang, Xiaoqing; Xu, Yuejuan; Liu, Deyuan; Geng, Juan; Chen, Sun; Jiang, Zhengwen; Fu, Qihua; Sun, Kun

2015-05-08

Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The aim of the study was to introduce a novel approach named CNVplex®, a high-throughput analysis technique designed for efficient detection of chromosomal CNVs, and to explore the prevalence of sub-chromosomal imbalances in 22q11.2 loci in patients with CHD from a single institute. We developed a novel technique, CNVplex®, for high-throughput detection of sub-chromosomal copy number aberrations. Modified from the multiplex ligation-dependent probe amplification (MLPA) method, it introduced a lengthening ligation system and four universal primer sets, which simplified the synthesis of probes and significantly improved the flexibility of the experiment. We used 110 samples, which were extensively characterized with chromosomal microarray analysis and MLPA, to validate the performance of the newly developed method. Furthermore, CNVplex® was used to screen for sub-chromosomal imbalances in 22q11.2 loci in 818 CHD patients consecutively enrolled from Shanghai Children's Medical Center. In the methodology development phase, CNVplex® detected all copy number aberrations that were previously identified with both chromosomal microarray analysis and MLPA, demonstrating 100% sensitivity and specificity. In the validation phase, 22q11.2 deletion and 22q11.2 duplication were detected in 39 and 1 of 818 patients with CHD by CNVplex®, respectively. Our data demonstrated that the frequency of 22q11.2 deletion varied among sub-groups of CHD patients. Notably, 22q11.2 deletion was more commonly observed in cases with conotruncal defect (CTD) than in cases with non-CTD (P<0.001). With higher resolution and more probes against selected chromosomal loci, CNVplex® also identified several individuals with small CNVs and alterations in other chromosomes. CNVplex® is sensitive and specific in its detection of CNVs, and it is an alternative to MLPA for batch screening of pathogenetic CNVs in known genomic loci.

Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach.

PubMed

Sacquin-Mora, S

2016-01-01

Flexibility is a central aspect of protein function, and ligand binding in enzymes involves a wide range of structural changes, ranging from large-scale domain movements to small loop or side-chain rearrangements. In order to understand how the mechanical properties of enzymes, and the mechanical variations that are induced by ligand binding, relate to enzymatic activity, we carried out coarse-grain Brownian dynamics simulations on a set of enzymes whose structures in the unbound and ligand-bound forms are available in the Protein Data Bank. Our results show that enzymes are remarkably heterogeneous objects from a mechanical point of view and that the local rigidity of individual residues is tightly connected to their part in the protein's overall structure and function. The systematic comparison of the rigidity of enzymes in their unbound and bound forms highlights the fact that small conformational changes can induce large mechanical effects, leading to either more or less flexibility depending on the enzyme's architecture and the location of its ligand-biding site. These mechanical variations target a limited number of specific residues that occupy key locations for enzymatic activity, and our approach thus offers a mean to detect perturbation-sensitive sites in enzymes, where the addition or removal of a few interactions will lead to important changes in the proteins internal dynamics. © 2016 Elsevier Inc. All rights reserved.

Comparative study of the digestive system of three species of tinamou. I. Crypturellus tataupa, Nothoprocta cinerascens, and Nothura maculosa (Aves: tinamidae).

PubMed

Chikilian, M; De Speroni, N B

1996-04-01

The morphology and histology, as well as the cytochemistry of complex carbohydrates, of the digestive system of Crypturellus tataupa (tataupa tinamou), Nothoprocta cinerascens (brushland tinamou), and Nothura maculosa (spotted tinamou) are described. The general morphology of the digestive system of these birds follows the basic model of the avian alimentary canal, although statistical analysis shows that the lengths of the organs are significantly different among the species. From cephalic to caudal regions the alimentary tract consists of esophagus, ingluvies or crop, proventriculus or glandular stomach, ventriculus or muscular stomach, small intestine, well-developed ceca, and rectum. Histologically, each section of the tract consists of four primary tissue layers: mucosa, submucosa, muscularis, and adventitia. Variations are found in the thickness of the esophageal epithelium, which shows the highest value in C. tataupa. In the proventriculus, the depth of the compound glands is greatest in N. cinerascens. The villi of the epithelial cells in the small intestine are most extensively developed in C. tataupa. Heterogeneity of mucins is detected not only in the surface coat of the alimentary tract but in the cellular content of the glands as well. Comparisons with the morphology of the digestive system of closely related and more advanced birds are made, and the possible relationship between morphological and cytochemical variation and the diet is discussed.

Just noticeable differences of open quotient and asymmetry coefficient in singing voice.

PubMed

Henrich, Nathalie; Sundin, Gunilla; Ambroise, Daniel; d'Alessandro, Christophe; Castellengo, Michèle; Doval, Boris

2003-12-01

This study aims to explore the perceptual relevance of the variations of glottal flow parameters and to what extent a small variation can be detected. Just Noticeable Differences (JNDs) have been measured for three values of open quotient (0.4, 0.6, and 0.8) and two values of asymmetry coefficient (2/3 and 0.8), and the effect of changes of vowel, pitch, vibrato, and amplitude parameters has been tested. Two main groups of subjects have been analyzed: a group of 20 untrained subjects and a group of 10 trained subjects. The results show that the JND for open quotient is highly dependent on the target value: an increase of the JND is noticed when the open quotient target value is increased. The relative JND is constant: deltaOq/Oq = 14% for the untrained and 10% for the trained. In the same way, the JND for asymmetry coefficient is also slightly dependent on the target value--an increase of the asymmetry coefficient value leads to a decrease of the JND. The results show that there is no effect from the selected vowel or frequency (two values have been tested), but that the addition of a vibrato has a small effect on the JND of open quotient. The choice of an amplitude parameter also has a great effect on the JND of open quotient.

Correlation among genetic variations of c-MET in Chinese patients with non-small cell lung cancer.

PubMed

Duan, Jianchun; Yang, Xiaodan; Zhao, Jun; Zhuo, Minglei; Wang, Zhijie; An, Tongtong; Bai, Hua; Wang, Jie

2018-01-05

The purpose of our research was to determine the correlation of amplification, protein expression and somatic mutation of c-MET in IIIb-IV stage NSCLC (Non-small cell lung cancer). We also explored correlation of c-MET variation with clinical outcome. c-MET expression was observed in 28.6% (56/196) cases, and among those 13.8% (27/196) were shown to be FISH positive. Only 2.67% patients in this study carried the c-MET mutation. Cases with c-MET FISH positive were all IHC positive ,but in IHC positive cases, only half were FISH positive. Among patients with IHC 2+ staining, 35.5% was FISH positive, while cases with IHC 3+ staining,64% was FISH positive. Both protein expression and copy number of c-MET did not significantly correlate with clinical prognosis in these patients treated with EGFR-TKIs. IHC could be used as a preliminary screening method for c-MET copy number amplification and should be confirmed by FISH only in IHC positive case which facilitate selection of ALK or MET inhibitor therapy. c-MET gene copy number, protein expression and somatic mutation for exon 14 were detected by fluorescent- In-Situ -Hybridization (FISH), Immunohistochemistry (IHC), and Denaturing-High-Performance-Liquid-Chromatography (DHPLC), respectively, in 196 NSCLC patients. The relationship between c-MET abnormalities and clinical outcome of targeted therapy was analyzed by McNemar's test.

Derivation of a respiration trigger signal in small animal list-mode PET based on respiration-induced variations of the ECG signal.

PubMed

Todica, Andrei; Lehner, Sebastian; Wang, Hao; Zacherl, Mathias J; Nekolla, Katharina; Mille, Erik; Xiong, Guoming; Bartenstein, Peter; la Fougère, Christian; Hacker, Marcus; Böning, Guido

2016-02-01

Raw PET list-mode data contains motion artifacts causing image blurring and decreased spatial resolution. Unless corrected, this leads to underestimation of the tracer uptake and overestimation of the lesion size, as well as inaccuracies with regard to left ventricular volume and ejection fraction (LVEF), especially in small animal imaging. A respiratory trigger signal from respiration-induced variations in the electro-cardiogram (ECG) was detected. Original and revised list-mode PET data were used for calculation of left ventricular function parameters using both respiratory gating techniques. For adequately triggered datasets we saw no difference in mean respiratory cycle period between the reference standard (RRS) and the ECG-based (ERS) methods (1120 ± 159 ms vs 1120 ± 159 ms; P = n.s.). While the ECG-based method showed somewhat higher signal noise (66 ± 22 ms vs 51 ± 29 ms; P < .001), both respiratory triggering techniques yielded similar estimates for EDV, ESV, LVEF (RRS: 387 ± 56 µL, 162 ± 34 µL, 59 ± 5%; ERS: 389 ± 59 µL, 163 ± 35 µL, 59 ± 4%; P = n.s.). This study showed that respiratory gating signals can be accurately derived from cardiac trigger information alone, without the additional requirement for dedicated measurement of the respiratory motion in rats.

An infrared small target detection method based on multiscale local homogeneity measure

NASA Astrophysics Data System (ADS)

Nie, Jinyan; Qu, Shaocheng; Wei, Yantao; Zhang, Liming; Deng, Lizhen

2018-05-01

Infrared (IR) small target detection plays an important role in the field of image detection area owing to its intrinsic characteristics. This paper presents a multiscale local homogeneity measure (MLHM) for infrared small target detection, which can enhance the performance of IR small target detection system. Firstly, intra-patch homogeneity of the target itself and the inter-patch heterogeneity between target and the local background regions are integrated to enhance the significant of small target. Secondly, a multiscale measure based on local regions is proposed to obtain the most appropriate response. Finally, an adaptive threshold method is applied to small target segmentation. Experimental results on three different scenarios indicate that the MLHM has good performance under the interference of strong noise.

RXTE Monitoring of the Anomalous X-ray Pulsar 1E 1048.1-5937: Long-Term Variability and the 2007 March Event

NASA Technical Reports Server (NTRS)

Dib, Rim; Kaspi, Victoria M.; Gavriil, Fotis P.

2009-01-01

After three years of no unusual activity, Anomalous X-ray Pulsar 1E 1048.1-5937 reactivated in 2007 March. We report on the detection of a large glitch (deltav/v = 1.63(2) x 10(exp -5)) on 2007 March 26 (MJD 54185.9), contemporaneous with the onset of a pulsed-flux flare, the third flare observed from this source in 10 years of monitoring with the Rossi X-ray Timing Explorer. Additionally, we report on a detailed study of the evolution of the timing properties, the pulsed flux, and the pulse profile of this source as measured by RXTE from 1996 July to 2008 January. In our timing study, we attempted phase coherent timing of all available observations. We show that in 2001, a timing anomaly of uncertain nature occurred near the rise of the first pulsed flux flare; we show that a likely glitch (deltav/v = 2.91(9) x 10(exp -6)) occurred in 2002, near the rise of the second flare, and we present a detailed description of the variations in the spin-down. In our pulsed flux study, we compare the decays of the three flares and discuss changes in the hardness ratio. In our pulse profile study, we show that the profile exhibited large variations near the peak of the first two flares, and several small short-term profile variations during the most recent flare. Finally, we report on the discovery of a small burst 27 days after the peak of the last flare, the fourth burst discovered from this source. We discuss the relationships between the observed properties in the framework of the magnetar model.

Quantifying Biomass and Bare Earth Changes from the Hayman Fire Using Multi-temporal Lidar

NASA Astrophysics Data System (ADS)

Stoker, J. M.; Kaufmann, M. R.; Greenlee, S. K.

2007-12-01

Small-footprint multiple-return lidar data collected in the Cheesman Lake property prior to the 2002 Hayman fire in Colorado provided an excellent opportunity to evaluate Lidar as a tool to predict and analyze fire effects on both soil erosion and overstory structure. Re-measuring this area and applying change detection techniques allowed for analyses at a high level of detail. Our primary objectives focused on the use of change detection techniques using multi-temporal lidar data to: (1) evaluate the effectiveness of change detection to identify and quantify areas of erosion or deposition caused by post-fire rain events and rehab activities; (2) identify and quantify areas of biomass loss or forest structure change due to the Hayman fire; and (3) examine effects of pre-fire fuels and vegetation structure derived from lidar data on patterns of burn severity. While we were successful in identifying areas where changes occurred, the original error bounds on the variation in actual elevations made it difficult, if not misleading to quantify volumes of material changed on a per pixel basis. In order to minimize these variations in the two datasets, we investigated several correction and co-registration methodologies. The lessons learned from this project highlight the need for a high level of flight planning and understanding of errors in a lidar dataset in order to correctly estimate and report quantities of vertical change. Directly measuring vertical change using only lidar without ancillary information can provide errors that could make quantifications confusing, especially in areas with steep slopes.

A microsensor for the detection of a single pathogenic bacterium using magnetotactic bacteria-based bio-carriers: simulations and preliminary experiments.

PubMed

Denomme, Ryan C; Lu, Zhao; Martel, Sylvain

2007-01-01

The proposed Magnetotactic Bacteria (MTB) based bio-carrier has the potential to greatly improve pathogenic bacteria detection time, specificity, and sensitivity. Microbeads are attached to the MTB and are modified with a coating of an antibody or phage that is specific to the target pathogenic bacteria. Using magnetic fields, the modified MTB are swept through a solution and the target bacteria present become attached to the microbeads (due to the coating). Then, the MTB are brought to the detection region and the number of pathogenic bacteria is determined. The high swimming speed and controllability of the MTB make this method ideal for the fast detection of small concentrations of specific bacteria. This paper focuses on an impedimetric detection system that will be used to identify if a target bacterium is attached to the microbead. The proposed detection system measures changes in electrical impedance as objects (MTB, microbeads, and pathogenic bacteria) pass through a set of microelectrodes embedded in a microfluidic device. FEM simulation is used to acquire the optimized parameters for the design of such a system. Specifically, factors such as electrode/detection channel geometry, object size and position, which have direct effects on the detection sensitivity for a single bacterium or microparticle, are investigated. Polymer microbeads and the MTB system with an E. coli bacterium are considered to investigate their impedance variations. Furthermore, preliminary experimental data using a microfabricated microfluidic device connected to an impedance analyzer are presented.

Automatic devices to take water samples and to raise trash screens at weirs

Treesearch

K. G. Reinhart; R. E. Leonard; G. E. Hart

1960-01-01

Experimentation on small watersheds is assuming increasing importance in watershed-management research. Much has been accomplished in developing adequate instrumentation for use in these experiments. Yet many problems still await solution. One difficulty encountered is that small streams are subject to wide variations in flow and that these variations are generally...

The Potential of Multicolor Photometry for Pulsating Subdwarf B Stars

NASA Astrophysics Data System (ADS)

Randall, S. K.; Fontaine, G.; Brassard, P.; Bergeron, P.

2005-12-01

We investigate the potential of multicolor photometry for partial mode identification in both long- and short-period variable subdwarf B stars. The technique presented is based on the fact that the frequency dependence of an oscillation's amplitude and phase bears the signature of the mode's degree index l, among other things. Unknown contributing factors can be eliminated through the evaluation of the amplitude ratios and phase differences arising from the brightness variation in different wavebands, theoretically enabling the inference of the degree index from observations in two or more bandpasses. Employing a designated model atmosphere code, we calculate the brightness variation expected across the visible disk during a pulsation cycle in terms of temperature, radius, and surface gravity perturbations to the emergent flux for representative EC 14026 and PG 1716 star models. Nonadiabatic effects are considered in detail and found to be significant from nonadiabatic pulsation calculations applied to our state-of-the-art models of subdwarf B stars. Our results indicate that the brightness variations observed in subdwarf B stars are caused primarily by changes in temperature and radius, with surface gravity perturbations playing a small role. For PG 1716 stars, temperature effects dominate in the limit of long periods with the result that the oscillatory amplitudes and phases lose their period dependence and nonadiabatic effects become unimportant. Outside this regime, however, their values are strongly influenced by both factors. We find that the phase shifts between brightness variations in different wavebands are generally small but may lie above the experimental detection threshold in certain cases. The prospect of mode discrimination seems much more promising on the basis of the corresponding amplitude ratios. While in EC 14026 stars the amplitude ratios predicted are very similar for modes with l=0, 1, or 2, they are well separated from those of modes with l=3, l=5, and l=4 or 6, each of which form a distinct group. For the case of the PG 1716 stars it should be possible to discriminate between modes with l=1, 2, 4, or 6 and those of degree indices l=3 and l=5. Identifying modes within a given group is challenging for both types of pulsator and requires multicolor photometry of extremely high quality. Nevertheless, we demonstrate that it is feasible using the example of the largest amplitude peak detected for the fast pulsator KPD 2109+4401 by Jeffery et al. Predicted color-amplitude ratios for a series of representative EC 14026 and PG 1716 stars are available upon request. Interested collaborators please contact S. K. Randall or G. Fontaine.

Application of advanced cytometric and molecular technologies to minimal residual disease monitoring

NASA Astrophysics Data System (ADS)

Leary, James F.; He, Feng; Reece, Lisa M.

2000-04-01

Minimal residual disease monitoring presents a number of theoretical and practical challenges. Recently it has been possible to meet some of these challenges by combining a number of new advanced biotechnologies. To monitor the number of residual tumor cells requires complex cocktails of molecular probes that collectively provide sensitivities of detection on the order of one residual tumor cell per million total cells. Ultra-high-speed, multi parameter flow cytometry is capable of analyzing cells at rates in excess of 100,000 cells/sec. Residual tumor selection marker cocktails can be optimized by use of receiver operating characteristic analysis. New data minimizing techniques when combined with multi variate statistical or neural network classifications of tumor cells can more accurately predict residual tumor cell frequencies. The combination of these techniques can, under at least some circumstances, detect frequencies of tumor cells as low as one cell in a million with an accuracy of over 98 percent correct classification. Detection of mutations in tumor suppressor genes requires insolation of these rare tumor cells and single-cell DNA sequencing. Rare residual tumor cells can be isolated at single cell level by high-resolution single-cell cell sorting. Molecular characterization of tumor suppressor gene mutations can be accomplished using a combination of single- cell polymerase chain reaction amplification of specific gene sequences followed by TA cloning techniques and DNA sequencing. Mutations as small as a single base pair in a tumor suppressor gene of a single sorted tumor cell have been detected using these methods. Using new amplification procedures and DNA micro arrays it should be possible to extend the capabilities shown in this paper to screening of multiple DNA mutations in tumor suppressor and other genes on small numbers of sorted metastatic tumor cells.

Method variation in the impact of missing data on response shift detection.

PubMed

Schwartz, Carolyn E; Sajobi, Tolulope T; Verdam, Mathilde G E; Sebille, Veronique; Lix, Lisa M; Guilleux, Alice; Sprangers, Mirjam A G

2015-03-01

Missing data due to attrition or item non-response can result in biased estimates and loss of power in longitudinal quality-of-life (QOL) research. The impact of missing data on response shift (RS) detection is relatively unknown. This overview article synthesizes the findings of three methods tested in this special section regarding the impact of missing data patterns on RS detection in incomplete longitudinal data. The RS detection methods investigated include: (1) Relative importance analysis to detect reprioritization RS in stroke caregivers; (2) Oort's structural equation modeling (SEM) to detect recalibration, reprioritization, and reconceptualization RS in cancer patients; and (3) Rasch-based item-response theory-based (IRT) models as compared to SEM models to detect recalibration and reprioritization RS in hospitalized chronic disease patients. Each method dealt with missing data differently, either with imputation (1), attrition-based multi-group analysis (2), or probabilistic analysis that is robust to missingness due to the specific objectivity property (3). Relative importance analyses were sensitive to the type and amount of missing data and imputation method, with multiple imputation showing the largest RS effects. The attrition-based multi-group SEM revealed differential effects of both the changes in health-related QOL and the occurrence of response shift by attrition stratum, and enabled a more complete interpretation of findings. The IRT RS algorithm found evidence of small recalibration and reprioritization effects in General Health, whereas SEM mostly evidenced small recalibration effects. These differences may be due to differences between the two methods in handling of missing data. Missing data imputation techniques result in different conclusions about the presence of reprioritization RS using the relative importance method, while the attrition-based SEM approach highlighted different recalibration and reprioritization RS effects by attrition group. The IRT analyses detected more recalibration and reprioritization RS effects than SEM, presumably due to IRT's robustness to missing data. Future research should apply simulation techniques in order to make conclusive statements about the impacts of missing data according to the type and amount of RS.

Methods for computational disease surveillance in infection prevention and control: Statistical process control versus Twitter's anomaly and breakout detection algorithms.

PubMed

Wiemken, Timothy L; Furmanek, Stephen P; Mattingly, William A; Wright, Marc-Oliver; Persaud, Annuradha K; Guinn, Brian E; Carrico, Ruth M; Arnold, Forest W; Ramirez, Julio A

2018-02-01

Although not all health care-associated infections (HAIs) are preventable, reducing HAIs through targeted intervention is key to a successful infection prevention program. To identify areas in need of targeted intervention, robust statistical methods must be used when analyzing surveillance data. The objective of this study was to compare and contrast statistical process control (SPC) charts with Twitter's anomaly and breakout detection algorithms. SPC and anomaly/breakout detection (ABD) charts were created for vancomycin-resistant Enterococcus, Acinetobacter baumannii, catheter-associated urinary tract infection, and central line-associated bloodstream infection data. Both SPC and ABD charts detected similar data points as anomalous/out of control on most charts. The vancomycin-resistant Enterococcus ABD chart detected an extra anomalous point that appeared to be higher than the same time period in prior years. Using a small subset of the central line-associated bloodstream infection data, the ABD chart was able to detect anomalies where the SPC chart was not. SPC charts and ABD charts both performed well, although ABD charts appeared to work better in the context of seasonal variation and autocorrelation. Because they account for common statistical issues in HAI data, ABD charts may be useful for practitioners for analysis of HAI surveillance data. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Three plot correlation-based small infrared target detection in dense sun-glint environment for infrared search and track

NASA Astrophysics Data System (ADS)

Kim, Sungho; Choi, Byungin; Kim, Jieun; Kwon, Soon; Kim, Kyung-Tae

2012-05-01

This paper presents a separate spatio-temporal filter based small infrared target detection method to address the sea-based infrared search and track (IRST) problem in dense sun-glint environment. It is critical to detect small infrared targets such as sea-skimming missiles or asymmetric small ships for national defense. On the sea surface, sun-glint clutters degrade the detection performance. Furthermore, if we have to detect true targets using only three images with a low frame rate camera, then the problem is more difficult. We propose a novel three plot correlation filter and statistics based clutter reduction method to achieve robust small target detection rate in dense sun-glint environment. We validate the robust detection performance of the proposed method via real infrared test sequences including synthetic targets.

Community composition of lacustrine small eukaryotes in hyper-eutrophic conditions in relation to top-down and bottom-up factors.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Debroas, Didier

2007-09-01

Small eukaryotes (0.2-5 microm) in hyper-eutrophic conditions were described using terminal restriction fragment length polymorphism and cloning-sequencing, and were related to environmental variables both by an experimental approach and by a temporal field study. In situ analysis showed marked temporal variations in the dominant terminal restriction fragments (T-RFs), which were related to environmental variables such as nutrient concentrations and metazooplankton composition. To monitor the responses of the small-eukaryote community to top-down (absence or presence of planktivorous fish) and bottom-up (low or high nitrogen and phosphorus addition) effects, a cross-classified design mesocosm experiment was used. Depending on the type of treatment, we recorded changes in the diversity of T-RFs, as well as modifications in phylogenetic composition. Centroheliozoa and Cryptophyta were found in all types of treatment, whereas Chlorophyta were specific to enclosures receiving high nutrient loadings, and were associated either with LKM11 and 'environmental sequences'. Cercozoa and Fungi were not detected in enclosures receiving high nutrient loadings and fishes. Our results showed that resources and top-down factors are both clearly involved in shaping the structure of small eukaryotes, not only autotrophs but also heterotrophs, via complex interactions and trophic cascades within a microbial loop, notably in response to nutrient loading.

Small subsidence of the 660-km discontinuity beneath Japan probed by ScS reverberations

NASA Astrophysics Data System (ADS)

Kato, Mamoru; Misawa, Mika; Kawakatsu, Hitoshi

We investigate layering structure in the mantle beneath Japan using ScS reverberation waveforms of two recent large deep events in the northwest Pacific. We estimate regional variation of the elastic and anelastic structure of the mantle as well as properties of the major velocity discontinuities by modeling broadband seismograms recorded at two dense networks, J-Array and FREESIA. The 660-km discontinuity is the deepest in the region where the stagnant subducting slab in the transition zone is tomographically imaged, but the subsidence is of ∼10 km, much smaller than previous estimates with SS precursors. No significant elevation is detected for the 410-km discontinuity.

Broadband mid-infrared measurements for shock induced chemistry

NASA Astrophysics Data System (ADS)

McGrane, Shawn; Bowlan, Pamela; Brown, Kathryn; Bolme, Cynthia; Cawkwell, Marc

2017-06-01

Vibrational absorption spectroscopy across the mid-infrared range is a ubiquitous diagnostic of chemical effects due to its sensitivity to small variations in bonding. At the high temperatures and pressures relevant to shock induced chemistry, vibrational spectral peaks become very broad, and accessing as much spectral range as possible with high time resolution can significantly aid in deducing chemical dynamics. Here, we report experiments using broadband (<500 cm-1 to >2000 cm-1) mid-infrared femtosecond supercontinua created by four wave mixing in filaments to perform absorption spectroscopy. These broadband mid-infrared supercontinua are detected through upconversion to visible light. Initial efforts to utilize these methods for measurement of chemical dynamics in shocked nitromethane will be reported.

New results on thermalization of electrons in GaAs

NASA Astrophysics Data System (ADS)

Hannak, Reinhard M.; Ruehle, Wolfgang W.

1994-05-01

The transition from a nonthermal into a thermal distribution of electrons at low densities (< 1014 cm-3) is traced on a picosecond time-scale by the time evolution of a band-to-acceptor transition in GaAs:Be. Two narrow, nonthermal electron distributions are detected during the first picoseconds originating from the heavy- and light-hole valence band, respectively. Measurements with circular polarization of excitation and luminescence confirm this assignment. The variation of their energetic peak-positions with excitation energy allows the experimental determination of the valence band dispersions for very small wave vectors near k equals 0, where only parabolic energy terms contribute to the dispersions. The results are consistent with the commonly used effective hole masses.

Low energy gamma ray emission from the Cygnus OB2 association

NASA Technical Reports Server (NTRS)

Chen, Wan; White, Richard L.

1992-01-01

According to our newly developed model of gamma-ray emission from chaotic early-type stellar winds, we predict the combined gamma-ray flux from the circumstellar winds of many very luminous early-type stars in the Cyg OB2 association can be detectable by the Energetic Gamma Ray Experiment Telescope (EGRET) (and maybe also by OSSE) on CGRO. Due to different radiation mechanisms, the gamma-ray spectrum from stellar winds can be quite different from that of CYG X-3; this spectral difference and the time-variation of Cyg X-3 flux will help to distinguish the gamma-ray components from different sources in this small region, which is spatially unresolvable by CGRO.

Detection and measurement of the intracellular calcium variation in follicular cells.

PubMed

Herrera-Navarro, Ana M; Terol-Villalobos, Iván R; Jiménez-Hernández, Hugo; Peregrina-Barreto, Hayde; Gonzalez-Barboza, José-Joel

2014-01-01

This work presents a new method for measuring the variation of intracellular calcium in follicular cells. The proposal consists in two stages: (i) the detection of the cell's nuclei and (ii) the analysis of the fluorescence variations. The first stage is performed via watershed modified transformation, where the process of labeling is controlled. The detection process uses the contours of the cells as descriptors, where they are enhanced with a morphological filter that homogenizes the luminance variation of the image. In the second stage, the fluorescence variations are modeled as an exponential decreasing function, where the fluorescence variations are highly correlated with the changes of intracellular free Ca(2+). Additionally, it is introduced a new morphological called medium reconstruction process, which helps to enhance the data for the modeling process. This filter exploits the undermodeling and overmodeling properties of reconstruction operators, such that it preserves the structure of the original signal. Finally, an experimental process shows evidence of the capabilities of the proposal.

Detection and Measurement of the Intracellular Calcium Variation in Follicular Cells

PubMed Central

Herrera-Navarro, Ana M.; Terol-Villalobos, Iván R.; Jiménez-Hernández, Hugo; Peregrina-Barreto, Hayde; Gonzalez-Barboza, José-Joel

2014-01-01

This work presents a new method for measuring the variation of intracellular calcium in follicular cells. The proposal consists in two stages: (i) the detection of the cell's nuclei and (ii) the analysis of the fluorescence variations. The first stage is performed via watershed modified transformation, where the process of labeling is controlled. The detection process uses the contours of the cells as descriptors, where they are enhanced with a morphological filter that homogenizes the luminance variation of the image. In the second stage, the fluorescence variations are modeled as an exponential decreasing function, where the fluorescence variations are highly correlated with the changes of intracellular free Ca2+. Additionally, it is introduced a new morphological called medium reconstruction process, which helps to enhance the data for the modeling process. This filter exploits the undermodeling and overmodeling properties of reconstruction operators, such that it preserves the structure of the original signal. Finally, an experimental process shows evidence of the capabilities of the proposal. PMID:25342958

Small-size pedestrian detection in large scene based on fast R-CNN

NASA Astrophysics Data System (ADS)

Wang, Shengke; Yang, Na; Duan, Lianghua; Liu, Lu; Dong, Junyu

2018-04-01

Pedestrian detection is a canonical sub-problem of object detection with high demand during recent years. Although recent deep learning object detectors such as Fast/Faster R-CNN have shown excellent performance for general object detection, they have limited success for small size pedestrian detection in large-view scene. We study that the insufficient resolution of feature maps lead to the unsatisfactory accuracy when handling small instances. In this paper, we investigate issues involving Fast R-CNN for pedestrian detection. Driven by the observations, we propose a very simple but effective baseline for pedestrian detection based on Fast R-CNN, employing the DPM detector to generate proposals for accuracy, and training a fast R-CNN style network to jointly optimize small size pedestrian detection with skip connection concatenating feature from different layers to solving coarseness of feature maps. And the accuracy is improved in our research for small size pedestrian detection in the real large scene.

Biotechnology Approaches to Life Detection

NASA Technical Reports Server (NTRS)

Steele, Andrew; McKay, David; Schweitzer, Mary

2001-01-01

The direct detection of organic biomarkers for living or fossil microbes on Mars by an in situ instrument is a worthy goal for future lander missions. Several new and innovative biotechnology approaches are being explored. Firstly we have proposed an instrument based on immunological reactions to specific antibodies to cause activation of fluorescent stains. Antibodies are raised or acquired to a variety of general and specific substances that might be in Mars soil. These antibodies are then combined with various fluorescent stains and applied to micron sized numbered spots on a small (2-3 cm) test plate where they become firmly attached after freeze drying. Using technology that has been developed for gene mining in DNA technology up to 10,000 tests per square inch can now be applied to a test plate. On Mars or the planet/moon of interest, a sample of soil from a trench or drill core is extracted with water and/or an organic solvent and ultrasonication and then applied to the test plate. Any substance, which has an antibody on the test plate, will react with its antibody and activate its fluorescent stain. At the moment a small UV light source will illuminate the test plate, which is observed with a small CCD camera, although other detection systems will be applied. The numbered spots that fluoresce indicate the presence of the tested-for substance, and the intensity indicates relative amounts. Furthermore with up to a thousand test plates available false positives and several variations of antibody can also be screened for. The entire instrument can be quite small and light, on the order of 10 cm in each dimension. A possible choice for light source may be small UV lasers at several wavelengths. Some of the wells or spots can contain simply standard fluorescent stains used to detect live cells, dead cells, DNA, etc. The stains in these spots may be directly activated, with no antibodies being necessary. The proposed system will look for three classes of biomarkers: those from extant life, such as DNA, those from extinct life such as hopanes, and those from organic compounds not necessarily associated with life such as PAHs, rocket exhaust contamination and other a/pre-biotic chemicals. Both monoclonal and polyclonal antibodies can be used. Monoclonal antibodies react with a very specific compound, but polyclonal antibodies may react to any of a whole family of compounds. Furthermore the technique of phage display to raise antibodies against classically non-antigenic molecules is also being considered. Additional information is contained in the original extended abstract.

Colloquium: Search for a drifting proton-electron mass ratio from H2

NASA Astrophysics Data System (ADS)

Ubachs, W.; Bagdonaite, J.; Salumbides, E. J.; Murphy, M. T.; Kaper, L.

2016-04-01

An overview is presented of the H2 quasar absorption method to search for a possible variation of the proton-electron mass ratio μ =mp/me on a cosmological time scale. The method is based on a comparison between wavelengths of absorption lines in the H2 Lyman and Werner bands as observed at high redshift with wavelengths of the same lines measured at zero redshift in the laboratory. For such comparison sensitivity coefficients to a relative variation of μ are calculated for all individual lines and included in the fitting routine deriving a value for Δ μ /μ . Details of the analysis of astronomical spectra, obtained with large 8-10 m class optical telescopes, equipped with high-resolution echelle grating based spectrographs, are explained. The methods and results of the laboratory molecular spectroscopy of H2, in particular, the laser-based metrology studies for the determination of rest wavelengths of the Lyman and Werner band absorption lines, are reviewed. Theoretical physics scenarios delivering a rationale for a varying μ are discussed briefly, as well as alternative spectroscopic approaches to probe variation of μ , other than the H2 method. Also a recent approach to detect a dependence of the proton-to-electron mass ratio on environmental conditions, such as the presence of strong gravitational fields, are highlighted. Currently some 56 H2 absorption systems are known and listed. Their usefulness to detect μ variation is discussed, in terms of column densities and brightness of background quasar sources, along with future observational strategies. The astronomical observations of ten quasar systems analyzed so far set a constraint on a varying proton-electron mass ratio of |Δ μ /μ |<5 ×1 0-6 (3 σ ), which is a null result, holding for redshifts in the range z =2.0 - 4.2 . This corresponds to look-back times of (10 - 12.4 )×109 years into cosmic history. Attempts to interpret the results from these ten H2 absorbers in terms of a spatial variation of μ are currently hampered by the small sample size and their coincidental distribution in a relatively narrow band across the sky.

Sources of Variation in a Two-Step Monitoring Protocol for Species Clustered in Conspicuous Points: Dolichotis patagonum as a Case Study.

PubMed

Alonso Roldán, Virginia; Bossio, Luisina; Galván, David E

2015-01-01

In species showing distributions attached to particular features of the landscape or conspicuous signs, counts are commonly made by making focal observations where animals concentrate. However, to obtain density estimates for a given area, independent searching for signs and occupancy rates of suitable sites is needed. In both cases, it is important to estimate detection probability and other possible sources of variation to avoid confounding effects on measurements of abundance variation. Our objective was to assess possible bias and sources of variation in a two-step protocol in which random designs were applied to search for signs while continuously recording video cameras were used to perform abundance counts where animals are concentrated, using mara (Dolichotis patagonum) as a case study. The protocol was successfully applied to maras within the Península Valdés protected area, given that the protocol was logistically suitable, allowed warrens to be found, the associated adults to be counted, and the detection probability to be estimated. Variability was documented in both components of the two-step protocol. These sources of variation should be taken into account when applying this protocol. Warren detectability was approximately 80% with little variation. Factors related to false positive detection were more important than imperfect detection. The detectability for individuals was approximately 90% using the entire day of observations. The shortest sampling period with a similar detection capacity than a day was approximately 10 hours, and during this period, the visiting dynamic did not show trends. For individual mara, the detection capacity of the camera was not significantly different from the observer during fieldwork. The presence of the camera did not affect the visiting behavior of adults to the warren. Application of this protocol will allow monitoring of the near-threatened mara providing a minimum local population size and a baseline for measuring long-term trends.

Tank-Binding Kinase 1 (TBK1) Gene and Open-Angle Glaucomas (An American Ophthalmological Society Thesis)

PubMed Central

Fingert, John H.; Robin, Alan L.; Scheetz, Todd E.; Kwon, Young H.; Liebmann, Jeffrey M.; Ritch, Robert; Alward, Wallace L.M.

2016-01-01

Purpose To investigate the role of TANK-binding kinase 1 (TBK1) gene copy-number variations (ie, gene duplications and triplications) in the pathophysiology of various open-angle glaucomas. Methods In previous studies, we discovered that copy-number variations in the TBK1 gene are associated with normal-tension glaucoma. Here, we investigated the prevalence of copy-number variations in cohorts of patients with other open-angle glaucomas—juvenile-onset open-angle glaucoma (n=30), pigmentary glaucoma (n=209), exfoliation glaucoma (n=225), and steroid-induced glaucoma (n=79)—using a quantitative polymerase chain reaction assay. Results No TBK1 gene copy-number variations were detected in patients with juvenile-onset open-angle glaucoma, pigmentary glaucoma, or steroid-induced glaucoma. A TBK1 gene duplication was detected in one (0.44%) of the 225 exfoliation glaucoma patients. Conclusions TBK1 gene copy-number variations (gene duplications and triplications) have been previously associated with normal-tension glaucoma. An exploration of other open-angle glaucomas detected a TBK1 copy-number variation in a patient with exfoliation glaucoma, which is the first example of a TBK1 mutation in a glaucoma patient with a diagnosis other than normal-tension glaucoma. A broader phenotypic range may be associated with TBK1 copy-number variations, although mutations in this gene are most often detected in patients with normal-tension glaucoma. PMID:27881886

Tank-Binding Kinase 1 (TBK1) Gene and Open-Angle Glaucomas (An American Ophthalmological Society Thesis).

PubMed

Fingert, John H; Robin, Alan L; Scheetz, Todd E; Kwon, Young H; Liebmann, Jeffrey M; Ritch, Robert; Alward, Wallace L M

2016-08-01

To investigate the role of TANK-binding kinase 1 ( TBK1 ) gene copy-number variations (ie, gene duplications and triplications) in the pathophysiology of various open-angle glaucomas. In previous studies, we discovered that copy-number variations in the TBK1 gene are associated with normal-tension glaucoma. Here, we investigated the prevalence of copy-number variations in cohorts of patients with other open-angle glaucomas-juvenile-onset open-angle glaucoma (n=30), pigmentary glaucoma (n=209), exfoliation glaucoma (n=225), and steroid-induced glaucoma (n=79)-using a quantitative polymerase chain reaction assay. No TBK1 gene copy-number variations were detected in patients with juvenile-onset open-angle glaucoma, pigmentary glaucoma, or steroid-induced glaucoma. A TBK1 gene duplication was detected in one (0.44%) of the 225 exfoliation glaucoma patients. TBK1 gene copy-number variations (gene duplications and triplications) have been previously associated with normal-tension glaucoma. An exploration of other open-angle glaucomas detected a TBK1 copy-number variation in a patient with exfoliation glaucoma, which is the first example of a TBK1 mutation in a glaucoma patient with a diagnosis other than normal-tension glaucoma. A broader phenotypic range may be associated with TBK1 copy-number variations, although mutations in this gene are most often detected in patients with normal-tension glaucoma.

A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data.

PubMed

Demidov, German; Simakova, Tamara; Vnuchkova, Julia; Bragin, Anton

2016-10-22

Multiplex polymerase chain reaction (PCR) is a common enrichment technique for targeted massive parallel sequencing (MPS) protocols. MPS is widely used in biomedical research and clinical diagnostics as the fast and accurate tool for the detection of short genetic variations. However, identification of larger variations such as structure variants and copy number variations (CNV) is still being a challenge for targeted MPS. Some approaches and tools for structural variants detection were proposed, but they have limitations and often require datasets of certain type, size and expected number of amplicons affected by CNVs. In the paper, we describe novel algorithm for high-resolution germinal CNV detection in the PCR-enriched targeted sequencing data and present accompanying tool. We have developed a machine learning algorithm for the detection of large duplications and deletions in the targeted sequencing data generated with PCR-based enrichment step. We have performed verification studies and established the algorithm's sensitivity and specificity. We have compared developed tool with other available methods applicable for the described data and revealed its higher performance. We showed that our method has high specificity and sensitivity for high-resolution copy number detection in targeted sequencing data using large cohort of samples.

THE TWO REGIMES OF PHOTOSPHERIC MOTIONS IN {alpha} HYDRA

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

Gray, David F., E-mail: dfgray@uwo.ca

2013-02-10

High-resolution spectroscopic observations of {alpha} Hya were acquired between 2003 and 2010. Analysis of line shifts, differential shifts, line widths, and line bisectors points to two regimes of velocity fields in the photosphere of {alpha} Hya: (1) normal granulation embedded in (2) large convection cells. Variations occur on a wide range of timescales, from several years on down. Radial velocity variations, which are irregular and span 786 m s{sup -1}, have a distribution consistent with a true mean rise velocity of the large cells of {approx}725 m s{sup -1} and a dispersion of {approx}220 m s{sup -1}. The distribution ofmore » granulation velocities, as measured from the widths of spectral lines, shows only small variations, consistent with the two regime concepts. On the multi-year timescale, radial velocity changes, small temperature variations ({approx}10 K), and small line-width variations ({approx}<0.8%) track each other, possibly with phase shifts. The granulation velocity gradient for {alpha} Hya is about half as large as the Sun's and no variation with time was seen, implying that any variation in velocity gradient from one large cell to the next must be less than a few percent. The asymmetry in the granulation velocity distribution, as specified in the flux deficit, is smaller than expected for {alpha} Hya's position in the HR diagram and appears to be variable.« less

Global patterns of kelp forest change over the past half-century.

PubMed

Krumhansl, Kira A; Okamoto, Daniel K; Rassweiler, Andrew; Novak, Mark; Bolton, John J; Cavanaugh, Kyle C; Connell, Sean D; Johnson, Craig R; Konar, Brenda; Ling, Scott D; Micheli, Fiorenza; Norderhaug, Kjell M; Pérez-Matus, Alejandro; Sousa-Pinto, Isabel; Reed, Daniel C; Salomon, Anne K; Shears, Nick T; Wernberg, Thomas; Anderson, Robert J; Barrett, Nevell S; Buschmann, Alejandro H; Carr, Mark H; Caselle, Jennifer E; Derrien-Courtel, Sandrine; Edgar, Graham J; Edwards, Matt; Estes, James A; Goodwin, Claire; Kenner, Michael C; Kushner, David J; Moy, Frithjof E; Nunn, Julia; Steneck, Robert S; Vásquez, Julio; Watson, Jane; Witman, Jon D; Byrnes, Jarrett E K

2016-11-29

Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = -0.018 y -1 ). Our analysis identified declines in 38% of ecoregions for which there are data (-0.015 to -0.18 y -1 ), increases in 27% of ecoregions (0.015 to 0.11 y -1 ), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.

Detection of long term persistence in time series of the Neuquen River (Argentina)

NASA Astrophysics Data System (ADS)

Seoane, Rafael; Paz González, Antonio

2014-05-01

In the Patagonian region (Argentina), previous hydrometeorological studies that have been developed using general circulation models show variations in annual mean flows. Future climate scenarios obtained from high-resolution models indicate decreases in total annual precipitation, and these scenarios are more important in the Neuquén river basin (23000 km2). The aim of this study was the estimation of long term persistence in the Neuquén River basin (Argentina). The detection of variations in the long range dependence term and long memory of time series was evaluated with the Hurst exponent. We applied rescaled adjusted range analysis (R/S) to time series of River discharges measured from 1903 to 2011 and this time series was divided into two subperiods: the first was from 1903 to 1970 and the second from 1970 to 2011. Results show a small increase in persistence for the second period. Our results are consistent with those obtained by Koch and Markovic (2007), who observed and estimated an increase of the H exponent for the period 1960-2000 in the Elbe River (Germany). References Hurst, H. (1951).Long term storage capacities of reservoirs". Trans. Am. Soc. Civil Engrs., 116:776-808. Koch and Markovic (2007). Evidences for Climate Change in Germany over the 20th Century from the Stochastic Analysis of hydro-meteorological Time Series, MODSIM07, International Congress on Modelling and Simulation, Christchurch, New Zealand.

Global patterns of kelp forest change over the past half-century

PubMed Central

Krumhansl, Kira A.; Okamoto, Daniel K.; Rassweiler, Andrew; Novak, Mark; Bolton, John J.; Cavanaugh, Kyle C.; Connell, Sean D.; Johnson, Craig R.; Konar, Brenda; Ling, Scott D.; Micheli, Fiorenza; Norderhaug, Kjell M.; Pérez-Matus, Alejandro; Sousa-Pinto, Isabel; Reed, Daniel C.; Salomon, Anne K.; Shears, Nick T.; Wernberg, Thomas; Anderson, Robert J.; Barrett, Nevell S.; Buschmann, Alejandro H.; Carr, Mark H.; Caselle, Jennifer E.; Derrien-Courtel, Sandrine; Edgar, Graham J.; Edwards, Matt; Estes, James A.; Goodwin, Claire; Kenner, Michael C.; Kushner, David J.; Nunn, Julia; Steneck, Robert S.; Vásquez, Julio; Watson, Jane; Witman, Jon D.

2016-01-01

Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = −0.018 y−1). Our analysis identified declines in 38% of ecoregions for which there are data (−0.015 to −0.18 y−1), increases in 27% of ecoregions (0.015 to 0.11 y−1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species. PMID:27849580

Automatic Telescope Search for Extrasolar Planets

NASA Technical Reports Server (NTRS)

Henry, Gregory W.

1998-01-01

We are using automatic photoelectric telescopes at the Tennessee State University Center for Automated Space Science to search for planets around nearby stars in our galaxy. Over the past several years, wc have developed the capability to make extremely precise measurements of brightness changes in Sun-like stars with automatic telescopes. Extensive quality control and calibration measurements result in a precision of 0.l% for a single nightly observation and 0.0270 for yearly means, far better than previously thought possible with ground-based observations. We are able, for the first time, to trace brightness changes in Sun-like stars that are of similar amplitude to brightness changes in the Sun, whose changes can be observed only with space-based radiometers. Recently exciting discoveries of the first extrasolar planets have been announced, based on the detection of very small radial-velocity variations that imply the existence of planets in orbit around several Sun-like stars. Our precise brightness measurements have been crucial for the confirmation of these discoveries by helping to eliminate alternative explanations for the radial-velocity variations. With our automatic telescopes, we are also searching for transits of these planets across the disks of their stars in order to conclusively verify their existence. The detection of transits would provide the first direct measurements of the sizes, masses, and densities of these planets and, hence, information on their compositions and origins.

Improving the quality of mass produced maps

USGS Publications Warehouse

Simley, J.

2001-01-01

Quality is critical in cartography because key decisions are often made based on the information the map communicates. The mass production of digital cartographic information to support geographic information science has now added a new dimension to the problem of cartographic quality, as problems once limited to small volumes can now proliferate in mass production programs. These problems can also affect the economics of map production by diverting a sizeable portion of production cost to pay for rework on maps with poor quality. Such problems are common to general industry-in response, the quality engineering profession has developed a number of successful methods to overcome these problems. Two important methods are the reduction of error through statistical analysis and addressing the quality environment in which people work. Once initial and obvious quality problems have been solved, outside influences periodically appear that cause adverse variations in quality and consequently increase production costs. Such errors can be difficult to detect before the customer is affected. However, a number of statistical techniques can be employed to detect variation so that the problem is eliminated before significant damage is caused. Additionally, the environment in which the workforce operates must be conductive to quality. Managers have a powerful responsibility to create this environment. Two sets of guidelines, known as Deming's Fourteen Points and ISO-9000, provide models for this environment.

Genetic variation in scaly hair-fin anchovy Setipinna tenuifilis (Engraulididae) based on the mitochondrial DNA control region.

PubMed

Xu, Shengyong; Song, Na; Lu, Zhichuang; Wang, Jun; Cai, Shanshan; Gao, Tianxiang

2014-06-01

Scaly hair-fin anchovy (Setipinna tenuifilis) is a small, pelagic and economical species and widely distributed in Chinese coastal water. However, resources of S. tenuifilis have been reduced due to overfishing. For better fishery management, it is necessary to understand the pattern of S. tenuifilis's biogeography. Genetic analyses were taken place to detect their population genetic variation. A total of 153 individuals from 7 locations (Dongying, Yantai, Qingdao, Nantong, Wenzhou, Xiamen and Beibu Bay) were sequenced at the 5' end of mtDNA control region. A 39-bp tandem repeated sequence was found at the 5' end of the segment and a polymorphism of tandem repeated sequence was detected among 7 populations. Both mismatch distribution analysis and neutrality tests showed S. tenuifilis had experienced a recent population expansion. The topology of neighbor-joining tree and Bayesian evolutionary tree showed no significant genealogical branches or clusters of samples corresponding to sampling locality. Hierarchical analysis of molecular variance and conventional pairwise population Fst value at group hierarchical level implied that there might have genetic divergence between southern group (population WZ, XM and BB) and northern group (population DY, YT, QD and NT). We concluded that there might have three different fishery management groups of S. tenuifilis and the late Pleistocene glacial event might have a crucial effect on present-day demography of S. tenuifilis in this region.

GRACE Hydrological estimates for small basins: Evaluating processing approaches on the High Plains Aquifer, USA

NASA Astrophysics Data System (ADS)

Longuevergne, Laurent; Scanlon, Bridget R.; Wilson, Clark R.

2010-11-01

The Gravity Recovery and Climate Experiment (GRACE) satellites provide observations of water storage variation at regional scales. However, when focusing on a region of interest, limited spatial resolution and noise contamination can cause estimation bias and spatial leakage, problems that are exacerbated as the region of interest approaches the GRACE resolution limit of a few hundred km. Reliable estimates of water storage variations in small basins require compromises between competing needs for noise suppression and spatial resolution. The objective of this study was to quantitatively investigate processing methods and their impacts on bias, leakage, GRACE noise reduction, and estimated total error, allowing solution of the trade-offs. Among the methods tested is a recently developed concentration algorithm called spatiospectral localization, which optimizes the basin shape description, taking into account limited spatial resolution. This method is particularly suited to retrieval of basin-scale water storage variations and is effective for small basins. To increase confidence in derived methods, water storage variations were calculated for both CSR (Center for Space Research) and GRGS (Groupe de Recherche de Géodésie Spatiale) GRACE products, which employ different processing strategies. The processing techniques were tested on the intensively monitored High Plains Aquifer (450,000 km2 area), where application of the appropriate optimal processing method allowed retrieval of water storage variations over a portion of the aquifer as small as ˜200,000 km2.

A Study of Sociolinguistic Variation in a Small Community: Puerto Rican Spanish in Amsterdam, New York

ERIC Educational Resources Information Center

Mumin, Zahir

2017-01-01

The objective of the current study is to contribute to the larger body of sociophonetic variation research by describing and analyzing Spanish as spoken in a small Puerto Rican community in the US. First, I describe phonological and morphosyntactic features of Spanish as used by four different groups of Puerto Rican informants in Amsterdam, New…

[A boy with Meier-Gorlin syndrome carrying a novel ORC6 mutation and uniparental disomy of chromosome 16].

PubMed

Li, Juan; Ding, Yu; Chang, Guoying; Cheng, Qing; Li, Xin; Wang, Jian; Wang, Xiumin; Shen, Yiping

2017-02-10

To identify the genetic cause for a 11-year-old Chinese boy with Meier-Gorlin syndrome (MGS). Chromosomal microarray analysis (CMA) was used to detect potential variations, while whole exome sequencing (WES) was used to identify sequence variants. Sanger sequencing was used to confirm the suspected variants. The boy has featured short stature, microtia, small patella, slender body build, craniofacial anomalies, and small testes with normal gonadotropin. A complete uniparental disomy of chromosome 16 was revealed by CMA. WES has identified a novel homozygous mutation c.67A>G (p.Lys23Glu) in ORC6 gene mapped to chromosome 16. As predicted by Alamut functional software, the mutation may affect the function of structural domain of the ORC6 protein. The patient is probably the first diagnosed MGS case in China, who carried a novel homozygous mutation of the ORC6 gene and uniparental disomy of chromosome 16. The effect of this novel mutation on the growth and development needs to be further investigated.

A comparison of two types of neural network for weld quality prediction in small scale resistance spot welding

NASA Astrophysics Data System (ADS)

Wan, Xiaodong; Wang, Yuanxun; Zhao, Dawei; Huang, YongAn

2017-09-01

Our study aims at developing an effective quality monitoring system in small scale resistance spot welding of titanium alloy. The measured electrical signals were interpreted in combination with the nugget development. Features were extracted from the dynamic resistance and electrode voltage curve. A higher welding current generally indicated a lower overall dynamic resistance level. A larger electrode voltage peak and higher change rate of electrode voltage could be detected under a smaller electrode force or higher welding current condition. Variation of the extracted features and weld quality was found more sensitive to the change of welding current than electrode force. Different neural network model were proposed for weld quality prediction. The back propagation neural network was more proper in failure load estimation. The probabilistic neural network model was more appropriate to be applied in quality level classification. A real-time and on-line weld quality monitoring system may be developed by taking advantages of both methods.

Tide-related variability of TAG hydrothermal activity observed by deep-sea monitoring system and OBSH

NASA Astrophysics Data System (ADS)

Fujioka, Kantaro; Kobayashi, Kazuo; Kato, Kazuhiro; Aoki, Misumi; Mitsuzawa, Kyohiko; Kinoshita, Masataka; Nishizawa, Azusa

1997-12-01

Hydrothermal activities were monitored by an ocean bottom seismometer with hydrophone (OBSH) and a composite measuring system (Manatee) including CTD, current meter, transmission meter and cameras at a small depression on the TAG hydrothermal mound in the Mid-Atlantic Ridge. Low-frequency pressure pulses detected by the hydrophone with semi-diurnal periodicity seem to correspond to cycles of hydrothermal upflow from a small and short-lived smoker vent close to the observing site. The peaks of pressure pulses are synchronous with the maximum gradient of areal strain decrease due to tidal load release. Microearthquakes with very near epicenters occur sporadically and do not appear to be directly correlatable to hydrothermal venting. Temporal variations in bottom water temperature also have semi-diurnal periodicity but are more complicated than the pressure events. Temperatures may be affected both by upwelling of hot water and by lateral flow of the bottom current changing its directions with ocean tide.

Solar Cycle Variability and Surface Differential Rotation from Ca II K-line Time Series Data

NASA Astrophysics Data System (ADS)

Scargle, Jeffrey D.; Keil, Stephen L.; Worden, Simon P.

2013-07-01

Analysis of over 36 yr of time series data from the NSO/AFRL/Sac Peak K-line monitoring program elucidates 5 components of the variation of the 7 measured chromospheric parameters: (a) the solar cycle (period ~ 11 yr), (b) quasi-periodic variations (periods ~ 100 days), (c) a broadband stochastic process (wide range of periods), (d) rotational modulation, and (e) random observational errors, independent of (a)-(d). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these parameters. Time-frequency analysis illuminates periodic and quasi-periodic signals, details of frequency modulation due to differential rotation, and in particular elucidates the rather complex harmonic structure (a) and (b) at timescales in the range ~0.1-10 yr. These results using only full-disk data suggest that similar analyses will be useful for detecting and characterizing differential rotation in stars from stellar light curves such as those being produced by NASA's Kepler observatory. Component (c) consists of variations over a range of timescales, in the manner of a 1/f random process with a power-law slope index that varies in a systematic way. A time-dependent Wilson-Bappu effect appears to be present in the solar cycle variations (a), but not in the more rapid variations of the stochastic process (c). Component (d) characterizes differential rotation of the active regions. Component (e) is of course not characteristic of solar variability, but the fact that the observational errors are quite small greatly facilitates the analysis of the other components. The data analyzed in this paper can be found at the National Solar Observatory Web site http://nsosp.nso.edu/cak_mon/, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.

SOLAR CYCLE VARIABILITY AND SURFACE DIFFERENTIAL ROTATION FROM Ca II K-LINE TIME SERIES DATA

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

Scargle, Jeffrey D.; Worden, Simon P.; Keil, Stephen L.

Analysis of over 36 yr of time series data from the NSO/AFRL/Sac Peak K-line monitoring program elucidates 5 components of the variation of the 7 measured chromospheric parameters: (a) the solar cycle (period {approx} 11 yr), (b) quasi-periodic variations (periods {approx} 100 days), (c) a broadband stochastic process (wide range of periods), (d) rotational modulation, and (e) random observational errors, independent of (a)-(d). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these parameters. Time-frequency analysis illuminates periodic and quasi-periodic signals, details of frequency modulation due to differential rotation, and in particular elucidates the rather complex harmonic structuremore » (a) and (b) at timescales in the range {approx}0.1-10 yr. These results using only full-disk data suggest that similar analyses will be useful for detecting and characterizing differential rotation in stars from stellar light curves such as those being produced by NASA's Kepler observatory. Component (c) consists of variations over a range of timescales, in the manner of a 1/f random process with a power-law slope index that varies in a systematic way. A time-dependent Wilson-Bappu effect appears to be present in the solar cycle variations (a), but not in the more rapid variations of the stochastic process (c). Component (d) characterizes differential rotation of the active regions. Component (e) is of course not characteristic of solar variability, but the fact that the observational errors are quite small greatly facilitates the analysis of the other components. The data analyzed in this paper can be found at the National Solar Observatory Web site http://nsosp.nso.edu/cak{sub m}on/, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.« less

Heritable Variation for Sex Ratio under Environmental Sex Determination in the Common Snapping Turtle (Chelydra Serpentina)

PubMed Central

Janzen, F. J.

1992-01-01

The magnitude of quantitative genetic variation for primary sex ratio was measured in families extracted from a natural population of the common snapping turtle (Chelydra serpentina), which possesses temperature-dependent sex determination (TSD). Eggs were incubated at three temperatures that produced mixed sex ratios. This experimental design provided estimates of the heritability of sex ratio in multiple environments and a test of the hypothesis that genotype X environment (G X E) interactions may be maintaining genetic variation for sex ratio in this population of C. serpentina. Substantial quantitative genetic variation for primary sex ratio was detected in all experimental treatments. These results in conjunction with the occurrence of TSD in this species provide support for three critical assumptions of Fisher's theory for the microevolution of sex ratio. There were statistically significant effects of family and incubation temperature on sex ratio, but no significant interaction was observed. Estimates of the genetic correlations of sex ratio across environments were highly positive and essentially indistinguishable from +1. These latter two findings suggest that G X E interaction is not the mechanism maintaining genetic variation for sex ratio in this system. Finally, although substantial heritable variation exists for primary sex ratio of C. serpentina under constant temperatures, estimates of the effective heritability of primary sex ratio in nature are approximately an order of magnitude smaller. Small effective heritability and a long generation time in C. serpentina imply that evolution of sex ratios would be slow even in response to strong selection by, among other potential agents, any rapid and/or substantial shifts in local temperatures, including those produced by changes in the global climate. PMID:1592234

Average of delta: a new quality control tool for clinical laboratories.

PubMed

Jones, Graham R D

2016-01-01

Average of normals is a tool used to control assay performance using the average of a series of results from patients' samples. Delta checking is a process of identifying errors in individual patient results by reviewing the difference from previous results of the same patient. This paper introduces a novel alternate approach, average of delta, which combines these concepts to use the average of a number of sequential delta values to identify changes in assay performance. Models for average of delta and average of normals were developed in a spreadsheet application. The model assessed the expected scatter of average of delta and average of normals functions and the effect of assay bias for different values of analytical imprecision and within- and between-subject biological variation and the number of samples included in the calculations. The final assessment was the number of patients' samples required to identify an added bias with 90% certainty. The model demonstrated that with larger numbers of delta values, the average of delta function was tighter (lower coefficient of variation). The optimal number of samples for bias detection with average of delta was likely to be between 5 and 20 for most settings and that average of delta outperformed average of normals when the within-subject biological variation was small relative to the between-subject variation. Average of delta provides a possible additional assay quality control tool which theoretical modelling predicts may be more valuable than average of normals for analytes where the group biological variation is wide compared with within-subject variation and where there is a high rate of repeat testing in the laboratory patient population. © The Author(s) 2015.

Visibility vs. biomass in flowers: exploring corolla allocation in Mediterranean entomophilous plants

PubMed Central

Herrera, Javier

2009-01-01

Background and Aims While pollinators may in general select for large, morphologically uniform floral phenotypes, drought stress has been proposed as a destabilizing force that may favour small flowers and/or promote floral variation within species. Methods The general validity of this concept was checked by surveying a taxonomically diverse array of 38 insect-pollinated Mediterranean species. The interplay between fresh biomass investment, linear size and percentage corolla allocation was studied. Allometric relationships between traits were investigated by reduced major-axis regression, and qualitative correlates of floral variation explored using general linear-model MANOVA. Key Results Across species, flowers were perfectly isometrical with regard to corolla allocation (i.e. larger flowers were just scaled-up versions of smaller ones and vice versa). In contrast, linear size and biomass varied allometrically (i.e. there were shape variations, in addition to variations in size). Most floral variables correlated positively and significantly across species, except corolla allocation, which was largely determined by family membership and floral symmetry. On average, species with bilateral flowers allocated more to the corolla than those with radial flowers. Plant life-form was immaterial to all of the studied traits. Flower linear size variation was in general low among conspecifics (coefficients of variation around 10 %), whereas biomass was in general less uniform (e.g. 200–400 mg in Cistus salvifolius). Significant among-population differences were detected for all major quantitative floral traits. Conclusions Flower miniaturization can allow an improved use of reproductive resources under prevailingly stressful conditions. The hypothesis that flower size reflects a compromise between pollinator attraction, water requirements and allometric constraints among floral parts is discussed. PMID:19258340

Detecting changes resulting from human pressure in a naturally quick-changing and heterogeneous environment: Spatial and temporal scales of variability in coastal lagoons

NASA Astrophysics Data System (ADS)

Pérez-Ruzafa, A.; Marcos, C.; Pérez-Ruzafa, I. M.; Barcala, E.; Hegazi, M. I.; Quispe, J.

2007-10-01

To detect changes in ecosystems due to human impact, experimental designs must include replicates at the appropriate scale to avoid pseudoreplication. Although coastal lagoons, with their highly variable environmental factors and biological assemblages, are relatively well-studied systems, very little is known about their natural scales of variation. In this study, we investigate the spatio-temporal scales of variability in the Mar Menor coastal lagoon (SE Spain) using structured hierarchical sampling designs, mixed and permutational multi-variate analyses of variance, and ordination multi-variate analyses applied to hydrographical parameters, nutrients, chlorophyll a and ichthyoplankton in the water column, and to macrophyte and fish benthic assemblages. Lagoon processes in the Mar Menor show heterogeneous patterns at different temporal and spatial scales. The water column characteristics (including nutrient concentration) showed small-scale spatio-temporal variability, from 10 0 to 10 1 km and from fortnightly to seasonally. Biological features (chlorophyll a concentration and ichthyoplankton assemblage descriptors) showed monthly changes and spatial patterns at the scale of 10 0 (chlorophyll a) - 10 1 km (ichthyoplankton). Benthic assemblages (macrophytes and fishes) showed significant differences between types of substrates in the same locality and between localities, according to horizontal gradients related with confinement in the lagoon, at the scale of 10 0-10 1 km. The vertical zonation of macrophyte assemblages (at scales of 10 1-10 2 cm) overlaps changes in substrata and horizontal gradients. Seasonal patterns in vegetation biomass were not significant, but the significant interaction between Locality and Season indicated that the seasons of maximum and minimum biomass depend on local environmental conditions. Benthic fish assemblages showed no significant patterns at the monthly scale but did show seasonal patterns.

Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping

PubMed Central

Wang, Xiaoming; Kudrna, David A.; Pan, Yonglong; Wang, Hao; Liu, Lin; Lin, Haiyan; Zhang, Jianwei; Song, Xiang; Goicoechea, Jose Luis; Wing, Rod A.; Zhang, Qifa; Luo, Meizhong

2014-01-01

Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html). PMID:24424778

Snapping shrimp sound production patterns on Caribbean coral reefs: relationships with celestial cycles and environmental variables

NASA Astrophysics Data System (ADS)

Lillis, Ashlee; Mooney, T. Aran

2018-06-01

The rich acoustic environment of coral reefs, including the sounds of a variety of fish and invertebrates, is a reflection of the structural complexity and biological diversity of these habitats. Emerging interest in applying passive acoustic monitoring and soundscape analysis to measure coral reef habitat characteristics and track ecological patterns is hindered by a poor understanding of the most common and abundant sound producers on reefs—the snapping shrimp. Here, we sought to address several basic biophysical drivers of reef sound by investigating acoustic activity patterns of snapping shrimp populations on two adjacent coral reefs using a detailed snap detection analysis routine to a high-resolution 2.5-month acoustic dataset from the US Virgin Islands. The reefs exhibited strong diel and lunar periodicity in snap rates and clear spatial differences in snapping levels. Snap rates peaked at dawn and dusk and were higher overall during daytime versus nighttime, a seldom-reported pattern in earlier descriptions of diel snapping shrimp acoustic activity. Small differences between the sites in snap rate rhythms were detected and illustrate how analyses of specific soundscape elements might reveal subtle between-reef variation. Snap rates were highly correlated with environmental variables, including water temperature and light, and were found to be sensitive to changes in oceanographic forcing. This study further establishes snapping shrimp as key players in the coral reef chorus and provides evidence that their acoustic output reflects a combination of environmental conditions, celestial influences, and spatial habitat variation. Effective application of passive acoustic monitoring in coral reef habitats using snap rates or snapping-influenced acoustic metrics will require a mechanistic understanding of the underlying spatial and temporal variation in snapping shrimp sound production across multiple scales.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

Population Census of a Large Common Tern Colony with a Small Unmanned Aircraft

PubMed Central

Chabot, Dominique; Craik, Shawn R.; Bird, David M.

2015-01-01

Small unmanned aircraft systems (UAS) may be useful for conducting high-precision, low-disturbance waterbird surveys, but limited data exist on their effectiveness. We evaluated the capacity of a small UAS to census a large (>6,000 nests) coastal Common tern (Sterna hirundo) colony of which ground surveys are particularly disruptive and time-consuming. We compared aerial photographic tern counts to ground nest counts in 45 plots (5-m radius) throughout the colony at three intervals over a nine-day period in order to identify sources of variation and establish a coefficient to estimate nest numbers from UAS surveys. We also compared a full colony ground count to full counts from two UAS surveys conducted the following day. Finally, we compared colony disturbance levels over the course of UAS flights to matched control periods. Linear regressions between aerial and ground counts in plots had very strong correlations in all three comparison periods (R 2 = 0.972–0.989, P < 0.001) and regression coefficients ranged from 0.928–0.977 terns/nest. Full colony aerial counts were 93.6% and 94.0%, respectively, of the ground count. Varying visibility of terns with ground cover, weather conditions and image quality, and changing nest attendance rates throughout incubation were likely sources of variation in aerial detection rates. Optimally timed UAS surveys of Common tern colonies following our method should yield population estimates in the 93–96% range of ground counts. Although the terns were initially disturbed by the UAS flying overhead, they rapidly habituated to it. Overall, we found no evidence of sustained disturbance to the colony by the UAS. We encourage colonial waterbird researchers and managers to consider taking advantage of this burgeoning technology. PMID:25874997

A fast and mobile system for registration of low-altitude visual and thermal aerial images using multiple small-scale UAVs

NASA Astrophysics Data System (ADS)

Yahyanejad, Saeed; Rinner, Bernhard

2015-06-01

The use of multiple small-scale UAVs to support first responders in disaster management has become popular because of their speed and low deployment costs. We exploit such UAVs to perform real-time monitoring of target areas by fusing individual images captured from heterogeneous aerial sensors. Many approaches have already been presented to register images from homogeneous sensors. These methods have demonstrated robustness against scale, rotation and illumination variations and can also cope with limited overlap among individual images. In this paper we focus on thermal and visual image registration and propose different methods to improve the quality of interspectral registration for the purpose of real-time monitoring and mobile mapping. Images captured by low-altitude UAVs represent a very challenging scenario for interspectral registration due to the strong variations in overlap, scale, rotation, point of view and structure of such scenes. Furthermore, these small-scale UAVs have limited processing and communication power. The contributions of this paper include (i) the introduction of a feature descriptor for robustly identifying corresponding regions of images in different spectrums, (ii) the registration of image mosaics, and (iii) the registration of depth maps. We evaluated the first method using a test data set consisting of 84 image pairs. In all instances our approach combined with SIFT or SURF feature-based registration was superior to the standard versions. Although we focus mainly on aerial imagery, our evaluation shows that the presented approach would also be beneficial in other scenarios such as surveillance and human detection. Furthermore, we demonstrated the advantages of the other two methods in case of multiple image pairs.

Tides and Decadal Variability

NASA Technical Reports Server (NTRS)

Ray, Richard D.

2003-01-01

This paper reviews the mechanisms by which oceanic tides and decadal variability in the oceans are connected. We distinguish between variability caused by tides and variability observed in the tides themselves. Both effects have been detected at some level. The most obvious connection with decadal timescales is through the 18.6-year precession of the moon's orbit plane. This precession gives rise to a small tide of the same period and to 18.6-year modulations in the phase and amplitudes of short-period tides. The 18.6-year "node tide" is very small, no more than 2 cm anywhere, and in sea level data it is dominated by the ocean's natural Variability. Some authors have naively attributed climate variations with periods near 19 years directly to the node tide, but the amplitude of the tide is too small for this mechanism to be operative. The more likely explanation (Loder and Garrett, JGR, 83, 1967-70, 1978) is that the 18.6-y modulations in short-period tides, especially h e principal tide M2, cause variations in ocean mixing, which is then observed in temperature and other climatic indicators. Tidally forced variability has also been proposed by some authors, either in response to occasional (and highly predictable) tidal extremes or as a nonlinear low-frequency oscillation caused by interactions between short-period tides. The former mechanism can produce only short-duration events hardly more significant than normal tidal ranges, but the latter mechanism can in principle induce low-frequency oscillations. The most recent proposal of this type is by Keeling and Whorf, who highlight the 1800-year spectral peak discovered by Bond et al. (1997). But the proposal appears contrived and should be considered, in the words of Munk et al. (2002), "as the most likely among unlikely candidates."

Techniques A: continuous waves

NASA Astrophysics Data System (ADS)

Beuthan, J.

1993-08-01

In a vast amount of medical diseases the biochemical and physiological changes of soft tissues are hardly detectable by conventional techniques of diagnostic imaging (x- ray, ultrasound, computer tomography, and MRI). The detectivity is low and the technical efforts are tremendous. On the other hand these pathologic variations induce significant changes of the optical tissue parameters which can be detected. The corresponding variations of the scattered light can most easily be detected and evaluated by infrared diaphanoscopy, even on optical thick tissue slices.

Life history of the Small Sandeel, Ammodytes tobianus, inferred from otolith microchemistry. A methodological approach

NASA Astrophysics Data System (ADS)

Laugier, F.; Feunteun, E.; Pecheyran, C.; Carpentier, A.

2015-11-01

Knowledge of life history and connectivity between essential ecological habitats are relevant for conservation and management of species and some natural tracers could be used to study the lifecycles of small or short-lived marine fishes. Although sandeels are central in marine food webs and are key species, there is incomplete knowledge about population mixing and migration patterns. For the first time the use of the otolith microchemistry on sandeel species is evaluated in the case of the Small Sandeel. Variations in microchemical fingerprints of 13 trace elements are performed with a Femtosecond LA-ICPM from the core to the margin of sagittal otolith and are compared within and between otoliths extracted from 34 fishes sampled in three different sites along the coast of the south-western English Channel in France. Firstly, preliminary investigations on the validity of the method revealed that Mg/Ca was the only ratio significantly dependant on fish ontogeny and sampling season. Secondly, the Mn/Ca, Zn/Ca, and Cu/Ca ratios enabled us to significantly discriminate among sampling sites. Thirdly, microchemical fingerprints of each life stage varied significantly among sampling sites but not within them, suggesting high site fidelity over relatively short distances. Finally, the fingerprints of all life stages were significantly different from those of the larval and metamorphosis stages. The otolith microchemistry could detect change of signature relative to the shift from a pelagic behaviour to a resident bentho-pelagic behaviour during the middle of the juvenile stage in Small Sandeels. Hence, analysis of trace element fingerprints in otoliths appears to be a valuable method to further studies on ontogenic habitat change, population mixing and variation of life history and be helpful for the management at local or regional scales of short-lived species such as those belonging to other Ammodytidae.

Genetic analysis of CHST6 and TGFBI in Turkish patients with corneal dystrophies: Five novel variations in CHST6

PubMed Central

Yaylacioglu Tuncay, Fulya; Kayman Kurekci, Gülsüm; Guntekin Ergun, Sezen; Pasaoglu, Ozge Tugce; Akata, Rustu Fikret; Dincer, Pervin Rukiye

2016-01-01

Purpose To identify pathogenic variations in carbohydrate sulfotransferase 6 (CHST6) and transforming growth factor, beta-induced (TGFBI) genes in Turkish patients with corneal dystrophy (CD). Methods In this study, patients with macular corneal dystrophy (MCD; n = 18), granular corneal dystrophy type 1 (GCD1; n = 12), and lattice corneal dystrophy type 1 (LCD1; n = 4), as well as 50 healthy controls, were subjected to clinical and genetic examinations. The level of antigenic keratan sulfate (AgKS) in the serum samples of patients with MCD was determined with enzyme-linked immunosorbent assay (ELISA) to immunophenotypically subtype the patients as MCD type I and MCD type II. DNA was isolated from venous blood samples from the patients and controls. Variations were analyzed with DNA sequencing in the coding region of CHST6 in patients with MCD and exons 4 and 12 in TGFBI in patients with LCD1 and GCD1. Clinical characteristics and the detected variations were evaluated to determine any existing genotype–phenotype correlations. Results The previously reported R555W mutation in TGFBI was detected in 12 patients with GCD1, and the R124C mutation in TGFBI was detected in four patients with LCD1. Serum AgKS levels indicated that 12 patients with MCD were in subgroup I, and five patients with MCD were in subgroup II. No genetic variation was detected in the coding region of CHST6 for three patients with MCD type II. In other patients with MCD, three previously reported missense variations (c. 1A>T, c.738C>G, and c.631 C>T), three novel missense variations (c.164 T>C, c.526 G>A, c. 610 C>T), and two novel frameshift variations (c.894_895 insG and c. 462_463 delGC) were detected. These variations did not exist in the control chromosomes, 1000 Genomes, and dbSNP. Conclusions This is the first molecular analysis of TGFBI and CHST6 in Turkish patients with different types of CD. We detected previously reported, well-known hot spot mutations in TGFBI in the patients with GCD1 and LCD1. Eight likely pathogenic variations in CHST6, five of them novel, were reported in patients with MCD, which enlarges the mutational spectrum of MCD. PMID:27829782

Genetic analysis of CHST6 and TGFBI in Turkish patients with corneal dystrophies: Five novel variations in CHST6.

PubMed

Yaylacioglu Tuncay, Fulya; Kayman Kurekci, Gülsüm; Guntekin Ergun, Sezen; Pasaoglu, Ozge Tugce; Akata, Rustu Fikret; Dincer, Pervin Rukiye

2016-01-01

To identify pathogenic variations in carbohydrate sulfotransferase 6 ( CHST6 ) and transforming growth factor, beta-induced ( TGFBI ) genes in Turkish patients with corneal dystrophy (CD). In this study, patients with macular corneal dystrophy (MCD; n = 18), granular corneal dystrophy type 1 (GCD1; n = 12), and lattice corneal dystrophy type 1 (LCD1; n = 4), as well as 50 healthy controls, were subjected to clinical and genetic examinations. The level of antigenic keratan sulfate (AgKS) in the serum samples of patients with MCD was determined with enzyme-linked immunosorbent assay (ELISA) to immunophenotypically subtype the patients as MCD type I and MCD type II. DNA was isolated from venous blood samples from the patients and controls. Variations were analyzed with DNA sequencing in the coding region of CHST6 in patients with MCD and exons 4 and 12 in TGFBI in patients with LCD1 and GCD1. Clinical characteristics and the detected variations were evaluated to determine any existing genotype-phenotype correlations. The previously reported R555W mutation in TGFBI was detected in 12 patients with GCD1, and the R124C mutation in TGFBI was detected in four patients with LCD1. Serum AgKS levels indicated that 12 patients with MCD were in subgroup I, and five patients with MCD were in subgroup II. No genetic variation was detected in the coding region of CHST6 for three patients with MCD type II. In other patients with MCD, three previously reported missense variations (c. 1A>T, c.738C>G, and c.631 C>T), three novel missense variations (c.164 T>C, c.526 G>A, c. 610 C>T), and two novel frameshift variations (c.894_895 insG and c. 462_463 delGC) were detected. These variations did not exist in the control chromosomes, 1000 Genomes, and dbSNP. This is the first molecular analysis of TGFBI and CHST6 in Turkish patients with different types of CD. We detected previously reported, well-known hot spot mutations in TGFBI in the patients with GCD1 and LCD1. Eight likely pathogenic variations in CHST6 , five of them novel, were reported in patients with MCD, which enlarges the mutational spectrum of MCD.

Device for detecting imminent failure of high-dielectric stress capacitors. [Patent application

DOEpatents

McDuff, G.G.

1980-11-05

A device is described for detecting imminent failure of a high-dielectric stress capacitor utilizing circuitry for detecting pulse width variations and pulse magnitude variations. Inexpensive microprocessor circuitry is utilized to make numerical calculations of digital data supplied by detection circuitry for comparison of pulse width data and magnitude data to determine if preselected ranges have been exceeded, thereby indicating imminent failure of a capacitor. Detection circuitry may be incorporated in transmission lines, pulse power circuitry, including laser pulse circuitry or any circuitry where capacitors or capacitor banks are utilized.

Device for detecting imminent failure of high-dielectric stress capacitors

DOEpatents

McDuff, George G.

1982-01-01

A device for detecting imminent failure of a high-dielectric stress capacitor utilizing circuitry for detecting pulse width variations and pulse magnitude variations. Inexpensive microprocessor circuitry is utilized to make numerical calculations of digital data supplied by detection circuitry for comparison of pulse width data and magnitude data to determine if preselected ranges have been exceeded, thereby indicating imminent failure of a capacitor. Detection circuitry may be incorporated in transmission lines, pulse power circuitry, including laser pulse circuitry or any circuitry where capacitors or capactior banks are utilized.

Dependence of the muon intensity on the atmospheric temperature measured by the GRAPES-3 experiment

NASA Astrophysics Data System (ADS)

Arunbabu, K. P.; Ahmad, S.; Chandra, A.; Dugad, S. R.; Gupta, S. K.; Hariharan, B.; Hayashi, Y.; Jagadeesan, P.; Jain, A.; Jhansi, V. B.; Kawakami, S.; Kojima, H.; Mohanty, P. K.; Morris, S. D.; Nayak, P. K.; Oshima, A.; Rao, B. S.; Reddy, L. V.; Shibata, S.; Tanaka, K.; Zuberi, M.

2017-09-01

The large area (560 m2) GRAPES-3 tracking muon telescope has been operating uninterruptedly at Ooty, India since 2001. Every day, it records 4 × 109 muons of ≥1 GeV with an angular resolution of ∼4°. The variation of atmospheric temperature affects the rate of decay of muons produced by the galactic cosmic rays (GCRs), which in turn modulates the muon intensity. By analyzing the GRAPES-3 data of six years (2005-2010), a small (amplitude ∼0.2%) seasonal variation (1 year (Yr) period) in the intensity of muons could be measured. The effective temperature 'Teff' of the upper atmosphere also displays a periodic variation with an amplitude of ∼1 K which was responsible for the observed seasonal variation in the muon intensity. At GeV energies, the muons detected by the GRAPES-3 are expected to be anti-correlated with Teff. The anti-correlation between the seasonal variation of Teff, and the muon intensity was used to measure the temperature coefficient αT by fast Fourier transform (FFT) technique. The magnitude of αT was found to scale with the assumed attenuation length 'λ' of the hadrons in the range λ = 80-180 g cm-2. However, the magnitude of the correction in the muon intensity was found to be almost independent of the value of λ used. For λ = 120 g cm-2 the value of temperature coefficient αT was found to be (- 0.17 ± 0.02)% K-1.

Analysis of new lactotransferrin gene variants in a case-control study related to periodontal disease in dog.

PubMed

Morinha, Francisco; Albuquerque, Carlos; Requicha, João; Dias, Isabel; Leitão, José; Gut, Ivo; Guedes-Pinto, Henrique; Viegas, Carlos; Bastos, Estela

2012-04-01

The molecular and genetic research has contributed to a better understanding of the periodontal disease (PD) in humans and has shown that many genes play a role in the predisposition and progression of this complex disease. Variations in human lactotransferrin (LTF) gene appear to affect anti-microbial functions of this molecule, influencing the PD susceptibility. PD is also a major health problem in small animal practice, being the most common inflammatory disease found in dogs. Nevertheless, the research in genetic predisposition to PD is an unexplored subject in this species. This work aims to contribute to the characterization of the genetic basis of canine PD. In order to identify genetic variations and verify its association with PD, was performed a molecular analysis of LTF gene in a case-control approach, including 40 dogs in the PD cases group and 50 dogs in the control group. In this study were detected and characterized eight new single nucleotide variations in the dog LTF gene. Genotype and allele frequencies of these variations showed no statistically significant differences between the control and PD cases groups. Our data do not give evidence for the contribution of these LTF variations to the genetic background of canine PD. Nevertheless, the sequence variant L/15_g.411C > T leads to an aminoacid change (Proline to Leucine) and was predicted to be possibly damaging to the LTF protein. Further investigations would be of extreme value to clarify the biological importance of these new findings.

Flagging and Correction of Pattern Noise in the Kepler Focal Plane Array

NASA Technical Reports Server (NTRS)

Kolodziejczak, Jeffery J.; Caldwell, Douglas A.; VanCleve, Jeffrey E.; Clarke, Bruce D.; Jenkins, Jon M.; Cote, Miles T.; Klaus, Todd C.; Argabright, Vic S.

2010-01-01

In order for Kepler to achieve its required less than 20 PPM photometric precision for magnitude 12 and brighter stars, instrument-induced variations in the CCD readout bias pattern (our "2D black image"), which are either fixed or slowly varying in time, must be identified and the corresponding pixels either corrected or removed from further data processing. The two principle sources of these readout bias variations are crosstalk between the 84 science CCDs and the 4 fine guidance sensor (FGS) CCDs and a high frequency amplifier oscillation on less than 40% of the CCD readout channels. The crosstalk produces a synchronous pattern in the 2D black image with time-variation observed in less than 10% of individual pixel bias histories. We will describe a method of removing the crosstalk signal using continuously-collected data from masked and over-clocked image regions (our "collateral data"), and occasionally-collected full-frame images and reverse-clocked readout signals. We use this same set to detect regions affected by the oscillating amplifiers. The oscillations manifest as time-varying moir pattern and rolling bands in the affected channels. Because this effect reduces the performance in only a small fraction of the array at any given time, we have developed an approach for flagging suspect data. The flags will provide the necessary means to resolve any potential ambiguity between instrument-induced variations and real photometric variations in a target time series. We will also evaluate the effectiveness of these techniques using flight data from background and selected target pixels.

Time-varying sodium absorption in the Type Ia supernova 2013gh

NASA Astrophysics Data System (ADS)

Ferretti, R.; Amanullah, R.; Goobar, A.; Johansson, J.; Vreeswijk, P. M.; Butler, R. P.; Cao, Y.; Cenko, S. B.; Doran, G.; Filippenko, A. V.; Freeland, E.; Hosseinzadeh, G.; Howell, D. A.; Lundqvist, P.; Mattila, S.; Nordin, J.; Nugent, P. E.; Petrushevska, T.; Valenti, S.; Vogt, S.; Wozniak, P.

2016-07-01

Context. Temporal variability of narrow absorption lines in high-resolution spectra of Type Ia supernovae (SNe Ia) is studied to search for circumstellar matter. Time series which resolve the profiles of absorption lines such as Na I D or Ca II H&K are expected to reveal variations due to photoionisation and subsequent recombination of the gases. The presence, composition, and geometry of circumstellar matter may hint at the elusive progenitor system of SNe Ia and could also affect the observed reddening law. Aims: To date, there are few known cases of time-varying Na I D absorption in SNe Ia, all of which occurred during relatively late phases of the supernova (SN) evolution. Photoionisation, however, is predicted to occur during the early phases of SNe Ia, when the supernovae peak in the ultraviolet. We attempt, therefore, to observe early-time absorption-line variations by obtaining high-resolution spectra of SNe before maximum light. Methods: We have obtained photometry and high-resolution spectroscopy of SNe Ia 2013gh and iPTF 13dge, to search for absorption-line variations. Furthermore, we study interstellar absorption features in relation to the observed photometric colours of the SNe. Results: Both SNe display deep Na I D and Ca II H&K absorption features. Furthermore, small but significant variations are detected in a feature of the Na I D profile of SN 2013gh. The variations are consistent with either geometric effects of rapidly moving or patchy gas clouds or photoionisation of Na I gas at R ≈ 1019 cm from the explosion. Conclusions: Our analysis indicates that it is necessary to focus on early phases to detect photoionisation effects of gases in the circumstellar medium of SNe Ia. Different absorbers such as Na I and Ca II can be used to probe for matter at different distances from the SNe. The nondetection of variations during early phases makes it possible to put limits on the abundance of the species at those distances. Full Tables 2 and 3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/592/A40

CNV-TV: a robust method to discover copy number variation from short sequencing reads.

PubMed

Duan, Junbo; Zhang, Ji-Gang; Deng, Hong-Wen; Wang, Yu-Ping

2013-05-02

Copy number variation (CNV) is an important structural variation (SV) in human genome. Various studies have shown that CNVs are associated with complex diseases. Traditional CNV detection methods such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) suffer from low resolution. The next generation sequencing (NGS) technique promises a higher resolution detection of CNVs and several methods were recently proposed for realizing such a promise. However, the performances of these methods are not robust under some conditions, e.g., some of them may fail to detect CNVs of short sizes. There has been a strong demand for reliable detection of CNVs from high resolution NGS data. A novel and robust method to detect CNV from short sequencing reads is proposed in this study. The detection of CNV is modeled as a change-point detection from the read depth (RD) signal derived from the NGS, which is fitted with a total variation (TV) penalized least squares model. The performance (e.g., sensitivity and specificity) of the proposed approach are evaluated by comparison with several recently published methods on both simulated and real data from the 1000 Genomes Project. The experimental results showed that both the true positive rate and false positive rate of the proposed detection method do not change significantly for CNVs with different copy numbers and lengthes, when compared with several existing methods. Therefore, our proposed approach results in a more reliable detection of CNVs than the existing methods.

Large scale variation in DNA copy number in chicken breeds

USDA-ARS?s Scientific Manuscript database

Background Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, c...

Statistical tests for whether a given set of independent, identically distributed draws comes from a specified probability density.

PubMed

Tygert, Mark

2010-09-21

We discuss several tests for determining whether a given set of independent and identically distributed (i.i.d.) draws does not come from a specified probability density function. The most commonly used are Kolmogorov-Smirnov tests, particularly Kuiper's variant, which focus on discrepancies between the cumulative distribution function for the specified probability density and the empirical cumulative distribution function for the given set of i.i.d. draws. Unfortunately, variations in the probability density function often get smoothed over in the cumulative distribution function, making it difficult to detect discrepancies in regions where the probability density is small in comparison with its values in surrounding regions. We discuss tests without this deficiency, complementing the classical methods. The tests of the present paper are based on the plain fact that it is unlikely to draw a random number whose probability is small, provided that the draw is taken from the same distribution used in calculating the probability (thus, if we draw a random number whose probability is small, then we can be confident that we did not draw the number from the same distribution used in calculating the probability).

Progress in the application of landform analysis in studies of semiarid erosion

USGS Publications Warehouse

Schumm, Stanley Alfred; Hadley, R.F.

1961-01-01

The analysis of topographic and hydrologic data gathered during studies of erosion in semiarid areas of Western United States show the following relation: (a) Mean annual sediment yield from small drainage basins is related to a ratio of basin relief to length; (b) mean annual runoff from small drainage basins is related to drainage density; (c) mean annual sediment yield per unit area decreases with increase in drainage area; (d) the form of some convex hill slopes is related to surficial creep; (e) asymmetry of drainage basins, including differences in hill-slope erosion and drainage density, is related to microclimatic variations on slopes of diverse exposure; .(f) the cutting of discontinuous gullies is closely related to steepening by deposition of the semiarid valley floor; (g) aggradation in ephemeral streams seems to be most prevalent in reaches where the ratio of contributing drainage area to channel length is relatively small; and (h) streamchannel shape, expressed as a width-depth ratio, is related to the percentage of silt-clay in bed and bank alluvium. The above relations cannot be detected without measurement of terrain characteristics. They further indicate the importance of quantitative terrain analysis in studies of erosion.

Serological and genomic evidence of Rift Valley fever virus during inter-epidemic periods in Mauritania.

PubMed

Rissmann, M; Eiden, M; El Mamy, B O; Isselmou, K; Doumbia, B; Ziegler, U; Homeier-Bachmann, T; Yahya, B; Groschup, M H

2017-04-01

Rift Valley fever virus (RVFV) is an emerging pathogen of major concern throughout Africa and the Arabian Peninsula, affecting both livestock and humans. In the past recurrent epidemics were reported in Mauritania and studies focused on the analysis of samples from affected populations during acute outbreaks. To verify characteristics and presence of RVFV during non-epidemic periods we implemented a multi-stage serological and molecular analysis. Serum samples of small ruminants, cattle and camels were obtained from Mauritania during an inter-epidemic period in 2012-2013. This paper presents a comparative analysis of potential variations and shifts of antibody presence and the capability of inter-epidemic infections in Mauritanian livestock. We observed distinct serological differences between tested species (seroprevalence: small ruminants 3·8%, cattle 15·4%, camels 32·0%). In one single bovine from Nouakchott, a recent RVF infection could be identified by the simultaneous detection of IgM antibodies and viral RNA. This study indicates the occurrence of a low-level enzootic RVFV circulation in livestock in Mauritania. Moreover, results indicate that small ruminants can preferably act as sentinels for RVF surveillance.

How the food supply harvestable by waders in the Wadden Sea depends on the variation in energy density, body weight, biomass, burying depth and behaviour of tidal-flat invertebrates

NASA Astrophysics Data System (ADS)

Zwarts, Leo; Wanink, Jan H.

For several reasons, waders in the Wadden Sea face a large seasonal and annual variation in their food supply. Observations on a tidal flat in the Dutch Wadden Sea have shown that: - (1) The average energy density of ten invertebrate prey species varies between 21 and 23 kJ·g -1 AFDW. In Scrobicularia plana and Mya arenaria, but not in Macoma balthica, the energy density is 10% lower in winter than in summer. - (2) Depending on the species, body weights of prey of similar size are 30 to 60% lower in winter than in summer. - (3) The year-to-year fluctuation in standing-crop biomass is larger in some species than in others, the difference depending mainly on the frequency of successful recruitment. The overall biomass of the macrobenthos in winter is half of that in summer, but the timing of the peak biomass differs per species. - (4) The burying depth varies per species: Cerastoderma edule live just beneath the surface, while M. balthica, S. plana, M. arenaria, Arenicola marina and Nereis diversicolor bury more deeply and the majority of these prey live out of reach of the bird's bill. In all six species, burying depth increases with size. There is no seasonal variation in depth of C. edule and M. arenaria, but the four other species live at most shallow depth in early summer and most deeply in midwinter. Burying depths in winter vary from year to year, but are unrelated to temperature. Neither has temperature any effect on depth within months. For knot Calidris canutus feeding on M. balthica, the fluctuation in the accessible fraction was the main source of variation in the biomass of prey that is actually harvestable, i.e. the biomass of prey of suitable size that is accessible. Accordingly, the paper reviews the available data on the temporal variations in accessibility, detectability, ingestibility, digestibility and profitability of prey for waders. Only a small part of the prey is harvestable since many accessible prey are ignored because of their low profitability, while many profitable prey are inaccessible. The profitability of prey depends on their size and weight but also on their depth in the mud, since handling time increases with burying depth. A simple biomechanical rule explains why the handling time of small prey increases with bill length and why large, long-billed waders ignore a disproportionately larger part of the small prey. The fraction detectable for visually feeding waders is usually very low, especially when the temperature of the substrate is below 3-6°C. Waders vary their prey choice over the year in response to the changes in the availability and profitability of their different prey species. The food supply harvestable by waders is much lower in winter than in summer. For waders wintering in the Wadden Sea, the food supply may be characterized as unpredictable and usually meagre. Waders wintering in NW Europe are concentrated in coastal sites where the average surface temperature is above 3°C. This probably cannot be explained by a greater burying depth, and only partly by a lower body condition, of prey in colder areas. Yet the harvestable fraction is lower in colder sites, especially for sight-feeding waders, as invertebrates are less active at low temperatures. However, the lower energetic cost of living and reduced chances of the prey being covered by ice may also contribute to the waders' preference for warmer sites.

Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data.

PubMed

Zhang, Peng; Li, Houqiang; Wang, Honghui; Wong, Stephen T C; Zhou, Xiaobo

2011-01-01

Peak detection is one of the most important steps in mass spectrometry (MS) analysis. However, the detection result is greatly affected by severe spectrum variations. Unfortunately, most current peak detection methods are neither flexible enough to revise false detection results nor robust enough to resist spectrum variations. To improve flexibility, we introduce peak tree to represent the peak information in MS spectra. Each tree node is a peak judgment on a range of scales, and each tree decomposition, as a set of nodes, is a candidate peak detection result. To improve robustness, we combine peak detection and common peak alignment into a closed-loop framework, which finds the optimal decomposition via both peak intensity and common peak information. The common peak information is derived and loopily refined from the density clustering of the latest peak detection result. Finally, we present an improved ant colony optimization biomarker selection method to build a whole MS analysis system. Experiment shows that our peak detection method can better resist spectrum variations and provide higher sensitivity and lower false detection rates than conventional methods. The benefits from our peak-tree-based system for MS disease analysis are also proved on real SELDI data.

Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition.

PubMed

Davoli, R; Gaffo, E; Zappaterra, M; Bortoluzzi, S; Zambonelli, P

2018-06-01

The identification of the molecular mechanisms regulating pathways associated with the potential for fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. Interactions of microRNAs (miRNAs) with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is far from saturation, and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations is still fragmentary. Using RNA-seq, we characterized the small RNA (sRNA) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs: 14 up-regulated (including ssc-miR-132, ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network were found to be expressed from backfat-related pig QTL. These results are informative for the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs and facilitate the prospective implementation of innovative strategies of pig genetic improvement based on genomic markers. © 2018 Stichting International Foundation for Animal Genetics.

Sensitivity of Honeybee Hygroreceptors to Slow Humidity Changes and Temporal Humidity Variation Detected in High Resolution by Mobile Measurements

PubMed Central

Tichy, Harald; Kallina, Wolfgang

2014-01-01

The moist cell and the dry cell on the antenna of the male honeybee were exposed to humidities slowly rising and falling at rates between –1.5%/s and +1.5%/s and at varying amplitudes in the 10 to 90% humidity range. The two cells respond to these slow humidity oscillations with oscillations in impulse frequency which depend not only on instantaneous humidity but also on the rate with which humidity changes. The impulse frequency of each cell was plotted as a function of these two parameters and regression planes were fitted to the data points of single oscillation periods. The regression slopes, which estimate sensitivity, rose with the amplitude of humidity oscillations. During large-amplitude oscillations, moist and dry cell sensitivity for instantaneous humidity and its rate of change was high. During small-amplitude oscillations, their sensitivity for both parameters was low, less exactly reflecting humidity fluctuations. Nothing is known about the spatial and temporal humidity variations a honeybee may encounter when flying through natural environments. Microclimatic parameters (absolute humidity, temperature, wind speed) were measured from an automobile traveling through different landscapes of Lower Austria. Landscape type affected extremes and mean values of humidity. Differences between peaks and troughs of humidity fluctuations were generally smaller in open grassy fields or deciduous forests than in edge habitats or forest openings. Overall, fluctuation amplitudes were small. In this part of the stimulus range, hygroreceptor sensitivity is not optimal for encoding instantaneous humidity and the rate of humidity change. It seems that honeybee's hygroreceptors are specialized for detecting large-amplitude fluctuations that are relevant for a specific behavior, namely, maintaining a sufficiently stable state of water balance. The results suggest that optimal sensitivity of both hygroreceptors is shaped not only by humidity oscillation amplitudes but also according to their impact on behavior. PMID:24901985

Spaceborne radar observations: A guide for Magellan radar-image analysis

NASA Technical Reports Server (NTRS)

Ford, J. P.; Blom, R. G.; Crisp, J. A.; Elachi, Charles; Farr, T. G.; Saunders, R. Stephen; Theilig, E. E.; Wall, S. D.; Yewell, S. B.

1989-01-01

Geologic analyses of spaceborne radar images of Earth are reviewed and summarized with respect to detecting, mapping, and interpreting impact craters, volcanic landforms, eolian and subsurface features, and tectonic landforms. Interpretations are illustrated mostly with Seasat synthetic aperture radar and shuttle-imaging-radar images. Analogies are drawn for the potential interpretation of radar images of Venus, with emphasis on the effects of variation in Magellan look angle with Venusian latitude. In each landform category, differences in feature perception and interpretive capability are related to variations in imaging geometry, spatial resolution, and wavelength of the imaging radar systems. Impact craters and other radially symmetrical features may show apparent bilateral symmetry parallel to the illumination vector at low look angles. The styles of eruption and the emplacement of major and minor volcanic constructs can be interpreted from morphological features observed in images. Radar responses that are governed by small-scale surface roughness may serve to distinguish flow types, but do not provide unambiguous information. Imaging of sand dunes is rigorously constrained by specific angular relations between the illumination vector and the orientation and angle of repose of the dune faces, but is independent of radar wavelength. With a single look angle, conditions that enable shallow subsurface imaging to occur do not provide the information necessary to determine whether the radar has recorded surface or subsurface features. The topographic linearity of many tectonic landforms is enhanced on images at regional and local scales, but the detection of structural detail is a strong function of illumination direction. Nontopographic tectonic lineaments may appear in response to contrasts in small-surface roughness or dielectric constant. The breakpoint for rough surfaces will vary by about 25 percent through the Magellan viewing geometries from low to high Venusian latitudes. Examples of anomalies and system artifacts that can affect image interpretation are described.

A robotic test of proprioception within the hemiparetic arm post-stroke.

PubMed

Simo, Lucia; Botzer, Lior; Ghez, Claude; Scheidt, Robert A

2014-04-30

Proprioception plays important roles in planning and control of limb posture and movement. The impact of proprioceptive deficits on motor function post-stroke has been difficult to elucidate due to limitations in current tests of arm proprioception. Common clinical tests only provide ordinal assessment of proprioceptive integrity (eg. intact, impaired or absent). We introduce a standardized, quantitative method for evaluating proprioception within the arm on a continuous, ratio scale. We demonstrate the approach, which is based on signal detection theory of sensory psychophysics, in two tasks used to characterize motor function after stroke. Hemiparetic stroke survivors and neurologically intact participants attempted to detect displacement- or force-perturbations robotically applied to their arm in a two-interval, two-alternative forced-choice test. A logistic psychometric function parameterized detection of limb perturbations. The shape of this function is determined by two parameters: one corresponds to a signal detection threshold and the other to variability of responses about that threshold. These two parameters define a space in which proprioceptive sensation post-stroke can be compared to that of neurologically-intact people. We used an auditory tone discrimination task to control for potential comprehension, attention and memory deficits. All but one stroke survivor demonstrated competence in performing two-alternative discrimination in the auditory training test. For the remaining stroke survivors, those with clinically identified proprioceptive deficits in the hemiparetic arm or hand had higher detection thresholds and exhibited greater response variability than individuals without proprioceptive deficits. We then identified a normative parameter space determined by the threshold and response variability data collected from neurologically intact participants. By plotting displacement detection performance within this normative space, stroke survivors with and without intact proprioception could be discriminated on a continuous scale that was sensitive to small performance variations, e.g. practice effects across days. The proposed method uses robotic perturbations similar to those used in ongoing studies of motor function post-stroke. The approach is sensitive to small changes in the proprioceptive detection of hand motions. We expect this new robotic assessment will empower future studies to characterize how proprioceptive deficits compromise limb posture and movement control in stroke survivors.

High-resolution remotely sensed small target detection by imitating fly visual perception mechanism.

PubMed

Huang, Fengchen; Xu, Lizhong; Li, Min; Tang, Min

2012-01-01

The difficulty and limitation of small target detection methods for high-resolution remote sensing data have been a recent research hot spot. Inspired by the information capture and processing theory of fly visual system, this paper endeavors to construct a characterized model of information perception and make use of the advantages of fast and accurate small target detection under complex varied nature environment. The proposed model forms a theoretical basis of small target detection for high-resolution remote sensing data. After the comparison of prevailing simulation mechanism behind fly visual systems, we propose a fly-imitated visual system method of information processing for high-resolution remote sensing data. A small target detector and corresponding detection algorithm are designed by simulating the mechanism of information acquisition, compression, and fusion of fly visual system and the function of pool cell and the character of nonlinear self-adaption. Experiments verify the feasibility and rationality of the proposed small target detection model and fly-imitated visual perception method.

Impact of respiratory motion correction and spatial resolution on lesion detection in PET: a simulation study based on real MR dynamic data

NASA Astrophysics Data System (ADS)

Polycarpou, Irene; Tsoumpas, Charalampos; King, Andrew P.; Marsden, Paul K.

2014-02-01

The aim of this study is to investigate the impact of respiratory motion correction and spatial resolution on lesion detectability in PET as a function of lesion size and tracer uptake. Real respiratory signals describing different breathing types are combined with a motion model formed from real dynamic MR data to simulate multiple dynamic PET datasets acquired from a continuously moving subject. Lung and liver lesions were simulated with diameters ranging from 6 to 12 mm and lesion to background ratio ranging from 3:1 to 6:1. Projection data for 6 and 3 mm PET scanner resolution were generated using analytic simulations and reconstructed without and with motion correction. Motion correction was achieved using motion compensated image reconstruction. The detectability performance was quantified by a receiver operating characteristic (ROC) analysis obtained using a channelized Hotelling observer and the area under the ROC curve (AUC) was calculated as the figure of merit. The results indicate that respiratory motion limits the detectability of lung and liver lesions, depending on the variation of the breathing cycle length and amplitude. Patients with large quiescent periods had a greater AUC than patients with regular breathing cycles and patients with long-term variability in respiratory cycle or higher motion amplitude. In addition, small (less than 10 mm diameter) or low contrast (3:1) lesions showed the greatest improvement in AUC as a result of applying motion correction. In particular, after applying motion correction the AUC is improved by up to 42% with current PET resolution (i.e. 6 mm) and up to 51% for higher PET resolution (i.e. 3 mm). Finally, the benefit of increasing the scanner resolution is small unless motion correction is applied. This investigation indicates high impact of respiratory motion correction on lesion detectability in PET and highlights the importance of motion correction in order to benefit from the increased resolution of future PET scanners.

Characterizing the nature of subpulse drifting in pulsars

NASA Astrophysics Data System (ADS)

Basu, Rahul; Mitra, Dipanjan

2018-04-01

We report a detailed study of subpulse drifting in four long-period pulsars. These pulsars were observed in the Meterwavelength Single-pulse Polarimetric Emission Survey and the presence of phase-modulated subpulse drifting was reported in each case. We carried out longer duration and more sensitive observations lasting 7000-12 000 periods in the frequency range 306-339 MHz. The drifting features were characterized in great detail, including the phase variations across the pulse window. For two pulsars, J0820-1350 and J1720-2933, the phases changed steadily across the pulse window. The pulsar J1034-3224 has five components. The leading component was very weak and was barely detectable in our single-pulse observations. The four trailing components showed subpulse drifting. The phase variations changed in alternate components with a reversal in the sign of the gradient. This phenomenon is known as bi-drifting. The pulsar J1555-3134 showed two distinct peak frequencies of comparable strengths in the fluctuation spectrum. The two peaks did not appear to be harmonically related and were most likely a result of different physical processes. Additionally, the long observations enabled us to explore the temporal variations of the drifting features. The subpulse drifting was largely constant with time but small fluctuations around a mean value were seen.

Nicotine and oxidative stress induced exomic variations are concordant and overrepresented in cancer-associated genes

PubMed Central

Bavarva, Jasmin H.; Tae, Hongseok; McIver, Lauren; Garner, Harold R.

2014-01-01

Although the connection between cancer and cigarette smoke is well established, nicotine is not characterized as a carcinogen. Here, we used exome sequencing to identify nicotine and oxidative stress-induced somatic mutations in normal human epithelial cells and its correlation with cancer. We identified over 6,400 SNVs, indels and microsatellites in each of the stress exposed cells relative to the control, of which, 2,159 were consistently observed at all nicotine doses. These included 429 nsSNVs including 158 novel and 79 cancer-associated. Over 80% of consistently nicotine induced variants overlap with variations detected in oxidative stressed cells, indicating that nicotine induced genomic alterations could be mediated through oxidative stress. Nicotine induced mutations were distributed across 1,585 genes, of which 49% were associated with cancer. MUC family genes were among the top mutated genes. Analysis of 591 lung carcinoma tumor exomes from The Cancer Genome Atlas (TCGA) revealed that 20% of non-small-cell lung cancer tumors in smokers have mutations in at least one of the MUC4, MUC6 or MUC12 genes in contrast to only 6% in non-smokers. These results indicate that nicotine induces genomic variations, promotes instability potentially mediated by oxidative stress, implicating nicotine in carcinogenesis, and establishes MUC genes as potential targets. PMID:24947164

Systematic Analysis of the Genetic Variability That Impacts SUMO Conjugation and Their Involvement in Human Diseases

NASA Astrophysics Data System (ADS)

Xu, Hao-Dong; Shi, Shao-Ping; Chen, Xiang; Qiu, Jian-Ding

2015-07-01

Protein function has been observed to rely on select essential sites instead of requiring all sites to be indispensable. Small ubiquitin-related modifier (SUMO) conjugation or sumoylation, which is a highly dynamic reversible process and its outcomes are extremely diverse, ranging from changes in localization to altered activity and, in some cases, stability of the modified, has shown to be especially valuable in cellular biology. Motivated by the significance of SUMO conjugation in biological processes, we report here on the first exploratory assessment whether sumoylation related genetic variability impacts protein functions as well as the occurrence of diseases related to SUMO. Here, we defined the SUMOAMVR as sumoylation related amino acid variations that affect sumoylation sites or enzymes involved in the process of connectivity, and categorized four types of potential SUMOAMVRs. We detected that 17.13% of amino acid variations are potential SUMOAMVRs and 4.83% of disease mutations could lead to SUMOAMVR with our system. More interestingly, the statistical analysis demonstrates that the amino acid variations that directly create new potential lysine sumoylation sites are more likely to cause diseases. It can be anticipated that our method can provide more instructive guidance to identify the mechanisms of genetic diseases.

Photometric long-term variations and superhump occurrence in the Classical Nova RR Pictoris

NASA Astrophysics Data System (ADS)

Fuentes-Morales, I.; Vogt, N.; Tappert, C.; Schmidtobreick, L.; Hambsch, F.-J.; Vučković, M.

2018-02-01

We present an analysis of all available time-resolved photometry from the literature and new light curves obtained in 2013-2014 for the old nova RR Pictoris. The well-known hump light curve phased with the orbital period reveals significant variations over the last 42 yr in shape, amplitude and other details which apparently are caused by long-term variations in the disc structure. In addition, we found evidence for the presence of superhumps in 2007, with the same period ( ˜ 9 per cent longer than the orbital period), as reported earlier by other authors from observations in 2005. Possibly, superhumps arise quickly in RR Pic, but are sporadic events, because in all the other observing runs analysed no significant superhump signal was detected. We also determined an actual version of the Stolz-Schoembs relation between superhump period and orbital period, analysing separately dwarf novae, classical novae and nova-like stars, and conclude that this relation is of general validity for all superhumpers among the cataclysmic variables (CVs), in spite of small but significant differences among the sub-types mentioned above. We emphasize the importance of such a study in context with the still open question of the interrelation between the different sub-classes of CVs, crucial for our understanding of the long-term CV evolution.

Constitutional sequence variation in the Fanconi anaemia group C (FANCC) gene in childhood acute myeloid leukaemia.

PubMed

Barber, Lisa M; McGrath, Helen E N; Meyer, Stefan; Will, Andrew M; Birch, Jillian M; Eden, Osborn B; Taylor, G Malcolm

2003-04-01

The extent to which genetic susceptibility contributes to the causation of childhood acute myeloid leukaemia (AML) is not known. The inherited bone marrow failure disorder Fanconi anaemia (FA) carries a substantially increased risk of AML, raising the possibility that constitutional variation in the FA (FANC) genes is involved in the aetiology of childhood AML. We have screened genomic DNA extracted from remission blood samples of 97 children with sporadic AML and 91 children with sporadic acute lymphoblastic leukaemia (ALL), together with 104 cord blood DNA samples from newborn children, for variations in the Fanconi anaemia group C (FANCC) gene. We found no evidence of known FANCC pathogenic mutations in children with AML, ALL or in the cord blood samples. However, we detected 12 different FANCC sequence variants, of which five were novel to this study. Among six FANCC variants leading to amino-acid substitutions, one (S26F) was present at a fourfold greater frequency in children with AML than in the cord blood samples (odds ratio: 4.09, P = 0.047; 95% confidence interval 1.08-15.54). Our results thus do not exclude the possibility that this polymorphic variant contributes to the risk of a small proportion of childhood AML.

Coffee Agroforests Remain Beneficial for Neotropical Bird Community Conservation across Seasons

PubMed Central

Peters, Valerie E.; Cooper, Robert J.; Carroll, C. Ron

2013-01-01

Coffee agroforestry systems and secondary forests have been shown to support similar bird communities but comparing these habitat types are challenged by potential biases due to differences in detectability between habitats. Furthermore, seasonal dynamics may influence bird communities differently in different habitat types and therefore seasonal effects should be considered in comparisons. To address these issues, we incorporated seasonal effects and factors potentially affecting bird detectability into models to compare avian community composition and dynamics between coffee agroforests and secondary forest fragments. In particular, we modeled community composition and community dynamics of bird functional groups based on habitat type (coffee agroforest vs. secondary forest) and season while accounting for variation in capture probability (i.e. detectability). The models we used estimated capture probability to be similar between habitat types for each dietary guild, but omnivores had a lower capture probability than frugivores and insectivores. Although apparent species richness was higher in coffee agroforest than secondary forest, model results indicated that omnivores and insectivores were more common in secondary forest when accounting for heterogeneity in capture probability. Our results largely support the notion that shade-coffee can serve as a surrogate habitat for secondary forest with respect to avian communities. Small coffee agroforests embedded within the typical tropical countryside matrix of secondary forest patches and small-scale agriculture, therefore, may host avian communities that resemble those of surrounding secondary forest, and may serve as viable corridors linking patches of forest within these landscapes. This information is an important step toward effective landscape-scale conservation in Neotropical agricultural landscapes. PMID:24058437

Improving the nowcasting of precipitation in an Alpine region with an enhanced radar echo tracking algorithm

NASA Astrophysics Data System (ADS)

Mecklenburg, S.; Joss, J.; Schmid, W.

2000-12-01

Nowcasting for hydrological applications is discussed. The tracking algorithm extrapolates radar images in space and time. It originates from the pattern recognition techniques TREC (Tracking Radar Echoes by Correlation, Rinehart and Garvey, J. Appl. Meteor., 34 (1995) 1286) and COTREC (Continuity of TREC vectors, Li et al., Nature, 273 (1978) 287). To evaluate the quality of the extrapolation, a parameter scheme is introduced, able to distinguish between errors in the position and the intensity of the predicted precipitation. The parameters for the position are the absolute error, the relative error and the error of the forecasted direction. The parameters for the intensity are the ratio of the medians and the variations of the rain rate (ratio of two quantiles) between the actual and the forecasted image. To judge the overall quality of the forecast, the correlation coefficient between the forecasted and the actual radar image has been used. To improve the forecast, three aspects have been investigated: (a) Common meteorological attributes of convective cells, derived from a hail statistics, have been determined to optimize the parameters of the tracking algorithm. Using (a), the forecast procedure modifications (b) and (c) have been applied. (b) Small-scale features have been removed by using larger tracking areas and by applying a spatial and temporal smoothing, since problems with the tracking algorithm are mainly caused by small-scale/short-term variations of the echo pattern or because of limitations caused by the radar technique itself (erroneous vectors caused by clutter or shielding). (c) The searching area and the number of searched boxes have been restricted. This limits false detections, which is especially useful in stratiform precipitation and for stationary echoes. Whereas a larger scale and the removal of small-scale features improve the forecasted position for the convective precipitation, the forecast of the stratiform event is not influenced, but limiting the search area leads to a slightly better forecast. The forecast of the intensity is successful for both precipitation events. Forecasting the variation of the rain rate calls for further investigation. Applying COTREC improves the forecast of the convective precipitation, especially for extrapolation times exceeding 30 min.

The 67P/Churyumov-Gerasimenko nucleus spectroscopic properties and their evolution over time

NASA Astrophysics Data System (ADS)

Fornasier, S.

2016-11-01

Comets are primitive small bodies witness of the Solar System formation. Our knowledge on cometary nuclei and on their evolution over time is very limited because they are dark, small, and thus faint objects, spatially unresolved by groundbased telescopes and masked by their atmosphere when they become brighter close to the Sun. Before the Rosetta mission, only 5 cometary nuclei have been directly imaged and investigated by space missions during relatively short fly-bys, catching thus a small fraction of the comet lifetime in its orbit. The Rosetta mission is orbiting around the 67P/Churyumov-Gerasimenko comet since August 2014, and provides the unique opportunity to continuously investigate the 67P nucleus during about 2 years, from large heliocentric distances (about 4 AU) to its perihelion passage (1.24 AU) and beyond. The OSIRIS cameras and VIRTIS spectrometer have shown that the 67P nucleus has a red spectral behavior with spectral properties similar to those of bare cometary nuclei, of primitive D-type asteroids like the Jupiter Trojans, and of the moderately red Transneptunians population (Sierks et al., 2015, Capaccioni et al., 2015). The surface is globally dominated by dehydrated and organic-rich refractory materials (Capaccioni et al., 2015), and shows some color heterogeneities. Three kind of terrains, from the spectrally bluer and water ice enriched terrains to the redder ones, associated mostly to dusty regions, have been identified by visible spectrophotometry from the first resolved images acquired in July-August 2014 (Fornasier et al., 2015), covering mostly the northern hemisphere of the nucleus. The southern hemisphere has become visible from Rosetta only since March 2015, and it shows a lack of spectrally red regions compared to the northern one, associated to the absence of wide spread smooth or dust covered terrains. Although water is the dominant volatile observed in the coma, exposed water ice has been detected only in small amounts in different regions of the comet (Pommerol et al., 2015; De Sanctis et al., 2015; Filacchione et al., 2016; Barucci et al. 2016). Thanks to the unprecedented spatial resolution, VIRTIS and OSIRIS instruments have detected the occurrence of water frost close to the morning shadows, putting in evidence the diurnal cycle of water. Seasonal color and spectral variations have also been observed when the comet approached perihelion, indicating that the increasing activity had progressively shed the surface dust, partially showing the underlying ice-rich layer. I will present an overview of the spectroscopic properties of the 67P nucleus and of their diurnal and seasonal variations over time and heliocentric distance.

Effective image differencing with convolutional neural networks for real-time transient hunting

NASA Astrophysics Data System (ADS)

Sedaghat, Nima; Mahabal, Ashish

2018-06-01

Large sky surveys are increasingly relying on image subtraction pipelines for real-time (and archival) transient detection. In this process one has to contend with varying point-spread function (PSF) and small brightness variations in many sources, as well as artefacts resulting from saturated stars and, in general, matching errors. Very often the differencing is done with a reference image that is deeper than individual images and the attendant difference in noise characteristics can also lead to artefacts. We present here a deep-learning approach to transient detection that encapsulates all the steps of a traditional image-subtraction pipeline - image registration, background subtraction, noise removal, PSF matching and subtraction - in a single real-time convolutional network. Once trained, the method works lightening-fast and, given that it performs multiple steps in one go, the time saved and false positives eliminated for multi-CCD surveys like Zwicky Transient Facility and Large Synoptic Survey Telescope will be immense, as millions of subtractions will be needed per night.

Human salivary glucose analysis by high-performance ion-exchange chromatography and pulsed amperometric detection.

PubMed

Gough, H; Luke, G A; Beeley, J A; Geddes, D A

1996-02-01

The aim of this project was to develop an analytical procedure with the required level of sensitivity for the determination of glucose concentrations in small volumes of unstimulated fasting whole saliva. The technique involves high-performance ion-exchange chromatography at high pH and pulsed amperometric detection. It has a high level of reproducibility, a sensitivity as low as 0.1 mumol/l and requires only 50 microliters samples (sensitivity = 0.002 pmol). Inhibition of glucose metabolism, by procedures such as collection into 0.1% (w/v) sodium fluoride, was shown to be essential if accurate results are to be obtained. Collection on to ice followed by storage at -20 degrees C was shown to be unsuitable and resulted in glucose loss by degradation. There were inter- and intraindividual variations in the glucose concentration in unstimulated mixed saliva (range; 0.02-0.4 mmol/l). The procedure can be used for the analysis of other salivary carbohydrates and for monitoring the clearance of dietary carbohydrates from the mouth.

Analysis of hop-derived terpenoids in beer and evaluation of their behavior using the stir bar-sorptive extraction method with GC-MS.

PubMed

Kishimoto, Toru; Wanikawa, Akira; Kagami, Noboru; Kawatsura, Katsuyuki

2005-06-15

Hop aroma components, which mainly comprise terpenoids, contribute to the character of beers. However, pretreatments are necessary before analyzing these components because of their trace levels and complicated matrixes. Here, the stir bar-sorptive extraction (SBSE) method was used to detect and quantify many terpenoids simultaneously from small samples. This simple technique showed low coefficients of variation, high accuracy, and low detection limits. An investigation of the behavior of terpenoids identified two distinct patterns of decreasing concentration during wort boiling. The first, which was seen in myrcene and linalool, involved a rapid decrease that was best fitted by a quadratic curve. The second, which was observed in beta-eudesmol, humulene, humulene epoxide I, beta-farnesene, caryophyllene, and geraniol, involved a gentle linear decrease. Conversely, the concentration of beta-damascenone increased after boiling. As the aroma composition depended on the hop variety, we also examined the relationship between terpenoid content and sensory analysis in beer.

Vector network analyzer ferromagnetic resonance spectrometer with field differential detection

NASA Astrophysics Data System (ADS)

Tamaru, S.; Tsunegi, S.; Kubota, H.; Yuasa, S.

2018-05-01

This work presents a vector network analyzer ferromagnetic resonance (VNA-FMR) spectrometer with field differential detection. This technique differentiates the S-parameter by applying a small binary modulation field in addition to the DC bias field to the sample. By setting the modulation frequency sufficiently high, slow sensitivity fluctuations of the VNA, i.e., low-frequency components of the trace noise, which limit the signal-to-noise ratio of the conventional VNA-FMR spectrometer, can be effectively removed, resulting in a very clean FMR signal. This paper presents the details of the hardware implementation and measurement sequence as well as the data processing and analysis algorithms tailored for the FMR spectrum obtained with this technique. Because the VNA measures a complex S-parameter, it is possible to estimate the Gilbert damping parameter from the slope of the phase variation of the S-parameter with respect to the bias field. We show that this algorithm is more robust against noise than the conventional algorithm based on the linewidth.

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.

PubMed

Chen, Zongliang; Wang, Baobao; Dong, Xiaomei; Liu, Han; Ren, Longhui; Chen, Jian; Hauck, Andrew; Song, Weibin; Lai, Jinsheng

2014-06-04

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing.

PubMed

Miyao, Akio; Nakagome, Mariko; Ohnuma, Takako; Yamagata, Harumi; Kanamori, Hiroyuki; Katayose, Yuichi; Takahashi, Akira; Matsumoto, Takashi; Hirochika, Hirohiko

2012-01-01

Somaclonal variation is a phenomenon that results in the phenotypic variation of plants regenerated from cell culture. One of the causes of somaclonal variation in rice is the transposition of retrotransposons. However, many aspects of the mechanisms that result in somaclonal variation remain undefined. To detect genome-wide changes in regenerated rice, we analyzed the whole-genome sequences of three plants independently regenerated from cultured cells originating from a single seed stock. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were detected in the genomes of the regenerated plants. The transposition of only Tos17 among 43 transposons examined was detected in the regenerated plants. Therefore, the SNPs and indels contribute to the somaclonal variation in regenerated rice in addition to the transposition of Tos17. The observed molecular spectrum was similar to that of the spontaneous mutations in Arabidopsis thaliana. However, the base change ratio was estimated to be 1.74 × 10(-6) base substitutions per site per regeneration, which is 248-fold greater than the spontaneous mutation rate of A. thaliana.

Quantifying the forcing effect of channel width variations on free bars: Morphodynamic modeling based on characteristic dissipative Galerkin scheme

NASA Astrophysics Data System (ADS)

Wu, Fu-Chun; Shao, Yun-Chuan; Chen, Yu-Chen

2011-09-01

The forcing effect of channel width variations on free bars is investigated in this study using a two-dimensional depth-averaged morphodynamic model. The novel feature of the model is the incorporation of a characteristic dissipative Galerkin (CDG) upwinding scheme in the bed evolution module. A correction for the secondary flows induced by streamline curvature is also included, allowing for simulations of bar growth and migration in channels with width variations beyond the small-amplitude regimes. The model is tested against a variety of experimental data ranging from purely forced and free bars to coexisting bed forms in the variable-width channel. The CDG scheme effectively dissipates local bed oscillations, thus sustains numerical stabilities. The results show that the global effect of width variations on bar height is invariably suppressive. Such effect increases with the dimensionless amplitude AC and wave number λC of width variations. For small AC, λC has little effects on bar height; for AC beyond small amplitudes, however, the suppressing effect depends on both AC and λC. The suppressing effect on bar length increases also with both AC and λC, but is much weaker than that on bar height. The global effect of width variations on bar celerity can be suppressive or enhancive, depending on the combination of AC and λC. For smaller λC, the effect on bar celerity is enhancive; for larger λC, bar celerity tends to increase at small AC but decreases for AC beyond small amplitudes. We present herein an unprecedented data set verifying the theoretical prediction on celerity enhancement. Full suppression of bar growth above the theoretically predicted threshold AC was not observed, regardless of the adopted amplitude of initial bed perturbation A. The global effects of width variations on free bars can be quantified using a forcing factor FC that integrates the effects of AC and λC. The suppressing effects on bar height and length are both proportional to FC2.16; the global effect on bar celerity is, however, a parabolic function of FC.

Wireless Metal Detection and Surface Coverage Sensing for All-Surface Induction Heating

PubMed Central

Kilic, Veli Tayfun; Unal, Emre; Demir, Hilmi Volkan

2016-01-01

All-surface induction heating systems, typically comprising small-area coils, face a major challenge in detecting the presence of a metallic vessel and identifying its partial surface coverage over the coils to determine which of the coils to power up. The difficulty arises due to the fact that the user can heat vessels made of a wide variety of metals (and their alloys). To address this problem, we propose and demonstrate a new wireless detection methodology that allows for detecting the presence of metallic vessels together with uniquely sensing their surface coverages while also identifying their effective material type in all-surface induction heating systems. The proposed method is based on telemetrically measuring simultaneously inductance and resistance of the induction coil coupled with the vessel in the heating system. Here, variations in the inductance and resistance values for an all-surface heating coil loaded by vessels (made of stainless steel and aluminum) at different positions were systematically investigated at different frequencies. Results show that, independent of the metal material type, unique identification of the surface coverage is possible at all freqeuncies. Additionally, using the magnitude and phase information extracted from the coupled coil impedance, unique identification of the vessel effective material is also achievable, this time independent of its surface coverage. PMID:26978367

Quantitative real-time in vivo detection of magnetic nanoparticles by their nonlinear magnetization

NASA Astrophysics Data System (ADS)

Nikitin, M. P.; Torno, M.; Chen, H.; Rosengart, A.; Nikitin, P. I.

2008-04-01

A novel method of highly sensitive quantitative detection of magnetic nanoparticles (MP) in biological tissues and blood system has been realized and tested in real time in vivo experiments. The detection method is based on nonlinear magnetic properties of MP and the related device can record a very small relative variation of nonlinear magnetic susceptibility up to 10-8 at room temperature, providing sensitivity of several nanograms of MP in 0.1ml volume. Real-time quantitative in vivo measurements of dynamics of MP concentration in blood flow have been performed. A catheter that carried the blood flow of a rat passed through the measuring device. After an MP injection, the quantity of MP in the circulating blood was continuously recorded. The method has also been used to evaluate the MP distribution between rat's organs. Its sensitivity was compared with detection of the radioactive MP based on isotope of Fe59. The comparison of magnetic and radioactive signals in the rat's blood and organ samples demonstrated similar sensitivity for both methods. However, the proposed magnetic method is much more convenient as it is safe, less expensive, and provides real-time measurements in vivo. Moreover, the sensitivity of the method can be further improved by optimization of the device geometry.

Asymdystopia: The Threat of Small Biases in Evaluations of Education Interventions That Need to Be Powered to Detect Small Impacts. NCEE 2018-4002

ERIC Educational Resources Information Center

Deke, John; Wei, Thomas; Kautz, Tim

2017-01-01

Evaluators of education interventions are increasingly designing studies to detect impacts much smaller than the 0.20 standard deviations that Cohen (1988) characterized as "small." While the need to detect smaller impacts is based on compelling arguments that such impacts are substantively meaningful, the drive to detect smaller impacts…

Use of next-generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia.

PubMed

Iacocca, Michael A; Wang, Jian; Dron, Jacqueline S; Robinson, John F; McIntyre, Adam D; Cao, Henian; Hegele, Robert A

2017-11-01

Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene ( LDLR ). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR ; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

PubMed Central

Gan, Mingyu; Liu, Qingyun; Yang, Chongguang; Gao, Qian; Luo, Tao

2016-01-01

Mixed infection by multiple Mycobacterium tuberculosis (MTB) strains is associated with poor treatment outcome of tuberculosis (TB). Traditional genotyping methods have been used to detect mixed infections of MTB, however, their sensitivity and resolution are limited. Deep whole-genome sequencing (WGS) has been proved highly sensitive and discriminative for studying population heterogeneity of MTB. Here, we developed a phylogenetic-based method to detect MTB mixed infections using WGS data. We collected published WGS data of 782 global MTB strains from public database. We called homogeneous and heterogeneous single nucleotide variations (SNVs) of individual strains by mapping short reads to the ancestral MTB reference genome. We constructed a phylogenomic database based on 68,639 homogeneous SNVs of 652 MTB strains. Mixed infections were determined if multiple evolutionary paths were identified by mapping the SNVs of individual samples to the phylogenomic database. By simulation, our method could specifically detect mixed infections when the sequencing depth of minor strains was as low as 1× coverage, and when the genomic distance of two mixed strains was as small as 16 SNVs. By applying our methods to all 782 samples, we detected 47 mixed infections and 45 of them were caused by locally endemic strains. The results indicate that our method is highly sensitive and discriminative for identifying mixed infections from deep WGS data of MTB isolates. PMID:27391214

panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.

PubMed

Povysil, Gundula; Tzika, Antigoni; Vogt, Julia; Haunschmid, Verena; Messiaen, Ludwine; Zschocke, Johannes; Klambauer, Günter; Hochreiter, Sepp; Wimmer, Katharina

2017-07-01

Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy-number variations (CNVs) in addition to single-nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics. © 2017 The Authors. Human Mutation published by Wiley Periodicals, Inc.

panelcn.MOPS: Copy‐number detection in targeted NGS panel data for clinical diagnostics

PubMed Central

Povysil, Gundula; Tzika, Antigoni; Vogt, Julia; Haunschmid, Verena; Messiaen, Ludwine; Zschocke, Johannes; Klambauer, Günter; Wimmer, Katharina

2017-01-01

Abstract Targeted next‐generation‐sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy‐number variations (CNVs) in addition to single‐nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user‐friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state‐of‐the‐art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user‐selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user‐friendliness rendering it highly suitable for routine clinical diagnostics. PMID:28449315

Population variability complicates the accurate detection of climate change responses.

PubMed

McCain, Christy; Szewczyk, Tim; Bracy Knight, Kevin

2016-06-01

The rush to assess species' responses to anthropogenic climate change (CC) has underestimated the importance of interannual population variability (PV). Researchers assume sampling rigor alone will lead to an accurate detection of response regardless of the underlying population fluctuations of the species under consideration. Using population simulations across a realistic, empirically based gradient in PV, we show that moderate to high PV can lead to opposite and biased conclusions about CC responses. Between pre- and post-CC sampling bouts of modeled populations as in resurvey studies, there is: (i) A 50% probability of erroneously detecting the opposite trend in population abundance change and nearly zero probability of detecting no change. (ii) Across multiple years of sampling, it is nearly impossible to accurately detect any directional shift in population sizes with even moderate PV. (iii) There is up to 50% probability of detecting a population extirpation when the species is present, but in very low natural abundances. (iv) Under scenarios of moderate to high PV across a species' range or at the range edges, there is a bias toward erroneous detection of range shifts or contractions. Essentially, the frequency and magnitude of population peaks and troughs greatly impact the accuracy of our CC response measurements. Species with moderate to high PV (many small vertebrates, invertebrates, and annual plants) may be inaccurate 'canaries in the coal mine' for CC without pertinent demographic analyses and additional repeat sampling. Variation in PV may explain some idiosyncrasies in CC responses detected so far and urgently needs more careful consideration in design and analysis of CC responses. © 2016 John Wiley & Sons Ltd.

Single-cell copy number variation detection

PubMed Central

2011-01-01

Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition and recurrent genome artifact corrections. We demonstrate that the proposed channel clone normalization significantly improves the copy number variation detection in both simulated and real single-cell array CGH data. PMID:21854607

High-throughput olfactory conditioning and memory retention test show variation in Nasonia parasitic wasps

PubMed Central

Hoedjes, K M; Steidle, J L M; Werren, J H; Vet, L E M; Smid, H M

2012-01-01

Most of our knowledge on learning and memory formation results from extensive studies on a small number of animal species. Although features and cellular pathways of learning and memory are highly similar in this diverse group of species, there are also subtle differences. Closely related species of parasitic wasps display substantial variation in memory dynamics and can be instrumental to understanding both the adaptive benefit of and mechanisms underlying this variation. Parasitic wasps of the genus Nasonia offer excellent opportunities for multidisciplinary research on this topic. Genetic and genomic resources available for Nasonia are unrivaled among parasitic wasps, providing tools for genetic dissection of mechanisms that cause differences in learning. This study presents a robust, high-throughput method for olfactory conditioning of Nasonia using a host encounter as reward. A T-maze olfactometer facilitates high-throughput memory retention testing and employs standardized odors of equal detectability, as quantified by electroantennogram recordings. Using this setup, differences in memory retention between Nasonia species were shown. In both Nasonia vitripennis and Nasonia longicornis, memory was observed up to at least 5 days after a single conditioning trial, whereas Nasonia giraulti lost its memory after 2 days. This difference in learning may be an adaptation to species-specific differences in ecological factors, for example, host preference. The high-throughput methods for conditioning and memory retention testing are essential tools to study both ultimate and proximate factors that cause variation in learning and memory formation in Nasonia and other parasitic wasp species. PMID:22804968