Attentional bias induced by solving simple and complex addition and subtraction problems.

PubMed

Masson, Nicolas; Pesenti, Mauro

2014-01-01

The processing of numbers has been shown to induce shifts of spatial attention in simple probe detection tasks, with small numbers orienting attention to the left and large numbers to the right side of space. Recently, the investigation of this spatial-numerical association has been extended to mental arithmetic with the hypothesis that solving addition or subtraction problems may induce attentional displacements (to the right and to the left, respectively) along a mental number line onto which the magnitude of the numbers would range from left to right, from small to large numbers. Here we investigated such attentional shifts using a target detection task primed by arithmetic problems in healthy participants. The constituents of the addition and subtraction problems (first operand; operator; second operand) were flashed sequentially in the centre of a screen, then followed by a target on the left or the right side of the screen, which the participants had to detect. This paradigm was employed with arithmetic facts (Experiment 1) and with more complex arithmetic problems (Experiment 2) in order to assess the effects of the operation, the magnitude of the operands, the magnitude of the results, and the presence or absence of a requirement for the participants to carry or borrow numbers. The results showed that arithmetic operations induce some spatial shifts of attention, possibly through a semantic link between the operation and space.

Analysis of the moderate resolution imaging spectroradiometer contextual algorithm for small fire detection, Journal of Applied Remote Sensing Vol.3

Treesearch

W. Wang; J.J. Qu; X. Hao; Y. Liu

2009-01-01

In the southeastern United States, most wildland fires are of low intensity. A substantial number of these fires cannot be detected by the MODIS contextual algorithm. To improve the accuracy of fire detection for this region, the remote-sensed characteristics of these fires have to be...

Are numbers, size and brightness equally efficient in orienting visual attention? Evidence from an eye-tracking study.

PubMed

Bulf, Hermann; Macchi Cassia, Viola; de Hevia, Maria Dolores

2014-01-01

A number of studies have shown strong relations between numbers and oriented spatial codes. For example, perceiving numbers causes spatial shifts of attention depending upon numbers' magnitude, in a way suggestive of a spatially oriented, mental representation of numbers. Here, we investigated whether this phenomenon extends to non-symbolic numbers, as well as to the processing of the continuous dimensions of size and brightness, exploring whether different quantitative dimensions are equally mapped onto space. After a numerical (symbolic Arabic digits or non-symbolic arrays of dots; Experiment 1) or a non-numerical cue (shapes of different size or brightness level; Experiment 2) was presented, participants' saccadic response to a target that could appear either on the left or the right side of the screen was registered using an automated eye-tracker system. Experiment 1 showed that, both in the case of Arabic digits and dot arrays, right targets were detected faster when preceded by large numbers, and left targets were detected faster when preceded by small numbers. Participants in Experiment 2 were faster at detecting right targets when cued by large-sized shapes and left targets when cued by small-sized shapes, whereas brightness cues did not modulate the detection of peripheral targets. These findings indicate that looking at a symbolic or a non-symbolic number induces attentional shifts to a peripheral region of space that is congruent with the numbers' relative position on a mental number line, and that a similar shift in visual attention is induced by looking at shapes of different size. More specifically, results suggest that, while the dimensions of number and size spontaneously map onto an oriented space, the dimension of brightness seems to be independent at a certain level of magnitude elaboration from the dimensions of spatial extent and number, indicating that not all continuous dimensions are equally mapped onto space.

Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells.

PubMed

Luo, Xian; Li, Liang

2017-11-07

In cellular metabolomics, it is desirable to carry out metabolomic profiling using a small number of cells in order to save time and cost. In some applications (e.g., working with circulating tumor cells in blood), only a limited number of cells are available for analysis. In this report, we describe a method based on high-performance chemical isotope labeling (CIL) nanoflow liquid chromatography mass spectrometry (nanoLC-MS) for high-coverage metabolomic analysis of small numbers of cells (i.e., ≤10000 cells). As an example, 12 C-/ 13 C-dansyl labeling of the metabolites in lysates of 100, 1000, and 10000 MCF-7 breast cancer cells was carried out using a new labeling protocol tailored to handle small amounts of metabolites. Chemical-vapor-assisted ionization in a captivespray interface was optimized for improving metabolite ionization and increasing robustness of nanoLC-MS. Compared to microflow LC-MS, the nanoflow system provided much improved metabolite detectability with a significantly reduced sample amount required for analysis. Experimental duplicate analyses of biological triplicates resulted in the detection of 1620 ± 148, 2091 ± 89 and 2402 ± 80 (n = 6) peak pairs or metabolites in the amine/phenol submetabolome from the 12 C-/ 13 C-dansyl labeled lysates of 100, 1000, and 10000 cells, respectively. About 63-69% of these peak pairs could be either identified using dansyl labeled standard library or mass-matched to chemical structures in human metabolome databases. We envisage the routine applications of this method for high-coverage quantitative cellular metabolomics using a starting material of 10000 cells. Even for analyzing 100 or 1000 cells, although the metabolomic coverage is reduced from the maximal coverage, this method can still detect thousands of metabolites, allowing the analysis of a large fraction of the metabolome and focused analysis of the detectable metabolites.

Monitoring of DSP toxins in small-sized plankton fraction of seawater collected in Mutsu Bay, Japan, by ELISA method: relation with toxin contamination of scallop.

PubMed

Imai, Ichiro; Sugioka, Hikaru; Nishitani, Goh; Mitsuya, Tadashi; Hamano, Yonekazu

2003-01-01

Monitorings were conducted on DSP toxins in mid-gut gland of scallop (mouse assay), cell numbers of toxic dinoflagellate species of Dinophysis, and diarrhetic shellfish poisoning (DSP) toxins in small-sized (0.7-5 microm) plankton fraction of seawater collected from surface (0 m) and 20 m depth at a station in Mutsu Bay, Aomori Prefecture, Japan, in 2000. A specific enzyme-linked immunosorbent assay (ELISA) was employed for the analysis of DSP toxins in small-sized plankton fraction using a mouse monoclonal anti-okadaic acid antibody which recognizes okadaic acid, dinophysistoxin-1, and dinophysistoxin-3. DSP toxins were detected twice in the mid-gut gland of scallops at 1.1-2.3 MU (mouse units) g(-1) on 26 June and at 0.6-1.2 MU g(-1) on 3 July, respectively. Relatively high cell densities of D. fortii were observed on 26 June and 11 September, and may only contribute to the bivalve toxicity during late June to early July. D. acuminata did not appear to be responsible for the toxicity of scallops in Mutsu Bay in 2000. ELISA monitoring of small-sized plankton fraction in seawater could detect DSP toxins two weeks before the detection of the toxin in scallops, and could do so two weeks after the loss of the bivalve toxicity by mouse assay. On 17 July, toxic D. fortii was detected at only small number, <10 cells l(-1), but DSP toxins were detected by the ELISA assay, suggesting a presence of other toxic small-sized plankton in seawater. For the purpose of reducing negative impacts of DSP occurrences, monitorings have been carried out hitherto on DSP toxins of bivalve tissues by mouse assay and on cell densities of "toxic" species of Dinophysis. Here we propose a usefulness of ELISA monitoring of plankton toxicity, especially in small-sized fraction, which are possible foods of mixotrophic Dinophysis, as a practical tool for detecting and predicting DSPs in coastal areas of fisheries grounds of bivalve aquaculture.

Improved microseismic event locations through large-N arrays and wave-equation imaging and inversion

NASA Astrophysics Data System (ADS)

Witten, B.; Shragge, J. C.

2016-12-01

The recent increased focus on small-scale seismicity, Mw < 4 has come about primarily for two reasons. First, there is an increase in induced seismicity related to injection operations primarily for wastewater disposal and hydraulic fracturing for oil and gas recovery and for geothermal energy production. While the seismicity associated with injection is sometimes felt, it is more often weak. Some weak events are detected on current sparse arrays; however, accurate location of the events often requires a larger number of (multi-component) sensors. This leads to the second reason for an increased focus on small magnitude seismicity: a greater number of seismometers are being deployed in large N-arrays. The greater number of sensors decreases the detection threshold and therefore significantly increases the number of weak events found. Overall, these two factors bring new challenges and opportunities. Many standard seismological location and inversion techniques are geared toward large, easily identifiable events recorded on a sparse number of stations. However, with large-N arrays we can detect small events by utilizing multi-trace processing techniques, and increased processing power equips us with tools that employ more complete physics for simultaneously locating events and inverting for P- and S-wave velocity structure. We present a method that uses large-N arrays and wave-equation-based imaging and inversion to jointly locate earthquakes and estimate the elastic velocities of the earth. The technique requires no picking and is thus suitable for weak events. We validate the methodology through synthetic and field data examples.

Exploitation of immunofluorescence for the quantification and characterization of small numbers of Pasteuria endospores.

PubMed

Costa, Sofia R; Kerry, Brian R; Bardgett, Richard D; Davies, Keith G

2006-12-01

The Pasteuria group of endospore-forming bacteria has been studied as a biocontrol agent of plant-parasitic nematodes. Techniques have been developed for its detection and quantification in soil samples, and these mainly focus on observations of endospore attachment to nematodes. Characterization of Pasteuria populations has recently been performed with DNA-based techniques, which usually require the extraction of large numbers of spores. We describe a simple immunological method for the quantification and characterization of Pasteuria populations. Bayesian statistics were used to determine an extraction efficiency of 43% and a threshold of detection of 210 endospores g(-1) sand. This provided a robust means of estimating numbers of endospores in small-volume samples from a natural system. Based on visual assessment of endospore fluorescence, a quantitative method was developed to characterize endospore populations, which were shown to vary according to their host.

Sensitive Detection Using Microfluidics and Nonlinear Amplification

DTIC Science & Technology

2011-07-22

Quantification of Nucleic Acids via Simultaneous Chemical Initiation of Recombinase Polymerase Amplification Reactions on SlipChip" 2011, 83, 3533... Amplification 5a. CONTRACT NUMBER 5b. GRANT NUMBER N00014-08-1-0936 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Rustem F. Ismagilov 5d. PROJECT NUMBER 5e...concentrations by combining controlled chemical autocatalytic amplification and stochastic confinement of small particles with the microfluidic

A net fishing enrichment strategy for colorimetric detection of E. coli O157:H7

USDA-ARS?s Scientific Manuscript database

The strict regulatory requirements for pathogen monitoring in food systems to ensure safety demands that the detection method can recognize small numbers of pathogens. Although significant efforts on the development of biosensors have been reported with marked improvement in sensitivity, appropriate...

Solid renal masses in adults

PubMed Central

Mittal, Mahesh Kumar; Sureka, Binit

2016-01-01

With the ever increasing trend of using cross-section imaging in today's era, incidental detection of small solid renal masses has dramatically multiplied. Coincidentally, the number of asymptomatic benign lesions being detected has also increased. The role of radiologists is not only to identify these lesions, but also go a one step further and accurately characterize various renal masses. Earlier detection of small renal cell carcinomas means identifying at the initial stage which has an impact on prognosis, patient management and healthcare costs. In this review article we share our experience with the typical and atypical solid renal masses encountered in adults in routine daily practice. PMID:28104933

New Transfer Theory Relationships for Signal and Noise Analyses of X-Ray Detectors

DTIC Science & Technology

2002-10-01

1 Oct 1999 - 30 Sep 2002 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER The Role of Neuropilin in Breast Cancer Metastasis 5b. GRANT NUMBER DAMD17-99-1...method available at present for the detection of breast cancer in screening programs. Unfortunately, it still misses many cancers , particularly in the...mammography holds the promise of improved specificity and sensitivity for the detection of small cancers . However, superior image quality can only be achieved

Deep ensemble learning of virtual endoluminal views for polyp detection in CT colonography

NASA Astrophysics Data System (ADS)

Umehara, Kensuke; Näppi, Janne J.; Hironaka, Toru; Regge, Daniele; Ishida, Takayuki; Yoshida, Hiroyuki

2017-03-01

Robust training of a deep convolutional neural network (DCNN) requires a very large number of annotated datasets that are currently not available in CT colonography (CTC). We previously demonstrated that deep transfer learning provides an effective approach for robust application of a DCNN in CTC. However, at high detection accuracy, the differentiation of small polyps from non-polyps was still challenging. In this study, we developed and evaluated a deep ensemble learning (DEL) scheme for reviewing of virtual endoluminal images to improve the performance of computer-aided detection (CADe) of polyps in CTC. Nine different types of image renderings were generated from virtual endoluminal images of polyp candidates detected by a conventional CADe system. Eleven DCNNs that represented three types of publically available pre-trained DCNN models were re-trained by transfer learning to identify polyps from the virtual endoluminal images. A DEL scheme that determines the final detected polyps by a review of the nine types of VE images was developed by combining the DCNNs using a random forest classifier as a meta-classifier. For evaluation, we sampled 154 CTC cases from a large CTC screening trial and divided the cases randomly into a training dataset and a test dataset. At 3.9 falsepositive (FP) detections per patient on average, the detection sensitivities of the conventional CADe system, the highestperforming single DCNN, and the DEL scheme were 81.3%, 90.7%, and 93.5%, respectively, for polyps ≥6 mm in size. For small polyps, the DEL scheme reduced the number of false positives by up to 83% over that of using a single DCNN alone. These preliminary results indicate that the DEL scheme provides an effective approach for improving the polyp detection performance of CADe in CTC, especially for small polyps.

An optical search for small comets

NASA Astrophysics Data System (ADS)

Mutel, R. L.; Fix, J. D.

2000-11-01

We have conducted an extensive optical search for small comets with the characteristics proposed by Frank et al. [1986] and Frank and Sigwarth [1993, 1997]. The observations were made using the 0.5-m reflector of the Iowa Robotic Observatory between September 1998 and June 1999. The search technique consisted of tracking a fixed point in the ecliptic plane at +/-9° geocentric solar phase angle. The telescope scan rate was chosen to track objects moving prograde at 10 km s-1 relative to the Earth at a distance of 55,000 km. The camera was multiply shuttered to discriminate against trails caused by cosmic rays and sensor imperfections. Of 6143 total images, we selected 2713 which were suitable for detection of objects with a magnitude 16.5 or brighter with 120 pixel trails. The sensitivity and reliability of the visual detection scheme were determined by extensive double-blind tests using synthetic trails added to over 500 search images. After careful visual inspection of all images, we found no trials consistent with small comets. This result strongly disagrees with previous optical searches of Yeates [1989] and Frank et al. [1990], whose detection rates and magnitudes, when converted to the present search, predict 65+/-22 detections. We conclude that at 99% confidence, the number density of any prograde objects in the ecliptic plane brighter than magnitude 16.5 with speeds near 10 km s-1 have a number density less than 5% of the small-comet density derived by Frank et al. [1990]. Any object fainter than this magnitude limit with a mass corresponding to the small-comet hypothesis (M>20,000kg) must have either an implausibly low geometric albedo (p<0.01) or a density larger than that of water.

Identification of pathogen genomic variants through an integrated pipeline

PubMed Central

2014-01-01

Background Whole-genome sequencing represents a powerful experimental tool for pathogen research. We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for finding single nucleotide and copy number variants as well as recombination events. Results We have validated our pipeline using four sets of Plasmodium falciparum drug resistant data containing 26 clones from 3D7 and Dd2 background strains, identifying an average of 11 single nucleotide variants per clone. We also identify 8 copy number variants with contributions to resistance, and report for the first time that all analyzed amplification events are in tandem. Conclusions The Platypus pipeline provides malaria researchers with a powerful tool to analyze short read sequencing data. It provides an accurate way to detect SNVs using known software packages, and a novel methodology for detection of CNVs, though it does not currently support detection of small indels. We have validated that the pipeline detects known SNVs in a variety of samples while filtering out spurious data. We bundle the methods into a freely available package. PMID:24589256

Improving Earth/Prediction Models to Improve Network Processing

NASA Astrophysics Data System (ADS)

Wagner, G. S.

2017-12-01

The United States Atomic Energy Detection System (USAEDS) primaryseismic network consists of a relatively small number of arrays andthree-component stations. The relatively small number of stationsin the USAEDS primary network make it both necessary and feasibleto optimize both station and network processing.Station processing improvements include detector tuning effortsthat use Receiver Operator Characteristic (ROC) curves to helpjudiciously set acceptable Type 1 (false) vs. Type 2 (miss) errorrates. Other station processing improvements include the use ofempirical/historical observations and continuous background noisemeasurements to compute time-varying, maximum likelihood probabilityof detection thresholds.The USAEDS network processing software makes extensive use of theazimuth and slowness information provided by frequency-wavenumberanalysis at array sites, and polarization analysis at three-componentsites. Most of the improvements in USAEDS network processing aredue to improvements in the models used to predict azimuth, slowness,and probability of detection. Kriged travel-time, azimuth andslowness corrections-and associated uncertainties-are computedusing a ground truth database. Improvements in station processingand the use of improved models for azimuth, slowness, and probabilityof detection have led to significant improvements in USADES networkprocessing.

MUSIC algorithm for location searching of dielectric anomalies from S-parameters using microwave imaging

NASA Astrophysics Data System (ADS)

Park, Won-Kwang; Kim, Hwa Pyung; Lee, Kwang-Jae; Son, Seong-Ho

2017-11-01

Motivated by the biomedical engineering used in early-stage breast cancer detection, we investigated the use of MUltiple SIgnal Classification (MUSIC) algorithm for location searching of small anomalies using S-parameters. We considered the application of MUSIC to functional imaging where a small number of dipole antennas are used. Our approach is based on the application of Born approximation or physical factorization. We analyzed cases in which the anomaly is respectively small and large in relation to the wavelength, and the structure of the left-singular vectors is linked to the nonzero singular values of a Multi-Static Response (MSR) matrix whose elements are the S-parameters. Using simulations, we demonstrated the strengths and weaknesses of the MUSIC algorithm in detecting both small and extended anomalies.

Automated Detection of Small Bodies by Space Based Observation

NASA Astrophysics Data System (ADS)

Bidstrup, P. R.; Grillmayer, G.; Andersen, A. C.; Haack, H.; Jorgensen, J. L.

The number of known comets and asteroids is increasing every year. Up till now this number is including approximately 250,000 of the largest minor planets, as they are usually referred. These discoveries are due to the Earth-based observation which has intensified over the previous decades. Additionally larger telescopes and arrays of telescopes are being used for exploring our Solar System. It is believed that all near- Earth and Main-Belt asteroids of diameters above 10 to 30 km have been discovered, leaving these groups of objects as observationally complete. However, the cataloguing of smaller bodies is incomplete as only a very small fraction of the expected number has been discovered. It is estimated that approximately 1010 main belt asteroids in the size range 1 m to 1 km are too faint to be observed using Earth-based telescopes. In order to observe these small bodies, space-based search must be initiated to remove atmospheric disturbances and to minimize the distance to the asteroids and thereby minimising the requirement for long camera integration times. A new method of space-based detection of moving non-stellar objects is currently being developed utilising the Advanced Stellar Compass (ASC) built for spacecraft attitude determination by Ørsted, Danish Technical University. The ASC serves as a backbone technology in the project as it is capable of fully automated distinction of known and unknown celestial objects. By only processing objects of particular interest, i.e. moving objects, it will be possible to discover small bodies with a minimum of ground control, with the ultimate ambition of a fully automated space search probe. Currently, the ASC is being mounted on the Flying Laptop satellite of the Institute of Space Systems, Universität Stuttgart. It will, after a launch into a low Earth polar orbit in 2008, test the detection method with the ASC equipment that already had significant in-flight experience. A future use of the ASC based automated detection of small bodies is currently on a preliminary stage and known as the Bering project - a deep space survey to the asteroid Main-Belt. With a successful detection method, the Bering mission is expected to discover approximately 6 new small objects per day and 1 will thus during the course of a few years discover 5,000-10,000 new sub-kilometer asteroids. Discovery of new small bodies can: 1) Provide further links between groups of meteorites. 2) Constrain the cratering rate at planetary surfaces and thus allow significantly improved cratering ages for terrains on Mars and other planets. 3) Help determine processes that transfer small asteroids from orbits in the asteroid Main-Belt to the inner Solar System. 2

Effectiveness of bed bug monitors for detecting and trapping bed bugs in apartments.

PubMed

Wang, Changlu; Tsai, Wan-Tien; Cooper, Richard; White, Jeffrey

2011-02-01

Bed bugs, Cimex lectularius L., are now considered a serious urban pest in the United States. Because they are small and difficult to find, there has been strong interest in developing and using monitoring tools to detect bed bugs and evaluate the results of bed bug control efforts. Several bed bug monitoring devices were developed recently, but their effectiveness is unknown. We comparatively evaluated three active monitors that contain attractants: CDC3000, NightWatch, and a home-made dry ice trap. The Climbup Insect Interceptor, a passive monitor (without attractants), was used for estimating the bed bug numbers before and after placing active monitors. The results of the Interceptors also were compared with the results of the active monitors. In occupied apartments, the relative effectiveness of the active monitors was: dry ice trap > CDC3000 > NightWatch. In lightly infested apartments, the Interceptor (operated for 7 d) trapped similar number of bed bugs as the dry ice trap (operated for 1 d) and trapped more bed bugs than CDC3000 and NightWatch (operated for 1 d). The Interceptor was also more effective than visual inspections in detecting the presence of small numbers of bed bugs. CDC3000 and the dry ice trap operated for 1 d were equally as effective as the visual inspections for detecting very low level of infestations, whereas 1-d deployment of NightWatch detected significantly lower number of infestations compared with visual inspections. NightWatch was designed to be able to operate for several consecutive nights. When operated for four nights, NightWatch trapped similar number of bed bugs as the Interceptors operated for 10 d after deployment of NightWatch. We conclude these monitors are effective tools in detecting early bed bug infestations and evaluating the results of bed bug control programs.

Modified Technique For Chemisorption Measurements

NASA Technical Reports Server (NTRS)

Schryer, David R.; Brown, Kenneth G.; Schryer, Jacqueline

1989-01-01

In measurements of chemisorption of CO on Pt/SnO2 catalyst observed that if small numbers of relatively large volumes of adsorbate gas are passed through sample, very little removal of CO detected. In these cases little or no CO has been chemisorbed on Pt/SnO2. Technique of using large number of small volumes of adsorbate gas to measure chemisorption applicable to many gas/material combinations other than CO on Pt/SnO2. Volume used chosen so that at least 10 percent of adsorbate gas removed during each exposure.

Design of DroDeASys (Drowsy Detection and Alarming System)

NASA Astrophysics Data System (ADS)

Juvale, Hrishikesh B.; Mahajan, Anant S.; Bhagwat, Ashwin A.; Badiger, Vishal T.; Bhutkar, Ganesh D.; Dhabe, Priyadarshan S.; Dhore, Manikrao L.

The paper discusses the Drowsy Detection & Alarming System that has been developed, using a non-intrusive approach. The system is basically developed to detect drivers dozing at the wheel at night time driving. The system uses a small infra-red night vision camera that points directly towards the driver`s face and monitors the driver`s eyes in order to detect fatigue. In such a case when fatigue is detected, a warning signal is issued to alert the driver. This paper discusses the algorithms that have been used to detect drowsiness. The decision whether the driver is dozing or not is taken depending on whether the eyes are open for a specific number of frames. If the eyes are found to be closed for a certain number of consecutive frames then the driver is alerted with an alarm.

FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs

PubMed Central

Huang, Kun; Doyle, Francis; Wurz, Zachary E.; Tenenbaum, Scott A.; Hammond, Reza K.

2017-01-01

Abstract Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play a variety of important regulatory roles in many eukaryotes. Their small size has made it challenging to study them directly in live cells. Here we describe an RNA-based fluorescent sensor for small RNA detection both in vitro and in vivo, adaptable for any small RNA. It utilizes an sxRNA switch for detection of miRNA–mRNA interactions combined with a fluorophore-binding sequence ‘Spinach’, a GFP-like RNA aptamer for which the RNA–fluorophore complex exhibits strong and consistent fluorescence under an excitation wavelength. Two example sensors, FASTmiR171 and FASTmiR122, can rapidly detect and quantify the levels of miR171 and miR122 in vitro. The sensors can determine relative levels of miRNAs in total RNA extracts with sensitivity similar to small RNA sequencing and northern blots. FASTmiR sensors were also used to estimate the copy number range of miRNAs in total RNA extracts. To localize and analyze the spatial distribution of small RNAs in live, single cells, tandem copies of FASTmiR122 were expressed in different cell lines. FASTmiR122 was able to quantitatively detect the differences in miR122 levels in Huh7 and HEK293T cells demonstrating its potential for tracking miRNA expression and localization in vivo. PMID:28586459

Single walled carbon nanotube-based stochastic resonance device with molecular self-noise source

NASA Astrophysics Data System (ADS)

Fujii, Hayato; Setiadi, Agung; Kuwahara, Yuji; Akai-Kasaya, Megumi

2017-09-01

Stochastic resonance (SR) is an intrinsic noise usage system for small-signal sensing found in various living creatures. The noise-enhanced signal transmission and detection system, which is probabilistic but consumes low power, has not been used in modern electronics. We demonstrated SR in a summing network based on a single-walled carbon nanotube (SWNT) device that detects small subthreshold signals with very low current flow. The nonlinear current-voltage characteristics of this SWNT device, which incorporated Cr electrodes, were used as the threshold level of signal detection. The adsorption of redox-active polyoxometalate molecules on SWNTs generated additional noise, which was utilized as a self-noise source. To form a summing network SR device, a large number of SWNTs were aligned parallel to each other between the electrodes, which increased the signal detection ability. The functional capabilities of the present small-size summing network SR device, which rely on dense nanomaterials and exploit intrinsic spontaneous noise at room temperature, offer a glimpse of future bio-inspired electronic devices.

Assessing the influence of small fires on trends in fire regime features at mainland Spain

NASA Astrophysics Data System (ADS)

Jiménez-Ruano, Adrián; Rodrigues Mimbrero, Marcos; de la Riva Fernández, Juan

2017-04-01

Small fires, i.e. fires smaller than 1 Ha, represent a huge proportion of total wildfire occurrence in the Mediterranean region. In the case of Spain, around 53% of fires in the period 1988-2013 fall into this category according to the Spanish EGIF statistics. However, the proportion of small fires is not stationary over time. Small fires are usually excluded from most analysis, given the chance of introducing or falling into temporal bias, being almost mandatory in those assessments using data before the 90s. Inconsistences and inhomogeneity problems related to the diversity of criteria and/or registration procedures among Autonomous Regions are found before that date, although it is widely agreed that small fires are consistently registered starting from 1988. Nevertheless, in terms of fire regimen characterization it is important to know to what extent small fires contribute to the overall fire behaviour. The aim of this study is to analyse spatial-temporal trends of several fire features such as total number of fires and burned area, number and burned area of natural and human fires, and the proportion of natural/human cause in the period 1988-2013 at province level (NUTS3). The analysis is conducted at the mainland Spain at annual and seasonal time scales. We are mainly interested in exploring differences in spatial-temporal trends including or excluding small fires and dealing with them separately as well. This allows determining the extent to which small fires may affect fire regime characterization. We employed a Mann-Kendall test for trend detection and Sen's slope to evaluate the magnitude of the change. Both tests were applied for each fire feature aggregated at NUTS3 level for both autumn-winter and spring-summer seasons. Our results show significant changes in the evolution of annual wildfire frequency; especially strong when small fires are accounted for. A similar outcome was observed in natural and human number fires during the spring-summer season. The increase in number of fires seems to be reversed during autumn-winter. At seasonal scale, the inclusion of small fires allows to detect significant trends in all of fire frequency features, except natural fires. In turn, neither burned area features do not significantly affect the trends through incorporating small fires. Therefore, the inclusion/exclusion of small fires do influence observed trends mostly in terms of fire frequency.

MUSIC algorithms for rebar detection

NASA Astrophysics Data System (ADS)

Solimene, Raffaele; Leone, Giovanni; Dell'Aversano, Angela

2013-12-01

The MUSIC (MUltiple SIgnal Classification) algorithm is employed to detect and localize an unknown number of scattering objects which are small in size as compared to the wavelength. The ensemble of objects to be detected consists of both strong and weak scatterers. This represents a scattering environment challenging for detection purposes as strong scatterers tend to mask the weak ones. Consequently, the detection of more weakly scattering objects is not always guaranteed and can be completely impaired when the noise corrupting data is of a relatively high level. To overcome this drawback, here a new technique is proposed, starting from the idea of applying a two-stage MUSIC algorithm. In the first stage strong scatterers are detected. Then, information concerning their number and location is employed in the second stage focusing only on the weak scatterers. The role of an adequate scattering model is emphasized to improve drastically detection performance in realistic scenarios.

Small-scale structure and 21cm fluctuations by primordial black holes

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

Gong, Jinn-Ouk; Kitajima, Naoya, E-mail: jinn-ouk.gong@apctp.org, E-mail: kitajima.naoya@f.mbox.nagoya-u.ac.jp

We discuss early structure formation of small scales sourced by primordial black holes (PBHs) which constitute a small part of present cold dark matter component. We calculate the mass function and power spectrum of haloes originated from the Poisson fluctuations of PBH number and show that the number of small haloes is significantly modified in the presence of PBHs even if their fraction accounts for only 10{sup −4}–10{sup −3} of total dark matter abundance. We then compute the subsequent 21cm signature from those haloes. We find that PBHs can provide major contributions at high redshifts within the detectability of futuremore » experiments such as Square Kilometer Array, and provide a forecast constraint on the PBH fraction.« less

Infrared Damage Detection System (IDDS) for Real-Time, Small-Scale Damage Monitoring

DTIC Science & Technology

2007-01-01

MM-YY) 2. REPORT TYPE 3. DATES COVERED (From - To) January 2007 Technical Paper 5a. CONTRACT NUMBER FA8650-04-C-5200 5b. GRANT NUMBER 4 ...PROJECT NUMBER 4347 5e. TASK NUMBER 27 6 . AUTHOR(S) George A. Hartman 5f. WORK UNIT NUMBER 03 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS... titanium alloys, titanium -aluminide intermetallics, and nickel-base superalloys. Various geometries have also been used; however, we will focus on the

Using Information From Prior Satellite Scans to Improve Cloud Detection Near the Day-Night Terminator

NASA Technical Reports Server (NTRS)

Yost, Christopher R.; Minnis, Patrick; Trepte, Qing Z.; Palikonda, Rabindra; Ayers, Jeffrey K.; Spangenberg, Doulas A.

2012-01-01

With geostationary satellite data it is possible to have a continuous record of diurnal cycles of cloud properties for a large portion of the globe. Daytime cloud property retrieval algorithms are typically superior to nighttime algorithms because daytime methods utilize measurements of reflected solar radiation. However, reflected solar radiation is difficult to accurately model for high solar zenith angles where the amount of incident radiation is small. Clear and cloudy scenes can exhibit very small differences in reflected radiation and threshold-based cloud detection methods have more difficulty setting the proper thresholds for accurate cloud detection. Because top-of-atmosphere radiances are typically more accurately modeled outside the terminator region, information from previous scans can help guide cloud detection near the terminator. This paper presents an algorithm that uses cloud fraction and clear and cloudy infrared brightness temperatures from previous satellite scan times to improve the performance of a threshold-based cloud mask near the terminator. Comparisons of daytime, nighttime, and terminator cloud fraction derived from Geostationary Operational Environmental Satellite (GOES) radiance measurements show that the algorithm greatly reduces the number of false cloud detections and smoothes the transition from the daytime to the nighttime clod detection algorithm. Comparisons with the Geoscience Laser Altimeter System (GLAS) data show that using this algorithm decreases the number of false detections by approximately 20 percentage points.

Detection of small orientation changes and the precision of visual working memory.

PubMed

Salmela, Viljami R; Saarinen, Jussi

2013-01-14

We investigated the precision of orientation representations with two tasks, change detection and recall. Previously change detection has been measured only with relatively large orientation changes compared to psychophysical thresholds. In the first experiment, we measured the observers' ability (d') to detect small changes in orientation (5-30°) with 1-4 Gabor items. With one item even a 10° change was well detected (average d'=2.5). As the amount of change increased to 30°, the d' increased to 5.2. When the number of items was increased, the d's gradually decreased. In the second experiment, we used a recall task and the observers adjusted the orientation of a probe Gabor to match the orientation of a Gabor held in the memory. The standard deviation (s.d.) of errors was calculated from the Gaussian distribution fitted to the data. As the number of items increased from 1 to 6, the s.d. increased from 8.6° to 19.6°. Even with six items, the observers did not make any random adjustments. The results show a square root relation between the d'/s.d. and the number of items. The d' in change detection is directly proportional to the square root of (1/n) and the orientation change. The increase of the s.d. in recall task is inversely proportional to square root of (1/n). The results suggest that limited resources and precision of representations, without additional assumptions, determine the memory performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

Application of the LDM algorithm to identify small lung nodules on low-dose MSCT scans

NASA Astrophysics Data System (ADS)

Zhao, Binsheng; Ginsberg, Michelle S.; Lefkowitz, Robert A.; Jiang, Li; Cooper, Cathleen; Schwartz, Lawrence H.

2004-05-01

In this work, we present a computer-aided detection (CAD) algorithm for small lung nodules on low-dose MSCT images. With this technique, identification of potential lung nodules is carried out with a local density maximum (LDM) algorithm, followed by reduction of false positives from the nodule candidates using task-specific 2-D/3-D features along with a knowledge-based nodule inclusion/exclusion strategy. Twenty-eight MSCT scans (40/80mAs, 120kVp, 5mm collimation/2.5mm reconstruction) from our lung cancer screening program that included at least one lung nodule were selected for this study. Two radiologists independently interpreted these cases. Subsequently, a consensus reading by both radiologists and CAD was generated to define a "gold standard". In total, 165 nodules were considered as the "gold standard" (average: 5.9 nodules/case; range: 1-22 nodules/case). The two radiologists detected 146 nodules (88.5%) and CAD detected 100 nodules (60.6%) with 8.7 false-positives/case. CAD detected an additional 19 nodules (6 nodules > 3mm and 13 nodules < 3mm) that had been missed by both radiologists. Preliminary results show that the CAD is capable of detecting small lung nodules with acceptable number of false-positives on low-dose MSCT scans and it can detect nodules that are otherwise missed by radiologists, though a majority are small nodules (< 3mm).

Compact Quantum Random Number Generator with Silicon Nanocrystals Light Emitting Device Coupled to a Silicon Photomultiplier

NASA Astrophysics Data System (ADS)

Bisadi, Zahra; Acerbi, Fabio; Fontana, Giorgio; Zorzi, Nicola; Piemonte, Claudio; Pucker, Georg; Pavesi, Lorenzo

2018-02-01

A small-sized photonic quantum random number generator, easy to be implemented in small electronic devices for secure data encryption and other applications, is highly demanding nowadays. Here, we propose a compact configuration with Silicon nanocrystals large area light emitting device (LED) coupled to a Silicon photomultiplier to generate random numbers. The random number generation methodology is based on the photon arrival time and is robust against the non-idealities of the detector and the source of quantum entropy. The raw data show high quality of randomness and pass all the statistical tests in national institute of standards and technology tests (NIST) suite without a post-processing algorithm. The highest bit rate is 0.5 Mbps with the efficiency of 4 bits per detected photon.

Occurrence of small Hsd plasmids in Salmonella typhi, Shigella boydii, and Escherichia coli.

PubMed Central

Yoshida, Y; Mise, K

1986-01-01

The natural occurrence of small Hsd (host specificity for DNA) plasmids was demonstrated in restriction endonuclease-producing strains of Salmonella typhi, Shigella boydii, and Escherichia coli. The five Hsd plasmids isolated were between 5.0 and 12.2 kilobases long. The copy number of all the Hsd plasmids was high (more than 10 copies per cell). Introduction of these small plasmids into E. coli strain 0 drastically lowered the efficiency of plating of the lambda.0 phages (the efficiency of plating was less than 5 X 10(-5) PFU-1). High restriction endonuclease activities were detected in the Hsd plasmid-positive strains because of the elevated copy numbers of the hsdR+ gene. The advantages of using E. coli strains containing the small Hsd plasmids for purification of type II restriction endonucleases are discussed. Images PMID:3003023

The Effect of Small Sample Size on Measurement Equivalence of Psychometric Questionnaires in MIMIC Model: A Simulation Study.

PubMed

Jamali, Jamshid; Ayatollahi, Seyyed Mohammad Taghi; Jafari, Peyman

2017-01-01

Evaluating measurement equivalence (also known as differential item functioning (DIF)) is an important part of the process of validating psychometric questionnaires. This study aimed at evaluating the multiple indicators multiple causes (MIMIC) model for DIF detection when latent construct distribution is nonnormal and the focal group sample size is small. In this simulation-based study, Type I error rates and power of MIMIC model for detecting uniform-DIF were investigated under different combinations of reference to focal group sample size ratio, magnitude of the uniform-DIF effect, scale length, the number of response categories, and latent trait distribution. Moderate and high skewness in the latent trait distribution led to a decrease of 0.33% and 0.47% power of MIMIC model for detecting uniform-DIF, respectively. The findings indicated that, by increasing the scale length, the number of response categories and magnitude DIF improved the power of MIMIC model, by 3.47%, 4.83%, and 20.35%, respectively; it also decreased Type I error of MIMIC approach by 2.81%, 5.66%, and 0.04%, respectively. This study revealed that power of MIMIC model was at an acceptable level when latent trait distributions were skewed. However, empirical Type I error rate was slightly greater than nominal significance level. Consequently, the MIMIC was recommended for detection of uniform-DIF when latent construct distribution is nonnormal and the focal group sample size is small.

The Effect of Small Sample Size on Measurement Equivalence of Psychometric Questionnaires in MIMIC Model: A Simulation Study

PubMed Central

Jafari, Peyman

2017-01-01

Evaluating measurement equivalence (also known as differential item functioning (DIF)) is an important part of the process of validating psychometric questionnaires. This study aimed at evaluating the multiple indicators multiple causes (MIMIC) model for DIF detection when latent construct distribution is nonnormal and the focal group sample size is small. In this simulation-based study, Type I error rates and power of MIMIC model for detecting uniform-DIF were investigated under different combinations of reference to focal group sample size ratio, magnitude of the uniform-DIF effect, scale length, the number of response categories, and latent trait distribution. Moderate and high skewness in the latent trait distribution led to a decrease of 0.33% and 0.47% power of MIMIC model for detecting uniform-DIF, respectively. The findings indicated that, by increasing the scale length, the number of response categories and magnitude DIF improved the power of MIMIC model, by 3.47%, 4.83%, and 20.35%, respectively; it also decreased Type I error of MIMIC approach by 2.81%, 5.66%, and 0.04%, respectively. This study revealed that power of MIMIC model was at an acceptable level when latent trait distributions were skewed. However, empirical Type I error rate was slightly greater than nominal significance level. Consequently, the MIMIC was recommended for detection of uniform-DIF when latent construct distribution is nonnormal and the focal group sample size is small. PMID:28713828

A comparison between minerals-modified glutamate medium and lauryl tryptose lactose broth for the enumeration of Escherichia coli and coliform organisms in water by the multiple tube method.

PubMed Central

1980-01-01

In a multi-laboratory trial, minerals-modified glutamate medium (MMGM) was compared with lauryl tryptose lactose broth (LTLB) in the multiple tube method for the enumeration of coliform organisms, including Escherichia coli, in water. Samples of raw and chlorinated waters yielded a total of 2313 positive tube-reactions with MMGM and 2174 with LTLB. These were interpreted either as E. coli; other coliform organisms; or as false positive reactions. The results at first reading (18 or 24 h) and at 48 h have been analysed statistically in terms of (i) most probable numbers of coliform organisms; (ii) positive reactions and their interpretation; and (iii) whether or not the sample yielded any E. coli or other coliform organisms. All three analyses indicated the same trends. For the detection of E. coli in raw waters LTLB was better than MMGM at 18-24 h, but MMGM was better at 48 h with waters containing small numbers of coliform organisms; for raw waters with greater numbers of organisms, both media performed equally well. Analysis of a subset of samples read at both 18 and 24 h indicated that the superiority of LTLB over MMGM with raw waters disappeared by 24 h. For chlorinated waters, LTLB yielded more positive gas reactions at 18-24 h, but fewer of these were E. coli than with MMGM; at 48 h MMGM was clearly better than LTLB for total coliform organisms including E. coli--especially if the numbers were small. MMGM therefore remains the medium of choice for the detection of E. coli as an indicator of faecal contamination of chlorinated drinking water supplies. It is also better for the detection of small numbers of E. coli in other waters. PMID:6762395

Radar waveform requirements for reliable detection of an aircraft-launched missile

NASA Astrophysics Data System (ADS)

Blair, W. Dale; Brandt-Pearce, Maite

1996-06-01

When tracking a manned aircraft with a phase array radar, detecting a missile launch (i.e., a target split) is particularly important because the missile can have a very small radar cross section (RCS) and drop below the horizon of the radar shortly after launch. Reliable detection of the launch is made difficult because the RCS of the missile is very small compared to that of the manned aircraft and the radar typically revisits a manned aircraft every few seconds. Furthermore, any measurements of the aircraft and missile taken shortly after the launch will be merged until the two targets are resolved in range, frequency, or space. In this paper, detection of the launched missile is addressed through the detection of the presence of target multiplicity with the in-phase and quadrature monopulse measurements. The probability of detecting the launch using monopulse processing will be studied with regard to the tracking signal-to-noise ratio and the number of pulses n the radar waveform.

Monitoring as a Means to Focus Research and Conservation - The Grassland Bird Monitoring Example

Treesearch

Brenda Dale; Michael Norton; Constance Downes; Brian Collins

2005-01-01

One recommendation of the Canadian Landbird Monitoring Strategy of Partners in Flight-Canada is to improve monitoring capability for rapidly declining grassland birds. In Canada, we lack statistical power for many grassland species because they are detected in small numbers, on a low number of routes, or show high year-to-year variability. In developing a Grassland...

Quantifying (dis)agreement between direct detection experiments in a halo-independent way

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

Feldstein, Brian; Kahlhoefer, Felix, E-mail: brian.feldstein@physics.ox.ac.uk, E-mail: felix.kahlhoefer@physics.ox.ac.uk

We propose an improved method to study recent and near-future dark matter direct detection experiments with small numbers of observed events. Our method determines in a quantitative and halo-independent way whether the experiments point towards a consistent dark matter signal and identifies the best-fit dark matter parameters. To achieve true halo independence, we apply a recently developed method based on finding the velocity distribution that best describes a given set of data. For a quantitative global analysis we construct a likelihood function suitable for small numbers of events, which allows us to determine the best-fit particle physics properties of darkmore » matter considering all experiments simultaneously. Based on this likelihood function we propose a new test statistic that quantifies how well the proposed model fits the data and how large the tension between different direct detection experiments is. We perform Monte Carlo simulations in order to determine the probability distribution function of this test statistic and to calculate the p-value for both the dark matter hypothesis and the background-only hypothesis.« less

Sea-Based Infrared Scene Interpretation by Background Type Classification and Coastal Region Detection for Small Target Detection

PubMed Central

Kim, Sungho

2015-01-01

Sea-based infrared search and track (IRST) is important for homeland security by detecting missiles and asymmetric boats. This paper proposes a novel scheme to interpret various infrared scenes by classifying the infrared background types and detecting the coastal regions in omni-directional images. The background type or region-selective small infrared target detector should be deployed to maximize the detection rate and to minimize the number of false alarms. A spatial filter-based small target detector is suitable for identifying stationary incoming targets in remote sea areas with sky only. Many false detections can occur if there is an image sector containing a coastal region, due to ground clutter and the difficulty in finding true targets using the same spatial filter-based detector. A temporal filter-based detector was used to handle these problems. Therefore, the scene type and coastal region information is critical to the success of IRST in real-world applications. In this paper, the infrared scene type was determined using the relationships between the sensor line-of-sight (LOS) and a horizontal line in an image. The proposed coastal region detector can be activated if the background type of the probing sector is determined to be a coastal region. Coastal regions can be detected by fusing the region map and curve map. The experimental results on real infrared images highlight the feasibility of the proposed sea-based scene interpretation. In addition, the effects of the proposed scheme were analyzed further by applying region-adaptive small target detection. PMID:26404308

Detection of small number of Giardia in biological materials prepared from stray dogs.

PubMed

Esmailikia, Leila; Ebrahimzade, Elahe; Shayan, Parviz; Amininia, Narges

2017-12-20

Giardia lamblia is an intestinal protozoa with intermittent and low shedding especially in dogs, and the detection of Giardia is accompanied with problems such as sampling and diagnostic method. The objective of this study was to detection of Giardia in biological materials with low number of parasite using parasitological and molecular methods, and also to determine whether the examined stray dogs harbor known zoonotic genotype of Giardia. For this aim 85 fecal and duodenal samples were studied from which 1 was positive by Trichrome staining of stool, 4 were positive by staining of duodenal samples. The nested PCR analysis with primers derived from 18 SrRNA showed that the specific PCR product could be amplified in 4 stool and 4 duodenal samples. All positive samples in staining analysis were also positive in nested PCR. No amplification could be observed by nested PCR with primers derived from β giardin gene due to the single copy of gene. Interestingly, the extracted DNA from old fixed stained Giardia positive smears could be also amplified with primers derived from 18SrRNA gene. The sequence analysis of nested PCR products showed that they belong to the genotype D. In conclusion, it is to denote that the Trichrome or Giemsa methods were not suitable for the detection of small number of this parasite in stool and the nested PCR with primers derived from 18S rRNA gene can replace the traditional methods successfully. For detection of Giardia in stool, primers derived from β giardin will not be recommended.

Driver genes in non-small cell lung cancer: Characteristics, detection methods, and targeted therapies

PubMed Central

He, Bing; Zhang, Hu-Qin

2017-01-01

Lung cancer is one of the most common causes of cancer-related death in the world. The large number of lung cancer cases is non-small cell lung cancer (NSCLC), which approximately accounting for 75% of lung cancer. Over the past years, our comprehensive knowledge about the molecular biology of NSCLC has been rapidly enriching, which has promoted the discovery of driver genes in NSCLC and directed FDA-approved targeted therapies. Of course, the targeted therapies based on driver genes provide a more exact option for advanced non-small cell lung cancer, improving the survival rate of patients. Now, we will review the landscape of driver genes in NSCLC including the characteristics, detection methods, the application of target therapy and challenges. PMID:28915704

Assessment of circulating copy number variant detection for cancer screening.

PubMed

Molparia, Bhuvan; Nichani, Eshaan; Torkamani, Ali

2017-01-01

Current high-sensitivity cancer screening methods, largely utilizing correlative biomarkers, suffer from false positive rates that lead to unnecessary medical procedures and debatable public health benefit overall. Detection of circulating tumor DNA (ctDNA), a causal biomarker, has the potential to revolutionize cancer screening. Thus far, the majority of ctDNA studies have focused on detection of tumor-specific point mutations after cancer diagnosis for the purpose of post-treatment surveillance. However, ctDNA point mutation detection methods developed to date likely lack either the scope or analytical sensitivity necessary to be useful for cancer screening, due to the low (<1%) ctDNA fraction derived from early stage tumors. On the other hand, tumor-derived copy number variant (CNV) detection is hypothetically a superior means of ctDNA-based cancer screening for many tumor types, given that, relative to point mutations, each individual tumor CNV contributes a much larger number of ctDNA fragments to the overall pool of circulating free DNA (cfDNA). A small number of studies have demonstrated the potential of ctDNA CNV-based screening in select cancer types. Here we perform an in silico assessment of the potential for ctDNA CNV-based cancer screening across many common cancers, and suggest ctDNA CNV detection shows promise as a broad cancer screening methodology.

Small-Angle Neutron Scattering on Crosslink Distribution of Epoxy Networks.

DTIC Science & Technology

1985-10-01

distinct second phase or heterogeneity has been detected. Small- angle X-ray scattering (SAXS), 1 nuclear magnetic resonance (NMR) ,2 electron ... paramagnetic resonance (EPR),3 and glass transition 4temperature (Tg) measurements reveal a second phase which is attri- . buted to a heterogeneous...FUNDING/SPONSORING lab. OFFICE SYMBOL 9. PROCUREMENT INSTRUMENT IDENTIFICATION NUMBER * ORGANIZATION I (If applticable)j F3361 5-84-C-5020 * Bc ADDRESS

Methodological Considerations When Quantifying High-Intensity Efforts in Team Sport Using Global Positioning System Technology.

PubMed

Varley, Matthew C; Jaspers, Arne; Helsen, Werner F; Malone, James J

2017-09-01

Sprints and accelerations are popular performance indicators in applied sport. The methods used to define these efforts using athlete-tracking technology could affect the number of efforts reported. This study aimed to determine the influence of different techniques and settings for detecting high-intensity efforts using global positioning system (GPS) data. Velocity and acceleration data from a professional soccer match were recorded via 10-Hz GPS. Velocity data were filtered using either a median or an exponential filter. Acceleration data were derived from velocity data over a 0.2-s time interval (with and without an exponential filter applied) and a 0.3-second time interval. High-speed-running (≥4.17 m/s 2 ), sprint (≥7.00 m/s 2 ), and acceleration (≥2.78 m/s 2 ) efforts were then identified using minimum-effort durations (0.1-0.9 s) to assess differences in the total number of efforts reported. Different velocity-filtering methods resulted in small to moderate differences (effect size [ES] 0.28-1.09) in the number of high-speed-running and sprint efforts detected when minimum duration was <0.5 s and small to very large differences (ES -5.69 to 0.26) in the number of accelerations when minimum duration was <0.7 s. There was an exponential decline in the number of all efforts as minimum duration increased, regardless of filtering method, with the largest declines in acceleration efforts. Filtering techniques and minimum durations substantially affect the number of high-speed-running, sprint, and acceleration efforts detected with GPS. Changes to how high-intensity efforts are defined affect reported data. Therefore, consistency in data processing is advised.

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.

NORAD's PARCS small satellite tests (1976 and 1978)

NASA Technical Reports Server (NTRS)

Kessler, D. J.

1985-01-01

NORAD sponsored small satellite tests in 1976 and 1978. The purpose of the tests was to use their more sensitive radar to determine the number of Earth orbiting objects which are not part of the official catalogue. Both tests used the PARCS radar. The characteristics of this radar are given. The detection capability of NORAD's operational system is estimated and compared to the PARC's radar sensitivity during these tests. The tests only slightly improved the detection capability, and the largest improvements were at the lowest and highest regions of its sensitivity range. The major conclusion of the test is that 17.7% of the objects detected were uncorrelated (i.e., not in the official catalogue). However, perhaps most significant is the altitutde and size distribution of detected objects are illustrated. The 1978 results are also summarized. This test concluded that at least 7% of the objects detected were not in the official catalogue. Another 6% of the detected objects were not tracked well enough to determine their status. Again, a large percentage of the detected objects at lower altitudes were not in the catalogue.

NORAD's PARCS small satellite tests (1976 and 1978)

NASA Astrophysics Data System (ADS)

Kessler, D. J.

1985-03-01

NORAD sponsored small satellite tests in 1976 and 1978. The purpose of the tests was to use their more sensitive radar to determine the number of Earth orbiting objects which are not part of the official catalogue. Both tests used the PARCS radar. The characteristics of this radar are given. The detection capability of NORAD's operational system is estimated and compared to the PARC's radar sensitivity during these tests. The tests only slightly improved the detection capability, and the largest improvements were at the lowest and highest regions of its sensitivity range. The major conclusion of the test is that 17.7% of the objects detected were uncorrelated (i.e., not in the official catalogue). However, perhaps most significant is the altitutde and size distribution of detected objects are illustrated. The 1978 results are also summarized. This test concluded that at least 7% of the objects detected were not in the official catalogue. Another 6% of the detected objects were not tracked well enough to determine their status. Again, a large percentage of the detected objects at lower altitudes were not in the catalogue.

The prevalence of antimicrobial-resistant Escherichia coli in two species of invasive alien mammals in Japan.

PubMed

Nakamura, Ichiro; Obi, Takeshi; Sakemi, Yoko; Nakayama, Ayano; Miyazaki, Kei; Ogura, Go; Tamaki, Masanobu; Oka, Tatsuzo; Takase, Kozo; Miyamoto, Atsushi; Kawamoto, Yasuhiro

2011-08-01

The prevalence of antimicrobial resistance in 128 Escherichia coli isolates was investigated in two species of invasive alien mammals (IAMs): the small Asian mongoose (SAM) and Japanese weasel (JW). The SAM is found on the main island of Okinawa, Japan, where a large number of livestock is available, and the JW is present on a small island, where is isolated from the main island, and have a small number of livestock. We focused on the two IAMs, inhabiting under the different environments, and compared their prevalence of antimicrobial-resistant E. coli. In the comparison of the frequencies of antimicrobial-resistant E. coli isolates between the SAM and JW, JW showed significantly higher prevalence of resistance against three drugs, ampicillin, chlortetracycline and nalidixic acid, compared with SAM's test results (P<0.05). The bla(TEM) gene and the aph1 gene were detected in 35 subjects (91%) of ampicillin-resistant isolates and 6 subjects (100%) of kanamycin-resistant isolates, respectively. The tet (A) gene was detected in 62 subjects (46%) of CTC-resistant isolates, and the tet (B) gene was detected in 25 subjects (8%) of those in IAM. The present results suggest that some IAMs were the carrier of antimicrobial-resistant bacteria and their genes, and the frequencies of these resistances were different between two IAM species.

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.

Acute carbon tetrachloride feeding induces damage of large but not small cholangiocytes from BDL rat liver.

PubMed

LeSage, G D; Glaser, S S; Marucci, L; Benedetti, A; Phinizy, J L; Rodgers, R; Caligiuri, A; Papa, E; Tretjak, Z; Jezequel, A M; Holcomb, L A; Alpini, G

1999-05-01

Bile duct damage and/or loss is limited to a range of duct sizes in cholangiopathies. We tested the hypothesis that CCl4 damages only large ducts. CCl4 or mineral oil was given to bile duct-ligated (BDL) rats, and 1, 2, and 7 days later small and large cholangiocytes were purified and evaluated for apoptosis, proliferation, and secretion. In situ, we measured apoptosis by morphometric and TUNEL analysis and the number of small and large ducts by morphometry. Two days after CCl4 administration, we found an increased number of small ducts and reduced number of large ducts. In vitro apoptosis was observed only in large cholangiocytes, and this was accompanied by loss of proliferation and secretion in large cholangiocytes and loss of choleretic effect of secretin. Small cholangiocytes de novo express the secretin receptor gene and secretin-induced cAMP response. Consistent with damage of large ducts, we detected cytochrome P-4502E1 (which CCl4 converts to its radicals) only in large cholangiocytes. CCl4 induces selective apoptosis of large ducts associated with loss of large cholangiocyte proliferation and secretion.

Quantification of Protozoa and Viruses from Small Water Volumes

PubMed Central

Bonilla, J. Alfredo; Bonilla, Tonya D.; Abdelzaher, Amir M.; Scott, Troy M.; Lukasik, Jerzy; Solo-Gabriele, Helena M.; Palmer, Carol J.

2015-01-01

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The goals of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation—IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels. PMID:26114244

Quantification of Protozoa and Viruses from Small Water Volumes.

PubMed

Bonilla, J Alfredo; Bonilla, Tonya D; Abdelzaher, Amir M; Scott, Troy M; Lukasik, Jerzy; Solo-Gabriele, Helena M; Palmer, Carol J

2015-06-24

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The aims of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation-IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels.

Extraction of advanced geospatial intelligence (AGI) from commercial synthetic aperture radar imagery

NASA Astrophysics Data System (ADS)

Kanberoglu, Berkay; Frakes, David

2017-04-01

The extraction of objects from advanced geospatial intelligence (AGI) products based on synthetic aperture radar (SAR) imagery is complicated by a number of factors. For example, accurate detection of temporal changes represented in two-color multiview (2CMV) AGI products can be challenging because of speckle noise susceptibility and false positives that result from small orientation differences between objects imaged at different times. These cases of apparent motion can result in 2CMV detection, but they obviously differ greatly in terms of significance. In investigating the state-of-the-art in SAR image processing, we have found that differentiating between these two general cases is a problem that has not been well addressed. We propose a framework of methods to address these problems. For the detection of the temporal changes while reducing the number of false positives, we propose using adaptive object intensity and area thresholding in conjunction with relaxed brightness optical flow algorithms that track the motion of objects across time in small regions of interest. The proposed framework for distinguishing between actual motion and misregistration can lead to more accurate and meaningful change detection and improve object extraction from a SAR AGI product. Results demonstrate the ability of our techniques to reduce false positives up to 60%.

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

Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D.

PubMed

Okamoto, Yuji; Goksungur, Meryem Tuba; Pehlivan, Davut; Beck, Christine R; Gonzaga-Jauregui, Claudia; Muzny, Donna M; Atik, Mehmed M; Carvalho, Claudia M B; Matur, Zeliha; Bayraktar, Serife; Boone, Philip M; Akyuz, Kaya; Gibbs, Richard A; Battaloglu, Esra; Parman, Yesim; Lupski, James R

2014-05-01

Copy-number variations as a mutational mechanism contribute significantly to human disease. Approximately one-half of the patients with Charcot-Marie-Tooth (CMT) disease have a 1.4 Mb duplication copy-number variation as the cause of their neuropathy. However, non-CMT1A neuropathy patients rarely have causative copy-number variations, and to date, autosomal-recessive disease has not been associated with copy-number variation as a mutational mechanism. We performed Agilent 8 × 60 K array comparative genomic hybridization on DNA from 12 recessive Turkish families with CMT disease. Additional molecular studies were conducted to detect breakpoint junctions and to evaluate gene expression levels in a family in which we detected an intragenic duplication copy-number variation. We detected an ~6.25 kb homozygous intragenic duplication in NDRG1, a gene known to be causative for recessive HMSNL/CMT4D, in three individuals from a Turkish family with CMT neuropathy. Further studies showed that this intragenic copy-number variation resulted in a homozygous duplication of exons 6-8 that caused decreased mRNA expression of NDRG1. Exon-focused high-resolution array comparative genomic hybridization enables the detection of copy-number variation carrier states in recessive genes, particularly small copy-number variations encompassing or disrupting single genes. In families for whom a molecular diagnosis has not been elucidated by conventional clinical assays, an assessment for copy-number variations in known CMT genes might be considered.

Development of a Flow Cytometry-Based Method for Rapid Detection of Escherichia coli and Shigella Spp. Using an Oligonucleotide Probe

PubMed Central

Xue, Yong; Wilkes, Jon G.; Moskal, Ted J.; Williams, Anna J.; Cooper, Willie M.; Nayak, Rajesh; Rafii, Fatemeh; Buzatu, Dan A.

2016-01-01

Standard methods to detect Escherichia coli contamination in food use the polymerase chain reaction (PCR) and agar culture plates. These methods require multiple incubation steps and take a long time to results. An improved rapid flow-cytometry based detection method was developed, using a fluorescence-labeled oligonucleotide probe specifically binding a16S rRNA sequence. The method positively detected 51 E. coli isolates as well as 4 Shigella species. All 27 non-E. coli strains tested gave negative results. Comparison of the new genetic assay with a total plate count (TPC) assay and agar plate counting indicated similar sensitivity, agreement between cytometry cell and colony counts. This method can detect a small number of E.coli cells in the presence of large numbers of other bacteria. This method can be used for rapid, economical, and stable detection of E. coli and Shigella contamination in the food industry and other contexts. PMID:26913737

Development of a Flow Cytometry-Based Method for Rapid Detection of Escherichia coli and Shigella Spp. Using an Oligonucleotide Probe.

PubMed

Xue, Yong; Wilkes, Jon G; Moskal, Ted J; Williams, Anna J; Cooper, Willie M; Nayak, Rajesh; Rafii, Fatemeh; Buzatu, Dan A

2016-01-01

Standard methods to detect Escherichia coli contamination in food use the polymerase chain reaction (PCR) and agar culture plates. These methods require multiple incubation steps and take a long time to results. An improved rapid flow-cytometry based detection method was developed, using a fluorescence-labeled oligonucleotide probe specifically binding a16S rRNA sequence. The method positively detected 51 E. coli isolates as well as 4 Shigella species. All 27 non-E. coli strains tested gave negative results. Comparison of the new genetic assay with a total plate count (TPC) assay and agar plate counting indicated similar sensitivity, agreement between cytometry cell and colony counts. This method can detect a small number of E.coli cells in the presence of large numbers of other bacteria. This method can be used for rapid, economical, and stable detection of E. coli and Shigella contamination in the food industry and other contexts.

Detection of Salmonella by indicator agar media and PCR as affected by alfalfa seed homogenates and native bacteria.

PubMed

Liao, C-H; Shollenberger, L M

2003-01-01

To investigate and prevent the undesirable effect of native bacteria and alfalfa seed homogenates on detection of Salmonella in alfalfa seeds by indicator agar media and polymerase chain reaction (PCR). The relative sensitivity of five indicator agar media, including modified semisolid RV (MSRV), xylose-lysine-Tergitol 4 (XLT4), Hektoen enteric agar (HEA), brilliant green agar (BGA) and bismuth sulphite agar (BSA), for detection of Salmonella in the presence of a large number of native bacteria from alfalfa seeds was examined. The detection limit as measured by the ratio between the numbers of native bacteria and Salmonella was estimated to be 10(6) to 1 for MSRV and 10(3) to 1 for XLT4, HEA, BGA or BSA. Presence of alfalfa seed homogenates markedly reduced the sensitivity of Salmonella detection by PCR. The minimal number of Salmonella detectable by PCR was determined to be 1-10 and 100-1000 CFU in the absence and presence of seed homogenate, respectively. Application of anti-Salmonella immunomagnetic beads permitted detection of 2-5 CFU of heat-injured cells in 25 g of seeds within 24 h by PCR. The MSRV medium is more sensitive than other indicator agars for detecting a small number of motile Salmonella in samples containing a large number of native bacteria. Application of immunomagnetic beads eliminates the PCR-inhibitory activity of seed homogenates and improves the detection of Salmonella in inoculated seeds. The results generated from this study will aid the seed distributors, sprout growers and public health officials to identify and recall the Salmonella-contaminated seed lots to be used for sprout production.

Labeling of stem cells with monocrystalline iron oxide for tracking and localization by magnetic resonance imaging

PubMed Central

Calzi, Sergio Li; Kent, David L.; Chang, Kyung-Hee; Padgett, Kyle R.; Afzal, Aqeela; Chandra, Saurav B.; Caballero, Sergio; English, Denis; Garlington, Wendy; Hiscott, Paul S.; Sheridan, Carl M.; Grant, Maria B.; Forder, John R.

2013-01-01

Precise localization of exogenously delivered stem cells is critical to our understanding of their reparative response. Our current inability to determine the exact location of small numbers of cells may hinder optimal development of these cells for clinical use. We describe a method using magnetic resonance imaging to track and localize small numbers of stem cells following transplantation. Endothelial progenitor cells (EPC) were labeled with monocrystalline iron oxide nanoparticles (MIONs) which neither adversely altered their viability nor their ability to migrate in vitro and allowed successful detection of limited numbers of these cells in muscle. MION-labeled stem cells were also injected into the vitreous cavity of mice undergoing the model of choroidal neovascularization, laser rupture of Bruch’s membrane. Migration of the MION-labeled cells from the injection site towards the laser burns was visualized by MRI. In conclusion, MION labeling of EPC provides a non-invasive means to define the location of small numbers of these cells. Localization of these cells following injection is critical to their optimization for therapy. PMID:19345699

Water-quality data for the Talkeetna River and four streams in National Parks, Cook Inlet basin, Alaska, 1998

USGS Publications Warehouse

Frenzel, Steven A.; Dorava, Joseph M.

1999-01-01

Five streams in the Cook Inlet Basin, Alaska, were sampled in 1998 to provide the National Park Service with baseline information on water quality. Four of these streams drain National Park Service land: Costello and Colorado Creeks in Denali National Park and Preserve, Johnson River in Lake Clark National Park and Preserve, and Kamishak River in Katmai National Park and Preserve. The fifth site was on the Talkeetna River, outside of national park boundaries. Samples of stream water, streambed sediments, and fish tissues were collected for chemical analyses. Biological and geomorphic information was also collected at each site. Nutrient concentrations in stream water were low and commonly were less than analytical detection limits. Analyses of fish tissues for 28 organochlorine compounds at Talkeetna River and Costello Creek produced just one detection. Hexachlorobenzene was detected at a concentration of 5.70 micrograms per kilogram in slimy sculpin from the Talkeetna River. Streambed sediment samples from the Talkeetna River had three organochlorine compounds at detectable levels; hexachlorobenzene was measured at 13 micrograms per kilogram and two other compounds were below the minimum reporting levels. At Colorado Creek, Johnson River, and Kamishak River, where fish samples were not collected, no organochlorine compounds were detected in streambed sediment samples. Several semivolatile organic compounds were detected at Colorado Creek and Costello Creek. Only one compound, dibenzothiophene, detected at Costello Creek at a concentration of 85 micrograms per kilogram was above the minimum reporting limit. No semivolatile organic compounds were detected at the Talkeetna, Kamishak, or Johnson Rivers. Trace elements were detected in both fish tissues and streambed sediments. Macroinvertebrate and fish samples contained few taxa at all sites. Total numbers of macroinvertebrate taxa ranged from 19 at the Johnson River to 38 at the Talkeetna River. Diptera were the most abundant and diverse order of macroinvertebrates at all sites. Total numbers of diptera taxa ranged from 8 at the Kamishak River to 19 at the Talkeetna River. Fish communities were represented by a maximum of nine taxa at the Talkeetna River and were absent at Colorado Creek. The Johnson River sampling site produced small numbers of juvenile Dolly Varden, and Costello Creek produced small numbers of both juvenile Dolly Varden and slimy sculpin.

A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts

PubMed Central

Onken, Arno; Dragoi, Valentin; Obermayer, Klaus

2012-01-01

Evaluating the importance of higher-order correlations of neural spike counts has been notoriously hard. A large number of samples are typically required in order to estimate higher-order correlations and resulting information theoretic quantities. In typical electrophysiology data sets with many experimental conditions, however, the number of samples in each condition is rather small. Here we describe a method that allows to quantify evidence for higher-order correlations in exactly these cases. We construct a family of reference distributions: maximum entropy distributions, which are constrained only by marginals and by linear correlations as quantified by the Pearson correlation coefficient. We devise a Monte Carlo goodness-of-fit test, which tests - for a given divergence measure of interest - whether the experimental data lead to the rejection of the null hypothesis that it was generated by one of the reference distributions. Applying our test to artificial data shows that the effects of higher-order correlations on these divergence measures can be detected even when the number of samples is small. Subsequently, we apply our method to spike count data which were recorded with multielectrode arrays from the primary visual cortex of anesthetized cat during an adaptation experiment. Using mutual information as a divergence measure we find that there are spike count bin sizes at which the maximum entropy hypothesis can be rejected for a substantial number of neuronal pairs. These results demonstrate that higher-order correlations can matter when estimating information theoretic quantities in V1. They also show that our test is able to detect their presence in typical in-vivo data sets, where the number of samples is too small to estimate higher-order correlations directly. PMID:22685392

Ommatidia of blow fly, house fly, and flesh fly: implication of their vision efficiency.

PubMed

Sukontason, Kabkaew L; Chaiwong, Tarinee; Piangjai, Somsak; Upakut, Sorawit; Moophayak, Kittikhun; Sukontason, Kom

2008-06-01

This work aims to elucidate the number of ommatidia or facets (the outwardly visible units of each ommatidium) for compound eyes in blow flies [Chrysomya megacephala (F.), Chrysomya rufifacies (Macquart), Chrysomya nigripes (Aubertin), Lucilia cuprina (Wiedemann)], house flies (Musca domestica L.), and flesh flies (Liosarcophaga dux Thomson) by manual counts of the corneal spreads. The head of the fly in each species was soaked in 20% potassium hydroxide solution at room temperature for 7 days, and the clear compound eye was dissected into six small parts, each of which was placed onto a slide and flattened using a coverslip. Images of each part were obtained using a microscope connected to a computer. The printed images of each part were magnified, and the total number of ommatidia per eye was manually counted. For males, the mean number of ommatidia was statistically different among all flies examined: L. dux (6,032) > C. rufifacies (5,356) > C. nigripes (4,798) > C. megacephala (4,376) > L. cuprina (3,665) > M. domestica (3,484). Likewise, the mean number of facets in females was statistically different: L. dux (6,086) > C. megacephala (5,641) > C. rufifacies (5,208) > C. nigripes (4,774) > L. cuprina (3,608) > M. domestica (3433). Scanning electron microscopy analysis of adult flies revealed the sexual dimorphism in the compound eye. Male C. megacephala had large ommatidia in the upper two thirds part and small ommatidia in the lower one third part, whereas only small ommatidia were detected in females. Dense postulate appearance was detected in the external surface of the corneal lens of the ommatidia of C. megacephala, C. rufifacies, and C. nigripes, while a mix of dense postulate appearance and variable groove array length was detected in L. cuprina and M. domestica. The probable functions of ommatidia are discussed with reference to other literature.

Fractal dimension of microbead assemblies used for protein detection.

PubMed

Hecht, Ariel; Commiskey, Patrick; Lazaridis, Filippos; Argyrakis, Panos; Kopelman, Raoul

2014-11-10

We use fractal analysis to calculate the protein concentration in a rotating magnetic assembly of microbeads of size 1 μm, which has optimized parameters of sedimentation, binding sites and magnetic volume. We utilize the original Forrest-Witten method, but due to the relatively small number of bead particles, which is of the order of 500, we use a large number of origins and also a large number of algorithm iterations. We find a value of the fractal dimension in the range 1.70-1.90, as a function of the thrombin concentration, which plays the role of binding the microbeads together. This is in good agreement with previous results from magnetorotation studies. The calculation of the fractal dimension using multiple points of reference can be used for any assembly with a relatively small number of particles. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of hyperspectral fluorescence images for poultry skin tumor inspection

NASA Astrophysics Data System (ADS)

Kong, Seong G.; Chen, Yud-Ren; Kim, Intaek; Kim, Moon S.

2004-02-01

We present a hyperspectral fluorescence imaging system with a fuzzy inference scheme for detecting skin tumors on poultry carcasses. Hyperspectral images reveal spatial and spectral information useful for finding pathological lesions or contaminants on agricultural products. Skin tumors are not obvious because the visual signature appears as a shape distortion rather than a discoloration. Fluorescence imaging allows the visualization of poultry skin tumors more easily than reflectance. The hyperspectral image samples obtained for this poultry tumor inspection contain 65 spectral bands of fluorescence in the visible region of the spectrum at wavelengths ranging from 425 to 711 nm. The large amount of hyperspectral image data is compressed by use of a discrete wavelet transform in the spatial domain. Principal-component analysis provides an effective compressed representation of the spectral signal of each pixel in the spectral domain. A small number of significant features are extracted from two major spectral peaks of relative fluorescence intensity that have been identified as meaningful spectral bands for detecting tumors. A fuzzy inference scheme that uses a small number of fuzzy rules and Gaussian membership functions successfully detects skin tumors on poultry carcasses. Spatial-filtering techniques are used to significantly reduce false positives.

Microfabricated silicon biosensors for microphysiometry

NASA Technical Reports Server (NTRS)

Bousse, L. J.; Libby, J. M.; Parce, J. W.

1993-01-01

Microphysiometers are biosensor devices that measure the metabolic rate of living cells by detecting the rate of extracellular acidification caused by a small number of cells. The cells are entrapped in a microvolume chamber, whose bottom surface is a silicon sensor chip. In a further miniaturization step, we have recently fabricated multichannel flow-through chips that will allow greater throughput and multiplicity. Microphysiometer technology can be applied to the detection of microorganisms. We describe the sensitive detection of bacteria and yeast. Further applications of microphysiometry to the characterization of microorganisms can be anticipated.

Detection and Estimation of an Optical Image by Photon-Counting Techniques. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Wang, Lily Lee

1973-01-01

Statistical description of a photoelectric detector is given. The photosensitive surface of the detector is divided into many small areas, and the moment generating function of the photo-counting statistic is derived for large time-bandwidth product. The detection of a specified optical image in the presence of the background light by using the hypothesis test is discussed. The ideal detector based on the likelihood ratio from a set of numbers of photoelectrons ejected from many small areas of the photosensitive surface is studied and compared with the threshold detector and a simple detector which is based on the likelihood ratio by counting the total number of photoelectrons from a finite area of the surface. The intensity of the image is assumed to be Gaussian distributed spatially against the uniformly distributed background light. The numerical approximation by the method of steepest descent is used, and the calculations of the reliabilities for the detectors are carried out by a digital computer.

Automatic extraction and processing of small RNAs on a multi-well/multi-channel (M&M) chip.

PubMed

Zhong, Runtao; Flack, Kenneth; Zhong, Wenwan

2012-12-07

The study of the regulatory roles in small RNAs can be accelerated by techniques that permit simple, low-cost, and rapid extraction of small RNAs from a small number of cells. In order to ensure highly specific and sensitive detection, the extracted RNAs should be free of the background nucleic acids and present stably in a small volume. To meet these criteria, we designed a multi-well/multi-channel (M&M) chip to carry out automatic and selective isolation of small RNAs via solid-phase extraction (SPE), followed by reverse-transcription (RT) to convert them to the more stable cDNAs in a final volume of 2 μL. Droplets containing buffers for RNA binding, washing, and elution were trapped in microwells, which were connected by one channel, and suspended in mineral oil. The silica magnetic particles (SMPs) for SPE were moved along the channel from well to well, i.e. in between droplets, by a fixed magnet and a translation stage, allowing the nucleic acid fragments to bind to the SMPs, be washed, and then be eluted for RT reaction within 15 minutes. RNAs shorter than 63 nt were selectively enriched from cell lysates, with recovery comparable to that of a commercial kit. Physical separation of the droplets on our M&M chip allowed the usage of multiple channels for parallel processing of multiple samples. It also permitted smooth integration with on-chip RT-PCR, which simultaneously detected the target microRNA, mir-191, expressed in fewer than 10 cancer cells. Our results have demonstrated that the M&M chip device is a valuable and cost-saving platform for studying small RNA expression patterns in a limited number of cells with reasonable sample throughput.

Predation, Competition, and Abiotic Disturbance: Population Dynamics of Small Mammals

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

Yunger, John A.; /Northern Illinois U. /Northern Illinois U.

Predation and food availability have been implicated in annual non-cyclic fluctuations of vertebrate prey at mid-latitudes. The timing and magnitude of these factors are unclear due to a lack of large-scale field experiments, little attention to interactions, and a failure to closely link vertebrate predators with their prey. From October 1992 to January 1996, small mammal populations were censused on eight 0.6 ha plots at monthly intervals in a 32-ha prairie restoration at Fermi National Accelerator Laboratory, Illinois. Terrestrial vertebrate predators were excluded after July 1993 from four of the eight plots and canid diets monitored. Both terrestrial and avianmore » vertebrate predators were excluded in March 1994. During 1993 small mammal densities (i.e., Microtus Pennsylvanicus, Peromyscus leucopus, and P. maniculatus) were relatively high. Following peak densities in late summer, Microtus numbers wer 2-3x greater on exclusion plots relative to controls due to preferential selection of Microtus by canids, as reflected in dits. Following an ice-storm and crash in small mammal numbers (particularly Microtus), vertebrate predator exclusion had no detectable effect on P. leucopus numbers, probably due to an abundance of alternative prey (i.e., Sylvilagus floridanus). Meadow vole numbers began to increase in Fall 1995, and a numerical effect of predator exclusion, similar to that in 1993, was observed. Predator exclusion had no detectable effect on the movements and spatial patterns of Microtus during 1993. There was a significant decrease in home range and a significant increase in home range overlap for P. leucopus on the predator exclusion plots. The change in spatial behavior may be due to interspecific competition with Microtus resulting from increased densities on exclusion plots. Thus, predators had an indirect effect on P. leucopus spatial patterns mediated through M. Pennsylvanicus. The role of food limitation was studied using natural and manipulative experiments. Unusually high acorn production in Fall 1994 resulted in increased P. leucopus numbers at one Fermilab site due to immigration since survivorship or reproduction were unaffected. A food supplementation experiment during October 1994-March 1995 induced a strong increase in P. leucopus numbers, due again to immigration, although reproduction also was advanced by two months.« less

Predation, Competition, and Abiotic Disturbance: Population Dynamics of Small Mammals

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

Yunger, John A.

Predation and food availability have been implicated in annual non-cyclic fluctuations of vertebrate prey at mid-latitudes. The timing and magnitude of these factors are unclear due to a lack of large-scale field experiments, little attention to interactions, and a failure to closely link vertebrate predators with their prey. From October 1992 to January 1996, small mammal populations were censused on eight 0.6 ha plots at monthly intervals in a 32-ha prairie restoration at Fermi National Accelerator Laboratory, Illinois. Terrestrial vertebrate predators were excluded after July 1993 from four of the eight plots and canid diets monitored. Both terrestrial and avianmore » vertebrate predators were excluded in March 1994. During 1993 small mammal densities (i.e., Microtus pennsylvanicus, Peromyscus leucopus, and P. maniculatus) were relatively high. Following peak densities in late summer, Microtus numbers were 2-3x greater on exclusion plots relative to controls due to preferential selection of Microtus by canids, as reflected in diets. Following an ice-storm and crash in small mammal numbers (particularly Microtus), vertebrate predator exclusion had no detectable effect on P. leucopus numbers, probably due to an abundance of alternative prey (i.e., Sylvilagus floridanus). Meadow vole numbers began to increase in Fall 1995, and a numerical effect of predator exclusion, similar to that in 1993, was observed. Predator exclusion had no detectable effect on the movements and spatial patterns of Microtus during 1993. There was a significant decrease in home range and a significant increase in home range overlap for £.. leucopus on the predator exclusion plots. The change in spatial behavior may be due to interspecific competition with Microtus resulting from increased densities on exclusion plots. Thus, predators had an indirect effect on .f.. leucopus spatial patterns mediated through M. pennsylvanicus. The role of food limitation was studied using natural and manipulative experiments. Unusually high acorn production in Fall 1994 resulted in increased f. leucopus numbers at one Fermilab site due to immigration since survivorship or reproduction were unaffected. A food supplementation experiment during October 1994-March 1995 induced a strong increase in f. leucopus numbers, due again to immigration, although reproduction also was advanced by two months.« less

Detection of quantitative trait loci causing abnormal spermatogenesis and reduced testis weight in the small testis (Smt) mutant mouse.

PubMed

Bolor, Hasbaira; Wakasugi, Noboru; Zhao, Wei Dong; Ishikawa, Akira

2006-04-01

The small testis (Smt) mutant mouse is characterized by a small testis of one third to one half the size of a normal testis, and its spermatogenesis is mostly arrested at early stages of meiosis, although a small number of spermatocytes at the late prophase of meiosis and a few spermatids can sometimes be seen. We performed quantitative trait locus (QTL) analysis of these spermatogenic traits and testis weight using 221 F2 males obtained from a cross between Smt and MOM (Mus musculus molossinus) mice. At the genome-wide 5% level, we detected two QTLs affecting meiosis on chromosomes 4 and 13, and two QTLs for paired testis weight as a percentage of body weight on chromosomes 4 and X. In addition, we found several QTLs for degenerated germ cells and multinuclear giant cells on chromosomes 4, 7 and 13. Interestingly, for cell degeneration, the QTL on chromosome 13 interacted epistatically with the QTL on chromosome 4. These results reveal polygenic participation in the abnormal spermatogenesis and small testis size in the Smt mutant.

Detection of fatigue cracks by nondestructive testing methods

NASA Technical Reports Server (NTRS)

Anderson, R. T.; Delacy, T. J.; Stewart, R. C.

1973-01-01

The effectiveness was assessed of various NDT methods to detect small tight cracks by randomly introducing fatigue cracks into aluminum sheets. The study included optimizing NDT methods calibrating NDT equipment with fatigue cracked standards, and evaluating a number of cracked specimens by the optimized NDT methods. The evaluations were conducted by highly trained personnel, provided with detailed procedures, in order to minimize the effects of human variability. These personnel performed the NDT on the test specimens without knowledge of the flaw locations and reported on the flaws detected. The performance of these tests was measured by comparing the flaws detected against the flaws present. The principal NDT methods utilized were radiographic, ultrasonic, penetrant, and eddy current. Holographic interferometry, acoustic emission monitoring, and replication methods were also applied on a reduced number of specimens. Generally, the best performance was shown by eddy current, ultrasonic, penetrant and holographic tests. Etching provided no measurable improvement, while proof loading improved flaw detectability. Data are shown that quantify the performances of the NDT methods applied.

Small UAS Detect and Avoid Requirements Necessary for Limited Beyond Visual Line of Sight (BVLOS) Operations

DOT National Transportation Integrated Search

2017-05-19

Potential sUAS BVLOS operational scenarios/use cases and DAA approaches were collected through a number of industry wide data calls. Every 333 Exemption holder was solicited for this same information. Summary information from more than 5,000 exemptio...

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.

PubMed

Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun

2018-02-28

Although single-cell RNA sequencing can reliably detect large-scale transcriptional programs, it is unclear whether it accurately captures the behavior of individual genes, especially those that express only in rare cells. Here, we use single-molecule RNA fluorescence in situ hybridization as a gold standard to assess trade-offs in single-cell RNA-sequencing data for detecting rare cell expression variability. We quantified the gene expression distribution for 26 genes that range from ubiquitous to rarely expressed and found that the correspondence between estimates across platforms improved with both transcriptome coverage and increased number of cells analyzed. Further, by characterizing the trade-off between transcriptome coverage and number of cells analyzed, we show that when the number of genes required to answer a given biological question is small, then greater transcriptome coverage is more important than analyzing large numbers of cells. More generally, our report provides guidelines for selecting quality thresholds for single-cell RNA-sequencing experiments aimed at rare cell analyses. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Multi-site evaluation of a computer aided detection (CAD) algorithm for small acute intra-cranial hemorrhage and development of a stand-alone CAD system ready for deployment in a clinical environment

NASA Astrophysics Data System (ADS)

Deshpande, Ruchi R.; Fernandez, James; Lee, Joon K.; Chan, Tao; Liu, Brent J.; Huang, H. K.

2010-03-01

Timely detection of Acute Intra-cranial Hemorrhage (AIH) in an emergency environment is essential for the triage of patients suffering from Traumatic Brain Injury. Moreover, the small size of lesions and lack of experience on the reader's part could lead to difficulties in the detection of AIH. A CT based CAD algorithm for the detection of AIH has been developed in order to improve upon the current standard of identification and treatment of AIH. A retrospective analysis of the algorithm has already been carried out with 135 AIH CT studies with 135 matched normal head CT studies from the Los Angeles County General Hospital/ University of Southern California Hospital System (LAC/USC). In the next step, AIH studies have been collected from Walter Reed Army Medical Center, and are currently being processed using the AIH CAD system as part of implementing a multi-site assessment and evaluation of the performance of the algorithm. The sensitivity and specificity numbers from the Walter Reed study will be compared with the numbers from the LAC/USC study to determine if there are differences in the presentation and detection due to the difference in the nature of trauma between the two sites. Simultaneously, a stand-alone system with a user friendly GUI has been developed to facilitate implementation in a clinical setting.

NRL SSD Research Achievements: 19601970. Volume 1

DTIC Science & Technology

2015-10-30

radio sources between declinations +10 and -20,” Mills, B.Y., Slee O.B., Hill, E.R. 1958, Australian J. Phys., 11 , 360-387 12. “SPEAR: Small Payload... 11 . SPONSOR / MONITOR’S REPORT NUMBER(S) 12. DISTRIBUTION / AVAILABILITY STATEMENT 13. SUPPLEMENTARY NOTES 14. ABSTRACT 15. SUBJECT TERMS 16...from a tour-de-force lunar occultation rocket experiment; and the First Detection of X-Ray Pulsations from the Crab Pulsar that matched the radio

Continuous, Real-Time Monitoring of Cocaine in Undiluted Blood Serum via a Microfluidic, Electrochemical Aptamer-Based Sensor

PubMed Central

Swensen, James S.; Xiao, Yi; Ferguson, Brian S.; Lubin, Arica A.; Lai, Rebecca Y.; Heeger, Alan J.; Plaxco, Kevin W.; Soh, H. Tom.

2009-01-01

The development of a biosensor system capable of continuous, real-time measurement of small-molecule analytes directly in complex, unprocessed aqueous samples has been a significant challenge, and successful implementation has been achieved for only a limited number of targets. Towards a general solution to this problem, we report here the Microfluidic Electrochemical Aptamer-based Sensor (MECAS) chip wherein we integrate target-specific DNA aptamers that fold, and thus generate an electrochemical signal, in response to the analyte with a microfluidic detection system. As a model, we demonstrate the continuous, real-time (~1 minute time resolution) detection of the small molecule drug cocaine at near physiological, low micromolar concentrations directly in undiluted, otherwise unmodified blood serum. We believe our approach of integrating folding-based electrochemical sensors with miniaturized detection systems may lay the ground work for the real-time, point-of-care detection of a wide variety of molecular targets. PMID:19271708

Small Proteins Can No Longer Be Ignored

PubMed Central

Storz, Gisela; Wolf, Yuri I.; Ramamurthi, Kumaran S.

2014-01-01

Small proteins, here defined as proteins of 50 amino acids or less in the absence of processing, have traditionally been overlooked due to challenges in their annotation and biochemical detection. In the past several years however, increasing numbers of small proteins have been identified either through the realization that mutations in “intergenic” regions actually are within unannotated small protein genes, or through the discovery that some small, regulatory RNAs (sRNAs) encode small proteins. These insights together with comparative sequence analysis indicate that tens if not hundreds of small proteins are synthesized in a given organism. This review will summarize what has been learned about the functions of several of these bacterial small proteins, most of which act at the membrane, illustrating the astonishing range of processes in which the small proteins act and pointing to several general conclusions. Important questions for future studies of these overlooked proteins also will be discussed. PMID:24606146

Crank angle detecting system for engines

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

Yuzawa, H.; Nishiyama, M.; Nakamura, K.

1988-05-31

An ignition system for a multi-cylinder internal combustion engine is described comprising: (a) engine cylinders in which spark plugs are installed respectively, (b) indicating means disposed so as to synchronize with an engine crankshaft and formed with a large number of slits and a small number of slits, the large number of slits being provided for indicating crankshaft angular positions and the small number of slits being provided for indicating predetermined piston strokes and wherein the small number of slits have mutually different widths from each other to distinguish between piston strokes of at least the groups of cylinders; (c)more » sensing means for sensing crankshaft angular positions in cooperation with the large number of slits of the indicating means and outputting a crank angle signal representing the crankshaft angular position and for sensing the predetermined piston strokes in cooperation with the small number of slits and outputting different width piston stroke signals corresponding to the different width slits; (d) discriminating means for identifying each cylinder group and outputting cylinder group identification signals on the basis of the different width stroke signals derived from the sensing means; (e) ignition timing determining means for generating an ignition timing signal on the basis of the crank angle signal; (f) ignition coil controlling means for generating ignition coil current signals corresponding to the cylinder group identification signals; and (g) ignition timing controlling means for generating cylinder group ignition signals in response to the ignition coil current signals and ignition timing signal so that the spark plugs of each cylinder group are ignited at a proper time.« less

Prevalence and Properties of Planets from Kepler and K2

NASA Astrophysics Data System (ADS)

Petigura, Erik; Marcy, Geoffrey W.; Howard, Andrew; Crossfield, Ian; Beichman, Charles; Sinukoff, Evan

2015-12-01

Discoveries from the prime Kepler mission demonstrated that small planets (< 3 Earth-radii) are common outcomes of planet formation around G, K, and M stars. While Kepler detected many such planets, all but a handful orbit faint, distant stars, which are not amenable to precise follow up measurements. NASA's K2 mission has the potential to increase the number of known small, transiting planets around bright stars by an order of magnitude. I will present the latest results from my team's efforts to detect, confirm, and characterize planets using the K2 mission. I will highlight some of the progress and remaining challenges involved with generating denoised K2 photometry and with detecting planets in the presence of severe instrument systematics. Among our recent discoveries are the K2-3 and K2-21 planetary systems: M dwarfs hosting multiple transiting Earth-size planets with low equilibrium temperatures. These systems offer a convenient laboratory for studying the bulk composition and atmospheric properties of small planets receiving low levels of stellar irradiation, where processes such as mass loss by photo-evaporation could play a weaker role.

Functionalized xenon as a biosensor

PubMed Central

Spence, Megan M.; Rubin, Seth M.; Dimitrov, Ivan E.; Ruiz, E. Janette; Wemmer, David E.; Pines, Alexander; Yao, Shao Qin; Tian, Feng; Schultz, Peter G.

2001-01-01

The detection of biological molecules and their interactions is a significant component of modern biomedical research. In current biosensor technologies, simultaneous detection is limited to a small number of analytes by the spectral overlap of their signals. We have developed an NMR-based xenon biosensor that capitalizes on the enhanced signal-to-noise, spectral simplicity, and chemical-shift sensitivity of laser-polarized xenon to detect specific biomolecules at the level of tens of nanomoles. We present results using xenon “functionalized” by a biotin-modified supramolecular cage to detect biotin–avidin binding. This biosensor methodology can be extended to a multiplexing assay for multiple analytes. PMID:11535830

Detection of Gene Rearrangements in Circulating Tumor Cells: Examples of ALK-, ROS1-, RET-Rearrangements in Non-Small-Cell Lung Cancer and ERG-Rearrangements in Prostate Cancer.

PubMed

Catelain, Cyril; Pailler, Emma; Oulhen, Marianne; Faugeroux, Vincent; Pommier, Anne-Laure; Farace, Françoise

2017-01-01

Circulating tumor cells (CTCs) hold promise as biomarkers to aid in patient treatment stratification and disease monitoring. Because the number of cells is a critical parameter for exploiting CTCs for predictive biomarker's detection, we developed a FISH (fluorescent in situ hybridization) method for CTCs enriched on filters (filter-adapted FISH [FA-FISH]) that was optimized for high cell recovery. To increase the feasibility and reliability of the analyses, we combined fluorescent staining and FA-FISH and developed a semi-automated microscopy method for optimal FISH signal identification in filtration-enriched CTCs . Here we present these methods and their use for the detection and characterization of ALK-, ROS1-, RET-rearrangement in CTCs from non-small-cell lung cancer and ERG-rearrangements in CTCs from prostate cancer patients.

Detection of fragments from internal insects in wheat samples using a laboratory entoleter

USDA-ARS?s Scientific Manuscript database

A simple, rapid method was developed for estimating the number of insect fragments in flour caused by hidden, internal-feeding insects in whole grains during storage. The method uses a small mechanical rotary device (entoleter), which accelerates whole wheat kernels to high speeds and projects them...

Detection of vapor nanobubbles by small angle neutron scattering (SANS)

NASA Astrophysics Data System (ADS)

Popov, Emilian; He, Lilin; Dominguez-Ontiveros, Elvis; Melnichenko, Yuri

2018-04-01

Experiments using boiling water on untreated (roughness 100-300 nm) metal surfaces using small-angle neutron scattering (SANS) show the appearance of structures that are 50-70 nm in size when boiling is present. The scattering signal disappears when the boiling ceases, and no change in the signal is detected at any surface temperature condition below saturation. This confirms that the signal is caused by vapor nanobubbles. Two boiling regimes are evaluated herein that differ by the degree of subcooling (3-10 °C). A polydisperse spherical model with a log-normal distribution fits the SANS data well. The size distribution indicates that a large number of nanobubbles exist on the surface during boiling, and some of them grow into large bubbles.

An empirical study of flight control software reliability

NASA Technical Reports Server (NTRS)

Dunham, J. R.; Pierce, J. L.

1986-01-01

The results of a laboratory experiment in flight control software reliability are reported. The experiment tests a small sample of implementations of a pitch axis control law for a PA28 aircraft with over 14 million pitch commands with varying levels of additive input and feedback noise. The testing which uses the method of n-version programming for error detection surfaced four software faults in one implementation of the control law. The small number of detected faults precluded the conduct of the error burst analyses. The pitch axis problem provides data for use in constructing a model in the prediction of the reliability of software in systems with feedback. The study is undertaken to find means to perform reliability evaluations of flight control software.

Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere.

PubMed

Schouten, Henk J; Vande Geest, Henri; Papadimitriou, Sofia; Bemer, Marian; Schaart, Jan G; Smulders, Marinus J M; Perez, Gabino Sanchez; Schijlen, Elio

2017-03-01

Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA. To prevent mutations due to in vitro propagation, we applied floral dip transformation of Arabidopsis thaliana. We re-sequenced the genomes of five primary transformants, and compared these to genomic sequences derived from a pool of four wild-type plants. By genome-wide comparisons, we identified ten small mutations in the genomes of the five transgenic plants, not correlated to the positions or number of T-DNA inserts. This mutation frequency is within the range of spontaneous mutations occurring during seed propagation in A. thaliana, as determined earlier. In addition, we detected small as well as large deletions specifically at the T-DNA insert sites. Furthermore, we detected partial T-DNA inserts, one of these a tiny 50-bp fragment originating from a central part of the T-DNA construct used, inserted into the plant genome without flanking other T-DNA. Because of its small size, we named this fragment a T-DNA splinter. As far as we know this is the first report of such a small T-DNA fragment insert in absence of any T-DNA border sequence. Finally, we found evidence for translocations from other chromosomes, flanking T-DNA inserts. In this study, we showed that next-generation sequencing (NGS) is a highly sensitive approach to detect T-DNA inserts in transgenic plants.

Super-Resolution Community Detection for Layer-Aggregated Multilayer Networks

PubMed Central

Taylor, Dane; Caceres, Rajmonda S.; Mucha, Peter J.

2017-01-01

Applied network science often involves preprocessing network data before applying a network-analysis method, and there is typically a theoretical disconnect between these steps. For example, it is common to aggregate time-varying network data into windows prior to analysis, and the trade-offs of this preprocessing are not well understood. Focusing on the problem of detecting small communities in multilayer networks, we study the effects of layer aggregation by developing random-matrix theory for modularity matrices associated with layer-aggregated networks with N nodes and L layers, which are drawn from an ensemble of Erdős–Rényi networks with communities planted in subsets of layers. We study phase transitions in which eigenvectors localize onto communities (allowing their detection) and which occur for a given community provided its size surpasses a detectability limit K*. When layers are aggregated via a summation, we obtain K∗∝O(NL/T), where T is the number of layers across which the community persists. Interestingly, if T is allowed to vary with L, then summation-based layer aggregation enhances small-community detection even if the community persists across a vanishing fraction of layers, provided that T/L decays more slowly than 𝒪(L−1/2). Moreover, we find that thresholding the summation can, in some cases, cause K* to decay exponentially, decreasing by orders of magnitude in a phenomenon we call super-resolution community detection. In other words, layer aggregation with thresholding is a nonlinear data filter enabling detection of communities that are otherwise too small to detect. Importantly, different thresholds generally enhance the detectability of communities having different properties, illustrating that community detection can be obscured if one analyzes network data using a single threshold. PMID:29445565

Super-Resolution Community Detection for Layer-Aggregated Multilayer Networks.

PubMed

Taylor, Dane; Caceres, Rajmonda S; Mucha, Peter J

2017-01-01

Applied network science often involves preprocessing network data before applying a network-analysis method, and there is typically a theoretical disconnect between these steps. For example, it is common to aggregate time-varying network data into windows prior to analysis, and the trade-offs of this preprocessing are not well understood. Focusing on the problem of detecting small communities in multilayer networks, we study the effects of layer aggregation by developing random-matrix theory for modularity matrices associated with layer-aggregated networks with N nodes and L layers, which are drawn from an ensemble of Erdős-Rényi networks with communities planted in subsets of layers. We study phase transitions in which eigenvectors localize onto communities (allowing their detection) and which occur for a given community provided its size surpasses a detectability limit K * . When layers are aggregated via a summation, we obtain [Formula: see text], where T is the number of layers across which the community persists. Interestingly, if T is allowed to vary with L , then summation-based layer aggregation enhances small-community detection even if the community persists across a vanishing fraction of layers, provided that T/L decays more slowly than ( L -1/2 ). Moreover, we find that thresholding the summation can, in some cases, cause K * to decay exponentially, decreasing by orders of magnitude in a phenomenon we call super-resolution community detection. In other words, layer aggregation with thresholding is a nonlinear data filter enabling detection of communities that are otherwise too small to detect. Importantly, different thresholds generally enhance the detectability of communities having different properties, illustrating that community detection can be obscured if one analyzes network data using a single threshold.

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.

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

PubMed Central

Yeri, Ashish; Courtright, Amanda; Reiman, Rebecca; Carlson, Elizabeth; Beecroft, Taylor; Janss, Alex; Siniard, Ashley; Richholt, Ryan; Balak, Chris; Rozowsky, Joel; Kitchen, Robert; Hutchins, Elizabeth; Winarta, Joseph; McCoy, Roger; Anastasi, Matthew; Kim, Seungchan; Huentelman, Matthew; Van Keuren-Jensen, Kendall

2017-01-01

Interest in circulating RNAs for monitoring and diagnosing human health has grown significantly. There are few datasets describing baseline expression levels for total cell-free circulating RNA from healthy control subjects. In this study, total extracellular RNA (exRNA) was isolated and sequenced from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 male college athletes ages 18–25 years. Many participants provided more than one sample, allowing us to investigate variability in an individual’s exRNA expression levels over time. Here we provide a systematic analysis of small exRNAs present in each biofluid, as well as an analysis of exogenous RNAs. The small RNA profile of each biofluid is distinct. We find that a large number of RNA fragments in plasma (63%) and urine (54%) have sequences that are assigned to YRNA and tRNA fragments respectively. Surprisingly, while many miRNAs can be detected, there are few miRNAs that are consistently detected in all samples from a single biofluid, and profiles of miRNA are different for each biofluid. Not unexpectedly, saliva samples have high levels of exogenous sequence that can be traced to bacteria. These data significantly contribute to the current number of sequenced exRNA samples from normal healthy individuals. PMID:28303895

Small volume low mechanical stress cytometry using computer-controlled Braille display microfluidics.

PubMed

Tung, Yi-Chung; Torisawa, Yu-suke; Futai, Nobuyuki; Takayama, Shuichi

2007-11-01

This paper describes a micro flow cytometer system designed for efficient and non-damaging analysis of samples with small numbers of precious cells. The system utilizes actuation of Braille-display pins for micro-scale fluid manipulation and a fluorescence microscope with a CCD camera for optical detection. The microfluidic chip is fully disposable and is composed of a polydimethylsiloxane (PDMS) slab with microchannel features sealed against a thin deformable PDMS membrane. The channels are designed with diffusers to alleviate pulsatile flow behaviors inherent in pin actuator-based peristaltic pumping schemes to maximize hydrodynamic focusing of samples with minimal disturbances in the laminar streams within the channel. A funnel connected to the microfluidic channel is designed for efficient loading of samples with small number of cells and is also positioned on the chip to prevent physical damages of the samples by the squeezing actions of Braille pins during actuation. The sample loading scheme was characterized by both computational fluidic dynamics (CFD) simulation and experimental observation. A fluorescein solution was first used for flow field investigation, followed by use of fluorescence beads with known relative intensities for optical detection performance calibration. Murine myoblast cells (C2C12) were exploited to investigate cell viability for the sample loading scheme of the device. Furthermore, human promyelocytic leukemia (HL60) cells stained by hypotonic DNA staining buffer were also tested in the system for cell cycle analysis. The ability to efficiently analyze cellular samples where the number of cells is small was demonstrated by analyzing cells from a single embryoid body derived from mouse embryonic stem cells. Consequently, the designed microfluidic device reported in this paper is promising for easy-to-use, small sample size flow cytometric analysis, and has potential to be further integrated with other Braille display-based microfluidic devices to facilitate a multi-functional lab-on-a-chip for mammalian cell manipulations.

Fragment size distribution in viscous bag breakup of a drop

NASA Astrophysics Data System (ADS)

Kulkarni, Varun; Bulusu, Kartik V.; Plesniak, Michael W.; Sojka, Paul E.

2015-11-01

In this study we examine the drop size distribution resulting from the fragmentation of a single drop in the presence of a continuous air jet. Specifically, we study the effect of Weber number, We, and Ohnesorge number, Oh on the disintegration process. The regime of breakup considered is observed between 12 <= We <= 16 for Oh <= 0.1. Experiments are conducted using phase Doppler anemometry. Both the number and volume fragment size probability distributions are plotted. The volume probability distribution revealed a bi-modal behavior with two distinct peaks: one corresponding to the rim fragments and the other to the bag fragments. This behavior was suppressed in the number probability distribution. Additionally, we employ an in-house particle detection code to isolate the rim fragment size distribution from the total probability distributions. Our experiments showed that the bag fragments are smaller in diameter and larger in number, while the rim fragments are larger in diameter and smaller in number. Furthermore, with increasing We for a given Ohwe observe a large number of small-diameter drops and small number of large-diameter drops. On the other hand, with increasing Oh for a fixed We the opposite is seen.

Seeking Beta: Experimental Considerations and Theoretical Implications Regarding the Detection of Curvature in Dose-Response Relationships for Chromosome Aberrations.

PubMed

Shuryak, Igor; Loucas, Bradford D; Cornforth, Michael N

2017-01-01

The concept of curvature in dose-response relationships figures prominently in radiation biology, encompassing a wide range of interests including radiation protection, radiotherapy and fundamental models of radiation action. In this context, the ability to detect even small amounts of curvature becomes important. Standard (ST) statistical approaches used for this purpose typically involve least-squares regression, followed by a test on sums of squares. Because we have found that these methods are not particularly robust, we investigated an alternative information theoretic (IT) approach, which involves Poisson regression followed by information-theoretic model selection. Our first objective was to compare the performances of the ST and IT methods by using them to analyze mFISH data on gamma-ray-induced simple interchanges in human lymphocytes, and on Monte Carlo simulated data. Real and simulated data sets that contained small-to-moderate curvature were deliberately selected for this exercise. The IT method tended to detect curvature with higher confidence than the ST method. The finding of curvature in the dose response for true simple interchanges is discussed in the context of fundamental models of radiation action. Our second objective was to optimize the design of experiments aimed specifically at detecting curvature. We used Monte Carlo simulation to investigate the following parameters. Constrained by available resources (i.e., the total number of cells to be scored) these include: the optimal number of dose points to use; the best way to apportion the total number of cells among these dose points; and the spacing of dose intervals. Counterintuitively, our simulation results suggest that 4-5 radiation doses were typically optimal, whereas adding more dose points may actually prove detrimental. Superior results were also obtained by implementing unequal dose spacing and unequal distributions in the number of cells scored at each dose.

Reflotron cholesterol measurement in general practice: accuracy and detection of errors.

PubMed

Ball, M J; Robertson, I K; Woods, M

1994-11-01

Comparison of cholesterol determinations by nurses using a Reflotron analyser in a general practice setting showed a good correlation with plasma cholesterol determinations by wet chemistry in a clinical biochemistry laboratory. A limited number of comparisons did, however, give a much lower result on the Reflotron. In an experimental situation, small sample volumes (which could result from poor technique) were shown to produce falsely low readings. A simple method which may immediately detect falsely low Reflotron readings is discussed.

Micro-satellite for space debris observation by optical sensors

NASA Astrophysics Data System (ADS)

Thillot, Marc; Brenière, Xavier; Midavaine, Thierry

2017-11-01

The purpose of this theoretical study carried out under CNES contract is to analyze the feasibility of small space debris detection and classification with an optical sensor on-board micro-satellite. Technical solutions based on active and passive sensors are analyzed and compared. For the most appropriated concept an optimization was made and theoretical performances in terms of number of detection versus class of diameter were calculated. Finally we give some preliminary physical sensor features to illustrate the concept (weight, volume, consumption,…).

A Comparative Study of Automated Infrasound Detectors - PMCC and AFD with Analyst Review.

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

Park, Junghyun; Hayward, Chris; Zeiler, Cleat

Automated detections calculated by the progressive multi-channel correlation (PMCC) method (Cansi, 1995) and the adaptive F detector (AFD) (Arrowsmith et al., 2009) are compared to the signals identified by five independent analysts. Each detector was applied to a four-hour time sequence recorded by the Korean infrasound array CHNAR. This array was used because it is composed of both small (<100 m) and large (~1000 m) aperture element spacing. The four hour time sequence contained a number of easily identified signals under noise conditions that have average RMS amplitudes varied from 1.2 to 4.5 mPa (1 to 5 Hz), estimated withmore » running five-minute window. The effectiveness of the detectors was estimated for the small aperture, large aperture, small aperture combined with the large aperture, and full array. The full and combined arrays performed the best for AFD under all noise conditions while the large aperture array had the poorest performance for both detectors. PMCC produced similar results as AFD under the lower noise conditions, but did not produce as dramatic an increase in detections using the full and combined arrays. Both automated detectors and the analysts produced a decrease in detections under the higher noise conditions. Comparing the detection probabilities with Estimated Receiver Operating Characteristic (EROC) curves we found that the smaller value of consistency for PMCC and the larger p-value for AFD had the highest detection probability. These parameters produced greater changes in detection probability than estimates of the false alarm rate. The detection probability was impacted the most by noise level, with low noise (average RMS amplitude of 1.7 mPa) having an average detection probability of ~40% and high noise (average RMS amplitude of 2.9 mPa) average detection probability of ~23%.« less

Detecting Noisy Events Using Waveform Cross-Correlation at Superarrays of Seismic Stations

NASA Astrophysics Data System (ADS)

von Seggern, D. H.; Tibuleac, I. M.

2007-12-01

Cross-correlation using master events, followed by stacking of the correlation series, has been shown to dramatically improve detection thresholds of small-to-medium seismic arrays. With the goal of lowering the detection threshold, determining relative magnitudes or moments, and characterizing sources by empirical Green's functions, we extend the cross-correlation methodology to include "superarrays" of seismic stations. The superarray concept naturally brings further benefits over conventional arrays and single-stations due to the fact that many distances and azimuths can be sampled. This extension is straightforward given the ease with which regional or global data from various stations or arrays can be currently accessed and combined into a single database. We demonstrate the capability of superarrays to detect and analyze events which lie below the detection threshold. This is aided by applying an F-statistic detector to the superarray cross-correlation stack and its components. Our first example illustrates the use of a superarray consisting of the Southern Great Basin Digital Seismic Network, a small-aperture array (NVAR) in Mina, Nevada and the Earthscope Transportable Array to detect events in California-Nevada areas. In our second example, we use a combination of small-to-medium arrays and single stations to study the rupture of the great Sumatra earthquake of 26 December 2004 and to detect its early aftershocks. The location and times of "detected" events are confirmed using a frequency- wavenumber method at the small-to-medium arrays. We propose that ad hoc superarrays can be used in many studies where conventional approaches previously used only single arrays or groups of single stations. The availability of near-real-time data from many networks and of archived data from, for instance, IRIS makes possible the easy assembly of superarrays. Furthermore, the continued improvement of seismic data availability and the continued growth in the number of world-wide seismic sensors will increasingly make superarrays an attractive choice for many studies.

Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species.

PubMed

Ferrero, Giulio; Cordero, Francesca; Tarallo, Sonia; Arigoni, Maddalena; Riccardo, Federica; Gallo, Gaetano; Ronco, Guglielmo; Allasia, Marco; Kulkarni, Neha; Matullo, Giuseppe; Vineis, Paolo; Calogero, Raffaele A; Pardini, Barbara; Naccarati, Alessio

2018-01-09

The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans. By analysing small RNA-sequencing data from 243 samples, we have identified and compared the most abundantly and uniformly expressed miRNAs and non-miRNA species of comparable size with the library preparation in four different specimens (plasma exosomes, stool, urine, and cervical scrapes). Eleven miRNAs were commonly detected among all different specimens while 231 miRNAs were globally unique across them. Classification analysis using these miRNAs provided an accuracy of 99.6% to recognize the sample types. piRNAs and tRNAs were the most represented non-miRNA small RNAs detected in all specimen types that were analysed, particularly in urine samples. With the present data, the most uniformly expressed small RNAs in each sample type were also identified. A signature of small RNAs for each specimen could represent a reference gene set in validation studies by RT-qPCR. Overall, the data reported hereby provide an insight of the constitution of the human miRNome and of other small non-coding RNAs in various specimens of healthy individuals.

Acoustic Sensing Based on Density Shift of Microspheres by Surface Binding of Gold Nanoparticles.

PubMed

Miyagawa, Akihisa; Inoue, Yoshinori; Harada, Makoto; Okada, Tetsuo

2017-01-01

Herein, we propose a concept for sensing based on density changes of microparticles (MPs) caused by a biochemical reaction. The MPs are levitated by a combined acoustic-gravitational force at a position determined by the density and compressibility. Importantly, the levitation is independent of the MPs sizes. When gold nanoparticles (AuNPs) are bound on the surface of polymer MPs through a reaction, the density of the MPs dramatically increases, and their levitation position in the acoustic-gravitational field is lowered. Because the shift of the levitation position is proportional to the number of AuNPs bound on one MP, we can determine the number of molecules involved in the reaction. The avidin-biotin reaction is used to demonstrate the effectiveness of this concept. The number of molecules involved in the reaction is very small because the reaction space is small for an MP; thus, the method has potential for highly sensitive detection.

Small- and Large-Effect Quantitative Trait Locus Interactions Underlie Variation in Yeast Sporulation Efficiency

PubMed Central

Lorenz, Kim; Cohen, Barak A.

2012-01-01

Quantitative trait loci (QTL) with small effects on phenotypic variation can be difficult to detect and analyze. Because of this a large fraction of the genetic architecture of many complex traits is not well understood. Here we use sporulation efficiency in Saccharomyces cerevisiae as a model complex trait to identify and study small-effect QTL. In crosses where the large-effect quantitative trait nucleotides (QTN) have been genetically fixed we identify small-effect QTL that explain approximately half of the remaining variation not explained by the major effects. We find that small-effect QTL are often physically linked to large-effect QTL and that there are extensive genetic interactions between small- and large-effect QTL. A more complete understanding of quantitative traits will require a better understanding of the numbers, effect sizes, and genetic interactions of small-effect QTL. PMID:22942125

The Utility of Malaria Rapid Diagnostic Tests as a Tool in Enhanced Surveillance for Malaria Elimination in Vanuatu

PubMed Central

Guintran, Jean-Olivier; Iata, Harry; Anderson, Karen; Nausien, Johnny; Gresty, Karryn J; Waters, Norman C.; Vestergaard, Lasse S.; Taleo, George; Cheng, Qin

2016-01-01

Background As part of efforts to eliminate malaria, Vanuatu has piloted the implementation of enhanced malaria surveillance and response strategies since 2011. This involves passive case detection (PCD) in health facilities, proactive case detection (Pro-ACD) and reactive case detection (Re-ACD) in communities using malaria rapid diagnostic tests (RDTs). While RDTs improve case management, their utility for detection of malaria infections in ACDs in this setting is unclear. Methods The utility of malaria RDTs as diagnostic tools was evaluated in PCD, in five rounds of Pro-ACDs and five rounds of Re-ACDs conducted in Tafea and Torba Provinces between 2011 and 2014. The number of malaria infections detected by RDTs was compared to that detected by PCR from collected used-RDTs. Results PCD in Tafea Province (2013) showed a RDT-positive rate of 0.21% (2/939) and a PCR-positive rate of 0.44% (2/453), indicating less than 1% of suspected malaria cases in Tafea Province were due to malaria. In Pro-ACDs conducted in Tafea and Torba Provinces, RDT-positive rates in 2013 and 2014 were 0.14% (3/2145) and 0% (0/2823), respectively, while the corresponding PCR-positive rates were 0.72% (9/1242) and 0.79% (9/1141). PCR identified villages in both provinces appearing to be transmission foci with a small number of low-density infections, mainly P. falciparum infections. In five rounds of Re-ACD, RDTs did not identify any additional infections while PCR detected only one among 173 subjects screened. Conclusions PCD and Pro-ACDs demonstrate that both Tafea and Torba Provinces in Vanuatu has achieved very low malaria prevalence. In these low-transmission areas, conducting Pro-ACD and Re-ACDs using RDTs appears not cost-effective and may have limited impact on interrupting malaria transmission due to the small number of infections identified by RDTs and considerable operational resources invested. More sensitive, field deployable and affordable diagnostic tools will improve malaria surveillance in malaria elimination settings. PMID:27902755

Tick Surveillance of Small Mammals Captured in Gyeonggi and Gangwon Provinces, Republic of Korea, 2004-2008

DTIC Science & Technology

2010-07-30

number of zoonotic pathogens: spotted fever group rickettsiae (Lee et al. 2003), Ehrlichia and Anaplasma spp. (Chae et al. 2003), Bartonella spp. (Kim...K.H. & Lee, S.H. (2003) Identification of the spotted fever group rickettsiae detected from Haemaphysalis longicornis in Korea. Microbiology and

Growth in the Number of SSN Tracked Orbital Objects

NASA Technical Reports Server (NTRS)

Stansbery, Eugene G.

2004-01-01

The number of objects in earth orbit tracked by the US Space Surveillance Network (SSN) has experienced unprecedented growth since March, 2003. Approximately 2000 orbiting objects have been added to the "Analyst list" of tracked objects. This growth is primarily due to the resumption of full power/full time operation of the AN/FPS-108 Cobra Dane radar located on Shemya Island, AK. Cobra Dane is an L-band (23-cm wavelength) phased array radar which first became operational in 1977. Cobra Dane was a "Collateral Sensor" in the SSN until 1994 when its communication link with the Space Control Center (SCC) was closed. NASA and the Air Force conducted tests in 1999 using Cobra Dane to detect and track small debris. These tests confirmed that the radar was capable of detecting and maintaining orbits on objects as small as 5-cm diameter. Subsequently, Cobra Dane was reconnected to the SSN and resumed full power/full time space surveillance operations on March 4, 2003. This paper will examine the new data and its implications to the understanding of the orbital debris environment and orbital safety.

Examining small molecule: HIV RNA interactions using arrayed imaging reflectometry

NASA Astrophysics Data System (ADS)

Chaimayo, Wanaruk; Miller, Benjamin L.

2014-03-01

Human Immunodeficiency Virus (HIV) has been the subject of intense research for more than three decades as it causes an uncurable disease: Acquired Immunodeficiency Syndrome, AIDS. In the pursuit of a medical treatment, RNAtargeted small molecules are emerging as promising targets. In order to understand the binding kinetics of small molecules and HIV RNA, association (ka) and dissociation (kd) kinetic constants must be obtained, ideally for a large number of sequences to assess selectivity. We have developed Aqueous Array Imaged Reflectometry (Aq-AIR) to address this challenge. Using a simple light interference phenomenon, Aq-AIR provides real-time high-throughput multiplex capabilities to detect binding of targets to surface-immobilized probes in a label-free microarray format. The second generation of Aq-AIR consisting of high-sensitivity CCD camera and 12-μL flow cell was fabricated. The system performance was assessed by real-time detection of MBNL1-(CUG)10 and neomycin B - HIV RNA bindings. The results establish this second-generation Aq-AIR to be able to examine small molecules binding to RNA sequences specific to HIV.

quenched-smFISH: Counting small RNA in Pathogenic Bacteria

NASA Astrophysics Data System (ADS)

Shepherd, Douglas; Li, Nan; Micheva-Viteva, Sofiya; Munsky, Brian; Hong-Geller, Elizabeth; Werner, James

2014-03-01

Here, we present a modification to single-molecule fluorescence in situ hybridization, quenched smFISH (q-smFISH), that enables quantitative detection and analysis of small RNA (sRNA) expressed in bacteria. We show that short nucleic acid targets can be detected when the background of unbound singly dye-labeled DNA oligomers is reduced through hybridization with a set of complementary DNA oligomers labeled with a fluorescence quencher. Exploiting an automated, multi-color wide-field microscope and GPU-accelerated data analysis package, we analyzed the statistics of sRNA expression in thousands of individual Yersinia pseudotuberculosis and Yersinia pestis bacteria before and during a simulated infection. Before infection, we find only a small fraction of either bacteria express the small RNAs YSR35 or YSP8. The copy numbers of these RNA are increased during simulated infection, suggesting a role in pathogenesis. The ability to directly quantify expression level changes of sRNA in single cells as a function of external stimuli provides key information on the role of sRNA in bacterial regulatory networks.

Design of large zoom for visible and infrared optical system in hemisphere space

NASA Astrophysics Data System (ADS)

Xing, Yang-guang; Li, Lin; Zhang, Juan

2018-01-01

In the field of space optical, the application of advanced optical instruments for related target detection and identification has become an advanced technology in modern optics. In order to complete the task of search in wide field of view and detailed investigation in small field of view, it is inevitable to use the structure of the zoom system to achieve a better observation for important targets. The innovation of this paper lies in using the zoom optical system in space detection, which achieve firstly military needs of searched target in the large field of view and recognized target in the small field of view. At the same time, this paper also completes firstly the design of variable focus optical detection system in the range of hemisphere space, the zoom optical system is working in the range of visible and infrared wavelengths, the perspective angle reaches 360 ° and the zoom ratio of the visible system is up to 15. The visible system has a zoom range of 60-900 mm, a detection band of 0.48-0.70μm, and a F-number of 2.0 to 5.0. The infrared system has a zoom range of 150 900mm, a detection band of 8-12μm, and a F-number of 1.2 to 3.0. The MTF of the visible zoom system is above 0.4 at spatial frequency of 45 lp / mm, and the infrared zoom system is above 0.4 at spatial frequency of 11 lp / mm. The design results show that the system has a good image quality.

Detection of Small Numbers of Campylobacter jejuni and Campylobacter coli Cells in Environmental Water, Sewage, and Food Samples by a Seminested PCR Assay

PubMed Central

Waage, Astrid S.; Vardund, Traute; Lund, Vidar; Kapperud, Georg

1999-01-01

A rapid and sensitive assay was developed for detection of small numbers of Campylobacter jejuni and Campylobacter coli cells in environmental water, sewage, and food samples. Water and sewage samples were filtered, and the filters were enriched overnight in a nonselective medium. The enrichment cultures were prepared for PCR by a rapid and simple procedure consisting of centrifugation, proteinase K treatment, and boiling. A seminested PCR based on specific amplification of the intergenic sequence between the two Campylobacter flagellin genes, flaA and flaB, was performed, and the PCR products were visualized by agarose gel electrophoresis. The assay allowed us to detect 3 to 15 CFU of C. jejuni per 100 ml in water samples containing a background flora consisting of up to 8,700 heterotrophic organisms per ml and 10,000 CFU of coliform bacteria per 100 ml. Dilution of the enriched cultures 1:10 with sterile broth prior to the PCR was sometimes necessary to obtain positive results. The assay was also conducted with food samples analyzed with or without overnight enrichment. As few as ≤3 CFU per g of food could be detected with samples subjected to overnight enrichment, while variable results were obtained for samples analyzed without prior enrichment. This rapid and sensitive nested PCR assay provides a useful tool for specific detection of C. jejuni or C. coli in drinking water, as well as environmental water, sewage, and food samples containing high levels of background organisms. PMID:10103261

An Automated Directed Spectral Search Methodology for Small Target Detection

NASA Astrophysics Data System (ADS)

Grossman, Stanley I.

Much of the current efforts in remote sensing tackle macro-level problems such as determining the extent of wheat in a field, the general health of vegetation or the extent of mineral deposits in an area. However, for many of the remaining remote sensing challenges being studied currently, such as border protection, drug smuggling, treaty verification, and the war on terror, most targets are very small in nature - a vehicle or even a person. While in typical macro-level problems the objective vegetation is in the scene, for small target detection problems it is not usually known if the desired small target even exists in the scene, never mind finding it in abundance. The ability to find specific small targets, such as vehicles, typifies this problem. Complicating the analyst's life, the growing number of available sensors is generating mountains of imagery outstripping the analysts' ability to visually peruse them. This work presents the important factors influencing spectral exploitation using multispectral data and suggests a different approach to small target detection. The methodology of directed search is presented, including the use of scene-modeled spectral libraries, various search algorithms, and traditional statistical and ROC curve analysis. The work suggests a new metric to calibrate analysis labeled the analytic sweet spot as well as an estimation method for identifying the sweet spot threshold for an image. It also suggests a new visualization aid for highlighting the target in its entirety called nearest neighbor inflation (NNI). It brings these all together to propose that these additions to the target detection arena allow for the construction of a fully automated target detection scheme. This dissertation next details experiments to support the hypothesis that the optimum detection threshold is the analytic sweet spot and that the estimation method adequately predicts it. Experimental results and analysis are presented for the proposed directed search techniques of spectral image based small target detection. It offers evidence of the functionality of the NNI visualization and also provides evidence that the increased spectral dimensionality of the 8-band Worldview-2 datasets provides noteworthy improvement in results over traditional 4-band multispectral datasets. The final experiment presents the results from a prototype fully automated target detection scheme in support of the overarching premise. This work establishes the analytic sweet spot as the optimum threshold defined as the point where error detection rate curves -- false detections vs. missing detections -- cross. At this point the errors are minimized while the detection rate is maximized. It then demonstrates that taking the first moment statistic of the histogram of calculated target detection values from a detection search with test threshold set arbitrarily high will estimate the analytic sweet spot for that image. It also demonstrates that directed search techniques -- when utilized with appropriate scene-specific modeled signatures and atmospheric compensations -- perform at least as well as in-scene search techniques 88% of the time and grossly under-performing only 11% of the time; the in-scene only performs as well or better 50% of the time. It further demonstrates the clear advantage increased multispectral dimensionality brings to detection searches improving performance in 50% of the cases while performing at least as well 72% of the time. Lastly, it presents evidence that a fully automated prototype performs as anticipated laying the groundwork for further research into fully automated processes for small target detection.

Damage identification using inverse methods.

PubMed

Friswell, Michael I

2007-02-15

This paper gives an overview of the use of inverse methods in damage detection and location, using measured vibration data. Inverse problems require the use of a model and the identification of uncertain parameters of this model. Damage is often local in nature and although the effect of the loss of stiffness may require only a small number of parameters, the lack of knowledge of the location means that a large number of candidate parameters must be included. This paper discusses a number of problems that exist with this approach to health monitoring, including modelling error, environmental effects, damage localization and regularization.

What errors do peer reviewers detect, and does training improve their ability to detect them?

PubMed

Schroter, Sara; Black, Nick; Evans, Stephen; Godlee, Fiona; Osorio, Lyda; Smith, Richard

2008-10-01

To analyse data from a trial and report the frequencies with which major and minor errors are detected at a general medical journal, the types of errors missed and the impact of training on error detection. 607 peer reviewers at the BMJ were randomized to two intervention groups receiving different types of training (face-to-face training or a self-taught package) and a control group. Each reviewer was sent the same three test papers over the study period, each of which had nine major and five minor methodological errors inserted. BMJ peer reviewers. The quality of review, assessed using a validated instrument, and the number and type of errors detected before and after training. The number of major errors detected varied over the three papers. The interventions had small effects. At baseline (Paper 1) reviewers found an average of 2.58 of the nine major errors, with no notable difference between the groups. The mean number of errors reported was similar for the second and third papers, 2.71 and 3.0, respectively. Biased randomization was the error detected most frequently in all three papers, with over 60% of reviewers rejecting the papers identifying this error. Reviewers who did not reject the papers found fewer errors and the proportion finding biased randomization was less than 40% for each paper. Editors should not assume that reviewers will detect most major errors, particularly those concerned with the context of study. Short training packages have only a slight impact on improving error detection.

Biomarkers for ALK and ROS1 in Lung Cancer: Immunohistochemistry and Fluorescent In Situ Hybridization.

PubMed

Luk, Peter P; Selinger, Christina I; Mahar, Annabelle; Cooper, Wendy A

2018-06-14

- A small proportion of non-small cell lung cancers harbor rearrangements of ALK or ROS1 genes, and these tumors are sensitive to targeted tyrosine kinase inhibitors. It is crucial for pathologists to accurately identify tumors with these genetic alterations to enable patients to access optimal treatments and avoid unnecessary side effects of less effective agents. Although a number of different techniques can be used to identify ALK- and ROS1-rearranged lung cancers, immunohistochemistry and fluorescence in situ hybridization are the mainstays. - To review the role of immunohistochemistry in assessment of ALK and ROS1 rearrangements in lung cancer, focusing on practical issues in comparison with other modalities such as fluorescence in situ hybridization. - This manuscript reviews the current literature on ALK and ROS1 detection using immunohistochemistry and fluorescence in situ hybridization as well as current recommendations. - Although fluorescence in situ hybridization remains the gold standard for detecting ALK and ROS1 rearrangement in non-small cell lung cancer, immunohistochemistry plays an important role and can be an effective screening method for detection of these genetic alterations, or a diagnostic test in the setting of ALK.

Detection of the Emerging Picornavirus Senecavirus A in Pigs, Mice, and Houseflies.

PubMed

Joshi, Lok R; Mohr, Kristin A; Clement, Travis; Hain, Kyle S; Myers, Bryan; Yaros, Joseph; Nelson, Eric A; Christopher-Hennings, Jane; Gava, Danielle; Schaefer, Rejane; Caron, Luizinho; Dee, Scott; Diel, Diego G

2016-06-01

Senecavirus A (SVA) is an emerging picornavirus that has been recently associated with an increased number of outbreaks of vesicular disease and neonatal mortality in swine. Many aspects of SVA infection biology and epidemiology remain unknown. Here, we present a diagnostic investigation conducted in swine herds affected by vesicular disease and increased neonatal mortality. Clinical and environmental samples were collected from affected and unaffected herds and were screened for the presence of SVA by real-time reverse transcriptase PCR and virus isolation. Notably, SVA was detected and isolated from vesicular lesions and tissues of affected pigs, environmental samples, mouse feces, and mouse small intestine. SVA nucleic acid was also detected in houseflies collected from affected farms and from a farm with no history of vesicular disease. Detection of SVA in mice and housefly samples and recovery of viable virus from mouse feces and small intestine suggest that these pests may play a role on the epidemiology of SVA. These results provide important information that may allow the development of improved prevention and control strategies for SVA. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Detection of the Emerging Picornavirus Senecavirus A in Pigs, Mice, and Houseflies

PubMed Central

Joshi, Lok R.; Mohr, Kristin A.; Clement, Travis; Hain, Kyle S.; Myers, Bryan; Yaros, Joseph; Nelson, Eric A.; Christopher-Hennings, Jane; Gava, Danielle; Schaefer, Rejane; Caron, Luizinho; Dee, Scott

2016-01-01

Senecavirus A (SVA) is an emerging picornavirus that has been recently associated with an increased number of outbreaks of vesicular disease and neonatal mortality in swine. Many aspects of SVA infection biology and epidemiology remain unknown. Here, we present a diagnostic investigation conducted in swine herds affected by vesicular disease and increased neonatal mortality. Clinical and environmental samples were collected from affected and unaffected herds and were screened for the presence of SVA by real-time reverse transcriptase PCR and virus isolation. Notably, SVA was detected and isolated from vesicular lesions and tissues of affected pigs, environmental samples, mouse feces, and mouse small intestine. SVA nucleic acid was also detected in houseflies collected from affected farms and from a farm with no history of vesicular disease. Detection of SVA in mice and housefly samples and recovery of viable virus from mouse feces and small intestine suggest that these pests may play a role on the epidemiology of SVA. These results provide important information that may allow the development of improved prevention and control strategies for SVA. PMID:27030489

Fast Neutron Detection Using Pixelated CdZnTe Spectrometers

NASA Astrophysics Data System (ADS)

Streicher, Michael; Goodman, David; Zhu, Yuefeng; Brown, Steven; Kiff, Scott; He, Zhong

2017-07-01

Fast neutrons are an important signature of special nuclear materials (SNMs). They have a low natural background rate and readily penetrate high atomic number materials that easily shield gamma-ray signatures. Therefore, they provide a complementary signal to gamma rays for detecting shielded SNM. Scattering kinematics dictate that a large nucleus (such as Cd or Te) will recoil with small kinetic energy after an elastic collision with a fast neutron. Charge carrier recombination and quenching further reduce the recorded energy deposited. Thus, the energy threshold of CdZnTe detectors must be very low in order to sense the small signals from these recoils. In this paper, the threshold was reduced to less than 5 keVee to demonstrate that the 5.9-keV X-ray line from 55Fe could be separated from electronic noise. Elastic scattering neutron interactions were observed as small energy depositions (less than 20 keVee) using digitally sampled pulse waveforms from pixelated CdZnTe detectors. Characteristic gamma-ray lines from inelastic neutron scattering were also observed.

Wireless sensor networks for heritage object deformation detection and tracking algorithm.

PubMed

Xie, Zhijun; Huang, Guangyan; Zarei, Roozbeh; He, Jing; Zhang, Yanchun; Ye, Hongwu

2014-10-31

Deformation is the direct cause of heritage object collapse. It is significant to monitor and signal the early warnings of the deformation of heritage objects. However, traditional heritage object monitoring methods only roughly monitor a simple-shaped heritage object as a whole, but cannot monitor complicated heritage objects, which may have a large number of surfaces inside and outside. Wireless sensor networks, comprising many small-sized, low-cost, low-power intelligent sensor nodes, are more useful to detect the deformation of every small part of the heritage objects. Wireless sensor networks need an effective mechanism to reduce both the communication costs and energy consumption in order to monitor the heritage objects in real time. In this paper, we provide an effective heritage object deformation detection and tracking method using wireless sensor networks (EffeHDDT). In EffeHDDT, we discover a connected core set of sensor nodes to reduce the communication cost for transmitting and collecting the data of the sensor networks. Particularly, we propose a heritage object boundary detecting and tracking mechanism. Both theoretical analysis and experimental results demonstrate that our EffeHDDT method outperforms the existing methods in terms of network traffic and the precision of the deformation detection.

Autonomous mine detection system (AMDS) neutralization payload module

NASA Astrophysics Data System (ADS)

Majerus, M.; Vanaman, R.; Wright, N.

2010-04-01

The Autonomous Mine Detection System (AMDS) program is developing a landmine and explosive hazards standoff detection, marking, and neutralization system for dismounted soldiers. The AMDS Capabilities Development Document (CDD) has identified the requirement to deploy three payload modules for small robotic platforms: mine detection and marking, explosives detection and marking, and neutralization. This paper addresses the neutralization payload module. There are a number of challenges that must be overcome for the neutralization payload module to be successfully integrated into AMDS. The neutralizer must meet stringent size, weight, and power (SWaP) requirements to be compatible with a small robot. The neutralizer must be effective against a broad threat, to include metal and plastic-cased Anti-Personnel (AP) and Anti-Tank (AT) landmines, explosive devices, and Unexploded Explosive Ordnance (UXO.) It must adapt to a variety of threat concealments, overburdens, and emplacement methods, to include soil, gravel, asphalt, and concrete. A unique neutralization technology is being investigated for adaptation to the AMDS Neutralization Module. This paper will describe review this technology and how the other two payload modules influence its design for minimizing SWaP. Recent modeling and experimental efforts will be included.

Detecting insect pollinator declines on regional and global scales

USGS Publications Warehouse

Lubuhn, Gretchen; Droege, Sam; Connor, Edward F.; Gemmill-Herren, Barbara; Potts, Simon G.; Minckley, Robert L.; Griswold, Terry; Jean, Robert; Kula, Emanuel; Roubik, David W.; Cane, Jim; Wright, Karen W.; Frankie, Gordon; Parker, Frank

2013-01-01

Recently there has been considerable concern about declines in bee communities in agricultural and natural habitats. The value of pollination to agriculture, provided primarily by bees, is >$200 billion/year worldwide, and in natural ecosystems it is thought to be even greater. However, no monitoring program exists to accurately detect declines in abundance of insect pollinators; thus, it is difficult to quantify the status of bee communities or estimate the extent of declines. We used data from 11 multiyear studies of bee communities to devise a program to monitor pollinators at regional, national, or international scales. In these studies, 7 different methods for sampling bees were used and bees were sampled on 3 different continents. We estimated that a monitoring program with 200-250 sampling locations each sampled twice over 5 years would provide sufficient power to detect small (2-5%) annual declines in the number of species and in total abundance and would cost U.S.$2,000,000. To detect declines as small as 1% annually over the same period would require >300 sampling locations. Given the role of pollinators in food security and ecosystem function, we recommend establishment of integrated regional and international monitoring programs to detect changes in pollinator communities.

Wireless Sensor Networks for Heritage Object Deformation Detection and Tracking Algorithm

PubMed Central

Xie, Zhijun; Huang, Guangyan; Zarei, Roozbeh; He, Jing; Zhang, Yanchun; Ye, Hongwu

2014-01-01

Deformation is the direct cause of heritage object collapse. It is significant to monitor and signal the early warnings of the deformation of heritage objects. However, traditional heritage object monitoring methods only roughly monitor a simple-shaped heritage object as a whole, but cannot monitor complicated heritage objects, which may have a large number of surfaces inside and outside. Wireless sensor networks, comprising many small-sized, low-cost, low-power intelligent sensor nodes, are more useful to detect the deformation of every small part of the heritage objects. Wireless sensor networks need an effective mechanism to reduce both the communication costs and energy consumption in order to monitor the heritage objects in real time. In this paper, we provide an effective heritage object deformation detection and tracking method using wireless sensor networks (EffeHDDT). In EffeHDDT, we discover a connected core set of sensor nodes to reduce the communication cost for transmitting and collecting the data of the sensor networks. Particularly, we propose a heritage object boundary detecting and tracking mechanism. Both theoretical analysis and experimental results demonstrate that our EffeHDDT method outperforms the existing methods in terms of network traffic and the precision of the deformation detection. PMID:25365458

The reliability and stability of visual working memory capacity.

PubMed

Xu, Z; Adam, K C S; Fang, X; Vogel, E K

2018-04-01

Because of the central role of working memory capacity in cognition, many studies have used short measures of working memory capacity to examine its relationship to other domains. Here, we measured the reliability and stability of visual working memory capacity, measured using a single-probe change detection task. In Experiment 1, the participants (N = 135) completed a large number of trials of a change detection task (540 in total, 180 each of set sizes 4, 6, and 8). With large numbers of both trials and participants, reliability estimates were high (α > .9). We then used an iterative down-sampling procedure to create a look-up table for expected reliability in experiments with small sample sizes. In Experiment 2, the participants (N = 79) completed 31 sessions of single-probe change detection. The first 30 sessions took place over 30 consecutive days, and the last session took place 30 days later. This unprecedented number of sessions allowed us to examine the effects of practice on stability and internal reliability. Even after much practice, individual differences were stable over time (average between-session r = .76).

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.

Fault detection and diagnosis in an industrial fed-batch cell culture process.

PubMed

Gunther, Jon C; Conner, Jeremy S; Seborg, Dale E

2007-01-01

A flexible process monitoring method was applied to industrial pilot plant cell culture data for the purpose of fault detection and diagnosis. Data from 23 batches, 20 normal operating conditions (NOC) and three abnormal, were available. A principal component analysis (PCA) model was constructed from 19 NOC batches, and the remaining NOC batch was used for model validation. Subsequently, the model was used to successfully detect (both offline and online) abnormal process conditions and to diagnose the root causes. This research demonstrates that data from a relatively small number of batches (approximately 20) can still be used to monitor for a wide range of process faults.

Nanobarcoding for improved nanoparticle detection in nanomedical biodistribution studies

NASA Astrophysics Data System (ADS)

Eustaquio, Trisha

Determination of the fate of nanoparticles (NPs) in a biological system, or NP biodistribution, is critical in evaluating a NP formulation for nanomedicine. Unlike small-molecule drugs, NPs impose unique challenges in the design of appropriate biodistribution studies due to their small size and subsequent detection signal. Current methods to determine NP biodistribution are greatly inadequate due to their limited detection thresholds. There is an overwhelming need for a sensitive and efficient imaging-based method that can (1) detect and measure small numbers of NPs of various types, ideally single NPs, (2) associate preferential NP uptake with histological cell type by preserving spatial information in samples, and (3) allow for relatively quick and accurate NP detection in in vitro (and possibly ex vivo) samples for comprehensive NP biodistribution studies. Herein, a novel method for improved NP detection is proposed, coined "nanobarcoding." Nanobarcoding utilizes a non-endogenous oligonucleotide, or "nanobarcode" (NB), conjugated to the NP surface to amplify the detection signal from a single NP via in situ polymerase chain reaction (ISPCR), and this signal amplification will facilitate rapid and precise detection of single NPs inside cells over large areas of sample such that more sophisticated studies can be performed on the NP-positive subpopulation. Moreover, nanobarcoding has the potential to be applied to the detection of more than one NP type to study the effects of physicochemical properties, targeting mechanisms, and route of entry on NP biodistribution. The nanobarcoding method was validated in vitro using NB-functionalized superparamagnetic iron oxide NPs (NB-SPIONs) as the model NP type for improved NP detection inside HeLa human cervical cancer cells, a cell line commonly used for ISPCR-mediated detection of human papilloma virus (HPV). Nanotoxicity effects of NB-SPIONs were also evaluated at the single-cell level using LEAP (Laser-Enabled Analysis and Processing, Intrexon, San Diego, CA), and NB-SPIONs were found to be less toxic than its precursor, carboxylated SPIONs (COOH-SPIONs).

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.

Counting polymers moving through a single ion channel

NASA Astrophysics Data System (ADS)

Bezrukov, Sergey M.; Vodyanoy, Igor; Parsegian, V. Adrian

1994-07-01

THE change in conductance of a small electrolyte-filled capillary owing to the passage of sub-micrometre-sized particles has long been used for particle counting and sizing. A commercial device for such measurements, the Coulter counter, is able to detect particles of sizes down to several tenths of a micrometre1-3. Nuclepore technology (in which pores are etched particle tracks) has extended the lower limit of size detection to 60-nm particles by using a capillary of diameter 0.45 μm (ref. 4). Here we show that natural channel-forming peptides incorporated into a bilayer lipid membrane can be used to detect the passage of single molecules with gyration radii as small as 5-15 Å. From our experiments with alamethicin pores we infer both the average number and the diffusion coefficients of poly(ethylene glycol) molecules in the pore. Our approach provides a means of observing the statistics and mechanics of flexible polymers moving within the confines of precisely defined single-molecule structures.

The Belousov-Zhabotinskii Reaction: Improving the Oregonator Model with the Arrhenius Equation

ERIC Educational Resources Information Center

Pellitero, Miguel Aller; Lamsfus, Carlos Alvarez; Borge, Javier

2013-01-01

Oscillating chemical reactions (OCRs) have been known since 1828, with the Belousov-Zhabotinskii (BZ) reaction the most studied example. Initially, OCRs were considered to be special cases due to the small number detected and because the oscillatory behavior did not seem to agree with the second law of thermodynamics. However, OCRs have become…

Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data

PubMed Central

Treutler, Hendrik; Neumann, Steffen

2016-01-01

Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92% of the cases. We make our methodology freely available as part of the Bioconductor packages xcms version 1.50.0 and CAMERA version 1.30.0. PMID:27775610

Detection of dietary DNA, protein, and glyphosate in meat, milk, and eggs.

PubMed

Van Eenennaam, A L; Young, A E

2017-07-01

Products such as meat, milk, and eggs from animals that have consumed genetically engineered (GE) feed are not currently subject to mandatory GE labeling requirements. Some voluntary "non-genetically modified organism" labeling has been associated with such products, indicating that the animals were not fed GE crops, as there are no commercialized GE food animals. This review summarizes the available scientific literature on the detection of dietary DNA and protein in animal products and briefly discusses the implications of mandatory GE labeling for products from animals that have consumed GE feed. Because glyphosate is used on some GE crops, the available studies on glyphosate residues in animal products are also reviewed. In GE crops, recombinant DNA (rDNA) makes up a small percentage of the plant's total DNA. The final amount of DNA in food/feed depends on many factors including the variable number and density of cells in the edible parts, the DNA-containing matrix, environmental conditions, and the specific transgenic event. Processing treatments and animals' digestive systems degrade DNA into small fragments. Available reports conclude that endogenous DNA and rDNA are processed in exactly the same way in the gastrointestinal tract and that they account for a very small proportion of food intake by weight. Small pieces of high copy number endogenous plant genes have occasionally been detected in meat and milk. Similarly sized pieces of rDNA have also been identified in meat, primarily fish, although detection is inconsistent. Dietary rDNA fragments have not been detected in chicken or quail eggs or in fresh milk from cows or goats. Collectively, studies have failed to identify full-length endogenous or rDNA transcripts or recombinant proteins in meat, milk, or eggs. Similarly, because mammals do not bioaccumulate glyphosate and it is rapidly excreted, negligible levels of glyphosate in cattle, pig and poultry meat, milk, and eggs have been reported. Despite consumer concern about the presence of trace concentrations of glyphosate that might have been applied to feed crops and/or the presence of rDNA or recombinant proteins in meat, milk, and eggs, the available data do not provide evidence to suggest that products from animals that have consumed approved GE feed crops differ in any distinguishable way from those derived from animals fed conventional feed or that products from animals fed GE feedstuffs pose novel health risks.

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo.

PubMed

Sakai, Kaori; Taconnat, Ludivine; Borrega, Nero; Yansouni, Jennifer; Brunaud, Véronique; Paysant-Le Roux, Christine; Delannoy, Etienne; Martin Magniette, Marie-Laure; Lepiniec, Loïc; Faure, Jean Denis; Balzergue, Sandrine; Dubreucq, Bertrand

2018-01-01

Genome-wide characterization of tissue- or cell-specific gene expression is a recurrent bottleneck in biology. We have developed a sensitive approach based on ultra-low RNA sequencing coupled to laser assisted microdissection for analyzing different tissues of the small Arabidopsis embryo. We first characterized the number of genes detected according to the quantity of tissue yield and total RNA extracted. Our results revealed that as low as 0.02 mm 2 of tissue and 50 pg of total RNA can be used without compromising the number of genes detected. The optimised protocol was used to compare the epidermal versus mesophyll cell transcriptomes of cotyledons at the torpedo-shaped stage of embryo development. The approach was validated by the recovery of well-known epidermal genes such AtML1 or AtPDF2 and genes involved in flavonoid and cuticular waxes pathways. Moreover, the interest and sensitivity of this approach were highlighted by the characterization of several transcription factors preferentially expressed in epidermal cells. This technical advance unlocks some current limitations of transcriptomic analyses and allows to investigate further and efficiently new biological questions for which only a very small amounts of cells need to be isolated. For instance, it paves the way to increasing the spatial accuracy of regulatory networks in developing small embryo of Arabidopsis or other plant tissues.

Flower detection and acuity of the Australian native stingless bee Tetragonula carbonaria Sm.

PubMed

Dyer, Adrian G; Streinzer, Martin; Garcia, Jair

2016-10-01

We tested the endemic Australian Tetragonula carbonaria bee as a model of how colour vision may allow these small bees to find flowers. In a Y-Maze apparatus, we presented stimuli that contained both chromatic- and green-receptor contrasts, or only had chromatic contrast to free flying bees. Stimuli were detected at visual angles of 9.5° and 9.3°, respectively. We next made morphological measurements of the compound eye under high magnification using a digital microscope, and despite a relatively small eye size with a surface area of 0.64 ± 0.02 mm(2), the compound eye contained 3010 ± 10 ommatidia. Measurements of diverging rays of light using antidromic illumination revealed a mean interommatidial angle in the frontal visual field measures 1.56° ± 0.10°. Finally, we calculate that the minimum number of ommatidia that need to be excited for object detection is 33, which is much higher than for object detection in bumblebees and for the detection of objects providing both colour and green contrasts by honeybees, but lower for the detection of an object lacking green contrast in honeybees. We discuss reasons that may explain potential tradeoff for foraging bees.

Sensitive and specific detection of viable Mycobacterium avium subsp. paratuberculosis in raw milk by the peptide-mediated magnetic separation-phage assay.

PubMed

Foddai, A C G; Grant, I R

2017-05-01

To validate an optimized peptide-mediated magnetic separation (PMS)-phage assay for detection of viable Mycobacterium avium subsp. paratuberculosis (MAP) in milk. Inclusivity, specificity and limit of detection 50% (LOD 50 ) of the optimized PMS-phage assay were assessed. Plaques were obtained for all 43 MAP strains tested. Of 12 other Mycobacterium sp. tested, only Mycobacterium bovis BCG produced small numbers of plaques. LOD 50 of the PMS-phage assay was 0·93 MAP cells per 50 ml milk, which was better than both PMS-qPCR and PMS-culture. When individual milks (n = 146) and bulk tank milk (BTM, n = 22) obtained from Johne's affected herds were tested by the PMS-phage assay, viable MAP were detected in 31 (21·2%) of 146 individual milks and 13 (59·1%) of 22 BTM, with MAP numbers detected ranging from 6-948 plaque-forming-units per 50 ml milk. PMS-qPCR and PMS-MGIT culture proved to be less sensitive tests than the PMS-phage assay. The optimized PMS-phage assay is the most sensitive and specific method available for the detection of viable MAP in milk. Further work is needed to streamline the PMS-phage assay, because the assay's multistep format currently makes it unsuitable for adoption by the dairy industry as a screening test. The inclusivity (ability to detect all MAP strains), specificity (ability to detect only MAP) and detection sensitivity (ability to detect low numbers of MAP) of the optimized PMS-phage assay have been comprehensively demonstrated for the first time. © 2017 The Society for Applied Microbiology.

Characterization of difference of Gaussian filters in the detection of mammographic regions

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

Catarious, David M. Jr.; Baydush, Alan H.; Floyd, Carey E. Jr.

2006-11-15

In this article, we present a characterization of the effect of difference of Gaussians (DoG) filters in the detection of mammographic regions. DoG filters have been used previously in mammographic mass computer-aided detection (CAD) systems. As DoG filters are constructed from the subtraction of two bivariate Gaussian distributions, they require the specification of three parameters: the size of the filter template and the standard deviations of the constituent Gaussians. The influence of these three parameters in the detection of mammographic masses has not been characterized. In this work, we aim to determine how the parameters affect (1) the physical descriptorsmore » of the detected regions (2) the true and false positive rates, and (3) the classification performance of the individual descriptors. To this end, 30 DoG filters are created from the combination of three template sizes and four values for each of the Gaussians' standard deviations. The filters are used to detect regions in a study database of 181 craniocaudal-view mammograms extracted from the Digital Database for Screening Mammography. To describe the physical characteristics of the identified regions, morphological and textural features are extracted from each of the detected regions. Differences in the mean values of the features caused by altering the DoG parameters are examined through statistical and empirical comparisons. The parameters' effects on the true and false positive rate are determined by examining the mean malignant sensitivities and false positives per image (FPpI). Finally, the effect on the classification performance is described by examining the variation in FPpI at the point where 81% of the malignant masses in the study database are detected. Overall, the findings of the study indicate that increasing the standard deviations of the Gaussians used to construct a DoG filter results in a dramatic decrease in the number of regions identified at the expense of missing a small number of malignancies. The sharp reduction in the number of identified regions allowed the identification of textural differences between large and small mammographic regions. We find that the classification performances of the features that achieve the lowest average FPpI are influenced by all three of the parameters.« less

A grey incidence algorithm to detect high-Z material using cosmic ray muons

NASA Astrophysics Data System (ADS)

He, W.; Xiao, S.; Shuai, M.; Chen, Y.; Lan, M.; Wei, M.; An, Q.; Lai, X.

2017-10-01

Muon scattering tomography (MST) is a method for using cosmic muons to scan cargo containers and vehicles for special nuclear materials. However, the flux of cosmic ray muons is low, in the real life application, the detection has to be done a short timescale with small numbers of muons. In this paper, we present a novel approach to detection of special nuclear material by using cosmic ray muons. We use the degree of grey incidence to distinguish typical waste fuel material, uranium, from low-Z material, medium-Z material and other high-Z materials of tungsten and lead. The result shows that using this algorithm, it is possible to detect high-Z materials with an acceptable timescale.

POLIX: A Thomson X-ray polarimeter for a small satellite mission

NASA Astrophysics Data System (ADS)

Paul, Biswajit; Gopala Krishna, M. R.; Puthiya Veetil, Rishin

2016-07-01

POLIX is a Thomson X-ray polarimeter for a small satellite mission of ISRO. The instrument consists of a collimator, a scatterer and a set proportional counters to detect the scattered X-rays. We will describe the design, specifications, sensitivity, and development status of this instrument and some of the important scientific goals. This instrument will provide unprecedented opportunity to measure X-ray polarisation in the medium energy range in a large number of sources of different classes with a minimum detectable linear polarisation degree of 2-3%. The prime objects for observation with this instrument are the X-ray bright accretion powered neutron stars, accreting black holes in different spectral states, rotation powered pulsars, magnetars, and active galactic nuclei. This instrument will be a bridge between the soft X-ray polarimeters and the Compton polarimeters.

Label-free virus detection using silicon photonic microring resonators

PubMed Central

McClellan, Melinda S.; Domier, Leslie L; Bailey, Ryan C.

2013-01-01

Viruses represent a continual threat to humans through a number of mechanisms, which include disease, bioterrorism, and destruction of both plant and animal food resources. Many contemporary techniques used for the detection of viruses and viral infections suffer from limitations such as the need for extensive sample preparation or the lengthy window between infection and measurable immune response, for serological methods. In order to develop a method that is fast, cost-effective, and features reduced sample preparation compared to many other virus detection methods, we report the application of silicon photonic microring resonators for the direct, label-free detection of intact viruses in both purified samples as well as in a complex, real-world analytical matrix. As a model system, we demonstrate the quantitative detection of Bean pod mottle virus, a pathogen of great agricultural importance, with a limit of detection of 10 ng/mL. By simply grinding a small amount of leaf sample in buffer with a mortar and pestle, infected leaves can be identified over a healthy control with a total analysis time of less than 45 min. Given the inherent scalability and multiplexing capability of the semiconductor-based technology, we feel that silicon photonic microring resonators are well-positioned as a promising analytical tool for a number of viral detection applications. PMID:22138465

Sensor array for toxic gas detection

DOEpatents

Stetter, Joseph R.; Zaromb, Solomon; Penrose, William R.

1987-01-01

A portable instrument for use in the field in detecting and identifying a hazardous component in air or other gas including an array of small sensors which upon exposure to the gas from a pattern of electrical responses, a source of standard response patterns characteristic of various components, and microprocessor means for comparing the sensor-formed response pattern with one or more standard patterns to thereby identify the component on a display. The number of responses may be increased beyond the number of sensors by changing the operating voltage, temperature or other condition associated with one or more sensors to provide a plurality of responses from each of one or more of the sensors. In one embodiment, the instrument is capable of identifying anyone of over 50-100 hazardous components.

Channel noise enhances signal detectability in a model of acoustic neuron through the stochastic resonance paradigm.

PubMed

Liberti, M; Paffi, A; Maggio, F; De Angelis, A; Apollonio, F; d'Inzeo, G

2009-01-01

A number of experimental investigations have evidenced the extraordinary sensitivity of neuronal cells to weak input stimulations, including electromagnetic (EM) fields. Moreover, it has been shown that biological noise, due to random channels gating, acts as a tuning factor in neuronal processing, according to the stochastic resonant (SR) paradigm. In this work the attention is focused on noise arising from the stochastic gating of ionic channels in a model of Ranvier node of acoustic fibers. The small number of channels gives rise to a high noise level, which is able to cause a spike train generation even in the absence of stimulations. A SR behavior has been observed in the model for the detection of sinusoidal signals at frequencies typical of the speech.

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.

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).

Medical Management of Small Abdominal Aortic Aneurysms

PubMed Central

Baxter, B. Timothy; Terrin, Michael C.; Dalman, Ronald L.

2013-01-01

Abdominal aortic aneurysm is a common condition that may be lethal when it is unrecognized. Current guidelines suggest repair as the aneurysm diameter reaches 5.0 to 5.5 cm. Most aortic aneurysms are detected incidentally when imaging is done for other purposes or through screening programs. Ninety percent of these aneurysms are below the threshold for intervention at the time of detection. A number of studies have sought to determine factors that lead to progression of aneurysmal disease that might be amenable to intervention during this period of observation. We review these studies and make recommendations for the medical management of small abdominal aortic aneurysms. On the basis of our current knowledge of the causes of aneurysm, a number of approaches have been proposed to prevent progression of aneurysmal disease. These include hemodynamic management, inhibition of inflammation, and protease inhibition. The American College of Cardiology/American Heart Association clinical practice guidelines rules of evidence have helped to define strength of evidence to support these approaches. Level A evidence (from large randomized trials) is available to indicate that observation of small aneurysms in men is safe up to a size of 5.5 cm and that propranolol does not inhibit aneurysm expansion. Level B evidence (from small randomized trials) suggests that roxithromycin or doxycycline will decrease the rate of aneurysm expansion. A number of studies agree that tobacco use is associated with an increased rate of aneurysm expansion. Level B and C evidence is available to suggest that 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors (statins) may inhibit aneurysm expansion. There are animal data but no human data demonstrating that angiotensin-converting enzyme inhibitors or losartan, an angiotensin receptor blocker, will decrease the rate of AAA expansion. A pharmacological agent without important side effects that inhibited aneurysm expansion could change current approaches to aneurysm treatment. Additional studies are needed to clarify the potential role of doxycycline, roxithromycin, and statin therapy in the progression of aneurysmal disease. PMID:18391122

A quantification of the effectiveness of EPID dosimetry and software-based plan verification systems in detecting incidents in radiotherapy

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

Bojechko, Casey; Phillps, Mark; Kalet, Alan

Purpose: Complex treatments in radiation therapy require robust verification in order to prevent errors that can adversely affect the patient. For this purpose, the authors estimate the effectiveness of detecting errors with a “defense in depth” system composed of electronic portal imaging device (EPID) based dosimetry and a software-based system composed of rules-based and Bayesian network verifications. Methods: The authors analyzed incidents with a high potential severity score, scored as a 3 or 4 on a 4 point scale, recorded in an in-house voluntary incident reporting system, collected from February 2012 to August 2014. The incidents were categorized into differentmore » failure modes. The detectability, defined as the number of incidents that are detectable divided total number of incidents, was calculated for each failure mode. Results: In total, 343 incidents were used in this study. Of the incidents 67% were related to photon external beam therapy (EBRT). The majority of the EBRT incidents were related to patient positioning and only a small number of these could be detected by EPID dosimetry when performed prior to treatment (6%). A large fraction could be detected by in vivo dosimetry performed during the first fraction (74%). Rules-based and Bayesian network verifications were found to be complimentary to EPID dosimetry, able to detect errors related to patient prescriptions and documentation, and errors unrelated to photon EBRT. Combining all of the verification steps together, 91% of all EBRT incidents could be detected. Conclusions: This study shows that the defense in depth system is potentially able to detect a large majority of incidents. The most effective EPID-based dosimetry verification is in vivo measurements during the first fraction and is complemented by rules-based and Bayesian network plan checking.« less

Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR.

PubMed

Hughesman, Curtis B; Lu, X J David; Liu, Kelly Y P; Zhu, Yuqi; Towle, Rebecca M; Haynes, Charles; Poh, Catherine F

2017-09-19

Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays. Furthermore, we demonstrate that the ability to target specific locations of the genome permits detection of clinically relevant oncogenic events such as small, submicroscopic homozygous deletions. Additional capabilities of the multiplexed ddPCR assay include the ability to infer ploidy level, quantify the change in copy number of target loci with high-level gains, and simultaneously assess the status and viral load for high-risk human papillomavirus types 16 and 18. This novel multiplexed ddPCR assay therefore may have clinical value in differentiating between benign oral lesions from those that are at risk of progressing to oral cancer.

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

PubMed Central

Feng, Hao; Conneely, Karen N.; Wu, Hao

2014-01-01

DNA methylation is an important epigenetic modification that has essential roles in cellular processes including gene regulation, development and disease and is widely dysregulated in most types of cancer. Recent advances in sequencing technology have enabled the measurement of DNA methylation at single nucleotide resolution through methods such as whole-genome bisulfite sequencing and reduced representation bisulfite sequencing. In DNA methylation studies, a key task is to identify differences under distinct biological contexts, for example, between tumor and normal tissue. A challenge in sequencing studies is that the number of biological replicates is often limited by the costs of sequencing. The small number of replicates leads to unstable variance estimation, which can reduce accuracy to detect differentially methylated loci (DML). Here we propose a novel statistical method to detect DML when comparing two treatment groups. The sequencing counts are described by a lognormal-beta-binomial hierarchical model, which provides a basis for information sharing across different CpG sites. A Wald test is developed for hypothesis testing at each CpG site. Simulation results show that the proposed method yields improved DML detection compared to existing methods, particularly when the number of replicates is low. The proposed method is implemented in the Bioconductor package DSS. PMID:24561809

Infrared hyperspectral imaging sensor for gas detection

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele

2000-11-01

A small light weight man portable imaging spectrometer has many applications; gas leak detection, flare analysis, threat warning, chemical agent detection, just to name a few. With support from the US Air Force and Navy, Pacific Advanced Technology has developed a small man portable hyperspectral imaging sensor with an embedded DSP processor for real time processing that is capable of remotely imaging various targets such as gas plums, flames and camouflaged targets. Based upon their spectral signature the species and concentration of gases can be determined. This system has been field tested at numerous places including White Mountain, CA, Edwards AFB, and Vandenberg AFB. Recently evaluation of the system for gas detection has been performed. This paper presents these results. The system uses a conventional infrared camera fitted with a diffractive optic that images as well as disperses the incident radiation to form spectral images that are collected in band sequential mode. Because the diffractive optic performs both imaging and spectral filtering, the lens system consists of only a single element that is small, light weight and robust, thus allowing man portability. The number of spectral bands are programmable such that only those bands of interest need to be collected. The system is entirely passive, therefore, easily used in a covert operation. Currently Pacific Advanced Technology is working on the next generation of this camera system that will have both an embedded processor as well as an embedded digital signal processor in a small hand held camera configuration. This will allow the implementation of signal and image processing algorithms for gas detection and identification in real time. This paper presents field test data on gas detection and identification as well as discuss the signal and image processing used to enhance the gas visibility. Flow rates as low as 0.01 cubic feet per minute have been imaged with this system.

Clustering-based energy-saving algorithm in ultra-dense network

NASA Astrophysics Data System (ADS)

Huang, Junwei; Zhou, Pengguang; Teng, Deyang; Zhang, Renchi; Xu, Hao

2017-06-01

In Ultra-dense Networks (UDN), dense deployment of low power small base stations will cause serious small cells interference and a large amount of energy consumption. The purpose of this paper is to explore the method of reducing small cells interference and energy saving system in UDN, and we innovatively propose a sleep-waking-active (SWA) scheme. The scheme decreases the user outage causing by failure to detect users’ service requests, shortens the opening time of active base stations directly switching to sleep mode; we further proposes a Vertex Surrounding Clustering(VSC) algorithm, which first colours the small cells with the most strongest interference and next extends to the adjacent small cells. VSC algorithm can use the least colour to stain the small cell, reduce the number of iterations and promote the efficiency of colouring. The simulation results show that SWA scheme can effectively improve the system Energy Efficiency (EE), the VSC algorithm can reduce the small cells interference and optimize the users’ Spectrum Efficiency (SE) and throughput.

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

Lipoprotein profile assessed by 2D-1H-NMR and subclinical atherosclerosis in children with familial hypercholesterolaemia.

PubMed

Rodríguez-Borjabad, Cèlia; Ibarretxe, Daiana; Girona, Josefa; Ferré, Raimon; Feliu, Albert; Amigó, Núria; Guijarro, Eugenio; Masana, Luis; Plana, Núria

2018-03-01

Familial hypercholesterolaemia (FH) is underdiagnosed in children. In addition to lipid concentrations, lipoprotein particle quantity and quality could influence cardiovascular risk. We aimed to perform a comprehensive plasma lipid study, including lipoprotein particle number and size assessment by two-dimensional nuclear magnetic resonance (2D-1H-NMR), in children with FH compared to non-affected children and to evaluate the clinical value of these factors as subclinical atherosclerosis biomarkers. One hundred eighty-three children participating in the broad "Hypercholesterolemia Early Detection Programme" (Decopin Project) were recruited. They were categorized as FH, if they had either a positive genetic test or clinical certainty, or as control children (CCh). Medical history, anthropometry and clinical variables were recorded. Standard biochemical measurements were performed. The lipoprotein profile was studied by 2D-1H-NMR. Carotid intima-media thickness (cIMT) was assessed by sonography in 177 children. FH children had a significant 36% increase in LDL particles. The small LDL fraction was increased by 33% compared to CCh. The relative relationship between large, medium and small LDL and the mean LDL particle size was similar between FH children and CCh. The total and small LDL particle numbers were directly associated with and contributed to the determination of the mean cIMT according to bivariate and multivariate analyses in FH children. The higher cholesterol levels of FH children are due to an overall increased number of all LDL particle subclasses, including a notable 33% increase in small LDL. Total and small LDL particle number shows a good correlation with cIMT in FH children. Copyright © 2018 Elsevier B.V. All rights reserved.

Attentional Capture of Objects Referred to by Spoken Language

ERIC Educational Resources Information Center

Salverda, Anne Pier; Altmann, Gerry T. M.

2011-01-01

Participants saw a small number of objects in a visual display and performed a visual detection or visual-discrimination task in the context of task-irrelevant spoken distractors. In each experiment, a visual cue was presented 400 ms after the onset of a spoken word. In experiments 1 and 2, the cue was an isoluminant color change and participants…

A Behavior-Genetic Study of Parenting Quality, Infant Attachment Security, and Their Covariation in a Nationally Representative Sample

ERIC Educational Resources Information Center

Roisman, Glenn I.; Fraley, R. Chris

2008-01-01

A number of relatively small-sample, genetically sensitive studies of infant attachment security have been published in the past several years that challenge the view that all psychological phenotypes are heritable and that environmental influences on child development--to the extent that they can be detected--serve to make siblings dissimilar.…

The Use of Quality Control and Data Mining Techniques for Monitoring Scaled Scores: An Overview. Research Report. ETS RR-12-20

ERIC Educational Resources Information Center

von Davier, Alina A.

2012-01-01

Maintaining comparability of test scores is a major challenge faced by testing programs that have almost continuous administrations. Among the potential problems are scale drift and rapid accumulation of errors. Many standard quality control techniques for testing programs, which can effectively detect and address scale drift for small numbers of…

Impact of muon detection thresholds on the separability of primary cosmic rays

NASA Astrophysics Data System (ADS)

Müller, S.; Engel, R.; Pierog, T.; Roth, M.

2018-01-01

Knowledge of the mass composition of cosmic rays in the transition region of galactic to extragalactic cosmic rays is needed to discriminate different astrophysical models on their origin, acceleration, and propagation. An important observable to separate different mass groups of cosmic rays is the number of muons in extensive air showers. We performed a CORSIKA simulation study to analyze the impact of the detection threshold of muons on the separation quality of different primary cosmic rays in the energy region of the ankle. Using only the number of muons as the composition-sensitive observable, we find a clear dependence of the separation power on the detection threshold for ideal measurements. Although the number of detected muons increases when lowering the threshold, the discrimination power is reduced. If statistical fluctuations for muon detectors of limited size are taken into account, the threshold dependence remains qualitatively the same for small distances to the shower core but is reduced for large core distances. We interpret the impact of the detection threshold of muons on the composition sensitivity in terms of a change of the correlation of the number of muons nμ with the shower maximum Xmax as function of the muon energy as a result of the underlying hadronic interactions and the shower geometry. We further investigate the role of muons produced in a shower by photon-air interactions and conclude that, in addition to the effect of the nμ -Xmax correlation, the separability of primaries is reduced as a consequence of the presence of more muons from photonuclear reactions in proton than in iron showers.

Salmonella enteritidis surveillance by egg immunology: impact of the sampling scheme on the release of contaminated table eggs.

PubMed

Klinkenberg, Don; Thomas, Ekelijn; Artavia, Francisco F Calvo; Bouma, Annemarie

2011-08-01

Design of surveillance programs to detect infections could benefit from more insight into sampling schemes. We address the effect of sampling schemes for Salmonella Enteritidis surveillance in laying hens. Based on experimental estimates for the transmission rate in flocks, and the characteristics of an egg immunological test, we have simulated outbreaks with various sampling schemes, and with the current boot swab program with a 15-week sampling interval. Declaring a flock infected based on a single positive egg was not possible because test specificity was too low. Thus, a threshold number of positive eggs was defined to declare a flock infected, and, for small sample sizes, eggs from previous samplings had to be included in a cumulative sample to guarantee a minimum flock level specificity. Effectiveness of surveillance was measured by the proportion of outbreaks detected, and by the number of contaminated table eggs brought on the market. The boot swab program detected 90% of the outbreaks, with 75% fewer contaminated eggs compared to no surveillance, whereas the baseline egg program (30 eggs each 15 weeks) detected 86%, with 73% fewer contaminated eggs. We conclude that a larger sample size results in more detected outbreaks, whereas a smaller sampling interval decreases the number of contaminated eggs. Decreasing sample size and interval simultaneously reduces the number of contaminated eggs, but not indefinitely: the advantage of more frequent sampling is counterbalanced by the cumulative sample including less recently laid eggs. Apparently, optimizing surveillance has its limits when test specificity is taken into account. © 2011 Society for Risk Analysis.

Quantile regression for the statistical analysis of immunological data with many non-detects.

PubMed

Eilers, Paul H C; Röder, Esther; Savelkoul, Huub F J; van Wijk, Roy Gerth

2012-07-07

Immunological parameters are hard to measure. A well-known problem is the occurrence of values below the detection limit, the non-detects. Non-detects are a nuisance, because classical statistical analyses, like ANOVA and regression, cannot be applied. The more advanced statistical techniques currently available for the analysis of datasets with non-detects can only be used if a small percentage of the data are non-detects. Quantile regression, a generalization of percentiles to regression models, models the median or higher percentiles and tolerates very high numbers of non-detects. We present a non-technical introduction and illustrate it with an implementation to real data from a clinical trial. We show that by using quantile regression, groups can be compared and that meaningful linear trends can be computed, even if more than half of the data consists of non-detects. Quantile regression is a valuable addition to the statistical methods that can be used for the analysis of immunological datasets with non-detects.

Apparatus and process for microbial detection and enumeration

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Grana, D. (Inventor)

1982-01-01

An apparatus and process for detecting and enumerating specific microorganisms from large volume samples containing small numbers of the microorganisms is presented. The large volume samples are filtered through a membrane filter to concentrate the microorganisms. The filter is positioned between two absorbent pads and previously moistened with a growth medium for the microorganisms. A pair of electrodes are disposed against the filter and the pad electrode filter assembly is retained within a petri dish by retainer ring. The cover is positioned on base of petri dish and sealed at the edges by a parafilm seal prior to being electrically connected via connectors to a strip chart recorder for detecting and enumerating the microorganisms collected on filter.

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.

PubMed

Jiang, Lan; Chen, Huidong; Pinello, Luca; Yuan, Guo-Cheng

2016-07-01

High-throughput single-cell technologies have great potential to discover new cell types; however, it remains challenging to detect rare cell types that are distinct from a large population. We present a novel computational method, called GiniClust, to overcome this challenge. Validation against a benchmark dataset indicates that GiniClust achieves high sensitivity and specificity. Application of GiniClust to public single-cell RNA-seq datasets uncovers previously unrecognized rare cell types, including Zscan4-expressing cells within mouse embryonic stem cells and hemoglobin-expressing cells in the mouse cortex and hippocampus. GiniClust also correctly detects a small number of normal cells that are mixed in a cancer cell population.

Modeling of a latent fault detector in a digital system

NASA Technical Reports Server (NTRS)

Nagel, P. M.

1978-01-01

Methods of modeling the detection time or latency period of a hardware fault in a digital system are proposed that explain how a computer detects faults in a computational mode. The objectives were to study how software reacts to a fault, to account for as many variables as possible affecting detection and to forecast a given program's detecting ability prior to computation. A series of experiments were conducted on a small emulated microprocessor with fault injection capability. Results indicate that the detecting capability of a program largely depends on the instruction subset used during computation and the frequency of its use and has little direct dependence on such variables as fault mode, number set, degree of branching and program length. A model is discussed which employs an analog with balls in an urn to explain the rate of which subsequent repetitions of an instruction or instruction set detect a given fault.

Comparison of four machine learning methods for object-oriented change detection in high-resolution satellite imagery

NASA Astrophysics Data System (ADS)

Bai, Ting; Sun, Kaimin; Deng, Shiquan; Chen, Yan

2018-03-01

High resolution image change detection is one of the key technologies of remote sensing application, which is of great significance for resource survey, environmental monitoring, fine agriculture, military mapping and battlefield environment detection. In this paper, for high-resolution satellite imagery, Random Forest (RF), Support Vector Machine (SVM), Deep belief network (DBN), and Adaboost models were established to verify the possibility of different machine learning applications in change detection. In order to compare detection accuracy of four machine learning Method, we applied these four machine learning methods for two high-resolution images. The results shows that SVM has higher overall accuracy at small samples compared to RF, Adaboost, and DBN for binary and from-to change detection. With the increase in the number of samples, RF has higher overall accuracy compared to Adaboost, SVM and DBN.

Minimum Energy-Variance Filters for the detection of compact sources in crowded astronomical images

NASA Astrophysics Data System (ADS)

Herranz, D.; Sanz, J. L.; López-Caniego, M.; González-Nuevo, J.

2006-10-01

In this paper we address the common problem of the detection and identification of compact sources, such as stars or far galaxies, in Astronomical images. The common approach, that consist in applying a matched filter to the data in order to remove noise and to search for intensity peaks above a certain detection threshold, does not work well when the sources to be detected appear in large number over small regions of the sky due to the effect of source overlapping and interferences among the filtered profiles of the sources. A new class of filter that balances noise removal with signal spatial concentration is introduced, then it is applied to simulated astronomical images of the sky at 857 GHz. We show that with the new filter it is possible to improve the ratio between true detections and false alarms with respect to the matched filter. For low detection thresholds, the improvement is ~ 40%.

Li 2Se as a Neutron Scintillator

DOE PAGES

Du, Mao-Hua; Shi, Hongliang; Singh, David J.

2015-06-23

We show that Li 2Se:Te is a potential neutron scintillator material based on density functional calculations. Li 2Se exhibits a number of properties favorable for efficient neutron detection, such as a high Li concentration for neutron absorption, a small effective atomic mass and a low density for reduced sensitivity to background gamma rays, and a small band gap for a high light yield. Our calculations show that Te doping should lead to the formation of deep acceptor complex V Li-Te Se, which can facilitate efficient light emission, similar to the emission activation in Te doped ZnSe.

Common Faults and Their Prioritization in Small Commercial Buildings: February 2017 - December 2017

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

Frank, Stephen M; Kim, Janghyun; Cai, Jie

To support an ongoing project at NREL titled 'An Open, Cloud-Based Platform for Whole-Building Fault Detection and Diagnostics' (work breakdown structure number 3.2.6.18 funded by the Department of Energy Building Technologies Office), this report documents faults that are commonly found in small commercial buildings (with a floor area of 10,000 ft2 or less) based on a literature review and discussions with building commissioning experts. It also provides a list of prioritized faults based on an estimation of the prevalence, energy impact, and financial impact of each fault.

Modulation of high frequency noise by engine tones of small boats.

PubMed

Pollara, Alexander; Sutin, Alexander; Salloum, Hady

2017-07-01

The effect of modulation of high frequency ship noise by propeller rotation frequencies is well known. This modulation is observed with the Detection of Envelope Modulation on Noise (DEMON) algorithm. Analysis of the DEMON spectrum allows the revolutions per minute and number of blades of the propeller to be determined. This work shows that the high frequency noise of a small boat can also be modulated by engine frequencies. Prior studies have not reported high frequency noise amplitude modulated at engine frequencies. This modulation is likely produced by bubbles from the engine exhaust system.

Occurrence of 1153 organic micropollutants in the aquatic environment of Vietnam.

PubMed

Chau, H T C; Kadokami, K; Duong, H T; Kong, L; Nguyen, T T; Nguyen, T Q; Ito, Y

2018-03-01

The rapid increase in the number and volume of chemical substances being used in modern society has been accompanied by a large number of potentially hazardous chemicals being found in environmental samples. In Vietnam, the monitoring of chemical substances is mainly limited to a small number of known pollutants in spite of rapid economic growth and urbanization, and there is an urgent need to examine a large number of chemicals to prevent impacts from expanding environmental pollution. However, it is difficult to analyze a large number of chemicals using existing methods, because they are time consuming and expensive. In the present study, we determined 1153 substances to grasp a pollution picture of microcontaminants in the aquatic environment. To achieve this objective, we have used two comprehensive analytical methods: (1) solid-phase extraction (SPE) and LC-TOF-MS analysis, and (2) SPE and GC-MS analysis. We collected 42 samples from northern (the Red River and Hanoi), central (Hue and Danang), and southern (Ho Chi Minh City and Saigon-Dongnai River) Vietnam. One hundred and sixty-five compounds were detected at least once. The compounds detected most frequently (>40 % samples) at μg/L concentrations were sterols (cholesterol, beta-sitosterol, stigmasterol, coprostanol), phthalates (bis(2-ethylhexyl) phthalate and di-n-butyl phthalate), and pharmaceutical and personal care products (caffeine, metformin). These contaminants were detected at almost the same detection frequency as in developed countries. The results reveal that surface waters in Vietnam, particularly in the center of large cities, are polluted by a large number of organic micropollutants, with households and business activities as the major sources. In addition, risk quotients (MEC/PNEC values) for nonylphenol, sulfamethoxazole, ampicillin, acetaminophen, erythromycin and clarithromycin were higher than 1, which indicates a possibility of adverse effects on aquatic ecosystems.

Limitations of malaria reactive case detection in an area of low and unstable transmission on the Myanmar-Thailand border.

PubMed

Parker, Daniel M; Landier, Jordi; von Seidlein, Lorenz; Dondorp, Arjen; White, Lisa; Hanboonkunupakarn, Borimas; Maude, Richard J; Nosten, François H

2016-11-25

Reactive case detection is an approach that has been proposed as a tool for malaria elimination in low-transmission settings. It is an intuitively justified approach based on the concept of space-time clustering of malaria cases. When an index malaria clinical case is detected, it triggers reactive screening and treatment in the index house and neighbouring houses. However, the efficacy of this approach at varying screening radii and malaria prevalence remains ill defined. Data were obtained from a detailed demographic and geographic surveillance study in four villages on the Myanmar-Thailand border. Clinical cases were recorded at village malaria clinics and were linked back to patients' residencies. These data were used to simulate the efficacy of reactive case detection for clinical cases using rapid diagnostic tests (RDT). Simulations took clinical cases in a given month and tabulated the number of cases that would have been detected in the following month at varying screening radii around the index houses. Simulations were run independently for both falciparum and vivax malaria. Each simulation of a reactive case detection effort was run in comparison with a strategy using random selection of houses for screening. In approximately half of the screenings for falciparum and 10% for vivax it would have been impossible to detect any malaria cases regardless of the screening strategy because the screening would have occurred during times when there were no cases. When geographically linked cases were present in the simulation, reactive case detection would have only been successful at detecting most malaria cases using larger screening radii (150-m radius and above). At this screening radius and above, reactive case detection does not perform better than random screening of an equal number of houses in the village. Screening within very small radii detects only a very small proportion of cases, but despite this low performance is better than random screening with the same sample size. The results of these simulations indicate that reactive case detection for clinical cases using RDTs has limited ability in halting transmission in regions of low and unstable transmission. This is linked to high spatial heterogeneity of cases, acquisition of malaria infections outside the village, as well missing asymptomatic infections. When cases are few and sporadic, reactive case detection would result in major time and budgetary losses.

Remote Sensing and Wetland Ecology: a South African Case Study.

PubMed

De Roeck, Els R; Verhoest, Niko E C; Miya, Mtemi H; Lievens, Hans; Batelaan, Okke; Thomas, Abraham; Brendonck, Luc

2008-05-26

Remote sensing offers a cost efficient means for identifying and monitoring wetlands over a large area and at different moments in time. In this study, we aim at providing ecologically relevant information on characteristics of temporary and permanent isolated open water wetlands, obtained by standard techniques and relatively cheap imagery. The number, surface area, nearest distance, and dynamics of isolated temporary and permanent wetlands were determined for the Western Cape, South Africa. Open water bodies (wetlands) were mapped from seven Landsat images (acquired during 1987 - 2002) using supervised maximum likelihood classification. The number of wetlands fluctuated over time. Most wetlands were detected in the winter of 2000 and 2002, probably related to road constructions. Imagery acquired in summer contained fewer wetlands than in winter. Most wetlands identified from Landsat images were smaller than one hectare. The average distance to the nearest wetland was larger in summer. In comparison to temporary wetlands, fewer, but larger permanent wetlands were detected. In addition, classification of non-vegetated wetlands on an Envisat ASAR radar image (acquired in June 2005) was evaluated. The number of detected small wetlands was lower for radar imagery than optical imagery (acquired in June 2002), probably because of deterioration of the spatial information content due the extensive pre-processing requirements of the radar image. Both optical and radar classifications allow to assess wetland characteristics that potentially influence plant and animal metacommunity structure. Envisat imagery, however, was less suitable than Landsat imagery for the extraction of detailed ecological information, as only large wetlands can be detected. This study has indicated that ecologically relevant data can be generated for the larger wetlands through relatively cheap imagery and standard techniques, despite the relatively low resolution of Landsat and Envisat imagery. For the characterisation of very small wetlands, high spatial resolution optical or radar images are needed. This study exemplifies the benefits of integrating remote sensing and ecology and hence stimulates interdisciplinary research of isolated wetlands.

Documenting Western Burrowing Owl Reproduction and Activity Patterns Using Motion-Activated Cameras

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

Hall, Derek B.; Greger, Paul D.

We used motion-activated cameras to monitor the reproduction and patterns of activity of the Burrowing Owl (Athene cunicularia) above ground at 45 burrows in south-central Nevada during the breeding seasons of 1999, 2000, 2001, and 2005. The 37 broods, encompassing 180 young, raised over the four years represented an average of 4.9 young per successful breeding pair. Young and adult owls were detected at the burrow entrance at all times of the day and night, but adults were detected more frequently during afternoon/early evening than were young. Motion-activated cameras require less effort to implement than other techniques. Limitations include photographingmore » only a small percentage of owl activity at the burrow; not detecting the actual number of eggs, young, or number fledged; and not being able to track individual owls over time. Further work is also necessary to compare the accuracy of productivity estimates generated from motion-activated cameras with other techniques.« less

A modular positron camera for the study of industrial processes

NASA Astrophysics Data System (ADS)

Leadbeater, T. W.; Parker, D. J.

2011-10-01

Positron imaging techniques rely on the detection of the back-to-back annihilation photons arising from positron decay within the system under study. A standard technique, called positron emitting particle tracking (PEPT) [1], uses a number of these detected events to rapidly determine the position of a positron emitting tracer particle introduced into the system under study. Typical applications of PEPT are in the study of granular and multi-phase materials in the disciplines of engineering and the physical sciences. Using components from redundant medical PET scanners a modular positron camera has been developed. This camera consists of a number of small independent detector modules, which can be arranged in custom geometries tailored towards the application in question. The flexibility of the modular camera geometry allows for high photon detection efficiency within specific regions of interest, the ability to study large and bulky systems and the application of PEPT to difficult or remote processes as the camera is inherently transportable.

Application of statistical process control to qualitative molecular diagnostic assays.

PubMed

O'Brien, Cathal P; Finn, Stephen P

2014-01-01

Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.

Detection of intensity bursts using Hawkes processes: An application to high-frequency financial data

NASA Astrophysics Data System (ADS)

Rambaldi, Marcello; Filimonov, Vladimir; Lillo, Fabrizio

2018-03-01

Given a stationary point process, an intensity burst is defined as a short time period during which the number of counts is larger than the typical count rate. It might signal a local nonstationarity or the presence of an external perturbation to the system. In this paper we propose a procedure for the detection of intensity bursts within the Hawkes process framework. By using a model selection scheme we show that our procedure can be used to detect intensity bursts when both their occurrence time and their total number is unknown. Moreover, the initial time of the burst can be determined with a precision given by the typical interevent time. We apply our methodology to the midprice change in foreign exchange (FX) markets showing that these bursts are frequent and that only a relatively small fraction is associated with news arrival. We show lead-lag relations in intensity burst occurrence across different FX rates and we discuss their relation with price jumps.

High Frequency Design Considerations for the Large Detector Number and Small Form Factor Dual Electron Spectrometer of the Fast Plasma Investigation on NASA's Magnetospheric Multiscale Mission

NASA Technical Reports Server (NTRS)

Kujawski, Joseph T.; Gliese, Ulrik B.; Cao, N. T.; Zeuch, M. A.; White, D.; Chornay, D. J; Lobell, J. V.; Avanov, L. A.; Barrie, A. C.; Mariano, A. J.;

The M31 Pixel Lensing PLAN Campaign: MACHO Lensing and Self-lensing Signals

NASA Astrophysics Data System (ADS)

Calchi Novati, S.; Bozza, V.; Bruni, I.; Dall'Ora, M.; De Paolis, F.; Dominik, M.; Gualandi, R.; Ingrosso, G.; Jetzer, Ph.; Mancini, L.; Nucita, A.; Safonova, M.; Scarpetta, G.; Sereno, M.; Strafella, F.; Subramaniam, A.; Gould, A.; PLAN Collaboration

2014-03-01

We present the final analysis of the observational campaign carried out by the PLAN (Pixel Lensing Andromeda) collaboration to detect a dark matter signal in form of MACHOs through the microlensing effect. The campaign consists of about 1 month/year observations carried out over 4 years (2007-2010) at the 1.5 m Cassini telescope in Loiano (Astronomical Observatory of BOLOGNA, OAB) plus 10 days of data taken in 2010 at the 2 m Himalayan Chandra Telescope monitoring the central part of M31 (two fields of about 13' × 12.'6). We establish a fully automated pipeline for the search and the characterization of microlensing flux variations. As a result, we detect three microlensing candidates. We evaluate the expected signal through a full Monte Carlo simulation of the experiment completed by an analysis of the detection efficiency of our pipeline. We consider both "self lensing" and "MACHO lensing" lens populations, given by M31 stars and dark matter halo MACHOs, in M31 and the Milky Way, respectively. The total number of events is consistent with the expected self-lensing rate. Specifically, we evaluate an expected signal of about two self-lensing events. As for MACHO lensing, for full 0.5(10-2) M ⊙ MACHO halos, our prediction is for about four (seven) events. The comparatively small number of expected MACHO versus self-lensing events, together with the small number statistics at our disposal, do not enable us to put strong constraints on that population. Rather, the hypothesis, suggested by a previous analysis, on the MACHO nature of OAB-07-N2, one of the microlensing candidates, translates into a sizeable lower limit for the halo mass fraction in form of the would-be MACHO population, f, of about 15% for 0.5 M ⊙ MACHOs.

The contactless detection of local normal transitions in superconducting coils by using Poynting’s vector method

NASA Astrophysics Data System (ADS)

Habu, K.; Kaminohara, S.; Kimoto, T.; Kawagoe, A.; Sumiyoshi, F.; Okamoto, H.

2010-11-01

We have developed a new monitoring system to detect an unusual event in the superconducting coils without direct contact on the coils, using Poynting's vector method. In this system, the potential leads and pickup coils are set around the superconducting coils to measure local electric and magnetic fields, respectively. By measuring the sets of magnetic and electric fields, the Poynting's vectors around the coil can be obtained. An unusual event in the coil can be detected as the result of the change of the Poynting's vector. This system has no risk of the voltage breakdown which may happen with the balance voltage method, because there is no need of direct contacts on the coil windings. In a previous paper, we have demonstrated that our system can detect the normal transitions in the Bi-2223 coil without direct contact on the coil windings by using a small test system. For our system to be applied to practical devices, it is necessary for the early detection of an unusual event in the coils to be able to detect local normal transitions in the coils. The signal voltages of the small sensors to measure local magnetic and electric fields are small. Although the increase in signals of the pickup coils is attained easily by an increase in the number of turns of the pickup coils, an increase in the signals of the potential lead is not easily attained. In this paper, a new method to amplify the signal of local electric fields around the coil is proposed. The validity of the method has been confirmed by measuring local electric fields around the Bi-2223 coil.

Detecting reciprocity at a global scale

PubMed Central

Frank, Morgan R.; Obradovich, Nick; Sun, Lijun; Woon, Wei Lee; LeVeck, Brad L.; Rahwan, Iyad

2018-01-01

Reciprocity stabilizes cooperation from the level of microbes all the way up to humans interacting in small groups, but does reciprocity also underlie stable cooperation between larger human agglomerations, such as nation states? Famously, evolutionary models show that reciprocity could emerge as a widespread strategy for achieving international cooperation. However, existing studies have only detected reciprocity-driven cooperation in a small number of country pairs. We apply a new method for detecting mutual influence in dynamical systems to a new large-scale data set that records state interactions with high temporal resolution. Doing so, we detect reciprocity between many country pairs in the international system and find that these reciprocating country pairs exhibit qualitatively different cooperative dynamics when compared to nonreciprocating pairs. Consistent with evolutionary theories of cooperation, reciprocating country pairs exhibit higher levels of stable cooperation and are more likely to punish instances of noncooperation. However, countries in reciprocity-based relationships are also quicker to forgive single acts of noncooperation by eventually returning to previous levels of mutual cooperation. By contrast, nonreciprocating pairs are more likely to exploit each other’s cooperation via higher rates of defection. Together, these findings provide the strongest evidence to date that reciprocity is a widespread mechanism for achieving international cooperation. PMID:29326983

Detecting reciprocity at a global scale.

PubMed

Frank, Morgan R; Obradovich, Nick; Sun, Lijun; Woon, Wei Lee; LeVeck, Brad L; Rahwan, Iyad

2018-01-01

Reciprocity stabilizes cooperation from the level of microbes all the way up to humans interacting in small groups, but does reciprocity also underlie stable cooperation between larger human agglomerations, such as nation states? Famously, evolutionary models show that reciprocity could emerge as a widespread strategy for achieving international cooperation. However, existing studies have only detected reciprocity-driven cooperation in a small number of country pairs. We apply a new method for detecting mutual influence in dynamical systems to a new large-scale data set that records state interactions with high temporal resolution. Doing so, we detect reciprocity between many country pairs in the international system and find that these reciprocating country pairs exhibit qualitatively different cooperative dynamics when compared to nonreciprocating pairs. Consistent with evolutionary theories of cooperation, reciprocating country pairs exhibit higher levels of stable cooperation and are more likely to punish instances of noncooperation. However, countries in reciprocity-based relationships are also quicker to forgive single acts of noncooperation by eventually returning to previous levels of mutual cooperation. By contrast, nonreciprocating pairs are more likely to exploit each other's cooperation via higher rates of defection. Together, these findings provide the strongest evidence to date that reciprocity is a widespread mechanism for achieving international cooperation.

Improved classification of small-scale urban watersheds using thematic mapper simulator data

NASA Technical Reports Server (NTRS)

Owe, M.; Ormsby, J. P.

1984-01-01

The utility of Landsat MSS classification methods in the case of small, highly urbanized hydrological basins containing complex land-use patterns is limited, and is plagued by misclassifications due to the spectral response similarity of many dissimilar surfaces. Landsat MSS data for the Conley Creek basin near Atlanta, Georgia, have been compared to thematic mapper simulator (TMS) data obtained on the same day by aircraft. The TMS data were able to alleviate many of the recurring patterns associated with MSS data, through bandwidth optimization, an increase of the number of spectral bands to seven, and an improvement of ground resolution to 30 m. The TMS is thereby able to detect small water bodies, powerline rights-of-way, and even individual buildings.

A reduced estimate of the number of kilometre-sized near-Earth asteroids.

PubMed

Rabinowitz, D; Helin, E; Lawrence, K; Pravdo, S

2000-01-13

Near-Earth asteroids are small (diameters < 10 km), rocky bodies with orbits that approach that of the Earth (they come within 1.3 AU of the Sun). Most have a chance of approximately 0.5% of colliding with the Earth in the next million years. The total number of such bodies with diameters > 1 km has been estimated to be in the range 1,000-2,000, which translates to an approximately 1% chance of a catastrophic collision with the Earth in the next millennium. These numbers are, however, poorly constrained because of the limitations of previous searches using photographic plates. (One kilometre is below the size of a body whose impact on the Earth would produce global effects.) Here we report an analysis of our survey for near-Earth asteroids that uses improved detection technologies. We find that the total number of asteroids with diameters > 1 km is about half the earlier estimates. At the current rate of discovery of near-Earth asteroids, 90% will probably have been detected within the next 20 years.

High-Density Dielectrophoretic Microwell Array for Detection, Capture, and Single-Cell Analysis of Rare Tumor Cells in Peripheral Blood.

PubMed

Morimoto, Atsushi; Mogami, Toshifumi; Watanabe, Masaru; Iijima, Kazuki; Akiyama, Yasuyuki; Katayama, Koji; Futami, Toru; Yamamoto, Nobuyuki; Sawada, Takeshi; Koizumi, Fumiaki; Koh, Yasuhiro

2015-01-01

Development of a reliable platform and workflow to detect and capture a small number of mutation-bearing circulating tumor cells (CTCs) from a blood sample is necessary for the development of noninvasive cancer diagnosis. In this preclinical study, we aimed to develop a capture system for molecular characterization of single CTCs based on high-density dielectrophoretic microwell array technology. Spike-in experiments using lung cancer cell lines were conducted. The microwell array was used to capture spiked cancer cells, and captured single cells were subjected to whole genome amplification followed by sequencing. A high detection rate (70.2%-90.0%) and excellent linear performance (R2 = 0.8189-0.9999) were noted between the observed and expected numbers of tumor cells. The detection rate was markedly higher than that obtained using the CellSearch system in a blinded manner, suggesting the superior sensitivity of our system in detecting EpCAM- tumor cells. Isolation of single captured tumor cells, followed by detection of EGFR mutations, was achieved using Sanger sequencing. Using a microwell array, we established an efficient and convenient platform for the capture and characterization of single CTCs. The results of a proof-of-principle preclinical study indicated that this platform has potential for the molecular characterization of captured CTCs from patients.

Tracking the Invasion of Small Numbers of Cells in Paper-Based Assays with Quantitative PCR.

PubMed

Truong, Andrew S; Lochbaum, Christian A; Boyce, Matthew W; Lockett, Matthew R

2015-11-17

Paper-based scaffolds are an attractive material for culturing mammalian cells in a three-dimensional environment. There are a number of previously published studies, which utilize these scaffolds to generate models of aortic valves, cardiac ischemia and reperfusion, and solid tumors. These models have largely relied on fluorescence imaging and microscopy to quantify cells in the scaffolds. We present here a polymerase chain reaction (PCR)-based method, capable of quantifying multiple cell types in a single culture with the aid of DNA barcodes: unique sequences of DNA introduced to the genome of individual cells or cell types through lentiviral transduction. PCR-based methods are highly specific and are amenable to high-throughput and multiplexed analyses. To validate this method, we engineered two different breast cancer lines to constitutively express either a green or red fluorescent protein. These cells lines allowed us to directly compare the ability of fluorescence imaging (of the fluorescent proteins) and qPCR (of the unique DNA sequences of the fluorescent proteins) to quantify known numbers of cells in the paper based-scaffolds. We also used both methods to quantify the distribution of these breast cell lines in homotypic and heterotypic invasion assays. In the paper-based invasion assays, a single sheet of paper containing cells suspended in a hydrogel was sandwiched between sheets of paper containing only hydrogel. The stack was incubated, and the cells invaded the adjacent layers. The individual sheets of the invasion assay were then destacked and the number of cells in each layer quantified. Our results show both methods can accurately detect cell populations of greater than 500 cells. The qPCR method can repeatedly and accurately detect as few as 50 cells, allowing small populations of highly invasive cells to be detected and differentiated from other cell types.

InSAR-detected Local Ground Inflation Prior to Small Phreatic Eruption

NASA Astrophysics Data System (ADS)

Kobayashi, T.; Morishita, Y.

2017-12-01

Phreatic eruptions may be related to transient pressure changes in subsurface regions of hydrothermal systems. It means that crustal deformation presumably proceeds with the pressure increase under the ground, which can be a kind of precursor. In this context, Mt. Hakone volcano is a good study target. This is because the crustal deformation has been successfully detected two months before small phreatic eruptions at an active geothermal area, called Owaku-dani. The anomalous activity such as an increase of seismicity started in the end of April, 2015. With this anomalous activity, SAR (ALOS-2) observations was conducted, and small but significant crustal deformation was detected in a local area with a diameter of 200 m with a displacement of 5 cm. The amount of deformation has increased with time although the spatial size has not changed, and resultantly the amount reached up to 60 cm. Finally, in the end of June, eruptions occurred just at the local crustal deformation area. It should be noted that the eruption started from the InSAR-detected inflational area. This is an excellent case that we were able to identify the location of small phreatic eruption in advance by detecting anomalous ground inflation. Further, we investigated whether or not the inflational deformation preceded the anomalous activity observed since the end of April. Applying InSAR time series analysis incorporating the phase linking method to C-band SAR data of RADARSAT-2 (RS2) and Sentinel-1A (S1), we successfully detected small but significant inflational ground deformation that has already proceeded since the end of 2014 at the latest. The amount of deformation reaches up to 3 cm during 4 months. The most striking point is that the spatial distribution is quite similar to the deformation detected by ALOS-2. It strongly suggests that the pressure increase in subsurface have already started before the anomalous activities such as seismic swarm and widely-distributed deformation have been identified. Acknowledgements: ALOS-2 and RS2 data were provided from JAXA under a cooperative research contract between GSI and JAXA, and in addition, for RS2 under a contract between JAXA and CSA. The ownership of ALOS-2 and RS2 data belong to JAXA and MDA, respectively. This study was supported by JSPS KAKENHI Grant Numbers JP16K1779.

Micro-optics for simultaneous multi-spectral imaging applied to chemical/biological and IED detection

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele

2012-06-01

Using diffractive micro-lenses configured in an array and placed in close proximity to the focal plane array will enable a small compact simultaneous multispectral imaging camera. This approach can be applied to spectral regions from the ultraviolet (UV) to the long-wave infrared (LWIR). The number of simultaneously imaged spectral bands is determined by the number of individually configured diffractive optical micro-lenses (lenslet) in the array. Each lenslet images at a different wavelength determined by the blaze and set at the time of manufacturing based on application. In addition, modulation of the focal length of the lenslet array with piezoelectric or electro-static actuation will enable spectral band fill-in allowing hyperspectral imaging. Using the lenslet array with dual-band detectors will increase the number of simultaneous spectral images by a factor of two when utilizing multiple diffraction orders. Configurations and concept designs will be presented for detection application for biological/chemical agents, buried IED's and reconnaissance. The simultaneous detection of multiple spectral images in a single frame of data enhances the image processing capability by eliminating temporal differences between colors and enabling a handheld instrument that is insensitive to motion.

Microwave emission from the coronae of late-type dwarf stars

NASA Technical Reports Server (NTRS)

Linsky, J. L.; Gary, D. E.

1983-01-01

VLA microwave observations of 14 late-type dwarf and subgiant stars and binary systems are examined. In this extensive set of observations, four sources at 6 cm (Chi-1 Ori, UV Cet, YY Gem, and Wolf 630AB) were detected and low upper limits for the remaining stars were found. The microwave luminosities of the nondetected F-K dwarfs are as small as 0.01 those of the dMe stars. The detected emission is slowly variable in all cases and is consistent with gyroresonant emission from thermal electrons spiraling in magnetic fields of about 300 gauss if the source sizes are as large as R/R(asterisk) = 3-4. This would correspond to magnetic fields that are probably in the range 0.001-0.0001 gauss at the photospheric level. An alternative mechanism is gyrosynchrotron emission from a relatively small number of electrons with effective temperature.

Development of a Strontium Magneto-Optical Trap for Probing Casimir-Polder Potentials

NASA Astrophysics Data System (ADS)

Martin, Paul J.

In recent years, cold atoms have been the centerpiece of many remarkably sensitive measurements, and much effort has been made to devise miniaturized quantum sensors and quantum information processing devices. At small distances, however, mechanical effects of the quantum vacuum begin to significantly impact the behavior of the cold-atom systems. A better understanding of how surface composition and geometry affect Casimir and Casimir-Polder potentials would benefit future engineering of small-scale devices. Unfortunately, theoretical solutions are limited and the number of experimental techniques that can accurately detect such short-range forces is relatively small. We believe the exemplary properties of atomic strontium--which have enabled unprecedented frequency metrology in optical lattice clocks--make it an ideal candidate for probing slight spectroscopic perturbations caused by vacuum fluctuations. To that end, we have constructed a magneto-optical trap for strontium to enable future study of atom-surface potentials, and the apparatus and proposed detection scheme are discussed herein. Of special note is a passively stable external-cavity diode laser we developed that is both affordable and competitive with high-end commercial options.

Current trends in nanobiosensor technology

PubMed Central

Wu, Diana; Langer, Robert S

2014-01-01

The development of tools and processes used to fabricate, measure, and image nanoscale objects has lead to a wide range of work devoted to producing sensors that interact with extremely small numbers (or an extremely small concentration) of analyte molecules. These advances are particularly exciting in the context of biosensing, where the demands for low concentration detection and high specificity are great. Nanoscale biosensors, or nanobiosensors, provide researchers with an unprecedented level of sensitivity, often to the single molecule level. The use of biomolecule-functionalized surfaces can dramatically boost the specificity of the detection system, but can also yield reproducibility problems and increased complexity. Several nanobiosensor architectures based on mechanical devices, optical resonators, functionalized nanoparticles, nanowires, nanotubes, and nanofibers have been demonstrated in the lab. As nanobiosensor technology becomes more refined and reliable, it is likely it will eventually make its way from the lab to the clinic, where future lab-on-a-chip devices incorporating an array of nanobiosensors could be used for rapid screening of a wide variety of analytes at low cost using small samples of patient material. PMID:21391305

Small impacts on the Giant Planet Jupiter

NASA Astrophysics Data System (ADS)

Hueso, Ricardo; Delcroix, Marc; Sanchez-Lavega, Agustin M.; Rojas, Jose Felix; María Gómez-Forrellad, Josep; Juaristi-Campillo, Jon

2017-10-01

Amateur video observations of Jupiter have shown five events of 1-s long flashes, each one observed by 2-3 observers geographically separated. The first three of these events occurred on June 3 2010, August 20 2010 and September 10 2012. Analysis of the light-curves of each flash shows that they most probably were caused by the impact of objects of 5-20 m depending on their density (Hueso et al., 2010, 2013) with a released energy comparable to superbolides on Earth similar to the Chelyabinsk airburst. The last two flashes on Jupiter were detected on 17 March 2016 and 26 May 2017 after a long pause in impacts detections of more than 3 years. In all of these cases no impact debri at the impact location was found in later observations.We present detailed light-curves of the five flashes. Photometric calibration of the images allows to constrain the size of the impacting objects. We estimate the flash observable characteristics of a Jupiter impact event that could leave an observable debri field on Jupiter’s atmosphere over a few days triggering fast observations. We also present results from a systematic search of impacts on >65,000 video amateur observations with a software specifically designed towards impact detection and based on differential photometry of frames over videos of Jupiter. From the observations of impacts and a statistical analysis of amateur observations the flux of small objects (5-20 m size) impacting Jupiter is predicted to be small (from 1 every 70 days to 1 every 12 days). A larger telescope than those used by amateurs could detect smaller impacts happening much more frequently. In spite of the uncertainties, these numbers imply that a dense number of observers are required to efficiently discover Jupiter impacts. The first three events were detected with Jupiter oppositions on September and December in 2010 and 2012 respectively and the last two events were detected with Jupiter oppositions in March and April 2017. We predict that more impacts will be found in the upcoming years with Jupiter opposition displaced towards the Summer in the Northern hemisphere where most amateur astronomers observe.References:Hueso et al. ApJ, 721L (2010).Hueso et al. A&A, 560, A55 (2013).

Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

PubMed

Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

2018-05-15

Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

SpeCond: a method to detect condition-specific gene expression

PubMed Central

2011-01-01

Transcriptomic studies routinely measure expression levels across numerous conditions. These datasets allow identification of genes that are specifically expressed in a small number of conditions. However, there are currently no statistically robust methods for identifying such genes. Here we present SpeCond, a method to detect condition-specific genes that outperforms alternative approaches. We apply the method to a dataset of 32 human tissues to determine 2,673 specifically expressed genes. An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html. PMID:22008066

Development of a rapid recombinase polymerase amplification assay for the detection of Streptococcus pneumoniae in whole blood.

PubMed

Clancy, Eoin; Higgins, Owen; Forrest, Matthew S; Boo, Teck Wee; Cormican, Martin; Barry, Thomas; Piepenburg, Olaf; Smith, Terry J

2015-10-29

Streptococcus pneumoniae is an important cause of microbial disease in humans. The introduction of multivalent vaccines has coincided with a dramatic decrease in the number of pneumococcal-related deaths. In spite of this, at a global level, pneumococcal infection remains an important cause of death among children under 5 years of age and in adults 65 years of age or older. In order to properly manage patients and control the spread of infection, a rapid and highly sensitive diagnostic method is needed for routine implementation, especially in resource-limited regions where pneumococcal disease is most prevalent. Using the gene encoding leader peptidase A as a molecular diagnostics target, a real-time RPA assay was designed and optimised for the detection of S. pneumoniae in whole blood. The performance of the assay was compared to real-time PCR in terms of its analytical limit of detection and specificity. The inhibitory effect of human genomic DNA on amplification was investigated. The potential clinical utility of the assay was investigated using a small number of clinical samples. The RPA assay has a limit of detection equivalent to PCR (4.0 and 5.1 genome equivalents per reaction, respectively) and was capable of detecting the equivalent of <1 colony forming unit of S. pneumoniae when spiked into human whole blood. The RPA assay was 100 % inclusive (38/38 laboratory reference strains and 19/19 invasive clinical isolates) and 100 % exclusive; differentiating strains of S. pneumoniae species from other viridans group streptococci, including S. pseudopneumoniae. When applied to the analysis of a small number (n = 11) of clinical samples (blood culture positive for S. pneumoniae), the RPA assay was demonstrated to be both rapid and sensitive. The RPA assay developed in this work is shown to be as sensitive and as specific as PCR. In terms of reaction kinetics, the RPA assay is shown to exceed those of the PCR, with the RPA running to completion in 20 minutes and capable generating a positive signal in as little as 6 minutes. This work represents a potentially suitable assay for application in point-of-care settings.

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C

PubMed Central

Oudelaar, A. Marieke; Davies, James O.J.; Downes, Damien J.; Higgs, Douglas R.

2017-01-01

Abstract Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000–20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations. PMID:29186505

eUnaG: a new ligand-inducible fluorescent reporter to detect drug transporter activity in live cells

PubMed Central

Yeh, Johannes T.-H.; Nam, Kwangho; Yeh, Joshua T.-H.; Perrimon, Norbert

2017-01-01

The absorption, distribution, metabolism and excretion (ADME) of metabolites and toxic organic solutes are orchestrated by the ATP-binding cassette (ABC) transporters and the organic solute carrier family (SLC) proteins. A large number of ABC and SLC transpoters exist; however, only a small number have been well characterized. To facilitate the analysis of these transporters, which is important for drug safety and physiological studies, we developed a sensitive genetically encoded bilirubin (BR)-inducible fluorescence sensor (eUnaG) to detect transporter-coupled influx/efflux of organic compounds. This sensor can be used in live cells to measure transporter activity, as excretion of BR depends on ABC and SLC transporters. Applying eUnaG in functional RNAi screens, we characterize l(2)03659 as a Drosophila multidrug resistant-associated ABC transporter. PMID:28176814

Anomaly clustering in hyperspectral images

NASA Astrophysics Data System (ADS)

Doster, Timothy J.; Ross, David S.; Messinger, David W.; Basener, William F.

2009-05-01

The topological anomaly detection algorithm (TAD) differs from other anomaly detection algorithms in that it uses a topological/graph-theoretic model for the image background instead of modeling the image with a Gaussian normal distribution. In the construction of the model, TAD produces a hard threshold separating anomalous pixels from background in the image. We build on this feature of TAD by extending the algorithm so that it gives a measure of the number of anomalous objects, rather than the number of anomalous pixels, in a hyperspectral image. This is done by identifying, and integrating, clusters of anomalous pixels via a graph theoretical method combining spatial and spectral information. The method is applied to a cluttered HyMap image and combines small groups of pixels containing like materials, such as those corresponding to rooftops and cars, into individual clusters. This improves visualization and interpretation of objects.

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

High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer

PubMed Central

Pailler, E.; Auger, N.; Lindsay, C. R.; Vielh, P.; Islas-Morris-Hernandez, A.; Borget, I.; Ngo-Camus, M.; Planchard, D.; Soria, J.-C.; Besse, B.; Farace, F.

2015-01-01

Background Genetic aberrations affecting the c-ros oncogene 1 (ROS1) tyrosine kinase gene have been reported in a small subset of patients with non-small-cell lung cancer (NSCLC). We evaluated whether ROS1-chromosomal rearrangements could be detected in circulating tumor cells (CTCs) and examined tumor heterogeneity of CTCs and tumor biopsies in ROS1-rearranged NSCLC patients. Patients and methods Using isolation by size of epithelial tumor cells (ISET) filtration and filter-adapted-fluorescence in situ hybridization (FA-FISH), ROS1 rearrangement was examined in CTCs from four ROS1-rearranged patients treated with the ROS1-inhibitor, crizotinib, and four ROS1-negative patients. ROS1-gene alterations observed in CTCs at baseline from ROS1-rearranged patients were compared with those present in tumor biopsies and in CTCs during crizotinib treatment. Numerical chromosomal instability (CIN) of CTCs was assessed by DNA content quantification and chromosome enumeration. Results ROS1 rearrangement was detected in the CTCs of all four patients with ROS1 rearrangement previously confirmed by tumor biopsy. In ROS1-rearranged patients, median number of ROS1-rearranged CTCs at baseline was 34.5 per 3 ml blood (range, 24–55). In ROS1-negative patients, median background hybridization of ROS1-rearranged CTCs was 7.5 per 3 ml blood (range, 7–11). Tumor heterogeneity, assessed by ROS1 copy number, was significantly higher in baseline CTCs compared with paired tumor biopsies in the three patients experiencing PR or SD (P < 0.0001). Copy number in ROS1-rearranged CTCs increased significantly in two patients who progressed during crizotinib treatment (P < 0.02). CTCs from ROS1-rearranged patients had a high DNA content and gain of chromosomes, indicating high levels of aneuploidy and numerical CIN. Conclusion We provide the first proof-of-concept that CTCs can be used for noninvasive and sensitive detection of ROS1 rearrangement in NSCLC patients. CTCs from ROS1-rearranged patients show considerable heterogeneity of ROS1-gene abnormalities and elevated numerical CIN, a potential mechanism to escape ROS1-inhibitor therapy in ROS1-rearranged NSCLC tumors. PMID:25846554

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.

[Role of C5b-9 expression in skeletal muscle blood vessels in necrotizing myopathy].

PubMed

Cong, Lu; Pu, Chuanqiang; Mao, Yanling; Liu, Jiexiao; Lu, Xianghui; Wang, Qian

2012-05-01

To investigate the expression of C5b-9 in the skeletal muscle blood vessels in patients with necrotizing myopathy and explore its role in the pathogenesis of this disease. The expression of C5b-9 and MHC-I in the skeletal muscular fibers and blood vessels in 4 patients with necrotizing myopathy was detected using enzymohistochemistry and immunohistochemistry. Focal or dispersive necrotic muscle fibers with obvious phagocytosis were observed in all the 4 patients. No inflammatory cell infiltration was found in the perimysium or perivascular regions. HE staining showed a decreased number of local small blood vessels, and the some small blood vessels showed thickened vascular walls. Immunohistochemistry detected prominent C5b-9 expression in the necrotic muscle fibers and the blood vessels, and diffuse strong C5b-9 expression was found in the vascular walls, vascular endothelial cells and the smooth muscle layer. No MHC-I deposition was detected in the muscular fibers and blood vessels. C5b-9 contributes to the pathogenesis of necrotizing myopathy mediated by pathologies in the blood vessels.

Development of a microplate-based fluorescence immunoassay using quantum dot streptavidin conjugates for enumeration of putative marine bacteria, Alteromonas sp., associated with a benthic harpacticoid copepod.

PubMed

Beckman, Erin M; Kawaguchi, Tomohiro; Chandler, G Thomas; Decho, Alan W

2008-12-01

Attached bacteria inhabit the surfaces of many marine animals--a process that may play important roles in the survival and transport through aquatic systems. However, efficient detection of these bacteria has been problematic, especially small aquatic animals such as benthic harpacticoid copepod. Quantum dots (QD) have recently emerged as a significant tool in immunofluorescence detection because of their unique properties compared to other fluorescent probes. In the present study, a polyclonal antibody was raised against the Gram-negative marine bacterium, Alteromonas sp. A microplate-based immunofluorescence bioassay using QD strepavidin conjugates was developed for quantifying putative Alteromonas sp. cells located on the surfaces of a marine harpacticoid copepod, Microarthridion littorale. The number of attached Alteromonas sp. was estimated to be 10(2)+/-8 CFU using this method. The QD approach, coupled to a microplate assay can potentially provide an efficient and accurate method for rapidly detecting multiple bacteria species attached to small invertebrate animals because of their unique excitation and emission characteristics.

Detection of nanoflare-heated plasma in the solar corona by the FOXSI-2 sounding rocket

NASA Astrophysics Data System (ADS)

Ishikawa, Shin-nosuke; Glesener, Lindsay; Krucker, Säm; Christe, Steven; Buitrago-Casas, Juan Camilo; Narukage, Noriyuki; Vievering, Juliana

2017-11-01

The processes that heat the solar and stellar coronae to several million kelvins, compared with the much cooler photosphere (5,800 K for the Sun), are still not well known1. One proposed mechanism is heating via a large number of small, unresolved, impulsive heating events called nanoflares2. Each event would heat and cool quickly, and the average effect would be a broad range of temperatures including a small amount of extremely hot plasma. However, detecting these faint, hot traces in the presence of brighter, cooler emission is observationally challenging. Here we present hard X-ray data from the second flight of the Focusing Optics X-ray Solar Imager (FOXSI-2), which detected emission above 7 keV from an active region of the Sun with no obvious individual X-ray flare emission. Through differential emission measure computations, we ascribe this emission to plasma heated above 10 MK, providing evidence for the existence of solar nanoflares. The quantitative evaluation of the hot plasma strongly constrains the coronal heating models.

Absorption spectroscopy at the limb of small transiting exoplanets

NASA Astrophysics Data System (ADS)

Ehrenreich, D.; Lecavelier Des Etangs, A.

2005-12-01

Planetary transits are a tremendous tool to probe into exoplanet atmospheres using the light from their parent stars (from 0.2 μm to ˜1 μm). The detection of atmospheric components in an extra-solar giant planet was performed using the Hubble Space Telescope (HST) with a sensitivity reaching ˜10-4 in relative absorption depth over ˜1 Å-wide features (Charbonneau et al., 2002). The next step is the detection and the characterization of smaller, possibly Earth-like worlds, which will require a sensitivity of ˜10-6. Fortunately, ˜0.1 μm-wide absorption bands of particular interest for small exoplanets do exist in this spectral domain. We developed a model to quantify the detectability of a variety of Earth-size planets harboring different kind of atmospheres. Key parameters are the density of the planet and the thickness of the atmosphere. We also evaluate in consequence the number of potential targets for a future space mission, and also find that K stars are best candidates. See Ehrenreich et al. (2005) for a complete description.

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.

PubMed

Bentzen, Amalie Kai; Marquard, Andrea Marion; Lyngaa, Rikke; Saini, Sunil Kumar; Ramskov, Sofie; Donia, Marco; Such, Lina; Furness, Andrew J S; McGranahan, Nicholas; Rosenthal, Rachel; Straten, Per Thor; Szallasi, Zoltan; Svane, Inge Marie; Swanton, Charles; Quezada, Sergio A; Jakobsen, Søren Nyboe; Eklund, Aron Charles; Hadrup, Sine Reker

2016-10-01

Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.

Label-free virus detection using silicon photonic microring resonators.

PubMed

McClellan, Melinda S; Domier, Leslie L; Bailey, Ryan C

2012-01-15

Viruses represent a continual threat to humans through a number of mechanisms, which include disease, bioterrorism, and destruction of both plant and animal food resources. Many contemporary techniques used for the detection of viruses and viral infections suffer from limitations such as the need for extensive sample preparation or the lengthy window between infection and measurable immune response, for serological methods. In order to develop a method that is fast, cost-effective, and features reduced sample preparation compared to many other virus detection methods, we report the application of silicon photonic microring resonators for the direct, label-free detection of intact viruses in both purified samples as well as in a complex, real-world analytical matrix. As a model system, we demonstrate the quantitative detection of Bean pod mottle virus, a pathogen of great agricultural importance, with a limit of detection of 10 ng/mL. By simply grinding a small amount of leaf sample in buffer with a mortar and pestle, infected leaves can be identified over a healthy control with a total analysis time of less than 45 min. Given the inherent scalability and multiplexing capability of the semiconductor-based technology, we feel that silicon photonic microring resonators are well-positioned as a promising analytical tool for a number of viral detection applications. Copyright © 2011 Elsevier B.V. All rights reserved.

Small Arrays for Seismic Intruder Detections: A Simulation Based Experiment

NASA Astrophysics Data System (ADS)

Pitarka, A.

2014-12-01

Seismic sensors such as geophones and fiber optic have been increasingly recognized as promising technologies for intelligence surveillance, including intruder detection and perimeter defense systems. Geophone arrays have the capability to provide cost effective intruder detection in protecting assets with large perimeters. A seismic intruder detection system uses one or multiple arrays of geophones design to record seismic signals from footsteps and ground vehicles. Using a series of real-time signal processing algorithms the system detects, classify and monitors the intruder's movement. We have carried out numerical experiments to demonstrate the capability of a seismic array to detect moving targets that generate seismic signals. The seismic source is modeled as a vertical force acting on the ground that generates continuous impulsive seismic signals with different predominant frequencies. Frequency-wave number analysis of the synthetic array data was used to demonstrate the array's capability at accurately determining intruder's movement direction. The performance of the array was also analyzed in detecting two or more objects moving at the same time. One of the drawbacks of using a single array system is its inefficiency at detecting seismic signals deflected by large underground objects. We will show simulation results of the effect of an underground concrete block at shielding the seismic signal coming from an intruder. Based on simulations we found that multiple small arrays can greatly improve the system's detection capability in the presence of underground structures. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344

Differential gene expression detection and sample classification using penalized linear regression models.

PubMed

Wu, Baolin

2006-02-15

Differential gene expression detection and sample classification using microarray data have received much research interest recently. Owing to the large number of genes p and small number of samples n (p > n), microarray data analysis poses big challenges for statistical analysis. An obvious problem owing to the 'large p small n' is over-fitting. Just by chance, we are likely to find some non-differentially expressed genes that can classify the samples very well. The idea of shrinkage is to regularize the model parameters to reduce the effects of noise and produce reliable inferences. Shrinkage has been successfully applied in the microarray data analysis. The SAM statistics proposed by Tusher et al. and the 'nearest shrunken centroid' proposed by Tibshirani et al. are ad hoc shrinkage methods. Both methods are simple, intuitive and prove to be useful in empirical studies. Recently Wu proposed the penalized t/F-statistics with shrinkage by formally using the (1) penalized linear regression models for two-class microarray data, showing good performance. In this paper we systematically discussed the use of penalized regression models for analyzing microarray data. We generalize the two-class penalized t/F-statistics proposed by Wu to multi-class microarray data. We formally derive the ad hoc shrunken centroid used by Tibshirani et al. using the (1) penalized regression models. And we show that the penalized linear regression models provide a rigorous and unified statistical framework for sample classification and differential gene expression detection.

Inspecting rapidly moving surfaces for small defects using CNN cameras

NASA Astrophysics Data System (ADS)

Blug, Andreas; Carl, Daniel; Höfler, Heinrich

2013-04-01

A continuous increase in production speed and manufacturing precision raises a demand for the automated detection of small image features on rapidly moving surfaces. An example are wire drawing processes where kilometers of cylindrical metal surfaces moving with 10 m/s have to be inspected for defects such as scratches, dents, grooves, or chatter marks with a lateral size of 100 μm in real time. Up to now, complex eddy current systems are used for quality control instead of line cameras, because the ratio between lateral feature size and surface speed is limited by the data transport between camera and computer. This bottleneck is avoided by "cellular neural network" (CNN) cameras which enable image processing directly on the camera chip. This article reports results achieved with a demonstrator based on this novel analogue camera - computer system. The results show that computational speed and accuracy of the analogue computer system are sufficient to detect and discriminate the different types of defects. Area images with 176 x 144 pixels are acquired and evaluated in real time with frame rates of 4 to 10 kHz - depending on the number of defects to be detected. These frame rates correspond to equivalent line rates on line cameras between 360 and 880 kHz, a number far beyond the available features. Using the relation between lateral feature size and surface speed as a figure of merit, the CNN based system outperforms conventional image processing systems by an order of magnitude.

Influence of field size on the physiological and skill demands of small-sided games in junior and senior rugby league players.

PubMed

Gabbett, Tim J; Abernethy, Bruce; Jenkins, David G

2012-02-01

The purpose of this study was to investigate the effect of changes in field size on the physiological and skill demands of small-sided games in elite junior and senior rugby league players. Sixteen elite senior rugby league players ([mean ± SE] age, 23.6 ± 0.5 years) and 16 elite junior rugby league players ([mean ± SE] age, 17.3 ± 0.3 years) participated in this study. On day 1, 2 teams played an 8-minute small-sided game on a small field (10-m width × 40-m length), whereas the remaining 2 teams played the small-sided game on a larger sized field (40-m width × 70-m length). On day 2, the groups were crossed over. Movement was recorded by a global positioning system unit sampling at 5 Hz. Games were filmed to count the number of possessions and the number and quality of disposals. The games played on a larger field resulted in a greater (p < 0.05) total distance covered, and distances covered in moderate, high, and very-high velocity movement intensities. Senior players covered more distance at moderate, high, and very-high intensities, and less distance at low and very-low intensities during small-sided games than junior players. Although increasing field size had no significant influence (p > 0.05) over the duration of recovery periods for junior players, larger field size significantly reduced (p < 0.05) the amount of short-, moderate-, and long-duration recovery periods in senior players. No significant between-group differences (p > 0.05) were detected for games played on a small or large field for the number or quality of skill involvements. These results suggest that increases in field size serve to increase the physiological demands of small-sided games but have minimal influence over the volume or quality of skill executions in elite rugby league players.

Enhancement of the Feature Extraction Capability in Global Damage Detection Using Wavelet Theory

NASA Technical Reports Server (NTRS)

Saleeb, Atef F.; Ponnaluru, Gopi Krishna

2006-01-01

The main objective of this study is to assess the specific capabilities of the defect energy parameter technique for global damage detection developed by Saleeb and coworkers. The feature extraction is the most important capability in any damage-detection technique. Features are any parameters extracted from the processed measurement data in order to enhance damage detection. The damage feature extraction capability was studied extensively by analyzing various simulation results. The practical significance in structural health monitoring is that the detection at early stages of small-size defects is always desirable. The amount of changes in the structure's response due to these small defects was determined to show the needed level of accuracy in the experimental methods. The arrangement of fine/extensive sensor network to measure required data for the detection is an "unlimited" ability, but there is a difficulty to place extensive number of sensors on a structure. Therefore, an investigation was conducted using the measurements of coarse sensor network. The white and the pink noises, which cover most of the frequency ranges that are typically encountered in the many measuring devices used (e.g., accelerometers, strain gauges, etc.) are added to the displacements to investigate the effect of noisy measurements in the detection technique. The noisy displacements and the noisy damage parameter values are used to study the signal feature reconstruction using wavelets. The enhancement of the feature extraction capability was successfully achieved by the wavelet theory.

Structural Damage Detection Using Virtual Passive Controllers

NASA Technical Reports Server (NTRS)

Lew, Jiann-Shiun; Juang, Jer-Nan

2001-01-01

This paper presents novel approaches for structural damage detection which uses the virtual passive controllers attached to structures, where passive controllers are energy dissipative devices and thus guarantee the closed-loop stability. The use of the identified parameters of various closed-loop systems can solve the problem that reliable identified parameters, such as natural frequencies of the open-loop system may not provide enough information for damage detection. Only a small number of sensors are required for the proposed approaches. The identified natural frequencies, which are generally much less sensitive to noise and more reliable than the identified natural frequencies, are used for damage detection. Two damage detection techniques are presented. One technique is based on the structures with direct output feedback controllers while the other technique uses the second-order dynamic feedback controllers. A least-squares technique, which is based on the sensitivity of natural frequencies to damage variables, is used for accurately identifying the damage variables.

Cerebral Microbleeds: A Field Guide to their Detection and Interpretation

PubMed Central

Greenberg, Steven M.; Vernooij, Meike W.; Cordonnier, Charlotte; Viswanathan, Anand; Salman, Rustam Al-Shahi; Warach, Steven; Launer, Lenore J.; Van Buchem, Mark A.; Breteler, Monique M.B.

2012-01-01

Summary Cerebral microbleeds (CMB) are increasingly recognized neuroimaging findings, occurring with cerebrovascular disease, dementia, and normal aging. Recent years have seen substantial progress, particularly in developing newer MRI methodologies for CMB detection and applying them to population-based elderly samples. This review focuses on these recent developments and their impact on two major questions: how CMB are detected, and how they should be interpreted. There is now ample evidence that prevalence and number of detected CMB varies with MRI characteristics such as pulse sequence, sequence parameters, spatial resolution, magnetic field strength, and post-processing, underlining the importance of MRI technique in interpreting studies. Recent investigations using sensitive techniques find the prevalence of CMB detected in community-dwelling elderly to be surprisingly high. We propose procedural guidelines for identifying CMB and suggest possible future approaches for elucidating the role of these common lesions as markers for, and potential contributors to, small vessel brain disease. PMID:19161908

Characterization of image heterogeneity using 2D Minkowski functionals increases the sensitivity of detection of a targeted MRI contrast agent.

PubMed

Canuto, Holly C; McLachlan, Charles; Kettunen, Mikko I; Velic, Marko; Krishnan, Anant S; Neves, Andre' A; de Backer, Maaike; Hu, D-E; Hobson, Michael P; Brindle, Kevin M

2009-05-01

A targeted Gd(3+)-based contrast agent has been developed that detects tumor cell death by binding to the phosphatidylserine (PS) exposed on the plasma membrane of dying cells. Although this agent has been used to detect tumor cell death in vivo, the differences in signal intensity between treated and untreated tumors was relatively small. As cell death is often spatially heterogeneous within tumors, we investigated whether an image analysis technique that parameterizes heterogeneity could be used to increase the sensitivity of detection of this targeted contrast agent. Two-dimensional (2D) Minkowski functionals (MFs) provided an automated and reliable method for parameterization of image heterogeneity, which does not require prior assumptions about the number of regions or features in the image, and were shown to increase the sensitivity of detection of the contrast agent as compared to simple signal intensity analysis. (c) 2009 Wiley-Liss, Inc.

Cortical areas involved in Arabic number reading.

PubMed

Roux, F-E; Lubrano, V; Lauwers-Cances, V; Giussani, C; Démonet, J-F

2008-01-15

Distinct functional pathways for processing words and numbers have been hypothesized from the observation of dissociated impairments of these categories in brain-damaged patients. We aimed to identify the cortical areas involved in Arabic number reading process in patients operated on for various brain lesions. Direct cortical electrostimulation was prospectively used in 60 brain mappings. We used object naming and two reading tasks: alphabetic script (sentences and number words) and Arabic number reading. Cortical areas involved in Arabic number reading were identified according to location, type of interference, and distinctness from areas associated with other language tasks. Arabic number reading was sustained by small cortical areas, often extremely well localized (<1 cm(2)). Over 259 language sites detected, 43 (17%) were exclusively involved in Arabic number reading (no sentence or word number reading interference detected in these sites). Specific Arabic number reading interferences were mainly found in three regions: the Broca area (Brodmann area 45), the anterior part of the dominant supramarginal gyrus (Brodmann area 40; p < 0.0001), and the temporal-basal area (Brodmann area 37; p < 0.05). Diverse types of interferences were observed (reading arrest, phonemic or semantic paraphasia). Error patterns were fairly similar across temporal, parietal, and frontal stimulation sites, except for phonemic paraphasias, which were found only in supramarginal gyrus. Our findings strongly support the fact that the acquisition through education of specific symbolic entities, such as Arabic numbers, could result in the segregation and the specialization of anatomically distinct brain areas.

Detecting Small Amounts of Gene Flow from Phylogenies of Alleles

PubMed Central

Slatkin, M.

1989-01-01

The method of coalescents is used to find the probability that none of the ancestors of alleles sampled from a population are immigrants. If that is the case for samples from two or more populations, then there would be concordance between the phylogenies of those alleles and the geographic locations from which they are drawn. This type of concordance has been found in several studies of mitochondrial DNA from natural populations. It is shown that if the number of sequences sampled from each population is reasonably large (10 or more), then this type of concordance suggests that the average number of individuals migrating between populations is likely to be relatively small (Nm < 1) but the possibility of occasional migrants cannot be excluded. The method is applied to the data of E. Bermingham and J. C. Avise on mtDNA from the bowfin, Amia calva. PMID:2714639

Radiation sensitivity of foodborne pathogens in meat byproducts with different packaging

NASA Astrophysics Data System (ADS)

Yong, Hae In; Kim, Hyun-Joo; Nam, Ki Chang; Kwon, Joong Ho; Jo, Cheorun

2015-10-01

The aim of this study was to determine radiation sensitivity of Escherichia coli O157:H7 and Listeria monocytogenes in edible meat byproducts. Seven beef byproducts (heart, liver, lung, lumen, omasum, large intestine, and small intestine) and four pork byproducts (heart, large intestine, liver, and small intestine) were used. Electron beam irradiation significantly reduced the numbers of pathogenic microorganisms in meat byproducts and no viable cells were detected in both aerobically- and vacuum-packaged samples irradiated at 4 kGy. Meat byproducts packed under vacuum had higher D10 value than the ones packed aerobically. No significant difference was observed between the D10 values of E. coli O157:H7 and L. monocytogenes inoculated in either aerobically or vacuum packaged samples. These results suggest that low-dose electron beam irradiation can significantly decrease microbial numbers and reduce the risk of meat byproduct contamination by the foodborne pathogens.

Unique insights into the intestinal absorption, transit, and subsequent biodistribution of polymer-derived microspheres

PubMed Central

Reineke, Joshua J.; Cho, Daniel Y.; Dingle, Yu-Ting; Morello, A. Peter; Jacob, Jules; Thanos, Christopher G.; Mathiowitz, Edith

2013-01-01

Polymeric microspheres (MSs) have received attention for their potential to improve the delivery of drugs with poor oral bioavailability. Although MSs can be absorbed into the absorptive epithelium of the small intestine, little is known about the physiologic mechanisms that are responsible for their cellular trafficking. In these experiments, nonbiodegradable polystyrene MSs (diameter range: 500 nm to 5 µm) were delivered locally to the jejunum or ileum or by oral administration to young male rats. Following administration, MSs were taken up rapidly (≤5 min) by the small intestine and were detected by transmission electron microscopy and confocal laser scanning microscopy. Gel permeation chromatography confirmed that polymer was present in all tissue samples, including the brain. These results confirm that MSs (diameter range: 500 nm to 5 µm) were absorbed by the small intestine and distributed throughout the rat. After delivering MSs to the jejunum or ileum, high concentrations of polystyrene were detected in the liver, kidneys, and lungs. The pharmacologic inhibitors chlorpromazine, phorbol 12-myristate 13-acetate, and cytochalasin D caused a reduction in the total number of MSs absorbed in the jejunum and ileum, demonstrating that nonphagocytic processes (including endocytosis) direct the uptake of MSs in the small intestine. These results challenge the convention that phagocytic cells such as the microfold cells solely facilitate MS absorption in the small intestine. PMID:23922388

Detection of Intermediate-Period Transiting Planets with a Network of Small Telescopes: transitsearch.org

NASA Astrophysics Data System (ADS)

Seagroves, Scott; Harker, Justin; Laughlin, Gregory; Lacy, Justin; Castellano, Tim

2003-12-01

We describe a project (transitsearch.org) currently attempting to discover transiting intermediate-period planets orbiting bright parent stars, and we simulate that project's performance. The discovery of such a transit would be an important astronomical advance, bridging the critical gap in understanding between HD 209458b and Jupiter. However, the task is made difficult by intrinsically low transit probabilities and small transit duty cycles. This project's efficient and economical strategy is to photometrically monitor stars that are known (from radial velocity surveys) to bear planets, using a network of widely spaced observers with small telescopes. These observers, each individually capable of precision (1%) differential photometry, monitor candidates during the time windows in which the radial velocity solution predicts a transit if the orbital inclination is close to 90°. We use Monte Carlo techniques to simulate the performance of this network, performing simulations with different configurations of observers in order to optimize coordination of an actual campaign. Our results indicate that transitsearch.org can reliably rule out or detect planetary transits within the current catalog of known planet-bearing stars. A distributed network of skilled amateur astronomers and small college observatories is a cost-effective method for discovering the small number of transiting planets with periods in the range 10 days

Sample size and the detection of a hump-shaped relationship between biomass and species richness in Mediterranean wetlands

USGS Publications Warehouse

Espinar, J.L.

2006-01-01

Questions: What is the observed relationship between biomass and species richness across both spatial and temporal scales in communities of submerged annual macrophytes? Does the number of plots sampled affect detection of hump-shaped pattern? Location: Don??ana National Park, southwestern Spain. Methods: A total of 102 plots were sampled during four hydrological cycles. In each hydrological cycle, the plots were distributed randomly along an environmental flooding gradient in three contrasted microhabitats located in the transition zone just below the upper marsh. In each plot (0.5 m x 0.5 m), plant density and above- and below-ground biomass of submerged vegetation were measured. The hump-shaped model was tested by using a generalized linear model (GLM). A bootstrap procedure was used to test the effect of the number of plots on the ability to detect hump-shaped patterns. Result: The area exhibited low species density with a range of 1 - 9 species and low values of biomass with a range of 0.2 - 87.6 g-DW / 0.25 m2. When data from all years and all microhabitats were combined, the relationships between biomass and species richness showed a hump-shaped pattern. The number of plots was large enough to allow detection of the hump-shaped pattern across microhabitats but it was too small to confirm the hump-shaped pattern within each individual microhabitat. Conclusion: This study provides evidence of hump-shaped patterns across microhabitats when GLM analysis is used. In communities of submerged annual macrophytes in Mediterranean wetlands, the highest species density occurs in intermediate values of biomass. The bootstrap procedure indicates that the number of plots affects the detection of hump-shaped patterns. ?? IAVS; Opulus Press.

Reduction of false-positives in a CAD scheme for automated detection of architectural distortion in digital mammography

NASA Astrophysics Data System (ADS)

de Oliveira, Helder C. R.; Mencattini, Arianna; Casti, Paola; Martinelli, Eugenio; di Natale, Corrado; Catani, Juliana H.; de Barros, Nestor; Melo, Carlos F. E.; Gonzaga, Adilson; Vieira, Marcelo A. C.

2018-02-01

This paper proposes a method to reduce the number of false-positives (FP) in a computer-aided detection (CAD) scheme for automated detection of architectural distortion (AD) in digital mammography. AD is a subtle contraction of breast parenchyma that may represent an early sign of breast cancer. Due to its subtlety and variability, AD is more difficult to detect compared to microcalcifications and masses, and is commonly found in retrospective evaluations of false-negative mammograms. Several computer-based systems have been proposed for automated detection of AD in breast images. The usual approach is automatically detect possible sites of AD in a mammographic image (segmentation step) and then use a classifier to eliminate the false-positives and identify the suspicious regions (classification step). This paper focus on the optimization of the segmentation step to reduce the number of FPs that is used as input to the classifier. The proposal is to use statistical measurements to score the segmented regions and then apply a threshold to select a small quantity of regions that should be submitted to the classification step, improving the detection performance of a CAD scheme. We evaluated 12 image features to score and select suspicious regions of 74 clinical Full-Field Digital Mammography (FFDM). All images in this dataset contained at least one region with AD previously marked by an expert radiologist. The results showed that the proposed method can reduce the false positives of the segmentation step of the CAD scheme from 43.4 false positives (FP) per image to 34.5 FP per image, without increasing the number of false negatives.

Quantum-state anomaly detection for arbitrary errors using a machine-learning technique

NASA Astrophysics Data System (ADS)

Hara, Satoshi; Ono, Takafumi; Okamoto, Ryo; Washio, Takashi; Takeuchi, Shigeki

2016-10-01

The accurate detection of small deviations in given density matrice is important for quantum information processing, which is a difficult task because of the intrinsic fluctuation in density matrices reconstructed using a limited number of experiments. We previously proposed a method for decoherence error detection using a machine-learning technique [S. Hara, T. Ono, R. Okamoto, T. Washio, and S. Takeuchi, Phys. Rev. A 89, 022104 (2014), 10.1103/PhysRevA.89.022104]. However, the previous method is not valid when the errors are just changes in phase. Here, we propose a method that is valid for arbitrary errors in density matrices. The performance of the proposed method is verified using both numerical simulation data and real experimental data.

Phase II: Automated System for Aneuploidy Detection in Sperm Final Report CRADA No. TC-1554-98

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

Wyrobek, W. J.; Dunlay, R. T.

This was a collaborative effort between the University of California, Lawrence Livermore National Laboratory (LLNL) and Cellomics, Inc. (formerly BioDx and Biological Detection, Inc.) to develop an automated system for detecting human sperm aneuploidy. Aneuploidy (an abnormal number of chromosomes) is one of the major categories of chromosomally abnormal sperm, which results in chromosomally defective pregnancies and babies. An automated system would be used for testing the effects of toxic agents and for other research and clinical applications. This collaborated effort was funded by a National Institutes of Environmental Health Services, Phase II, Small Business Innovation Research Program (SBIR) grantmore » to Cellornics (Contract No. N44-ES-82004).« less

Most probable number methodology for quantifying dilute concentrations and fluxes of Escherichia coli O157:H7 in surface waters.

PubMed

Jenkins, M B; Endale, D M; Fisher, D S; Gay, P A

2009-02-01

To better understand the transport and enumeration of dilute densities of Escherichia coli O157:H7 in agricultural watersheds, we developed a culture-based, five tube-multiple dilution most probable number (MPN) method. The MPN method combined a filtration technique for large volumes of surface water with standard selective media, biochemical and immunological tests, and a TaqMan confirmation step. This method determined E. coli O157:H7 concentrations as low as 0.1 MPN per litre, with a 95% confidence level of 0.01-0.7 MPN per litre. Escherichia coli O157:H7 densities ranged from not detectable to 9 MPN per litre for pond inflow, from not detectable to 0.9 MPN per litre for pond outflow and from not detectable to 8.3 MPN per litre for within pond. The MPN methodology was extended to mass flux determinations. Fluxes of E. coli O157:H7 ranged from <27 to >10(4) MPN per hour. This culture-based method can detect small numbers of viable/culturable E. coli O157:H7 in surface waters of watersheds containing animal agriculture and wildlife. This MPN method will improve our understanding of the transport and fate of E. coli O157:H7 in agricultural watersheds, and can be the basis of collections of environmental E. coli O157:H7.

A unified large/small-scale dynamo in helical turbulence

NASA Astrophysics Data System (ADS)

Bhat, Pallavi; Subramanian, Kandaswamy; Brandenburg, Axel

2016-09-01

We use high resolution direct numerical simulations (DNS) to show that helical turbulence can generate significant large-scale fields even in the presence of strong small-scale dynamo action. During the kinematic stage, the unified large/small-scale dynamo grows fields with a shape-invariant eigenfunction, with most power peaked at small scales or large k, as in Subramanian & Brandenburg. Nevertheless, the large-scale field can be clearly detected as an excess power at small k in the negatively polarized component of the energy spectrum for a forcing with positively polarized waves. Its strength overline{B}, relative to the total rms field Brms, decreases with increasing magnetic Reynolds number, ReM. However, as the Lorentz force becomes important, the field generated by the unified dynamo orders itself by saturating on successively larger scales. The magnetic integral scale for the positively polarized waves, characterizing the small-scale field, increases significantly from the kinematic stage to saturation. This implies that the small-scale field becomes as coherent as possible for a given forcing scale, which averts the ReM-dependent quenching of overline{B}/B_rms. These results are obtained for 10243 DNS with magnetic Prandtl numbers of PrM = 0.1 and 10. For PrM = 0.1, overline{B}/B_rms grows from about 0.04 to about 0.4 at saturation, aided in the final stages by helicity dissipation. For PrM = 10, overline{B}/B_rms grows from much less than 0.01 to values of the order the 0.2. Our results confirm that there is a unified large/small-scale dynamo in helical turbulence.

Ammocoetes of Pacific lamprey are not susceptible to common fish rhabdoviruses of the U.S. Pacific Northwest

USGS Publications Warehouse

Kurath, Gael; Jolley, C J.; Thompson, Tarin M.; Thompson, D.; Whitesel, A.T.; Gutenberger, S.; Winton, James R.

2013-01-01

Pacific Lampreys Entosphenus tridentatus have experienced severe population declines in recent years and efforts to develop captive rearing programs are under consideration. However, there is limited knowledge of their life history, ecology, and potential to harbor or transmit pathogens that may cause infectious disease. As a measure of the possible risks associated with introducing wild lampreys into existing fish culture facilities, larval lampreys (ammocoetes) were tested for susceptibility to infection and mortality caused by experimental exposures to the fish rhabdovirus pathogens: infectious hematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV). Two IHNV isolates, representing the U and M genogroups, and one VHSV isolate from the IVa genotype were each delivered to groups of ammocoetes by immersion at moderate and high viral doses, and by intraperitoneal injection. Ammocoetes were then held in triplicate tanks with no substrate or sediment. During 41 d of observation postchallenge there was low or no mortality in all groups, and no virus was detected in the small number of fish that died. Ammocoetes sampled for incidence of infection at 6 and 12 d after immersion challenges also had no detectable virus, and no virus was detected in surviving fish from any group. A small number of ammocoetes sampled 6 d after the injection challenge had detectable virus, but at levels below the original quantity of virus injected. Overall there was no evidence of infection, replication, or persistence of any of the viruses in any of the treatment groups. Our results suggest that Pacific Lampreys are highly unlikely to serve as hosts that maintain or transmit these viruses.

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

PubMed Central

Najmanovich, Rafael

2013-01-01

IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder. PMID:24555058

[Automated detection of estrus and mastitis in dairy cows].

PubMed

de Mol, R M

2001-02-15

The development and test of detection models for oestrus and mastitis in dairy cows is described in a PhD thesis that was defended in Wageningen on June 5, 2000. These models were based on sensors for milk yield, milk temperature, electrical conductivity of milk, and cow activity and concentrate intake, and on combined processing of the sensor data. The models alert farmers to cows that need attention, because of possible oestrus or mastitis. A first detection model for cows, milked twice a day, was based on time series models for the sensor variables. A time series model describes the dependence between successive observations. The parameters of the time series models were fitted on-line for each cow after each milking by means of a Kalman filter, a mathematical method to estimate the state of a system on-line. The Kalman filter gives the best estimate of the current state of a system based on all preceding observations. This model was tested for 2 years on two experimental farms, and under field conditions on four farms over several years. A second detection model, for cow milked in an automatic milking system (AMS), was based on a generalization of the first model. Two data sets (one small, one large) were used for testing. The results for oestrus detection were good for both models. The results for mastitis detection were varying (in some cases good, in other cases moderate). Fuzzy logic was used to classify mastitis and oestrus alerts with both detection models, to reduce the number of false positive alerts. Fuzzy logic makes approximate reasoning possible, where statements can be partly true or false. Input for the fuzzy logic model were alerts from the detection models and additional information. The number of false positive alerts decreased considerably, while the number of detected cases remained at the same level. These models make automated detection possible in practice.

Model observer for assessing digital breast tomosynthesis for multi-lesion detection in the presence of anatomical noise

NASA Astrophysics Data System (ADS)

Wen, Gezheng; Markey, Mia K.; Miner Haygood, Tamara; Park, Subok

2018-02-01

Model observers are widely used in task-based assessments of medical image quality. The presence of multiple abnormalities in a single set of images, such as in multifocal multicentric breast cancer (MFMC), has an immense clinical impact on treatment planning and survival outcomes. Detecting multiple breast tumors is challenging as MFMC is relatively uncommon, and human observers do not know the number or locations of tumors a priori. Digital breast tomosynthesis (DBT), in which an x-ray beam sweeps over a limited angular range across the breast, has the potential to improve the detection of multiple tumors. However, prior studies of DBT image quality all focus on unifocal breast cancers. In this study, we extended our 2D multi-lesion (ML) channelized Hotelling observer (CHO) into a 3D ML-CHO that detects multiple lesions from volumetric imaging data. Then we employed the 3D ML-CHO to identify optimal DBT acquisition geometries for detection of MFMC. Digital breast phantoms with multiple embedded synthetic lesions were scanned by simulated DBT scanners of different geometries (wide/narrow angular span, different number of projections per scan) to simulate MFMC cases. With new implementations of 3D partial least squares (PLS) and modified Laguerre-Gauss (LG) channels, the 3D ML-CHO made detection decisions based upon the overall information from individual DBT slices and their correlations. Our evaluation results show that: (1) the 3D ML-CHO could achieve good detection performance with a small number of channels, and 3D PLS channels on average outperform the counterpart LG channels; (2) incorporating locally varying anatomical backgrounds and their correlations as in the 3D ML-CHO is essential for multi-lesion detection; (3) the most effective DBT geometry for detection of MFMC may vary when the task of clinical interest changes, and a given DBT geometry may not yield images that are equally informative for detecting MF, MC, and unifocal cancers.

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA

PubMed Central

Cohen, K. Bretonnel; Verspoor, Karin; Johnson, Helen L.; Roeder, Chris; Ogren, Philip V.; Baumgartner, William A.; White, Elizabeth; Tipney, Hannah; Hunter, Lawrence

2013-01-01

We approached the problems of event detection, argument identification, and negation and speculation detection in the BioNLP’09 information extraction challenge through concept recognition and analysis. Our methodology involved using the OpenDMAP semantic parser with manually written rules. The original OpenDMAP system was updated for this challenge with a broad ontology defined for the events of interest, new linguistic patterns for those events, and specialized coordination handling. We achieved state-of-the-art precision for two of the three tasks, scoring the highest of 24 teams at precision of 71.81 on Task 1 and the highest of 6 teams at precision of 70.97 on Task 2. We provide a detailed analysis of the training data and show that a number of trigger words were ambiguous as to event type, even when their arguments are constrained by semantic class. The data is also shown to have a number of missing annotations. Analysis of a sampling of the comparatively small number of false positives returned by our system shows that major causes of this type of error were failing to recognize second themes in two-theme events, failing to recognize events when they were the arguments to other events, failure to recognize nontheme arguments, and sentence segmentation errors. We show that specifically handling coordination had a small but important impact on the overall performance of the system. The OpenDMAP system and the rule set are available at http://bionlp.sourceforge.net. PMID:25937701

A framework for optimizing micro-CT in dual-modality micro-CT/XFCT small-animal imaging system

NASA Astrophysics Data System (ADS)

Vedantham, Srinivasan; Shrestha, Suman; Karellas, Andrew; Cho, Sang Hyun

2017-09-01

Dual-modality Computed Tomography (CT)/X-ray Fluorescence Computed Tomography (XFCT) can be a valuable tool for imaging and quantifying the organ and tissue distribution of small concentrations of high atomic number materials in small-animal system. In this work, the framework for optimizing the micro-CT imaging system component of the dual-modality system is described, either when the micro-CT images are concurrently acquired with XFCT and using the x-ray spectral conditions for XFCT, or when the micro-CT images are acquired sequentially and independently of XFCT. This framework utilizes the cascaded systems analysis for task-specific determination of the detectability index using numerical observer models at a given radiation dose, where the radiation dose is determined using Monte Carlo simulations.

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

Ensembles of novelty detection classifiers for structural health monitoring using guided waves

NASA Astrophysics Data System (ADS)

Dib, Gerges; Karpenko, Oleksii; Koricho, Ermias; Khomenko, Anton; Haq, Mahmoodul; Udpa, Lalita

2018-01-01

Guided wave structural health monitoring uses sparse sensor networks embedded in sophisticated structures for defect detection and characterization. The biggest challenge of those sensor networks is developing robust techniques for reliable damage detection under changing environmental and operating conditions (EOC). To address this challenge, we develop a novelty classifier for damage detection based on one class support vector machines. We identify appropriate features for damage detection and introduce a feature aggregation method which quadratically increases the number of available training observations. We adopt a two-level voting scheme by using an ensemble of classifiers and predictions. Each classifier is trained on a different segment of the guided wave signal, and each classifier makes an ensemble of predictions based on a single observation. Using this approach, the classifier can be trained using a small number of baseline signals. We study the performance using Monte-Carlo simulations of an analytical model and data from impact damage experiments on a glass fiber composite plate. We also demonstrate the classifier performance using two types of baseline signals: fixed and rolling baseline training set. The former requires prior knowledge of baseline signals from all EOC, while the latter does not and leverages the fact that EOC vary slowly over time and can be modeled as a Gaussian process.

ORCHID - a computer simulation of the reliability of an NDE inspection system

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

Moles, M.D.C.

1987-03-01

CANDU pressurized heavy water reactors contain several hundred horizontally-mounted zirconium alloy pressure tubes. Following a pressure tube failure, a pressure tube inspection system called CIGARette was rapidly designed, manufactured and put in operation. Defects called hydride blisters were found to be the cause of the failure, and were detected using a combination of eddy current and ultrasonic scans. A number of improvements were made to CIGARette during the inspection period. The ORCHID computer program models the operation of the delivery system, eddy current and ultrasonic systems by imitating the on-reactor decision-making procedure. ORCHID predicts that during the early stage ofmore » development, less than one blistered tube in three would be detected, while less than one in two would be detected in the middle development stage. However, ORCHID predicts that during the late development stage, probability of detection will be over 90%, primarily due to the inclusion of axial ultrasonic scans (a procedural modification). Rotational and axial slip could severely reduce probability of detection. Comparison of CIGARette's inspection data with ORCHID's predictions indicate that the latter are compatible with the actual inspection results, through the numbers are small and data uncertain. It should be emphasized that the CIGARette system has been essentially replaced with the much more reliable CIGAR system.« less

Multigrid contact detection method

NASA Astrophysics Data System (ADS)

He, Kejing; Dong, Shoubin; Zhou, Zhaoyao

2007-03-01

Contact detection is a general problem of many physical simulations. This work presents a O(N) multigrid method for general contact detection problems (MGCD). The multigrid idea is integrated with contact detection problems. Both the time complexity and memory consumption of the MGCD are O(N) . Unlike other methods, whose efficiencies are influenced strongly by the object size distribution, the performance of MGCD is insensitive to the object size distribution. We compare the MGCD with the no binary search (NBS) method and the multilevel boxing method in three dimensions for both time complexity and memory consumption. For objects with similar size, the MGCD is as good as the NBS method, both of which outperform the multilevel boxing method regarding memory consumption. For objects with diverse size, the MGCD outperform both the NBS method and the multilevel boxing method. We use the MGCD to solve the contact detection problem for a granular simulation system based on the discrete element method. From this granular simulation, we get the density property of monosize packing and binary packing with size ratio equal to 10. The packing density for monosize particles is 0.636. For binary packing with size ratio equal to 10, when the number of small particles is 300 times as the number of big particles, the maximal packing density 0.824 is achieved.

Automatic Detection of Lung and Liver Lesions in 3-D Positron Emission Tomography Images: A Pilot Study

NASA Astrophysics Data System (ADS)

Lartizien, Carole; Marache-Francisco, Simon; Prost, Rémy

2012-02-01

Positron emission tomography (PET) using fluorine-18 deoxyglucose (18F-FDG) has become an increasingly recommended tool in clinical whole-body oncology imaging for the detection, diagnosis, and follow-up of many cancers. One way to improve the diagnostic utility of PET oncology imaging is to assist physicians facing difficult cases of residual or low-contrast lesions. This study aimed at evaluating different schemes of computer-aided detection (CADe) systems for the guided detection and localization of small and low-contrast lesions in PET. These systems are based on two supervised classifiers, linear discriminant analysis (LDA) and the nonlinear support vector machine (SVM). The image feature sets that serve as input data consisted of the coefficients of an undecimated wavelet transform. An optimization study was conducted to select the best combination of parameters for both the SVM and the LDA. Different false-positive reduction (FPR) methods were evaluated to reduce the number of false-positive detections per image (FPI). This includes the removal of small detected clusters and the combination of the LDA and SVM detection maps. The different CAD schemes were trained and evaluated based on a simulated whole-body PET image database containing 250 abnormal cases with 1230 lesions and 250 normal cases with no lesion. The detection performance was measured on a separate series of 25 testing images with 131 lesions. The combination of the LDA and SVM score maps was shown to produce very encouraging detection performance for both the lung lesions, with 91% sensitivity and 18 FPIs, and the liver lesions, with 94% sensitivity and 10 FPIs. Comparison with human performance indicated that the different CAD schemes significantly outperformed human detection sensitivities, especially regarding the low-contrast lesions.

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

PubMed

Uppal, Karan; Soltow, Quinlyn A; Strobel, Frederick H; Pittard, W Stephen; Gernert, Kim M; Yu, Tianwei; Jones, Dean P

2013-01-16

Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation. xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites. xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.

Molecular Profiles for Lung Cancer Pathogenesis and Detection in U.S. Veterans

DTIC Science & Technology

2013-10-01

All small RNA sequencing and microarray data has been deposited in GEO under the accession number GSE48798. References 1. Hwang HW, Mendell JT (2006...searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send...histologically normal airway epithelium and tumor. We have validated this approach and the data will allow us to identify novel pathways for lung

Diffraction Pattern Analysis as an Optical Inspection Technique

DTIC Science & Technology

1991-08-01

BACKGROUND Diameters of fiber samples have commonly been measured manually with an optical microscope. Marcuse and Presby developed an automatic...by analyzing the back-scattered light when a beam of laser light impinged upon the fiber [2]. Presby and Marcuse extended this back-scattering tech...be im- proved further in order to become a feasible method for detecting a small number of blocked openings in CRT screens. 20 REFERENCES 1. Marcuse

Simulation-based power calculation for designing interrupted time series analyses of health policy interventions.

PubMed

Zhang, Fang; Wagner, Anita K; Ross-Degnan, Dennis

2011-11-01

Interrupted time series is a strong quasi-experimental research design to evaluate the impacts of health policy interventions. Using simulation methods, we estimated the power requirements for interrupted time series studies under various scenarios. Simulations were conducted to estimate the power of segmented autoregressive (AR) error models when autocorrelation ranged from -0.9 to 0.9 and effect size was 0.5, 1.0, and 2.0, investigating balanced and unbalanced numbers of time periods before and after an intervention. Simple scenarios of autoregressive conditional heteroskedasticity (ARCH) models were also explored. For AR models, power increased when sample size or effect size increased, and tended to decrease when autocorrelation increased. Compared with a balanced number of study periods before and after an intervention, designs with unbalanced numbers of periods had less power, although that was not the case for ARCH models. The power to detect effect size 1.0 appeared to be reasonable for many practical applications with a moderate or large number of time points in the study equally divided around the intervention. Investigators should be cautious when the expected effect size is small or the number of time points is small. We recommend conducting various simulations before investigation. Copyright © 2011 Elsevier Inc. All rights reserved.

Estimating wind-turbine-caused bird and bat fatality when zero carcasses are observed.

PubMed

Huso, Manuela M P; Dalthorp, Dan; Dail, David; Madsen, Lisa

2015-07-01

Many wind-power facilities in the United States have established effective monitoring programs to determine turbine-caused fatality rates of birds and bats, but estimating the number of fatalities of rare species poses special difficulties. The loss of even small numbers of individuals may adversely affect fragile populations, but typically, few (if any) carcasses are observed during monitoring. If monitoring design results in only a small proportion of carcasses detected, then finding zero carcasses may give little assurance that the number of actual fatalities is small. Fatality monitoring at wind-power facilities commonly involves conducting experiments to estimate the probability (g) an individual will be observed, accounting for the possibilities that it falls in an unsearched area, is scavenged prior to detection, or remains undetected even when present. When g < 1, the total carcass count (X) underestimates the total number of fatalities (M). Total counts can be 0 when M is small or when M is large and g < 1. Distinguishing these two cases is critical when estimating fatality of a rare species. Observing no individuals during searches may erroneously be interpreted as evidence of absence. We present an approach that uses Bayes' theorem to construct a posterior distribution for M, i.e., P(M \\ X, ĝ), reflecting the observed carcass count and previously estimated g. From this distribution, we calculate two values important to conservation: the probability that M is below a predetermined limit and the upper bound (M*) of the 100(1 - α)% credible interval for M. We investigate the dependence of M* on α, g, and the prior distribution of M, asking what value of g is required to attain a desired M for a given α. We found that when g < -0.15, M* was clearly influenced by the mean and variance of ĝ and the choice of prior distribution for M, but the influence of these factors is minimal when g > -0.45. Further, we develop extensions for temporal replication that can inform prior distributions of M and methods for combining information across several areas or time periods. We apply the method to data collected at a wind-power facility where scheduled searches yielded X = 0 raptor carcasses.

First Detected Arrival of a Quantum Walker on an Infinite Line

NASA Astrophysics Data System (ADS)

Thiel, Felix; Barkai, Eli; Kessler, David A.

2018-01-01

The first detection of a quantum particle on a graph is shown to depend sensitively on the distance ξ between the detector and initial location of the particle, and on the sampling time τ . Here, we use the recently introduced quantum renewal equation to investigate the statistics of first detection on an infinite line, using a tight-binding lattice Hamiltonian with nearest-neighbor hops. Universal features of the first detection probability are uncovered and simple limiting cases are analyzed. These include the large ξ limit, the small τ limit, and the power law decay with the attempt number of the detection probability over which quantum oscillations are superimposed. For large ξ the first detection probability assumes a scaling form and when the sampling time is equal to the inverse of the energy band width nonanalytical behaviors arise, accompanied by a transition in the statistics. The maximum total detection probability is found to occur for τ close to this transition point. When the initial location of the particle is far from the detection node we find that the total detection probability attains a finite value that is distance independent.

Sources of Salmonella on broiler carcasses during transportation and processing: modes of contamination and methods of control.

PubMed

Corry, Janet E L; Allen, V M; Hudson, W R; Breslin, M F; Davies, R H

2002-01-01

The prevalence and types of salmonella in broiler chickens during transportation and during slaughter and dressing were studied. This was part of a comprehensive investigation of salmonellas in two UK poultry companies, which aimed to find the origins and mechanisms of salmonella contamination. Salmonellas were isolated using cultural methods. Serovars of Salmonella detected during rearing were usually also found in a small proportion of birds on the day of slaughter and on the carcasses at various points during processing. There was little evidence of salmonellas spreading to large numbers of carcasses during processing. Many serovars found in the feedmills or hatcheries were also detected in the birds during rearing and/or slaughter. Transport crates were contaminated with salmonellas after washing and disinfection. Prevalence of salmonellas fell in the two companies during this survey. A small number of serovars predominated in the processing plants of each company. These serovars originated from the feed mills. Reasons for transport crate contamination were: (1) inadequate cleaning, resulting in residual faecal soiling; (2) disinfectant concentration and temperature of disinfectant too low; (3) contaminated recycled flume water used to soak the crates. Efforts to control salmonella infection in broilers need to concentrate on crate cleaning and disinfection and hygiene in the feed mills.

Optical imaging of hemoglobin oxygen saturation using a small number of spectral images for endoscopic application.

PubMed

Saito, Takaaki; Yamaguchi, Hiroshi

2015-01-01

Tissue hypoxia is associated with tumor and inflammatory diseases, and detection of hypoxia is potentially useful for their detailed diagnosis. An endoscope system that can optically observe hemoglobin oxygen saturation (StO2) would enable minimally invasive, real-time detection of lesion hypoxia in vivo. Currently, point measurement of tissue StO2 via endoscopy is possible using the commercial fiber-optic oximeter T-Stat, which is based on visible light spectroscopy at many wavelengths. For clinical use, however, imaging of StO2 is desirable to assess the distribution of tissue oxygenation around a lesion. Here, we describe our StO2 imaging technique based on a small number of wavelength ranges in the visible range. By assuming a homogeneous tissue, we demonstrated that tissue StO2 can be obtained independently from the scattering property and blood concentration of tissue using four spectral bands. We developed a prototype endoscope system and used it to observe tissue-simulating phantoms. The StO2 (%) values obtained using our technique agreed with those from the T-Stat within 10%. We also showed that tissue StO2 can be derived using three spectral band if the scattering property is fixed at preliminarily measured values.

Automatic rock detection for in situ spectroscopy applications on Mars

NASA Astrophysics Data System (ADS)

Mahapatra, Pooja; Foing, Bernard H.

A novel algorithm for rock detection has been developed for effectively utilising Mars rovers, and enabling autonomous selection of target rocks that require close-contact spectroscopic measurements. The algorithm demarcates small rocks in terrain images as seen by cameras on a Mars rover during traverse. This information may be used by the rover for selection of geologically relevant sample rocks, and (in conjunction with a rangefinder) to pick up target samples using a robotic arm for automatic in situ determination of rock composition and mineralogy using, for example, a Raman spectrometer. Determining rock samples within the region that are of specific interest without physically approaching them significantly reduces time, power and risk. Input images in colour are converted to greyscale for intensity analysis. Bilateral filtering is used for texture removal while preserving rock boundaries. Unsharp masking is used for contrast enhance-ment. Sharp contrasts in intensities are detected using Canny edge detection, with thresholds that are calculated from the image obtained after contrast-limited adaptive histogram equalisation of the unsharp masked image. Scale-space representations are then generated by convolving this image with a Gaussian kernel. A scale-invariant blob detector (Laplacian of the Gaussian, LoG) detects blobs independently of their sizes, and therefore requires a multi-scale approach with automatic scale se-lection. The scale-space blob detector consists of convolution of the Canny edge-detected image with a scale-normalised LoG at several scales, and finding the maxima of squared LoG response in scale-space. After the extraction of local intensity extrema, the intensity profiles along rays going out of the local extremum are investigated. An ellipse is fitted to the region determined by significant changes in the intensity profiles. The fitted ellipses are overlaid on the original Mars terrain image for a visual estimation of the rock detection accuracy, and the number of ellipses are counted. Since geometry and illumination have the least effect on small rocks, the proposed algorithm is effective in detecting small rocks (or bigger rocks at larger distances from the camera) that consist of a small fraction of image pixels. Acknowledgements: The first author would like to express her gratitude to the European Space Agency (ESA/ESTEC) and the International Lunar Exploration Working Group (ILEWG) for their support of this work.

Detection of Cheating by Decimation Algorithm

NASA Astrophysics Data System (ADS)

Yamanaka, Shogo; Ohzeki, Masayuki; Decelle, Aurélien

2015-02-01

We expand the item response theory to study the case of "cheating students" for a set of exams, trying to detect them by applying a greedy algorithm of inference. This extended model is closely related to the Boltzmann machine learning. In this paper we aim to infer the correct biases and interactions of our model by considering a relatively small number of sets of training data. Nevertheless, the greedy algorithm that we employed in the present study exhibits good performance with a few number of training data. The key point is the sparseness of the interactions in our problem in the context of the Boltzmann machine learning: the existence of cheating students is expected to be very rare (possibly even in real world). We compare a standard approach to infer the sparse interactions in the Boltzmann machine learning to our greedy algorithm and we find the latter to be superior in several aspects.

Mixture models with entropy regularization for community detection in networks

NASA Astrophysics Data System (ADS)

Chang, Zhenhai; Yin, Xianjun; Jia, Caiyan; Wang, Xiaoyang

2018-04-01

Community detection is a key exploratory tool in network analysis and has received much attention in recent years. NMM (Newman's mixture model) is one of the best models for exploring a range of network structures including community structure, bipartite and core-periphery structures, etc. However, NMM needs to know the number of communities in advance. Therefore, in this study, we have proposed an entropy regularized mixture model (called EMM), which is capable of inferring the number of communities and identifying network structure contained in a network, simultaneously. In the model, by minimizing the entropy of mixing coefficients of NMM using EM (expectation-maximization) solution, the small clusters contained little information can be discarded step by step. The empirical study on both synthetic networks and real networks has shown that the proposed model EMM is superior to the state-of-the-art methods.

Moving object detection in top-view aerial videos improved by image stacking

NASA Astrophysics Data System (ADS)

Teutsch, Michael; Krüger, Wolfgang; Beyerer, Jürgen

2017-08-01

Image stacking is a well-known method that is used to improve the quality of images in video data. A set of consecutive images is aligned by applying image registration and warping. In the resulting image stack, each pixel has redundant information about its intensity value. This redundant information can be used to suppress image noise, resharpen blurry images, or even enhance the spatial image resolution as done in super-resolution. Small moving objects in the videos usually get blurred or distorted by image stacking and thus need to be handled explicitly. We use image stacking in an innovative way: image registration is applied to small moving objects only, and image warping blurs the stationary background that surrounds the moving objects. Our video data are coming from a small fixed-wing unmanned aerial vehicle (UAV) that acquires top-view gray-value images of urban scenes. Moving objects are mainly cars but also other vehicles such as motorcycles. The resulting images, after applying our proposed image stacking approach, are used to improve baseline algorithms for vehicle detection and segmentation. We improve precision and recall by up to 0.011, which corresponds to a reduction of the number of false positive and false negative detections by more than 3 per second. Furthermore, we show how our proposed image stacking approach can be implemented efficiently.

Covalently functionalized noble metal nanoparticles for molecular imprinted polymer biosensors: Synthesis, characterization, and SERS detection

NASA Astrophysics Data System (ADS)

Volkert, Anna Allyse

This dissertation evaluates how gold nanoparticle structure and local environment influence resulting sensor function when using these nanomaterials for complex sample analysis. Molecular imprinted polymers (MIPs), a class of plastic antibodies, are engineered and incorporated into these nanosensors thereby facilitating the quantitative detection of a variety of small molecules when Raman spectroscopy and surface enhanced Raman scattering (SERS) are used for detection. First, homogeneous seeded growth gold nanosphere synthesis is evaluated as a function of ionic double layer composition and thickness. Systematically increasing the citrate concentration during synthesis improves nanomaterial shape homogeneity; however, further elevations of citrate concentration increase the number of internal and/or external atomic defects in the nanomaterials which leads to decreasing solution-phase stability. Next, spherical gold nanoparticles are modified with self-assembled monolayer (SAM), modeled using interfacial energy calculations, and experimental characterized using transmission electron microscopy, NMR, extinction spectroscopy, zeta potential, X-ray photoelectron spectroscopy, and flocculation studies to assess the morphology, surface chemistry, optical properties, surface charge, SAM packing density, and nanoparticle stability, respectively. The number of molecules on the nanostructures increases with increasing ionic strength (by decreasing the electrostatic interfacial energy between assembled molecules) which subsequently promotes nanoparticle stability. Third, plastic antibodies that recognize three drugs commonly used to treat migraines are engineered. These methacrylate-based MIPs are synthesized, extracted, characterized, and used to quantitatively and directly detect over-the-counter drugs in complex samples using Raman microscopy. These results along with numerical approximation methods to estimate drug binding site densities and dissociation constants with the MIPs serve as a foundation for understanding how modest recognition selectivity of MIPs coupled with shifts in the vibrational energy modes from the drugs upon hydrogen binding to the polymer backbone promote sensitive and selective drug detection in complex samples. Finally, nanomaterial incorporation into MIPs for applications in SERS-based biosensors is evaluated. Importantly, gold nanorod concentration increases the detectability of the same drugs using MIPs as pre-concentration and recognition elements. This combination of materials, theory, and applications forms a solid foundation which should aid in the design and development of MIP nanobiosensors for specific and sensitive detection of small molecules in complex matrices.

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface.

PubMed

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-06-05

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

PubMed Central

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states. PMID:26046669

Micro-Doppler extraction of a small UAV in a non-line-of-sight urban scenario

NASA Astrophysics Data System (ADS)

Gustavsson, Magnus; Andersson, Åsa; Johansson, Tommy; Jonsson, Rolf; Karlsson, Nils; Nilsson, Stefan

2017-05-01

The appearance of small UAVs on the commercial market poses a real threat to both civilian safety and to military operations. In open terrain a radar can detect and track even small UAVs at long distances. In an urban environment with limited line-of-sight and strong static and non-static background, this capability can be severely reduced. The radar cross section of these UAVs are normally small compared to the background. However, the rotors of the UAVs produce a characteristic micro-Doppler signature that can be exploited for detection and classification. In this paper, we investigate in an experimental set-up whether it is possible in the radar non-line-of-sight to retrieve the micro-Doppler signature of the UAV rotors. This is done by exploring up to three multipath bounces in the measured signal. The measurements were made with a semi-monostatic single receiver-transmitter radar system operating at X-band in a pulsed single frequency mode. The radar response of the UAV, with plastic and metallic rotors, was measured at several positions inside a 4 m wide corridor with metallic walls. In this paper, data from one line-of-sight and two non-line-ofsight positions are presented. Results show that we are able to detect the micro-Doppler of the rotors and to retrieve the number of revolutions per minute, for both rotor types. Free space Finite-Difference Time-Domain calculations have also been performed on a CAD-model of the UAV rotor to determine the optimal choice of polarization and the short-time Fourier transform filter length.

Sensitivity of Noncontrast Computed Tomography for Small Renal Calculi With Endoscopy as the Gold Standard.

PubMed

Bhojani, Naeem; Paonessa, Jessica E; El Tayeb, Marawan M; Williams, James C; Hameed, Tariq A; Lingeman, James E

2018-04-03

To compare the sensitivity of noncontrast computed tomography (CT) with endoscopy for detection of renal calculi. Imaging modalities for detection of nephrolithiasis have centered on abdominal x-ray, ultrasound, and noncontrast CT. Sensitivities of 58%-62% (abdominal x-ray), 45% (ultrasound), and 95%-100% (CT) have been previously reported. However, these results have never been correlated with endoscopic findings. Idiopathic calcium oxalate stone formers with symptomatic calculi requiring ureteroscopy were studied. At the time of surgery, the number and the location of all calculi within the kidney were recorded followed by basket retrieval. Each calculus was measured and sent for micro-CT and infrared spectrophotometry. All CT scans were reviewed by the same genitourinary radiologist who was blinded to the endoscopic findings. The radiologist reported on the number, location, and size of each calculus. Eighteen renal units were studied in 11 patients. Average time from CT scan to ureteroscopy was 28.6 days. The mean number of calculi identified per kidney was 9.2 ± 6.1 for endoscopy and 5.9 ± 4.1 for CT (P <.004). The mean size of total renal calculi (sum of the longest stone diameters) per kidney was 22.4 ± 17.1 mm and 18.2 ± 13.2 mm for endoscopy and CT, respectively (P = .06). CT scan underreports the number of renal calculi, probably missing some small stones and being unable to distinguish those lying in close proximity to one another. However, the total stone burden seen by CT is, on average, accurate when compared with that found on endoscopic examination. Copyright © 2018 Elsevier Inc. All rights reserved.

Preselection of EGFR mutations in non-small-cell lung cancer patients by immunohistochemistry: comparison with DNA-sequencing, EGFR wild-type expression, gene copy number gain and clinicopathological data.

PubMed

Gaber, Rania; Watermann, Iris; Kugler, Christian; Vollmer, Ekkehard; Perner, Sven; Reck, Martin; Goldmann, Torsten

2017-01-01

Targeting epidermal growth factor receptor (EGFR) in patients with non-small-cell lung cancer (NSCLC) having EGFR mutations is associated with an improved overall survival. The aim of this study is to verify, if EGFR mutations detected by immunohistochemistry (IHC) is a convincing way to preselect patients for DNA-sequencing and to figure out, the statistical association between EGFR mutation, wild-type EGFR overexpression, gene copy number gain, which are the main factors inducing EGFR tumorigenic activity and the clinicopathological data. Two hundred sixteen tumor tissue samples of primarily chemotherapeutic naïve NSCLC patients were analyzed for EGFR mutations E746-A750del and L858R and correlated with DNA-sequencing. Two hundred six of which were assessed by IHC, using 6B6 and 43B2 specific antibodies followed by DNA-sequencing of positive cases and 10 already genotyped tumor tissues were also included to investigate debugging accuracy of IHC. In addition, EGFR wild-type overexpression was IHC evaluated and EGFR gene copy number determination was performed by fluorescence in situ hybridization (FISH). Forty-one÷206 (19.9%) cases were positive for mutated EGFR by IHC. Eight of them had EGFR mutations of exons 18-21 by DNA-sequencing. Hit rate of 10 already genotyped NSCLC mutated cases was 90% by IHC. Positive association was found between EGFR mutations determined by IHC and both EGFR overexpression and increased gene copy number (p=0.002 and p<0.001, respectively). Additionally, positive association was detected between EGFR mutations, high tumor grade and clinical stage (p<0.001). IHC staining with mutation specific antibodies was demonstrated as a possible useful screening test to preselect patients for DNA-sequencing.

LSDCat: Detection and cataloguing of emission-line sources in integral-field spectroscopy datacubes

NASA Astrophysics Data System (ADS)

Herenz, Edmund Christian; Wisotzki, Lutz

2017-06-01

We present a robust, efficient, and user-friendly algorithm for detecting faint emission-line sources in large integral-field spectroscopic datacubes together with the public release of the software package Line Source Detection and Cataloguing (LSDCat). LSDCat uses a three-dimensional matched filter approach, combined with thresholding in signal-to-noise, to build a catalogue of individual line detections. In a second pass, the detected lines are grouped into distinct objects, and positions, spatial extents, and fluxes of the detected lines are determined. LSDCat requires only a small number of input parameters, and we provide guidelines for choosing appropriate values. The software is coded in Python and capable of processing very large datacubes in a short time. We verify the implementation with a source insertion and recovery experiment utilising a real datacube taken with the MUSE instrument at the ESO Very Large Telescope. The LSDCat software is available for download at http://muse-vlt.eu/science/tools and via the Astrophysics Source Code Library at http://ascl.net/1612.002

Fluorescence based explosive detection: from mechanisms to sensory materials.

PubMed

Sun, Xiangcheng; Wang, Ying; Lei, Yu

2015-11-21

The detection of explosives is one of the current pressing concerns in global security. In the past few decades, a large number of emissive sensing materials have been developed for the detection of explosives in vapor, solution, and solid states through fluorescence methods. In recent years, great efforts have been devoted to develop new fluorescent materials with various sensing mechanisms for detecting explosives in order to achieve super-sensitivity, ultra-selectivity, as well as fast response time. This review article starts with a brief introduction on various sensing mechanisms for fluorescence based explosive detection, and then summarizes in an exhaustive and systematic way the state-of-the-art of fluorescent materials for explosive detection with a focus on the research in the recent 5 years. A wide range of fluorescent materials, such as conjugated polymers, small fluorophores, supramolecular systems, bio-inspired materials and aggregation induced emission-active materials, and their sensing performance and sensing mechanism are the centerpiece of this review. Finally, conclusions and future outlook are presented and discussed.

Detection of potato beetle damage using remote sensing from small unmanned aircraft systems

NASA Astrophysics Data System (ADS)

Hunt, E. Raymond; Rondon, Silvia I.

2017-04-01

Colorado potato beetle (CPB) adults and larvae devour leaves of potato and other solanaceous crops and weeds, and may quickly develop resistance to pesticides. With early detection of CPB damage, more options are available for precision integrated pest management, which reduces the amount of pesticides applied in a field. Remote sensing with small unmanned aircraft systems (sUAS) has potential for CPB detection because low flight altitudes allow image acquisition at very high spatial resolution. A five-band multispectral sensor and up-looking incident light sensor were mounted on a six-rotor sUAS, which was flown at altitudes of 60 and 30 m in June 2014. Plants went from visibly undamaged to having some damage in just 1 day. Whole-plot normalized difference vegetation index (NDVI) and the number of pixels classified as damaged (0.70≤NDVI≤0.80) were not correlated with visible CPB damage ranked from least to most. Area of CPB damage estimated using object-based image analysis was highly correlated to the visual ranking of damage. Furthermore, plant height calculated using structure-from-motion point clouds was related to CPB damage, but this method required extensive operator intervention for success. Object-based image analysis has potential for early detection based on high spatial resolution sUAS remote sensing.

The complete mitochondrial genome of Rapana venosa (Gastropoda, Muricidae).

PubMed

Sun, Xiujun; Yang, Aiguo

2016-01-01

The complete mitochondrial (mt) genome of the veined rapa whelk, Rapana venosa, was determined using genome walking techniques in this study. The total length of the mt genome sequence of R. venosa was 15,271 bp, which is comparable to the reported Muricidae mitogenomes to date. It contained 13 protein-coding genes, 21 transfer RNA genes, and two ribosomal RNA genes. A bias towards a higher representation of nucleotides A and T (69%) was detected in the mt genome of R. venosa. A small number of non-coding nucleotides (302 bp) was detected, and the largest non-coding region was 74 bp in length.

Counterfactuality of ‘counterfactual’ communication

NASA Astrophysics Data System (ADS)

Vaidman, L.

2015-11-01

The counterfactuality of the recently proposed protocols for direct quantum communication is analyzed. It is argued that the protocols can be counterfactual only for one value of the transmitted bit. The protocols achieve a reduced probability of detection of the particle in the transmission channel by increasing the number of paths in the channel. However, this probability is not lower than the probability of detecting a particle actually passing through such a multi-path channel, which was found to be surprisingly small. The relation between security and counterfactuality of the protocols is discussed. An analysis of counterfactuality of the protocols in the framework of the Bohmian interpretation is performed.

Cost-appropriateness of whole body vs limited bone imaging for suspected focal sports injuries

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

Nagle, C.E.

Bone imaging has been recognized as a useful diagnostic tool in detecting the presence of focal musculoskeletal injury when radiographs are normal. A retrospective review of bone images in a small number of amateur athletes indicates that secondary injuries were commonly detected at sites different from the site of musculoskeletal pain being evaluated for injury. While a larger study will be necessary to confirm the data, this review suggests that it is medically justified and cost-appropriate to perform imaging of the entire skeleton as opposed to imaging limited to the anatomic site of pain and suspected injury.

Incomplete Detection of Nonclassical Phase-Space Distributions

NASA Astrophysics Data System (ADS)

Bohmann, M.; Tiedau, J.; Bartley, T.; Sperling, J.; Silberhorn, C.; Vogel, W.

2018-02-01

We implement the direct sampling of negative phase-space functions via unbalanced homodyne measurement using click-counting detectors. The negativities significantly certify nonclassical light in the high-loss regime using a small number of detectors which cannot resolve individual photons. We apply our method to heralded single-photon states and experimentally demonstrate the most significant certification of nonclassicality for only two detection bins. By contrast, the frequently applied Wigner function fails to directly indicate such quantum characteristics for the quantum efficiencies present in our setup without applying additional reconstruction algorithms. Therefore, we realize a robust and reliable approach to characterize nonclassical light in phase space under realistic conditions.

Why small-scale cannabis growers stay small: five mechanisms that prevent small-scale growers from going large scale.

PubMed

Hammersvik, Eirik; Sandberg, Sveinung; Pedersen, Willy

2012-11-01

Over the past 15-20 years, domestic cultivation of cannabis has been established in a number of European countries. New techniques have made such cultivation easier; however, the bulk of growers remain small-scale. In this study, we explore the factors that prevent small-scale growers from increasing their production. The study is based on 1 year of ethnographic fieldwork and qualitative interviews conducted with 45 Norwegian cannabis growers, 10 of whom were growing on a large-scale and 35 on a small-scale. The study identifies five mechanisms that prevent small-scale indoor growers from going large-scale. First, large-scale operations involve a number of people, large sums of money, a high work-load and a high risk of detection, and thus demand a higher level of organizational skills than for small growing operations. Second, financial assets are needed to start a large 'grow-site'. Housing rent, electricity, equipment and nutrients are expensive. Third, to be able to sell large quantities of cannabis, growers need access to an illegal distribution network and knowledge of how to act according to black market norms and structures. Fourth, large-scale operations require advanced horticultural skills to maximize yield and quality, which demands greater skills and knowledge than does small-scale cultivation. Fifth, small-scale growers are often embedded in the 'cannabis culture', which emphasizes anti-commercialism, anti-violence and ecological and community values. Hence, starting up large-scale production will imply having to renegotiate or abandon these values. Going from small- to large-scale cannabis production is a demanding task-ideologically, technically, economically and personally. The many obstacles that small-scale growers face and the lack of interest and motivation for going large-scale suggest that the risk of a 'slippery slope' from small-scale to large-scale growing is limited. Possible political implications of the findings are discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

A Comparison of the effectiveness of Mammographic Film-Screen and Standard Film-Screen in the Detection of Small Bone Fractures

PubMed Central

Sani, Karim Ghazikhanlou; Jafari, Mahmoodreza; Rostampoor, Nima

2011-01-01

The use of mammography film-screen is limited in general radiography. The purpose of this study was to compare the effectiveness of mammographic film-screen and standard film-screen systems in the detection of small bone fractures. Radiographs were taken from patients' extremities and neck areas using mammography film-screen and standard film-screen (n=57 each). Fourteen other radiographs were taken from other views (predominantly oblique views), making a total number of 128 radiographs. Paired radiographs, taken from the same areas, were compared by two radiologists in terms of image visual sharpness, presence of bony fractures, and soft tissue injuries. The surface dose received by patients in the two systems was also compared. The radiographs taken by mammography film-screen had a statistically better visual sharpness compared to those taken by the standard film-screen system. However, there was no statistically significant difference between the diagnostic accuracy of the two systems. Mammography film-screen was able to detect only one out of 57 lesions, whereas standard film-screen system did not detec any lesion. The surface dose received by patients in mammography film-screen was higher than that in standard film-screen system. The findings of the present study suggest that mammography film-screen may be recommended as a diagnostic tool for the detection of small fractures of tinny parts of body such as fingers, hand or foot. They also suggest that mammography film-screen has no advantage over standard film-screen for radiography of thick body parts such as neck and knee. PMID:23115417

Clinical utility of scintimammography: From the Anger-camera to new dedicated devices

NASA Astrophysics Data System (ADS)

Schillaci, Orazio; Danieli, Roberta; Romano, Pasquale; Cossu, Elsa; Simonetti, Giovanni

2006-12-01

Scintimammography is a functional imaging technique which uses a radiation detection camera to detect radionuclide tracers in the patient's breasts. Tracers are designed to accumulate in tumours more than in healthy tissue: the most used are Tc-99 m sestamibi and Tc-99 m tetrofosmin. Scintimammography is useful in some clinical indications as an adjunct to mammography: it is recommended for those lesions where additional information is required to reach a definitive diagnosis. Patients with dubious mammograms may benefit from this test, as well as women with dense breasts or with implants. Scintimammography is a valuable diagnostic tool also in patients with locally advanced breast cancer for monitoring and predicting response to neoadjuvant chemotherapy. Nevertheless, using an Anger-camera this technique shows a high sensitivity only for cancers >1 cm. Since other modalities are increasingly employed for the early identification of small abnormalities, the issue of detecting small cancers is critical for the future development and clinical utility of breast imaging with radiopharmaceuticals. The use of high-resolution cameras dedicated for breast imaging is the best option to improve the detection of small cancers: they allow higher flexibility in patient positioning, and the availability of mammography-like projections. Moreover, the detector can be placed directly in contact with the breast allowing a mild compression with reduction of the breast's thickness, thus increasing the target-to-background ratio and the sensitivity. These new devices have the potential of increasing the total number of breast scintigraphies performed thereby enhancing the role of nuclear medicine in breast cancer imaging.

[Diagnostics and antimicrobial therapy of severe community-acquired pneumonia].

PubMed

Sinopalnikov, A I; Zaitsev, A A

2015-04-01

In the current paper authors presented the latest information concerning etiology of severe community-acquired pneumonia. Most cases are caused by a relatively small number ofpathogenic bacterial and viral natures. The frequency of detection of various pathogens of severe community-acquired pneumonia may vary greatly depending on the region, season and clinical profile of patients, availability of relevant risk factors. Authors presented clinical characteristics of severe community-acquired pneumonia and comparative evaluation of a number of scales to assess the risk of adverse outcome of the disease. Diagnosis of severe community-acquired pneumonia includes the following: collecting of epidemiological history, identification of pneumonia, detection of sepsis and identification of multiple organ dysfunction syndrome, detection of acute respiratory failure, assessment of comorbidity. Authors gave recommendations concerning evaluation of the clinical manifestations of the disease, the use of instrumental and laboratory methods for diagnosis of severe community-acquired pneumonia. To select the mode of antimicrobial therapy is most important local monitoring antimicrobial resistance of pathogens. The main criteria for the effectiveness of treatment are to reduce body temperature, severe intoxication, respiratory and organ failure.

Propensity score to detect baseline imbalance in cluster randomized trials: the role of the c-statistic.

PubMed

Leyrat, Clémence; Caille, Agnès; Foucher, Yohann; Giraudeau, Bruno

2016-01-22

Despite randomization, baseline imbalance and confounding bias may occur in cluster randomized trials (CRTs). Covariate imbalance may jeopardize the validity of statistical inferences if they occur on prognostic factors. Thus, the diagnosis of a such imbalance is essential to adjust statistical analysis if required. We developed a tool based on the c-statistic of the propensity score (PS) model to detect global baseline covariate imbalance in CRTs and assess the risk of confounding bias. We performed a simulation study to assess the performance of the proposed tool and applied this method to analyze the data from 2 published CRTs. The proposed method had good performance for large sample sizes (n =500 per arm) and when the number of unbalanced covariates was not too small as compared with the total number of baseline covariates (≥40% of unbalanced covariates). We also provide a strategy for pre selection of the covariates needed to be included in the PS model to enhance imbalance detection. The proposed tool could be useful in deciding whether covariate adjustment is required before performing statistical analyses of CRTs.

Estimation of walrus populations on sea ice with infrared imagery and aerial photography

USGS Publications Warehouse

Udevitz, M.S.; Burn, D.M.; Webber, M.A.

2008-01-01

Population sizes of ice-associated pinnipeds have often been estimated with visual or photographic aerial surveys, but these methods require relatively slow speeds and low altitudes, limiting the area they can cover. Recent developments in infrared imagery and its integration with digital photography could allow substantially larger areas to be surveyed and more accurate enumeration of individuals, thereby solving major problems with previous survey methods. We conducted a trial survey in April 2003 to estimate the number of Pacific walruses (Odobenus rosmarus divergens) hauled out on sea ice around St. Lawrence Island, Alaska. The survey used high altitude infrared imagery to detect groups of walruses on strip transects. Low altitude digital photography was used to determine the number of walruses in a sample of detected groups and calibrate the infrared imagery for estimating the total number of walruses. We propose a survey design incorporating this approach with satellite radio telemetry to estimate the proportion of the population in the water and additional low-level flights to estimate the proportion of the hauled-out population in groups too small to be detected in the infrared imagery. We believe that this approach offers the potential for obtaining reliable population estimates for walruses and other ice-associated pinnipeds. ?? 2007 by the Society for Marine Mammalogy.

Matched filter based detection of floating mines in IR spacetime

NASA Astrophysics Data System (ADS)

Borghgraef, Alexander; Lapierre, Fabian; Philips, Wilfried; Acheroy, Marc

2009-09-01

Ship-based automatic detection of small floating objects on an agitated sea surface remains a hard problem. Our main concern is the detection of floating mines, which proved a real threat to shipping in confined waterways during the first Gulf War, but applications include salvaging,search-and-rescue and perimeter or harbour defense. IR video was chosen for its day-and-night imaging capability, and its availability on military vessels. Detection is difficult because a rough sea is seen as a dynamic background of moving objects with size order, shape and temperature similar to those of the floating mine. We do find a determinant characteristic in the target's periodic motion, which differs from that of the propagating surface waves composing the background. The classical detection and tracking approaches give bad results when applied to this problem. While background detection algorithms assume a quasi-static background, the sea surface is actually very dynamic, causing this category of algorithms to fail. Kalman or particle filter algorithms on the other hand, which stress temporal coherence, suffer from tracking loss due to occlusions and the great noise level of the image. We propose an innovative approach. This approach uses the periodicity of the objects movement and thus its temporal coherence. The principle is to consider the video data as a spacetime volume similar to a hyperspectral data cube by replacing the spectral axis with a temporal axis. We can then apply algorithms developed for hyperspectral detection problems to the detection of small floating objects. We treat the detection problem using multilinear algebra, designing a number of finite impulse response filters (FIR) maximizing the target response. The algorithm was applied to test footage of practice mines in the infrared.

Hallmarks in prostate cancer imaging with Ga68-PSMA-11-PET/CT with reference to detection limits and quantitative properties.

PubMed

Sanchez-Crespo, Alejandro; Jussing, Emma; Björklund, Ann-Charlotte; Pokrovskaja Tamm, Katja

2018-04-04

Gallium-68-labeled prostate-specific antigen positron emission tomography/computed tomography imaging (Ga68-PSMA-11-PET/CT) has emerged as a potential gold standard for prostate cancer (PCa) diagnosis. However, the imaging limitations of this technique at the early state of PCa recurrence/metastatic spread are still not well characterized. The aim of this study was to determine the quantitative properties and the fundamental imaging limits of Ga68-PSMA-11-PET/CT in localizing small PCa cell deposits. The human PCa LNCaP cells (PSMA expressing) were grown and collected as single cell suspension or as 3D-spheroids at different cell numbers and incubated with Ga68-PSMA-11. Thereafter, human HCT116 cells (PSMA negative) were added to a total cell number of 2 × 10 5 cells per tube. The tubes were then pelleted and the supernatant aspirated. A whole-body PET/CT scanner with a clinical routine protocol was used for imaging the pellets inside of a cylindrical water phantom with increasing amounts of background activity. The actual activity bound to the cells was also measured in an automatic gamma counter. Imaging detection limits and activity recovery coefficients as a function of LNCaP cell number were obtained. The effect of Ga68-PSMA-11 mass concentration on cell binding was also investigated in samples of LnCaP cells incubated with increasing concentrations of radioligand. A total of 1 × 10 4 LNCaP cells mixed in a pellet of 2 × 10 5 cells were required to reach a 50% detection probability with Ga68-PSMA-11-PET/CT without background. With a background level of 1 kBq/ml, between 4 × 10 5 and 1 × 10 6 cells are required. The radioligand equilibrium dissociation constant was 27.05 nM, indicating high binding affinity. Hence, the specific activity of the radioligand has a profound effect on image quantification. Ga68-PSMA-11-PET detects a small number of LNCaP cells even when they are mixed in a population of non-PSMA expressing cells and in the presence of background. The obtained image detection limits and characteristic quantification properties of Ga68-PSMA-11-PET/CT are essential hallmarks for the individualization of patient management. The use of the standardized uptake value for Ga68-PSMA-11-PET/CT image quantification should be precluded.

Power and money in cluster randomized trials: when is it worth measuring a covariate?

PubMed

Moerbeek, Mirjam

2006-08-15

The power to detect a treatment effect in cluster randomized trials can be increased by increasing the number of clusters. An alternative is to include covariates into the regression model that relates treatment condition to outcome. In this paper, formulae are derived in order to evaluate both strategies on basis of their costs. It is shown that the strategy that uses covariates is more cost-efficient in detecting a treatment effect when the costs to measure these covariates are small and the correlation between the covariates and outcome is sufficiently large. The minimum required correlation depends on the cluster size, and the costs to recruit a cluster and to measure the covariate, relative to the costs to recruit a person. Measuring a covariate that varies at the person level only is recommended when cluster sizes are small and the costs to recruit and measure a cluster are large. Measuring a cluster level covariate is recommended when cluster sizes are large and the costs to recruit and measure a cluster are small. An illustrative example shows the use of the formulae in a practical setting. Copyright 2006 John Wiley & Sons, Ltd.

Probing the Small-scale Structure in Strongly Lensed Systems via Transdimensional Inference

NASA Astrophysics Data System (ADS)

Daylan, Tansu; Cyr-Racine, Francis-Yan; Diaz Rivero, Ana; Dvorkin, Cora; Finkbeiner, Douglas P.

2018-02-01

Strong lensing is a sensitive probe of the small-scale density fluctuations in the Universe. We implement a pipeline to model strongly lensed systems using probabilistic cataloging, which is a transdimensional, hierarchical, and Bayesian framework to sample from a metamodel (union of models with different dimensionality) consistent with observed photon count maps. Probabilistic cataloging allows one to robustly characterize modeling covariances within and across lens models with different numbers of subhalos. Unlike traditional cataloging of subhalos, it does not require model subhalos to improve the goodness of fit above the detection threshold. Instead, it allows the exploitation of all information contained in the photon count maps—for instance, when constraining the subhalo mass function. We further show that, by not including these small subhalos in the lens model, fixed-dimensional inference methods can significantly mismodel the data. Using a simulated Hubble Space Telescope data set, we show that the subhalo mass function can be probed even when many subhalos in the sample catalogs are individually below the detection threshold and would be absent in a traditional catalog. The implemented software, Probabilistic Cataloger (PCAT) is made publicly available at https://github.com/tdaylan/pcat.

Two classes of small antisense RNAs in fungal RNA silencing triggered by non-integrative transgenes

PubMed Central

Nicolás, Francisco E.; Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M.

2003-01-01

Transformation of Mucor circinelloides with self-replicative plasmids containing a wild-type copy of the carotenogenic gene carB causes silencing of the carB function in 3% of transformants. Genomic analyses revealed a relationship between silenced phenotype and number of copies of plasmids. This phenotype results from a reduction of the steady-state levels of carB mRNA, a reduction that is not due to differences in the level of transcription, indicating that silencing is post-transcriptional. Small sense and antisense RNAs have been found to be associated with gene silencing in M.circinelloides. Two size classes of small antisense RNAs, differentially accumulated during the vegetative growth of silenced transformants, have been detected: a long 25-nucleotide RNA and a short 21-nucleotide RNA. Secondary sense and antisense RNAs corresponding to sequences of the endogenous gene downstream of the initial triggering molecule have also been detected, revealing the existence of spreading of RNA targeting in fungi. These findings, together with the self-replicative nature of the triggering molecules, make M.circinelloides a suitable organism for investigating some unresolved questions in RNA silencing. PMID:12881432

Multiplex PCR for diagnosis of Theileria uilenbergi, Theileria luwenshuni, and Theileria ovis in small ruminants.

PubMed

Zhang, Xiao; Liu, Zhijie; Yang, Jifei; Chen, Ze; Guan, Guiquan; Ren, Qiaoyun; Liu, Aihong; Luo, Jianxun; Yin, Hong; Li, Youquan

2014-02-01

Infections with Theileria sp. may cause significant economic losses to the sheep industry. Species identification based on microscopic examination is difficult, and more suitable methods are required for the rapid detection and identification of Theileria sp, in clinical specimens. In this study, a multiplex polymerase chain reaction (mPCR) assay was developed to simultaneously identify three individual Theileria species in small ruminants. Three pairs of specific, sensitive primers were designed on the basis of the 5.8S ribosomal RNA gene (Theileria luwenshuni and Theileria ovis) and the 18S ribosomal RNA gene (Theileria uilenbergi) to generate target products of 303, 884, and 530 bp, respectively. Standard DNA for each of the three species was extracted from blood recovered from infected sheep, and a preliminary study was conducted on 56 sheep to verify the reliability of the system. Optimal PCR conditions, including primer concentration, annealing time, and the number of amplification cycles, were established. The assay sensitivity under these conditions was 10(-3) % parasitemia, and its specificity was 100 %. The results of the study suggest that mPCR represents a simple, efficient test method as a practical alternative for the rapid detection and identification of Theileria species in small ruminants.

Nanoporous Glass Integrated in Volumetric Bar-Chart Chip for Point-of-Care Diagnostics of Non-Small Cell Lung Cancer.

PubMed

Li, Ying; Xuan, Jie; Song, Yujun; Qi, Wenjin; He, Bangshun; Wang, Ping; Qin, Lidong

2016-01-26

Point-of-care (POC) testing has the potential to enable rapid, low-cost, and large-scale screening. POC detection of a multiplexed biomarker panel can facilitate the early diagnosis of non-small cell lung cancer (NSCLC) and, thus, may allow for more timely surgical intervention for life-saving treatment. Herein, we report the nanoporous glass (NPG) integrated volumetric bar-chart chip (V-Chip) for POC detection of the three NSCLC biomarkers CEA, CYFRA 21-1, and SCCA, by the naked eye. The 3D nanostructures in the NPG membrane efficiently increase the number of binding sites for antibodies and decrease the diffusion distance between antibody and antigen, enabling the low detection limit and rapid analysis time of the NPG-V-Chip. We utilized the NPG-V-Chip to test the NSCLC biomarker panel and found that the limit of detection can reach 50 pg/mL (10-fold improvement over the original V-Chip), and the total assay time can be decreased from 4 to 0.5 h. We then detected CEA in 21 serum samples from patients with common cancers, and the on-chip results showed good correlation with the clinical results. We further assayed 10 lung cancer samples using the device and confirmed the results obtained using conventional ELISA methods. In summary, the NPG-V-Chip platform has the ability of multiplex, low detection limit, low cost, lack of need for accessory equipment, and rapid analysis time, which may render the V-Chip a useful platform for quantitative POC detection in resource-limited settings and personalized diagnostics.

Identifying High-Risk Patients without Labeled Training Data: Anomaly Detection Methodologies to Predict Adverse Outcomes

PubMed Central

Syed, Zeeshan; Saeed, Mohammed; Rubinfeld, Ilan

2010-01-01

For many clinical conditions, only a small number of patients experience adverse outcomes. Developing risk stratification algorithms for these conditions typically requires collecting large volumes of data to capture enough positive and negative for training. This process is slow, expensive, and may not be appropriate for new phenomena. In this paper, we explore different anomaly detection approaches to identify high-risk patients as cases that lie in sparse regions of the feature space. We study three broad categories of anomaly detection methods: classification-based, nearest neighbor-based, and clustering-based techniques. When evaluated on data from the National Surgical Quality Improvement Program (NSQIP), these methods were able to successfully identify patients at an elevated risk of mortality and rare morbidities following inpatient surgical procedures. PMID:21347083

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.

Providing structural modules with self-integrity monitoring

NASA Astrophysics Data System (ADS)

Walton, W. B.; Ibanez, P.; Yessaie, G.

1988-08-01

With the advent of complex space structures (i.e., U.S. Space Station), the need for methods for remotely detecting structural damage will become greater. Some of these structures will have hundreds of individual structural elements (i.e., strut members). Should some of them become damaged, it could be virtually impossible to detect it using visual or similar inspection techniques. The damage of only a few individual members may or may not be a serious problem. However, should a significant number of the members be damaged, a significant problem could be created. The implementation of an appropriate remote damage detection scheme would greatly reduce the likelihood of a serious problem related to structural damage ever occurring. This report presents the results of the research conducted on remote structural damage detection approaches and the related mathematical algorithms. The research was conducted for the Small Business Innovation and Research (SBIR) Phase 2 National Aeronautics and Space Administration (NASA) Contract NAS7-961.

Magnetic resonance force microscopy of paramagnetic electron spins at millikelvin temperatures.

PubMed

Vinante, A; Wijts, G; Usenko, O; Schinkelshoek, L; Oosterkamp, T H

2011-12-06

Magnetic resonance force microscopy (MRFM) is a powerful technique to detect a small number of spins that relies on force detection by an ultrasoft magnetically tipped cantilever and selective magnetic resonance manipulation of the spins. MRFM would greatly benefit from ultralow temperature operation, because of lower thermomechanical noise and increased thermal spin polarization. Here we demonstrate MRFM operation at temperatures as low as 30 mK, thanks to a recently developed superconducting quantum interference device (SQUID)-based cantilever detection technique, which avoids cantilever overheating. In our experiment, we detect dangling bond paramagnetic centres on a silicon surface down to millikelvin temperatures. Fluctuations of such defects are supposedly linked to 1/f magnetic noise and decoherence in SQUIDs, as well as in several superconducting and single spin qubits. We find evidence that spin diffusion has a key role in the low-temperature spin dynamics.

Designed Strategies for Fluorescence-Based Biosensors for the Detection of Mycotoxins

PubMed Central

Sharma, Atul; Khan, Reem; Catanante, Gaelle; Sherazi, Tauqir A.; Bhand, Sunil; Hayat, Akhtar; Marty, Jean Louis

2018-01-01

Small molecule toxins such as mycotoxins with low molecular weight are the most widely studied biological toxins. These biological toxins are responsible for food poisoning and have the potential to be used as biological warfare agents at the toxic dose. Due to the poisonous nature of mycotoxins, effective analysis techniques for quantifying their toxicity are indispensable. In this context, biosensors have been emerged as a powerful tool to monitors toxins at extremely low level. Recently, biosensors based on fluorescence detection have attained special interest with the incorporation of nanomaterials. This review paper will focus on the development of fluorescence-based biosensors for mycotoxin detection, with particular emphasis on their design as well as properties such as sensitivity and specificity. A number of these fluorescent biosensors have shown promising results in food samples for the detection of mycotoxins, suggesting their future potential for food applications. PMID:29751687

Analysis of a Smartphone-Based Architecture with Multiple Mobility Sensors for Fall Detection

PubMed Central

Santoyo-Ramón, Jose Antonio; Cano-García, Jose Manuel

2016-01-01

During the last years, many research efforts have been devoted to the definition of Fall Detection Systems (FDSs) that benefit from the inherent computing, communication and sensing capabilities of smartphones. However, employing a smartphone as the unique sensor in a FDS application entails several disadvantages as long as an accurate characterization of the patient’s mobility may force to transport this personal device on an unnatural position. This paper presents a smartphone-based architecture for the automatic detection of falls. The system incorporates a set of small sensing motes that can communicate with the smartphone to help in the fall detection decision. The deployed architecture is systematically evaluated in a testbed with experimental users in order to determine the number and positions of the sensors that optimize the effectiveness of the FDS, as well as to assess the most convenient role of the smartphone in the architecture. PMID:27930736

Efficient surveillance for healthcare-associated infections spreading between hospitals

PubMed Central

Ciccolini, Mariano; Donker, Tjibbe; Grundmann, Hajo; Bonten, Marc J. M.; Woolhouse, Mark E. J.

2014-01-01

Early detection of new or novel variants of nosocomial pathogens is a public health priority. We show that, for healthcare-associated infections that spread between hospitals as a result of patient movements, it is possible to design an effective surveillance system based on a relatively small number of sentinel hospitals. We apply recently developed mathematical models to patient admission data from the national healthcare systems of England and The Netherlands. Relatively short detection times are achieved once 10–20% hospitals are recruited as sentinels and only modest reductions are seen as more hospitals are recruited thereafter. Using a heuristic optimization approach to sentinel selection, the same expected time to detection can be achieved by recruiting approximately half as many hospitals. Our study provides a robust evidence base to underpin the design of an efficient sentinel hospital surveillance system for novel nosocomial pathogens, delivering early detection times for reduced expenditure and effort. PMID:24469791

Designed Strategies for Fluorescence-Based Biosensors for the Detection of Mycotoxins.

PubMed

Sharma, Atul; Khan, Reem; Catanante, Gaelle; Sherazi, Tauqir A; Bhand, Sunil; Hayat, Akhtar; Marty, Jean Louis

2018-05-11

Small molecule toxins such as mycotoxins with low molecular weight are the most widely studied biological toxins. These biological toxins are responsible for food poisoning and have the potential to be used as biological warfare agents at the toxic dose. Due to the poisonous nature of mycotoxins, effective analysis techniques for quantifying their toxicity are indispensable. In this context, biosensors have been emerged as a powerful tool to monitors toxins at extremely low level. Recently, biosensors based on fluorescence detection have attained special interest with the incorporation of nanomaterials. This review paper will focus on the development of fluorescence-based biosensors for mycotoxin detection, with particular emphasis on their design as well as properties such as sensitivity and specificity. A number of these fluorescent biosensors have shown promising results in food samples for the detection of mycotoxins, suggesting their future potential for food applications.

Providing structural modules with self-integrity monitoring

NASA Technical Reports Server (NTRS)

Walton, W. B.; Ibanez, P.; Yessaie, G.

1988-01-01

With the advent of complex space structures (i.e., U.S. Space Station), the need for methods for remotely detecting structural damage will become greater. Some of these structures will have hundreds of individual structural elements (i.e., strut members). Should some of them become damaged, it could be virtually impossible to detect it using visual or similar inspection techniques. The damage of only a few individual members may or may not be a serious problem. However, should a significant number of the members be damaged, a significant problem could be created. The implementation of an appropriate remote damage detection scheme would greatly reduce the likelihood of a serious problem related to structural damage ever occurring. This report presents the results of the research conducted on remote structural damage detection approaches and the related mathematical algorithms. The research was conducted for the Small Business Innovation and Research (SBIR) Phase 2 National Aeronautics and Space Administration (NASA) Contract NAS7-961.

Analysis of a Smartphone-Based Architecture with Multiple Mobility Sensors for Fall Detection.

PubMed

Casilari, Eduardo; Santoyo-Ramón, Jose Antonio; Cano-García, Jose Manuel

2016-01-01

During the last years, many research efforts have been devoted to the definition of Fall Detection Systems (FDSs) that benefit from the inherent computing, communication and sensing capabilities of smartphones. However, employing a smartphone as the unique sensor in a FDS application entails several disadvantages as long as an accurate characterization of the patient's mobility may force to transport this personal device on an unnatural position. This paper presents a smartphone-based architecture for the automatic detection of falls. The system incorporates a set of small sensing motes that can communicate with the smartphone to help in the fall detection decision. The deployed architecture is systematically evaluated in a testbed with experimental users in order to determine the number and positions of the sensors that optimize the effectiveness of the FDS, as well as to assess the most convenient role of the smartphone in the architecture.

Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies.

PubMed

Bianchi, Diana W; Chudova, Darya; Sehnert, Amy J; Bhatt, Sucheta; Murray, Kathryn; Prosen, Tracy L; Garber, Judy E; Wilkins-Haug, Louise; Vora, Neeta L; Warsof, Stephen; Goldberg, James; Ziainia, Tina; Halks-Miller, Meredith

2015-07-14

Understanding the relationship between aneuploidy detection on noninvasive prenatal testing (NIPT) and occult maternal malignancies may explain results that are discordant with the fetal karyotype and improve maternal clinical care. To evaluate massively parallel sequencing data for patterns of copy-number variations that might prospectively identify occult maternal malignancies. Case series identified from 125,426 samples submitted between February 15, 2012, and September 30, 2014, from asymptomatic pregnant women who underwent plasma cell-free DNA sequencing for clinical prenatal aneuploidy screening. Analyses were conducted in a clinical laboratory that performs DNA sequencing. Among the clinical samples, abnormal results were detected in 3757 (3%); these were reported to the ordering physician with recommendations for further evaluation. NIPT for fetal aneuploidy screening (chromosomes 13, 18, 21, X, and Y). Detailed genome-wide bioinformatics analysis was performed on available sequencing data from 8 of 10 women with known cancers. Genome-wide copy-number changes in the original NIPT samples and in subsequent serial samples from individual patients when available are reported. Copy-number changes detected in NIPT sequencing data in the known cancer cases were compared with the types of aneuploidies detected in the overall cohort. From a cohort of 125,426 NIPT results, 3757 (3%) were positive for 1 or more aneuploidies involving chromosomes 13, 18, 21, X, or Y. From this set of 3757 samples, 10 cases of maternal cancer were identified. Detailed clinical and sequencing data were obtained in 8. Maternal cancers most frequently occurred with the rare NIPT finding of more than 1 aneuploidy detected (7 known cancers among 39 cases of multiple aneuploidies by NIPT, 18% [95% CI, 7.5%-33.5%]). All 8 cases that underwent further bioinformatics analysis showed unique patterns of nonspecific copy-number gains and losses across multiple chromosomes. In 1 case, blood was sampled after completion of treatment for colorectal cancer and the abnormal pattern was no longer evident. In this preliminary study, a small number of cases of occult malignancy were subsequently diagnosed among pregnant women whose noninvasive prenatal testing results showed discordance with the fetal karyotype. The clinical importance of these findings will require further research.

Highly efficient circulating tumor cell isolation from whole blood and label-free enumeration using polymer-based microfluidics with an integrated conductivity sensor.

PubMed

Adams, André A; Okagbare, Paul I; Feng, Juan; Hupert, Matuesz L; Patterson, Don; Göttert, Jost; McCarley, Robin L; Nikitopoulos, Dimitris; Murphy, Michael C; Soper, Steven A

2008-07-09

A novel microfluidic device that can selectively and specifically isolate exceedingly small numbers of circulating tumor cells (CTCs) through a monoclonal antibody (mAB) mediated process by sampling large input volumes (>/=1 mL) of whole blood directly in short time periods (<37 min) was demonstrated. The CTCs were concentrated into small volumes (190 nL), and the number of cells captured was read without labeling using an integrated conductivity sensor following release from the capture surface. The microfluidic device contained a series (51) of high-aspect ratio microchannels (35 mum width x 150 mum depth) that were replicated in poly(methyl methacrylate), PMMA, from a metal mold master. The microchannel walls were covalently decorated with mABs directed against breast cancer cells overexpressing the epithelial cell adhesion molecule (EpCAM). This microfluidic device could accept inputs of whole blood, and its CTC capture efficiency was made highly quantitative (>97%) by designing capture channels with the appropriate widths and heights. The isolated CTCs were readily released from the mAB capturing surface using trypsin. The released CTCs were then enumerated on-device using a novel, label-free solution conductivity route capable of detecting single tumor cells traveling through the detection electrodes. The conductivity readout provided near 100% detection efficiency and exquisite specificity for CTCs due to scaling factors and the nonoptimal electrical properties of potential interferences (erythrocytes or leukocytes). The simplicity in manufacturing the device and its ease of operation make it attractive for clinical applications requiring one-time use operation.

Highly Efficient Circulating Tumor Cell Isolation from Whole Blood and Label-Free Enumeration Using Polymer-Based Microfluidics with an Integrated Conductivity Sensor

PubMed Central

Adams, André A.; Okagbare, Paul I.; Feng, Juan; Hupert, Matuesz L.; Patterson, Don; Göttert, Jost; McCarley, Robin L.; Nikitopoulos, Dimitris; Murphy, Michael C.; Soper, Steven A.

2008-01-01

A novel microfluidic device that can selectively and specifically isolate exceedingly small numbers of circulating tumor cells (CTCs) through a monoclonal antibody (mAB) mediated process by sampling large input volumes (≥1 mL) of whole blood directly in short time periods (<37 min) was demonstrated. The CTCs were concentrated into small volumes (190 nL), and the number of cells captured was read without labeling using an integrated conductivity sensor following release from the capture surface. The microfluidic device contained a series (51) of high-aspect ratio microchannels (35 μm width × 150 μm depth) that were replicated in poly(methyl methacrylate), PMMA, from a metal mold master. The microchannel walls were covalently decorated with mABs directed against breast cancer cells overexpressing the epithelial cell adhesion molecule (EpCAM). This microfluidic device could accept inputs of whole blood, and its CTC capture efficiency was made highly quantitative (>97%) by designing capture channels with the appropriate widths and heights. The isolated CTCs were readily released from the mAB capturing surface using trypsin. The released CTCs were then enumerated on-device using a novel, label-free solution conductivity route capable of detecting single tumor cells traveling through the detection electrodes. The conductivity readout provided near 100% detection efficiency and exquisite specificity for CTCs due to scaling factors and the nonoptimal electrical properties of potential interferences (erythrocytes or leukocytes). The simplicity in manufacturing the device and its ease of operation make it attractive for clinical applications requiring one-time use operation. PMID:18557614

High-Power Vehicle-Towed TEM for Small Ordnance Detection at Depth

DTIC Science & Technology

2014-02-01

Operations,100A Donner Dr,Oak Ridge,TN, 37830 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10...T. Jeffrey Gamey Battelle, 100A Donner Dr., Oak Ridge, TN 37830 (865) 599-0820 gameytj@battelle.org Geophysicist – Principle Investigator...William Doll Battelle, 100A Donner Dr., Oak Ridge, TN 37830 (865) 599-6165 dollw@battelle.org Geophysicist – modeling assessment, data collection, data

Squamous Cell Cancer of The Lung with Synchronous Renal Cell Carcinoma

PubMed Central

Ateş, İhsan; Yazıcı, Ozan; Ateş, Hale; Yazılıtaş, Doğan; Özcan, Ayşe Naz; Ağaçkıran, Yetkin; Zengin, Nurullah

2016-01-01

Coexistence of two or more primary cancers is a relatively rare case. Not with standing that the coexistence of multiple primary cancers is often discussed in the literature, there is a small number of publications concerning the coexistence of squamous cell lung carcinoma and renal cancer. In this case report, detection of both squamous cell lung carcinoma and primary renal cancer in one male patient is going to be discussed. PMID:29404140

Design of a New Ultracompact Resonant Plasmonic Multi-Analyte Label-Free Biosensing Platform

PubMed Central

De Palo, Maripina; Ciminelli, Caterina

2017-01-01

In this paper, we report on the design of a bio-multisensing platform for the selective label-free detection of protein biomarkers, carried out through a 3D numerical algorithm. The platform includes a number of biosensors, each of them is based on a plasmonic nanocavity, consisting of a periodic metal structure to be deposited on a silicon oxide substrate. Light is strongly confined in a region with extremely small size (=1.57 μm2), to enhance the light-matter interaction. A surface sensitivity Ss = 1.8 nm/nm has been calculated together with a detection limit of 128 pg/mm2. Such performance, together with the extremely small footprint, allow the integration of several devices on a single chip to realize extremely compact lab-on-chip microsystems. In addition, each sensing element of the platform has a good chemical stability that is guaranteed by the selection of gold for its fabrication. PMID:28783075

Method to improve cancerous lesion detection sensitivity in a dedicated dual-head scintimammography system

DOEpatents

Kieper, Douglas Arthur [Seattle, WA; Majewski, Stanislaw [Morgantown, WV; Welch, Benjamin L [Hampton, VA

2012-07-03

An improved method for enhancing the contrast between background and lesion areas of a breast undergoing dual-head scintimammographic examination comprising: 1) acquiring a pair of digital images from a pair of small FOV or mini gamma cameras compressing the breast under examination from opposing sides; 2) inverting one of the pair of images to align or co-register with the other of the images to obtain co-registered pixel values; 3) normalizing the pair of images pixel-by-pixel by dividing pixel values from each of the two acquired images and the co-registered image by the average count per pixel in the entire breast area of the corresponding detector; and 4) multiplying the number of counts in each pixel by the value obtained in step 3 to produce a normalization enhanced two dimensional contrast map. This enhanced (increased contrast) contrast map enhances the visibility of minor local increases (uptakes) of activity over the background and therefore improves lesion detection sensitivity, especially of small lesions.

Method to improve cancerous lesion detection sensitivity in a dedicated dual-head scintimammography system

DOEpatents

Kieper, Douglas Arthur [Newport News, VA; Majewski, Stanislaw [Yorktown, VA; Welch, Benjamin L [Hampton, VA

2008-10-28

An improved method for enhancing the contrast between background and lesion areas of a breast undergoing dual-head scintimammographic examination comprising: 1) acquiring a pair of digital images from a pair of small FOV or mini gamma cameras compressing the breast under examination from opposing sides; 2) inverting one of the pair of images to align or co-register with the other of the images to obtain co-registered pixel values; 3) normalizing the pair of images pixel-by-pixel by dividing pixel values from each of the two acquired images and the co-registered image by the average count per pixel in the entire breast area of the corresponding detector; and 4) multiplying the number of counts in each pixel by the value obtained in step 3 to produce a normalization enhanced two dimensional contrast map. This enhanced (increased contrast) contrast map enhances the visibility of minor local increases (uptakes) of activity over the background and therefore improves lesion detection sensitivity, especially of small lesions.

The physical and microbiological quality of chicken meat in the different type of enterprise poultry slaughterhouse: a case study in Karanganyar District

NASA Astrophysics Data System (ADS)

Hertanto, B. S.; Nurmalasari, C. D. A.; Nuhriawangsa, A. M. P.; Cahyadi, M.; Kartikasari, L. R.

2018-01-01

The aim of this study was to determine the physical and microbiological quality of chicken meat produced by the different type of enterprise slaughterhouse in Karanganyar District. The number of 20 poultry slaughterhouses was determined by convenience sampling method. The samples of chicken meat were randomly collected from medium enterprise poultry slaughterhouses (n=12) and small enterprise poultry slaughterhouses (n=8). A survey was carried out among poultry slaughterhouses in Karanganyar District. All the samples were subjected to physical quality consisted of pH test, texture, and color, while microbiological quality consisted of total plate count, microbial detection of Escherichia coli and Salmonella. The data were analyzed using descriptive quantitative analysis. The study showed that chicken meat in 6 small enterprise slaughterhouses and 11 medium enterprise slaughterhouses had normal pH of 5.81 - 6.3. Color and texture of chicken meats had relatively normal in both small and medium enterprise slaughterhouses. The total plate count of chicken meat showed in both small and medium enterprise slaughterhouses was <1x106 CFU/gr. The test of bacterial contamination showed that 3 of small and medium enterprise slaughterhouses were positively contaminated by Escherichia coli of >1x101 CFU/gr, and Salmonella was detected in 1 medium enterprise slaughterhouse. The overall results of the study suggest that the potential risk of chicken meat contamination depends on the processing of chicken meat in poultry slaughterhouses.

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.

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.

Small Near-Earth Asteroids in the Palomar Transient Factory Survey: A Real-Time Streak-detection System

NASA Astrophysics Data System (ADS)

Waszczak, Adam; Prince, Thomas A.; Laher, Russ; Masci, Frank; Bue, Brian; Rebbapragada, Umaa; Barlow, Tom; Surace, Jason; Helou, George; Kulkarni, Shrinivas

2017-03-01

Near-Earth asteroids (NEAs) in the 1-100 meter size range are estimated to be ˜1,000 times more numerous than the ˜15,000 currently cataloged NEAs, most of which are in the 0.5-10 kilometer size range. Impacts from 10-100 meter size NEAs are not statistically life-threatening, but may cause significant regional damage, while 1-10 meter size NEAs with low velocities relative to Earth are compelling targets for space missions. We describe the implementation and initial results of a real-time NEA-discovery system specialized for the detection of small, high angular rate (visually streaked) NEAs in Palomar Transient Factory (PTF) images. PTF is a 1.2-m aperture, 7.3 deg2 field of view (FOV) optical survey designed primarily for the discovery of extragalactic transients (e.g., supernovae) in 60-second exposures reaching ˜20.5 visual magnitude. Our real-time NEA discovery pipeline uses a machine-learned classifier to filter a large number of false-positive streak detections, permitting a human scanner to efficiently and remotely identify real asteroid streaks during the night. Upon recognition of a streaked NEA detection (typically within an hour of the discovery exposure), the scanner triggers follow-up with the same telescope and posts the observations to the Minor Planet Center for worldwide confirmation. We describe our 11 initial confirmed discoveries, all small NEAs that passed 0.3-15 lunar distances from Earth. Lastly, we derive useful scaling laws for comparing streaked-NEA-detection capabilities of different surveys as a function of their hardware and survey-pattern characteristics. This work most directly informs estimates of the streak-detection capabilities of the Zwicky Transient Facility (ZTF, planned to succeed PTF in 2017), which will apply PTF’s current resolution and sensitivity over a 47-deg2 FOV.

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

Simultaneous multispectral framing infrared camera using an embedded diffractive optical lenslet array

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele

2011-06-01

Recent advances in micro-optical element fabrication using gray scale technology have opened up the opportunity to create simultaneous multi-spectral imaging with fine structure diffractive lenses. This paper will discuss an approach that uses diffractive optical lenses configured in an array (lenslet array) and placed in close proximity to the focal plane array which enables a small compact simultaneous multispectral imaging camera [1]. The lenslet array is designed so that all lenslets have a common focal length with each lenslet tuned for a different wavelength. The number of simultaneous spectral images is determined by the number of individually configured lenslets in the array. The number of spectral images can be increased by a factor of 2 when using it with a dual-band focal plane array (MWIR/LWIR) by exploiting multiple diffraction orders. In addition, modulation of the focal length of the lenslet array with piezoelectric actuation will enable spectral bin fill-in allowing additional spectral coverage while giving up simultaneity. Different lenslet array spectral imaging concept designs are presented in this paper along with a unique concept for prefiltering the radiation focused on the detector. This approach to spectral imaging has applications in the detection of chemical agents in both aerosolized form and as a liquid on a surface. It also can be applied to the detection of weaponized biological agent and IED detection in various forms from manufacturing to deployment and post detection during forensic analysis.

Planetary Nebulae in the UWISH2 survey

NASA Astrophysics Data System (ADS)

Gledhill, T. M.; Froebrich, D.; Campbell-White, J.; Jones, A. M.

2018-06-01

Near-infrared imaging in the 1 - 0 S(1) emission line of molecular hydrogen is able to detect planetary nebulae (PNe) that are hidden from optical emission line surveys. We present images of 307 objects from the UWISH2 survey of the northern Galactic Plane, and with the aid of mid-infrared colour diagnostics draw up a list of 291 PN candidates. The majority, 183, are new detections and 85 per cent of these are not present in H α surveys of the region. We find that more than half (54 per cent) of objects have a bipolar morphology and that some objects previously considered as elliptical or point-source in H α imaging, appear bipolar in UWISH2 images. By considering a small subset of objects for which physical radii are available from the H α surface brightness-radius relation, we find evidence that the H2 surface brightness remains roughly constant over a factor 20 range of radii from 0.03 to 0.6 pc, encompassing most of the visible lifetime of a PN. This leads to the H α surface brightness becoming comparable to that of H2 at large radius (>0.5 pc). By combining the number of UWISH2 PNe without H α detection with an estimate of the PN detection efficiency in H2 emission, we estimate that PN numbers from H α surveys may underestimate the true PN number by a factor between 1.5 and 2.5 within the UWISH2 survey area.

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.

Compact and cost effective instrument for detecting drug precursors in different environments based on fluorescence polarization

NASA Astrophysics Data System (ADS)

Antolín-Urbaneja, J. C.; Eguizabal, I.; Briz, N.; Dominguez, A.; Estensoro, P.; Secchi, A.; Varriale, A.; Di Giovanni, S.; D'Auria, S.

2013-05-01

Several techniques for detecting chemical drug precursors have been developed in the last decade. Most of them are able to identify molecules at very low concentration under lab conditions. Other commercial devices are able to detect a fixed number and type of target substances based on a single detection technique providing an absence of flexibility with respect to target compounds. The construction of compact and easy to use detection systems providing screening for a large number of compounds being able to discriminate them with low false alarm rate and high probability of detection is still an open concern. Under CUSTOM project, funded by the European Commission within the FP7, a stand-alone portable sensing device based on multiple techniques is being developed. One of these techniques is based on the LED induced fluorescence polarization to detect Ephedrine and Benzyl Methyl Keton (BMK) as a first approach. This technique is highly selective with respect to the target compounds due to the generation of properly engineered fluorescent proteins which are able to bind the target analytes, as it happens in an "immune-type reaction". This paper deals with the advances in the design, construction and validation of the LED induced fluorescence sensor to detect BMK analytes. This sensor includes an analysis module based on high performance LED and PMT detector, a fluidic system to dose suitable quantities of reagents and some printed circuit boards, all of them fixed in a small structure (167mm × 193mm × 228mm) with the capability of working as a stand-alone application.

Evaluation of Strategies to Control a Potential Outbreak of Foot-and-Mouth Disease in Sweden.

PubMed

Dórea, Fernanda C; Nöremark, Maria; Widgren, Stefan; Frössling, Jenny; Boklund, Anette; Halasa, Tariq; Ståhl, Karl

2017-01-01

To minimize the potential consequences of an introduction of foot-and-mouth disease (FMD) in Europe, European Union (EU) member states are required to present a contingency plan. This study used a simulation model to study potential outbreak scenarios in Sweden and evaluate the best control strategies. The model was informed by the Swedish livestock structure using herd information from cattle, pig, and small ruminant holdings in the country. The contact structure was based on animal movement data and studies investigating the movements between farms of veterinarians, service trucks, and other farm visitors. All scenarios of outbreak control included depopulation of detected herds, 3 km protection and 10 km surveillance zones, movement tracing, and 3 days national standstill. The effect of availability of surveillance resources, i.e., number of field veterinarians per day, and timeliness of enforcement of interventions, was assessed. With the estimated currently available resources, an FMD outbreak in Sweden is expected to be controlled (i.e., last infected herd detected) within 3 weeks of detection in any evaluated scenario. The density of farms in the area where the epidemic started would have little impact on the time to control the outbreak, but spread in high density areas would require more surveillance resources, compared to areas of lower farm density. The use of vaccination did not result in a reduction in the expected number of infected herds. Preemptive depopulation was able to reduce the number of infected herds in extreme scenarios designed to test a combination of worst-case conditions of virus introduction and spread, but at the cost of doubling the number of herds culled. This likely resulted from a combination of the small outbreaks predicted by the spread model, and the high efficacy of the basic control measures evaluated, under the conditions of the Swedish livestock industry, and considering the assumed control resources available. The results indicate that the duration and extent of FMD outbreaks could be kept limited in Sweden using the EU standard control strategy and a 3 days national standstill.

Evaluation of Strategies to Control a Potential Outbreak of Foot-and-Mouth Disease in Sweden

PubMed Central

Dórea, Fernanda C.; Nöremark, Maria; Widgren, Stefan; Frössling, Jenny; Boklund, Anette; Halasa, Tariq; Ståhl, Karl

2017-01-01

To minimize the potential consequences of an introduction of foot-and-mouth disease (FMD) in Europe, European Union (EU) member states are required to present a contingency plan. This study used a simulation model to study potential outbreak scenarios in Sweden and evaluate the best control strategies. The model was informed by the Swedish livestock structure using herd information from cattle, pig, and small ruminant holdings in the country. The contact structure was based on animal movement data and studies investigating the movements between farms of veterinarians, service trucks, and other farm visitors. All scenarios of outbreak control included depopulation of detected herds, 3 km protection and 10 km surveillance zones, movement tracing, and 3 days national standstill. The effect of availability of surveillance resources, i.e., number of field veterinarians per day, and timeliness of enforcement of interventions, was assessed. With the estimated currently available resources, an FMD outbreak in Sweden is expected to be controlled (i.e., last infected herd detected) within 3 weeks of detection in any evaluated scenario. The density of farms in the area where the epidemic started would have little impact on the time to control the outbreak, but spread in high density areas would require more surveillance resources, compared to areas of lower farm density. The use of vaccination did not result in a reduction in the expected number of infected herds. Preemptive depopulation was able to reduce the number of infected herds in extreme scenarios designed to test a combination of worst-case conditions of virus introduction and spread, but at the cost of doubling the number of herds culled. This likely resulted from a combination of the small outbreaks predicted by the spread model, and the high efficacy of the basic control measures evaluated, under the conditions of the Swedish livestock industry, and considering the assumed control resources available. The results indicate that the duration and extent of FMD outbreaks could be kept limited in Sweden using the EU standard control strategy and a 3 days national standstill. PMID:28791298

Quantitation of mRNAs for α 1-acid glycoprotein and for serum albumin in livers of normal, stressed, fasted, and refed rats. [ 125I or 131I radioimmunoassay for protein products of specific mRNA activity

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

Harris, Linda Jean

1978-01-01

A new procedure for determining the relative levels of a specific mRNA species was developed and applied to mRNA for rat serum albumin (RSA) and α 1-AGP) in rat liver. The method is a radioimmunoassay ( 125In or 131I) for the completed protein, but which also detects antigenic determinants in nascent polypeptide chains on plysomes synthesizing the specific protein. Results show that 24 hs after stressing the rat by turpentine injection the total number of polysomes per mg DNA has increased by 20 to 25%; however, the number of RSA synthesizing polysomes per mg DNA has decreased slightly. In ratsmore » fasted for 6 days, the number of RSA synthesizing polysomes per mg polysomal RNA is only slightly below normal, but the total number of RSA synthesizing polysomes per mg DNA has decreased by 40%. Again, it is seen that RSA mRNA levels do not decrease as sharply as the rate of RSA synthesis. Twelve hours after refeeding the rats, the number of RSA synthesizing polysomes begins to increase, reaching a peak two to three times normal levels 24 to 48 hours after commencement of refeeding. During the first 24 hs after turpentine injection, there is a linear increase in the number of α 1-AGP synthesizing polysomes. The increase is smaller during the next 24 hs and there is a small decrease between 48 and 72 hs. The serum concentrations of α 1-AGP following turpentine treatment reflect these changes in polysome levels. It was not possible to compare the number of α 1-AGP synthesizing polysomes in livers of normal, fasted, and refed rats because the levels detected were only slightly higher than those seen in rat and rat kidney polysome controls. This background activity must be eliminated before the technique can be applied to quantitating mRNA for proteins synthesized in very small quantities. This technique offers several advantages over other procedures commonly used to quantitate mRNA. (ERB)« less

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

PubMed

Leung, Kaston; Klaus, Anders; Lin, Bill K; Laks, Emma; Biele, Justina; Lai, Daniel; Bashashati, Ali; Huang, Yi-Fei; Aniba, Radhouane; Moksa, Michelle; Steif, Adi; Mes-Masson, Anne-Marie; Hirst, Martin; Shah, Sohrab P; Aparicio, Samuel; Hansen, Carl L

2016-07-26

The genomes of large numbers of single cells must be sequenced to further understanding of the biological significance of genomic heterogeneity in complex systems. Whole genome amplification (WGA) of single cells is generally the first step in such studies, but is prone to nonuniformity that can compromise genomic measurement accuracy. Despite recent advances, robust performance in high-throughput single-cell WGA remains elusive. Here, we introduce droplet multiple displacement amplification (MDA), a method that uses commercially available liquid dispensing to perform high-throughput single-cell MDA in nanoliter volumes. The performance of droplet MDA is characterized using a large dataset of 129 normal diploid cells, and is shown to exceed previously reported single-cell WGA methods in amplification uniformity, genome coverage, and/or robustness. We achieve up to 80% coverage of a single-cell genome at 5× sequencing depth, and demonstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA product to achieve a median allelic dropout of 15%, and using whole genome sequencing to achieve false and true positive rates of 9.66 × 10(-6) and 68.8%, respectively, in a G1-phase cell. We further show that droplet MDA allows for the detection of copy number variants (CNVs) as small as 30 kb in single cells of an ovarian cancer cell line and as small as 9 Mb in two high-grade serous ovarian cancer samples using only 0.02× depth. Droplet MDA provides an accessible and scalable method for performing robust and accurate CNV and SNV measurements on large numbers of single cells.

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.

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).

Size distribution and growth rate of crystal nuclei near critical undercooling in small volumes

NASA Astrophysics Data System (ADS)

Kožíšek, Z.; Demo, P.

2017-11-01

Kinetic equations are numerically solved within standard nucleation model to determine the size distribution of nuclei in small volumes near critical undercooling. Critical undercooling, when first nuclei are detected within the system, depends on the droplet volume. The size distribution of nuclei reaches the stationary value after some time delay and decreases with nucleus size. Only a certain maximum size of nuclei is reached in small volumes near critical undercooling. As a model system, we selected recently studied nucleation in Ni droplet [J. Bokeloh et al., Phys. Rev. Let. 107 (2011) 145701] due to available experimental and simulation data. However, using these data for sample masses from 23 μg up to 63 mg (corresponding to experiments) leads to the size distribution of nuclei, when no critical nuclei in Ni droplet are formed (the number of critical nuclei < 1). If one takes into account the size dependence of the interfacial energy, the size distribution of nuclei increases to reasonable values. In lower volumes (V ≤ 10-9 m3) nucleus size reaches some maximum extreme size, which quickly increases with undercooling. Supercritical clusters continue their growth only if the number of critical nuclei is sufficiently high.

Using an AMACR (P504S)/34betaE12/p63 cocktail for the detection of small focal prostate carcinoma in needle biopsy specimens.

PubMed

Jiang, Zhong; Li, Cuizhen; Fischer, Andrew; Dresser, Karen; Woda, Bruce A

2005-02-01

We assessed the usefulness of immunohistochemical analysis with a 3-antibody cocktail (alpha-methylacyl coenzyme A racemase [AMACR, or P504S], 34betaE12, p63) and a double-chromogen reaction for detection of limited prostate cancer in 138 needle biopsy specimens, including 82 with small foci of prostatic adenocarcinoma and 56 benign prostates. When carcinoma was present, red cytoplasmic granular staining (AMACR) in the malignant glands and cells and dark brown nuclear (p63) and cytoplasmic (34betaE12) staining in basal cells of adjacent nonmalignant glands were found. Of 82 cases of small foci of prostatic adenocarcinoma, 78 (95%) expressed AMACR; all malignant glands were negative for basal cell staining. All benign glands adjacent to malignant glands were recognized easily by basal cell marker positivity and little or no AMACR expression. No benign glands were simultaneously positive for AMACR and negative for basal cell markers (specificity, 100%). There were no differences in intensity and numbers of positive glands with double-chromogen staining compared with using 1-color staining. Our results indicate that immunohistochemistry with a 3-antibody cocktail and double chromogen is a simple and easy assay that can be used as a routine test, which overcomes the problems of studying small lesions in prostate needle biopsies with multiple immunohistochemical stains.

Quantile-based permutation thresholds for quantitative trait loci hotspots.

PubMed

Neto, Elias Chaibub; Keller, Mark P; Broman, Andrew F; Attie, Alan D; Jansen, Ritsert C; Broman, Karl W; Yandell, Brian S

2012-08-01

Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume "omic" data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.

How long is enough to detect terrestrial animals? Estimating the minimum trapping effort on camera traps

PubMed Central

Si, Xingfeng; Kays, Roland

2014-01-01

Camera traps is an important wildlife inventory tool for estimating species diversity at a site. Knowing what minimum trapping effort is needed to detect target species is also important to designing efficient studies, considering both the number of camera locations, and survey length. Here, we take advantage of a two-year camera trapping dataset from a small (24-ha) study plot in Gutianshan National Nature Reserve, eastern China to estimate the minimum trapping effort actually needed to sample the wildlife community. We also evaluated the relative value of adding new camera sites or running cameras for a longer period at one site. The full dataset includes 1727 independent photographs captured during 13,824 camera days, documenting 10 resident terrestrial species of birds and mammals. Our rarefaction analysis shows that a minimum of 931 camera days would be needed to detect the resident species sufficiently in the plot, and c. 8700 camera days to detect all 10 resident species. In terms of detecting a diversity of species, the optimal sampling period for one camera site was c. 40, or long enough to record about 20 independent photographs. Our analysis of evaluating the increasing number of additional camera sites shows that rotating cameras to new sites would be more efficient for measuring species richness than leaving cameras at fewer sites for a longer period. PMID:24868493

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.

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

Ensembles of novelty detection classifiers for structural health monitoring using guided waves

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

Dib, Gerges; Karpenko, Oleksii; Koricho, Ermias

Guided wave structural health monitoring uses sparse sensor networks embedded in sophisticated structures for defect detection and characterization. The biggest challenge of those sensor networks is developing robust techniques for reliable damage detection under changing environmental and operating conditions. To address this challenge, we develop a novelty classifier for damage detection based on one class support vector machines. We identify appropriate features for damage detection and introduce a feature aggregation method which quadratically increases the number of available training observations.We adopt a two-level voting scheme by using an ensemble of classifiers and predictions. Each classifier is trained on a differentmore » segment of the guided wave signal, and each classifier makes an ensemble of predictions based on a single observation. Using this approach, the classifier can be trained using a small number of baseline signals. We study the performance using monte-carlo simulations of an analytical model and data from impact damage experiments on a glass fiber composite plate.We also demonstrate the classifier performance using two types of baseline signals: fixed and rolling baseline training set. The former requires prior knowledge of baseline signals from all environmental and operating conditions, while the latter does not and leverages the fact that environmental and operating conditions vary slowly over time and can be modeled as a Gaussian process.« less

High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer.

PubMed

Pailler, E; Auger, N; Lindsay, C R; Vielh, P; Islas-Morris-Hernandez, A; Borget, I; Ngo-Camus, M; Planchard, D; Soria, J-C; Besse, B; Farace, F

2015-07-01

Genetic aberrations affecting the c-ros oncogene 1 (ROS1) tyrosine kinase gene have been reported in a small subset of patients with non-small-cell lung cancer (NSCLC). We evaluated whether ROS1-chromosomal rearrangements could be detected in circulating tumor cells (CTCs) and examined tumor heterogeneity of CTCs and tumor biopsies in ROS1-rearranged NSCLC patients. Using isolation by size of epithelial tumor cells (ISET) filtration and filter-adapted-fluorescence in situ hybridization (FA-FISH), ROS1 rearrangement was examined in CTCs from four ROS1-rearranged patients treated with the ROS1-inhibitor, crizotinib, and four ROS1-negative patients. ROS1-gene alterations observed in CTCs at baseline from ROS1-rearranged patients were compared with those present in tumor biopsies and in CTCs during crizotinib treatment. Numerical chromosomal instability (CIN) of CTCs was assessed by DNA content quantification and chromosome enumeration. ROS1 rearrangement was detected in the CTCs of all four patients with ROS1 rearrangement previously confirmed by tumor biopsy. In ROS1-rearranged patients, median number of ROS1-rearranged CTCs at baseline was 34.5 per 3 ml blood (range, 24-55). In ROS1-negative patients, median background hybridization of ROS1-rearranged CTCs was 7.5 per 3 ml blood (range, 7-11). Tumor heterogeneity, assessed by ROS1 copy number, was significantly higher in baseline CTCs compared with paired tumor biopsies in the three patients experiencing PR or SD (P < 0.0001). Copy number in ROS1-rearranged CTCs increased significantly in two patients who progressed during crizotinib treatment (P < 0.02). CTCs from ROS1-rearranged patients had a high DNA content and gain of chromosomes, indicating high levels of aneuploidy and numerical CIN. We provide the first proof-of-concept that CTCs can be used for noninvasive and sensitive detection of ROS1 rearrangement in NSCLC patients. CTCs from ROS1-rearranged patients show considerable heterogeneity of ROS1-gene abnormalities and elevated numerical CIN, a potential mechanism to escape ROS1-inhibitor therapy in ROS1-rearranged NSCLC tumors. © The Author 2015. Published by Oxford University Press on behalf of the European Society for Medical Oncology.

Debris Detector Verification by Hvi-Tests

NASA Astrophysics Data System (ADS)

Bauer, Waldemar; Drolshagen, Gerhard; Vörsmann, Peter; Romberg, Oliver; Putzar, Robin

Information regarding Space Debris (SD) or Micrometeoroids (MM) impacting on spacecraft (S/C) or payloads (P/L) can be obtained by using environmental models e.g. MASTER (ESA) or ORDEM (NASA). The validation of such models is performed by comparison of simulated results with measured or orbital observed data. The latter is utilised for large particles and can be obtained from ground based or space based radars or telescopes. Data regarding very small but abundant particles can also be gained by analysis of retrieved hardware (e.g. Hubble Space Telescope, Space Shuttle Windows), which are brought from orbit back to Earth. Furthermore, in-situ impact detectors are an essential source for information on small size meteoroids and space debris. These kind of detectors are placed in orbit and collect impact data regarding SD and MM, sending data near real time via telemetry. Compared to the impact data which is gained by analysis of retrieved surfaces, the detected data comprise additional information regarding exact impact time and, depending on the type of detector, on the orbit and particles composition. Nevertheless, existing detectors have limitations. Since the detection area is small, statistically meaningful number of impacts are obtained for very small particles only. Measurements of particles in the size range of hundreds of microns to mm which are potentially damaging to S/C require larger sensor areas. To make use of the advantages of in-situ impact detectors and to increase the amount of impact data an innovative impact detector concept is currently under development at DLR in Bremen. Different to all previous impact detectors the Solar Generator based Impact Detector (SOLID) is not an add-on component on the S/C. SOLID makes use of existing subsystems of the S/C and adopts them for impact detection purposes. Since the number of impacts on a target in space depends linearly on the exposed area, the S/C solar panels offer a unique opportunity to use them for impact detection. Considering that the SOLID method could be applied to several S/Cs in different orbits, the spatial coverage in space concerning SD and MM can be significantly increased. In this way the method allows to generate large amount of impact data, which can be used for environmental model validation. This paper focuses on the verification of the SOLID method by Hypervelocity Impact (HVI) tests performed at Fraunhofer EMI. The test set-up as well as achieved results are presented and discussed.

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.

Are We Really Missing Small Galaxies?

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2018-02-01

One long-standing astrophysical puzzle is that of so-called missing dwarf galaxies: the number of small dwarf galaxies that we observe is far fewer than that predicted by theory. New simulations, however, suggest that perhaps theres no mystery after all.Missing DwarfsDark-matter cosmological simulations predict many small galaxy halos for every large halo that forms. [The Via Lactea project]Models of a lambda-cold-dark-matter (CDM) universe predict the distribution of galaxy halo sizes throughout the universe, suggesting there should be many more small galaxies than large ones. In what has become known as the missing dwarf problem, however, we find that while we observe the expected numbers of galaxies at the larger end of the scale, we dont see nearly enough small galaxies to match the predictions.Are these galaxies actually missing? Are our predictions wrong? Or are the galaxies there and were just not spotting them? A recent study led by Alyson Brooks (Rutgers University) uses new simulations to explore whatscausing the difference between theory and observation.The fraction of detectable halos as a function of velocity, according to the authors simulations. Below 35 km/s, the detectability of the galaxies drops precipitously. [Brooks et al. 2017]Simulating Galactic VelocitiesBecause we cant weigh a galaxy directly, one proxy used for galaxy mass is its circular velocity; the more massive a galaxy, the faster gas and stars rotate around its center. The discrepancy between models and observations lies in whats known as the galaxy velocity function, which describes the number density of galaxies for a given circular velocity. While theory and observations agree for galaxies with circular velocities above 100 km/s, theory predicts far more dwarfs below this velocity than we observe.To investigate this problem, Brooks and collaborators ran a series of cosmological simulations based on our understanding of a CDM universe. Instead of exploring the result using only dark matter, however, the team included baryons in their simulations. They then produced mock observations of the resulting galaxy velocities to see what an observed velocity function would look like for their simulated galaxies.No Problem After All?Comparison of theoretical velocity functions to observations. The black dashed line shows the original, dark-matter-only model predictions; the black solid line includes the effects of detectability. Blue lines show the authors new model, including the effects of detectability and inclusion of baryons. The red and teal data points from observations match this corrected model well. [Brooks et al. 2017]Based on their baryon-inclusive simulations, Brooks and collaborators argue that there are two main factors that have contributed to the seeming theory/observation mismatch of the missing dwarf problem:Galaxies with low velocities arent detectable by our current surveys.The authors found that the detectable fraction of their simulated galaxies plunges as soon as galaxy velocity drops below 35 km/s. They conclude that were probably unable to see a large fraction of the smallest galaxies.Were not correctly inferring the circular velocity of the galaxies.Circular velocity is usually measured by looking at the line width of a gas tracer like HI. The authors find that this doesnt trace the full potential wells of the dwarf galaxies, however, resulting in an incorrect interpretation of their velocities.The authors show that the inclusion of these effects in the theoretical model significantly changes the predicted shape of the galaxy velocity function. This new function beautifully matches observations, neatly eliminating the missing dwarf problem. Perhaps this long-standing mystery has been a problem of interpretation all along!CitationAlyson M. Brooks et al 2017 ApJ 850 97. doi:10.3847/1538-4357/aa9576

A Survey on Aflatoxin M1 Content in Sheep and Goat Milk Produced in Sardinia Region, Italy (2005-2013).

PubMed

Virdis, Salvatore; Scarano, Christian; Spanu, Vincenzo; Murittu, Gavino; Spanu, Carlo; Ibba, Ignazio; De Santis, Enrico Pietro Luigi

2014-12-09

In the present work the results of a survey conducted in Sardinia Region on Aflatoxin M 1 (AFM 1 ) contamination in milk of small ruminants from 2005 to 2013 are reported. A total of 517 sheep and 88 goat milk samples from bulk tank, tank trucks and silo tank milk were collected. Analyses were performed by the Regional Farmers Association laboratory using high-performance liquid chromatography following the ISO 14501:1998 standard. None of the sheep milk samples analysed during 2005-2012 showed AFM 1 contamination. In sheep milk samples collected in 2013, 8 out of 172 (4.6%) were contaminated by AFM 1 with a concentration (mean±SD) of 12.59±14.05 ng/L. In one bulk tank milk sample 58.82 ng/L AFM 1 was detected, exceeding the EU limit. In none of goat milk samples analysed from 2010 to 2012 AFM 1 was detected. In 2013, 9 out of 66 goat milk samples (13.6%) showed an AFM 1 concentration of 47.21±19.58 ng/L. Two of these samples exceeded the EU limit, with concentrations of 62.09 and 138.6 ng/L. Higher contamination frequency and concentration rates were detected in bulk tank milk samples collected at farm than in bulk milk truck or silo samples, showing a dilution effect on AFM 1 milk content along small ruminants supply chain. The rate and levels of AFM 1 contamination in sheep and goat milk samples were lower than other countries. However, the small number of milk samples analysed for AFM 1 in Sardinia Region in 2005-2013 give evidence that food business operators check programmes should be improved to ensure an adequate monitoring of AFM 1 contamination in small ruminant dairy chain.

Small median tumor diameter at cure threshold (<20 mm) among aggressive non-small cell lung cancers in male smokers predicts both chest X-ray and CT screening outcomes in a novel simulation framework.

PubMed

Goldwasser, Deborah L; Kimmel, Marek

2013-01-01

The effectiveness of population-wide lung cancer screening strategies depends on the underlying natural course of lung cancer. We evaluate the expected stage distribution in the Mayo CT screening study under an existing simulation model of non-small cell lung cancer (NSCLC) progression calibrated to the Mayo lung project (MLP). Within a likelihood framework, we evaluate whether the probability of 5-year NSCLC survival conditional on tumor diameter at detection depends significantly on screening detection modality, namely chest X-ray and computed tomography. We describe a novel simulation framework in which tumor progression depends on cellular proliferation and mutation within a stem cell compartment of the tumor. We fit this model to randomized trial data from the MLP and produce estimates of the median radiologic size at the cure threshold. We examine the goodness of model fit with respect to radiologic tumor size and 5-year NSCLC survival among incident cancers in both the MLP and Mayo CT studies. An existing model of NSCLC progression under-predicts the number of advanced-stage incident NSCLCs among males in the Mayo CT study (p-value = 0.004). The probability of 5-year NSCLC survival conditional on tumor diameter depends significantly on detection modality (p-value = 0.0312). In our new model, selected solution sets having a median tumor diameter of 16.2-22.1 mm at cure threshold among aggressive NSCLCs predict both MLP and Mayo CT outcomes. We conclude that the median lung tumor diameter at cure threshold among aggressive NSCLCs in male smokers may be small (<20 mm). Copyright © 2012 UICC.

A new code for automatic detection and analysis of the lineament patterns for geophysical and geological purposes (ADALGEO)

NASA Astrophysics Data System (ADS)

Soto-Pinto, C.; Arellano-Baeza, A.; Sánchez, G.

2013-08-01

We present a new numerical method for automatic detection and analysis of changes in lineament patterns caused by seismic and volcanic activities. The method is implemented as a series of modules: (i) normalization of the image contrast, (ii) extraction of small linear features (stripes) through convolution of the part of the image in the vicinity of each pixel with a circular mask or through Canny algorithm, and (iii) posterior detection of main lineaments using the Hough transform. We demonstrate that our code reliably detects changes in the lineament patterns related to the stress evolution in the Earth's crust: specifically, a significant number of new lineaments appear approximately one month before an earthquake, while one month after the earthquake the lineament configuration returns to its initial state. Application of our software to the deformations caused by volcanic activity yields the opposite results: the number of lineaments decreases with the onset of microseismicity. This discrepancy can be explained assuming that the plate tectonic earthquakes are caused by the compression and accumulation of stress in the Earth's crust due to subduction of tectonic plates, whereas in the case of volcanic activity we deal with the inflation of a volcano edifice due to elevation of pressure and magma intrusion and the resulting stretching of the surface.

A Parallel Finite Set Statistical Simulator for Multi-Target Detection and Tracking

NASA Astrophysics Data System (ADS)

Hussein, I.; MacMillan, R.

2014-09-01

Finite Set Statistics (FISST) is a powerful Bayesian inference tool for the joint detection, classification and tracking of multi-target environments. FISST is capable of handling phenomena such as clutter, misdetections, and target birth and decay. Implicit within the approach are solutions to the data association and target label-tracking problems. Finally, FISST provides generalized information measures that can be used for sensor allocation across different types of tasks such as: searching for new targets, and classification and tracking of known targets. These FISST capabilities have been demonstrated on several small-scale illustrative examples. However, for implementation in a large-scale system as in the Space Situational Awareness problem, these capabilities require a lot of computational power. In this paper, we implement FISST in a parallel environment for the joint detection and tracking of multi-target systems. In this implementation, false alarms and misdetections will be modeled. Target birth and decay will not be modeled in the present paper. We will demonstrate the success of the method for as many targets as we possibly can in a desktop parallel environment. Performance measures will include: number of targets in the simulation, certainty of detected target tracks, computational time as a function of clutter returns and number of targets, among other factors.

Potential role of Alternaria and Cladosporium species in canine lymphoplasmacytic rhinitis.

PubMed

Mercier, E; Peters, I R; Billen, F; Battaille, G; Clercx, C; Day, M J; Peeters, D

2013-04-01

To evaluate the possible role of Alternaria and Cladosporium species in the pathogenesis of canine lymphoplasmacytic rhinitis by comparing the amount of specific fungal DNA in nasal mucosal biopsies between dogs without nasal neoplasia and those with lymphoplasmacytic rhinitis or nasal neoplasia. Quantitative real-time polymerase chain reaction (qPCR) assays detecting DNA from Alternaria and Cladosporium fungi were applied to nasal mucosal biopsies collected from dogs with lymphoplasmacytic rhinitis (n = 8), dogs with nasal neoplasia (n = 10) and control animals (n = 10). A copy number for each sample was calculated using a standard curve of known copy number and differences amongst groups were assessed using Kruskal-Wallis tests. No significant difference was found between the groups. Low levels of Alternaria DNA (10-100 copies/PCR) were detected in one sample; very low levels of DNA (<10 copies/qPCR) were detected in 6 samples, and 21 samples were negative. Low levels of Cladosporium DNA were detected in 2 samples; very low levels of DNA in 18; and 8 were negative. Results of this study reveal that Alternaria and Cladosporium species are part of the canine nasal flora, and that these fungi are probably not involved in the pathogenesis of lymphoplasmacytic rhinitis. © 2013 British Small Animal Veterinary Association.

The adsorption of helium atoms on small cationic gold clusters.

PubMed

Goulart, Marcelo; Gatchell, Michael; Kranabetter, Lorenz; Kuhn, Martin; Martini, Paul; Gitzl, Norbert; Rainer, Manuel; Postler, Johannes; Scheier, Paul; Ellis, Andrew M

2018-04-04

Adducts formed between small gold cluster cations and helium atoms are reported for the first time. These binary ions, Aun+Hem, were produced by electron ionization of helium nanodroplets doped with neutral gold clusters and were detected using mass spectrometry. For a given value of n, the distribution of ions as a function of the number of added helium atoms, m, has been recorded. Peaks with anomalously high intensities, corresponding to so-called magic number ions, are identified and interpreted in terms of the geometric structures of the underlying Aun+ ions. These features can be accounted for by planar structures for Aun+ ions with n ≤ 7, with the addition of helium having no significant effect on the structures of the underlying gold cluster ions. According to ion mobility studies and some theoretical predictions, a 3-D structure is expected for Au8+. However, the findings for Au8+ in this work are more consistent with a planar structure.

Single-electron random-number generator (RNG) for highly secure ubiquitous computing applications

NASA Astrophysics Data System (ADS)

Uchida, Ken; Tanamoto, Tetsufumi; Fujita, Shinobu

2007-11-01

Since the security of all modern cryptographic techniques relies on unpredictable and irreproducible digital keys generated by random-number generators (RNGs), the realization of high-quality RNG is essential for secure communications. In this report, a new RNG, which utilizes single-electron phenomena, is proposed. A room-temperature operating silicon single-electron transistor (SET) having nearby an electron pocket is used as a high-quality, ultra-small RNG. In the proposed RNG, stochastic single-electron capture/emission processes to/from the electron pocket are detected with high sensitivity by the SET, and result in giant random telegraphic signals (GRTS) on the SET current. It is experimentally demonstrated that the single-electron RNG generates extremely high-quality random digital sequences at room temperature, in spite of its simple configuration. Because of its small-size and low-power properties, the single-electron RNG is promising as a key nanoelectronic device for future ubiquitous computing systems with highly secure mobile communication capabilities.

Matching algorithm of missile tail flame based on back-propagation neural network

NASA Astrophysics Data System (ADS)

Huang, Da; Huang, Shucai; Tang, Yidong; Zhao, Wei; Cao, Wenhuan

2018-02-01

This work presents a spectral matching algorithm of missile plume detection that based on neural network. The radiation value of the characteristic spectrum of the missile tail flame is taken as the input of the network. The network's structure including the number of nodes and layers is determined according to the number of characteristic spectral bands and missile types. We can get the network weight matrixes and threshold vectors through training the network using training samples, and we can determine the performance of the network through testing the network using the test samples. A small amount of data cause the network has the advantages of simple structure and practicality. Network structure composed of weight matrix and threshold vector can complete task of spectrum matching without large database support. Network can achieve real-time requirements with a small quantity of data. Experiment results show that the algorithm has the ability to match the precise spectrum and strong robustness.

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

PubMed Central

Ghai, Rohit; Mizuno, Carolina Megumi; Picazo, Antonio; Camacho, Antonio; Rodriguez-Valera, Francisco

2013-01-01

We describe a deep-branching lineage of marine Actinobacteria with very low GC content (33%) and the smallest free living cells described yet (cell volume ca. 0.013 μm3), even smaller than the cosmopolitan marine photoheterotroph, ‘Candidatus Pelagibacter ubique'. These microbes are highly related to 16S rRNA sequences retrieved by PCR from the Pacific and Atlantic oceans 20 years ago. Metagenomic fosmids allowed a virtual genome reconstruction that also indicated very small genomes below 1 Mb. A new kind of rhodopsin was detected indicating a photoheterotrophic lifestyle. They are estimated to be ~4% of the total numbers of cells found at the site studied (the Mediterranean deep chlorophyll maximum) and similar numbers were estimated in all tropical and temperate photic zone metagenomes available. Their geographic distribution mirrors that of picocyanobacteria and there appears to be an association between these microbial groups. A new sub-class, ‘Candidatus Actinomarinidae' is proposed to designate these microbes. PMID:23959135

Clinical utility of circulating tumour cell detection in non-small-cell lung cancer.

PubMed

Fusi, Alberto; Metcalf, Robert; Krebs, Matthew; Dive, Caroline; Blackhall, Fiona

2013-12-01

Recent years have witnessed increased interest in the detection of circulating tumour cells (CTCs) for diagnosis, monitoring, and treatment decision making in patients with cancer. Factors that have led to accelerated research in this field include advances in technologies for examination of intact CTCs, personalised medicine with treatment selection according to molecular characteristics, and continued lack of understanding of the biology of treatment resistance and metastasis. CTCs offer promise as a surrogate for tissue where there is insufficient tissue for molecular analysis and where there is a requirement to serially monitor molecular changes in cancer cells through treatment or on progression. In patients with either small cell or non-small cell lung cancer (NSCLC), there is evidence that CTC number is prognostic and that CTCs counted before and after treatment mirror treatment response. In patients with molecularly defined subtypes of NSCLC, CTCs demonstrate the same molecular changes as the cancer cells of the tumour. However, CTCs are not quite ready for "primetime" in the lung cancer clinic. There are still more questions than answers with respect to the optimal technologies for their detection and analysis, their biological significance, and their clinical utility. Despite this the current pace of progress in CTC technology development seems set to make "liquid biopsies" a clinical reality within the next decade. For the everyday clinician and clinical trialist, it will be important to maintain knowledge of the strengths and weaknesses of the technologies and evolving evidence base for CTCs as a routinely used diagnostic tool.

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.

Use of dye to distinguish salt and protein crystals under microcrystallization conditions

NASA Technical Reports Server (NTRS)

Cosenza, Larry (Inventor); Gester, Thomas E. (Inventor); Bray, Terry L. (Inventor); DeLucas, Lawrence J. (Inventor); Hamrick, David T. (Inventor)

2007-01-01

An improved method of screening crystal growth conditions is provided wherein molecules are crystallized from solutions containing dyes. These dyes are selectively incorporated or associated with crystals of particular character thereby rendering crystals of particular character colored and improving detection of the dyed crystals. A preferred method involves use of dyes in protein solutions overlayed by oil. Use of oil allows the use of small volumes of solution and facilitates the screening of large numbers of crystallization conditions in arrays using automated devices that dispense appropriate solutions to generate crystallization trials, overlay crystallization trials with an oil, provide appropriate conditions conducive to crystallization and enhance detection of dyed (colored) or undyed (uncolored) crystals that result.

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

Setio, Arnaud A. A., E-mail: arnaud.arindraadiyoso@radboudumc.nl; Jacobs, Colin; Gelderblom, Jaap

Purpose: Current computer-aided detection (CAD) systems for pulmonary nodules in computed tomography (CT) scans have a good performance for relatively small nodules, but often fail to detect the much rarer larger nodules, which are more likely to be cancerous. We present a novel CAD system specifically designed to detect solid nodules larger than 10 mm. Methods: The proposed detection pipeline is initiated by a three-dimensional lung segmentation algorithm optimized to include large nodules attached to the pleural wall via morphological processing. An additional preprocessing is used to mask out structures outside the pleural space to ensure that pleural and parenchymalmore » nodules have a similar appearance. Next, nodule candidates are obtained via a multistage process of thresholding and morphological operations, to detect both larger and smaller candidates. After segmenting each candidate, a set of 24 features based on intensity, shape, blobness, and spatial context are computed. A radial basis support vector machine (SVM) classifier was used to classify nodule candidates, and performance was evaluated using ten-fold cross-validation on the full publicly available lung image database consortium database. Results: The proposed CAD system reaches a sensitivity of 98.3% (234/238) and 94.1% (224/238) large nodules at an average of 4.0 and 1.0 false positives/scan, respectively. Conclusions: The authors conclude that the proposed dedicated CAD system for large pulmonary nodules can identify the vast majority of highly suspicious lesions in thoracic CT scans with a small number of false positives.« less

Outliers to the peak energy-isotropic energy relation in gamma-ray bursts

NASA Astrophysics Data System (ADS)

Nakar, Ehud; Piran, Tsvi

2005-06-01

The peak energy-isotropic energy (EpEi) relation is among the most intriguing recent discoveries concerning gamma-ray bursts (GRBs). It can have numerous implications for our understanding of the emission mechanism of the bursts and for the application of GRBs to cosmological studies. However, this relation has been verified only for a small sample of bursts with measured redshifts. We propose here a test of whether a burst with an unknown redshift can potentially satisfy the EpEi relation. Applying this test to a large sample of BATSE bursts, we find that a significant fraction of those bursts cannot satisfy this relation. Our test is sensitive only to dim and hard bursts, and therefore this relation might still hold as an inequality (i.e. there are no intrinsically bright and soft bursts). We conclude that the observed relation seen in the sample of bursts with known redshift might be influenced by observational biases and the inability to locate and to localize well hard and weak bursts that have only a small number of photons. In particular, we point out that the threshold for detection, localization and redshift measurement is essentially higher than the threshold for detection alone. We predict that Swift will detect some hard and weak bursts that would be outliers to the EpEi relation. However, we cannot quantify this prediction. We stress the importance of understanding the detection-localization-redshift threshold for the coming Swift detections.

Axion searches with microwave filters: the RADES project

NASA Astrophysics Data System (ADS)

Álvarez Melcón, Alejandro; Arguedas Cuendis, Sergio; Cogollos, Cristian; Díaz-Morcillo, Alejandro; Döbrich, Babette; Gallego, Juan Daniel; Gimeno, Benito; Irastorza, Igor G.; José Lozano-Guerrero, Antonio; Malbrunot, Chloé; Navarro, Pablo; Peña Garay, Carlos; Redondo, Javier; Vafeiadis, Theodoros; Wuensch, Walter

2018-05-01

We propose, design and construct a variant of the conventional axion haloscope concept that could be competitive in the search for dark matter axions of masses in the decade 10–100 μeV. Theses masses are located somewhat above the mass range in which existing experiments have reached sensitivity to benchmark QCD axion models. Our haloscope consists of an array of small microwave cavities connected by rectangular irises, in an arrangement commonly used in radio-frequency filters. The size of the unit cavity determines the main resonant frequency, while the possibility to connect a large number of cavities allows to reach large detection volumes. We develop the theoretical framework of the detection concept, and present design prescriptions to optimize detection capabilities. We describe the design and realization of a first small-scale prototype of this concept, called Relic Axion Detector Exploratory Setup (RADES). It consists of a copper-coated stainless steel five-cavities microwave filter with the detecting mode operating at around 8.4 GHz. This structure has been electromagnetically characterized at 2 K and 298 K, and it is now placed in ultra-high vacuum in one of the twin-bores of the 9 T CAST dipole magnet at CERN. We describe the data acquisition system developed for relic axion detection, and present preliminary results of the electromagnetic properties of the microwave filter, which show the potential of filters to reach QCD axion window sensitivity at X-band frequencies.

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.

Habitat selection by green turtles in a spatially heterogeneous benthic landscape in Dry Tortugas National Park, Florida

USGS Publications Warehouse

Fujisaki, Ikuko; Hart, Kristen M.; Sartain-Iverson, Autumn R.

2016-01-01

We examined habitat selection by green turtles Chelonia mydas at Dry Tortugas National Park, Florida, USA. We tracked 15 turtles (6 females and 9 males) using platform transmitter terminals (PTTs); 13 of these turtles were equipped with additional acoustic transmitters. Location data by PTTs comprised periods of 40 to 226 d in varying months from 2009 to 2012. Core areas were concentrated in shallow water (mean bathymetry depth of 7.7 m) with a comparably dense coverage of seagrass; however, the utilization distribution overlap index indicated a low degree of habitat sharing. The probability of detecting a turtle on an acoustic receiver was inversely associated with the distance from the receiver to turtle capture sites and was lower in shallower water. The estimated daily detection probability of a single turtle at a given acoustic station throughout the acoustic array was small (<0.1 in any year), and that of multiple turtle detections was even smaller. However, the conditional probability of multiple turtle detections, given at least one turtle detection at a receiver, was much higher despite the small number of tagged turtles in each year (n = 1 to 5). Also, multiple detections of different turtles at a receiver frequently occurred within a few minutes (40%, or 164 of 415, occurred within 1 min). Our numerical estimates of core area overlap, co-occupancy probabilities, and habitat characterization for green turtles could be used to guide conservation of the area to sustain the population of this species.

Multivariate optical element platform for compressed detection of fluorescence markers

NASA Astrophysics Data System (ADS)

Priore, Ryan J.; Swanstrom, Joseph A.

2014-05-01

The success of a commercial fluorescent diagnostic assay is dependent on the selection of a fluorescent biomarker; due to the broad nature of fluorescence biomarker emission profiles, only a small number of fluorescence biomarkers may be discriminated from each other as a function of excitation source. Multivariate Optical Elements (MOEs) are thin-film devices that encode a broad band, spectroscopic pattern allowing a simple broadband detector to generate a highly sensitive and specific detection for a target analyte. MOEs have historically been matched 1:1 to a discrete analyte or class prediction; however, MOE filter sets are capable of sensing projections of the original sparse spectroscopic space enabling a small set of MOEs to discriminate a multitude of target analytes. This optical regression can offer real-time measurements with relatively high signal-to-noise ratios that realize the advantages of multiplexed detection and pattern recognition in a simple optical instrument. The specificity advantage of MOE-based sensors allows fluorescent biomarkers that were once incapable of discrimination from one another via optical band pass filters to be employed in a common assay panel. A simplified MOE-based sensor may ultimately reduce the requirement for highly trained operators as well as move certain life science applications like disease prognostication from the laboratory to the point of care. This presentation will summarize the design and fabrication of compressed detection MOE filter sets for detecting multiple fluorescent biomarkers simultaneously with strong spectroscopic interference as well as comparing the detection performance of the MOE sensor with traditional optical band pass filter methodologies.

Prognostic value of the frequency of vascular invasion in stage I non-small cell lung cancer.

PubMed

Okada, Satoshi; Mizuguchi, Shinjiro; Izumi, Nobuhiro; Komatsu, Hiroaki; Toda, Michihito; Hara, Kantaro; Okuno, Takahiro; Shibata, Toshihiko; Wanibuchi, Hideki; Nishiyama, Noritoshi

2017-01-01

There is no standard pathological method for determining vessel invasion in lung cancer. Herein, we examine whether vessel invasion can be accurately assessed using hematoxylin-eosin staining alone, and investigate the prognostic impact of the presence and frequency of vessel invasion in lung cancer. Vessel invasion was assessed by hematoxylin-eosin, Victoria blue, and D2-40 in 251 completely resected stage I non-small cell lung cancer patients. Vessel invasion was classified into 3 grades according to the number of invaded vessels. Using hematoxylin-eosin and Victoria blue, vascular invasion was detected in 27 (10.8 %) and 75 (29.9 %) of patients, respectively. Lymphatic permeation was detected in 126 (50.2 %) and 70 (27.9 %) of patients using hematoxylin-eosin and D2-40 staining. Hematoxylin-eosin staining did not accurately detect a high frequency of vessel invasion; only 5 and 21.7 % of high-frequency vascular invasion and lymphatic permeation cases diagnosed with Victoria blue and D2-40 were detected. Multivariate analysis based on elastic stain and immunostaining indicated that plural invasion, a high frequency of vascular invasion (hazard ratio 4.00), and a high frequency of lymphatic permeation (hazard ratio 2.30) were independent predictors of cancer recurrence within 3 years. Likewise, an age ≥70 years, male, and a high frequency of vascular invasion (hazard ratio 3.41) were independent predictors of overall survival. Vascular invasion should be confirmed by elastic stains, and the frequency, not but the presence, of vascular invasion is a powerful independent prognostic factor in completely resected stage I non-small cell lung cancer patients.

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.

Longer mean colonoscopy withdrawal time is associated with increased adenoma detection: evidence from the Bowel Cancer Screening Programme in England.

PubMed

Lee, T J W; Blanks, R G; Rees, C J; Wright, K C; Nickerson, C; Moss, S M; Chilton, A; Goddard, A F; Patnick, J; McNally, R J Q; Rutter, M D

2013-01-01

Increasing colonoscopy withdrawal time (CWT) is thought to be associated with increasing adenoma detection rate (ADR). Current English guidelines recommend a minimum CWT of 6 minutes. It is known that in the Bowel Cancer Screening Programme (BCSP) in England there is wide variation in CWT. The aim of this observational study was to examine the relationship between CWT and ADR. The study examined data from 31 088 colonoscopies by 147 screening program colonoscopists. Colonoscopists were grouped in four levels of mean CWT ( < 7, 7 - 8.9, 9 - 10.9, and ≥ 11 minutes). Univariable and multivariable analysis (binary logistic and negative binomial regression) were used to explore the relationship between CWT, ADR, mean number of adenomas and number of right-sided and advanced adenomas. In colonoscopists with a mean CWT < 7 minutes, the mean ADR was 42.5 % compared with 47.1 % in the ≥ 11-minute group (P < 0.001). The mean number of adenomas detected per procedure increased from 0.77 to 0.94, respectively (P < 0.001). The increase in adenoma detection was mainly of subcentimeter or proximal adenomas; there was no increase in the detection of advanced adenomas. Regression models showed an increase in ADR from 43 % to 46.5 % for mean CWT times ranging from 6 to 10 minutes. This study demonstrates that longer mean withdrawal times are associated with increasing adenoma detection, mainly of small or right-sided adenomas. However, beyond 10 minutes the increase in ADR is minimal. Mean withdrawal times longer than 6 minutes are not associated with increased detection of advanced adenomas. Withdrawal time remains an important quality metric of colonoscopy. © Georg Thieme Verlag KG Stuttgart · New York.

Unsupervised Learning —A Novel Clustering Method for Rolling Bearing Faults Identification

NASA Astrophysics Data System (ADS)

Kai, Li; Bo, Luo; Tao, Ma; Xuefeng, Yang; Guangming, Wang

2017-12-01

To promptly process the massive fault data and automatically provide accurate diagnosis results, numerous studies have been conducted on intelligent fault diagnosis of rolling bearing. Among these studies, such as artificial neural networks, support vector machines, decision trees and other supervised learning methods are used commonly. These methods can detect the failure of rolling bearing effectively, but to achieve better detection results, it often requires a lot of training samples. Based on above, a novel clustering method is proposed in this paper. This novel method is able to find the correct number of clusters automatically the effectiveness of the proposed method is validated using datasets from rolling element bearings. The diagnosis results show that the proposed method can accurately detect the fault types of small samples. Meanwhile, the diagnosis results are also relative high accuracy even for massive samples.

A SIMPLE AND EFFECTIVE MULTIPLEX PCR TECHNIQUE FOR DETECTING HUMAN PATHOGENIC TAENIA EGGS IN HOUSEFLIES.

PubMed

Pornruseetriratn, Siritavee; Maipanich, Wanna; Sa-nguankiat, Surapol; Pubampen, Somchit; Poodeepiyasawat, Akkarin; Thaenkham, Urusa

2017-01-01

Taenia solium, T. saginata, and T. asiatica are cestode pathogens causing taeniasis in humans. Houseflies can transfer Taenia eggs to food. However, houseflies are thought to carry only small numbers of Taenia eggs, sometimes fewer than 10. Although several PCR-based methods have been developed to detect Taenia DNA, these require more than 10 eggs for adequate detection. We developed a multiplex PCR method with high specificity for the discrimination among the eggs of the three Taenia species, T. solium, T. saginata, and T. asiatica, using 18S ribosomal DNA (rDNA) as a genetic marker. This technique was found to be highly sensitive, capable of identifying the Taenia species from only one egg. This multiplex PCR technique using 18S rDNA specific primers should be suitable to diagnose Taenia eggs.

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.

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways.

PubMed

Libis, Vincent; Delépine, Baudoin; Faulon, Jean-Loup

2016-10-21

Detection of chemical signals is critical for cells in nature as well as in synthetic biology, where they serve as inputs for designer circuits. Important progress has been made in the design of signal processing circuits triggering complex biological behaviors, but the range of small molecules recognized by sensors as inputs is limited. The ability to detect new molecules will increase the number of synthetic biology applications, but direct engineering of tailor-made sensors takes time. Here we describe a way to immediately expand the range of biologically detectable molecules by systematically designing metabolic pathways that transform nondetectable molecules into molecules for which sensors already exist. We leveraged computer-aided design to predict such sensing-enabling metabolic pathways, and we built several new whole-cell biosensors for molecules such as cocaine, parathion, hippuric acid, and nitroglycerin.

Adaptation of a military FTS to civilian air toxics measurements

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

Engel, J.R.; Dorval, R.K.

1994-12-31

In many ways, the military problem of chemical agent detection is similar to the civilian problem of toxic and related air pollutants detection. A recent program to design a next generation Fourier transform spectrometer (FTS) based chemical agent detection system has been funded by the US Army. This program has resulted in an FTS system that has a number of characteristics that make it suitable for applications to the civilian measurement problem. Low power, low weight, and small size lead to low installation, operating and maintenance costs. Innovative use of diode lasers in place of HeNe reference sources leads tomore » long lifetimes and high reliability. Absolute scan position servos allow for highly efficient offset scanning. This paper will relate the performance of this system to present air monitoring requirements.« less

Embedded Disposable Functionalized Electrochemical Biosensor with a 3D-Printed Flow Cell for Detection of Hepatic Oval Cells (HOCs).

PubMed

Damiati, Samar; Peacock, Martin; Leonhardt, Stefan; Damiati, Laila; Baghdadi, Mohammed A; Becker, Holger; Kodzius, Rimantas; Schuster, Bernhard

2018-02-14

Hepatic oval cells (HOCs) are considered the progeny of the intrahepatic stem cells that are found in a small population in the liver after hepatocyte proliferation is inhibited. Due to their small number, isolation and capture of these cells constitute a challenging task for immunosensor technology. This work describes the development of a 3D-printed continuous flow system and exploits disposable screen-printed electrodes for the rapid detection of HOCs that over-express the OV6 marker on their membrane. Multiwall carbon nanotube (MWCNT) electrodes have a chitosan film that serves as a scaffold for the immobilization of oval cell marker antibodies (anti-OV6-Ab), which enhance the sensitivity of the biomarker and makes the designed sensor specific for oval cells. The developed sensor can be easily embedded into the 3D-printed flow cell to allow cells to be exposed continuously to the functionalized surface. The continuous flow is intended to increase capture of most of the target cells in the specimen. Contact angle measurements were performed to characterize the nature and quality of the modified sensor surface, and electrochemical measurements (cyclic voltammetry (CV) and square wave voltammetry (SWV)) were performed to confirm the efficiency and selectivity of the fabricated sensor to detect HOCs. The proposed method is valuable for capturing rare cells and could provide an effective tool for cancer diagnosis and detection.

MT-PCR panel detection of canine parvovirus (CPV-2): Vaccine and wild-type CPV-2 can be difficult to differentiate in canine diagnostic fecal samples.

PubMed

Meggiolaro, Maira N; Ly, Anna; Rysnik-Steck, Benjamin; Silva, Carolina; Zhang, Joshua; Higgins, Damien P; Muscatello, Gary; Norris, Jacqueline M; Krockenberger, Mark; Šlapeta, Jan

2017-06-01

Canine parvovirus (CPV-2) remains an important cause of devastating enteritis in young dogs. It can be successfully prevented with live attenuated CPV-2 vaccines when given at the appropriate age and in the absence of maternal antibody interference. Rapid diagnosis of parvoviral enteritis in young dogs is essential to ensuring suitable barrier nursing protocols within veterinary hospitals. The current diagnostic trend is to use multiplexed PCR panels to detect an array of pathogens commonly responsible for diarrhea in dogs. The multiplexed PCR assays do not distinguish wild from vaccine CPV-2. They are highly sensitive and detect even a low level of virus shedding, such as those caused by the CPV-2 vaccine. The aim of this study was to identify the CPV-2 subtypes detected in diagnostic specimens and rule out occult shedding of CPV-2 vaccine strains. For a total of 21 samples that tested positive for CPV-2 in a small animal fecal pathogens diagnostic multiplexed tandem PCR (MT-PCR) panel during 2014-2016 we partially characterized the VP2 gene of CPV-2. Vaccine CPV-2 strain, wild type CPV-2a subtypes and vaccine-like CPV-2b subtypes were detected. High copy number was indicative of wild-type CPV-2a presence, but presence of vaccine-like CPV-2b had a variable copy number in fecal samples. A yardstick approach to a copy number or C t -value to discriminate vaccine strain from a wild type virus of CPV-2 can be, in some cases, potentially misleading. Therefore, discriminating vaccine strain from a wild type subtype of CPV-2 remains ambitious. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Arctic Regional Communications Small SATellite (ARCSAT)

NASA Technical Reports Server (NTRS)

Casas, Joseph; Kress, Martin; Sims, William; Spehn, Stephen; Jaeger, Talbot; Sanders, Devon

2013-01-01

Traditional satellite missions are extremely complex and expensive to design, build, test, launch and operate. Consequently many complementary operational, exploration and research satellite missions are being formulated as a growing part of the future space community capabilities using formations of small, distributed, simple to launch and inexpensive highly capable small scale satellites. The Arctic Regional Communications small SATellite (ARCSAT) initiative would launch a Mini-Satellite "Mothership" into Polar or Sun Sync low-earth-orbit (LEO). Once on orbit, the Mothership would perform orbital insertion of four internally stored independently maneuverable nanosatellites, each containing electronically steerable antennas and reconfigurable software-defined radios. Unlike the traditional geostationary larger complex satellite communication systems, this LEO communications system will be comprised of initially a five small satellite formation that can be later incrementally increased in the total number of satellites for additional data coverage. ARCSAT will provide significant enabling capabilities in the Arctic for autonomous voice and data communications relay, Maritime Domain Awareness (MDA), data-extraction from unattended sensors, and terrestrial Search & Rescue (SAR) beacon detection missions throughout the "data starved desert" of the Arctic Region.

Contribution of Infrasound to IDC Reviewed Event Bulletin

NASA Astrophysics Data System (ADS)

Bittner, Paulina; Polich, Paul; Gore, Jane; Ali, Sherif Mohamed; Medinskaya, Tatiana; Mialle, Pierrick

2016-04-01

Until 2003 two waveform technologies, i.e. seismic and hydroacoustic were used to detect and locate events included in the International Data Centre (IDC) Reviewed Event Bulletin (REB). The first atmospheric event was published in the REB in 2003 but infrasound detections could not be used by the Global Association (GA) Software due to the unmanageable high number of spurious associations. Offline improvements of the automatic processing took place to reduce the number of false detections to a reasonable level. In February 2010 the infrasound technology was reintroduced to the IDC operations and has contributed to both automatic and reviewed IDC bulletins. The primary contribution of infrasound technology is to detect atmospheric events. These events may also be observed at seismic stations, which will significantly improve event location. Examples of REB events, which were detected by the International Monitoring System (IMS) infrasound network were fireballs (e.g. Bangkok fireball, 2015), volcanic eruptions (e.g. Calbuco, Chile 2015) and large surface explosions (e.g. Tjanjin, China 2015). Query blasts and large earthquakes belong to events primarily recorded at seismic stations of the IMS network but often detected at the infrasound stations. Presence of infrasound detection associated to an event from a mining area indicates a surface explosion. Satellite imaging and a database of active mines can be used to confirm the origin of such events. This presentation will summarize the contribution of 6 years of infrasound data to IDC bulletins and provide examples of events recorded at the IMS infrasound network. Results of this study may help to improve location of small events with observations on infrasound stations.

Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site

PubMed Central

Yang, Chunyan; Wang, Lin; Wang, Wenzhi; Zhao, Guigang; Geng, Yupeng; Yu, Douglas W.

2017-01-01

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish. PMID:28505200

Whole exome sequencing is an efficient, sensitive and specific method of mutation detection in osteogenesis imperfecta and Marfan syndrome

PubMed Central

McInerney-Leo, Aideen M; Marshall, Mhairi S; Gardiner, Brooke; Coucke, Paul J; Van Laer, Lut; Loeys, Bart L; Summers, Kim M; Symoens, Sofie; West, Jennifer A; West, Malcolm J; Paul Wordsworth, B; Zankl, Andreas; Leo, Paul J; Brown, Matthew A; Duncan, Emma L

2013-01-01

Osteogenesis imperfecta (OI) and Marfan syndrome (MFS) are common Mendelian disorders. Both conditions are usually diagnosed clinically, as genetic testing is expensive due to the size and number of potentially causative genes and mutations. However, genetic testing may benefit patients, at-risk family members and individuals with borderline phenotypes, as well as improving genetic counseling and allowing critical differential diagnoses. We assessed whether whole exome sequencing (WES) is a sensitive method for mutation detection in OI and MFS. WES was performed on genomic DNA from 13 participants with OI and 10 participants with MFS who had known mutations, with exome capture followed by massive parallel sequencing of multiplexed samples. Single nucleotide polymorphisms (SNPs) and small indels were called using Genome Analysis Toolkit (GATK) and annotated with ANNOVAR. CREST, exomeCopy and exomeDepth were used for large deletion detection. Results were compared with the previous data. Specificity was calculated by screening WES data from a control population of 487 individuals for mutations in COL1A1, COL1A2 and FBN1. The target capture of five exome capture platforms was compared. All 13 mutations in the OI cohort and 9/10 in the MFS cohort were detected (sensitivity=95.6%) including non-synonymous SNPs, small indels (<10 bp), and a large UTR5/exon 1 deletion. One mutation was not detected by GATK due to strand bias. Specificity was 99.5%. Capture platforms and analysis programs differed considerably in their ability to detect mutations. Consumable costs for WES were low. WES is an efficient, sensitive, specific and cost-effective method for mutation detection in patients with OI and MFS. Careful selection of platform and analysis programs is necessary to maximize success. PMID:24501682

Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site.

PubMed

Cai, Wang; Ma, Zhuxin; Yang, Chunyan; Wang, Lin; Wang, Wenzhi; Zhao, Guigang; Geng, Yupeng; Yu, Douglas W

2017-01-01

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish.

Modeling epidemics on adaptively evolving networks: A data-mining perspective.

PubMed

Kattis, Assimakis A; Holiday, Alexander; Stoica, Ana-Andreea; Kevrekidis, Ioannis G

2016-01-01

The exploration of epidemic dynamics on dynamically evolving ("adaptive") networks poses nontrivial challenges to the modeler, such as the determination of a small number of informative statistics of the detailed network state (that is, a few "good observables") that usefully summarize the overall (macroscopic, systems-level) behavior. Obtaining reduced, small size accurate models in terms of these few statistical observables--that is, trying to coarse-grain the full network epidemic model to a small but useful macroscopic one--is even more daunting. Here we describe a data-based approach to solving the first challenge: the detection of a few informative collective observables of the detailed epidemic dynamics. This is accomplished through Diffusion Maps (DMAPS), a recently developed data-mining technique. We illustrate the approach through simulations of a simple mathematical model of epidemics on a network: a model known to exhibit complex temporal dynamics. We discuss potential extensions of the approach, as well as possible shortcomings.

Estimating wind-turbine-caused bird and bat fatality when zero carcasses are observed

USGS Publications Warehouse

Huso, Manuela M.P.; Dalthorp, Daniel; Dail, David; Madsen, Lisa

2015-01-01

Many wind-power facilities in the United States have established effective monitoring programs to determine turbine-caused fatality rates of birds and bats, but estimating the number of fatalities of rare species poses special difficulties. The loss of even small numbers of individuals may adversely affect fragile populations, but typically, few (if any) carcasses are observed during monitoring. If monitoring design results in only a small proportion of carcasses detected, then finding zero carcasses may give little assurance that the number of actual fatalities is small. Fatality monitoring at wind-power facilities commonly involves conducting experiments to estimate the probability (g) an individual will be observed, accounting for the possibilities that it falls in an unsearched area, is scavenged prior to detection, or remains undetected even when present. When g < 1, the total carcass count (X) underestimates the total number of fatalities (M). Total counts can be 0 when M is small or when M is large and g ≪1. Distinguishing these two cases is critical when estimating fatality of a rare species. Observing no individuals during searches may erroneously be interpreted as evidence of absence. We present an approach that uses Bayes' theorem to construct a posterior distribution for M, i.e., P(M | X, ĝ), reflecting the observed carcass count and previously estimated g. From this distribution, we calculate two values important to conservation: the probability that M is below a predetermined limit and the upper bound (M*) of the 100(1 − α)% credible interval for M. We investigate the dependence of M* on α, g, and the prior distribution of M, asking what value of g is required to attain a desired M* for a given α. We found that when g < ~0.15, M* was clearly influenced by the mean and variance of ĝ and the choice of prior distribution for M, but the influence of these factors is minimal when g > ~0.45. Further, we develop extensions for temporal replication that can inform prior distributions of M and methods for combining information across several areas or time periods. We apply the method to data collected at a wind-power facility where scheduled searches yielded X = 0 raptor carcasses

Assessment of the role of circulating breast cancer cells in tumor formation and metastatic potential using in vivo flow cytometry

NASA Astrophysics Data System (ADS)

Hwu, Derrick; Boutrus, Steven; Greiner, Cherry; Dimeo, Theresa; Kuperwasser, Charlotte; Georgakoudi, Irene

2011-04-01

The identification of breast cancer patients who will ultimately progress to metastatic disease is of significant clinical importance. The quantification and assessment of circulating tumor cells (CTCs) has been proposed as one strategy to monitor treatment effectiveness and disease prognosis. However, CTCs have been an elusive population of cells to study because of their small number and difficulties associated with isolation protocols. In vivo flow cytometry (IVFC) can overcome these limitations and provide insights in the role these cells play during primary and metastatic tumor growth. In this study, we used two-color IVFC to examine, for up to ten weeks following orthotopic implantation, changes in the number of circulating human breast cells expressing GFP and a population of circulating hematopoietic cells with strong autofluorescence. We found that the number of detected CTCs in combination with the number of red autofluorescent cells (650 to 690 nm) during the first seven days following implantation was predictive in development of tumor formation and metastasis eight weeks later. These results suggest that the combined detection of these two cell populations could offer a novel approach in the monitoring and prognosis of breast cancer progression, which in turn could aid significantly in their effective treatment.

Copy Number Variants in Obesity-Related Syndromes: Review and Perspectives on Novel Molecular Approaches

PubMed Central

Koiffmann, Celia Priszkulnik

2012-01-01

In recent decades, obesity has reached epidemic proportions worldwide and became a major concern in public health. Despite heritability estimates of 40 to 70% and the long-recognized genetic basis of obesity in a number of rare cases, the list of common obesity susceptibility variants by the currently published genome-wide association studies (GWASs) only explain a small proportion of the individual variation in risk of obesity. It was not until very recently that GWASs of copy number variants (CNVs) in individuals with extreme phenotypes reported a number of large and rare CNVs conferring high risk to obesity, and specifically deletions on chromosome 16p11.2. In this paper, we comment on the recent advances in the field of genetics of obesity with an emphasis on the genes and genomic regions implicated in highly penetrant forms of obesity associated with developmental disorders. Array genomic hybridization in this patient population has afforded discovery opportunities for CNVs that have not previously been detectable. This information can be used to generate new diagnostic arrays and sequencing platforms, which will likely enhance detection of known genetic conditions with the potential to elucidate new disease genes and ultimately help in developing a next-generation sequencing protocol relevant to clinical practice. PMID:23316347

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…

Solving the relativistic inverse stellar problem through gravitational waves observation of binary neutron stars

NASA Astrophysics Data System (ADS)

Abdelsalhin, Tiziano; Maselli, Andrea; Ferrari, Valeria

2018-04-01

The LIGO/Virgo Collaboration has recently announced the direct detection of gravitational waves emitted in the coalescence of a neutron star binary. This discovery allows, for the first time, to set new constraints on the behavior of matter at supranuclear density, complementary with those coming from astrophysical observations in the electromagnetic band. In this paper we demonstrate the feasibility of using gravitational signals to solve the relativistic inverse stellar problem, i.e., to reconstruct the parameters of the equation of state (EoS) from measurements of the stellar mass and tidal Love number. We perform Bayesian inference of mock data, based on different models of the star internal composition, modeled through piecewise polytropes. Our analysis shows that the detection of a small number of sources by a network of advanced interferometers would allow to put accurate bounds on the EoS parameters, and to perform a model selection among the realistic equations of state proposed in the literature.

Modeling the distribution of illicit oily discharges detected by aerial surveillance in western Canadian marine waters.

PubMed

Serra-Sogas, Norma; O'Hara, Patrick D; Canessa, Rosaline

2014-10-15

Oily discharges from vessel operations have been documented in Canada's Pacific region by the National Aerial Surveillance Program (NASP) since the early 1990s. We explored a number of regression methods to explain the distribution and counts per grid cell of oily discharges detected from 1998 to 2007 using independent predictor variables, while trying to address the large number of zeros present in the data. Best-fit models indicate that discharges are generally concentrated close to shore typically in association with small harbours, and with major commercial and tourist centers. Oily discharges were also concentrated in Barkley Sound and at the entrance of Juan de Fuca Strait. The identification of important factors associated with discharge patterns, and predicting discharge rates in areas with surveillance effort can be used to inform future surveillance. Model output can also be used as inputs for risk models for existing conditions and as baseline for future scenarios. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

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.

Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing.

PubMed

Li, Feng; Kaczor-Urbanowicz, Karolina Elżbieta; Sun, Jie; Majem, Blanca; Lo, Hsien-Chun; Kim, Yong; Koyano, Kikuye; Liu Rao, Shannon; Young Kang, So; Mi Kim, Su; Kim, Kyoung-Mee; Kim, Sung; Chia, David; Elashoff, David; Grogan, Tristan R; Xiao, Xinshu; Wong, David T W

2018-04-23

It was recently discovered that abundant and stable extracellular RNA (exRNA) species exist in bodily fluids. Saliva is an emerging biofluid for biomarker development for noninvasive detection and screening of local and systemic diseases. Use of RNA-Sequencing (RNA-Seq) to profile exRNA is rapidly growing; however, no single preparation and analysis protocol can be used for all biofluids. Specifically, RNA-Seq of saliva is particularly challenging owing to high abundance of bacterial contents and low abundance of salivary exRNA. Given the laborious procedures needed for RNA-Seq library construction, sequencing, data storage, and data analysis, saliva-specific and optimized protocols are essential. We compared different RNA isolation methods and library construction kits for long and small RNA sequencing. The role of ribosomal RNA (rRNA) depletion also was evaluated. The miRNeasy Micro Kit (Qiagen) showed the highest total RNA yield (70.8 ng/mL cell-free saliva) and best small RNA recovery, and the NEBNext library preparation kits resulted in the highest number of detected human genes [5649-6813 at 1 reads per kilobase RNA per million mapped (RPKM)] and small RNAs [482-696 microRNAs (miRNAs) and 190-214 other small RNAs]. The proportion of human RNA-Seq reads was much higher in rRNA-depleted saliva samples (41%) than in samples without rRNA depletion (14%). In addition, the transfer RNA (tRNA)-derived RNA fragments (tRFs), a novel class of small RNAs, were highly abundant in human saliva, specifically tRF-4 (4%) and tRF-5 (15.25%). Our results may help in selection of the best adapted methods of RNA isolation and small and long RNA library constructions for salivary exRNA studies. © 2018 American Association for Clinical Chemistry.

Technical Letter Report Development of Flaw Size Distribution Tables Including Effects of Flaw Depth Sizing Errors for Draft 10CFR 50.61a (Alternate PTS Rule) JCN-N6398, Task 4

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

Simonen, Fredric A.; Gosselin, Stephen R.; Doctor, Steven R.

2013-04-22

This document describes a new method to determine whether the flaws in a particular reactor pressure vessel are consistent with the assumptions regarding the number and sizes of flaws used in the analyses that formed the technical justification basis for the new voluntary alternative Pressurized Thermal Shock (PTS) rule (Draft 10 CFR 50.61a). The new methodology addresses concerns regarding prior methodology because ASME Code Section XI examinations do not detect all fabrication flaws, they have higher detection performance for some flaw types, and there are flaw sizing errors always present (e.g., significant oversizing of small flaws and systematic under sizingmore » of larger flaws). The new methodology allows direct comparison of ASME Code Section XI examination results with values in the PTS draft rule Tables 2 and 3 in order to determine if the number and sizes of flaws detected by an ASME Code Section XI examination are consistent with those assumed in the probabilistic fracture mechanics calculations performed in support of the development of 10 CFR 50.61a.« less

Reduction in training time of a deep learning model in detection of lesions in CT

NASA Astrophysics Data System (ADS)

Makkinejad, Nazanin; Tajbakhsh, Nima; Zarshenas, Amin; Khokhar, Ashfaq; Suzuki, Kenji

2018-02-01

Deep learning (DL) emerged as a powerful tool for object detection and classification in medical images. Building a well-performing DL model, however, requires a huge number of images for training, and it takes days to train a DL model even on a cutting edge high-performance computing platform. This study is aimed at developing a method for selecting a "small" number of representative samples from a large collection of training samples to train a DL model for the could be used to detect polyps in CT colonography (CTC), without compromising the classification performance. Our proposed method for representative sample selection (RSS) consists of a K-means clustering algorithm. For the performance evaluation, we applied the proposed method to select samples for the training of a massive training artificial neural network based DL model, to be used for the classification of polyps and non-polyps in CTC. Our results show that the proposed method reduce the training time by a factor of 15, while maintaining the classification performance equivalent to the model trained using the full training set. We compare the performance using area under the receiveroperating- characteristic curve (AUC).

Multi-categorical deep learning neural network to classify retinal images: A pilot study employing small database.

PubMed

Choi, Joon Yul; Yoo, Tae Keun; Seo, Jeong Gi; Kwak, Jiyong; Um, Terry Taewoong; Rim, Tyler Hyungtaek

2017-01-01

Deep learning emerges as a powerful tool for analyzing medical images. Retinal disease detection by using computer-aided diagnosis from fundus image has emerged as a new method. We applied deep learning convolutional neural network by using MatConvNet for an automated detection of multiple retinal diseases with fundus photographs involved in STructured Analysis of the REtina (STARE) database. Dataset was built by expanding data on 10 categories, including normal retina and nine retinal diseases. The optimal outcomes were acquired by using a random forest transfer learning based on VGG-19 architecture. The classification results depended greatly on the number of categories. As the number of categories increased, the performance of deep learning models was diminished. When all 10 categories were included, we obtained results with an accuracy of 30.5%, relative classifier information (RCI) of 0.052, and Cohen's kappa of 0.224. Considering three integrated normal, background diabetic retinopathy, and dry age-related macular degeneration, the multi-categorical classifier showed accuracy of 72.8%, 0.283 RCI, and 0.577 kappa. In addition, several ensemble classifiers enhanced the multi-categorical classification performance. The transfer learning incorporated with ensemble classifier of clustering and voting approach presented the best performance with accuracy of 36.7%, 0.053 RCI, and 0.225 kappa in the 10 retinal diseases classification problem. First, due to the small size of datasets, the deep learning techniques in this study were ineffective to be applied in clinics where numerous patients suffering from various types of retinal disorders visit for diagnosis and treatment. Second, we found that the transfer learning incorporated with ensemble classifiers can improve the classification performance in order to detect multi-categorical retinal diseases. Further studies should confirm the effectiveness of algorithms with large datasets obtained from hospitals.

Detecting gait abnormalities after concussion or mild traumatic brain injury: A systematic review of single-task, dual-task, and complex gait.

PubMed

Fino, Peter C; Parrington, Lucy; Pitt, Will; Martini, Douglas N; Chesnutt, James C; Chou, Li-Shan; King, Laurie A

2018-05-01

While a growing number of studies have investigated the effects of concussion or mild traumatic brain injury (mTBI) on gait, many studies use different experimental paradigms and outcome measures. The path for translating experimental studies for objective clinical assessments of gait is unclear. This review asked 2 questions: 1) is gait abnormal after concussion/mTBI, and 2) what gait paradigms (single-task, dual-task, complex gait) detect abnormalities after concussion. Data sources included MEDLINE/PubMed, Scopus, Web of Science, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) accessed on March 14, 2017. Original research articles reporting gait outcomes in people with concussion or mTBI were included. Studies of moderate, severe, or unspecified TBI, and studies without a comparator were excluded. After screening 233 articles, 38 studies were included and assigned to one or more sections based on the protocol and reported outcomes. Twenty-six articles reported single-task simple gait outcomes, 24 reported dual-task simple gait outcomes, 21 reported single-task complex gait outcomes, and 10 reported dual-task complex gait outcomes. Overall, this review provides evidence for two conclusions: 1) gait is abnormal acutely after concussion/mTBI but generally resolves over time; and 2) the inconsistency of findings, small sample sizes, and small number of studies examining homogenous measures at the same time-period post-concussion highlight the need for replication across independent populations and investigators. Future research should concentrate on dual-task and complex gait tasks, as they showed promise for detecting abnormal locomotor function outside of the acute timeframe. Additionally, studies should provide detailed demographic and clinical characteristics to enable more refined comparisons across studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Potential Drug-Drug Interactions in a Cohort of Elderly, Polymedicated Primary Care Patients on Antithrombotic Treatment.

PubMed

Schneider, Katharina Luise; Kastenmüller, Kathrin; Weckbecker, Klaus; Bleckwenn, Markus; Böhme, Miriam; Stingl, Julia Carolin

2018-06-01

Drug-drug interactions (DDIs) are an important risk factor for adverse drug reactions. Older, polymedicated patients are particularly affected. Although antithrombotics have been detected as high-risk drugs for DDIs, data on older patients exposed to them are scarce. Baseline data of 365 IDrug study outpatients (≥ 60 years, use of an antithrombotic and one or more additional long-term drug) were analyzed regarding potential drug-drug interactions (pDDIs) with a clinical decision support system. Data included prescription and self-medication drugs. The prevalence of having one or more pDDI was 85.2%. The median number of alerts per patient was three (range 0-17). For 58.4% of the patients, potential severe/contraindicated interactions were detected. Antiplatelets and non-steroidal anti-inflammatory drugs (NSAIDs) showed the highest number of average pDDI alert involvements per use (2.9 and 2.2, respectively). For NSAIDs, also the highest average number of severe/contraindicated alert involvements per use (1.2) was observed. 91.8% of all pDDI involvements concerned the 25 most frequently used drug classes. 97.5% of the severe/contraindicated pDDIs were attributed to only nine different potential clinical manifestations. The most common management recommendation for severe/contraindicated pDDIs was to intensify monitoring. Number of drugs was the only detected factor significantly associated with increased number of pDDIs (p < 0.001). The findings indicate a high risk for pDDIs in older, polymedicated patients on antithrombotics. As a consequence of patients' frequently similar drug regimens, the variety of potential clinical manifestations was small. Awareness of these pDDI symptoms and the triggering drugs as well as patients' self-medication use may contribute to increased patient safety.

Optimization of self-aligned double patterning (SADP)-compliant layout designs using pattern matching for sub-20nm metal routing

NASA Astrophysics Data System (ADS)

Wang, Lynn T.-N.; Schroeder, Uwe Paul; Madhavan, Sriram

2017-03-01

A pattern-based methodology for optimizing SADP-compliant layout designs is developed based on identifying cut mask patterns and replacing them with pre-characterized fixing solutions. A pattern-based library of difficult-tomanufacture cut patterns with pre-characterized fixing solutions is built. A pattern-based engine searches for matching patterns in the decomposed layouts. When a match is found, the engine opportunistically replaces the detected pattern with a pre-characterized fixing solution. The methodology was demonstrated on a 7nm routed metal2 block. A small library of 30 cut patterns increased the number of more manufacturable cuts by 38% and metal-via enclosure by 13% with a small parasitic capacitance impact of 0.3%.

Best Phd thesis Prize: Statistical analysis of ALFALFA galaxies: insights in galaxy

NASA Astrophysics Data System (ADS)

Papastergis, E.

2013-09-01

We use the rich dataset of local universe galaxies detected by the ALFALFA 21cm survey to study the statistical properties of gas-bearing galaxies. In particular, we measure the number density of galaxies as a function of their baryonic mass ("baryonic mass function") and rotational velocity ("velocity width function"), and we characterize their clustering properties ("two-point correlation function"). These statistical distributions are determined by both the properties of dark matter on small scales, as well as by the complex baryonic processes through which galaxies form over cosmic time. We interpret the ALFALFA measurements with the aid of publicly available cosmological N-body simulations and we present some key results related to galaxy formation and small-scale cosmology.

An expanding universe of small proteins.

PubMed

Hobbs, Errett C; Fontaine, Fanette; Yin, Xuefeng; Storz, Gisela

2011-04-01

Historically, small proteins (sproteins) of less than 50 amino acids, in their final processed forms or genetically encoded as such, have been understudied. However, both serendipity and more recent focused efforts have led to the identification of a number of new sproteins in both Gram-negative and Gram-positive bacteria. Increasing evidence demonstrates that sproteins participate in a wide array of cellular processes and exhibit great diversity in their mechanisms of action, yet general principles of sprotein function are emerging. This review highlights examples of sproteins that participate in cell signaling, act as antibiotics and toxins, and serve as structural proteins. We also describe roles for sproteins in detecting and altering membrane features, acting as chaperones, and regulating the functions of larger proteins. Published by Elsevier Ltd.

Weak Perturbations of Biochemical Oscillators

NASA Astrophysics Data System (ADS)

Gailey, Paul

2001-03-01

Biochemical oscillators may play important roles in gene regulation, circadian rhythms, physiological signaling, and sensory processes. These oscillations typically occur inside cells where the small numbers of reacting molecules result in fluctuations in the oscillation period. Some oscillation mechanisms have been reported that resist fluctuations and produce more stable oscillations. In this paper, we consider the use of biochemical oscillators as sensors by comparing inherent fluctuations with the effects of weak perturbations to one of the reactants. Such systems could be used to produce graded responses to weak stimuli. For example, a leading hypothesis to explain geomagnetic navigation in migrating birds and other animals is based on magnetochemical reactions. Because the magnitude of magnetochemical effects is small at geomagnetic field strengths, a sensitive, noise resistant detection scheme would be required.

Optimal strategies for observation of active galactic nuclei variability with Imaging Atmospheric Cherenkov Telescopes

NASA Astrophysics Data System (ADS)

Giomi, Matteo; Gerard, Lucie; Maier, Gernot

2016-07-01

Variable emission is one of the defining characteristic of active galactic nuclei (AGN). While providing precious information on the nature and physics of the sources, variability is often challenging to observe with time- and field-of-view-limited astronomical observatories such as Imaging Atmospheric Cherenkov Telescopes (IACTs). In this work, we address two questions relevant for the observation of sources characterized by AGN-like variability: what is the most time-efficient way to detect such sources, and what is the observational bias that can be introduced by the choice of the observing strategy when conducting blind surveys of the sky. Different observing strategies are evaluated using simulated light curves and realistic instrument response functions of the Cherenkov Telescope Array (CTA), a future gamma-ray observatory. We show that strategies that makes use of very small observing windows, spread over large periods of time, allows for a faster detection of the source, and are less influenced by the variability properties of the sources, as compared to strategies that concentrate the observing time in a small number of large observing windows. Although derived using CTA as an example, our conclusions are conceptually valid for any IACTs facility, and in general, to all observatories with small field of view and limited duty cycle.

Embedded fiber optic sensors for monitoring processing, quality and structural health of resin transfer molded components

NASA Astrophysics Data System (ADS)

Keulen, C.; Rocha, B.; Yildiz, M.; Suleman, A.

2011-07-01

Due to their small size and flexibility fiber optics can be embedded into composite materials with little negative effect on strength and reliability of the host material. Fiber optic sensors such as Fiber Bragg Gratings (FBG) or Etched Fiber Sensors (EFS) can be used to detect a number of relevant parameters such as flow, degree of cure, quality and structural health throughout the life of a composite component. With a detection algorithm these embedded sensors can be used to detect damage in real time while the component remains in service. This paper presents the research being conducted on the use of fiber optic sensors for process and Structural Health Monitoring (SHM) of Resin Transfer Molded (RTM) composite structures. Fiber optic sensors are used at all life stages of an RTM composite panel. A laboratory scale RTM apparatus was developed with the capability of visually monitoring the resin filling process. A technique for embedding fiber optic sensors with this apparatus has also been developed. Both FBGs and EFSs have been embedded in composite panels using the apparatus. EFSs to monitor the fabrication process, specifically resin flow have been embedded and shown to be capable of detecting the presence of resin at various locations as it is injected into the mold. Simultaneously these sensors were multiplexed on the same fiber with FBGs, which have the ability to measure strain. Since multiple sensors can be multiplexed on a single fiber the number of ingress/egress locations required per sensor can be significantly reduced. To characterize the FBGs for strain detection tensile test specimens with embedded FBG sensors have been produced. These specimens have been instrumented with a resistive strain gauge for benchmarking. Both specimens and embedded sensors were characterized through tensile testing. Furthermore FBGs have been embedded into composite panels in a manner that is conducive to detection of Lamb waves generated with a centrally located PZT. To sense Lamb waves a high speed, high precision sensing technique is required to acquire data from embedded FBGs due to the high velocities and small strain amplitudes of these guided waves. A technique based on a filter consisting of a tunable FBG was developed. Since this filter is not dependant on moving parts, tests executed with this filter concluded with the detection of Lamb waves, removing the influence of temperature and operational strains. A damage detection algorithm was developed to detect and localize cracks and delaminations.

Improved computer-aided detection of small polyps in CT colonography using interpolation for curvature estimationa

PubMed Central

Liu, Jiamin; Kabadi, Suraj; Van Uitert, Robert; Petrick, Nicholas; Deriche, Rachid; Summers, Ronald M.

2011-01-01

Purpose: Surface curvatures are important geometric features for the computer-aided analysis and detection of polyps in CT colonography (CTC). However, the general kernel approach for curvature computation can yield erroneous results for small polyps and for polyps that lie on haustral folds. Those erroneous curvatures will reduce the performance of polyp detection. This paper presents an analysis of interpolation’s effect on curvature estimation for thin structures and its application on computer-aided detection of small polyps in CTC. Methods: The authors demonstrated that a simple technique, image interpolation, can improve the accuracy of curvature estimation for thin structures and thus significantly improve the sensitivity of small polyp detection in CTC. Results: Our experiments showed that the merits of interpolating included more accurate curvature values for simulated data, and isolation of polyps near folds for clinical data. After testing on a large clinical data set, it was observed that sensitivities with linear, quadratic B-spline and cubic B-spline interpolations significantly improved the sensitivity for small polyp detection. Conclusions: The image interpolation can improve the accuracy of curvature estimation for thin structures and thus improve the computer-aided detection of small polyps in CTC. PMID:21859029

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

Masoumi, Ali; Vilenkin, Alexander; Yamada, Masaki, E-mail: ali@cosmos.phy.tufts.edu, E-mail: vilenkin@cosmos.phy.tufts.edu, E-mail: Masaki.Yamada@tufts.edu

In the landscape perspective, our Universe begins with a quantum tunneling from an eternally-inflating parent vacuum, followed by a period of slow-roll inflation. We investigate the tunneling process and calculate the probability distribution for the initial conditions and for the number of e-folds of slow-roll inflation, modeling the landscape by a small-field one-dimensional random Gaussian potential. We find that such a landscape is fully consistent with observations, but the probability for future detection of spatial curvature is rather low, P ∼ 10{sup −3}.

Using of dynamic speckled speckles with a small number of scatterers for study of suspension of Chlamydia

NASA Astrophysics Data System (ADS)

Ulyanov, Sergey; Filonova, Nadezhda; Ulianova, Onega; Utz, Sergey; Moiseeva, Yulia; Subbotina, Irina; Kalduzova, Irina; Larionova, Olga; Feodorova, Valentina

2018-04-01

Theory of formation of speckled speckles at diffraction of focused Gaussian beam in the suspension, containing of Chlamydia trachomatis (CT) is presented. Optical model of scattering of light in suspension of Chlamydia is suggested. Formula for bandwidth of spectrum of intensity fluctuations in speckled speckles is derived. It has been demonstrated, that speckle-microscopy can be used for detection of CT bacteria for any concentration of the relevant cells in suspension.

Exploring the Feasibility of Reputation Models for Improving P2P Routing under Churn

NASA Astrophysics Data System (ADS)

Sànchez-Artigas, Marc; García-López, Pedro; Herrera, Blas

Reputation mechanisms help peer-to-peer (P2P) networks to detect and avoid unreliable or uncooperative peers. Recently, it has been discussed that routing protocols can be improved by conditioning routing decisions to the past behavior of forwarding peers. However, churn — the continuous process of node arrival and departure — may severely hinder the applicability of rating mechanisms. In particular, short lifetimes mean that reputations are often generated from a small number of transactions.

Proceedings of the Ground-Water Detection Workshop Held at Vicksburg, Mississippi on 12-14 January 1982.

DTIC Science & Technology

1984-12-01

shales and hard aquiferic car- bonates. Therefore, small confined and perched aquifers can occur in a number of localities. The basement complex...the region that extends from Saudia Arabia all the way into Algeria, Morocco, and Tunisia is from older to younger strata. The major aquifer in the... aquifers all the way down the stratigraphic section--a phreatic one at the top, then semi- confined and confined aquifers until we get to upper

High Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment Monitoring of Prostate Cancer

DTIC Science & Technology

2012-07-01

number of high resolution PET experiments including the dual-ring small field- of-view configuration shown at left in Figure 5 . The benchtop system...detectors having 26 x 40 arrays of 1mm x 1mm x 1mm detector elements is shown at right in Figure 5 . Detectors used for probe experiments shown in...Figure 13). In the series of experiments geared towards PET application, but with the results applicable to the present single gamma case, we have

Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.

PubMed

Ferreira, Diogo C; van der Linden, Marx G; de Oliveira, Leandro C; Onuchic, José N; de Araújo, Antônio F Pereira

2016-04-01

Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations. © 2016 Wiley Periodicals, Inc.

Finding Cardinality Heavy-Hitters in Massive Traffic Data and Its Application to Anomaly Detection

NASA Astrophysics Data System (ADS)

Ishibashi, Keisuke; Mori, Tatsuya; Kawahara, Ryoichi; Hirokawa, Yutaka; Kobayashi, Atsushi; Yamamoto, Kimihiro; Sakamoto, Hitoaki; Asano, Shoichiro

We propose an algorithm for finding heavy hitters in terms of cardinality (the number of distinct items in a set) in massive traffic data using a small amount of memory. Examples of such cardinality heavy-hitters are hosts that send large numbers of flows, or hosts that communicate with large numbers of other hosts. Finding these hosts is crucial to the provision of good communication quality because they significantly affect the communications of other hosts via either malicious activities such as worm scans, spam distribution, or botnet control or normal activities such as being a member of a flash crowd or performing peer-to-peer (P2P) communication. To precisely determine the cardinality of a host we need tables of previously seen items for each host (e. g., flow tables for every host) and this may infeasible for a high-speed environment with a massive amount of traffic. In this paper, we use a cardinality estimation algorithm that does not require these tables but needs only a little information called the cardinality summary. This is made possible by relaxing the goal from exact counting to estimation of cardinality. In addition, we propose an algorithm that does not need to maintain the cardinality summary for each host, but only for partitioned addresses of a host. As a result, the required number of tables can be significantly decreased. We evaluated our algorithm using actual backbone traffic data to find the heavy-hitters in the number of flows and estimate the number of these flows. We found that while the accuracy degraded when estimating for hosts with few flows, the algorithm could accurately find the top-100 hosts in terms of the number of flows using a limited-sized memory. In addition, we found that the number of tables required to achieve a pre-defined accuracy increased logarithmically with respect to the total number of hosts, which indicates that our method is applicable for large traffic data for a very large number of hosts. We also introduce an application of our algorithm to anomaly detection. With actual traffic data, our method could successfully detect a sudden network scan.

Small Business Procurement Event

DTIC Science & Technology

2014-08-13

Small Business Procurement Event 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK...NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Department of the Navy,Office of Small Business Programs,720 Kennon...distribution unlimited 13. SUPPLEMENTARY NOTES NDIA 27th Navy Gold Coast Small Business Procurement Event, 12-13 Aug 2014, San Diego, CA. 14. ABSTRACT

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.

MET exon 14 skipping defines a unique molecular class of non-small cell lung cancer.

PubMed

Zheng, Difan; Wang, Rui; Ye, Ting; Yu, Su; Hu, Haichuan; Shen, Xuxia; Li, Yuan; Ji, Hongbin; Sun, Yihua; Chen, Haiquan

2016-07-05

Recurrent MET exon 14 splicing has been revealed in lung cancers and is a promising therapeutic target. Because we have limited knowledge about the natural history of MET mutant tumors, the current study was aiming to determine the clinical and pathological characteristics in non-small cell lung cancers (NSCLC). Twenty-three patients (1.3%) were positive for MET exon 14 skipping. Patients with MET exon 14 skipping displayed unique characteristics: female, non-smokers, earlier pathology stage and older age. MET exon 14 skipping indicated an early event as other drivers in lung cancer, while MET copy number gain was more likely a late event in lung cancer. Overall survival (OS) of patients harboring MET exon 14 skipping was longer than patients with KRAS mutation. Almost four-fifths of the lung tumors with MET exon 14 skipping had EGFR and/or HER2 gene copy number gains. EGFR inhibitor showed moderate antitumor activity in treatment of a patient harboring MET exon 14 skipping. From October 2007 to June 2013, we screened 1770 patients with NSCLC and correlated MET status with clinical pathologic characteristics and mutations in EGFR, KRAS, BRAF, HER2, and ALK. Quantitative Real-Time PCR was used to detect MET gene copy number gain. Immunohistochemistry (IHC) was also performed to screen MET exon 14 skipping. Clinicopathological characteristics and survival information were analyzed. MET exon 14 skipping was detected in 1.3% (23/1770) of the Chinese patients with NSCLC. MET exon 14 skipping defined a new molecular subset of NSCLC with identifiable clinical characteristics. The therapeutic EGFR inhibitors might be an alternative treatment for patients with MET mutant NSCLC.

[Usefulness of continuous glucose monitoring system (CGMS) in monitoring glycaemic profile in small children with diabetes type 1].

PubMed

Głowińska-Olszewska, Barbara; Urban, Mirosława; Peczyńska, Jadwiga; Florys, Bozena; Kowalewski, Marek

2005-01-01

Improved methods of diabetes therapy result in a near normoglycaemic state in many patients. This leads however unfortunately to more frequent hypoglycaemic incidents. Particularly small children, whose nervous system is not fully mature, are at high risk of central nervous system damage in case of hypoglycaemia. A new method of detail monitoring of glycaemia provides CGMS system. The aim of the study was to compare the glycaemic profile, with high attention to hypoglycaemia in groups of young and older children with diabetes type 1, using CGMS and routine glucose meter. We studied 32 children with diabetes type 1. Children were divided into groups: group I--small children, n=17 (<7 yrs of age), mean age 5,8 years, with disease duration--2,46 years, with mean HbA1c level--7,22%, and group II--older children, n=15 (>10 years of age), mean age--12 years, with disease duration--3 years, with HbA1c level--7,21%. Continuous glucose monitoring system (CGMS), by MiniMed, was applied in outpatient or hospital conditions, after short training of patient and parents; together with routine glucose meter measurements, 4-8 times/24 hours. In 9 patients from small children group CGMS was repeated after 2 months. Hypoglycaemic incidents detected with CGMS were similar in both groups: 4,6 in I group vs. 4,2 in II group (ns). Hypoglycaemic incidents found with meter were lower in I group--1,6 vs. 2,3 in II group (ns). Mean hypoglycaemic time/24 hour was longer in small children group: 101 min vs. 74 min in group II (p<00,05). In I group we found higher number of hypoglycaemic incidents during the night compared to group II--1,7 vs. 0,8 (p<00,05) and longer duration of night hypoglycaemia: in I group--56 min vs. 32 min in group II (p<00,05). Repeated CGMS study in 9 children from I group revealed decreased mean time of hypoglycaemia/24 hours from 134 min/24 h to 90 min/24 h (p<00,05) and decreased time of night hypoglycaemia from 65 min to 40 min (p<00,05), with a comparable number of hypoglycaemic incidents. Hypoglycaemic incidents found with routine meter measurements in small children were 1,6 vs. 4,6 hypoglycaemia found with CGMS (p<00,05), in the older children group routine measurement found 2,3 hypoglycaemia vs. 4,2 detected with CGMS (ns). 1. CGMS can be particularly usefull in monitoring glucose profile and detecting hypoglycaemia incidents, mainly nocturnal in small children. 2. CGMS allows to verify meal dose of insulin and to decrease postprandial hyperglycaemia. 3. Modification of insulin therapy on the base of CGMS helps to decrease the time of hypoglycaemia and hyperglycemia, particularly during the night.

The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel

PubMed Central

Laurie, Cathy C.; Chasalow, Scott D.; LeDeaux, John R.; McCarroll, Robert; Bush, David; Hauge, Brian; Lai, Chaoqiang; Clark, Darryl; Rocheford, Torbert R.; Dudley, John W.

2004-01-01

In one of the longest-running experiments in biology, researchers at the University of Illinois have selected for altered composition of the maize kernel since 1896. Here we use an association study to infer the genetic basis of dramatic changes that occurred in response to selection for changes in oil concentration. The study population was produced by a cross between the high- and low-selection lines at generation 70, followed by 10 generations of random mating and the derivation of 500 lines by selfing. These lines were genotyped for 488 genetic markers and the oil concentration was evaluated in replicated field trials. Three methods of analysis were tested in simulations for ability to detect quantitative trait loci (QTL). The most effective method was model selection in multiple regression. This method detected ∼50 QTL accounting for ∼50% of the genetic variance, suggesting that >50 QTL are involved. The QTL effect estimates are small and largely additive. About 20% of the QTL have negative effects (i.e., not predicted by the parental difference), which is consistent with hitchhiking and small population size during selection. The large number of QTL detected accounts for the smooth and sustained response to selection throughout the twentieth century. PMID:15611182

Improved In vivo Assessment of Pulmonary Fibrosis in Mice using X-Ray Dark-Field Radiography

NASA Astrophysics Data System (ADS)

Yaroshenko, Andre; Hellbach, Katharina; Yildirim, Ali Önder; Conlon, Thomas M.; Fernandez, Isis Enlil; Bech, Martin; Velroyen, Astrid; Meinel, Felix G.; Auweter, Sigrid; Reiser, Maximilian; Eickelberg, Oliver; Pfeiffer, Franz

2015-12-01

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease with a median life expectancy of 4-5 years after initial diagnosis. Early diagnosis and accurate monitoring of IPF are limited by a lack of sensitive imaging techniques that are able to visualize early fibrotic changes at the epithelial-mesenchymal interface. Here, we report a new x-ray imaging approach that directly visualizes the air-tissue interfaces in mice in vivo. This imaging method is based on the detection of small-angle x-ray scattering that occurs at the air-tissue interfaces in the lung. Small-angle scattering is detected with a Talbot-Lau interferometer, which provides the so-called x-ray dark-field signal. Using this imaging modality, we demonstrate-for the first time-the quantification of early pathogenic changes and their correlation with histological changes, as assessed by stereological morphometry. The presented radiography method is significantly more sensitive in detecting morphological changes compared with conventional x-ray imaging, and exhibits a significantly lower radiation dose than conventional x-ray CT. As a result of the improved imaging sensitivity, this new imaging modality could be used in future to reduce the number of animals required for pulmonary research studies.

Viral metagenomic analysis of feces of wild small carnivores

PubMed Central

2014-01-01

Background Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores. PMID:24886057

Development of a surface-enhanced Raman technique for biomarker studies on Mars.

PubMed

Dunn, Darrell S; Sridhar, Narasi; Miller, Michael A; Price, Kendra T; Pabalan, Roberto; Abrajano, Teofilo A

2007-01-01

Raman spectroscopy has been identified as a potentially useful tool to collect evidence of past or present life on extraterrestrial bodies. However, it is limited by its inherently low signal strength. In this investigation, laboratory tests were conducted using surface-enhanced Raman spectroscopy (SERS) in an "inverted" mode to detect the presence of organic compounds that may be similar to possible biomarkers present on Mars. SERS was used to overcome the inherently low signal intensity of Raman spectroscopy and was an effective method for detecting small concentrations of organic compounds on a number of surfaces. For small organic molecules, dissolution of the molecule to be analyzed in a suitable solvent and depositing it on a prepared SERS substrate for analysis is possible. However, for larger molecules, an "inverted" SERS (iSERS) technique was shown to be effective. In iSERS, nanoparticles of silver or gold were deposited on the mineral substrate/organic compound to be analyzed. Benzotriazole, benzoic acid, and phthalic acid were used as test organic analogs and the iSERS technique was able to detect femtomole levels of the analytes. The interference from various mineral substrates was also examined. Different methods of depositing silver particles were evaluated, including ion beam-assisted vapor deposition and deposition from aqueous colloidal suspensions.

Effectiveness of cross polarized light and fluorescence diagnosis for detection of sub-clinical and clinical actinic keratosis during imiquimod treatment.

PubMed

Ortonne, Jean-Paul; Gupta, Girish; Ortonne, Nicolas; Duteil, Luc; Queille, Catherine; Mallefet, Pascal

2010-07-01

During treatment of actinic keratosis (AK) lesions with imiquimod sub-clinical lesions often become visible. It is, however, unclear whether these sub-clinical lesions would be detectable beforehand. The aim of this pilot study was to compare two techniques, cross polarized light photography (CPL) and fluorescence diagnosis (FD) using methyllevulinic acid and illumination with Wood's lamp for their ability to detect sub-clinical lesions. These findings were also compared with biopsy results taken before and after treatment with imiquimod 5% cream or vehicle. Twelve patients with at least five clinically visible AK lesions in a single contiguous 20 cm(2) area on the head were recruited. Patient eligibility was determined at the screening visit, when they were randomized to treatment. The randomization was 3:1, active to vehicle (nine treated with imiquimod, three with vehicle cream) for a total duration of 24 weeks (six clinic visits). Patients were assessed for baseline AK lesion counts (clinical and sub-clinical) at the screening visit and final counts at week 20. The number of clinically observed AK lesions was significantly lower at week 12 and week 20 compared with baseline following imiquimod treatment versus vehicle. The number of counted lesions were significantly higher using the CPL method compared with clinical counting with imiquimod treatment at baseline (8.3 +/- 3.4 vs 5.8 +/- 1.3; P = 0.027) and week 20 (4.8 +/- 2.4 vs 3.0 +/- 1.7; P = 0.02) but not in the vehicle group. The FD lesion counting method did not show a significant increase in the number of detected lesions compared with clinical analysis in the imiquimod and placebo groups but when comparisons were performed using pooled data (treatments and visits combined) the results were significant. The number of sub-clinical and clinical AK lesions detected during treatment with imiquimod can be better demonstrated using the methods of CPL and FD, but statistical significance was reached only using the CPL method. This is only a preliminary study with a small number of patients and as a result it is difficult to conclude both statistical and clinical significance. However, results were encouraging and indicate that larger studies are needed to demonstrate the relevance of these two new methods for improved detection of clinical and especially sub-clinical AK lesions.

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

Role of Computer Aided Diagnosis (CAD) in the detection of pulmonary nodules on 64 row multi detector computed tomography.

PubMed

Prakashini, K; Babu, Satish; Rajgopal, K V; Kokila, K Raja

2016-01-01

To determine the overall performance of an existing CAD algorithm with thin-section computed tomography (CT) in the detection of pulmonary nodules and to evaluate detection sensitivity at a varying range of nodule density, size, and location. A cross-sectional prospective study was conducted on 20 patients with 322 suspected nodules who underwent diagnostic chest imaging using 64-row multi-detector CT. The examinations were evaluated on reconstructed images of 1.4 mm thickness and 0.7 mm interval. Detection of pulmonary nodules, initially by a radiologist of 2 years experience (RAD) and later by CAD lung nodule software was assessed. Then, CAD nodule candidates were accepted or rejected accordingly. Detected nodules were classified based on their size, density, and location. The performance of the RAD and CAD system was compared with the gold standard that is true nodules confirmed by consensus of senior RAD and CAD together. The overall sensitivity and false-positive (FP) rate of CAD software was calculated. Of the 322 suspected nodules, 221 were classified as true nodules on the consensus of senior RAD and CAD together. Of the true nodules, the RAD detected 206 (93.2%) and 202 (91.4%) by the CAD. CAD and RAD together picked up more number of nodules than either CAD or RAD alone. Overall sensitivity for nodule detection with the CAD program was 91.4%, and FP detection per patient was 5.5%. The CAD showed comparatively higher sensitivity for nodules of size 4-10 mm (93.4%) and nodules in hilar (100%) and central (96.5%) location when compared to RAD's performance. CAD performance was high in detecting pulmonary nodules including the small size and low-density nodules. CAD even with relatively high FP rate, assists and improves RAD's performance as a second reader, especially for nodules located in the central and hilar region and for small nodules by saving RADs time.

Photoacoustic sensor for medical diagnostics

NASA Astrophysics Data System (ADS)

Wolff, Marcus; Groninga, Hinrich G.; Harde, Hermann

2004-03-01

The development of new optical sensor technologies has a major impact on the progress of diagnostic methods. Of the permanently increasing number of non-invasive breath tests, the 13C-Urea Breath Test (UBT) for the detection of Helicobacter pylori is the most prominent. However, many recent developments, like the detection of cancer by breath test, go beyond gastroenterological applications. We present a new detection scheme for breath analysis that employs an especially compact and simple set-up. Photoacoustic Spectroscopy (PAS) represents an offset-free technique that allows for short absorption paths and small sample cells. Using a single-frequency diode laser and taking advantage of acoustical resonances of the sample cell, we performed extremely sensitive and selective measurements. The smart data processing method contributes to the extraordinary sensitivity and selectivity as well. Also, the reasonable acquisition cost and low operational cost make this detection scheme attractive for many biomedical applications. The experimental set-up and data processing method, together with exemplary isotope-selective measurements on carbon dioxide, are presented.

Biosensors for Non-Invasive Detection of Celiac Disease Biomarkers in Body Fluids.

PubMed

Pasinszki, Tibor; Krebsz, Melinda

2018-06-16

Celiac disease is a chronic gluten-initiated autoimmune disorder that predominantly damages the mucosa of the small intestine in genetically-susceptible individuals. It affects a large and increasing number of the world’s population. The diagnosis of this disease and monitoring the response of patients to the therapy, which is currently a life-long gluten-free diet, require the application of reliable, rapid, sensitive, selective, simple, and cost-effective analytical tools. Celiac disease biomarker detection in full blood, serum, or plasma offers a non-invasive way to do this and is well-suited to being the first step of diagnosis. Biosensors provide a novel and alternative way to perform conventional techniques in biomarker sensing, in which electrode material and architecture play important roles in achieving sensitive, selective, and stable detection. There are many opportunities to build and modify biosensor platforms using various materials and detection methods, and the aim of the present review is to summarize developments in this field.

A Small Angle Scattering Sensor System for the Characterization of Combustion Generated Particulate

NASA Technical Reports Server (NTRS)

Feikema, Douglas A.; Kim, W.; Sivathanu, Yudaya

2007-01-01

One of the critical issues for the US space program is fire safety of the space station and future launch vehicles. A detailed understanding of the scattering signatures of particulate is essential for the development of a false alarm free fire detection system. This paper describes advanced optical instrumentation developed and applied for fire detection. The system is being designed to determine four important physical properties of disperse fractal aggregates and particulates including size distribution, number density, refractive indices, and fractal dimension. Combustion generated particulate are the primary detection target; however, in order to discriminate from other particulate, non-combustion generated particles should also be characterized. The angular scattering signature is measured and analyzed using two photon optical laser scattering. The Rayleigh-Debye-Gans (R-D-G) scattering theory for disperse fractal aggregates is utilized. The system consists of a pulsed laser module, detection module and data acquisition system and software to analyze the signals. The theory and applications are described.

Cerebral microbleeds: a guide to detection and interpretation.

PubMed

Greenberg, Steven M; Vernooij, Meike W; Cordonnier, Charlotte; Viswanathan, Anand; Al-Shahi Salman, Rustam; Warach, Steven; Launer, Lenore J; Van Buchem, Mark A; Breteler, Monique Mb

2009-02-01

Cerebral microbleeds (CMBs) are increasingly recognised neuroimaging findings in individuals with cerebrovascular disease and dementia, and in normal ageing. There has been substantial progress in the understanding of CMBs in recent years, particularly in the development of newer MRI methods for the detection of CMBs and the application of these techniques to population-based samples of elderly people. In this Review, we focus on these recent developments and their effects on two main questions: how CMBs are detected, and how CMBs should be interpreted. The number of CMBs detected depends on MRI characteristics, such as pulse sequence, sequence parameters, spatial resolution, magnetic field strength, and image post-processing, emphasising the importance of taking into account MRI technique in the interpretation of study results. Recent investigations with sensitive MRI techniques have indicated a high prevalence of CMBs in community-dwelling elderly people. We propose a procedural guide for identification of CMBs and suggest possible future approaches for elucidating the role of these common lesions as markers for, and contributors to, small-vessel brain disease.

Site specific probability of passive acoustic detection of humpback whale calls from single fixed hydrophones.

PubMed

Helble, Tyler A; D'Spain, Gerald L; Hildebrand, John A; Campbell, Gregory S; Campbell, Richard L; Heaney, Kevin D

2013-09-01

Passive acoustic monitoring of marine mammal calls is an increasingly important method for assessing population numbers, distribution, and behavior. A common mistake in the analysis of marine mammal acoustic data is formulating conclusions about these animals without first understanding how environmental properties such as bathymetry, sediment properties, water column sound speed, and ocean acoustic noise influence the detection and character of vocalizations in the acoustic data. The approach in this paper is to use Monte Carlo simulations with a full wave field acoustic propagation model to characterize the site specific probability of detection of six types of humpback whale calls at three passive acoustic monitoring locations off the California coast. Results show that the probability of detection can vary by factors greater than ten when comparing detections across locations, or comparing detections at the same location over time, due to environmental effects. Effects of uncertainties in the inputs to the propagation model are also quantified, and the model accuracy is assessed by comparing calling statistics amassed from 24,690 humpback units recorded in the month of October 2008. Under certain conditions, the probability of detection can be estimated with uncertainties sufficiently small to allow for accurate density estimates.

Types and numbers of sensilla on antennae and maxillary palps of small and large houseflies, Musca domestica (Diptera, Muscidae).

PubMed

Smallegange, Renate C; Kelling, Frits J; Den Otter, Cornelis J

2008-12-01

Houseflies, Musca domestica, obtained from a high-larval-density culture were significantly (ca. 1.5 times) smaller than those from a low-larval-density culture. The same held true for their antennae and maxillary palps. Structure, number, and distribution of sensilla on antennae and palps of small and large flies were investigated using Scanning electron microscopy and Transmission electron microscopy. In each funiculus three pits were present, two (Type I) consisting of several compartments and one (Type II) of one compartment. Four types of olfactory sensilla were detected: trichoid sensilla on the funiculi, basiconic sensilla on funiculi and palps, grooved sensilla on funiculi and in pits Type I, and clavate sensilla on funiculi and in pits Type II. Type I pits also contained striated sensilla (presumably hygroreceptors). Mechanosensory bristles were present on scapes, pedicels, and palps. Noninnervated microtrichia were found on the palps and all antennal segments. The large houseflies possessed nearly twice as much sensilla as the small flies. So far, we did not observe differences in behavior between small and large flies. We assumed that small flies, being olfactory less equipped than large flies, may be able to compensate for this by, e.g., visual cues or by their olfactory sensilla being more sensitive than those of large flies. To be able to answer these questions careful studies have to be done on the behavioral responses of small and large flies to environmental stimuli. In addition, electrophysiological studies should be performed to reveal whether the responses of individual sensilla of flies reared under different conditions have been changed. 2008 Wiley-Liss, Inc.

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.

Repeated Solid-state Dewetting of Thin Gold Films for Nanogap-rich Plasmonic Nanoislands.

PubMed

Kang, Minhee; Park, Sang-Gil; Jeong, Ki-Hun

2015-10-15

This work reports a facile wafer-level fabrication for nanogap-rich gold nanoislands for highly sensitive surface enhanced Raman scattering (SERS) by repeating solid-state thermal dewetting of thin gold film. The method provides enlarged gold nanoislands with small gap spacing, which increase the number of electromagnetic hotspots and thus enhance the extinction intensity as well as the tunability for plasmon resonance wavelength. The plasmonic nanoislands from repeated dewetting substantially increase SERS enhancement factor over one order-of-magnitude higher than those from a single-step dewetting process and they allow ultrasensitive SERS detection of a neurotransmitter with extremely low Raman activity. This simple method provides many opportunities for engineering plasmonics for ultrasensitive detection and highly efficient photon collection.

Repeated Solid-state Dewetting of Thin Gold Films for Nanogap-rich Plasmonic Nanoislands

PubMed Central

Kang, Minhee; Park, Sang-Gil; Jeong, Ki-Hun

2015-01-01

This work reports a facile wafer-level fabrication for nanogap-rich gold nanoislands for highly sensitive surface enhanced Raman scattering (SERS) by repeating solid-state thermal dewetting of thin gold film. The method provides enlarged gold nanoislands with small gap spacing, which increase the number of electromagnetic hotspots and thus enhance the extinction intensity as well as the tunability for plasmon resonance wavelength. The plasmonic nanoislands from repeated dewetting substantially increase SERS enhancement factor over one order-of-magnitude higher than those from a single-step dewetting process and they allow ultrasensitive SERS detection of a neurotransmitter with extremely low Raman activity. This simple method provides many opportunities for engineering plasmonics for ultrasensitive detection and highly efficient photon collection. PMID:26469768

Clearance of chlamydial elementary bodies from the conjunctival sac

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

Taylor, H.R.; Velez, V.L.

1987-07-01

The rate of disappearance of inactivated Chlamydia trachomatis elementary body (EB) preparations from the conjunctival sac was studied in monkeys. Direct fluorescent antibody (DFA) cytology showed that the majority of EB had been cleared from the eye within 24 hr of the inoculation of 1 X 10(6) inactivated EB, although small numbers of EB could be detected for up to 144 hr. The rate of clearance in normal and ocular immune animals did not differ, and formalin-killed and UV-inactivated EBs disappeared at a comparable rate. These studies suggest that chlamydial EB are cleared relatively quickly from the eye and supportmore » the notion that EBs detected by DFA cytology indicate the presence of current infection.« less

Automated Information System (AIS) Alarm System

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

Hunteman, W.

1997-05-01

The Automated Information Alarm System is a joint effort between Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratory to demonstrate and implement, on a small-to-medium sized local area network, an automated system that detects and automatically responds to attacks that use readily available tools and methodologies. The Alarm System will sense or detect, assess, and respond to suspicious activities that may be detrimental to information on the network or to continued operation of the network. The responses will allow stopping, isolating, or ejecting the suspicious activities. The number of sensors, the sensitivity of the sensors, themore » assessment criteria, and the desired responses may be set by the using organization to meet their local security policies.« less

Tracing Low-Mass Star Formation in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Petr-Gotzens, Monika; Zivkov, V.; Oliveira, J.

2017-06-01

Star formation in low metallicity environments is evidently occurring under different conditions than in our Milky Way. Lower metallicity implies a lower dust to gas ratio, most likely leading to less cooling efficiency at high density molecular cores where low mass stars are expected to form. We outline a project that aims to identify the low mass pre-main sequence populations within the Large and Small Magellanic Cloud. We developed an automatic detection algorithm that systematically analyses near-infrared colour-magnitude diagrammes constructed from the VMC (VISTA Magellanic Clouds) public survey data. In this poster we present our first results that show that we are able to detect significant numbers of PMS stars with masses down to 1.5 solar mass.

Investigations on the 1.7 micron residual absorption feature in the vegetation reflection spectrum

NASA Technical Reports Server (NTRS)

Verdebout, J.; Jacquemoud, S.; Andreoli, G.; Hosgood, B.; Sieber, A.

1993-01-01

The detection and interpretation of the weak absorption features associated with the biochemical components of vegetation is of great potential interest to a variety of applications ranging from classification to global change studies. This recent subject is also challenging because the spectral signature of the biochemicals is only detectable as a small distortion of the infrared spectrum which is mainly governed by water. Furthermore, the interpretation is complicated by complexity of the molecules (lignin, cellulose, starch, proteins) which contain a large number of different and common chemical bonds. In this paper, we present investigations on the absorption feature centered at 1.7 micron; these were conducted both on AVIRIS data and laboratory reflectance spectra of leaves.

Design and Analysis of Cost-Efficient Sensor Deployment for Tracking Small UAS with Agent-Based Modeling.

PubMed

Shin, Sangmi; Park, Seongha; Kim, Yongho; Matson, Eric T

2016-04-22

Recently, commercial unmanned aerial systems (UAS) have gained popularity. However, these UAS are potential threats to people in terms of safety in public places, such as public parks or stadiums. To reduce such threats, we consider a design, modeling, and evaluation of a cost-efficient sensor system that detects and tracks small UAS. In this research, we focus on discovering the best sensor deployments by simulating different types and numbers of sensors in a designated area, which provide reasonable detection rates at low costs. Also, the system should cover the crowded areas more thoroughly than vacant areas to reduce direct threats to people underneath. This research study utilized the Agent-Based Modeling (ABM) technique to model a system consisting of independent and heterogeneous agents that interact with each other. Our previous work presented the ability to apply ABM to analyze the sensor configurations with two types of radars in terms of cost-efficiency. The results from the ABM simulation provide a list of candidate configurations and deployments that can be referred to for applications in the real world environment.

Design and Analysis of Cost-Efficient Sensor Deployment for Tracking Small UAS with Agent-Based Modeling

PubMed Central

Shin, Sangmi; Park, Seongha; Kim, Yongho; Matson, Eric T.

2016-01-01

Recently, commercial unmanned aerial systems (UAS) have gained popularity. However, these UAS are potential threats to people in terms of safety in public places, such as public parks or stadiums. To reduce such threats, we consider a design, modeling, and evaluation of a cost-efficient sensor system that detects and tracks small UAS. In this research, we focus on discovering the best sensor deployments by simulating different types and numbers of sensors in a designated area, which provide reasonable detection rates at low costs. Also, the system should cover the crowded areas more thoroughly than vacant areas to reduce direct threats to people underneath. This research study utilized the Agent-Based Modeling (ABM) technique to model a system consisting of independent and heterogeneous agents that interact with each other. Our previous work presented the ability to apply ABM to analyze the sensor configurations with two types of radars in terms of cost-efficiency. The results from the ABM simulation provide a list of candidate configurations and deployments that can be referred to for applications in the real world environment. PMID:27110790

Fast Neutron Detection using Pixelated CdZnTe Spectrometers

DOE PAGES

Streicher, Michael; Goodman, David; Zhu, Yuefeng; ...

2017-05-29

One important important signature of special nuclear materials (SNM) are fast neutrons. Fast neutrons have a low natural background rate and readily penetrate high atomic number materials which easily shield gamma-ray signatures. Thus, fast neutrons provide a complementary signal to gamma rays for detecting shielded SNM. Scattering kinematics dictate that a large nucleus (such as Cd or Te) will recoil with small kinetic energy after an elastic collision with a fast neutron. Charge carrier recombination and quenching further reduce the recorded energy deposited. Thus, the energy threshold of CdZnTe detectors must be very low in order to sense the smallmore » signals from these recoils. Here, the threshold was reduced to less than 5 keVee to demonstrate that the 5.9 keV x-ray line from 55Fe could be separated from electronic noise. Elastic scattering neutron interactions were observed as small energy depositions (less than 20 keVee) using digitally-sampled pulse waveforms from pixelated CdZnTe detectors. Characteristic gamma-ray lines from inelastic neutron scattering were also observed.« less

Search for Sugars and Related Compounds in Residues Produced from the UV Irradiation of Astrophysical Ice Analogs

NASA Technical Reports Server (NTRS)

Sandford, S. A.; Nuevo, M.; Materese, C. K.; Cooper, G. W.

2015-01-01

A large variety of organics of biological and prebiotic interests have been detected in meteorites, including one sugar and several sugar acids and sugar alcohols [1]. The presence of these compounds in meteorites, along with amino acids, amphiphiles, and nucleobases [2-4], indicates that molecules essential to life can be formed abiotically under astrophysical conditions. This hypothesis is supported by extensive laboratory studies involving the formation of complex organic molecules from the ultraviolet (UV) irradiation of astrophysical ice analogs (H2O, CO, CO2, CH3OH, CH4, NH3, etc.). These studies show that the organic residues recovered at room temperature contain many of the same compounds as those found in meteorites[3,58]. However, to the best of our knowledge, no systematic search for the presence of sugars and sugar derivatives in such laboratory residues have been reported to date. Only a limited number of small (greater than 4 C atoms) sugar-related compounds such as glycerol and glyceric acid [9], and more recently small (2-4 C atoms) aldehydes [10] have been detected in residues.

Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys

PubMed Central

Berry, David; Gutierrez, Tony

2017-01-01

Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira, and Thalassolituus, as well as the Alphaproteobacterial genus Thalassospira. Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys. PMID:28567035

Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys.

PubMed

Berry, David; Gutierrez, Tony

2017-01-01

Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira , and Thalassolituus , as well as the Alphaproteobacterial genus Thalassospira . Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys.

Accounting for imperfect detection and survey bias in statistical analysis of presence-only data

USGS Publications Warehouse

Dorazio, Robert M.

2014-01-01

Using mathematical proof and simulation-based comparisons, I demonstrate that biases induced by errors in detection or biased selection of survey locations can be reduced or eliminated by using the hierarchical model to analyse presence-only data in conjunction with counts observed in planned surveys. I show that a relatively small number of high-quality data (from planned surveys) can be used to leverage the information in presence-only observations, which usually have broad spatial coverage but may not be informative of both occurrence and detectability of individuals. Because a variety of sampling protocols can be used in planned surveys, this approach to the analysis of presence-only data is widely applicable. In addition, since the point-process model is formulated at the level of an individual, it can be extended to account for biological interactions between individuals and temporal changes in their spatial distributions.

Defect Detection in Superconducting Radiofrequency Cavity Surface Using C + + and OpenCV

NASA Astrophysics Data System (ADS)

Oswald, Samantha; Thomas Jefferson National Accelerator Facility Collaboration

2014-03-01

Thomas Jefferson National Accelerator Facility (TJNAF) uses superconducting radiofrequency (SRF) cavities to accelerate an electron beam. If theses cavities have a small particle or defect, it can degrade the performance of the cavity. The problem at hand is inspecting the cavity for defects, little bubbles of niobium on the surface of the cavity. Thousands of pictures have to be taken of a single cavity and then looked through to see how many defects were found. A C + + program with Open Source Computer Vision (OpenCV) was constructed to reduce the number of hours searching through the images and finds all the defects. Using this code, the SRF group is now able to use the code to identify defects in on-going tests of SRF cavities. Real time detection is the next step so that instead of taking pictures when looking at the cavity, the camera will detect all the defects.

Wearable vital parameters monitoring system

NASA Astrophysics Data System (ADS)

Caramaliu, Radu Vadim; Vasile, Alexandru; Bacis, Irina

2015-02-01

The system we propose monitors body temperature, heart rate and beside this, it tracks if the person who wears it suffers a faint. It uses a digital temperature sensor, a pulse sensor and a gravitational acceleration sensor to monitor the eventual faint or small heights free falls. The system continuously tracks the GPS position when available and stores the last valid data. So, when measuring abnormal vital parameters the module will send an SMS, using the GSM cellular network , with the person's social security number, the last valid GPS position for that person, the heart rate, the body temperature and, where applicable, a valid fall alert or non-valid fall alert. Even though such systems exist, they contain only faint detection or heart rate detection. Usually there is a strong correlation between low/high heart rate and an eventual faint. Combining both features into one system results in a more reliable detection device.

Review: Magnetic Fields of O-Type Stars

NASA Astrophysics Data System (ADS)

Wade, G. A.; MiMeS Collaboration

2015-04-01

Since 2002, strong, organized magnetic fields have been firmly detected at the surfaces of about 10 Galactic O-type stars. In this paper I will review the characteristics of the inferred fields of individual stars as well as the overall population. I will discuss the extension of the “magnetic desert,” first inferred among the A-type stars, to O stars up to 60 M⊙. I will discuss the interaction of the winds of the magnetic stars with the fields above their surfaces, generating complex “dynamical magnetosphere” structures detected in optical and UV lines, and in X-ray lines and continuum. Finally, I will discuss the detection of a small number of variable O stars in the LMC and SMC that exhibit spectral characteristics analogous to the known Galactic magnetic stars, and that almost certainly represent the first known examples of extragalactic magnetic stars.

Observer performance in semi-automated microbleed detection

NASA Astrophysics Data System (ADS)

Kuijf, Hugo J.; Brundel, Manon; de Bresser, Jeroen; Viergever, Max A.; Biessels, Geert Jan; Geerlings, Mirjam I.; Vincken, Koen L.

2013-03-01

Cerebral microbleeds are small bleedings in the human brain, detectable with MRI. Microbleeds are associated with vascular disease and dementia. The number of studies involving microbleed detection is increasing rapidly. Visual rating is the current standard for detection, but is a time-consuming process, especially at high-resolution 7.0 T MR images, has limited reproducibility and is highly observer dependent. Recently, multiple techniques have been published for the semi-automated detection of microbleeds, attempting to overcome these problems. In the present study, a 7.0 T dual-echo gradient echo MR image was acquired in 18 participants with microbleeds from the SMART study. Two experienced observers identified 54 microbleeds in these participants, using a validated visual rating scale. The radial symmetry transform (RST) can be used for semi-automated detection of microbleeds in 7.0 T MR images. In the present study, the results of the RST were assessed by two observers and 47 microbleeds were identified: 35 true positives and 12 extra positives (microbleeds that were missed during visual rating). Hence, after scoring a total number of 66 microbleeds could be identified in the 18 participants. The use of the RST increased the average sensitivity of observers from 59% to 69%. More importantly, inter-observer agreement (ICC and Dice's coefficient) increased from 0.85 and 0.64 to 0.98 and 0.96, respectively. Furthermore, the required rating time was reduced from 30 to 2 minutes per participant. By fine-tuning the RST, sensitivities up to 90% can be achieved, at the cost of extra false positives.

Forecast Verification: Identification of small changes in weather forecasting skill

NASA Astrophysics Data System (ADS)

Weatherhead, E. C.; Jensen, T. L.

2017-12-01

Global and regonal weather forecasts have improved over the past seven decades most often because of small, incrmental improvements. The identificaiton and verification of forecast improvement due to proposed small changes in forecasting can be expensive and, if not carried out efficiently, can slow progress in forecasting development. This presentation will look at the skill of commonly used verification techniques and show how the ability to detect improvements can depend on the magnitude of the improvement, the number of runs used to test the improvement, the location on the Earth and the statistical techniques used. For continuous variables, such as temperture, wind and humidity, the skill of a forecast can be directly compared using a pair-wise statistical test that accommodates the natural autocorrelation and magnitude of variability. For discrete variables, such as tornado outbreaks, or icing events, the challenges is to reduce the false alarm rate while improving the rate of correctly identifying th discrete event. For both continuus and discrete verification results, proper statistical approaches can reduce the number of runs needed to identify a small improvement in forecasting skill. Verification within the Next Generation Global Prediction System is an important component to the many small decisions needed to make stat-of-the-art improvements to weather forecasting capabilities. The comparison of multiple skill scores with often conflicting results requires not only appropriate testing, but also scientific judgment to assure that the choices are appropriate not only for improvements in today's forecasting capabilities, but allow improvements that will come in the future.

Axonal degeneration and regeneration in sensory roots in a genital herpes model.

PubMed

Soffer, D; Martin, J R

1989-01-01

In a mouse model of genital herpes simplex virus type 2 (HSV-2) infection, roots of the lower spinal cord were examined 5 days to 6 months after inoculation. Using immunoperoxidase methods on paraffin sections, viral antigen was found in sensory ganglia, their proximal roots and distal nerves on days 5 and 6 after infection. In Epon sections, most mice had focal sensory root abnormalities in lower thoracic, lumbar or sacral levels. At days 7 and 10, lesions showed chiefly nerve fiber degeneration, particularly of large myelinated fibers. At 2 weeks, lesions contained relatively large bundles of small unmyelinated fibers with immature axon-Schwann cell relationships. From 3 to 6 weeks, lesions again contained many more small unmyelinated fibers than normal but, in increasing proportions, axons in bundles were isolated from their neighbors by Schwann cell cytoplasm, and Schwann cells having 1:1 relationships with axons showed mesaxon or thin myelin sheath formation. At later times, the proportion of small unmyelinated axons decreased in parallel with increased numbers of small myelinated axons. By 6 months, affected roots showed a relative reduction in large myelinated fibers, increased proportions of small myelinated fibers and Schwann cell nuclei. Numbers of unmyelinated fibers were reduced relative to 3- to 6-week lesions. Axonal degeneration and regeneration appears to be the chief pathological change in sensory roots in this model. If regenerated fibers arise from latently infected neurons, then establishment of latency is not a relatively silent event, but is associated with major long-lasting, morphologically detectable effects.

Camera trap placement and the potential for bias due to trails and other features

PubMed Central

Forrester, Tavis D.

2017-01-01

Camera trapping has become an increasingly widespread tool for wildlife ecologists, with large numbers of studies relying on photo capture rates or presence/absence information. It is increasingly clear that camera placement can directly impact this kind of data, yet these biases are poorly understood. We used a paired camera design to investigate the effect of small-scale habitat features on species richness estimates, and capture rate and detection probability of several mammal species in the Shenandoah Valley of Virginia, USA. Cameras were deployed at either log features or on game trails with a paired camera at a nearby random location. Overall capture rates were significantly higher at trail and log cameras compared to their paired random cameras, and some species showed capture rates as much as 9.7 times greater at feature-based cameras. We recorded more species at both log (17) and trail features (15) than at their paired control cameras (13 and 12 species, respectively), yet richness estimates were indistinguishable after 659 and 385 camera nights of survey effort, respectively. We detected significant increases (ranging from 11–33%) in detection probability for five species resulting from the presence of game trails. For six species detection probability was also influenced by the presence of a log feature. This bias was most pronounced for the three rodents investigated, where in all cases detection probability was substantially higher (24.9–38.2%) at log cameras. Our results indicate that small-scale factors, including the presence of game trails and other features, can have significant impacts on species detection when camera traps are employed. Significant biases may result if the presence and quality of these features are not documented and either incorporated into analytical procedures, or controlled for in study design. PMID:29045478

Camera trap placement and the potential for bias due to trails and other features.

PubMed

Kolowski, Joseph M; Forrester, Tavis D

2017-01-01

Camera trapping has become an increasingly widespread tool for wildlife ecologists, with large numbers of studies relying on photo capture rates or presence/absence information. It is increasingly clear that camera placement can directly impact this kind of data, yet these biases are poorly understood. We used a paired camera design to investigate the effect of small-scale habitat features on species richness estimates, and capture rate and detection probability of several mammal species in the Shenandoah Valley of Virginia, USA. Cameras were deployed at either log features or on game trails with a paired camera at a nearby random location. Overall capture rates were significantly higher at trail and log cameras compared to their paired random cameras, and some species showed capture rates as much as 9.7 times greater at feature-based cameras. We recorded more species at both log (17) and trail features (15) than at their paired control cameras (13 and 12 species, respectively), yet richness estimates were indistinguishable after 659 and 385 camera nights of survey effort, respectively. We detected significant increases (ranging from 11-33%) in detection probability for five species resulting from the presence of game trails. For six species detection probability was also influenced by the presence of a log feature. This bias was most pronounced for the three rodents investigated, where in all cases detection probability was substantially higher (24.9-38.2%) at log cameras. Our results indicate that small-scale factors, including the presence of game trails and other features, can have significant impacts on species detection when camera traps are employed. Significant biases may result if the presence and quality of these features are not documented and either incorporated into analytical procedures, or controlled for in study design.

Moving standard deviation and moving sum of outliers as quality tools for monitoring analytical precision.

PubMed

Liu, Jiakai; Tan, Chin Hon; Badrick, Tony; Loh, Tze Ping

2018-02-01

An increase in analytical imprecision (expressed as CV a ) can introduce additional variability (i.e. noise) to the patient results, which poses a challenge to the optimal management of patients. Relatively little work has been done to address the need for continuous monitoring of analytical imprecision. Through numerical simulations, we describe the use of moving standard deviation (movSD) and a recently described moving sum of outlier (movSO) patient results as means for detecting increased analytical imprecision, and compare their performances against internal quality control (QC) and the average of normal (AoN) approaches. The power of detecting an increase in CV a is suboptimal under routine internal QC procedures. The AoN technique almost always had the highest average number of patient results affected before error detection (ANPed), indicating that it had generally the worst capability for detecting an increased CV a . On the other hand, the movSD and movSO approaches were able to detect an increased CV a at significantly lower ANPed, particularly for measurands that displayed a relatively small ratio of biological variation to CV a. CONCLUSION: The movSD and movSO approaches are effective in detecting an increase in CV a for high-risk measurands with small biological variation. Their performance is relatively poor when the biological variation is large. However, the clinical risks of an increase in analytical imprecision is attenuated for these measurands as an increased analytical imprecision will only add marginally to the total variation and less likely to impact on the clinical care. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Cancer-cells on a chip for label-free optic detection of secreted molecules

NASA Astrophysics Data System (ADS)

Berthuy, Ophélie I.; Blum, Loïc. J.; Marquette, Christophe A.

2015-05-01

To unravel cell complexity, living-cell chips have been developed that allow delivery of experimental stimuli but also measurement of the resulting cellular responses. We have been developing a new concept for multiplexed detection of biomolecules secreted by different cancer cells. In the present report, we are making the proof of concept of cell small populations (from 1 to 100 cells) spotting, culture and secretion detection on a gold surface. For that purpose, antibodies and different cell lines were spotted using a piezoelectric spotter. In order to keep the cells in a hydrated environment during the robotized micropipetting and to address different cell lines on a single chip, a biocompatible alginate polymer was used. This approach enables the encapsulation of the cell in a very small volume (30 nL), directly on the substrate and permits a precise control of the number of cells in each alginate bead. After 24h of culture, the adherent cells are ready for surface plasmon resonance imaging (SPRi) experimentation. To enable the detection of secreted proteins, various antibodies are immobilized in an organized manner on a SPRi sensor and permitted the multiplex detection of different proteins secreted by the different cultured cell lines. Evidence of the real-time detection will be presented for Prostate Specific Antigen (PSA) and β-2-microglobulin (B2M) secreted by prostate cancer cells following induction by dihydrotestosterone (DHT). Different kinetics for the two secreted proteins were then demonstrated and precisely determined using the chip. There is no doubt that our chip will, in a near future, be applied to more multiplexed and complex biological secretion systems for which kinetic data are at the moment not reachable using standard cellular biology tools.

Postoperative Management of Multiple Primary Cancers Associated with Non-small Cell Lung Cancer.

PubMed

Shoji, Fumihiro; Yamazaki, Koji; Miura, Naoko; Katsura, Masakazu; Oku, Yuka; Takeo, Sadanori; Maehara, Yoshihiko

2018-06-01

Modern treatment for primary cancers has improved survival. Therefore, increased numbers of patients with multiple primary cancers (MPC) associated with lung cancer may be expected. The aim of the present study was to report MPC associated with lung cancer and discuss patients' characteristics and postoperative management. Overall, 973 consecutive patients who underwent surgery for non-small cell lung cancer (NSCLC) were retrospectively studied. NSCLC with MPC was observed in 148 patients (15.2%). MPC comprised 24 synchronous (2.5%) and 124 metachronous (12.7%) diseases. Of the 124 metachronous patients, NSCLC was detected before cancers were detected in other organs (lung cancer first (LCF)) in 25 (20.2%) patients and subsequently in other organs after treatment (other organs, primary cancer-first (OCF)) in 99 (79.8%) patients. MPC was significantly associated with advanced age (p<0.0001) and chronic obstructive pulmonary disease (COPD) (p=0.0040). The leading sites of MPC in patients with synchronous tumors and those with OCF were the digestive organs. In contrast, the leading site of MPC in patients with LCF was the lung. In the latter, at least two primary lung cancers were detected within 5 years as well as 5 years after surgery for the treatment of the first detected lung cancer, while primary cancers of other organs were detected within 5 years. Advanced age and COPD may represent a high-risk of MPCs. Therefore, we recommend careful follow-up to detect MPC in the lung as well as the digestive organs beyond 5 years after treatment of the first cancer. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Investigation of the Microstructural Changes and Hardness Variations of Sub-Zero Treated Cr-V Ledeburitic Tool Steel Due to the Tempering Treatment

NASA Astrophysics Data System (ADS)

Jurči, Peter; Dománková, Mária; Ptačinová, Jana; Pašák, Matej; Kusý, Martin; Priknerová, Petra

2018-03-01

The microstructure and tempering response of Cr-V ledeburitic steel Vanadis 6 subjected to sub-zero treatment at - 196 °C for 4 h have been examined with reference to the same steel after conventional heat treatment. The obtained experimental results infer that sub-zero treatment significantly reduces the retained austenite amount, makes an overall refinement of microstructure, and induces a significant increase in the number and population density of small globular carbides with a size 100-500 nm. At low tempering temperatures, the transient M3C-carbides precipitated, whereas their number was enhanced by sub-zero treatment. The presence of chromium-based M7C3 precipitates was evidenced after tempering at the temperature of normal secondary hardening; this phase was detected along with the M3C. Tempering above 470 °C converts almost all the retained austenite in conventionally quenched specimens while the transformation of retained austenite is rather accelerated in sub-zero treated material. As a result of tempering, a decrease in the population density of small globular carbides was recorded; however, the number of these particles retained much higher in sub-zero treated steel. Elevated hardness of sub-zero treated steel can be referred to more completed martensitic transformation and enhanced number of small globular carbides; this state is retained up to a tempering temperature of around 500 °C in certain extent. Correspondingly, lower as-tempered hardness of sub-zero treated steel tempered above 500 °C is referred to much lower contribution of the transformation of retained austenite, and to an expectedly lower amount of precipitated alloy carbides.

The Newcomb-Benford law in its relation to some common distributions.

PubMed

Formann, Anton K

2010-05-07

An often reported, but nevertheless persistently striking observation, formalized as the Newcomb-Benford law (NBL), is that the frequencies with which the leading digits of numbers occur in a large variety of data are far away from being uniform. Most spectacular seems to be the fact that in many data the leading digit 1 occurs in nearly one third of all cases. Explanations for this uneven distribution of the leading digits were, among others, scale- and base-invariance. Little attention, however, found the interrelation between the distribution of the significant digits and the distribution of the observed variable. It is shown here by simulation that long right-tailed distributions of a random variable are compatible with the NBL, and that for distributions of the ratio of two random variables the fit generally improves. Distributions not putting most mass on small values of the random variable (e.g. symmetric distributions) fail to fit. Hence, the validity of the NBL needs the predominance of small values and, when thinking of real-world data, a majority of small entities. Analyses of data on stock prices, the areas and numbers of inhabitants of countries, and the starting page numbers of papers from a bibliography sustain this conclusion. In all, these findings may help to understand the mechanisms behind the NBL and the conditions needed for its validity. That this law is not only of scientific interest per se, but that, in addition, it has also substantial implications can be seen from those fields where it was suggested to be put into practice. These fields reach from the detection of irregularities in data (e.g. economic fraud) to optimizing the architecture of computers regarding number representation, storage, and round-off errors.

Edge detection of optical subaperture image based on improved differential box-counting method

NASA Astrophysics Data System (ADS)

Li, Yi; Hui, Mei; Liu, Ming; Dong, Liquan; Kong, Lingqin; Zhao, Yuejin

2018-01-01

Optical synthetic aperture imaging technology is an effective approach to improve imaging resolution. Compared with monolithic mirror system, the image of optical synthetic aperture system is often more complex at the edge, and as a result of the existence of gap between segments, which makes stitching becomes a difficult problem. So it is necessary to extract the edge of subaperture image for achieving effective stitching. Fractal dimension as a measure feature can describe image surface texture characteristics, which provides a new approach for edge detection. In our research, an improved differential box-counting method is used to calculate fractal dimension of image, then the obtained fractal dimension is mapped to grayscale image to detect edges. Compared with original differential box-counting method, this method has two improvements as follows: by modifying the box-counting mechanism, a box with a fixed height is replaced by a box with adaptive height, which solves the problem of over-counting the number of boxes covering image intensity surface; an image reconstruction method based on super-resolution convolutional neural network is used to enlarge small size image, which can solve the problem that fractal dimension can't be calculated accurately under the small size image, and this method may well maintain scale invariability of fractal dimension. The experimental results show that the proposed algorithm can effectively eliminate noise and has a lower false detection rate compared with the traditional edge detection algorithms. In addition, this algorithm can maintain the integrity and continuity of image edge in the case of retaining important edge information.

Silver enhancement of nanogold and undecagold

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

Hainfield, J.F.; Furuya, F.R.

1995-07-01

A recent advance in immunogold technology has been the use of molecular gold instead of colloidal gold. A number of advantages are realized by this approach, such as stable covalent, site-specific attachment, small probe size and absence of aggregates for improved penetration. Silver enhancement has led to improved and unique results for electron and light microscopy, as well as their use with blots and gels. Most previous work with immunogold silver staining has been done with colloidal gold particles. More recently, large gold compounds (``clusters``) having a definite number of gold atoms and defined organic shell, have been used, frequentlymore » with improved results. These gold dusters, large compared to simple compounds, are, however, at the small end of the colloidal gold scale in size; undecagold is 0.8 nm and Nanogold is 1.4 nm. They may be used in practically all applications where colloidal gold is used (Light and electron microscopy, dot blots, etc.) and in some unique applications, where at least the larger colloidal golds don`t work, such as running gold labeled proteins on gels (which are later detected by silver enhancement). The main differences between gold clusters and colloidal golds are the small size of the dusters and their covalent attachment to antibodies or other molecules.« less

Accuracy or precision: Implications of sample design and methodology on abundance estimation

USGS Publications Warehouse

Kowalewski, Lucas K.; Chizinski, Christopher J.; Powell, Larkin A.; Pope, Kevin L.; Pegg, Mark A.

2015-01-01

Sampling by spatially replicated counts (point-count) is an increasingly popular method of estimating population size of organisms. Challenges exist when sampling by point-count method, and it is often impractical to sample entire area of interest and impossible to detect every individual present. Ecologists encounter logistical limitations that force them to sample either few large-sample units or many small sample-units, introducing biases to sample counts. We generated a computer environment and simulated sampling scenarios to test the role of number of samples, sample unit area, number of organisms, and distribution of organisms in the estimation of population sizes using N-mixture models. Many sample units of small area provided estimates that were consistently closer to true abundance than sample scenarios with few sample units of large area. However, sample scenarios with few sample units of large area provided more precise abundance estimates than abundance estimates derived from sample scenarios with many sample units of small area. It is important to consider accuracy and precision of abundance estimates during the sample design process with study goals and objectives fully recognized, although and with consequence, consideration of accuracy and precision of abundance estimates is often an afterthought that occurs during the data analysis process.

An Observational Upper Limit on the Interstellar Number Density of Asteroids and Comets

NASA Astrophysics Data System (ADS)

Engelhardt, Toni; Jedicke, Robert; Vereš, Peter; Fitzsimmons, Alan; Denneau, Larry; Beshore, Ed; Meinke, Bonnie

2017-03-01

We derived 90% confidence limits (CLs) on the interstellar number density ({ρ }{IS}{CL}) of interstellar objects (ISOs; comets and asteroids) as a function of the slope of their size-frequency distribution (SFD) and limiting absolute magnitude. To account for gravitational focusing, we first generated a quasi-realistic ISO population to ˜ 750 {au} from the Sun and propagated it forward in time to generate a steady state population of ISOs with heliocentric distance < 50 {au}. We then simulated the detection of the synthetic ISOs using pointing data for each image and average detection efficiencies for each of three contemporary solar system surveys—Pan-STARRS1, the Mt. Lemmon Survey, and the Catalina Sky Survey. These simulations allowed us to determine the surveys’ combined ISO detection efficiency under several different but realistic modes of identifying ISOs in the survey data. Some of the synthetic detected ISOs had eccentricities as small as 1.01, which is in the range of the largest eccentricities of several known comets. Our best CL of {ρ }{IS}{CL}=1.4× {10}-4 {{au}}-3 implies that the expectation that extra-solar systems form like our solar system, eject planetesimals in the same way, and then distribute them throughout the Galaxy, is too simplistic, or that the SFD or behavior of ISOs as they pass through our solar system is far from expectation.

Simple Random Sampling-Based Probe Station Selection for Fault Detection in Wireless Sensor Networks

PubMed Central

Huang, Rimao; Qiu, Xuesong; Rui, Lanlan

2011-01-01

Fault detection for wireless sensor networks (WSNs) has been studied intensively in recent years. Most existing works statically choose the manager nodes as probe stations and probe the network at a fixed frequency. This straightforward solution leads however to several deficiencies. Firstly, by only assigning the fault detection task to the manager node the whole network is out of balance, and this quickly overloads the already heavily burdened manager node, which in turn ultimately shortens the lifetime of the whole network. Secondly, probing with a fixed frequency often generates too much useless network traffic, which results in a waste of the limited network energy. Thirdly, the traditional algorithm for choosing a probing node is too complicated to be used in energy-critical wireless sensor networks. In this paper, we study the distribution characters of the fault nodes in wireless sensor networks, validate the Pareto principle that a small number of clusters contain most of the faults. We then present a Simple Random Sampling-based algorithm to dynamic choose sensor nodes as probe stations. A dynamic adjusting rule for probing frequency is also proposed to reduce the number of useless probing packets. The simulation experiments demonstrate that the algorithm and adjusting rule we present can effectively prolong the lifetime of a wireless sensor network without decreasing the fault detected rate. PMID:22163789

Simple random sampling-based probe station selection for fault detection in wireless sensor networks.

PubMed

Huang, Rimao; Qiu, Xuesong; Rui, Lanlan

2011-01-01

Fault detection for wireless sensor networks (WSNs) has been studied intensively in recent years. Most existing works statically choose the manager nodes as probe stations and probe the network at a fixed frequency. This straightforward solution leads however to several deficiencies. Firstly, by only assigning the fault detection task to the manager node the whole network is out of balance, and this quickly overloads the already heavily burdened manager node, which in turn ultimately shortens the lifetime of the whole network. Secondly, probing with a fixed frequency often generates too much useless network traffic, which results in a waste of the limited network energy. Thirdly, the traditional algorithm for choosing a probing node is too complicated to be used in energy-critical wireless sensor networks. In this paper, we study the distribution characters of the fault nodes in wireless sensor networks, validate the Pareto principle that a small number of clusters contain most of the faults. We then present a Simple Random Sampling-based algorithm to dynamic choose sensor nodes as probe stations. A dynamic adjusting rule for probing frequency is also proposed to reduce the number of useless probing packets. The simulation experiments demonstrate that the algorithm and adjusting rule we present can effectively prolong the lifetime of a wireless sensor network without decreasing the fault detected rate.

Clover: Compiler directed lightweight soft error resilience

DOE PAGES

Liu, Qingrui; Lee, Dongyoon; Jung, Changhee; ...

2015-05-01

This paper presents Clover, a compiler directed soft error detection and recovery scheme for lightweight soft error resilience. The compiler carefully generates soft error tolerant code based on idem-potent processing without explicit checkpoint. During program execution, Clover relies on a small number of acoustic wave detectors deployed in the processor to identify soft errors by sensing the wave made by a particle strike. To cope with DUE (detected unrecoverable errors) caused by the sensing latency of error detection, Clover leverages a novel selective instruction duplication technique called tail-DMR (dual modular redundancy). Once a soft error is detected by either themore » sensor or the tail-DMR, Clover takes care of the error as in the case of exception handling. To recover from the error, Clover simply redirects program control to the beginning of the code region where the error is detected. Lastly, the experiment results demonstrate that the average runtime overhead is only 26%, which is a 75% reduction compared to that of the state-of-the-art soft error resilience technique.« less

Radiation detection and situation management by distributed sensor networks

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

Jan, Frigo; Mielke, Angela; Cai, D Michael

Detection of radioactive materials in an urban environment usually requires large, portal-monitor-style radiation detectors. However, this may not be a practical solution in many transport scenarios. Alternatively, a distributed sensor network (DSN) could complement portal-style detection of radiological materials through the implementation of arrays of low cost, small heterogeneous sensors with the ability to detect the presence of radioactive materials in a moving vehicle over a specific region. In this paper, we report on the use of a heterogeneous, wireless, distributed sensor network for traffic monitoring in a field demonstration. Through wireless communications, the energy spectra from different radiation detectorsmore » are combined to improve the detection confidence. In addition, the DSN exploits other sensor technologies and algorithms to provide additional information about the vehicle, such as its speed, location, class (e.g. car, truck), and license plate number. The sensors are in-situ and data is processed in real-time at each node. Relevant information from each node is sent to a base station computer which is used to assess the movement of radioactive materials.« less

Antibody-Mediated Small Molecule Detection Using Programmable DNA-Switches.

PubMed

Rossetti, Marianna; Ippodrino, Rudy; Marini, Bruna; Palleschi, Giuseppe; Porchetta, Alessandro

2018-06-13

The development of rapid, cost-effective, and single-step methods for the detection of small molecules is crucial for improving the quality and efficiency of many applications ranging from life science to environmental analysis. Unfortunately, current methodologies still require multiple complex, time-consuming washing and incubation steps, which limit their applicability. In this work we present a competitive DNA-based platform that makes use of both programmable DNA-switches and antibodies to detect small target molecules. The strategy exploits both the advantages of proximity-based methods and structure-switching DNA-probes. The platform is modular and versatile and it can potentially be applied for the detection of any small target molecule that can be conjugated to a nucleic acid sequence. Here the rational design of programmable DNA-switches is discussed, and the sensitive, rapid, and single-step detection of different environmentally relevant small target molecules is demonstrated.

Assessment of Environmental and Hereditary Influence on Development of Pituitary Tumors Using Dermatoglyphic Traits and Their Potential as Screening Markers.

PubMed

Gradiser, Marina; Matovinovic Osvatic, Martina; Dilber, Dario; Bilic-Curcic, Ines

2016-03-17

The aim of this study was to assess environmental and hereditary influence on development of pituitary tumors using dermatoglyphic traits. The study was performed on 126 patients of both genders with pituitary tumors (60 non-functional and 66 functional pituitary tumor patients) in comparison to the control group of 400 phenotypically healthy individuals. Statistical analysis of quantitative and qualitative traits of digito-palmar dermatoglyphics was performed, and hormonal status was determined according to the standard protocols. Although we did not find markers that could specifically distinguish functional from non-functional tumors, we have found markers predisposing to the development of tumors in general (a small number of ridges between triradius of both hands, a smaller number of ridges between the triradius of c-d rc R), those for endocrine dysfunction (increased number of arches and reduced number of whorls, difference of pattern distribution in the I3 and I4 interdigital space), and some that could potentially be attributed to patients suffering from pituitary tumors (small number of ridges for variables FRR 5, smaller number of ridges in the FRL 4 of both hands and difference of pattern distribution at thenar of I1 and I2 interdigital space). The usage of dermatoglyphic traits as markers of predisposition of pituitary tumor development could facilitate the earlier detection of patients in addition to standard methods, and possibly earlier treatment and higher survival rate. Finally, our results are consistent with the hypothesis about multifactorial nature of pituitary tumor etiology comprised of both gene instability and environmental factors.

Assessment of Environmental and Hereditary Influence on Development of Pituitary Tumors Using Dermatoglyphic Traits and Their Potential as Screening Markers

PubMed Central

Gradiser, Marina; Matovinovic Osvatic, Martina; Dilber, Dario; Bilic-Curcic, Ines

2016-01-01

The aim of this study was to assess environmental and hereditary influence on development of pituitary tumors using dermatoglyphic traits. The study was performed on 126 patients of both genders with pituitary tumors (60 non-functional and 66 functional pituitary tumor patients) in comparison to the control group of 400 phenotypically healthy individuals. Statistical analysis of quantitative and qualitative traits of digito-palmar dermatoglyphics was performed, and hormonal status was determined according to the standard protocols. Although we did not find markers that could specifically distinguish functional from non-functional tumors, we have found markers predisposing to the development of tumors in general (a small number of ridges between triradius of both hands, a smaller number of ridges between the triradius of c–d rc R), those for endocrine dysfunction (increased number of arches and reduced number of whorls, difference of pattern distribution in the I3 and I4 interdigital space), and some that could potentially be attributed to patients suffering from pituitary tumors (small number of ridges for variables FRR 5, smaller number of ridges in the FRL 4 of both hands and difference of pattern distribution at thenar of I1 and I2 interdigital space). The usage of dermatoglyphic traits as markers of predisposition of pituitary tumor development could facilitate the earlier detection of patients in addition to standard methods, and possibly earlier treatment and higher survival rate. Finally, our results are consistent with the hypothesis about multifactorial nature of pituitary tumor etiology comprised of both gene instability and environmental factors. PMID:26999178

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates

USGS Publications Warehouse

Hobbs, Michael T.; Brehme, Cheryl S.

2017-01-01

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing.

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates.

PubMed

Hobbs, Michael T; Brehme, Cheryl S

2017-01-01

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing.

An Unconditional Test for Change Point Detection in Binary Sequences with Applications to Clinical Registries.

PubMed

Ellenberger, David; Friede, Tim

2016-08-05

Methods for change point (also sometimes referred to as threshold or breakpoint) detection in binary sequences are not new and were introduced as early as 1955. Much of the research in this area has focussed on asymptotic and exact conditional methods. Here we develop an exact unconditional test. An unconditional exact test is developed which assumes the total number of events as random instead of conditioning on the number of observed events. The new test is shown to be uniformly more powerful than Worsley's exact conditional test and means for its efficient numerical calculations are given. Adaptions of methods by Berger and Boos are made to deal with the issue that the unknown event probability imposes a nuisance parameter. The methods are compared in a Monte Carlo simulation study and applied to a cohort of patients undergoing traumatic orthopaedic surgery involving external fixators where a change in pin site infections is investigated. The unconditional test controls the type I error rate at the nominal level and is uniformly more powerful than (or to be more precise uniformly at least as powerful as) Worsley's exact conditional test which is very conservative for small sample sizes. In the application a beneficial effect associated with the introduction of a new treatment procedure for pin site care could be revealed. We consider the new test an effective and easy to use exact test which is recommended in small sample size change point problems in binary sequences.

Radiofrequency ablation in primary non-small cell lung cancer: What a radiologist needs to know

PubMed Central

Bhatia, Shivank; Pereira, Keith; Mohan, Prasoon; Narayanan, Govindarajan; Wangpaichitr, Medhi; Savaraj, Niramol

2016-01-01

Lung cancer continues to be one of the leading causes of death worldwide. In advanced cases of lung cancer, a multimodality approach is often applied, however with poor local control rates. In early non-small cell lung cancer (NSCLC), surgery is the standard of care. Only 15-30% of patients are eligible for surgical resection. Improvements in imaging and treatment delivery systems have provided new tools to better target these tumors. Stereotactic body radiation therapy (SBRT) has evolved as the next best option. The role of radiofrequency ablation (RFA) is also growing. Currently, it is a third-line option in stage 1 NSCLC, when SBRT cannot be performed. More recent studies have demonstrated usefulness in recurrent tumors and some authors have also suggested combination of RFA with other modalities in larger tumors. Following the National Lung Screening Trial (NLST), screening by low-dose computed tomography (CT) has demonstrated high rates of early-stage lung cancer detection in high-risk populations. Hence, even considering the current role of RFA as a third-line option, in view of increasing numbers of occurrences detected, the number of potential RFA candidates may see a steep uptrend. In view of all this, it is imperative that interventional radiologists be familiar with the techniques of lung ablation. The aim of this article is to discuss the procedural technique of RFA in the lung and review the current evidence regarding RFA for NSCLC. PMID:27081229

Effects of amyloid and small vessel disease on white matter network disruption.

PubMed

Kim, Hee Jin; Im, Kiho; Kwon, Hunki; Lee, Jong Min; Ye, Byoung Seok; Kim, Yeo Jin; Cho, Hanna; Choe, Yearn Seong; Lee, Kyung Han; Kim, Sung Tae; Kim, Jae Seung; Lee, Jae Hong; Na, Duk L; Seo, Sang Won

2015-01-01

There is growing evidence that the human brain is a large scale complex network. The structural network is reported to be disrupted in cognitively impaired patients. However, there have been few studies evaluating the effects of amyloid and small vessel disease (SVD) markers, the common causes of cognitive impairment, on structural networks. Thus, we evaluated the association between amyloid and SVD burdens and structural networks using diffusion tensor imaging (DTI). Furthermore, we determined if network parameters predict cognitive impairments. Graph theoretical analysis was applied to DTI data from 232 cognitively impaired patients with varying degrees of amyloid and SVD burdens. All patients underwent Pittsburgh compound-B (PiB) PET to detect amyloid burden, MRI to detect markers of SVD, including the volume of white matter hyperintensities and the number of lacunes, and detailed neuropsychological testing. The whole-brain network was assessed by network parameters of integration (shortest path length, global efficiency) and segregation (clustering coefficient, transitivity, modularity). PiB retention ratio was not associated with any white matter network parameters. Greater white matter hyperintensity volumes or lacunae numbers were significantly associated with decreased network integration (increased shortest path length, decreased global efficiency) and increased network segregation (increased clustering coefficient, increased transitivity, increased modularity). Decreased network integration or increased network segregation were associated with poor performances in attention, language, visuospatial, memory, and frontal-executive functions. Our results suggest that SVD alters white matter network integration and segregation, which further predicts cognitive dysfunction.

A Wide-field Survey for Transiting Hot Jupiters and Eclipsing Pre-main-sequence Binaries in Young Stellar Associations

NASA Astrophysics Data System (ADS)

Oelkers, Ryan J.; Macri, Lucas M.; Marshall, Jennifer L.; DePoy, Darren L.; Lambas, Diego G.; Colazo, Carlos; Stringer, Katelyn

2016-09-01

The past two decades have seen a significant advancement in the detection, classification, and understanding of exoplanets and binaries. This is due, in large part, to the increase in use of small-aperture telescopes (<20 cm) to survey large areas of the sky to milli-mag precision with rapid cadence. The vast majority of the planetary and binary systems studied to date consists of main-sequence or evolved objects, leading to a dearth of knowledge of properties at early times (<50 Myr). Only a dozen binaries and one candidate transiting Hot Jupiter are known among pre-main-sequence objects, yet these are the systems that can provide the best constraints on stellar formation and planetary migration models. The deficiency in the number of well characterized systems is driven by the inherent and aperiodic variability found in pre-main-sequence objects, which can mask and mimic eclipse signals. Hence, a dramatic increase in the number of young systems with high-quality observations is highly desirable to guide further theoretical developments. We have recently completed a photometric survey of three nearby (<150 pc) and young (<50 Myr) moving groups with a small-aperture telescope. While our survey reached the requisite photometric precision, the temporal coverage was insufficient to detect Hot Jupiters. Nevertheless, we discovered 346 pre-main-sequence binary candidates, including 74 high-priority objects for further study. This paper includes data taken at The McDonald Observatory of The University of Texas at Austin.

Electron microscopic quantification of collagen fibril diameters in the rabbit medial collateral ligament: a baseline for comparison.

PubMed

Frank, C; Bray, D; Rademaker, A; Chrusch, C; Sabiston, P; Bodie, D; Rangayyan, R

1989-01-01

To establish a normal baseline for comparison, thirty-one thousand collagen fibril diameters were measured in calibrated transmission electron (TEM) photomicrographs of normal rabbit medial collateral ligaments (MCL's). A new automated method of quantitation was used to compare statistically fibril minimum diameter distributions in one midsubstance location in both MCL's from six animals at 3 months of age (immature) and three animals at 10 months of age (mature). Pooled results demonstrate that rabbit MCL's have statistically different (p less than 0.001) mean minimum diameters at these two ages. Interanimal differences in mean fibril minimum diameters were also significant (p less than 0.001) and varied by 20% to 25% in both mature and immature animals. Finally, there were significant differences (p less than 0.001) in mean diameters and distributions from side-to-side in all animals. These mean left-to-right differences were less than 10% in all mature animals but as much as 62% in some immature animals. Statistical analysis of these data demonstrate that animal-to-animal comparisons using these protocols require a large number of animals with appropriate numbers of fibrils being measured to detect small intergroup differences. With experiments which compare left to right ligaments, far fewer animals are required to detect similarly small differences. These results demonstrate the necessity for rigorous control of sampling, an extensive normal baseline and statistically confirmed experimental designs in any TEM comparisons of collagen fibril diameters.

Analysis of gene expression in small numbers of purified hemopoietic progenitor cells by RT-PCR.

PubMed

Ziegler, B L; Lamping, C P; Thoma, S J; Fliedner, T M

1995-05-01

Primitive hemopoietic stem cells represent the most probable targets for genetic alterations due to exposure to ionizing irradiation or chemical carcinogens. We have applied a two-step protocol for the purification of CD34+HLA-DR-/low hemopoietic progenitor cells from cord blood (CB). CD34+ cells were isolated by monoclonal antibody (mAb) against CD34 (My10) and immunomagnetic beads. Beads were cleaved off the CD34+ cells by enzymatic treatment with chymopapain. Due to chymopapain-resistance of epitopes recognized by the used mAbs purity control of CD34+ cells and separation into CD34+HLA-DR-/low and CD34+HLA-DR+ subsets could be performed by using flow cytometry. Two miniaturized procedures were applied to isolate poly(A)+ mRNA for the reverse transcription polymerase chain reaction (RT-PCR) from small numbers of CD34+HLA-DR-/low cells. In five experiments, the mean purity of immunomagnetically isolated CD34+ cells was 93.8% +/- 3.9. Flow cytometry sorting of CD34+ cells resulted in pure CD34+HLA-DR-/low populations (purity > 98.8%; range 98.8% to 99.9%; viability > 96%) with an average yield of 2600 +/- 800 cells/5 x 10(7) low density CB cells. By RT-PCR using both poly(A)+ mRNA isolation procedures, sequences corresponding to CD34 and beta 2-microglobulin were amplified from as few as 20 cells. Furthermore, a sequence-independent RT-PCR (SIP-RT-PCR) was applied to amplify the cDNA derived from five erythroblasts isolated from a burst-forming unit-erythroid (BFU-E). Upon hybridization, full-length c-fos message was detected in the SIP-RT-PCR amplified material. Our data demonstrate that gene expression can be detected at the transcriptional level in small numbers of hemopoietic progenitor cells. In addition, the SIP-RT-PCR may allow the amplification of unique mRNA species when subtractive hybridization procedures are performed. The presented data should be useful to analyze gene expression in rare subsets of radiation-exposed immature hemopoietic stem/progenitor cells.

Development of Temperature Sensitive Paints for the Detection of Small Temperature Differences

NASA Technical Reports Server (NTRS)

Oglesby, Donald M.; Upchurch, Billy T.; Sealey, Bradley S.; Leighty, Bradley D.; Burkett, Cecil G., Jr.; Jalali, Amir

1997-01-01

Temperature sensitive paints (TSP s) have recently been used to detect small temperature differences on aerodynamic model surfaces. These types of applications impose stringent performance requirements on a paint system. The TSP s must operate over a broad temperature range, must be physically robust (cannot chip or peel), must be polishable to at least the smoothness of the model surface, and must have sufficient sensitivity to detect small temperature differences. TSP coatings based on the use of metal complexes in polymer binders were developed at NASA Langley Research Center which meet most of the requirements for detection of small temperature differences under severe environmental conditions.

Detection of small earthquakes with dense array data: example from the San Jacinto fault zone, southern California

NASA Astrophysics Data System (ADS)

Meng, Haoran; Ben-Zion, Yehuda

2018-01-01

We present a technique to detect small earthquakes not included in standard catalogues using data from a dense seismic array. The technique is illustrated with continuous waveforms recorded in a test day by 1108 vertical geophones in a tight array on the San Jacinto fault zone. Waveforms are first stacked without time-shift in nine non-overlapping subarrays to increase the signal-to-noise ratio. The nine envelope functions of the stacked records are then multiplied with each other to suppress signals associated with sources affecting only some of the nine subarrays. Running a short-term moving average/long-term moving average (STA/LTA) detection algorithm on the product leads to 723 triggers in the test day. Using a local P-wave velocity model derived for the surface layer from Betsy gunshot data, 5 s long waveforms of all sensors around each STA/LTA trigger are beamformed for various incident directions. Of the 723 triggers, 220 are found to have localized energy sources and 103 of these are confirmed as earthquakes by verifying their observation at 4 or more stations of the regional seismic network. This demonstrates the general validity of the method and allows processing further the validated events using standard techniques. The number of validated events in the test day is >5 times larger than that in the standard catalogue. Using these events as templates can lead to additional detections of many more earthquakes.

Embedded Disposable Functionalized Electrochemical Biosensor with a 3D-Printed Flow Cell for Detection of Hepatic Oval Cells (HOCs)

PubMed Central

Peacock, Martin; Leonhardt, Stefan; Damiati, Laila; Baghdadi, Mohammed A.; Schuster, Bernhard

2018-01-01

Hepatic oval cells (HOCs) are considered the progeny of the intrahepatic stem cells that are found in a small population in the liver after hepatocyte proliferation is inhibited. Due to their small number, isolation and capture of these cells constitute a challenging task for immunosensor technology. This work describes the development of a 3D-printed continuous flow system and exploits disposable screen-printed electrodes for the rapid detection of HOCs that over-express the OV6 marker on their membrane. Multiwall carbon nanotube (MWCNT) electrodes have a chitosan film that serves as a scaffold for the immobilization of oval cell marker antibodies (anti-OV6-Ab), which enhance the sensitivity of the biomarker and makes the designed sensor specific for oval cells. The developed sensor can be easily embedded into the 3D-printed flow cell to allow cells to be exposed continuously to the functionalized surface. The continuous flow is intended to increase capture of most of the target cells in the specimen. Contact angle measurements were performed to characterize the nature and quality of the modified sensor surface, and electrochemical measurements (cyclic voltammetry (CV) and square wave voltammetry (SWV)) were performed to confirm the efficiency and selectivity of the fabricated sensor to detect HOCs. The proposed method is valuable for capturing rare cells and could provide an effective tool for cancer diagnosis and detection. PMID:29443890

TEAM: efficient two-locus epistasis tests in human genome-wide association study.

PubMed

Zhang, Xiang; Huang, Shunping; Zou, Fei; Wang, Wei

2010-06-15

As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene-gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach.

Comparative performance of two quantitative safety signalling methods: implications for use in a pharmacovigilance department.

PubMed

Almenoff, June S; LaCroix, Karol K; Yuen, Nancy A; Fram, David; DuMouchel, William

2006-01-01

There is increasing interest in using disproportionality-based signal detection methods to support postmarketing safety surveillance activities. Two commonly used methods, empirical Bayes multi-item gamma Poisson shrinker (MGPS) and proportional reporting ratio (PRR), perform differently with respect to the number and types of signals detected. The goal of this study was to compare and analyse the performance characteristics of these two methods, to understand why they differ and to consider the practical implications of these differences for a large, industry-based pharmacovigilance department. We compared the numbers and types of signals of disproportionate reporting (SDRs) obtained with MGPS and PRR using two postmarketing safety databases and a simulated database. We recorded signal counts and performed a qualitative comparison of the drug-event combinations signalled by the two methods as well as a sensitivity analysis to better understand how the thresholds commonly used for these methods impact their performance. PRR detected more SDRs than MGPS. We observed that MGPS is less subject to confounding by demographic factors because it employs stratification and is more stable than PRR when report counts are low. Simulation experiments performed using published empirical thresholds demonstrated that PRR detected false-positive signals at a rate of 1.1%, while MGPS did not detect any statistical false positives. In an attempt to separate the effect of choice of signal threshold from more fundamental methodological differences, we performed a series of experiments in which we modified the conventional threshold values for each method so that each method detected the same number of SDRs for the example drugs studied. This analysis, which provided quantitative examples of the relationship between the published thresholds for the two methods, demonstrates that the signalling criterion published for PRR has a higher signalling frequency than that published for MGPS. The performance differences between the PRR and MGPS methods are related to (i) greater confounding by demographic factors with PRR; (ii) a higher tendency of PRR to detect false-positive signals when the number of reports is small; and (iii) the conventional thresholds that have been adapted for each method. PRR tends to be more 'sensitive' and less 'specific' than MGPS. A high-specificity disproportionality method, when used in conjunction with medical triage and investigation of critical medical events, may provide an efficient and robust approach to applying quantitative methods in routine postmarketing pharmacovigilance.

ISOCAM observations of the Hubble Deep Field reduced with the PRETI method

NASA Astrophysics Data System (ADS)

Aussel, H.; Cesarsky, C. J.; Elbaz, D.; Starck, J. L.

1999-02-01

We have developed a new ISOCAM data reduction technique based on wavelet analysis, especially designed for the detection of faint sources in mid-infrared surveys. This method, the Pattern REcognition Technique for Isocam data (PRETI) has been used to reduce the observations of the Hubble Deep Field (HDF) and flanking fields with ISOCAM at 6.75 (LW2) and 15 mu m (LW3) (Rowan-Robinson et al. \\cite{RowanRobinson}). Simulations of ISOCAM data allow us to test the photometric accuracy and completeness of the reduction. According to these simulations, the PRETI source list is 95% complete in the 15 mu m band at 200 mu Jy and in the 6.75 mu m band at 65 mu Jy, using detection thresholds which minimize the number of false detections. We detect 49 objects in the ISO-HDF at high confidence secure level, 42 in the LW3 filter, 3 in the LW2 filter, and 4 in both filters. An additional, less secure, list of 100 sources is presented, of which 89 are detected at 15 mu m only, 7 at 6.75 mu m only and 4 in both filters. All ISO-HDF objects detected in the HDF itself have optical or infrared counterparts, except for one from the additional list. All except one of the radio sources detected in the field by Fomalont et al. (\\cite{Fomalont}) are detected with ISOCAM. Using a precise correction for the field of view distortion of ISOCAM allows us to separate blended sources. This, together with the fact that PRETI allows to correct data on the tail of cosmic rays glitches, lead us to produce deeper source lists than previous authors. Our list of bright sources agree with those of Désert et al. (\\cite{IAS}) in both filters, and with those of Goldschmidt et al. (\\cite{Goldschmidt}) in the LW3 filter, with systematic difference in photometry. Number counts derived from our results show an excess by a factor of 10 with respect to the prediction of a no evolution model (Franceschini \\cite{Franceschini98}) in the LW3 band. On the contrary, the number of sources in the LW2 band is compatible with the prediction of such a model, but with greater uncertainties, given the small number of detections. Based on observations with the Infrared Space Observatory (ISO). ISO is an ESA project with instruments funded by ESA Member States (especially the PI countries: France, Germany, The Netherlands and the United Kingdom) and with participation of ISAS and NASA.

Extraction of Extended Small-Scale Objects in Digital Images

NASA Astrophysics Data System (ADS)

Volkov, V. Y.

2015-05-01

Detection and localization problem of extended small-scale objects with different shapes appears in radio observation systems which use SAR, infra-red, lidar and television camera. Intensive non-stationary background is the main difficulty for processing. Other challenge is low quality of images, blobs, blurred boundaries; in addition SAR images suffer from a serious intrinsic speckle noise. Statistics of background is not normal, it has evident skewness and heavy tails in probability density, so it is hard to identify it. The problem of extraction small-scale objects is solved here on the basis of directional filtering, adaptive thresholding and morthological analysis. New kind of masks is used which are open-ended at one side so it is possible to extract ends of line segments with unknown length. An advanced method of dynamical adaptive threshold setting is investigated which is based on isolated fragments extraction after thresholding. Hierarchy of isolated fragments on binary image is proposed for the analysis of segmentation results. It includes small-scale objects with different shape, size and orientation. The method uses extraction of isolated fragments in binary image and counting points in these fragments. Number of points in extracted fragments is normalized to the total number of points for given threshold and is used as effectiveness of extraction for these fragments. New method for adaptive threshold setting and control maximises effectiveness of extraction. It has optimality properties for objects extraction in normal noise field and shows effective results for real SAR images.

A nonparametric method for assessment of interactions in a median regression model for analyzing right censored data.

PubMed

Lee, MinJae; Rahbar, Mohammad H; Talebi, Hooshang

2018-01-01

We propose a nonparametric test for interactions when we are concerned with investigation of the simultaneous effects of two or more factors in a median regression model with right censored survival data. Our approach is developed to detect interaction in special situations, when the covariates have a finite number of levels with a limited number of observations in each level, and it allows varying levels of variance and censorship at different levels of the covariates. Through simulation studies, we compare the power of detecting an interaction between the study group variable and a covariate using our proposed procedure with that of the Cox Proportional Hazard (PH) model and censored quantile regression model. We also assess the impact of censoring rate and type on the standard error of the estimators of parameters. Finally, we illustrate application of our proposed method to real life data from Prospective Observational Multicenter Major Trauma Transfusion (PROMMTT) study to test an interaction effect between type of injury and study sites using median time for a trauma patient to receive three units of red blood cells. The results from simulation studies indicate that our procedure performs better than both Cox PH model and censored quantile regression model based on statistical power for detecting the interaction, especially when the number of observations is small. It is also relatively less sensitive to censoring rates or even the presence of conditionally independent censoring that is conditional on the levels of covariates.

A high-throughput assay format for determination of nitrate reductase and nitrite reductase enzyme activities

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

McNally, N.; Liu, Xiang Yang; Choudary, P.V.

1997-01-01

The authors describe a microplate-based high-throughput procedure for rapid assay of the enzyme activities of nitrate reductase and nitrite reductase, using extremely small volumes of reagents. The new procedure offers the advantages of rapidity, small sample size-nanoliter volumes, low cost, and a dramatic increase in the throughput sample number that can be analyzed simultaneously. Additional advantages can be accessed by using microplate reader application software packages that permit assigning a group type to the wells, recording of the data on exportable data files and exercising the option of using the kinetic or endpoint reading modes. The assay can also bemore » used independently for detecting nitrite residues/contamination in environmental/food samples. 10 refs., 2 figs.« less

Composition of uroliths in small domestic animals in the United Kingdom.

PubMed

Rogers, Keith D; Jones, Boyd; Roberts, Larry; Rich, Michael; Montalto, Nicola; Beckett, Sophie

2011-05-01

The mineral composition of 7819 small animal uroliths in the UK was determined by semi-quantitative X-ray diffraction over a period of 90 months from 2002 to 2010. Canine and feline uroliths constituted 97% of the study population and the mineral phase detected most frequently was struvite (43%), followed by calcium oxalate (41%). Uroliths from crossbreeds, Dalmatians, Yorkshire terriers and Shih Tzus accounted for almost 30% of all canine uroliths, with the highest frequency in Dalmatians, which had a predominance of urate uroliths. The average ages of dogs and cats with uroliths were 7.0 years and 7.4 years, respectively. The ratio of the number of dogs presenting with struvite compared to oxalate phases reached a maximum at 3years of age. Copyright © 2010 Elsevier Ltd. All rights reserved.

The diagnostic performance of expert dermoscopists vs a computer-vision system on small-diameter melanomas.

PubMed

Friedman, Robert J; Gutkowicz-Krusin, Dina; Farber, Michele J; Warycha, Melanie; Schneider-Kels, Lori; Papastathis, Nicole; Mihm, Martin C; Googe, Paul; King, Roy; Prieto, Victor G; Kopf, Alfred W; Polsky, David; Rabinovitz, Harold; Oliviero, Margaret; Cognetta, Armand; Rigel, Darrell S; Marghoob, Ashfaq; Rivers, Jason; Johr, Robert; Grant-Kels, Jane M; Tsao, Hensin

2008-04-01

To evaluate the performance of dermoscopists in diagnosing small pigmented skin lesions (diameter

Compilation of 1990 annual reports of the Navy ELF communications system ecological monitoring program. Volume 2: Tabs C thru F

NASA Astrophysics Data System (ADS)

Zapotosky, J. E.

1991-08-01

This portion of the report includes monitoring of and data for arthropoda and earthworms; pollinating insects; and small mammals and nesting birds. During the 1990 growing season the ELF antenna was operated more frequently than in prior years. This provides 2 years of intermittent ELF exposure for the biological systems to react to the radiation, one year of very limited exposure and greater exposure in 1990. Arthropod and earthworm sampling was conducted at intervals of two weeks from early May to late October. High voltage transmission lines and magnetic fields have been shown to affect honeybee reproduction, survival, orientation, and nest structure. ELF EM fields could have similar effects on native megachild bees. Changes in cell length, number of cells per nest, number of leaver per cell, orientation of nest entrances, and time to collect a round leaf pierce to cap a cell were monitored. We have not detected significant changes that could be attributed to ELF EM fields. Small mammal and nesting bird biological studies in the western Upper Peninsula of Michigan for the year 1990 are reported.

Materials emission of chemicals--PVC flooring materials.

PubMed

Lundgren, B; Jonsson, B; Ek-Olausson, B

1999-09-01

Data of chemical emissions from flooring materials have been collected and investigated in a database known as METS. The emission tests are performed using the Field and Laboratory Emission Cell (FLEC). The emission rates of total volatile organic compounds (TVOC) in the boiling point range of hexane to octadecane varies from around 4,000 micrograms/(m2.h) to less than 10 micrograms/(m2.h). Results obtained 1994/95 are presented and compared with the results obtained in 1992 for similar materials. The tests are performed 4 weeks and 26 weeks after the manufacturing of the material. The emission rates of TVOC decrease on the average approximately 60% from 4 to 26 weeks. The differences and trends in emission rates of individual chemicals and their use are discussed. For many VOCs emission rates decrease rapidly and become near to or below 2 micrograms/(m2.h) (the detection limit) after 26 weeks. For a small number of individual compounds the emission rate decrease little over 26 weeks. A small number of chemicals are singled out for particular interest in a health and comfort evaluation based on the emission results.

Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.

PubMed

Kupas, Katrin; Ultsch, Alfred; Klebe, Gerhard

2008-05-15

A new method to discover similar substructures in protein binding pockets, independently of sequence and folding patterns or secondary structure elements, is introduced. The solvent-accessible surface of a binding pocket, automatically detected as a depression on the protein surface, is divided into a set of surface patches. Each surface patch is characterized by its shape as well as by its physicochemical characteristics. Wavelets defined on surfaces are used for the description of the shape, as they have the great advantage of allowing a comparison at different resolutions. The number of coefficients to describe the wavelets can be chosen with respect to the size of the considered data set. The physicochemical characteristics of the patches are described by the assignment of the exposed amino acid residues to one or more of five different properties determinant for molecular recognition. A self-organizing neural network is used to project the high-dimensional feature vectors onto a two-dimensional layer of neurons, called a map. To find similarities between the binding pockets, in both geometrical and physicochemical features, a clustering of the projected feature vector is performed using an automatic distance- and density-based clustering algorithm. The method was validated with a small training data set of 109 binding cavities originating from a set of enzymes covering 12 different EC numbers. A second test data set of 1378 binding cavities, extracted from enzymes of 13 different EC numbers, was then used to prove the discriminating power of the algorithm and to demonstrate its applicability to large scale analyses. In all cases, members of the data set with the same EC number were placed into coherent regions on the map, with small distances between them. Different EC numbers are separated by large distances between the feature vectors. A third data set comprising three subfamilies of endopeptidases is used to demonstrate the ability of the algorithm to detect similar substructures between functionally related active sites. The algorithm can also be used to predict the function of novel proteins not considered in training data set. 2007 Wiley-Liss, Inc.

Monitoring a large number of pesticides and transformation products in water samples from Spain and Italy.

PubMed

Rousis, Nikolaos I; Bade, Richard; Bijlsma, Lubertus; Zuccato, Ettore; Sancho, Juan V; Hernandez, Felix; Castiglioni, Sara

2017-07-01

Assessing the presence of pesticides in environmental waters is particularly challenging because of the huge number of substances used which may end up in the environment. Furthermore, the occurrence of pesticide transformation products (TPs) and/or metabolites makes this task even harder. Most studies dealing with the determination of pesticides in water include only a small number of analytes and in many cases no TPs. The present study applied a screening method for the determination of a large number of pesticides and TPs in wastewater (WW) and surface water (SW) from Spain and Italy. Liquid chromatography coupled to high-resolution mass spectrometry (HRMS) was used to screen a database of 450 pesticides and TPs. Detection and identification were based on specific criteria, i.e. mass accuracy, fragmentation, and comparison of retention times when reference standards were available, or a retention time prediction model when standards were not available. Seventeen pesticides and TPs from different classes (fungicides, herbicides and insecticides) were found in WW in Italy and Spain, and twelve in SW. Generally, in both countries more compounds were detected in effluent WW than in influent WW, and in SW than WW. This might be due to the analytical sensitivity in the different matrices, but also to the presence of multiple sources of pollution. HRMS proved a good screening tool to determine a large number of substances in water and identify some priority compounds for further quantitative analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Continuous detection of weak sensory signals in afferent spike trains: the role of anti-correlated interspike intervals in detection performance.

PubMed

Goense, J B M; Ratnam, R

2003-10-01

An important problem in sensory processing is deciding whether fluctuating neural activity encodes a stimulus or is due to variability in baseline activity. Neurons that subserve detection must examine incoming spike trains continuously, and quickly and reliably differentiate signals from baseline activity. Here we demonstrate that a neural integrator can perform continuous signal detection, with performance exceeding that of trial-based procedures, where spike counts in signal- and baseline windows are compared. The procedure was applied to data from electrosensory afferents of weakly electric fish (Apteronotus leptorhynchus), where weak perturbations generated by small prey add approximately 1 spike to a baseline of approximately 300 spikes s(-1). The hypothetical postsynaptic neuron, modeling an electrosensory lateral line lobe cell, could detect an added spike within 10-15 ms, achieving near ideal detection performance (80-95%) at false alarm rates of 1-2 Hz, while trial-based testing resulted in only 30-35% correct detections at that false alarm rate. The performance improvement was due to anti-correlations in the afferent spike train, which reduced both the amplitude and duration of fluctuations in postsynaptic membrane activity, and so decreased the number of false alarms. Anti-correlations can be exploited to improve detection performance only if there is memory of prior decisions.

Small target pre-detection with an attention mechanism

NASA Astrophysics Data System (ADS)

Wang, Yuehuan; Zhang, Tianxu; Wang, Guoyou

2002-04-01

We introduce the concept of predetection based on an attention mechanism to improve the efficiency of small-target detection by limiting the image region of detection. According to the characteristics of small-target detection, local contrast is taken as the only feature in predetection and a nonlinear sampling model is adopted to make the predetection adaptive to detect small targets with different area sizes. To simplify the predetection itself and decrease the false alarm probability, neighboring nodes in the sampling grid are used to generate a saliency map, and a short-term memory is adopted to accelerate the `pop-out' of targets. We discuss the fact that the proposed approach is simple enough in computational complexity. In addition, even in a cluttered background, attention can be led to targets in a satisfying few iterations, which ensures that the detection efficiency will not be decreased due to false alarms. Experimental results are presented to demonstrate the applicability of the approach.

Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

PubMed Central

Pöschko, Maria Theresia; Rodin, Victor V.; Schlagnitweit, Judith; Müller, Norbert; Desvaux, Hervé

2017-01-01

The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements. PMID:28067218

Dual-foci detection in photoacoustic computed tomography with coplanar light illumination and acoustic detection: a phantom study.

PubMed

Lin, Xiangwei; Liu, Chengbo; Meng, Jing; Gong, Xiaojing; Lin, Riqiang; Sun, Mingjian; Song, Liang

2018-05-01

A dual-foci transducer with coplanar light illumination and acoustic detection was applied for the first time. It overcame the small directivity angle, low-sensitivity, and large datasets in conventional circular scanning or array-based photoacoustic computed tomography (PACT). The custom-designed transducer is focused on both the scanning plane with virtual-point detection and the elevation direction for large field of view (FOV) cross-sectional imaging. Moreover, a coplanar light illumination and acoustic detection configuration can provide ring-shaped light irradiation with highly efficient acoustic detection, which in principle has a better adaptability when imaging samples of irregular surfaces. Phantom experiments showed that our PACT system can achieve high resolution (∼0.5  mm), enhanced signal-to-noise ratio (16-dB improvement), and a more complete structure in a greater FOV with an equal number of sampling points compared with the results from a flat aperture transducer. This study provides the proof of concept for the fabrication of a sparse array with the dual-foci property and large aperture size for high-quality, low-cost, and high-speed photoacoustic imaging. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Evaluation of the DIRAMIC system for detection of urinary tract infections and for Escherichia coli identification.

PubMed

Travieso Ruiz, Fernando; Roura Carmona, Gloria; Romay Penabad, Cheyla; Contreras Alarcón, Rolando

2004-01-01

The use of the DIRAMIC system for the detection of urinary tract infections (UTI) and the possibility to identify Escherichia coli in the same culture media was evaluated. The results from DIRAMIC detection system were compared to counts of colony forming units per milliliter (CFU/ml) of urine inoculated in CLED Medium; 884 urine specimens were processed taking > or =10(4) CFU/ml as criteria of positive urine culture counts. For E. coli identification, substrates for the determination of beta-glucuronidase and tryptophanase were incorporated to the culture medium and named DETID-Ec. Outputs were compared to those from API RAPIDEC-ur strips. The DIRAMIC system can detect UTI, with a sensitivity and specificity of 82.25 and 94.49%, respectively. It was possible to identify E. coli during detection with 87.50% of sensitivity and 95.96% of specificity. The small volumes of culture medium used in the DIRAMIC system as well as the short times for the detection make the system a rapid and economical method for screening UTI. Furthermore, by using DETID-Ec culture medium the time and the number of biochemical tests necessary for the E. coli identification are lowered.

Distributed Fault Detection Based on Credibility and Cooperation for WSNs in Smart Grids.

PubMed

Shao, Sujie; Guo, Shaoyong; Qiu, Xuesong

2017-04-28

Due to the increasingly important role in monitoring and data collection that sensors play, accurate and timely fault detection is a key issue for wireless sensor networks (WSNs) in smart grids. This paper presents a novel distributed fault detection mechanism for WSNs based on credibility and cooperation. Firstly, a reasonable credibility model of a sensor is established to identify any suspicious status of the sensor according to its own temporal data correlation. Based on the credibility model, the suspicious sensor is then chosen to launch fault diagnosis requests. Secondly, the sending time of fault diagnosis request is discussed to avoid the transmission overhead brought about by unnecessary diagnosis requests and improve the efficiency of fault detection based on neighbor cooperation. The diagnosis reply of a neighbor sensor is analyzed according to its own status. Finally, to further improve the accuracy of fault detection, the diagnosis results of neighbors are divided into several classifications to judge the fault status of the sensors which launch the fault diagnosis requests. Simulation results show that this novel mechanism can achieve high fault detection ratio with a small number of fault diagnoses and low data congestion probability.

Distributed Fault Detection Based on Credibility and Cooperation for WSNs in Smart Grids

PubMed Central

Shao, Sujie; Guo, Shaoyong; Qiu, Xuesong

2017-01-01

Due to the increasingly important role in monitoring and data collection that sensors play, accurate and timely fault detection is a key issue for wireless sensor networks (WSNs) in smart grids. This paper presents a novel distributed fault detection mechanism for WSNs based on credibility and cooperation. Firstly, a reasonable credibility model of a sensor is established to identify any suspicious status of the sensor according to its own temporal data correlation. Based on the credibility model, the suspicious sensor is then chosen to launch fault diagnosis requests. Secondly, the sending time of fault diagnosis request is discussed to avoid the transmission overhead brought about by unnecessary diagnosis requests and improve the efficiency of fault detection based on neighbor cooperation. The diagnosis reply of a neighbor sensor is analyzed according to its own status. Finally, to further improve the accuracy of fault detection, the diagnosis results of neighbors are divided into several classifications to judge the fault status of the sensors which launch the fault diagnosis requests. Simulation results show that this novel mechanism can achieve high fault detection ratio with a small number of fault diagnoses and low data congestion probability. PMID:28452925

Secondary syphilis in HIV positive individuals: correlation with histopathologic findings, CD4 counts, and quantity of treponemes in microscopic sections.

PubMed

Rosa, Gabriela; Procop, Gary W; Schold, Jesse D; Piliang, Melissa P

2016-10-01

Although syphilis is uncommon, infection rates are much higher in HIV-infected individuals than the general population. A proposed explanation is impaired cellular immunity with HIV infection. A search of one institution yielded 10 patients with a diagnosis of secondary syphilis on skin biopsy, positive syphilis serology and available CD4 counts. We evaluated 11 biopsies from the 10 patients. We correlated the patients' CD4 counts with the histologic findings and with the number of treponemes on skin biopsies, highlighted by immunohistochemistry (IHC). We also compared the detection of spirochetes in silver stained sections (e.g. Warthin-Starry) with T. pallidum IHC. All biopsies were assessed for various histologic features. The sensitivity of IHC to detect treponemes was 64% and of silver stain was 9% (p-value 0.04). The number of treponemes on the biopsies was determined by IHC. High numbers of spirochetes (i.e. >100 per 10 hpf) were only seen in patients with CD4 counts less than 250 cells/ml. The most consistent histologic finding was a moderate to severe lymphoplasmacytic infiltrate. Although the study is small, it appears that a higher number of spirochetes is associated with CD4 counts less than 250 cell/ml. The T. pallidum IHC stain was vastly superior to the Warthin-Starry stain. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Super-resolution reconstruction of hyperspectral images.

PubMed

Akgun, Toygar; Altunbasak, Yucel; Mersereau, Russell M

2005-11-01

Hyperspectral images are used for aerial and space imagery applications, including target detection, tracking, agricultural, and natural resource exploration. Unfortunately, atmospheric scattering, secondary illumination, changing viewing angles, and sensor noise degrade the quality of these images. Improving their resolution has a high payoff, but applying super-resolution techniques separately to every spectral band is problematic for two main reasons. First, the number of spectral bands can be in the hundreds, which increases the computational load excessively. Second, considering the bands separately does not make use of the information that is present across them. Furthermore, separate band super-resolution does not make use of the inherent low dimensionality of the spectral data, which can effectively be used to improve the robustness against noise. In this paper, we introduce a novel super-resolution method for hyperspectral images. An integral part of our work is to model the hyperspectral image acquisition process. We propose a model that enables us to represent the hyperspectral observations from different wavelengths as weighted linear combinations of a small number of basis image planes. Then, a method for applying super resolution to hyperspectral images using this model is presented. The method fuses information from multiple observations and spectral bands to improve spatial resolution and reconstruct the spectrum of the observed scene as a combination of a small number of spectral basis functions.

Multi-sensor field trials for detection and tracking of multiple small unmanned aerial vehicles flying at low altitude

NASA Astrophysics Data System (ADS)

Laurenzis, Martin; Hengy, Sebastien; Hommes, Alexander; Kloeppel, Frank; Shoykhetbrod, Alex; Geibig, Thomas; Johannes, Winfried; Naz, Pierre; Christnacher, Frank

2017-05-01

Small unmanned aerial vehicles (UAV) flying at low altitude are becoming more and more a serious threat in civilian and military scenarios. In recent past, numerous incidents have been reported where small UAV were flying in security areas leading to serious danger to public safety or privacy. The detection and tracking of small UAV is a widely discussed topic. Especially, small UAV flying at low altitude in urban environment or near background structures and the detection of multiple UAV at the same time is challenging. Field trials were carried out to investigate the detection and tracking of multiple UAV flying at low altitude with state of the art detection technologies. Here, we present results which were achieved using a heterogeneous sensor network consisting of acoustic antennas, small frequency modulated continuous wave (FMCW) RADAR systems and optical sensors. While acoustics, RADAR and LiDAR were applied to monitor a wide azimuthal area (360°) and to simultaneously track multiple UAV, optical sensors were used for sequential identification with a very narrow field of view.

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates

PubMed Central

2017-01-01

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing. PMID:28981533

The cost of large numbers of hypothesis tests on power, effect size and sample size.

PubMed

Lazzeroni, L C; Ray, A

2012-01-01

Advances in high-throughput biology and computer science are driving an exponential increase in the number of hypothesis tests in genomics and other scientific disciplines. Studies using current genotyping platforms frequently include a million or more tests. In addition to the monetary cost, this increase imposes a statistical cost owing to the multiple testing corrections needed to avoid large numbers of false-positive results. To safeguard against the resulting loss of power, some have suggested sample sizes on the order of tens of thousands that can be impractical for many diseases or may lower the quality of phenotypic measurements. This study examines the relationship between the number of tests on the one hand and power, detectable effect size or required sample size on the other. We show that once the number of tests is large, power can be maintained at a constant level, with comparatively small increases in the effect size or sample size. For example at the 0.05 significance level, a 13% increase in sample size is needed to maintain 80% power for ten million tests compared with one million tests, whereas a 70% increase in sample size is needed for 10 tests compared with a single test. Relative costs are less when measured by increases in the detectable effect size. We provide an interactive Excel calculator to compute power, effect size or sample size when comparing study designs or genome platforms involving different numbers of hypothesis tests. The results are reassuring in an era of extreme multiple testing.

Northern Blot Detection of Virus-Derived Small Interfering RNAs in Caenorhabditis elegans Using Nonradioactive Oligo Probes.

PubMed

Long, Tianyun; Lu, Rui

2017-01-01

Northern blot analysis has been widely used as a tool for detection and characterization of specific RNA molecules. When coupled with radioactive probe northern blot allows for robust detection and characterization of small RNA molecules of trace amount. Here, we describe the detection and size characterization of virus-derived small interfering RNAs (vsiRNAs) in C. elegans using nonradioactive DNA oligo probes in northern blotting. Our protocol allows for the detection and characterization of not only primary vsiRNAs but also secondary vsiRNAs, a class of single-stranded vsiRNAs that has distinct migration pattern, and can be easily adapted to the detection of vsiRNAs in other organisms.

Some observations on sympatric populations of the malaria vectors Anopheles leucosphyrus and Anopheles balabacensis in a village-forest setting in South Kalimantan.

PubMed

Harbach, R E; Baimai, V; Sukowati, S

1987-06-01

Human bait collections of biting anopheline mosquitoes were made on five consecutive nights during September 1986 in a remote village located in a heavily forested area of South Kalimantan, Indonesia. Anopheles leucosphyrus and An. balabacensis comprised 97.7% of the total number of specimens collected outside houses in the village. Anopheles balabacensis were slightly fewer in total numbers than leucosphyrus. Mosquitoes were collected simultaneously in the village and the forest on two nights. The numbers of leucosphyrus and balabacensis biting in the forest were small in comparison with the populations encountered in the village. Approximately 75% of the specimens were checked individually for sporozoite infections using ELISA for P. falciparum and P. vivax. Sporozoites of P. falciparum were detected in one specimen of leucosphyrus and one of balabacensis. The sporozoite infection rate was 1.0% for leucosphyrus and 1.3% for balabacensis.

Readily releasable pool of synaptic vesicles measured at single synaptic contacts.

PubMed

Trigo, Federico F; Sakaba, Takeshi; Ogden, David; Marty, Alain

2012-10-30

To distinguish between different models of vesicular release in brain synapses, it is necessary to know the number of vesicles of transmitter that can be released immediately at individual synapses by a high-calcium stimulus, the readily releasable pool (RRP). We used direct stimulation by calcium uncaging at identified, single-site inhibitory synapses to investigate the statistics of vesicular release and the size of the RRP. Vesicular release, detected as quantal responses in the postsynaptic neuron, showed an unexpected stochastic variation in the number of quanta from stimulus to stimulus at high intracellular calcium, with a mean of 1.9 per stimulus and a maximum of three or four. The results provide direct measurement of the RRP at single synaptic sites. They are consistent with models in which release proceeds from a small number of vesicle docking sites with an average occupancy around 0.7.

Characterization of the Oxidation State of 229 Th Recoils Implanted in MgF2 for the Search of the Low-lying 229 Th Isomeric State

NASA Astrophysics Data System (ADS)

Barker, Beau; Meyer, Edmund; Schacht, Mike; Collins, Lee; Wilkerson, Marianne; Zhao, Xinxin

2016-05-01

The low-lying (7.8 eV) isomeric state in 229 Th has the potential to become a nuclear frequency standard. 229 Th recoils from 233 U decays have been collected in MgF2 for use in the direct search of the transition. Of interest is the oxidation state of the implanted 229 Th atoms as this can have an influence on the decay mechanisms and photon emission rate. Too determine the oxidation state of the implanted 229 Th recoils we have employed laser induced florescence (LIF), and plan-wave pseudopotential DFT calculations to search for emission from thorium ions in oxidation states less than + 4. Our search focused on detecting emission from Th3+ ions. The DFT calculations predicted the Th3+ state to be the most likely to be present in the crystal after Th4+. We also calculated the band structure for the Th3+ doped MgF2 crystal. For LIF spectra a number of excitation wavelengths were employed, emission spectra in the visible to near-IR were recorded along with time-resolved emission spectra. We have found no evidence for Th3+ in the MgF2 plates. We also analyzed the detection limit of our apprentice and found that the minimum number of Th3+ atoms that we could detect is quite small compared to the number of implanted 229 Th recoils. The number of implanted 229 Th recoils was derived from a γ-ray spectrum by monitoring emission from the daughters of 228 Th. These were present in the MgF2 plates due to a 232 U impurity, which decays to 228 Th, in the source. LA-UR-16-20442.

Mycobacterium smegmatis strain for detection of Mycobacterium tuberculosis by PCR used as internal control for inhibition of amplification and for quantification of bacteria.

PubMed Central

Kolk, A H; Noordhoek, G T; de Leeuw, O; Kuijper, S; van Embden, J D

1994-01-01

For the detection of Mycobacterium tuberculosis by PCR, the IS6110 sequence was used. A modified target was constructed by insertion of 56 nucleotides in the IS6110 insertion element of Mycobacterium bovis BCG. This modified insertion sequence was integrated into the genome of Mycobacterium smegmatis, a mycobacterium species which does not contain the IS6110 element. When DNA from the modified M. smegmatis 1008 strain was amplified with IS6110-specific primers INS1 and INS2, a band of 301 bp was seen on agarose gel, whereas the PCR product of M. tuberculosis complex DNA was a 245-bp fragment with these primers. The addition of a small number of M. smegmatis 1008 cells to clinical samples before DNA purification enables the detection of problems which may be due to the loss of DNA in the isolation procedure or to the presence of inhibitors. The presence of inhibitors of the amplification reaction can be confirmed by the addition of M. smegmatis 1008 DNA after the DNA isolation procedure. Furthermore, competition between the different target DNAs of M. smegmatis 1008 DNA and M. tuberculosis complex DNA enables the estimation of the number of IS6110 elements in the clinical sample. Images PMID:8051267

Application of airborne thermal imagery to surveys of Pacific walrus

USGS Publications Warehouse

Burn, D.M.; Webber, M.A.; Udevitz, M.S.

2006-01-01

We conducted tests of airborne thermal imagery of Pacific walrus to determine if this technology can be used to detect walrus groups on sea ice and estimate the number of walruses present in each group. In April 2002 we collected thermal imagery of 37 walrus groups in the Bering Sea at spatial resolutions ranging from 1-4 m. We also collected high-resolution digital aerial photographs of the same groups. Walruses were considerably warmer than the background environment of ice, snow, and seawater and were easily detected in thermal imagery. We found a significant linear relation between walrus group size and the amount of heat measured by the thermal sensor at all 4 spatial resolutions tested. This relation can be used in a double-sampling framework to estimate total walrus numbers from a thermal survey of a sample of units within an area and photographs from a subsample of the thermally detected groups. Previous methods used in visual aerial surveys of Pacific walrus have sampled only a small percentage of available habitat, resulting in population estimates with low precision. Results of this study indicate that an aerial survey using a thermal sensor can cover as much as 4 times the area per hour of flight time with greater reliability than visual observation.

Diabetic retinopathy grading by digital curvelet transform.

PubMed

Hajeb Mohammad Alipour, Shirin; Rabbani, Hossein; Akhlaghi, Mohammad Reza

2012-01-01

One of the major complications of diabetes is diabetic retinopathy. As manual analysis and diagnosis of large amount of images are time consuming, automatic detection and grading of diabetic retinopathy are desired. In this paper, we use fundus fluorescein angiography and color fundus images simultaneously, extract 6 features employing curvelet transform, and feed them to support vector machine in order to determine diabetic retinopathy severity stages. These features are area of blood vessels, area, regularity of foveal avascular zone, and the number of micro-aneurisms therein, total number of micro-aneurisms, and area of exudates. In order to extract exudates and vessels, we respectively modify curvelet coefficients of color fundus images and angiograms. The end points of extracted vessels in predefined region of interest based on optic disk are connected together to segment foveal avascular zone region. To extract micro-aneurisms from angiogram, first extracted vessels are subtracted from original image, and after removing detected background by morphological operators and enhancing bright small pixels, micro-aneurisms are detected. 70 patients were involved in this study to classify diabetic retinopathy into 3 groups, that is, (1) no diabetic retinopathy, (2) mild/moderate nonproliferative diabetic retinopathy, (3) severe nonproliferative/proliferative diabetic retinopathy, and our simulations show that the proposed system has sensitivity and specificity of 100% for grading.

Inventory of forest and rangeland and detection of forest stress

NASA Technical Reports Server (NTRS)

Heller, R. C. (Principal Investigator); Aldrich, R. C.; Weber, F. P.; Driscoll, R. S.

1973-01-01

The author has identified the following significant results. Three small scales of CIR photography were interpreted to determine the number of bark beetle-killed trees detected in each of six spot size categories. A procedure was developed to predict the probability of detecting spots in each spot size category and in turn to estimate the number of infestations and dead trees even on the smallest scale. Statistical tests of the data indicated that the linear model did not fit the data and that other models should be tested. As a result of daily monitoring of Black Hills radiometric instruments it was possible to show the spectral energy relationships in the ponderosa pine ecosystems over time. These data have been helpful for comparison with radiance signatures extracted from ERTS-1 bulk 70mm using precision microdensitometry. Effects of atmospheric interference were shown by a 30 percent increase in scene radiance on channel 4 of the satellite imagery. A calibration and scaling technique was developed and tested to enable interpretation of ERTS-1 bulk and precision data for the Atlanta test site. The technique includes calibration of a photographic copy system for the I2S image combiner and the production of scaled overlays of grid coordinate systems, study area locations, and outline maps of county boundaries.

A binned clustering algorithm to detect high-Z material using cosmic muons

NASA Astrophysics Data System (ADS)

Thomay, C.; Velthuis, J. J.; Baesso, P.; Cussans, D.; Morris, P. A. W.; Steer, C.; Burns, J.; Quillin, S.; Stapleton, M.

2013-10-01

We present a novel approach to the detection of special nuclear material using cosmic rays. Muon Scattering Tomography (MST) is a method for using cosmic muons to scan cargo containers and vehicles for special nuclear material. Cosmic muons are abundant, highly penetrating, not harmful for organic tissue, cannot be screened against, and can easily be detected, which makes them highly suited to the use of cargo scanning. Muons undergo multiple Coulomb scattering when passing through material, and the amount of scattering is roughly proportional to the square of the atomic number Z of the material. By reconstructing incoming and outgoing tracks, we can obtain variables to identify high-Z material. In a real life application, this has to happen on a timescale of 1 min and thus with small numbers of muons. We have built a detector system using resistive plate chambers (RPCs): 12 layers of RPCs allow for the readout of 6 x and 6 y positions, by which we can reconstruct incoming and outgoing tracks. In this work we detail the performance of an algorithm by which we separate high-Z targets from low-Z background, both for real data from our prototype setup and for MC simulation of a cargo container-sized setup. (c) British Crown Owned Copyright 2013/AWE

Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples.

PubMed

Zhao, Qi; Liu, Yuanning; Zhang, Ning; Hu, Menghan; Zhang, Hao; Joshi, Trupti; Xu, Dong

2018-01-01

In recent years, an increasing number of studies have reported the presence of plant miRNAs in human samples, which resulted in a hypothesis asserting the existence of plant-derived exogenous microRNA (xenomiR). However, this hypothesis is not widely accepted in the scientific community due to possible sample contamination and the small sample size with lack of rigorous statistical analysis. This study provides a systematic statistical test that can validate (or invalidate) the plant-derived xenomiR hypothesis by analyzing 388 small RNA sequencing data from human samples in 11 types of body fluids/tissues. A total of 166 types of plant miRNAs were found in at least one human sample, of which 14 plant miRNAs represented more than 80% of the total plant miRNAs abundance in human samples. Plant miRNA profiles were characterized to be tissue-specific in different human samples. Meanwhile, the plant miRNAs identified from microbiome have an insignificant abundance compared to those from humans, while plant miRNA profiles in human samples were significantly different from those in plants, suggesting that sample contamination is an unlikely reason for all the plant miRNAs detected in human samples. This study also provides a set of testable synthetic miRNAs with isotopes that can be detected in situ after being fed to animals.

Non-small cell lung carcinoma therapy using mTOR-siRNA.

PubMed

Matsubara, Hirochika; Sakakibara, Kenji; Kunimitsu, Tamo; Matsuoka, Hiroyasu; Kato, Kaori; Oyachi, Noboru; Dobashi, Yoh; Matsumoto, Masahiko

2012-01-01

Molecular targeting agents play important roles in non-small-cell lung cancer (NSCLC) therapy. Published studies have investigated new drugs categorized as molecular targeting agents that inhibit the mammalian target of rapamycin (mTOR). We focused on a small interfering RNA (siRNA) that specifically inhibits mTOR and has fewer side effects. To evaluate the antitumor effects of the siRNA, cell proliferation, apoptosis, and migration were assessed. In the study group, the siRNA was transfected into NSCLC cells. The number of cells present after 6 days of culture was counted to determine changes in cell proliferation. The level of apoptosis was evaluated by the detection of DNA-histone complexes in the cytoplasmic fraction using an absorption spectrometer. Changes in migration were evaluated by calculating the number of cells that passed through a specific filter using a commercial chemotaxis assay kit. mTOR-siRNA transfection inhibited cell proliferation as indicated by 37.3% (p = 0.034) decrease in the number of cells compared with the control cells. Analysis of the level of apoptosis in NSCLC cells revealed 16.7% (p = 0.016) increase following mTOR-siRNA transfection, and mTOR-siRNA transfection significantly inhibited cell migration by 39.2% (p = 0.0001). We confirmed that mTOR-siRNA induces apoptosis and inhibits the proliferation and migration of NSCLC cells in vitro. Further studies using mTOR-siRNA may aid in the development of an alternative therapy that maximizes the antineoplastic effect of mTOR inhibition.

Non-small cell lung carcinoma therapy using mTOR-siRNA

PubMed Central

Matsubara, Hirochika; Sakakibara, Kenji; Kunimitsu, Tamo; Matsuoka, Hiroyasu; Kato, Kaori; Oyachi, Noboru; Dobashi, Yoh; Matsumoto, Masahiko

2012-01-01

Molecular targeting agents play important roles in non-small-cell lung cancer (NSCLC) therapy. Published studies have investigated new drugs categorized as molecular targeting agents that inhibit the mammalian target of rapamycin (mTOR). We focused on a small interfering RNA (siRNA) that specifically inhibits mTOR and has fewer side effects. To evaluate the antitumor effects of the siRNA, cell proliferation, apoptosis, and migration were assessed. In the study group, the siRNA was transfected into NSCLC cells. The number of cells present after 6 days of culture was counted to determine changes in cell proliferation. The level of apoptosis was evaluated by the detection of DNA-histone complexes in the cytoplasmic fraction using an absorption spectrometer. Changes in migration were evaluated by calculating the number of cells that passed through a specific filter using a commercial chemotaxis assay kit. mTOR-siRNA transfection inhibited cell proliferation as indicated by 37.3% (p = 0.034) decrease in the number of cells compared with the control cells. Analysis of the level of apoptosis in NSCLC cells revealed 16.7% (p = 0.016) increase following mTOR-siRNA transfection, and mTOR-siRNA transfection significantly inhibited cell migration by 39.2% (p = 0.0001). We confirmed that mTOR-siRNA induces apoptosis and inhibits the proliferation and migration of NSCLC cells in vitro. Further studies using mTOR-siRNA may aid in the development of an alternative therapy that maximizes the antineoplastic effect of mTOR inhibition. PMID:22400071

X-ray intravital microscopy for functional imaging in rat hearts using synchrotron radiation coronary microangiography

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

Umetani, K.; Fukushima, K.

2013-03-15

An X-ray intravital microscopy technique was developed to enable in vivo visualization of the coronary, cerebral, and pulmonary arteries in rats without exposure of organs and with spatial resolution in the micrometer range and temporal resolution in the millisecond range. We have refined the system continually in terms of the spatial resolution and exposure time. X-rays transmitted through an object are detected by an X-ray direct-conversion type detector, which incorporates an X-ray SATICON pickup tube. The spatial resolution has been improved to 6 {mu}m, yielding sharp images of small arteries. The exposure time has been shortened to around 2 msmore » using a new rotating-disk X-ray shutter, enabling imaging of beating rat hearts. Quantitative evaluations of the X-ray intravital microscopy technique were extracted from measurements of the smallest-detectable vessel size and detection of the vessel function. The smallest-diameter vessel viewed for measurements is determined primarily by the concentration of iodinated contrast material. The iodine concentration depends on the injection technique. We used ex vivo rat hearts under Langendorff perfusion for accurate evaluation. After the contrast agent is injected into the origin of the aorta in an isolated perfused rat heart, the contrast agent is delivered directly into the coronary arteries with minimum dilution. The vascular internal diameter response of coronary arterial circulation is analyzed to evaluate the vessel function. Small blood vessels of more than about 50 {mu}m diameters were visualized clearly at heart rates of around 300 beats/min. Vasodilation compared to the control was observed quantitatively using drug manipulation. Furthermore, the apparent increase in the number of small vessels with diameters of less than about 50 {mu}m was observed after the vasoactive agents increased the diameters of invisible small blood vessels to visible sizes. This technique is expected to offer the potential for direct investigation of mechanisms of vascular dysfunctions.« less

[The hazards of hospitals and selected public buildings of Legionella pneumophila].

PubMed

Sikora, Agnieszka; Kozioł-Montewka, Maria; Wójtowicz-Bobin, Małgorzata; Gładysz, Iwona; Dobosz, Paulina

2013-11-01

The registered infection and outbreaks of epidemic tend to monitor potential reservoirs of Legionella infection. According to the Act of 29 March 2007 on the requirements for the quality of water intended for human consumption are required to test for the presence and number of Legionella in the water system of hospitals. In case of detection of L. pneumophila serogroup 1 (SG 1) or increased above normal number other serogroups of bacteria it is necessary to eradicate these bacteria from the water system. The aim of this study was to assess the degree of contamination of the water supply system of selected public buildings and analyze the effectiveness of disinfection methods for the elimination of L. pneumophila in hot water systems. The materials for this study were hot and cold water samples which were collected from the water supply system of 23 different objects. Enumeration of Legionella bacteria in water samples was determined by membrane filtration (FM) and/or by surface inoculation methods according to the standards: PN-ISO 11731: 2002: "The quality of the water. Detection and enumeration of Legionella" and PN-EN ISO 11731-2: 2008: "Water quality--Detection and enumeration of Legionella--Part 2: Methodology of membrane filtration for water with a small number of bacteria". L. pneumophila was present in 164 samples of hot water, which accounted for 76.99%. In all tested water samples L. pneumophila SG 2-14 strains were detected. The most virulent strain--L. pneumophila SG 1 was not detected. In examined 23 objects in 12 of L. pneumophila exceed acceptable levels > 100 CFU/100 ml. The presence of L. pneumophila SG 2-14 demonstrated in all examined objects, indicating the risk of infection, and the need for permanent monitoring of the water system supply. The thermal disinfection is the most common, inexpensive, and effective method of control of L. pneumophila used in examined objects, but does not eliminate bacterial biofilm. Disinfection using the filters stopped of L. pneumophila, and was the method of complementary thermal disinfection. Chlorine dioxide is a very effective biocide for large numbers of L. pneumophila in water systems.

Daily rhythmicity of body temperature in the dog.

PubMed

Refinetti, R; Piccione, G

2003-08-01

Research over the past 50 years has demonstrated the existence of circadian or daily rhythmicity in the body core temperature of a large number of mammalian species. However, previous studies have failed to identify daily rhythmicity of body temperature in dogs. We report here the successful recording of daily rhythms of rectal temperature in female Beagle dogs. The low robustness of the rhythms (41% of maximal robustness) and the small range of excursion (0.5 degrees C) are probably responsible for previous failures in detecting rhythmicity in dogs.

Device characteristics of antenna-coupled metal-insulator-metal diodes (rectenna) using Al2O3, TiO2, and Cr2O3 as insulator layer for energy harvesting applications

NASA Astrophysics Data System (ADS)

Inac, Mesut; Shafique, Atia; Ozcan, Meric; Gurbuz, Yasar

2015-09-01

Antenna-coupled metal-insulator-metal devices are most potent candidate for future energy harvesting devices. The reason for that they are ultra-high speed devices that can rectify the electromagnetic radiation at high frequencies. In addition to their speed, they are also small devices that can have more number of devices in unit area. In this work, it is aimed design and develop a device which can harvest and detect IR radiation.

A study of the far infrared counterparts of new candidates for planetary nebulae

NASA Astrophysics Data System (ADS)

Iyengar, K. V. K.

1986-05-01

The IRAS Point Source Catalog was searched for infrared counterparts of the fourteen new candidates for planetary nebulae of low surface brightness detected by Hartl and Tritton (1985). Five of these candidates were identified with sources in the Catalog. All five nebulae are found in regions of high cirrus flux at 100 microns, and all have both point sources and small size extended sources with numbers varying from field to field. The infrared emission from these nebulae is connected with dust temperatures of about 100 K, characteristic of planetary nebulae.