Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks.

PubMed

Deininger, Lisa; Patel, Ekta; Clench, Malcolm R; Sears, Vaughn; Sammon, Chris; Francese, Simona

2016-06-01

A bottom up in situ proteomic method has been developed enabling the mapping of multiple blood signatures on the intact ridges of blood fingermarks by Matrix Assisted Laser Desorption Mass Spectrometry Imaging (MALDI-MSI). This method, at a proof of concept stage, builds upon recently published work demonstrating the opportunity to profile and identify multiple blood signatures in bloodstains via a bottom up proteomic approach. The present protocol addresses the limitation of the previously developed profiling method with respect to destructivity; destructivity should be avoided for evidence such as blood fingermarks, where the ridge detail must be preserved in order to provide the associative link between the biometric information and the events of bloodshed. Using a blood mark reference model, trypsin concentration and spraying conditions have been optimised within the technical constraints of the depositor eventually employed; the application of MALDI-MSI and Ion Mobility MS have enabled the detection, confirmation and visualisation of blood signatures directly onto the ridge pattern. These results are to be considered a first insight into a method eventually informing investigations (and judicial debates) of violent crimes in which the reliable and non-destructive detection and mapping of blood in fingermarks is paramount to reconstruct the events of bloodshed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fingermark ridge drift.

PubMed

De Alcaraz-Fossoul, Josep; Roberts, Katherine A; Feixat, Carme Barrot; Hogrebe, Gregory G; Badia, Manel Gené

2016-01-01

Distortions of the fingermark topography are usually considered when comparing latent and exemplar fingerprints. These alterations are characterized as caused by an extrinsic action, which affects entire areas of the deposition and alters the overall flow of a series of contiguous ridges. Here we introduce a novel visual phenomenon that does not follow these principles, named fingermark ridge drift. An experiment was designed that included variables such as type of secretion (eccrine and sebaceous), substrate (glass and polystyrene), and degrees of exposure to natural light (darkness, shade, and direct light) indoors. Fingermarks were sequentially visualized with titanium dioxide powder, photographed and analyzed. The comparison between fresh and aged depositions revealed that under certain environmental conditions an individual ridge could randomly change its original position regardless of its unaltered adjacent ridges. The causes of the drift phenomenon are not well understood. We believe it is exclusively associated with intrinsic natural aging processes of latent fingermarks. This discovery will help explain the detection of certain dissimilarities at the minutiae/ridge level; determine more accurate "hits"; identify potentially erroneous corresponding points; and rethink identification protocols, especially the criteria of "no single minutiae discrepancy" for a positive identification. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Application of acid-modified Imperata cylindrica powder for latent fingerprint development.

PubMed

Low, Wei Zeng; Khoo, Bee Ee; Aziz, Zalina Binti Abdul; Low, Ling Wei; Teng, Tjoon Tow; bin Abdullah, Ahmad Fahmi Lim

2015-09-01

A novel powdering material that utilizes acid-modified Imperata cylindrica (IC) powder for the development of fingermarks was studied. Experiments were carried out to determine the suitability, adherence quality and sensitivity of the acid-modified IC powder. Fingermarks of different constituents (eccrine, sebaceous and natural fingermarks) on different types of surfaces were used. Acid-modified IC powder was also used to develop fingermarks of different ages as well as aged fingermarks recovered from the water. From the visual inspection, acid-modified IC powder was able to interact with different fingermark constituents and produced distinct ridge details on the examined surfaces. It was also able to develop aged fingermarks and fingermarks that were submerged in water. A statistical comparison was made against the Sirchie® Hi-Fi black powder in terms of the powders' sensitivity and quality of the developed natural fingermarks. The image quality was analyzed using MITRE's Image Quality of Fingerprint (IQF) software. From the experiments, acid-modified IC powder has the potential as a fingermark development powder, although natural fingermarks developed by Sirchie® black powder showed better quality and sensitivity based on the results of the statistical comparison. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Solid-state acquisition of fingermark topology using dense columnar thin films.

PubMed

Lakhtakia, Akhlesh; Shaler, Robert C; Martín-Palma, Raúl J; Motyka, Michael A; Pulsifer, Drew P

2011-05-01

Various vacuum techniques are employed to develop fingermarks on evidentiary items. In this work, a vacuum was used to deposit columnar thin films (CTFs) on untreated, cyanoacrylate-fumed or dusted fingermarks on a limited selection of nonporous surfaces (microscope glass slides and evidence tape). CTF deposition was not attempted on fingermarks deposited on porous surfaces. The fingermarks were placed in a vacuum chamber with the fingermark side facing an evaporating source boat containing either chalcogenide glass or MgF(2). Thermal evaporation of chalcogenide glass or MgF(2) under a 1 μTorr vacuum for 30 min formed dense CTFs on fingermark ridges, capturing the topographical features. The results show that it is possible to capture fingermark topology using CTFs on selected untreated, vacuumed cyanoacrylate-fumed or black powder-dusted nonporous surfaces. Additionally, the results suggested this might be a mechanism to help elucidate the sequence of deposition. © 2011 American Academy of Forensic Sciences.

Comparison of the columnar-thin-film and vacuum-metal-deposition techniques to develop sebaceous fingermarks on nonporous substrates.

PubMed

Williams, Stephanie F; Pulsifer, Drew P; Shaler, Robert C; Ramotowski, Robert S; Brazelle, Shelly; Lakhtakia, Akhlesh

2015-03-01

Both the columnar-thin-film (CTF) and the vacuum-metal-deposition (VMD) techniques for visualizing sebaceous fingermarks require the deposition of a material thereon in a vacuum chamber. Despite that similarity, there are many differences between the two techniques. The film deposited with the CTF technique has a columnar morphology, but the film deposited with the VMD technique comprises discrete islands. A split-print methodology on a variety of fingermarked substrates was used to determine that the CTF technique is superior for developing fingermarks on clear sandwich bags and partial bloody fingermarks on stainless steel. Both techniques are similar in their ability to develop fingermarks on glass but the CTF technique yields higher contrast. The VMD technique is superior for developing fingermarks on white grocery bags and the smooth side of Gloss Finish Scotch Multitask(™) tape. Neither technique worked well for fingermarks on black garbage bags. © 2014 American Academy of Forensic Sciences.

Latent fingermark development on a range of porous substrates using ninhydrin analogs--a comparison with ninhydrin and 1,8-diazofluoren.

PubMed

Berdejo, Stephanie; Rowe, Mark; Bond, John W

2012-03-01

Three relatively new reagents for developing latent fingermarks on porous substrates, 1,2-indandione (IND), 5-methylthioninhydrin (5-MTN), and lawsone, are compared with the more widely used ninhydrin and 1,8-diazofluoren (DFO). Developed latent fingermark visualization on 10 different substrates comprising colored papers, cardboard, and cellophane rather than conventional printer and writing/notepad paper is assessed using latent fingermark deposits from 48 donors. Results show improved fluorescent fingermark visualization using IND compared with DFO on a range of colored cardboards and thick white paper, thus extending the range of substrates known to yield improved visualization with IND. Adding zinc chloride to IND failed to yield any further improvement in fluorescent fingermark visualization. 5-MTN (with and without zinc chloride posttreatment) showed no improvement in visualization compared with ninhydrin and DFO although visible fingermarks were developed. Lawsone produced fluorescent visible fingermarks only with white substrates, which were inferior to those produced with DFO. © 2011 American Academy of Forensic Sciences.

The analysis of latent fingermarks on polymer banknotes using MALDI-MS.

PubMed

Scotcher, K; Bradshaw, R

2018-06-08

In September 2016, the UK adopted a new Bank of England (BoE) £5 polymer banknote, followed by the £10 polymer banknote in September 2017. They are designed to be cleaner, stronger and have increased counterfeit resilience; however, fingermark development can be problematic from the polymer material as various security features and coloured/textured areas have been found to alter the effectiveness of conventional fingermark enhancement techniques (FETs). As fingermarks are one of the most widely used forms of identification in forensic cases, it is important that maximum ridge detail be obtained in order to allow for comparison. This research explores the use of matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) profiling and imaging for the analysis of fingermarks deposited on polymer banknotes. The proposed methodology was able to obtain both physical and chemical information from fingermarks deposited in a range of scenarios including; different note areas, depletion series, aged samples and following conventional FETs. The analysis of forensically important molecular targets within these fingermarks was also explored, focussing specifically on cocaine. The ability of MALDI-MS to provide ridge detail and chemical information highlights the forensic applicability of this technique and potential for the analysis of fingermarks deposited onto this problematic surface.

An update on MALDI mass spectrometry based technology for the analysis of fingermarks - stepping into operational deployment.

PubMed

Francese, S; Bradshaw, R; Denison, N

2017-07-10

Since 2009, when Matrix Assisted Laser Desorption Ionisation Mass Spectrometry Imaging (MALDI MSI) was firstly reported for the molecular mapping of latent fingermarks, the range of information and operational capabilities have steadily increased. Pioneering work from our Fingermark Research Group exploited different modalities, including Profiling (MALDI MSP), tandem mass spectrometry (MS/MS) and Ion Mobility MS/MS; a number of methodologies were also developed to conquer a main challenge, namely profiling the suspect and their actions prior to or whilst committing the crime. Suspect profiling here is no longer based on behavioural science but complements this discipline and the investigations by detecting and visualising the molecular make-up of fingermarks onto the identifying ridges. This forensic opportunity provides the link between the biometric information (ridge detail) and the corpus delicti or intelligence on the circumstances of the crime. In 2013, a review was published covering the research work and developments of four years supported by the Home Office, UK, and the local regional Police with some insights (and comparison) into similar research being reported employing other mass spectrometric techniques. The present review is an extensive update on the MALDI MS based methods' achievements, limitations and work in progress in fingermark analysis; it also offers an outlook on further necessary research into this subject. The main highlights are the increased number of possible information retrievable around a suspect and the more extended compatibility of this technology. The latter has allowed MALDI MS based methods to integrate well with current forensic fingerprinting, leading to the investigation of real police casework.

The Reed-Stanton press rig for the generation of reproducible fingermarks: Towards a standardised methodology for fingermark research.

PubMed

Reed, H; Stanton, A; Wheat, J; Kelley, J; Davis, L; Rao, W; Smith, A; Owen, D; Francese, S

2016-01-01

In the search for better or new methods/techniques to visualise fingermarks or to analyse them exploiting their chemical content, fingermarks inter-variability may hinder the assessment of the method effectiveness. Variability is due to changes in the chemical composition of the fingermarks between different donors and within the same donor, as well as to differential contact time, pressure and angle. When validating a method or comparing it with existing ones, it is not always possible to account for this type of variability. One way to compensate for these issues is to employ, in the early stages of the method development, a device generating reproducible fingermarks. Here the authors present their take on such device, as well as quantitatively describing its performance and benefits against the manual production of marks. Finally a short application is illustrated for the use of this device, at the method developmental stages, in an emerging area of fingerprinting research concerning the retrieval of chemical intelligence from fingermarks. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Thermal development of latent fingermarks on porous surfaces--further observations and refinements.

PubMed

Song, Di Fei; Sommerville, Daniel; Brown, Adam G; Shimmon, Ronald G; Reedy, Brian J; Tahtouh, Mark

2011-01-30

In a further study of the thermal development of fingermarks on paper and similar surfaces, it is demonstrated that direct contact heating of the substrate using coated or ceramic surfaces at temperatures in excess of 230°C produces results superior to those obtained using hot air. Fingermarks can also be developed in this way on other cellulose-based substrates such as wood and cotton fabric, though ridge detail is difficult to obtain in the latter case. Fluorescence spectroscopy indicates that the phenomena observed during the thermal development of fingermarks can be reproduced simply by heating untreated white copy paper or filter paper, or these papers treated with solutions of sodium chloride or alanine. There is no evidence to suggest that the observed fluorescence of fingermarks heated on paper is due to a reaction of fingermark constituents on or with the paper. Instead, we maintain that the ridge contrast observed first as fluorescence, and later as brown charring, is simply an acceleration of the thermal degradation of the paper. Thermal degradation of cellulose, a major constituent of paper and wood, is known to give rise to a fluorescent product if sufficient oxygen is available [1-5]. However, the absence of atmospheric oxygen has only a slight effect on the thermal development of fingermarks, indicating that there is sufficient oxygen already present in paper to allow the formation of the fluorescent and charred products. In a depletion study comparing thermal development of fingermarks on paper with development using ninhydrin, the thermal technique was found to be as sensitive as ninhydrin for six out of seven donors. When thermal development was used in sequence with ninhydrin and DFO, it was found that only fingermarks that had been developed to the fluorescent stage (a few seconds of heating) could subsequently be developed with the other reagents. In the reverse sequence, no useful further development was noted for fingermarks that were treated thermally after having been developed with ninhydrin or DFO. Aged fingermarks, including marks from 1-year-old university examination papers were successfully developed using the thermal technique. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Development of latent fingermarks on thermal paper: preliminary investigation into use of iodine fuming.

PubMed

Jasuja, Om Prakash; Singh, Gagandeep

2009-11-20

Thermal paper finds its extensive use in the modern day life and could act as a vital piece of physical evidence carrying latent fingermarks. A large number of citations are available in literature suggesting various techniques to develop these marks but all are suffering with one or the other drawbacks such as complex and cumbersome procedure, pre- or post-treatment, background coloration and efficiency to develop aged fingermarks. In present study, a very simple and novel method involving iodine fuming has been suggested to develop fingermarks which were not only permanent but also without any background coloration. The suggested method does not involve any pre- or post-treatment of the substrate and was able to develop very old fingermarks (upto >1 year). In this study an attempt has been made to explain the reaction mechanism of the process. In case of different types of thermal papers, presence of different substituents on leuco dye (lactone ring) structure resulted in development of different colored fingermarks upon reaction with iodine. Sebaceous material laden marks have been found to be more intensely developed as compared to eccrine marks, and the difference was more pronounced in case of aged fingermarks.

The thermal visualisation of latent fingermarks on metallic surfaces.

PubMed

Wightman, G; O'Connor, D

2011-01-30

Recent published research has lead to improved techniques for recovering latent fingermarks from metallic surfaces. The present study corroborates and extends some of the work carried out by Bond [1-3], but an alternative mechanism is proposed for the thermal visualisation of fingermarks based on differential oxidation and the production of interference colours that improve contrast. Fingermarks treated at low temperature could be reheated to enhance recovery, but an upper temperature limit occurs beyond which the mark degrades. The mechanism of enhancement is discussed. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Observations on the effects of image processing functions on fingermark data in the Fourier domain

NASA Astrophysics Data System (ADS)

Bramble, Simon K.; Fabrizi, Paola M.

1995-09-01

One of the image processing functions used for the enhancement of laten fingermark images is the Fourier transform. This paper describes some effects of spatial resolution, zero-filling and windowing on fingermark data in the Fourier domain. It is shown that with an understanding of the fingermark structure it is possible to determine the approximate prosition of the frequency data in the Fourier domain corresponding to the fingermark image detail. The effect of attenuation of frequency data on a zero-filled image is shown to be different to the same attenuation on a non-zero-filled image. The effects of windowing spatial data on the frequency data are also highlighted and compared with the same data after the application of a Hanning window.

Optical properties of drug metabolites in latent fingermarks

PubMed Central

Shen, Yao; Ai, Qing

2016-01-01

Drug metabolites usually have structures of split-ring resonators (SRRs), which might lead to negative permittivity and permeability in electromagnetic field. As a result, in the UV-vis region, the latent fingermarks images of drug addicts and non drug users are inverse. The optical properties of latent fingermarks are quite different between drug addicts and non-drug users. This is a technic superiority for crime scene investigation to distinguish them. In this paper, we calculate the permittivity and permeability of drug metabolites using tight-binding model. The latent fingermarks of smokers and non-smokers are given as an example. PMID:26838730

A novel method for the photographic recovery of fingermark impressions from ammunition cases using digital imaging.

PubMed

Porter, Glenn; Ebeyan, Robert; Crumlish, Charles; Renshaw, Adrian

2015-03-01

The photographic preservation of fingermark impression evidence found on ammunition cases remains problematic due to the cylindrical shape of the deposition substrate preventing complete capture of the impression in a single image. A novel method was developed for the photographic recovery of fingermarks from curved surfaces using digital imaging. The process involves the digital construction of a complete impression image made from several different images captured from multiple camera perspectives. Fingermark impressions deposited onto 9-mm and 0.22-caliber brass cartridge cases and a plastic 12-gauge shotgun shell were tested using various image parameters, including digital stitching method, number of images per 360° rotation of shell, image cropping, and overlap. The results suggest that this method may be successfully used to recover fingermark impression evidence from the surfaces of ammunition cases or other similar cylindrical surfaces. © 2014 American Academy of Forensic Sciences.

Metabolite mapping by consecutive nanostructure and silver-assisted mass spectrometry imaging on tissue sections.

PubMed

Gustafsson, O J R; Guinan, T M; Rudd, D; Kobus, H; Benkendorff, K; Voelcker, N H

2017-06-30

Nanostructure-based mass spectrometry imaging (MSI) is a promising technology for molecular imaging of small molecules, without the complex chemical background typically encountered in matrix-assisted molecular imaging approaches. Here, we have enhanced these surfaces with silver (Ag) to provide a second tier of MSI data from a single sample. MSI data was acquired through the application of laser desorption/ionization mass spectrometry to biological samples imprinted onto desorption/ionization on silicon (DIOS) substrates. Following initial analysis, ultra-thin Ag layers were overlaid onto the followed by MSI analysis (Ag-DIOS MSI). This approach was first demonstrated for fingermark small molecules including environmental contaminants and sebum components. Subsequently, this bimodal method was translated to lipids and metabolites in fore-stomach sections from a 6-bromoisatin chemopreventative murine mouse model. DIOS MSI allowed mapping of common ions in fingermarks as well as 6-bromoisatin metabolites and lipids in murine fore-stomach. Furthermore, DIOS MSI was complemented by the Ag-DIOS MSI of Ag-adductable lipids such as wax esters in fingermarks and cholesterol in murine fore-stomach. Gastrointestinal acid condensation products of 6-bromoisatin, such as the 6,6'-dibromoindirubin mapped herein, are very challenging to isolate and characterize. By re-analyzing the same tissue imprints, this metabolite was readily detected by DIOS, placed in a tissue-specific spatial context, and subsequently overlaid with additional lipid distributions acquired using Ag-DIOS MSI. The ability to place metabolite and lipid classes in a tissue-specific context makes this novel method suited to MSI analyses where the collection of additional information from the same sample maximises resource use, and also maximises the number of annotated small molecules, in particular for metabolites that are typically undetectable with traditional platforms. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The interaction of fingermark deposits on metal surfaces and potential ways for visualisation.

PubMed

Wightman, G; Emery, F; Austin, C; Andersson, I; Harcus, L; Arju, G; Steven, C

2015-04-01

The interaction of fingermark deposits on metals has been examined by a variety of techniques. Visualisation by film growth has been the main area of investigation through: thermal oxidation, anodising, peroxide solution, and the interaction with vapour of iodine and ammonium sulphide. Corrosion of the underlying metal has also been examined as an alternative means of visualisation. Confocal microscopy was used to look at the film thickness and corrosion products around the prints. Scanning electron microscopy and energy dispersion of X-rays (SEM-EDX) examined a number of metal samples to investigate film growth and the elemental distribution. The observations suggest that differential oxidation was occurring as well as corrosion into the metal. Fingermark deposits on metals can corrode into the metal depending on the reactivity of the metal and leave a recoverable mark. However, fingermark deposits can also alter the rate of chemical reaction of the substrate metal by oxidation. In some cases organic matter can inhibit reaction, both when forming an oxide layer and when corroding the metal. However, signs of third level detail from pore contact may also be visible and the monovalent ions from salts could also influence film growth. Whilst further work would need to be carried out to decide whether any of these techniques may have application in fingermark recovery, this study does suggest that fingermarks on metals may be recoverable after incidents such as fires or immersion in water. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Thermally evaporated conformal thin films on non-traditional/non-planar substrates

NASA Astrophysics Data System (ADS)

Pulsifer, Drew Patrick

Conformal thin films have a wide variety of uses in the microelectronics, optics, and coatings industries. The ever-increasing capabilities of these conformal thin films have enabled tremendous technological advancement in the last half century. During this period, new thin-film deposition techniques have been developed and refined. While these techniques have remarkable performance for traditional applications which utilize planar substrates such as silicon wafers, they are not suitable for the conformal coating of non-traditional substrates such as biological material. The process of thermally evaporating a material under vacuum conditions is one of the oldest thin-film deposition techniques which is able to produce functional film morphologies. A drawback of thermally evaporated thin films is that they are not intrinsically conformal. To overcome this, while maintaining the advantages of thermal evaporation, a procedure for varying the substrates orientation with respect to the incident vapor flux during deposition was developed immediately prior to the research undertaken for this doctoral dissertation. This process was shown to greatly improve the conformality of thermally evaporated thin films. This development allows for several applications of thermally evaporated conformal thin films on non-planar/non-traditional substrates. Three settings in which to evaluate the improved conformal deposition of thermally evaporated thin films were investigated for this dissertation. In these settings the thin-film morphologies are of different types. In the first setting, a bioreplication approach was used to fabricate artificial visual decoys for the invasive species Agrilus planipennis, commonly known as the emerald ash borer (EAB). The mating behavior of this species involves an overflying EAB male pouncing on an EAB female at rest on an ash leaflet before copulation. The male spots the female on the leaflet by visually detecting the iridescent green color of the female's elytra. As rearing EAB and then deploying dead females as decoys is both arduous and inconvenient, the development of an artificial decoy would be of great interest to entomologists and foresters. A dead female EAB was used to make a negative die of nickel and a positive die of epoxy. The process of fabricating the paired dies utilized thermally evaporated conformal thin films in several critical steps. In order to conformally coat the EAB with nickel, the substrate stage holding the female EAB was periodically rocked and rotated during the deposition. This process was designed to result in a uniform thin film of ˜ 500-nm thickness with dense morphology. The nickel film was then reinforced through an electroforming process and mounted in a fixture which allowed it to be heated electrically. The corresponding positive die was replicated from the negative die through a series of successive castings. The final EAB positive die was fabricated from a hard epoxy material and attached to a fixture which allowed it to be heated while being pressed into the negative die. Decoys were then made by first depositing a quarter-wave-stack Bragg reflector on a polymer sheet and then stamping it with the pair of matched negative and positive dies to take the shape of the upper surface of an EAB female. As nearly 100 decoys were fabricated from just one EAB female, this bioreplication process is industrially scalable. Preliminary results from field trapping tests are indicative of success. For the second setting, a method of developing latent fingermarks with thermally evaporated conformal thin films was developed. Fingermarks have long been used to identify the individual who left them behind when he/she touched an object with the friction ridges of his/her hands. In many cases the fingermark which is left behind consists of sebaceous secretions which are not clearly visible under normal conditions. In order to make the fingermarks visible and identifiable, they are traditionally developed by either a physical technique which relies on a material preferentially sticking to sebaceous materials or a chemical technique which relies on a reaction with material within the fingermark. In this application, a columnar thin film (CTF) is deposited conformally over both the fingermark and the underlying substrate. The CTF is produced by the conformal-evaporated-film-by-rotation method, wherein the substrate with the fingermark upon it is held obliquely with respect to a vapor flux in a vacuum chamber. The substrate is then rapidly rotated about its surface normal resulting in a conformal film with columnar morphology. This technique was optimized for several substrates and compared with traditional development techniques. CTF development was found to be superior to traditional techniques in several cases. Use of the CTF was investigated for several types of particularly difficult to develop fingermarks such as those which consist of both bloody and nonbloody areas, and fingermarks on fired cartridge casings. The CTF technique's sensitivity was also compared to that of traditional development techniques. Finally, the CTF technique was compared with another thin film deposition technique called vacuum-metal deposition. (Abstract shortened by UMI.).

Fingermark visualisation on uncirculated £5 (Bank of England) polymer notes: Initial process comparison studies.

PubMed

Downham, Rory P; Brewer, Eleigh R; King, Roberto S P; Luscombe, Aoife M; Sears, Vaughn G

2017-06-01

Experiments were conducted to investigate the effectiveness of a range of fingermark visualisation processes on brand new, uncirculated, £5 polymer banknotes (and their test note predecessors), as produced by the Bank of England (BoE). In the main study of this paper, a total of 14 individual processes were investigated on BoE £5 polymer banknotes, which included both 'Category A' processes (as recommended in the Home Office Fingermark Visualisation Manual) as well as recently developed processes, including fpNatural ® 2 powder (cuprorivaite) from Foster+Freeman and a vacuum metal deposition sequence that evaporates silver followed by zinc. Results from this preliminary investigation indicate that fpNatural ® 2, multimetal deposition, Wet Powder ™ Black, iron oxide powder suspension and black magnetic powder are the most effective processes on these uncirculated £5 BoE polymer banknotes, when viewed under "primary viewing" conditions (white light or fluorescence). Additional fingermarks were visualised on the polymer banknotes following the subsequent use of reflected infrared imaging and lifting techniques, and with the benefit of these techniques taken into consideration, the aforementioned processes remained amongst the most effective overall. This work provides initial insight into fingermark visualisation strategies for BoE £5 polymer banknotes, and the need for further studies in order to generate mature operational guidance is emphasised. Copyright © 2017 Elsevier B.V. All rights reserved.

Beyond the ridge pattern: multi-informative analysis of latent fingermarks by MALDI mass spectrometry.

PubMed

Francese, S; Bradshaw, R; Ferguson, L S; Wolstenholme, R; Clench, M R; Bleay, S

2013-08-07

After over a century, fingerprints are still one of the most powerful means of biometric identification. The conventional forensic workflow for suspect identification consists of (i) recovering latent marks from crime scenes using the appropriate enhancement technique and (ii) obtaining an image of the mark to compare either against known suspect prints and/or to search in a Fingerprint Database. The suspect is identified through matching the ridge pattern and local characteristics of the ridge pattern (minutiae). However successful, there are a number of scenarios in which this process may fail; they include the recovery of partial, distorted or smudged marks, poor quality of the image resulting from inadequacy of the enhancement technique applied, extensive scarring/abrasion of the fingertips or absence of suspect's fingerprint records in the database. In all of these instances it would be very desirable to have a technology able to provide additional information from a fingermark exploiting its endogenous and exogenous chemical content. This opportunity could potentially provide new investigative leads, especially when the fingermark comparison and match process fails. We have demonstrated that Matrix Assisted Laser Desorption Ionisation Mass Spectrometry and Mass Spectrometry Imaging (MALDI MSI) can provide multiple images of the same fingermark in one analysis simultaneous with additional intelligence. Here, a review on the pioneering use and development of MALDI MSI for the analysis of latent fingermarks is presented along with the latest achievements on the forensic intelligence retrievable.

Typing DNA profiles from previously enhanced fingerprints using direct PCR.

PubMed

Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Linacre, Adrian

2017-07-01

Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many samples, be the key to success if there is limited sample DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite; silver aluminium; HiFi Volcano silk black; or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold ® DNA polymerase to boost the PCR. Ninety eight out of 160 samples (61%) were considered 'up-loadable' to the Australian National Criminal Investigation DNA Database (NCIDD). The method described required a minimum of working steps, equipment and reagents, and was completed within 4h. Direct PCR allows the generation of DNA profiles from enhanced prints without the need to increase PCR cycle numbers beyond manufacturer's recommendations. Particular emphasis was placed on preventing contamination by applying strict protocols and avoiding the use of previously used fingerprint brushes. Based on this extensive survey, the data provided indicate minimal effects of any of these four powders on the chance of obtaining DNA profiles from enhanced fingermarks. Copyright © 2017 Elsevier B.V. All rights reserved.

Using spectral information in forensic imaging.

PubMed

Miskelly, Gordon M; Wagner, John H

2005-12-20

Improved detection of forensic evidence by combining narrow band photographic images taken at a range of wavelengths is dependent on the substance of interest having a significantly different spectrum from the underlying substrate. While some natural substances such as blood have distinctive spectral features which are readily distinguished from common colorants, this is not true for visualization agents commonly used in forensic science. We now show that it is possible to select reagents with narrow spectral features that lead to increased visibility using digital cameras and computer image enhancement programs even if their coloration is much less intense to the unaided eye than traditional reagents. The concept is illustrated by visualising latent fingermarks on paper with the zinc complex of Ruhemann's Purple, cyanoacrylate-fumed fingerprints with Eu(tta)(3)(phen), and soil prints with 2,6-bis(benzimidazol-2-yl)-4-[4'-(dimethylamino)phenyl]pyridine [BBIDMAPP]. In each case background correction is performed at one or two wavelengths bracketing the narrow absorption or emission band of these compounds. However, compounds with sharp spectral features would also lead to improved detection using more advanced algorithms such as principal component analysis.

Latent fingermark visualisation using reduced-pressure sublimation of copper phthalocyanine.

PubMed

Williams, Geraint; ap Llwyd Dafydd, Hefin; Watts, Alun; McMurray, Neil

2011-01-30

The sublimation of copper phthalocyanine (CuPc) at a temperature of 400°C under conditions of reduced pressure is shown to be an effective method of developing latent fingermarks on certain types of surface. Preliminary experiments on a limited selection of surfaces including paper, plastic and ceramic tiles were carried out using a simple apparatus consisting of a vacuum desiccator and a resistive heater. CuPc from the gas phase condenses preferentially on fingermark deposits, revealing deep blue patterns with excellent ridge detail clarity on light coloured surfaces. The technique is shown to be most effective on porous surfaces such as paper, but relatively ineffective on non-porous ceramic and plastic surfaces. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Determination of efficacy of fingermark enhancement reagents; the use of propyl chloroformate for the derivatization of fingerprint amino acids extracted from paper.

PubMed

Mink, Tineke; Voorhaar, Annelies; Stoel, Reinoud; de Puit, Marcel

2013-09-01

The analysis of the constituents of fingerprints has been described numerous times, mainly with the purpose of determining the aging effect on fingerprints or showing the differences between donors or groups of donors. In this paper we describe the use of derivatized amino acids to determine the efficacy of the visualization reagents 1,8-diazafluoren-9-one (DFO) and ninhydrin. At present certain conditions are used for the application of these reagents, as determined by trial-and-error investigations, to the effect on fingerprints. The recovery of amino acids from a porous surface can be used as a measure for the efficacy of a visualization agent. In this paper we describe a method for the determination of the amount of amino acid left after reaction with well known fingerprint visualization reagents. This will allow a more scientific approach to method development for fingermark enhancement techniques. Furthermore, investigations on the influence of the concentration of fingermark amino acids, the order of application of and exposure time to reagents and the influence of age of the amino acids were carried out. These studies have resulted in a broader understanding of the mechanism involved in visualization of fingermarks using DFO and ninhydrin. Copyright © 2013 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

A novel monodisperse SiO2@C-dot for the rapid and facile identification of latent fingermarks using self-quenching resistant solid-state fluorescence.

PubMed

Peng, Di; Liu, Xiang; Huang, Mengjun; Wang, Dan; Liu, Renlong

2018-04-24

Solid powder fluorescence shows great potential for application in medicine, biology, and engineering, especially in the identification of latent fingermarks in forensic science. However, conventional developing methods suffer from some drawbacks, such as low contrast, low sensitivity, low selectivity, and high toxicity. To conquer these challenges, novel SiO2@C-dot microspheres were prepared via a facile one-pot hydrothermal method by using citric acid as a carbon source and aminosilane as a nitrogen source. Interestingly, the results showed that the resultant powders possess good monodispersity, high fluorescence emission, and resistance to self-quenching. Additionally, the mechanism for the solid-state fluorescence of SiO2@C-dot compounds was also investigated. More importantly, the fingermarks on various surfaces, including transparent glasses, ceramic tiles, transparent plastics, aluminum alloys, plastic cards, painted woods, artificial leathers, and Chinese paper money, developed by the powders have indicated well-defined papillary ridges under a 365 nm UV lamp. The novel strategy of using monodisperse SiO2@C-dot microspheres as a fluorescent label for developing latent fingermarks showed greater advantages compared to conventional methods, which was also demonstrated using the automatic fingerprint identification system. It is simple, rapid, low-cost, nontoxic, and effective, and is expected to be a promising alternative for the development of latent fingerprints in forensic science.

A comparison of the use of vacuum metal deposition versus cyanoacrylate fuming for visualisation of fingermarks and grab impressions on fabrics.

PubMed

Fraser, Joanna; Deacon, Paul; Bleay, Stephen; Bremner, David H

2014-03-01

Both vacuum metal deposition (VMD) and cyanoacrylate fuming (CAF) are techniques used to visualise latent fingermarks on smooth non-porous surfaces such as plastic and glass. VMD was initially investigated in the 1970s as to its effectiveness for visualising prints on fabrics, but was abandoned when radioactive sulphur dioxide was found to be more effective. However, interest in VMD was resurrected in the 1990s when CAF was also used routinely. We now report on studies to determine whether VMD or CAF is the more effective technique for the detection of marks on fabrics. Four different fabrics, nylon, polyester, polycotton and cotton, were utilised during this study, along with 15 donors who ranged in their age and ability to leave fingermarks, from good to medium to poor, thus reflecting the general population. Once samples were collected they were kept for a determined time (1, 2, 3, 4, 5, 6, 7, 14, 21 or 28 days) and then treated using either the gold and zinc metal VMD process or standard cyanoacrylate fuming. The smoother fabrics, such as nylon, consistently produced greater ridge detail whereas duller fabrics, like cotton tended only to show empty prints and impressions of where the fabric had been touched, rather than any ridge details. The majority of fabrics did however allow the development of touch marks that could be targeted for DNA taping which potentially could lead to a DNA profile. Of the two techniques VMD was around 5 times more effective than CAF, producing a greater amount of ridge detail, palmar flexion creases and target areas on more samples and fabrics. Copyright © 2013 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

DNA Profiles from Fingerprint Lifts-Enhancing the Evidential Value of Fingermarks Through Successful DNA Typing.

PubMed

Subhani, Zuhaib; Daniel, Barbara; Frascione, Nunzianda

2018-05-25

This study evaluated the compatibility of the most common enhancement methods and lifting techniques with DNA profiling. Emphasis is placed on modern lifting techniques (i.e., gelatin lifters and Isomark™) and historical fingerprint lifts for which limited research has been previously conducted. A total of 180 fingerprints were deposited on a glass surface, enhanced, lifted, and processed for DNA typing. DNA could be extracted and profiled for all the powders and lifts tested and from both groomed fingerprints and natural prints with no significant difference in the percentage of profile recovered. DNA profiles could also be obtained from historical fingerprint lifts (79.2% of 72 lifts) with one or more alleles detected. These results demonstrate the compatibility between different powder/lift combinations and DNA profiling therefore augmenting the evidential value of fingerprints in forensic casework. © 2018 American Academy of Forensic Sciences.

Forensic applications of desorption electrospray ionisation mass spectrometry (DESI-MS).

PubMed

Morelato, Marie; Beavis, Alison; Kirkbride, Paul; Roux, Claude

2013-03-10

Desorption electrospray ionisation mass spectrometry (DESI-MS) is an emerging analytical technique that enables in situ mass spectrometric analysis of specimens under ambient conditions. It has been successfully applied to a large range of forensically relevant materials. This review assesses and highlights forensic applications of DESI-MS including the analysis and detection of illicit drugs, explosives, chemical warfare agents, inks and documents, fingermarks, gunshot residues and drugs of abuse in urine and plasma specimens. The minimal specimen preparation required for analysis and the sensitivity of detection achieved offer great advantages, especially in the field of forensic science. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Fingerprint deposition on nitrocellulose and polyvinylidene difluoride membranes using alkaline phosphatase.

PubMed

Kurien, Biji T; Danda, Debashish; Scofield, R Hal

2015-01-01

Dactyloscopy or fingerprint identification is a vital part of forensic evidence. Identification with fingerprints has been known since the finding of finger impressions on the clay surface of Babylonian legal contracts almost 4,000 years ago. The skin on the fingers and palms appears as grooves and ridges when observed under a microscope. A unique fingerprint is produced by the patterns of these friction skin ridges. Visible fingerprints can be deposited on solid surfaces. Colored inks have been used to deposit fingermarks on documents. Herein, we show that alkaline phosphatase can be used to transfer prints from fingers or palm to nitrocellulose or polyvinylidene difluoride membranes. The prints can be detected by using the nitro blue tetrazolium/5-bromo-4-chloro-3-indolyl phosphate method of detection.

A comparison between atmospheric/humidity and vacuum cyanoacrylate fuming of latent fingermarks.

PubMed

Farrugia, Kevin J; Fraser, Joanna; Friel, Lauren; Adams, Duncan; Attard-Montalto, Nicola; Deacon, Paul

2015-12-01

A number of pseudo-operational trials were set up to compare the atmospheric/humidity and vacuum cyanoacrylate fuming processes on plastic carrier bags. The fuming processes were compared using two-step cyanoacrylate fuming with basic yellow 40 (BY40) staining and a one-step fluorescent cyanoacrylate fuming, Lumicyano 4%. Preliminary work using planted fingermarks and split depletions were performed to identify the optimum vacuum fuming conditions. The first pseudo-operational trial compared the different fuming conditions (atmospheric/humidity vs. vacuum) for the two-step process where an additional 50% more marks were detected with the atmospheric/humidity process. None of the marks by the vacuum process could be observed visually; however, a significant number of marks were detected by fluorescence after BY40 staining. The second trial repeated the same work in trial 1 using the one-step cyanoacrylate process, Lumicyano at a concentration of 4%. Trial 2 provided comparable results to trial 1 and all the items were then re-treated with Lumicyano 4% at atmospheric/humidity conditions before dyeing with BY40 to provide the sequences of process A (Lumicyano 4% atmospheric-Lumicyano 4% atmospheric-BY40) and process B (Lumicyano 4% vacuum-Lumicyano 4% atmospheric-BY40). The number of marks (visual and fluorescent) was counted after each treatment with a substantial increase in the number of detected marks in the second and third treatments of the process. The increased detection rate after the double Lumicyano process was unexpected and may have important implications. Trial 3 was performed to investigate whether the amount of cyanoacrylate and/or fuming time had an impact on the results observed in trial 2 whereas trial 4 assessed if the double process using conventional cyanoacrylate, rather than Lumicyano 4%, provided an increased detection rate. Trials 3 and 4 confirmed that doubling the amount of Lumicyano 4% cyanoacrylate and fuming time produced a lower detection rate than the double process with Lumicyano 4%. Furthermore, the double process with conventional cyanoacrylate did not provide any benefit. Scanning electron microscopy was also performed to investigate the morphology of the cyanoacrylate polymer under different conditions. The atmospheric/humidity process appears to be superior to the vacuum process for both the two-step and one-step cyanoacrylate fuming, although the two-step process performed better in comparison to the one-step process under vacuum conditions. Nonetheless, the use of vacuum cyanoacrylate fuming may have certain operational advantages and its use does not adversely affect subsequent cyanoacrylate fuming with atmospheric/humidity conditions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

DNA recovery from latent fingermarks treated with an infrared fluorescent fingerprint powder.

PubMed

Al Oleiwi, Abdulrahman; Hussain, Imtiaz; McWhorter, Allyce; Sutton, Raul; King, Roberto S P

2017-08-01

The effect of the infrared fluorescent fingermark visualisation powder, fpNatural 1™, on the recovery of both the quantity and quality of touch DNA from fingerprints deposited on glass slides, was investigated using qPCR and STR typing. Four donors each deposited replicate marks, which were either left untreated (n=5) or treated by dusting with fpNatural 1™ (n=5). Each sample was swabbed using the double swab technique, before being extracted using the EZNA Forensic DNA kit and then DNA quantitated before being subjected to DNA profile analysis. Results showed that there was no significant effect of fpNatural 1™ on either the quantity or quality of recovered DNA. This suggests that fpNatural 1™ may prove a good choice of powder for regular use at crime scenes or in the laboratory. The fpNatural 1™ properties of low density, water immiscibility and low DNA affinity may account for these positive outcomes. Copyright © 2017 Elsevier B.V. All rights reserved.

Straightforward fabrication of black nano silica dusting powder for latent fingerprint imaging

NASA Astrophysics Data System (ADS)

Komalasari, Isna; Krismastuti, Fransiska Sri Herwahyu; Elishian, Christine; Handayani, Eka Mardika; Nugraha, Willy Cahya; Ketrin, Rosi

2017-11-01

Imaging of latent fingerprint pattern (aka fingermark) is one of the most important and accurate detection methods in forensic investigation because of the characteristic of individual fingerprint. This detection technique relies on the mechanical adherence of fingerprint powder to the moisture and oily component of the skin left on the surface. The particle size of fingerprint powder is one of the critical parameter to obtain excellent fingerprint image. This study develops a simple, cheap and straightforward method to fabricate Nano size black dusting fingerprint powder based on Nano silica and applies the powder to visualize latent fingerprint. The nanostructured silica was prepared from tetraethoxysilane (TEOS) and then modified with Nano carbon, methylene blue and sodium acetate to color the powder. Finally, as a proof-of-principle, the ability of this black Nano silica dusting powder to image latent fingerprint is successfully demonstrated and the results show that this fingerprint powder provides clearer fingerprint pattern compared to the commercial one highlighting the potential application of the nanostructured silica in forensic science.

A validation study of the 1,2-indandione reagent for operational use in the UK: Part 2 - Optimization of processing conditions.

PubMed

Nicolasora, Niko; Downham, Rory; Dyer, Rachel-May; Hussey, Laura; Luscombe, Aoife; Sears, Vaughn

2018-05-02

This paper contains details of work carried out to identify the most effective processing conditions for the optimized 1,2-indandione/zn formulation developed for use under UK conditions. Using direct measurements of fluorescence taken from test spots of amino acids and eccrine sweat during oven processing, complemented with experiments on real fingermarks, it was established that processing temperatures above 120°C in the oven were detrimental to the fluorescence of the developed mark. Alternative methods of development to oven processing were found to be effective, but less controllable. High levels of humidification were also found to be detrimental to the fluorescence of 1,2-indandione developed marks, and oven processing at 100°C and 0% relative humidity is therefore recommended for further studies. It has also been shown that 1,2-indandione can develop fingermarks at temperatures as low as 20°C, making it a candidate for use at crime scenes. Copyright © 2018. Published by Elsevier B.V.

Performance of 1,2-indanedione and the need for sequential treatment of fingerprints.

PubMed

Mangle, Milery Figuera; Xu, Xioama; de Puit, M

2015-09-01

The use of 1,2-indanedione-ZnCl2 (IND-Zn) for the visualisation of fingermarks on porous materials has been widely accepted. The use of the reagent in comparison with others has been well described. To what extent IND or IND-Zn reacts with amino acids, in comparison to ninhydrin, has not been described to date. In this technical note we describe the analysis of amino acids with LCMS with the purpose of understanding the reactivity of ninhydrin, IND-Zn and the sequence thereof. The consumption of amino acids by these visualisation reagents is a feature we propose to use for calculations on the reactivity of these reagents. By using recently developed methods for the quantification of amino acids, we determined the consumption of these entities by visualisation reagents. We show that the differences in reactivity between IND and ninhydrin are not as big as the differences between 1,8-diazafluoren-9-one (DFO) and ninhydrin. We also show that it is of great importance to use IND-Zn and ninhydrin in sequence, in order to fully consume the amino acids present in fingermarks. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

DNA decontamination of fingerprint brushes.

PubMed

Szkuta, Bianca; Oorschot, Roland A H van; Ballantyne, Kaye N

2017-08-01

Genetic profiling of DNA collected from fingerprints that have been exposed to various enhancement techniques is routine in many forensic laboratories. As a result of direct contact with fingermark residues during treatment, there is concern around the DNA contamination risk of dusting fingermarks with fingerprint brushes. Previous studies have demonstrated the potential for cross-contamination between evidentiary items through various mechanisms, highlighting the risk of using the same fingerprint brush to powder multiple surfaces within and between crime-scenes. Experiments were performed to assess the contamination risk of reused fingerprint brushes through the transfer of dried saliva and skin deposits from and to glass surfaces with new unused squirrel hair and fiberglass brushes. Additional new unused brushes and brushes previously used in casework were also tested for their ability to contaminate samples. In addition, the ability to eradicate DNA from used squirrel hair and fiberglass fingerprint brushes was assessed using a 1% sodium hypochlorite solution and a 5% solution of a commercially available alternative, Virkon. DNA profiling results from surfaces contacted by treated and untreated brushes were compared to determine the effectiveness of the devised cleaning protocol. Brush durability was also assessed over multiple wash/rinse/dry cycles with both agents. Varying amounts of DNA-containing material were collected and transferred by squirrel hair and fiberglass brushes, with detectability on the secondary surface dependent on the biological nature of the material being transferred. The impact of DNA contamination from dirty fingerprint brushes was most apparent in simulations involving the transfer of dried saliva and brushes previously used in casework, while minimal transfer of touch DNA was observed. Alarmingly, large quantities of DNA were found to reside on new unused squirrel hair brushes, while no DNA was detected on new unused fiberglass brushes or brushes sold as DNA-free. Squirrel hair brushes were easily and effectively cleaned with both hypochlorite and Virkon, with no evidence of DNA transfer between exhibits by treated brushes. Brushes were still deemed useable after multiple cleaning cycles with either agent. In contrast, fiberglass bristles became tangled and matted when wet and could not be cleaned effectively using either method. It is recommended they are disposed of following use. Each laboratory should consider their current circumstances before adapting a cleaning method. The implementation of a program to monitor the effectiveness of the cleaning regime is also advised. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of one-step luminescent cyanoacrylate fuming.

PubMed

Khuu, Alicia; Chadwick, Scott; Spindler, Xanthe; Lam, Rolanda; Moret, Sébastien; Roux, Claude

2016-06-01

One-step luminescent cyanoacrylates have recently been introduced as an alternative to the conventional cyanoacrylate fuming methods. These new techniques do not require the application of a luminescent post-treatment in order to enhance cyanoacrylate-developed fingermarks. In this study, three one-step polymer cyanoacrylates: CN Yellow Crystals (Aneval Inc.), PolyCyano UV (Foster+Freeman Ltd.) and PECA Multiband (BVDA), and one monomer cyanoacrylate: Lumikit™ (Crime Scene Technology), were evaluated against a conventional two-step cyanoacrylate fuming method (Cyanobloom (Foster+Freeman Ltd.) with rhodamine 6G stain). The manufacturers' recommended conditions or conditions compatible with the MVC™ 1000/D (Foster+Freeman Ltd.) were assessed with fingermarks aged for up to 8 weeks on non-porous and semi-porous substrates. Under white light, Cyanobloom generally gave better development than the one-step treatments across the substrates. Similarly when viewed under the respective luminescent conditions, Cyanobloom with rhodamine 6G stain resulted in improved contrast against the one-step treatments except on polystyrene, where PolyCyano UV and PECA Multiband gave better visualisation. Rhodamine 6G post-treatment of one-step samples did not significantly enhance the contrast of any of the one-step treatments against Cyanobloom/rhodamine 6G-treated samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

Gupta, Bipin Kumar, E-mail: bipinbhu@yahoo.com; Kumar, Arun; Amity Institute of Applied Science, Amity University, Noida, Uttar Pradesh 201303

Herein, a novel green emitting long-persistent Sr{sub 3}SiAl{sub 4}O{sub 11}:Eu{sup 2+}/Dy{sup 3+} phosphor was synthesized in a single phase form using facile solid state reaction method under the reducing atmosphere of 10% H{sub 2} and 90% N{sub 2}. The resulting phosphor exhibits hyper-sensitive strong broad green emission, peaking at 510 nm upon 340 nm excitation wavelength, which is attributed to the 4f{sup 6}5d{sup 1}-4f{sup 7} transitions of emission center of europium (Eu{sup 2+}) ions. Moreover, the incorporation of dysprosium (Dy{sup 3+}) ions, which act as effective hole trap centers with appropriate depth, largely enhances the photoluminescence characteristics and greatly improves the persistentmore » intense luminescence behavior of Sr{sub 3}SiAl{sub 4}O{sub 11}:Eu{sup 2+}/Dy{sup 3+} phosphor under ultraviolet (UV) excitation. In addition, with the optimum doping concentration and sufficient UV excitation time period, the as-synthesized phosphor can be persisted afterglow for time duration ∼4 h with maximum luminescence intensity. Thus, these results suggest that this phosphor could be expected as an ultimate choice for next generation advanced luminescent materials in security applications such as latent finger-marks detection, photo-masking induced phosphorescent images, and security code detection.« less

Likelihood ratio data to report the validation of a forensic fingerprint evaluation method.

PubMed

Ramos, Daniel; Haraksim, Rudolf; Meuwly, Didier

2017-02-01

Data to which the authors refer to throughout this article are likelihood ratios (LR) computed from the comparison of 5-12 minutiae fingermarks with fingerprints. These LRs data are used for the validation of a likelihood ratio (LR) method in forensic evidence evaluation. These data present a necessary asset for conducting validation experiments when validating LR methods used in forensic evidence evaluation and set up validation reports. These data can be also used as a baseline for comparing the fingermark evidence in the same minutiae configuration as presented in (D. Meuwly, D. Ramos, R. Haraksim,) [1], although the reader should keep in mind that different feature extraction algorithms and different AFIS systems used may produce different LRs values. Moreover, these data may serve as a reproducibility exercise, in order to train the generation of validation reports of forensic methods, according to [1]. Alongside the data, a justification and motivation for the use of methods is given. These methods calculate LRs from the fingerprint/mark data and are subject to a validation procedure. The choice of using real forensic fingerprint in the validation and simulated data in the development is described and justified. Validation criteria are set for the purpose of validation of the LR methods, which are used to calculate the LR values from the data and the validation report. For privacy and data protection reasons, the original fingerprint/mark images cannot be shared. But these images do not constitute the core data for the validation, contrarily to the LRs that are shared.

Eu2+,Dy3+ codoped SrAl2O4 nanocrystalline phosphor for latent fingerprint detection in forensic applications

NASA Astrophysics Data System (ADS)

Sharma, Vishal; Das, Amrita; Kumar, Vinay

2016-01-01

In this work, europium and dysprosium doped strontium aluminate (SrAl2O4:Eu2+,Dy3+) nanophosphor is synthesized and its novel application for the detection of latent fingerprints on various contact surfaces is reported. The SrAl2O4:Eu2+,Dy3+ is synthesized using a combustion method and shows long-lasting afterglow luminescence. The powder particles are characterized using field emission scanning electron microscopy (FE-SEM), SEM-energy dispersive x-ray analysis, x-ray diffraction and photoluminescence spectrophotometry. The FE-SEM image analysis reveals that the nanoparticles are mostly 8-15 nm in size with an irregular spherical shape. This nano-structured powder was applied to fresh and aged fingerprints deposited on porous, semi-porous and non-porous contact surfaces, such as ordinary colored paper, glossy paper, glass, aluminum foil, a yellow foil chocolate wrapper, a soft drink can, a PET bottle, a compact disc and a computer mouse. The results are reproducible and show great sensitivity and high contrast in the developed fingermark regions on these surfaces. These nanophosphor particles also show a strong and long-lasting afterglow property, making them a suitable candidate for use as a fingerprint developing agent on luminescent and highly patterned surfaces. These kinds of powders have shown that they can remove the interference from background luminescence, which is not possible using ordinary luminescent fingerprinting powders.

Spectroscopic detection of exogenous materials in latent fingerprints treated with powders and lifted off with adhesive tapes.

PubMed

Banas, A; Banas, K; Breese, M B H; Loke, J; Lim, S K

2014-07-01

Fingerprint evidence offers great value to criminal investigations since it is an internationally recognized and established means of human identification. With recent advances in modern technology, scientists have started analyzing not only the ridge patterns of fingerprints but also substances which can be found within them. The aim of this work was to determine whether Fourier transform infrared (FTIR) spectromicroscopy could be used to detect contamination in a fingerprint which was dusted with powder (a technique already recognized as an effective and reliable method for developing latent fingerprints) and subsequently lifted off with adhesive tape. Explosive materials (pentaerythritol tetranitrate, C-4, TNT) and noncontrolled substances (sugar, aspirin) were used to prepare contaminated fingerprints on various substrates. Freshly deposited fingermarks with powders which were lifted off with adhesive tapes (provided by Singapore Police Force) were analyzed using a Bruker Hyperion 2000 microscope at the ISMI beamline (Singapore Synchrotron Light Source) with an attenuated total reflection objective. FTIR spectroscopy is a nondestructive technique which requires almost no sample preparation. Further, the fingerprint under analysis remains in pristine condition, allowing subsequent analysis if necessary. All analyzed substances were successfully distinguished using their FTIR spectra in powdered and lifted fingerprints. This method has the potential to significantly impact forensic science by greatly enhancing the information that can be obtained from the study of fingerprints.

The use of fingerprints available on the web in false identity documents: Analysis from a forensic intelligence perspective.

PubMed

Girelli, Carlos Magno Alves

2016-05-01

Fingerprints present in false identity documents were found on the web. In some cases, laterally reversed (mirrored) images of a same fingerprint were observed in different documents. In the present work, 100 fingerprints images downloaded from the web, as well as their reversals obtained by image editing, were compared between themselves and against the database of the Brazilian Federal Police AFIS, in order to better understand trends about this kind of forgery in Brazil. Some image editing effects were observed in the analyzed fingerprints: addition of artifacts (such as watermarks), image rotation, image stylization, lateral reversal and tonal reversal. Discussion about lateral reversals' detection is presented in this article, as well as suggestion to reduce errors due to missed HIT decisions between reversed fingerprints. The present work aims to highlight the importance of the fingerprints' analysis when performing document examination, especially when only copies of documents are available, something very common in Brazil. Besides the intrinsic features of the fingermarks considered in three levels of details by ACE-V methodology, some visual features of the fingerprints images can be helpful to identify sources of forgeries and modus operandi, such as: limits and image contours, fails in the friction ridges caused by excess or lack of inking and presence of watermarks and artifacts arising from the background. Based on the agreement of such features in fingerprints present in different identity documents and also on the analysis of the time and location where the documents were seized, it is possible to highlight potential links between apparently unconnected crimes. Therefore, fingerprints have potential to reduce linkage blindness and the present work suggests the analysis of fingerprints when profiling false identity documents, as well as the inclusion of fingerprints features in the profile of the documents. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Organic solvent and temperature-enhanced ion chromatography-high resolution mass spectrometry for the determination of low molecular weight organic and inorganic anions.

PubMed

Gilchrist, Elizabeth S; Nesterenko, Pavel N; Smith, Norman W; Barron, Leon P

2015-03-20

There has recently been increased interest in coupling ion chromatography (IC) to high resolution mass spectrometry (HRMS) to enable highly sensitive and selective analysis. Herein, the first comprehensive study focusing on the direct coupling of suppressed IC to HRMS without the need for post-suppressor organic solvent modification is presented. Chromatographic selectivity and added HRMS sensitivity offered by organic solvent-modified IC eluents on a modern hyper-crosslinked polymeric anion-exchange resin (IonPac AS18) are shown using isocratic eluents containing 5-50 mM hydroxide with 0-80% methanol or acetonitrile for a range of low molecular weight anions (<165 Da). Comprehensive experiments on IC thermodynamics over a temperature range between 20-45 °C with the eluent containing up to 60% of acetonitrile or methanol revealed markedly different retention behaviour and selectivity for the selected analytes on the same polymer based ion-exchange resin. Optimised sensitivity with HRMS was achieved with as low as 30-40% organic eluent content. Analytical performance characteristics are presented and compared with other IC-MS based works. This study also presents the first application of IC-HRMS to forensic detection of trace low-order anionic explosive residues in latent human fingermarks. Copyright © 2015 Elsevier B.V. All rights reserved.

Laser desorption/ionization mass spectrometry of lipids using etched silver substrates.

PubMed

Schnapp, Andreas; Niehoff, Ann-Christin; Koch, Annika; Dreisewerd, Klaus

2016-07-15

Silver-assisted laser desorption/ionization mass spectrometry can be used for the analysis of small molecules. For example, adduct formation with silver cations enables the molecular analysis of long-chain hydrocarbons, which are difficult to ionize via conventional matrix-assisted laser desorption ionization (MALDI). Here we used highly porous silver foils, produced by etching with nitric acid, as sample substrates for LDI mass spectrometry. As model system for the analysis of complex lipid mixtures, cuticular extracts of fruit flies (Drosophila melanogaster) and worker bees (Apis mellifera) were investigated. The mass spectra obtained by spotting extract onto the etched silver substrates demonstrate the sensitive detection of numerous lipid classes such as long-chain saturated and unsaturated hydrocarbons, fatty acyl alcohols, wax esters, and triacylglycerols. MS imaging of cuticular surfaces with a lateral resolution of a few tens of micrometers became possible after blotting, i.e., after transferring lipids by physical contact with the substrate. The examples of pheromone-producing male hindwings of the squinting bush brown butterfly (Bicyclus anynana) and a fingermark are shown. Because the substrates are also easy to produce, they provide a viable alternative to colloidal silver nanoparticles and other so far described silver substrates. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysing and exemplifying forensic conclusion criteria in terms of Bayesian decision theory.

PubMed

Biedermann, A; Bozza, S; Taroni, F

2018-03-01

There is ongoing discussion in forensic science and the law about the nature of the conclusions reached based on scientific evidence, and on how such conclusions - and conclusion criteria - may be justified by rational argument. Examples, among others, are encountered in fields such as fingermarks (e.g., 'this fingermark comes from Mr. A's left thumb'), handwriting examinations (e.g., 'the questioned signature is that of Mr. A'), kinship analyses (e.g., 'Mr. A is the father of child C') or anthropology (e.g., 'these are human remains'). Considerable developments using formal methods of reasoning based on, for example (Bayesian) decision theory, are available in literature, but currently such reference principles are not explicitly used in operational forensic reporting and ensuing decision-making. Moreover, applied examples, illustrating the principles, are scarce. A potential consequence of this in practical proceedings, and hence a cause of concern, is that underlying ingredients of decision criteria (such as losses quantifying the undesirability of adverse decision consequences), are not properly dealt with. There is merit, thus, in pursuing the study and discussion of practical examples, demonstrating that formal decision-theoretic principles are not merely conceptual considerations. Actually, these principles can be shown to underpin practical decision-making procedures and existing legal decision criteria, though often not explicitly apparent as such. In this paper, we will present such examples and discuss their properties from a Bayesian decision-theoretic perspective. We will argue that these are essential concepts for an informed discourse on decision-making across forensic disciplines and the development of a coherent view on this topic. We will also emphasize that these principles are of normative nature in the sense that they provide standards against which actual judgment and decision-making may be compared. Most importantly, these standards are justified independently of peoples' observable decision behaviour, and of whether or not one endorses these formal methods of reasoning. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Electrochromic enhancement of latent fingerprints by poly(3,4-ethylenedioxythiophene).

PubMed

Brown, Rachel M; Hillman, A Robert

2012-06-28

Spatially selective electrodeposition of poly-3,4-ethylenedioxythiophene (PEDOT) thin films on metallic surfaces is shown to be an effective means of visualizing latent fingerprints. The technique exploits the fingerprint deposit as an insulating mask, such that electrochemical processes (here, polymer deposition) may only take place on deposit-free areas of the surface between the ridges of the fingerprint deposit; the end result is a negative image of the fingermark. Use of a surfactant (sodium dodecylsulphate, SDS) to solubilise the EDOT monomer allows the use of an aqueous electrolyte. Electrochemical (coulometric) data provide a total assay of deposited material, yielding spatially averaged film thicknesses, which are commensurate with substantive filling of the trenches between fingerprint deposit ridges, but not overfilling to the extent that the ridge detail is covered. This is confirmed by optical microscopy and AFM images, which show continuous polymer deposition within the trenches and good definition at the ridge edges. Stainless steel substrates treated in this manner and transferred to background electrolyte (aqueous sulphuric acid) showed enhanced fingerprints when the contrast between the polymer background and fingerprint deposit was optimised using the electrochromic properties of the PEDOT films. The facility of the method to reveal fingerprints of various ages and subjected to plausible environmental histories was demonstrated. Comparison of this enhancement methodology with commonly used fingerprint enhancement methods (dusting with powder, application of wet powder suspensions and cyanoacrylate fuming) showed promising performance in selected scenarios of practical interest.

Infrared spectroscopy and spectroscopic imaging in forensic science.

PubMed

Ewing, Andrew V; Kazarian, Sergei G

2017-01-16

Infrared spectroscopy and spectroscopic imaging, are robust, label free and inherently non-destructive methods with a high chemical specificity and sensitivity that are frequently employed in forensic science research and practices. This review aims to discuss the applications and recent developments of these methodologies in this field. Furthermore, the use of recently emerged Fourier transform infrared (FT-IR) spectroscopic imaging in transmission, external reflection and Attenuated Total Reflection (ATR) modes are summarised with relevance and potential for forensic science applications. This spectroscopic imaging approach provides the opportunity to obtain the chemical composition of fingermarks and information about possible contaminants deposited at a crime scene. Research that demonstrates the great potential of these techniques for analysis of fingerprint residues, explosive materials and counterfeit drugs will be reviewed. The implications of this research for the examination of different materials are considered, along with an outlook of possible future research avenues for the application of vibrational spectroscopic methods to the analysis of forensic samples.

Columnar-thin-film acquisition of fingermark topology

NASA Astrophysics Data System (ADS)

Shaler, Robert C.; Lakhtakia, Akhlesh; Rogers, Jessica W.; Pulsifer, Drew P.; Martín-Palma, Raúl J.

2010-08-01

Fingerprint visualization obtained from physical evidence taken from crime scenes for subsequent comparison typically requires the use of physical and chemical techniques. One physical technique to visualize or develop sebaceous fingerprints on various surfaces employs the deposition of metals such as gold and zinc thereon. We have developed a different vacuum technology: the conformal-evaporated-film-by-rotation technique to deposit dense columnar thin films (CTFs) on latent fingerprints on different types of surfaces. Sample fingerprints, acting as nonplanar substrates, deposited on different surfaces were placed in a vacuum chamber with the fingerprint side facing a boat containing an evaporant material such as chalcogenide glass. Thermal evaporation of the solid material led to the formation of a dense CTF on the fingerprint, thereby capturing the topographical texture with high resolution. Our results show that it is possible to acquire the topology of latent fingerprints on non-porous surfaces. Additionally, deposition of CTFs on overlapping fingerprints suggested ours may be a technique for elucidating the sequence of deposition of the fingerprints at the scene.

A guideline for the validation of likelihood ratio methods used for forensic evidence evaluation.

PubMed

Meuwly, Didier; Ramos, Daniel; Haraksim, Rudolf

2017-07-01

This Guideline proposes a protocol for the validation of forensic evaluation methods at the source level, using the Likelihood Ratio framework as defined within the Bayes' inference model. In the context of the inference of identity of source, the Likelihood Ratio is used to evaluate the strength of the evidence for a trace specimen, e.g. a fingermark, and a reference specimen, e.g. a fingerprint, to originate from common or different sources. Some theoretical aspects of probabilities necessary for this Guideline were discussed prior to its elaboration, which started after a workshop of forensic researchers and practitioners involved in this topic. In the workshop, the following questions were addressed: "which aspects of a forensic evaluation scenario need to be validated?", "what is the role of the LR as part of a decision process?" and "how to deal with uncertainty in the LR calculation?". The questions: "what to validate?" focuses on the validation methods and criteria and "how to validate?" deals with the implementation of the validation protocol. Answers to these questions were deemed necessary with several objectives. First, concepts typical for validation standards [1], such as performance characteristics, performance metrics and validation criteria, will be adapted or applied by analogy to the LR framework. Second, a validation strategy will be defined. Third, validation methods will be described. Finally, a validation protocol and an example of validation report will be proposed, which can be applied to the forensic fields developing and validating LR methods for the evaluation of the strength of evidence at source level under the following propositions. Copyright © 2016. Published by Elsevier B.V.

Multi-isotope tracers to investigate processes in the Elbe, Weser and Ems river catchment using B, Mo, Sr, and Pb isotope ratios assessed by MC ICP-MS

NASA Astrophysics Data System (ADS)

Irrgeher, Johanna; Reese, Anna; Zimmermann, Tristan; Prohaska, Thomas; Retzmann, Anika; Wieser, Michael E.; Zitek, Andreas; Proefrock, Daniel

2017-04-01

Environmental monitoring of complex ecosystems requires reliable sensitive techniques based on sound analytical strategies to identify the source, fate and sink of elements and matter. Isotopic signatures can serve to trace pathways by making use of specific isotopic fingermarks or to distinguish between natural and anthropogenic sources. The presented work shows the potential of using the isotopic variation of Sr, Pb (as well-established isotopic systems), Mo and B (as novel isotopic system) assessed by MC ICP-MS in water and sediment samples to study aquatic ecosystem transport processes. The isotopic variation of Sr, Pb, Mo and B was determined in different marine and estuarine compartments covering the catchment of the German Wadden Sea and its main tributaries, the Elbe, Weser and Ems River. The varying elemental concentrations, the complex matrix and the expected small variations in the isotopic composition required the development and application of reliable analytical measurement approaches as well as suited metrological data evaluation strategies. Aquatic isoscapes were created using ArcGIS® by relating spatial isotopic data with geographical and geological maps. The elemental and isotopic distribution maps show large variation for different parameters and also reflect the numerous impact factors (e.g. geology, anthropogenic sources) influencing the catchment area.

Moiré deflectometry-based position detection for optical tweezers.

PubMed

Khorshad, Ali Akbar; Reihani, S Nader S; Tavassoly, Mohammad Taghi

2017-09-01

Optical tweezers have proven to be indispensable tools for pico-Newton range force spectroscopy. A quadrant photodiode (QPD) positioned at the back focal plane of an optical tweezers' condenser is commonly used for locating the trapped object. In this Letter, for the first time, to the best of our knowledge, we introduce a moiré pattern-based detection method for optical tweezers. We show, both theoretically and experimentally, that this detection method could provide considerably better position sensitivity compared to the commonly used detection systems. For instance, position sensitivity for a trapped 2.17 μm polystyrene bead is shown to be 71% better than the commonly used QPD-based detection method. Our theoretical and experimental results are in good agreement.

Occurrence and behavior of the herbicide Prometon in the hydrologic system

USGS Publications Warehouse

Capel, P.D.; Spexet, A.H.; Larson, S.J.

1999-01-01

Prometon, a triazine herbicide, is used for total vegetation control on industrial sites, on noncrop areas on farms, in and under asphalt, and to a small extent by homeowners. Prometon has often been detected in surface water and groundwater in studies reported in the literature, but its presence is seldom discussed, partly because of its infrequent inclusion on lists of herbicides used in either agricultural or urban areas. In recent large-scale studies by the U.S. Geological Survey, prometon has been the most commonly detected herbicide in surface water and groundwater in urban areas and the third and fourth most commonly detected herbicide in groundwater and surface water, respectively, in agricultural areas. It also has been detected in rain. The frequent detection of prometon in the environment is discussed in relation to its use practices and predicted environmental behavior. Prometon is compared to atrazine, a structurally similar agricultural triazine herbicide that is one of the most studied and most commonly detected herbicides found in the hydrologic environment. The environmental data presented here demonstrate the wide-scale occurrence of prometon in all components of the hydrologic system, particularly in the surface water and groundwater of urban areas.Prometon, a triazine herbicide, is used for total vegetation control on industrial sites, on noncrop areas on farms, in and under asphalt, and to a small extent by homeowners. Prometon has often been detected in surface water and groundwater in studies reported in the literature, but its presence is seldom discussed, partly because of its infrequent inclusion on lists of herbicides used in either agricultural or urban areas. In recent large-scale studies by the U.S. Geological Survey, prometon has been the most commonly detected herbicide in surface water and groundwater in urban areas and the third and fourth most commonly detected herbicide in groundwater and surface water, respectively, in agricultural areas. It also has been detected in rain. The frequent detection of prometon in the environment is discussed in relation to its use practices and predicted environmental behavior. Prometon is compared to atrazine, a structurally similar agricultural triazine herbicide that is one of the most studied and most commonly detected herbicides found in the hydrologic environment. The environmental data presented here demonstrate the wide-scale occurrence of prometon in all components of the hydrologic system, particularly in the surface water and groundwater of urban areas.

Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data.

PubMed

Zhang, Peng; Li, Houqiang; Wang, Honghui; Wong, Stephen T C; Zhou, Xiaobo

2011-01-01

Peak detection is one of the most important steps in mass spectrometry (MS) analysis. However, the detection result is greatly affected by severe spectrum variations. Unfortunately, most current peak detection methods are neither flexible enough to revise false detection results nor robust enough to resist spectrum variations. To improve flexibility, we introduce peak tree to represent the peak information in MS spectra. Each tree node is a peak judgment on a range of scales, and each tree decomposition, as a set of nodes, is a candidate peak detection result. To improve robustness, we combine peak detection and common peak alignment into a closed-loop framework, which finds the optimal decomposition via both peak intensity and common peak information. The common peak information is derived and loopily refined from the density clustering of the latest peak detection result. Finally, we present an improved ant colony optimization biomarker selection method to build a whole MS analysis system. Experiment shows that our peak detection method can better resist spectrum variations and provide higher sensitivity and lower false detection rates than conventional methods. The benefits from our peak-tree-based system for MS disease analysis are also proved on real SELDI data.

Detection of nonauthorized genetically modified organisms using differential quantitative polymerase chain reaction: application to 35S in maize.

PubMed

Cankar, Katarina; Chauvensy-Ancel, Valérie; Fortabat, Marie-Noelle; Gruden, Kristina; Kobilinsky, André; Zel, Jana; Bertheau, Yves

2008-05-15

Detection of nonauthorized genetically modified organisms (GMOs) has always presented an analytical challenge because the complete sequence data needed to detect them are generally unavailable although sequence similarity to known GMOs can be expected. A new approach, differential quantitative polymerase chain reaction (PCR), for detection of nonauthorized GMOs is presented here. This method is based on the presence of several common elements (e.g., promoter, genes of interest) in different GMOs. A statistical model was developed to study the difference between the number of molecules of such a common sequence and the number of molecules identifying the approved GMO (as determined by border-fragment-based PCR) and the donor organism of the common sequence. When this difference differs statistically from zero, the presence of a nonauthorized GMO can be inferred. The interest and scope of such an approach were tested on a case study of different proportions of genetically modified maize events, with the P35S promoter as the Cauliflower Mosaic Virus common sequence. The presence of a nonauthorized GMO was successfully detected in the mixtures analyzed and in the presence of (donor organism of P35S promoter). This method could be easily transposed to other common GMO sequences and other species and is applicable to other detection areas such as microbiology.

Automated Detection of a Crossing Contact Based on Its Doppler Shift

DTIC Science & Technology

2009-03-01

contacts in passive sonar systems. A common approach is the application of high- gain processing followed by successive classification criteria. Most...contacts in passive sonar systems. A common approach is the application of high-gain processing followed by successive classification criteria...RESEARCH MOTIVATION The trade-off between the false alarm and detection probability is fundamental in radar and sonar . (Chevalier, 2002) A common

Validation and application of a quantitative real-time PCR assay to detect common wheat adulteration of durum wheat for pasta production.

PubMed

Carloni, Elisa; Amagliani, Giulia; Omiccioli, Enrica; Ceppetelli, Veronica; Del Mastro, Michele; Rotundo, Luca; Brandi, Giorgio; Magnani, Mauro

2017-06-01

Pasta is the Italian product par excellence and it is now popular worldwide. Pasta of a superior quality is made with pure durum wheat. In Italy, addition of Triticum aestivum (common wheat) during manufacturing is not allowed and, without adequate labeling, its presence is considered an adulteration. PCR-related techniques can be employed for the detection of common wheat contaminations. In this work, we demonstrated that a previously published method for the detection of T. aestivum, based on the gliadin gene, is inadequate. Moreover, a new molecular method, based on DNA extraction from semolina and real-time PCR determination of T. aestivum in Triticum spp., was validated. This multiplex real-time PCR, based on the dual-labeled probe strategy, guarantees target detection specificity and sensitivity in a short period of time. Moreover, the molecular analysis of common wheat contamination in commercial wheat and flours is described for the first time. Copyright © 2016 Elsevier Ltd. All rights reserved.

An endogenous reference gene of common and durum wheat for detection of genetically modified wheat.

PubMed

Imai, Shinjiro; Tanaka, Keiko; Nishitsuji, Yasuyuki; Kikuchi, Yosuke; Matsuoka, Yasuyuki; Arami, Shin-Ichiro; Sato, Megumi; Haraguchi, Hiroyuki; Kurimoto, Youichi; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

2012-01-01

To develop a method for detecting GM wheat that may be marketed in the near future, we evaluated the proline-rich protein (PRP) gene as an endogenous reference gene of common wheat (Triticum aestivum L.) and durum wheat (Triticum durum L.). Real-time PCR analysis showed that only DNA of wheat was amplified and no amplification product was observed for phylogenetically related cereals, indicating that the PRP detection system is specific to wheat. The intensities of the amplification products and Ct values among all wheat samples used in this study were very similar, with no nonspecific or additional amplification, indicating that the PRP detection system has high sequence stability. The limit of detection was estimated at 5 haploid genome copies. The PRP region was demonstrated to be present as a single or double copy in the common wheat haploid genome. Furthermore, the PRP detection system showed a highly linear relationship between Ct values and the amount of plasmid DNA, indicating that an appropriate calibration curve could be constructed for quantitative detection of GM wheat. All these results indicate that the PRP gene is a suitable endogenous reference gene for PCR-based detection of GM wheat.

Organic Chemical Concentrations and Reproductive Biomarkers in Common Carp (Cyprinus carpio) Collected from Two Areas in Lake Mead, Nevada, May 1999-May 2000

USGS Publications Warehouse

Goodbred, Steven L.; Leiker, Thomas J.; Patiño, Reynaldo; Jenkins, Jill A.; Denslow, Nancy D.; Orsak, Erik; Rosen, Michael R.

2007-01-01

The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, National Park Service, Bureau of Reclamation, and Nevada Department of Wildlife, collected and assessed data to determine the general health and reproductive status of common carp (Cyprinus carpio) at two study areas in Lake Mead, Nevada, during May 1999-May 2000. These data will form the basis of interpretations and provide a comparison for continuing studies on the health of the ecosystem in Lake Mead. One study area, Las Vegas Bay, is in the western part of Lake Mead. Las Vegas Bay receives inflows from Las Vegas Wash, which is predominantly tertiary-treated wastewater effluent, and to a lesser extent stormwater runoff from Las Vegas, Henderson, and other nearby communities, and from ground water underlying Las Vegas Valley. The other study area, Overton Arm, is in the northern extent of Lake Mead. Overton Arm receives inflow from the Virgin and Muddy Rivers, which historically are not influenced by wastewater effluent. Both sexes of common carp were collected bimonthly for 12 months using boat-mounted electrofishing gear (a direct electric current is used to temporarily immobilize fish for capture) to determine their health and reproductive status and any relation between these factors and environmental contaminants. This report presents fish tissue chemistry, organic chemical compound concentrations, and biomarker data for 83 male common carp collected from Las Vegas Bay, similar organic chemistry results for 15 male common carp, and similar biomarker measures for 80 male common carp collected from Overton Arm. Tissue chemistry results also are presented for 16 female common carp and biomarker measures for 79 female common carp collected from Las Vegas Bay, and tissue chemistry results for 15 female common carp and biomarker measures for 81 female common carp collected from Overton Arm. Thirty-three organic chemical compounds plus total concentrations for four groups of compounds (chlordanes, polychlorinated biphenyls [PCBs], brominated diphenyl ethers [BDEs], and triclosans) were analyzed from extracts of whole-body tissue using gas chromatography/mass spectrometry in male common carp from Las Vegas Bay during May 1999 through May 2000. All 33 compounds were detected in at least one sample of whole-body tissue from male common carp collected in Las Vegas Bay. In Overton Arm, 37 organic compounds plus total concentrations of three groups of compounds (PCBs, BDEs, and triclosans) were analyzed in male common carp where 20 (54 percent) of the compounds were detected. Sixteen of the 33 compounds detected in male common carp from Las Vegas Bay and 10 compounds detected in males from Overton Arm have the potential to disrupt the endocrine system in fish in Lake Mead. During May and June 1999, the mean concentration of all organic compounds detected in male common carp was 670 micrograms per kilogram from Las Vegas Bay and 109 micrograms per kilogram from Overton Arm. Twenty-seven organic compounds plus total PCBs were analyzed from extracts of whole-body tissue in female common carp collected in Las Vegas Bay and Overton Arm during May 1999. Twenty-four (86 percent) of these compounds were detected in at least one sample of whole-body tissue from female common carp collected from Las Vegas Bay while 10 (36 percent) chemical compounds were detected in female common carp from Overton Arm during that same period. Median concentrations of all chemical compounds were higher in female common carp from Las Vegas Bay compared to those collected from Overton Arm except Dacthal (DCPA), which was similar between sites. Biomarker measures obtained for male and female common carp include gonadosomatic index (percentage of gonad weight to total body weight), plasma vitellogenin (a phospholipid protein normally produced by female common carp and other oviparous fish), and condition factor [body weight/(fork length)3]. Biomarker measures for male c

Anthropogenic organic compounds in source water of selected community water systems that use groundwater, 2002-05

USGS Publications Warehouse

Hopple, Jessica A.; Delzer, Gregory C.; Kingsbury, James A.

2009-01-01

Source water, defined as groundwater collected from a community water system well prior to water treatment, was sampled from 221 wells during October 2002 to July 2005 and analyzed for 258 anthropogenic organic compounds. Most of these compounds are unregulated in drinking water and include pesticides and pesticide degradates, gasoline hydrocarbons, personal-care and domestic-use products, and solvents. The laboratory analytical methods used in the study have detection levels that commonly are 100 to 1,000 times lower than State and Federal standards and guidelines for protecting water quality. Detections of anthropogenic organic compounds do not necessarily indicate a concern to human health but rather help to identify emerging issues and track changes in occurrence and concentrations over time. Less than one-half (120) of the 258 compounds were detected in at least one source-water sample. Chloroform, in 36 percent of samples, was the most commonly detected of the 12 compounds that were in about 10 percent or more of source-water samples. The herbicides atrazine, metolachlor, prometon, and simazine also were among the commonly detected compounds. The commonly detected degradates of atrazine - deethylatrazine and deisopropylatrazine - as well as degradates of acetochlor and alachlor, generally were detected at concentrations similar to or greater than concentrations of the parent herbicide. The compounds perchloroethene, trichloroethene, 1,1,1-trichloroethane, methyl tert-butyl ether, and cis-1,2-dichloroethene also were detected commonly. The most commonly detected compounds in source-water samples generally were among those detected commonly across the country and reported in previous studies by the U.S. Geological Survey's National Water-Quality Assessment Program. Relatively few compounds were detected at concentrations greater than human-health benchmarks, and 84 percent of the concentrations were two or more orders of magnitude less than benchmarks. Five compounds (perchloroethene, trichloroethene, 1,2-dibromoethane, acrylonitrile, and dieldrin) were detected at concentrations greater than their human-health benchmark. The human-health benchmarks used for comparison were U.S. Environmental Protection Agency Maximum Contaminant Levels (MCLs) for regulated compounds and Health-Based Screening Levels developed by the U.S. Geological Survey in collaboration with the U.S. Environmental Protection Agency and other agencies for unregulated compounds. About one-half of all detected compounds do not have human-health benchmarks or adequate toxicity information to evaluate results in a human-health context. Ninety-four source-water and finished-water (water that has passed through all the treatment processes but prior to distribution) sites were sampled at selected community water systems during June 2004 to September 2005. Most of the samples were analyzed for compounds that were detected commonly or at relatively high concentrations during the initial source-water sampling. The majority of the finished-water samples represented water blended with water from one or more other wells. Thirty-four samples were from water systems that did not blend water from sampled wells with water from other wells prior to distribution. The comparison of source- and finished-water samples represents an initial assessment of whether compounds present in source water also are present in finished water and is not intended as an evaluation of water-treatment efficacy. The treatment used at the majority of the community water systems sampled is disinfection, which, in general, is not designed to remove the compounds monitored in this study. Concentrations of all compounds detected in finished water were less than their human-health benchmarks. Two detections of perchloroethene and one detection of trichloroethene in finished water had concentrations within an order of magnitude of the MCL. Concentrations of disinfection by-products were

Applicability of the ParaDNA(®) Screening System to Seminal Samples.

PubMed

Tribble, Nicholas D; Miller, Jamie A D; Dawnay, Nick; Duxbury, Nicola J

2015-05-01

Seminal fluid represents a common biological material recovered from sexual assault crime scenes. Such samples can be prescreened using different techniques to determine cell type and relative amount before submitting for full STR profiling. The ParaDNA(®) Screening System is a novel forensic test which identifies the presence of DNA through amplification and detection of two common STR loci (D16S539 and TH01) and the Amelogenin marker. The detection of the Y allele in samples could provide a useful tool in the triage and submission of sexual assault samples by enforcement authorities. Male template material was detected on a range of common sexual assault evidence items including cotton pillow cases, condoms, swab heads and glass surfaces and shows a detection limit of 1 in 1000 dilution of neat semen. These data indicate this technology has the potential to be a useful tool for the detection of male donor DNA in sexual assault casework. © 2015 American Academy of Forensic Sciences.

Development of a PCR assay to detect cyprinid herpesvirus 1 in koi and common carp.

PubMed

Viadanna, Pedro H O; Miller-Morgan, Tim; Peterson, Trace; Way, Keith; Stone, David M; Marty, Gary D; Pilarski, Fabiana; Hedrick, Ronald P; Waltzek, Thomas B

2017-02-08

Cyprinid herpesvirus 1 (CyHV1) infects all scaled and color varieties of common carp Cyprinus carpio, including koi. While it is most often associated with unsightly growths known as 'carp pox,' the underlying lesion (epidermal hyperplasia) can arise from a variety of disease processes. CyHV1-induced epidermal hyperplasia may occur transiently in response to water temperature, and thus histopathology cannot be used in isolation to assess CyHV1 infection status. To address this problem, here we describe a PCR assay targeted to the putative thymidine kinase gene of CyHV1. The PCR assay generates a 141 bp amplicon and reliably detects down to 10 copies of control plasmid DNA sequence (analytic sensitivity). The PCR does not cross-detect genomic DNA from cyprinid herpesvirus 2 and 3 (analytic specificity). The CyHV1 PCR effectively detected viral DNA in koi and common carp sampled from various locations in the UK, USA, Brazil, and Japan. Viral DNA was detected in both normal appearing and grossly affected epidermal tissues from koi experiencing natural epizootics. The new CyHV1 PCR provides an additional approach to histopathology for the rapid detection of CyHV1. Analysis of the thymidine kinase gene sequences determined for 7 PCR-positive carp originating from disparate geographical regions identified 3 sequence types, with 1 type occurring in both koi and common carp.

Optimizing study design for multi-species avian monitoring programmes

Treesearch

Jamie S. Sanderlin; William M. Block; Joseph L. Ganey

2014-01-01

Many monitoring programmes are successful at monitoring common species, whereas rare species, which are often of highest conservation concern, may be detected infrequently. Study designs that increase the probability of detecting rare species at least once over the study period, while collecting adequate data on common species, strengthen programme ability to address...

Viruses and Bacteria in the Etiology of the Common Cold

PubMed Central

Mäkelä, Mika J.; Puhakka, Tuomo; Ruuskanen, Olli; Leinonen, Maija; Saikku, Pekka; Kimpimäki, Marko; Blomqvist, Soile; Hyypiä, Timo; Arstila, Pertti

1998-01-01

Two hundred young adults with common colds were studied during a 10-month period. Virus culture, antigen detection, PCR, and serology with paired samples were used to identify the infection. Viral etiology was established for 138 of the 200 patients (69%). Rhinoviruses were detected in 105 patients, coronavirus OC43 or 229E infection was detected in 17, influenza A or B virus was detected in 12, and single infections with parainfluenza virus, respiratory syncytial virus, adenovirus, and enterovirus were found in 14 patients. Evidence for bacterial infection was found in seven patients. Four patients had a rise in antibodies against Chlamydia pneumoniae, one had a rise in antibodies against Haemophilus influenzae, one had a rise in antibodies against Streptococcus pneumoniae, and one had immunoglobulin M antibodies against Mycoplasma pneumoniae. The results show that although approximately 50% of episodes of the common cold were caused by rhinoviruses, the etiology can vary depending on the epidemiological situation with regard to circulating viruses. Bacterial infections were rare, supporting the concept that the common cold is almost exclusively a viral disease. PMID:9466772

Molecular commonality detection using an artificial enzyme membrane for in situ one-stop biosurveillance.

PubMed

Ikeno, Shinya; Asakawa, Hitoshi; Haruyama, Tetsuya

2007-08-01

Biodetection and biosensing have been developed based on the concept of sensitivity toward specific molecules. However, current demand may require more levelheaded or far-sighted methods, especially in the field of biological safety and security. In the fields of hygiene, public safety, and security including fighting bioterrorism, the detection of biological contaminants, e.g., microorganisms, spores, and viruses, is a constant challenge. However, there is as yet no sophisticated method of detecting such contaminants in situ without oversight. The authors focused their attention on diphosphoric acid anhydride, which is a structure common to all biological phosphoric substances. Interestingly, biological phosphoric substances are peculiar substances present in all living things and include many different substances, e.g., ATP, ADP, dNTP, pyrophosphate, and so forth, all of which have a diphosphoric acid anhydride structure. The authors took this common structure as the basis of their development of an artificial enzyme membrane with selectivity for the structure common to all biological phosphoric substances and studied the possibility of its application to in situ biosurveillance sensors. The artificial enzyme membrane-based amperometric biosensor developed by the authors can detect various biological phosphoric substances, because it has a comprehensive molecular selectivity for the structure of these biological phosphoric substances. This in situ detection method of the common diphosphoric acid anhydride structure brings a unique advantage to the fabrication of in situ biosurveillance sensors for monitoring biological contaminants, e.g., microorganism, spores, and viruses, without an oversight, even if they were transformed.

Raman detection of improvised explosive device (IED) material fabricated using drop-on-demand inkjet technology on several real world surfaces

NASA Astrophysics Data System (ADS)

Farrell, Mikella E.; Holthoff, Ellen L.; Pellegrino, Paul M.

2015-05-01

The requirement to detect hazardous materials (i.e., chemical, biological, and explosive) on a host of materials has led to the development of hazard detection systems. These new technologies and their capabilities could have immediate uses for the US military, national security agencies, and environmental response teams in efforts to keep people secure and safe. In particular, due to the increasing use by terrorists, the detection of common explosives and improvised explosive device (IED) materials have motivated research efforts toward detecting trace (i.e., particle level) quantities on multiple commonly encountered surfaces (e.g., textiles, metals, plastics, natural products, and even people). Non-destructive detection techniques can detect trace quantities of explosive materials; however, it can be challenging in the presence of a complex chemical background. One spectroscopic technique gaining increased attention for detection is Raman. One popular explosive precursor material is ammonium nitrate (AN). The material AN has many agricultural applications, however it can also be used in the fabrication of IEDs or homemade explosives (HMEs). In this paper, known amounts of AN will be deposited using an inkjet printer into several different common material surfaces (e.g., wood, human hair, textiles, metals, plastics). The materials are characterized with microscope images and by collecting Raman spectral data. In this report the detection and identification of AN will be demonstrated.

Pesticides in Ground Water of the Maryland Coastal Plain

USGS Publications Warehouse

Denver, Judith M.; Ator, Scott W.

2006-01-01

Selected pesticides are detectable at low levels (generally less than 0.1 microgram per liter) in unconfined ground water in many parts of the Maryland Coastal Plain. Samples were recently collected (2001-04) from 47 wells in the Coastal Plain and analyzed for selected pesticides and degradate compounds (products of pesticide degradation). Most pesticide degradation occurs in the soil zone before infiltration to the water table, and degradates of selected pesticides were commonly detected in ground water, often at higher concentrations than their respective parent compounds. Pesticides and their degradates often occur in ground water in mixtures of multiple compounds, reflecting similar patterns in usage. All measured concentrations in ground water were below established standards for drinking water, and nearly all were below other health-based guidelines. Although drinking-water standards and guidelines are typically much higher than observed concentrations in ground water, they do not exist for many detected compounds (particularly degradates), or for mixtures of multiple compounds. The distribution of observed pesticide compounds reflects known usage patterns, as well as chemical properties and environmental factors that affect the fate and transport of these compounds in the environment. Many commonly used pesticides, such as glyphosate, pendimethalin, and 2,4-D were not detected in ground water, likely because they were sorbed onto organic matter or degraded in the soil zone. Others that are more soluble and (or) persistent, like atrazine, metolachlor, and several of their degradates, were commonly detected in ground water where they have been used. Atrazine, for example, an herbicide used primarily on corn, was most commonly detected in ground water on the Eastern Shore (where agriculture is common), particularly where soils are well drained. Conversely, dieldrin, an insecticide previously used heavily for termite control, was detected only on the Western Shore, where urban land is more common. Use of dieldrin was suspended in 1987, but this compound is relatively persistent in the environment, and several decades are typically required for ground water to move completely through the surficial aquifer. U.S. Department of the Interior U.S. Geological Survey USGS Fact Sheet FS 2006-3119 2006 Location of the Maryland Coastal Plain.

Etiology of Childhood Diarrhea Following Rotavirus Vaccine Introduction: A Prospective, Population-Based Study in Nicaragua

PubMed Central

Becker-Dreps, Sylvia; Bucardo, Filemon; Vilchez, Samuel; Zambrana, Luis Enrique; Liu, Lan; Weber, David J.; Peña, Rodolfo; Barclay, Leslie; Vinjé, Jan; Hudgens, Michael G.; Nordgren, Johan; Svensson, Lennart; Morgan, Douglas R.; Espinoza, Félix; Paniagua, Margarita

2014-01-01

Background Nicaragua was the first developing nation to implement routine immunization with the pentavalent rotavirus vaccine (RV5). In this RV5-immunized population, understanding infectious etiologies of childhood diarrhea is necessary to direct diarrhea treatment and prevention efforts. Methods We followed a population-based sample of children less than 5 years in León, Nicaragua for diarrhea episodes through household visits. Information was obtained on RV5 history and sociodemographics. Stool samples collected during diarrhea episodes and among healthy children underwent laboratory analysis for viral, bacterial, and parasitic enteropathogens. Detection frequency and incidence of each enteropathogen was calculated. Results The 826 children in the cohort experienced 677 diarrhea episodes during 607.5 child-years of exposure time (1.1 episodes per child-year). At least one enteropathogen was detected among 61.1% of the 337 diarrheal stools collected. The most common enteropathogens among diarrheal stools were: norovirus (20.4%), sapovirus (16.6%), enteropathogenic Escherichia coli (EPEC, 11.3%), Entamoeba histolytica/dispar (8.3%), Giardia lamblia (8.0%), and enterotoxigenic E.coli (ETEC, 7.7%), with rotavirus detected among 5.3% of diarrheal stools. EPEC and ETEC were frequently detected among stools from healthy children. Among children with diarrhea, norovirus was more commonly detected among younger children (< 2 years) and G. lamblia was more commonly detected among older children (2-4 years). The mean age of rotavirus detection was 34.6 months. Conclusions In this Central American community following RV5 introduction, rotavirus was not commonly detected among children with diarrhea. Prevention and appropriate management of norovirus and sapovirus should be considered to further reduce the burden of diarrheal disease. PMID:24879131

A specific endogenous reference for genetically modified common bean (Phaseolus vulgaris L.) DNA quantification by real-time PCR targeting lectin gene.

PubMed

Venturelli, Gustavo L; Brod, Fábio C A; Rossi, Gabriela B; Zimmermann, Naíra F; Oliveira, Jaison P; Faria, Josias C; Arisi, Ana C M

2014-11-01

The Embrapa 5.1 genetically modified (GM) common bean was approved for commercialization in Brazil. Methods for the quantification of this new genetically modified organism (GMO) are necessary. The development of a suitable endogenous reference is essential for GMO quantification by real-time PCR. Based on this, a new taxon-specific endogenous reference quantification assay was developed for Phaseolus vulgaris L. Three genes encoding common bean proteins (phaseolin, arcelin, and lectin) were selected as candidates for endogenous reference. Primers targeting these candidate genes were designed and the detection was evaluated using the SYBR Green chemistry. The assay targeting lectin gene showed higher specificity than the remaining assays, and a hydrolysis probe was then designed. This assay showed high specificity for 50 common bean samples from two gene pools, Andean and Mesoamerican. For GM common bean varieties, the results were similar to those obtained for non-GM isogenic varieties with PCR efficiency values ranging from 92 to 101 %. Moreover, this assay presented a limit of detection of ten haploid genome copies. The primers and probe developed in this work are suitable to detect and quantify either GM or non-GM common bean.

Rapid diagnosis of common deletional α-thalassemia in the Chinese population by qPCR based on identical primer homologous fragments.

PubMed

Long, Ju

2016-05-01

In China, -(SEA), -α(3.7) and -α(4.2) are common deletional α-thalassemia alleles. Gap-PCR is the currently used detection method for these alleles, whose disadvantages include time-consuming procedure and increased potential for PCR product contamination. Therefore, this detection method needs to be improved. Based on identical-primer homologous fragments, a qPCR system was developed for deletional α-thalassemia genotyping, which was composed of a group of quantitatively-related primers and their corresponding probes plus two groups of qualitatively-related primers and their corresponding probes. In order to verify the accuracy of the qPCR system, known genotype samples and random samples are employed. The standard curve result demonstrated that designed primers and probes all yielded good amplification efficiency. In the tests of known genotype samples and random samples, sample detection results were consistent with verification results. In detecting αα, -(SEA), -α(3.7) and -α(4.2) alleles, deletional α-thalassemia alleles are accurately detected by this method. In addition, this method is provided with a wider detection range, greater speed and reduced PCR product contamination risk when compared with current common gap-PCR detection reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

Are You Ready for [a] Roundup?--What Chemistry Has to Do with Genetic Modifications

NASA Astrophysics Data System (ADS)

Pöpping, Bert

2001-06-01

Genetically modified crops are grown in most parts of the world nowadays. These transgenic plants have new properties such as herbicide tolerance or insect resistance that often cannot be introduced by conventional breeding. Using examples of very common transgenic varieties, the article explains how the knowledge of metabolic pathways and genetic information is used to design these plants and how the same knowledge is used to detect them. It reviews why detection of genetic modifications in plants has become necessary and describes the most common detection methods, from immunological assays to polymerase chain reaction and real-time detection.

Defining a region of optimization based on engine usage data

DOEpatents

Jiang, Li; Lee, Donghoon; Yilmaz, Hakan; Stefanopoulou, Anna

2015-08-04

Methods and systems for engine control optimization are provided. One or more operating conditions of a vehicle engine are detected. A value for each of a plurality of engine control parameters is determined based on the detected one or more operating conditions of the vehicle engine. A range of the most commonly detected operating conditions of the vehicle engine is identified and a region of optimization is defined based on the range of the most commonly detected operating conditions of the vehicle engine. The engine control optimization routine is initiated when the one or more operating conditions of the vehicle engine are within the defined region of optimization.

Glint-induced false alarm reduction in signature adaptive target detection

NASA Astrophysics Data System (ADS)

Crosby, Frank J.

2002-07-01

The signal adaptive target detection algorithm developed by Crosby and Riley uses target geometry to discern anomalies in local backgrounds. Detection is not restricted based on specific target signatures. The robustness of the algorithm is limited by an increased false alarm potential. The base algorithm is extended to eliminate one common source of false alarms in a littoral environment. This common source is glint reflected on the surface of water. The spectral and spatial transience of glint prevent straightforward characterization and complicate exclusion. However, the statistical basis of the detection algorithm and its inherent computations allow for glint discernment and the removal of its influence.

Detection of genetically modified organisms (GMOs) using isothermal amplification of target DNA sequences.

PubMed

Lee, David; La Mura, Maurizio; Allnutt, Theo R; Powell, Wayne

2009-02-02

The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR). Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

The Hidden Snake in the Grass: Superior Detection of Snakes in Challenging Attentional Conditions

PubMed Central

Soares, Sandra C.; Lindström, Björn; Esteves, Francisco; Öhman, Arne

2014-01-01

Snakes have provided a serious threat to primates throughout evolution. Furthermore, bites by venomous snakes still cause significant morbidity and mortality in tropical regions of the world. According to the Snake Detection Theory (SDT Isbell, 2006; 2009), the vital need to detect camouflaged snakes provided strong evolutionary pressure to develop astute perceptual capacity in animals that were potential targets for snake attacks. We performed a series of behavioral tests that assessed snake detection under conditions that may have been critical for survival. We used spiders as the control stimulus because they are also a common object of phobias and rated negatively by the general population, thus commonly lumped together with snakes as “evolutionary fear-relevant”. Across four experiments (N = 205) we demonstrate an advantage in snake detection, which was particularly obvious under visual conditions known to impede detection of a wide array of common stimuli, for example brief stimulus exposures, stimuli presentation in the visual periphery, and stimuli camouflaged in a cluttered environment. Our results demonstrate a striking independence of snake detection from ecological factors that impede the detection of other stimuli, which suggests that, consistent with the SDT, they reflect a specific biological adaptation. Nonetheless, the empirical tests we report are limited to only one aspect of this rich theory, which integrates findings across a wide array of scientific disciplines. PMID:25493937

The Hidden Snake in the Grass: Superior Detection of Snakes in Challenging Attentional Conditions.

PubMed

Soares, Sandra C; Lindström, Björn; Esteves, Francisco; Ohman, Arne

2014-01-01

Snakes have provided a serious threat to primates throughout evolution. Furthermore, bites by venomous snakes still cause significant morbidity and mortality in tropical regions of the world. According to the Snake Detection Theory (SDT Isbell, 2006; 2009), the vital need to detect camouflaged snakes provided strong evolutionary pressure to develop astute perceptual capacity in animals that were potential targets for snake attacks. We performed a series of behavioral tests that assessed snake detection under conditions that may have been critical for survival. We used spiders as the control stimulus because they are also a common object of phobias and rated negatively by the general population, thus commonly lumped together with snakes as "evolutionary fear-relevant". Across four experiments (N = 205) we demonstrate an advantage in snake detection, which was particularly obvious under visual conditions known to impede detection of a wide array of common stimuli, for example brief stimulus exposures, stimuli presentation in the visual periphery, and stimuli camouflaged in a cluttered environment. Our results demonstrate a striking independence of snake detection from ecological factors that impede the detection of other stimuli, which suggests that, consistent with the SDT, they reflect a specific biological adaptation. Nonetheless, the empirical tests we report are limited to only one aspect of this rich theory, which integrates findings across a wide array of scientific disciplines.

Detection methods and performance criteria for genetically modified organisms.

PubMed

Bertheau, Yves; Diolez, Annick; Kobilinsky, André; Magin, Kimberly

2002-01-01

Detection methods for genetically modified organisms (GMOs) are necessary for many applications, from seed purity assessment to compliance of food labeling in several countries. Numerous analytical methods are currently used or under development to support these needs. The currently used methods are bioassays and protein- and DNA-based detection protocols. To avoid discrepancy of results between such largely different methods and, for instance, the potential resulting legal actions, compatibility of the methods is urgently needed. Performance criteria of methods allow evaluation against a common standard. The more-common performance criteria for detection methods are precision, accuracy, sensitivity, and specificity, which together specifically address other terms used to describe the performance of a method, such as applicability, selectivity, calibration, trueness, precision, recovery, operating range, limit of quantitation, limit of detection, and ruggedness. Performance criteria should provide objective tools to accept or reject specific methods, to validate them, to ensure compatibility between validated methods, and be used on a routine basis to reject data outside an acceptable range of variability. When selecting a method of detection, it is also important to consider its applicability, its field of applications, and its limitations, by including factors such as its ability to detect the target analyte in a given matrix, the duration of the analyses, its cost effectiveness, and the necessary sample sizes for testing. Thus, the current GMO detection methods should be evaluated against a common set of performance criteria.

A Kalman-Filter-Based Common Algorithm Approach for Object Detection in Surgery Scene to Assist Surgeon's Situation Awareness in Robot-Assisted Laparoscopic Surgery

PubMed Central

2018-01-01

Although the use of the surgical robot is rapidly expanding for various medical treatments, there still exist safety issues and concerns about robot-assisted surgeries due to limited vision through a laparoscope, which may cause compromised situation awareness and surgical errors requiring rapid emergency conversion to open surgery. To assist surgeon's situation awareness and preventive emergency response, this study proposes situation information guidance through a vision-based common algorithm architecture for automatic detection and tracking of intraoperative hemorrhage and surgical instruments. The proposed common architecture comprises the location of the object of interest using feature texture, morphological information, and the tracking of the object based on Kalman filter for robustness with reduced error. The average recall and precision of the instrument detection in four prostate surgery videos were 96% and 86%, and the accuracy of the hemorrhage detection in two prostate surgery videos was 98%. Results demonstrate the robustness of the automatic intraoperative object detection and tracking which can be used to enhance the surgeon's preventive state recognition during robot-assisted surgery. PMID:29854366

Feature selection from hyperspectral imaging for guava fruit defects detection

NASA Astrophysics Data System (ADS)

Mat Jafri, Mohd. Zubir; Tan, Sou Ching

2017-06-01

Development of technology makes hyperspectral imaging commonly used for defect detection. In this research, a hyperspectral imaging system was setup in lab to target for guava fruits defect detection. Guava fruit was selected as the object as to our knowledge, there is fewer attempts were made for guava defect detection based on hyperspectral imaging. The common fluorescent light source was used to represent the uncontrolled lighting condition in lab and analysis was carried out in a specific wavelength range due to inefficiency of this particular light source. Based on the data, the reflectance intensity of this specific setup could be categorized in two groups. Sequential feature selection with linear discriminant (LD) and quadratic discriminant (QD) function were used to select features that could potentially be used in defects detection. Besides the ordinary training method, training dataset in discriminant was separated in two to cater for the uncontrolled lighting condition. These two parts were separated based on the brighter and dimmer area. Four evaluation matrixes were evaluated which are LD with common training method, QD with common training method, LD with two part training method and QD with two part training method. These evaluation matrixes were evaluated using F1-score with total 48 defected areas. Experiment shown that F1-score of linear discriminant with the compensated method hitting 0.8 score, which is the highest score among all.

HIV resistance testing and detected drug resistance in Europe.

PubMed

Schultze, Anna; Phillips, Andrew N; Paredes, Roger; Battegay, Manuel; Rockstroh, Jürgen K; Machala, Ladislav; Tomazic, Janez; Girard, Pierre M; Januskevica, Inga; Gronborg-Laut, Kamilla; Lundgren, Jens D; Cozzi-Lepri, Alessandro

2015-07-17

To describe regional differences and trends in resistance testing among individuals experiencing virological failure and the prevalence of detected resistance among those individuals who had a genotypic resistance test done following virological failure. Multinational cohort study. Individuals in EuroSIDA with virological failure (>1 RNA measurement >500 on ART after >6 months on ART) after 1997 were included. Adjusted odds ratios (aORs) for resistance testing following virological failure and aORs for the detection of resistance among those who had a test were calculated using logistic regression with generalized estimating equations. Compared to 74.2% of ART-experienced individuals in 1997, only 5.1% showed evidence of virological failure in 2012. The odds of resistance testing declined after 2004 (global P < 0.001). Resistance was detected in 77.9% of the tests, NRTI resistance being most common (70.3%), followed by NNRTI (51.6%) and protease inhibitor (46.1%) resistance. The odds of detecting resistance were lower in tests done in 1997-1998, 1999-2000 and 2009-2010, compared to those carried out in 2003-2004 (global P < 0.001). Resistance testing was less common in Eastern Europe [aOR 0.72, 95% confidence interval (CI) 0.55-0.94] compared to Southern Europe, whereas the detection of resistance given that a test was done was less common in Northern (aOR 0.29, 95% CI 0.21-0.39) and Central Eastern (aOR 0.47, 95% CI 0.29-0.76) Europe, compared to Southern Europe. Despite a concurrent decline in virological failure and testing, drug resistance was commonly detected. This suggests a selective approach to resistance testing. The regional differences identified indicate that policy aiming to minimize the emergence of resistance is of particular relevance in some European regions, notably in the countries in Eastern Europe.

Robust Scale Transformation Methods in IRT True Score Equating under Common-Item Nonequivalent Groups Design

ERIC Educational Resources Information Center

He, Yong

2013-01-01

Common test items play an important role in equating multiple test forms under the common-item nonequivalent groups design. Inconsistent item parameter estimates among common items can lead to large bias in equated scores for IRT true score equating. Current methods extensively focus on detection and elimination of outlying common items, which…

Imaging of common breast implants and implant-related complications: A pictorial essay

PubMed Central

Shah, Amisha T; Jankharia, Bijal B

2016-01-01

The number of women undergoing breast implant procedures is increasing exponentially. It is, therefore, imperative for a radiologist to be familiar with the normal and abnormal imaging appearances of common breast implants. Diagnostic imaging studies such as mammography, ultrasonography, and magnetic resonance imaging are used to evaluate implant integrity, detect abnormalities of the implant and its surrounding capsule, and detect breast conditions unrelated to implants. Magnetic resonance imaging of silicone breast implants, with its high sensitivity and specificity for detecting implant rupture, is the most reliable modality to asses implant integrity. Whichever imaging modality is used, the overall aim of imaging breast implants is to provide the pertinent information about implant integrity, detect implant failures, and to detect breast conditions unrelated to the implants, such as cancer. PMID:27413269

Imaging of common breast implants and implant-related complications: A pictorial essay.

PubMed

Shah, Amisha T; Jankharia, Bijal B

2016-01-01

The number of women undergoing breast implant procedures is increasing exponentially. It is, therefore, imperative for a radiologist to be familiar with the normal and abnormal imaging appearances of common breast implants. Diagnostic imaging studies such as mammography, ultrasonography, and magnetic resonance imaging are used to evaluate implant integrity, detect abnormalities of the implant and its surrounding capsule, and detect breast conditions unrelated to implants. Magnetic resonance imaging of silicone breast implants, with its high sensitivity and specificity for detecting implant rupture, is the most reliable modality to asses implant integrity. Whichever imaging modality is used, the overall aim of imaging breast implants is to provide the pertinent information about implant integrity, detect implant failures, and to detect breast conditions unrelated to the implants, such as cancer.

Can hyperspectral remote sensing detect species specific biochemicals?

USDA-ARS?s Scientific Manuscript database

Discrimination of a few plants scattered among many plants is a goal common to detection of agricultural weeds and invasive species. Detection of clandestinely grown Cannabis sativa L. is in many ways a special case of weed detection. Remote sensing technology provides an automated, computer based,...

[Laser induced fluorescence spectrum characteristics of common edible oil and fried cooking oil].

PubMed

Mu, Tao-tao; Chen, Si-ying; Zhang, Yin-chao; Chen, He; Guo, Pan; Ge, Xian-ying; Gao, Li-lei

2013-09-01

In order to detect the trench oil the authors built a trench oil rapid detection system based on laser induced fluorescence detection technology. This system used 355 nm laser as excitation light source. The authors collected the fluorescence spectrum of a variety of edible oil and fried cooking oil (a kind of trench oil) and then set up a fluorescence spectrum database by taking advantage of the trench oil detection system It was found that the fluorescence characteristics of fried cooking oil and common edible oil were obviously different. Then it could easily realize the oil recognition and trench oil rapid detection by using principal component analysis and BP neural network, and the overall recognition rate could reach as high as 97.5%. Experiments showed that laser induced fluorescence spectrum technology was fast, non-contact, and highly sensitive. Combined with BP neural network, it would become a new technique to detect the trench oil.

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%.

Rapid detection of α-thalassaemia variants using droplet digital PCR.

PubMed

Lee, T-Y; Lai, M-I; Ramachandran, V; Tan, J A M A; Teh, L-K; Othman, R; Hussein, N H; George, E

2016-08-01

Alpha thalassaemia is a highly prevalent disease globally and is a well-known public health problem in Malaysia. The deletional forms of the mutation are the most common forms found in alpha thalassaemia. The three most common deletional alpha thalassaemia found in this region include --(SEA) deletion, -α(3.7) rightward and -α(4.2) leftward deletions. The prevalence rate of triplication alpha cases such as ααα(anti3.7) and ααα(anti4.2) is not known in Malaysia although it plays a role in exacerbating the clinical phenotypes in beta thalassaemia carriers. Recently, there have been more reported cases of rare alpha thalassaemia mutations due to the advancement of molecular techniques involved in thalassaemia detections. Therefore, it is essential to develop a new method which allows the detection of different alpha thalassaemia mutations including the rare ones simultaneously and accurately. The purpose of this study was to design an assay for the detection of triplications, common and rare deletional alpha thalassaemia using droplet digital PCR (ddPCR). This is a quantitative detection method to measure the changes of copy number which can detect deletions, duplications and triplications of the alpha globin gene simultaneously. In conclusion, ddPCR is an alternative method for rapid detection of alpha thalassaemia variants in Malaysia. © 2016 John Wiley & Sons Ltd.

Detection of nidoviruses in live pythons and boas.

PubMed

Marschang, Rachel E; Kolesnik, Ekaterina

2017-02-09

Nidoviruses have recently been described as a putative cause of severe respiratory disease in pythons in the USA and Europe. The objective of this study was to establish the use of a conventional PCR for the detection of nidoviruses in samples from live animals and to extend the list of susceptible species. A PCR targeting a portion of ORF1a of python nidoviruses was used to detect nidoviruses in diagnostic samples from live boas and pythons. A total of 95 pythons, 84 boas and 22 snakes of unknown species were included in the study. Samples tested included oral swabs and whole blood. Nidoviruses were detected in 27.4% of the pythons and 2.4% of the boas tested. They were most commonly detected in ball pythons (Python [P.] regius) and Indian rock pythons (P. molurus), but were also detected for the first time in other python species, including Morelia spp. and Boa constrictor. Oral swabs were most commonly tested positive. The PCR described here can be used for the detection of nidoviruses in oral swabs from live snakes. These viruses appear to be relatively common among snakes in captivity in Europe and screening for these viruses should be considered in the clinical work-up. Nidoviruses are believed to be an important cause of respiratory disease in pythons, but can also infect boas. Detection of these viruses in live animals is now possible and can be of interest both in diseased animals as well as in quarantine situations.

Estimating the Effects of Detection Heterogeneity and Overdispersion on Trends Estimated from Avian Point Counts

EPA Science Inventory

Point counts are a common method for sampling avian distribution and abundance. Though methods for estimating detection probabilities are available, many analyses use raw counts and do not correct for detectability. We use a removal model of detection within an N-mixture approa...

The use of PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) to detect bacterial and fungal colonization in healthy military service members.

PubMed

Vetor, Ryan; Murray, Clinton K; Mende, Katrin; Melton-Kreft, Rachel; Akers, Kevin S; Wenke, Joseph; Spirk, Tracy; Guymon, Charles; Zera, Wendy; Beckius, Miriam L; Schnaubelt, Elizabeth R; Ehrlich, Garth; Vento, Todd J

2016-07-22

The role of microbial colonization in disease is complex. Novel molecular tools to detect colonization offer theoretical improvements over traditional methods. We evaluated PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) as a screening tool to study colonization of healthy military service members. We assessed 101 healthy Soldiers using PCR/ESI-TOF-MS on nares, oropharynx, and groin specimens for the presence of gram-positive and gram-negative bacteria (GNB), fungi, and antibiotic resistance genes. A second set of swabs was processed by traditional culture, followed by identification using the BD Phoenix automated system; comparison between PCR/ESI-TOF-MS and culture was carried out only for GNB. Using PCR/ESI-TOF-MS, at least one colonizing organism was found on each individual: mean (SD) number of organisms per subject of 11.8(2.8). The mean number of organisms in the nares, groin and oropharynx was 3.8(1.3), 3.8(1.4) and 4.2(2), respectively. The most commonly detected organisms were aerobic gram-positive bacteria: primarily coagulase-negative Staphylococcus (101 subjects: 341 organisms), Streptococcus pneumoniae (54 subjects: 57 organisms), Staphylococcus aureus (58 subjects: 80 organisms) and Nocardia asteroides (45 subjects: 50 organisms). The mecA gene was found in 96 subjects. The most commonly found GNB was Haemophilus influenzae (20 subjects: 21 organisms) and the most common anaerobe was Propionibacterium acnes (59 subjects). Saccharomyces species (30 subjects) were the most common fungi detected. Only one GNB (nares E. coli) was identified in the same subject by both diagnostic systems. PCR/ESI-TOF-MS detected common colonizing organisms and identified more typically-virulent bacteria in asymptomatic, healthy adults. PCR/ESI-TOF-MS appears to be a useful method for detecting bacterial and fungal organisms, but further clinical correlation and validation studies are needed.

Extended linear detection range for optical tweezers using image-plane detection scheme

NASA Astrophysics Data System (ADS)

Hajizadeh, Faegheh; Masoumeh Mousavi, S.; Khaksar, Zeinab S.; Reihani, S. Nader S.

2014-10-01

Ability to measure pico- and femto-Newton range forces using optical tweezers (OT) strongly relies on the sensitivity of its detection system. We show that the commonly used back-focal-plane detection method provides a linear response range which is shorter than that of the restoring force of OT for large beads. This limits measurable force range of OT. We show, both theoretically and experimentally, that utilizing a second laser beam for tracking could solve the problem. We also propose a new detection scheme in which the quadrant photodiode is positioned at the plane optically conjugate to the object plane (image plane). This method solves the problem without need for a second laser beam for the bead sizes that are commonly used in force spectroscopy applications of OT, such as biopolymer stretching.

Development of an event-specific hydrolysis probe quantitative real-time polymerase chain reaction assay for Embrapa 5.1 genetically modified common bean (Phaseolus vulgaris).

PubMed

Treml, Diana; Venturelli, Gustavo L; Brod, Fábio C A; Faria, Josias C; Arisi, Ana C M

2014-12-10

A genetically modified (GM) common bean event, namely Embrapa 5.1, resistant to the bean golden mosaic virus (BGMV), was approved for commercialization in Brazil. Brazilian regulation for genetically modified organism (GMO) labeling requires that any food containing more than 1% GMO be labeled. The event-specific polymerase chain reaction (PCR) method has been the primary trend for GMO identification and quantitation because of its high specificity based on the flanking sequence. This work reports the development of an event-specific assay, named FGM, for Embrapa 5.1 detection and quantitation by use of SYBR Green or hydrolysis probe. The FGM assay specificity was tested for Embrapa 2.3 event (a noncommercial GM common bean also resistant to BGMV), 46 non-GM common bean varieties, and other crop species including maize, GM maize, soybean, and GM soybean. The FGM assay showed high specificity to detect the Embrapa 5.1 event. Standard curves for the FGM assay presented a mean efficiency of 95% and a limit of detection (LOD) of 100 genome copies in the presence of background DNA. The primers and probe developed are suitable for the detection and quantitation of Embrapa 5.1.

A negative association between bromadiolone exposure and nestling body condition in common kestrels: management implications for vole outbreaks.

PubMed

Martínez-Padilla, Jesús; López-Idiáquez, David; López-Perea, Jhon J; Mateo, Rafael; Paz, Alfonso; Viñuela, Javier

2017-02-01

Vole outbreaks have been extensively described, along with their impacts on humans, particularly in agricultural areas. The use of rodenticides is a common legal practice to minimise crop damage induced by high vole density for biocidal use. However, rodenticides can have negative direct and indirect impacts on non-target species that feed on voles. We studied whether the use of a second-generation anticoagulant rodenticide (SGAR), bromadiolone, can be detected in the blood of fledglings of wild common kestrels Falco tinnunculus in two areas of central Spain, exploring its possible indirect effects. We found that 16.9% of fledglings had a detectable concentration of bromadiolone in their blood, with an average concentration of 0.248 ± 0.023 ng mL -1 . Fledglings with bromadiolone in their blood, regardless of the concentration, had 6.7% lower body mass than those without detectable bromadiolone. The use of bromadiolone was detectable in the blood of alive non-target species. Detected bromadiolone in blood may reduce the body condition of nestlings, potentially reducing their fitness. The source of bromadiolone found in nestlings needs to be determined in future studies to derive accurate management advice. However, we urge the discontinuation of official SGAR distribution to farmers and their use in agrarian lands to minimise damage of voles on crops, particularly where common kestrels breed, and encourage the use of alternative effective practices. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Simultaneous Detection of Both RNA and DNA Viruses Infecting Dry Bean and Occurrence of Mixed Infections by BGYMV, BCMV and BCMNV in the Central-West Region of Mexico

PubMed Central

Chiquito-Almanza, Elizabeth; Acosta-Gallegos, Jorge A.; García-Álvarez, Nadia C.; Garrido-Ramírez, Eduardo R.; Montero-Tavera, Victor; Guevara-Olvera, Lorenzo; Anaya-López, José L.

2017-01-01

A multiplex reverse transcription polymerase chain reaction (RT-PCR) assay was developed to simultaneously detect bean common mosaic virus (BCMV), bean common mosaic necrotic virus (BCMNV), and bean golden yellow mosaic virus (BGYMV) from common bean leaves dried with silica gel using a single total nucleic acid extraction cetyl trimethyl ammonium bromide (CTAB) method. A mixture of five specific primers was used to amplify three distinct fragments corresponding to 272 bp from the AC1 gene of BGYMV as well as 469 bp and 746 bp from the CP gene of BCMV and BCMNV, respectively. The three viruses were detected in a single plant or in a bulk of five plants. The multiplex RT-PCR was successfully applied to detect these three viruses from 187 field samples collected from 23 municipalities from the states of Guanajuato, Nayarit and Jalisco, Mexico. Rates of single infections were 14/187 (7.5%), 41/187 (21.9%), and 35/187 (18.7%), for BGYMV, BCMV, and BCMNV, respectively; 29/187 (15.5%) samples were co-infected with two of these viruses and 10/187 (5.3%) with the three viruses. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting these viruses in the common bean and can be used for routine molecular diagnosis and epidemiological studies. PMID:28358318

Using a Linear Regression Method to Detect Outliers in IRT Common Item Equating

ERIC Educational Resources Information Center

He, Yong; Cui, Zhongmin; Fang, Yu; Chen, Hanwei

2013-01-01

Common test items play an important role in equating alternate test forms under the common item nonequivalent groups design. When the item response theory (IRT) method is applied in equating, inconsistent item parameter estimates among common items can lead to large bias in equated scores. It is prudent to evaluate inconsistency in parameter…

Detection probability of cliff-nesting raptors during helicopter and fixed-wing aircraft surveys in western Alaska

USGS Publications Warehouse

Booms, T.L.; Schempf, P.F.; McCaffery, B.J.; Lindberg, M.S.; Fuller, M.R.

2010-01-01

We conducted repeated aerial surveys for breeding cliff-nesting raptors on the Yukon Delta National Wildlife Refuge (YDNWR) in western Alaska to estimate detection probabilities of Gyrfalcons (Falco rusticolus), Golden Eagles (Aquila chrysaetos), Rough-legged Hawks (Buteo lagopus), and also Common Ravens (Corvus corax). Using the program PRESENCE, we modeled detection histories of each species based on single species occupancy modeling. We used different observers during four helicopter replicate surveys in the Kilbuck Mountains and five fixed-wing replicate surveys in the Ingakslugwat Hills near Bethel, AK. During helicopter surveys, Gyrfalcons had the highest detection probability estimate (p^;p^ 0.79; SE 0.05), followed by Golden Eagles (p^=0.68; SE 0.05), Common Ravens (p^=0.45; SE 0.17), and Rough-legged Hawks (p^=0.10; SE 0.11). Detection probabilities from fixed-wing aircraft in the Ingakslugwat Hills were similar to those from the helicopter in the Kilbuck Mountains for Gyrfalcons and Golden Eagles, but were higher for Common Ravens (p^=0.85; SE 0.06) and Rough-legged Hawks (p^=0.42; SE 0.07). Fixed-wing aircraft provided detection probability estimates and SEs in the Ingakslugwat Hills similar to or better than those from helicopter surveys in the Kilbucks and should be considered for future cliff-nesting raptor surveys where safe, low-altitude flight is possible. Overall, detection probability varied by observer experience and in some cases, by study area/aircraft type.

Organic Compounds in Potomac River Water Used for Public Supply near Washington, D.C., 2003-05

USGS Publications Warehouse

Brayton, Michael J.; Denver, Judith M.; Delzer, Gregory C.; Hamilton, Pixie A.

2008-01-01

Organic compounds studied in this U.S. Geological Survey (USGS) assessment generally are man-made, including, in part, pesticides, solvents, gasoline hydrocarbons, personal care and domestic-use products, and refrigerants and propellants. A total of 85 of 277 compounds were detected at least once among the 25 samples collected approximately monthly during 2003-05 at the intake of the Washington Aqueduct, one of several community water systems on the Potomac River upstream from Washington, D.C. The diversity of compounds detected indicate a variety of different sources and uses (including wastewater discharge, industrial, agricultural, domestic, and others) and different pathways (including treated wastewater outfalls located upstream, overland runoff, and ground-water discharge) to drinking-water supplies. Seven compounds were detected year-round in source-water intake samples, including selected herbicide compounds commonly used in the Potomac River Basin and in other agricultural areas across the United States. Two-thirds of the 26 compounds detected most commonly in source water (in at least 20 percent of the samples) also were detected most commonly in finished water (after treatment but prior to distribution). Concentrations for all detected compounds in source and finished water generally were less than 0.1 microgram per liter and always less than human-health benchmarks, which are available for about one-half of the detected compounds. On the basis of this screening-level assessment, adverse effects to human health are expected to be negligible (subject to limitations of available human-health benchmarks).

Detecting Signals of Disproportionate Reporting from Singapore's Spontaneous Adverse Event Reporting System: An Application of the Sequential Probability Ratio Test.

PubMed

Chan, Cheng Leng; Rudrappa, Sowmya; Ang, Pei San; Li, Shu Chuen; Evans, Stephen J W

2017-08-01

The ability to detect safety concerns from spontaneous adverse drug reaction reports in a timely and efficient manner remains important in public health. This paper explores the behaviour of the Sequential Probability Ratio Test (SPRT) and ability to detect signals of disproportionate reporting (SDRs) in the Singapore context. We used SPRT with a combination of two hypothesised relative risks (hRRs) of 2 and 4.1 to detect signals of both common and rare adverse events in our small database. We compared SPRT with other methods in terms of number of signals detected and whether labelled adverse drug reactions were detected or the reaction terms were considered serious. The other methods used were reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN) and Gamma Poisson Shrinker (GPS). The SPRT produced 2187 signals in common with all methods, 268 unique signals, and 70 signals in common with at least one other method, and did not produce signals in 178 cases where two other methods detected them, and there were 403 signals unique to one of the other methods. In terms of sensitivity, ROR performed better than other methods, but the SPRT method found more new signals. The performances of the methods were similar for negative predictive value and specificity. Using a combination of hRRs for SPRT could be a useful screening tool for regulatory agencies, and more detailed investigation of the medical utility of the system is merited.

Prenatal diagnosis of fetuses with increased nuchal translucency using an approach based on quantitative fluorescent polymerase chain reaction and genomic microarray.

PubMed

Pan, Min; Han, Jin; Zhen, Li; Yang, Xin; Li, Ru; Liao, Can; Li, Dong-Zhi

2016-02-01

To assess the clinical value of prenatal diagnosis of fetuses with increased nuchal translucency (NT) using an approach based on quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray (CMA). From January 2013 to October 2014, we included 175 pregnancies with fetal NT ≥ 3.5mm at 11-13 weeks' gestation who received chorionic villus sampling. QF-PCR was first used to rapidly detect common aneuploidies. The cases with a normal QF-PCR result were analyzed by CMA. Of the 175 cases, common aneuploidies were detected by QF-PCR in 53 (30.2%) cases (30 cases of trisomy 21, 12 cases of monosomy X, 7 cases of trisomy 18, 3 cases of trisomy 13 and 1 case of 47, XXY). Among the 122 cases with a normal QF-PCR result, microarray detected additional pathogenic copy number variants (CNVs) in 5.7% (7/122) of cases. Four cases would have expected to be detectable by conventional karyotyping because of large deletions/duplications (>10 Mb), leaving three cases (2.5%; 3/118) with pathogenic CNVs only detectable by CMA. It is rational to use a diagnostic strategy in which CMA is preceded by the less expensive, rapid, QF-PCR to detect common aneuploidies. CMA allows detection of a number of pathogenic chromosomal aberrations in fetuses with a high NT. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Serum paraquat concentration detected by spectrophotometry in patients with paraquat poisoning

PubMed Central

Li, Chang-bin; Li, Xin-hua; Wang, Zhen; Jiang, Cheng-hua; Peng, Ai

2011-01-01

BACKGROUND: Paraquat (PQ) is a world-wide used herbicide and also a type of common poison for suicide and accidental poisoning. Numerous studies have proved that the concentration of serum PQ plays an important role in prognosis. Spectrophotometry, including common spectrophotometry and second-derivative spectrophotometry, is commonly used for PQ detection in primary hospitals. So far, lack of systematic research on the reliability of the method and the correlation between clinical features of patients with PQ poisoning and the test results has restricted the clinical use of spectrophotometry. This study aimed to evaluate the reliability and value of spectrophotometry in detecting the concentration of serum PQ. METHODS: The wavelengths for detecting the concentration of serum PQ by common and second-derivative spectrophotometry were determined. Second-derivative spectrophotometry was applied to detect the concentration of serum PQ. The linear range and precision for detection of PQ concentration by this method were confirmed. The concentration of serum PQ shown by second-derivative spectrophotometry and HPLC were compared in 8 patients with PQ poisoning. Altogether 21 patients with acute poisoning 4 hours after PQ ingestion treated in the period of October 2008 to September 2010 were retrospectively reviewed. The patients were divided into higher and lower than 1.8 μg/mL groups based on their concentrations of serum PQ measured by second-derivative spectrophotometry on admission. The severity of clinical manifestations between the two groups were analyzed with Student's t test or Fisher's exact test. RESULTS: The absorption peak of 257 nm could not be found when common spectrophotometry was used to detect the PQ concentration in serum. The calibration curve in the 0.4–8.0 μg/mL range for PQ concentration shown by second-derivative spectrophotometry obeyed Beer's law with r=0.996. The average recovery rates of PQ were within a range of 95.0% to 99.5%, relative standard deviation (RSD) was within 1.35% to 5.41% (n=6), and the lower detection limit was 0.05 μg/mL. The PQ concentrations in serum of 8 patients with PQ poisoning shown by second-derivative spectrophotometry were consistent with the quantitative determinations by HPLC (r=0.995, P<0.0001). The survival rate was 22.2% in patients whose PQ concentration in serum was more than 1.8 μg/mL, and the incidences of acidosis, oliguria and pneumomediastinum in these patients were 55.6%, 55.6% and 77.8%, respectively. These clinical manifestations were different significantly from those of the patients whose PQ concentration in serum was less than 1.8 μg/mL (P<0.05). CONCLUSIONS: For common spectrophotometry, the wavelength at 257 nm was not suitable for detecting serum PQ as no absorbance was shown. Second-derivative spectrophotometry was reliable for detecting serum paraquat concentration. Serum PQ concentration detected by second-derivative spectrophotometry could be used to predict the severity of clinical manifestations of patients with PQ poisoning, and PQ content higher than 1.8 μg/mL 4 hours after ingestion could be an important predictive factor for poor prognosis. PMID:25215006

Magnetic resonance imaging in the new paradigm for the diagnosis of prostate cancer.

PubMed

Vilanova, J C; Catalá, V

For various reasons, prostate cancer is a major public health problem. It is a very common cancer, but has a very low mortality rate because it comprises two types of disease: one insignificant, indolent, and much more common, and the other aggressive, significant, and much less common. The routine diagnostic approach to prostate cancer has been systematic blind biopsies, which has low detection rates and might detect low risk, insignificant prostate cancer, leading to overdiagnosis and overtreatment of indolent cancers. The possibility of including multiparametric magnetic resonance imaging in the diagnostic management to improve the detection of aggressive cancer while reducing the overdiagnosis of indolent cancer represents a change in the diagnostic management. This article updates knowledge about the diagnostic management of prostate cancer including multiparametric magnetic resonance imaging. Copyright © 2016 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

Bioassays of quorum sensing compounds using Agrobacterium tumefaciens and Chromobacterium violaceum.

PubMed

Chu, Weihua; Vattem, Dhiraj A; Maitin, Vatsala; Barnes, Mary B; McLean, Robert J C

2011-01-01

In most bacteria, a global level of regulation exists involving intercellular communication via the production and response to cell density-dependent signal molecules. This cell density-dependent regulation has been termed quorum sensing (QS). QS is a global regulator, which has been associated with a number of important features in bacteria including virulence regulation and biofilm formation. Consequently, there is considerable interest in understanding, detecting, and inhibiting QS. Acyl homoserine lactones (acyl HSLs) are used as extracellular QS signals by a variety of Gram-negative bacteria. Chromobacterium violaceum, a Gram-negative bacterium commonly found in soil and water, produces the characteristic purple pigment violacein, the production of which is regulated by acyl HSL-mediated QS. Based on this readily observed pigmentation phenotype, C. violaceum strains can be used to detect various aspects of acyl HSL-mediated QS activity. In another commonly used bioassay organism, Agrobacterium tumefaciens, QS can be detected by the use of a reporter gene such as lacZ. Here, we describe several commonly used approaches incorporating C. violaceum and A. tumefaciens that can be used to detect acyl HSLs and QS inhibition.

Organic Compounds in Clackamas River Water Used for Public Supply near Portland, Oregon, 2003-05

USGS Publications Warehouse

Carpenter, Kurt D.; McGhee, Gordon

2009-01-01

Organic compounds studied in this U.S. Geological Survey (USGS) assessment generally are man-made, including pesticides, gasoline hydrocarbons, solvents, personal care and domestic-use products, disinfection by-products, and manufacturing additives. In all, 56 compounds were detected in samples collected approximately monthly during 2003-05 at the intake for the Clackamas River Water plant, one of four community water systems on the lower Clackamas River. The diversity of compounds detected suggests a variety of different sources and uses (including wastewater discharges, industrial, agricultural, domestic, and others) and different pathways to drinking-water supplies (point sources, precipitation, overland runoff, ground-water discharge, and formation during water treatment). A total of 20 organic compounds were commonly detected (in at least 20 percent of the samples) in source water and (or) finished water. Fifteen compounds were commonly detected in source water, and five of these compounds (benzene, m- and p-xylene, diuron, simazine, and chloroform) also were commonly detected in finished water. With the exception of gasoline hydrocarbons, disinfection by-products, chloromethane, and the herbicide diuron, concentrations in source and finished water were less than 0.1 microgram per liter and always less than human-health benchmarks, which are available for about 60 percent of the compounds detected. On the basis of this screening-level assessment, adverse effects to human health are assumed to be negligible (subject to limitations of available human-health benchmarks).

Enhanced Detectability of Community Structure in Multilayer Networks through Layer Aggregation.

PubMed

Taylor, Dane; Shai, Saray; Stanley, Natalie; Mucha, Peter J

2016-06-03

Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different, but potentially related, types of interactions, and it is important to understand limitations on the detectability of community structure in these networks. Using random matrix theory, we analyze detectability limitations for multilayer (specifically, multiplex) stochastic block models (SBMs) in which L layers are derived from a common SBM. We study the effect of layer aggregation on detectability for several aggregation methods, including summation of the layers' adjacency matrices for which we show the detectability limit vanishes as O(L^{-1/2}) with increasing number of layers, L. Importantly, we find a similar scaling behavior when the summation is thresholded at an optimal value, providing insight into the common-but not well understood-practice of thresholding pairwise-interaction data to obtain sparse network representations.

"Utilizing" signal detection theory.

PubMed

Lynn, Spencer K; Barrett, Lisa Feldman

2014-09-01

What do inferring what a person is thinking or feeling, judging a defendant's guilt, and navigating a dimly lit room have in common? They involve perceptual uncertainty (e.g., a scowling face might indicate anger or concentration, for which different responses are appropriate) and behavioral risk (e.g., a cost to making the wrong response). Signal detection theory describes these types of decisions. In this tutorial, we show how incorporating the economic concept of utility allows signal detection theory to serve as a model of optimal decision making, going beyond its common use as an analytic method. This utility approach to signal detection theory clarifies otherwise enigmatic influences of perceptual uncertainty on measures of decision-making performance (accuracy and optimality) and on behavior (an inverse relationship between bias magnitude and sensitivity optimizes utility). A "utilized" signal detection theory offers the possibility of expanding the phenomena that can be understood within a decision-making framework. © The Author(s) 2014.

“UTILIZING” SIGNAL DETECTION THEORY

PubMed Central

Lynn, Spencer K.; Barrett, Lisa Feldman

2014-01-01

What do inferring what a person is thinking or feeling, deciding to report a symptom to your doctor, judging a defendant’s guilt, and navigating a dimly lit room have in common? They involve perceptual uncertainty (e.g., a scowling face might indicate anger or concentration, which engender different appropriate responses), and behavioral risk (e.g., a cost to making the wrong response). Signal detection theory describes these types of decisions. In this tutorial we show how, by incorporating the economic concept of utility, signal detection theory serves as a model of optimal decision making, beyond its common use as an analytic method. This utility approach to signal detection theory highlights potentially enigmatic influences of perceptual uncertainty on measures of decision-making performance (accuracy and optimality) and on behavior (a functional relationship between bias and sensitivity). A “utilized” signal detection theory offers the possibility of expanding the phenomena that can be understood within a decision-making framework. PMID:25097061

Automatic detection of typical dust devils from Mars landscape images

NASA Astrophysics Data System (ADS)

Ogohara, Kazunori; Watanabe, Takeru; Okumura, Susumu; Hatanaka, Yuji

2018-02-01

This paper presents an improved algorithm for automatic detection of Martian dust devils that successfully extracts tiny bright dust devils and obscured large dust devils from two subtracted landscape images. These dust devils are frequently observed using visible cameras onboard landers or rovers. Nevertheless, previous research on automated detection of dust devils has not focused on these common types of dust devils, but on dust devils that appear on images to be irregularly bright and large. In this study, we detect these common dust devils automatically using two kinds of parameter sets for thresholding when binarizing subtracted images. We automatically extract dust devils from 266 images taken by the Spirit rover to evaluate our algorithm. Taking dust devils detected by visual inspection to be ground truth, the precision, recall and F-measure values are 0.77, 0.86, and 0.81, respectively.

VarDetect: a nucleotide sequence variation exploratory tool

PubMed Central

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

2008-01-01

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

Value of multiplex PCR to determine the bacterial and viral aetiology of pneumonia in school-age children.

PubMed

Aydemir, Yusuf; Aydemir, Özlem; Pekcan, Sevgi; Özdemir, Mehmet

2017-02-01

Conventional methods for the aetiological diagnosis of community-acquired pneumonia (CAP) are often insufficient owing to low sensitivity and the long wait for the results of culture and particularly serology, and it often these methods establish a diagnosis in only half of cases. To evaluate the most common bacterial and viral agents in CAP using a fast responsive PCR method and investigate the relationship between clinical/laboratory features and aetiology, thereby contributing to empirical antibiotic selection and reduction of treatment failure. In children aged 4-15 years consecutively admitted with a diagnosis of CAP, the 10 most commonly detected bacterial and 12 most commonly detected viral agents were investigated by induced sputum using bacterial culture and multiplex PCR methods. Clinical and laboratory features were compared between bacterial and viral pneumonia. In 78 patients, at least one virus was detected in 38 (48.7%) and at least one bacterium in 32 (41%). In addition, both bacteria and viruses were detected in 16 (20.5%) patients. Overall, the agent detection rate was 69.2%. The most common viruses were respiratory syncytial virus and influenza and the most frequently detected bacteria were S. pneumoniae and H. influenzae. PCR was superior to culture for bacterial isolation (41% vs 13%, respectively). Fever, wheezing and radiological features were not helpful in differentiating between bacterial and viral CAP. White blood cell count, CRP and ESR values were significantly higher in the bacterial/mixed aetiology group than in the viral aetiology group. In CAP, multiplex PCR is highly reliable, superior in detecting multiple pathogens and rapidly identifies aetiological agents. Clinical features are poor for differentiation between bacterial and viral infections. The use of PCR methods allow physicians to provide more appropriate antimicrobial therapy, resulting in a better response to treatment, and it may be possible for use as a routine service if costs can be reduced.

Capturing and Displaying Uncertainty in the Common Tactical/Environmental Picture

DTIC Science & Technology

2003-09-30

multistatic active detection, and incorporated this characterization into a Bayesian track - before - detect system called, the Likelihood Ratio Tracker (LRT...prediction uncertainty in a track before detect system for multistatic active sonar. The approach has worked well on limited simulation data. IMPACT

The importance of cone beam CT in the radiological detection of osteomalacia.

PubMed

Cakur, B; Sümbüllü, M A; Dagistan, S; Durna, D

2012-01-01

Although osteomalacia is one of the most common osteometabolic diseases among the elderly, there is no case in the literature that presents the effects of osteomalacia in detail using cone beam CT (CBCT). While thin and porous bones are the most common radiographic sign of the disease, the radiological hallmarks are pseudofractures (Looser's zone). We coincidentally detected osteomalacia in a 23-year-old female and we showed the pseudofracture on CBCT images. In the present case, we aim to present the images of osteomalacia that were detected by CBCT in detail. CBCT has an important value in screening for osteomalacia.

The importance of cone beam CT in the radiological detection of osteomalacia

PubMed Central

Çakur, B; Sümbüllü, M A; Dağistan, S; Durna, D

2012-01-01

Although osteomalacia is one of the most common osteometabolic diseases among the elderly, there is no case in the literature that presents the effects of osteomalacia in detail using cone beam CT (CBCT). While thin and porous bones are the most common radiographic sign of the disease, the radiological hallmarks are pseudofractures (Looser's zone). We coincidentally detected osteomalacia in a 23-year-old female and we showed the pseudofracture on CBCT images. In the present case, we aim to present the images of osteomalacia that were detected by CBCT in detail. CBCT has an important value in screening for osteomalacia. PMID:22074877

Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

PubMed Central

Mee, Edward T.; Preston, Mark D.; Minor, Philip D.; Schepelmann, Silke; Huang, Xuening; Nguyen, Jenny; Wall, David; Hargrove, Stacey; Fu, Thomas; Xu, George; Li, Li; Cote, Colette; Delwart, Eric; Li, Linlin; Hewlett, Indira; Simonyan, Vahan; Ragupathy, Viswanath; Alin, Voskanian-Kordi; Mermod, Nicolas; Hill, Christiane; Ottenwälder, Birgit; Richter, Daniel C.; Tehrani, Arman; Jacqueline, Weber-Lehmann; Cassart, Jean-Pol; Letellier, Carine; Vandeputte, Olivier; Ruelle, Jean-Louis; Deyati, Avisek; La Neve, Fabio; Modena, Chiara; Mee, Edward; Schepelmann, Silke; Preston, Mark; Minor, Philip; Eloit, Marc; Muth, Erika; Lamamy, Arnaud; Jagorel, Florence; Cheval, Justine; Anscombe, Catherine; Misra, Raju; Wooldridge, David; Gharbia, Saheer; Rose, Graham; Ng, Siemon H.S.; Charlebois, Robert L.; Gisonni-Lex, Lucy; Mallet, Laurent; Dorange, Fabien; Chiu, Charles; Naccache, Samia; Kellam, Paul; van der Hoek, Lia; Cotten, Matt; Mitchell, Christine; Baier, Brian S.; Sun, Wenping; Malicki, Heather D.

2016-01-01

Background Unbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity. Methods A common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay. Results Fifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories. Conclusion The study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories. PMID:26709640

Portable thin layer chromatography for field detection of explosives and propellants

NASA Astrophysics Data System (ADS)

Satcher, Joe H.; Maienschein, Jon L.; Pagoria, Philip F.; Racoveanu, Ana; Carman, M. Leslie; Whipple, Richard E.; Reynolds, John G.

2012-06-01

A field deployable detection kit for explosives and propellants using thin layer chromatography (TLC) has been developed at Lawrence Livermore National Laboratory (LLNL). The chemistry of the kit has been modified to allow for field detection of propellants (through propellant stabilizers), military explosives, peroxide explosives, nitrates and inorganic oxidizer precursors. For many of these target analytes, the detection limit is in the μg to pg range. A new miniaturized, bench prototype, field portable TLC (Micro TLC) kit has also been developed for the detection and identification of common military explosives. It has been demonstrated in a laboratory environment and is ready for field-testing. The kit is comprised of a low cost set of commercially available components specifically assembled for rapid identification needed in the field and identifies the common military explosives: HMX, RDX, Tetryl, Explosive D or picric acid, and TNT all on one plate. Additional modifications of the Micro TLC system have been made with fluorescent organosilicon co-polymer coatings to detect a large suite of explosives.

A Comparison of Source Code Plagiarism Detection Engines

NASA Astrophysics Data System (ADS)

Lancaster, Thomas; Culwin, Fintan

2004-06-01

Automated techniques for finding plagiarism in student source code submissions have been in use for over 20 years and there are many available engines and services. This paper reviews the literature on the major modern detection engines, providing a comparison of them based upon the metrics and techniques they deploy. Generally the most common and effective techniques are seen to involve tokenising student submissions then searching pairs of submissions for long common substrings, an example of what is defined to be a paired structural metric. Computing academics are recommended to use one of the two Web-based detection engines, MOSS and JPlag. It is shown that whilst detection is well established there are still places where further research would be useful, particularly where visual support of the investigation process is possible.

Emergence of carp edema virus (CEV) and its significance to European common carp and koi Cyprinus carpio.

PubMed

Way, K; Haenen, O; Stone, D; Adamek, M; Bergmann, S M; Bigarré, L; Diserens, N; El-Matbouli, M; Gjessing, M C; Jung-Schroers, V; Leguay, E; Matras, M; Olesen, N J; Panzarin, V; Piačková, V; Toffan, A; Vendramin, N; Vesel, T; Waltzek, T

2017-10-18

Carp edema virus disease (CEVD), also known as koi sleepy disease, is caused by a poxvirus associated with outbreaks of clinical disease in koi and common carp Cyprinus carpio. Originally characterised in Japan in the 1970s, international trade in koi has led to the spread of CEV, although the first recognised outbreak of the disease outside of Japan was not reported until 1996 in the USA. In Europe, the disease was first recognised in 2009 and, as detection and diagnosis have improved, more EU member states have reported CEV associated with disease outbreaks. Although the structure of the CEV genome is not yet elucidated, molecular epidemiology studies have suggested distinct geographical populations of CEV infecting both koi and common carp. Detection and identification of cases of CEVD in common carp were unreliable using the original PCR primers. New primers for conventional and quantitative PCR (qPCR) have been designed that improve detection, and their sequences are provided in this paper. The qPCR primers have successfully detected CEV DNA in archive material from investigations of unexplained carp mortalities conducted >15 yr ago. Improvement in disease management and control is possible, and the principles of biosecurity, good health management and disease surveillance, applied to koi herpesvirus disease, can be equally applied to CEVD. However, further research studies are needed to fill the knowledge gaps in the disease pathogenesis and epidemiology that, currently, prevent an accurate assessment of the likely impact of CEVD on European koi and common carp aquaculture and on wild carp stocks.

Rapid Target Detection in High Resolution Remote Sensing Images Using Yolo Model

NASA Astrophysics Data System (ADS)

Wu, Z.; Chen, X.; Gao, Y.; Li, Y.

2018-04-01

Object detection in high resolution remote sensing images is a fundamental and challenging problem in the field of remote sensing imagery analysis for civil and military application due to the complex neighboring environments, which can cause the recognition algorithms to mistake irrelevant ground objects for target objects. Deep Convolution Neural Network(DCNN) is the hotspot in object detection for its powerful ability of feature extraction and has achieved state-of-the-art results in Computer Vision. Common pipeline of object detection based on DCNN consists of region proposal, CNN feature extraction, region classification and post processing. YOLO model frames object detection as a regression problem, using a single CNN predicts bounding boxes and class probabilities in an end-to-end way and make the predict faster. In this paper, a YOLO based model is used for object detection in high resolution sensing images. The experiments on NWPU VHR-10 dataset and our airport/airplane dataset gain from GoogleEarth show that, compare with the common pipeline, the proposed model speeds up the detection process and have good accuracy.

Personalized features for attention detection in children with Attention Deficit Hyperactivity Disorder.

PubMed

Fahimi, Fatemeh; Guan, Cuntai; Wooi Boon Goh; Kai Keng Ang; Choon Guan Lim; Tih Shih Lee

2017-07-01

Measuring attention from electroencephalogram (EEG) has found applications in the treatment of Attention Deficit Hyperactivity Disorder (ADHD). It is of great interest to understand what features in EEG are most representative of attention. Intensive research has been done in the past and it has been proven that frequency band powers and their ratios are effective features in detecting attention. However, there are still unanswered questions, like, what features in EEG are most discriminative between attentive and non-attentive states? Are these features common among all subjects or are they subject-specific and must be optimized for each subject? Using Mutual Information (MI) to perform subject-specific feature selection on a large data set including 120 ADHD children, we found that besides theta beta ratio (TBR) which is commonly used in attention detection and neurofeedback, the relative beta power and theta/(alpha+beta) (TBAR) are also equally significant and informative for attention detection. Interestingly, we found that the relative theta power (which is also commonly used) may not have sufficient discriminative information itself (it is informative only for 3.26% of ADHD children). We have also demonstrated that although these features (relative beta power, TBR and TBAR) are the most important measures to detect attention on average, different subjects have different set of most discriminative features.

Experimental evidence that primate trichromacy is well suited for detecting primate social colour signals.

PubMed

Hiramatsu, Chihiro; Melin, Amanda D; Allen, William L; Dubuc, Constance; Higham, James P

2017-06-14

Primate trichromatic colour vision has been hypothesized to be well tuned for detecting variation in facial coloration, which could be due to selection on either signal wavelengths or the sensitivities of the photoreceptors themselves. We provide one of the first empirical tests of this idea by asking whether, when compared with other visual systems, the information obtained through primate trichromatic vision confers an improved ability to detect the changes in facial colour that female macaque monkeys exhibit when they are proceptive. We presented pairs of digital images of faces of the same monkey to human observers and asked them to select the proceptive face. We tested images that simulated what would be seen by common catarrhine trichromatic vision, two additional trichromatic conditions and three dichromatic conditions. Performance under conditions of common catarrhine trichromacy, and trichromacy with narrowly separated LM cone pigments (common in female platyrrhines), was better than for evenly spaced trichromacy or for any of the dichromatic conditions. These results suggest that primate trichromatic colour vision confers excellent ability to detect meaningful variation in primate face colour. This is consistent with the hypothesis that social information detection has acted on either primate signal spectral reflectance or photoreceptor spectral tuning, or both. © 2017 The Authors.

Experimental evidence that primate trichromacy is well suited for detecting primate social colour signals

PubMed Central

Higham, James P.

2017-01-01

Primate trichromatic colour vision has been hypothesized to be well tuned for detecting variation in facial coloration, which could be due to selection on either signal wavelengths or the sensitivities of the photoreceptors themselves. We provide one of the first empirical tests of this idea by asking whether, when compared with other visual systems, the information obtained through primate trichromatic vision confers an improved ability to detect the changes in facial colour that female macaque monkeys exhibit when they are proceptive. We presented pairs of digital images of faces of the same monkey to human observers and asked them to select the proceptive face. We tested images that simulated what would be seen by common catarrhine trichromatic vision, two additional trichromatic conditions and three dichromatic conditions. Performance under conditions of common catarrhine trichromacy, and trichromacy with narrowly separated LM cone pigments (common in female platyrrhines), was better than for evenly spaced trichromacy or for any of the dichromatic conditions. These results suggest that primate trichromatic colour vision confers excellent ability to detect meaningful variation in primate face colour. This is consistent with the hypothesis that social information detection has acted on either primate signal spectral reflectance or photoreceptor spectral tuning, or both. PMID:28615496

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens.

PubMed

Raja, B; Goux, H J; Marapadaga, A; Rajagopalan, S; Kourentzi, K; Willson, R C

2017-08-01

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens. The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection. The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established. Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens. © 2017 The Society for Applied Microbiology.

46 CFR 113.10-5 - Common return.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 4 2011-10-01 2011-10-01 false Common return. 113.10-5 Section 113.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING COMMUNICATION AND ALARM SYSTEMS AND EQUIPMENT Fire and Smoke Detecting and Alarm Systems § 113.10-5 Common return. A conductor...

46 CFR 113.10-5 - Common return.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 4 2014-10-01 2014-10-01 false Common return. 113.10-5 Section 113.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING COMMUNICATION AND ALARM SYSTEMS AND EQUIPMENT Fire and Smoke Detecting and Alarm Systems § 113.10-5 Common return. A conductor...

46 CFR 113.10-5 - Common return.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Common return. 113.10-5 Section 113.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING COMMUNICATION AND ALARM SYSTEMS AND EQUIPMENT Fire and Smoke Detecting and Alarm Systems § 113.10-5 Common return. A conductor...

46 CFR 113.10-5 - Common return.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 4 2012-10-01 2012-10-01 false Common return. 113.10-5 Section 113.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING COMMUNICATION AND ALARM SYSTEMS AND EQUIPMENT Fire and Smoke Detecting and Alarm Systems § 113.10-5 Common return. A conductor...

46 CFR 113.10-5 - Common return.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 4 2013-10-01 2013-10-01 false Common return. 113.10-5 Section 113.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING COMMUNICATION AND ALARM SYSTEMS AND EQUIPMENT Fire and Smoke Detecting and Alarm Systems § 113.10-5 Common return. A conductor...

CT Colonography with Computer-aided Detection: Recognizing the Causes of False-Positive Reader Results

PubMed Central

Dachman, Abraham H.; Wroblewski, Kristen; Vannier, Michael W.; Horne, John M.

2014-01-01

Computed tomography (CT) colonography is a screening modality used to detect colonic polyps before they progress to colorectal cancer. Computer-aided detection (CAD) is designed to decrease errors of detection by finding and displaying polyp candidates for evaluation by the reader. CT colonography CAD false-positive results are common and have numerous causes. The relative frequency of CAD false-positive results and their effect on reader performance on the basis of a 19-reader, 100-case trial shows that the vast majority of CAD false-positive results were dismissed by readers. Many CAD false-positive results are easily disregarded, including those that result from coarse mucosa, reconstruction, peristalsis, motion, streak artifacts, diverticulum, rectal tubes, and lipomas. CAD false-positive results caused by haustral folds, extracolonic candidates, diminutive lesions (<6 mm), anal papillae, internal hemorrhoids, varices, extrinsic compression, and flexural pseudotumors are almost always recognized and disregarded. The ileocecal valve and tagged stool are common sources of CAD false-positive results associated with reader false-positive results. Nondismissable CAD soft-tissue polyp candidates larger than 6 mm are another common cause of reader false-positive results that may lead to further evaluation with follow-up CT colonography or optical colonoscopy. Strategies for correctly evaluating CAD polyp candidates are important to avoid pitfalls from common sources of CAD false-positive results. ©RSNA, 2014 PMID:25384290

Presence of selected chemicals of emerging concern in water and bottom sediment from the St. Louis River, St. Louis Bay, and Superior Bay, Minnesota and Wisconsin, 2010

USGS Publications Warehouse

Christensen, Victoria G.; Lee, Kathy E.; Kieta, Kristen A.; Elliott, Sarah M.

2012-01-01

The St. Louis Bay of Lake Superior receives substantial urban runoff, wastewater treatment plant effluent, and industrial effluent. In 1987, the International Joint Commission designated the St. Louis Bay portion of the lower St. Louis River as one of the Great Lakes Areas of Concern. Concerns exist about the potential effects of chemicals of emerging concern on aquatic biota because many of these chemicals, including endocrine active chemicals, have been shown to affect the endocrine systems of fish. To determine the occurrence of chemicals of emerging concern in the St. Louis River, the St. Louis Bay, and Superior Bay, the U.S. Geological Survey in cooperation with the Minnesota Pollution Control Agency and the Wisconsin Department of Natural Resources collected water and bottom-sediment samples from 40 sites from August through October 2010. The objectives of this study were to (1) identify the extent to which chemicals of emerging concern, including pharmaceuticals, hormones, and other organic chemicals, occur in the St. Louis River, St. Louis Bay, and Superior Bay, and (2) identify the extent to which the chemicals may have accumulated in bottom sediment of the study area. Samples were analyzed for selected wastewater indicators, hormones, sterols, bisphenol A, and human-health pharmaceuticals. During this study, 33 of 89 chemicals of emerging concern were detected among all water samples collected and 56 of 104 chemicals of emerging concern were detected in bottom-sediment samples. The chemical N,N-diethyl-meta-toluamide (DEET) was the most commonly detected chemical in water samples and 2,6-dimethylnaphthalene was the most commonly detected chemical in bottom-sediment samples. In general, chemicals of emerging concern were detected at a higher frequency in bottom-sediment samples than in water samples. Estrone (a steroid hormone) and hexahydrohexamethyl cyclopentabensopyran (a synthetic fragrance) were the most commonly detected endocrine active chemicals in water samples; beta-sitosterol (a plant sterol), estrone, and 4-tert-octylphenol (an alkylphenol) were the most commonly detected endocrine active chemicals in bottom-sediment samples. The greater detection frequency of chemicals in bottom-sediment samples compared to the detection frequency in water samples indicates that bottom sediment is an important sink for chemicals of emerging concern. At least one polycyclic aromatic hydrocarbon was detected in every sample; and in most samples, all nine polycyclic aromatic hydrocarbons included in analyses were detected. Bottom sediment collected from Superior Bay had the most polycyclic aromatic hydrocarbon detections of the sediment sampling locations.

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.

Improving Accuracy in Detecting Acoustic Onsets

ERIC Educational Resources Information Center

Duyck, Wouter; Anseel, Frederik; Szmalec, Arnaud; Mestdagh, Pascal; Tavernier, Antoine; Hartsuiker, Robert J.

2008-01-01

In current cognitive psychology, naming latencies are commonly measured by electronic voice keys that detect when sound exceeds a certain amplitude threshold. However, recent research (e.g., K. Rastle & M. H. Davis, 2002) has shown that these devices are particularly inaccurate in precisely detecting acoustic onsets. In this article, the authors…

Ultra-sensitive detection using integrated waveguide technologies

USDA-ARS?s Scientific Manuscript database

There is a pressing need to detect analytes at very low concentrations, such as food- and water-borne pathogens (e.g. E. coli O157:H7) and biothreat agents (e.g., anthrax, toxins). Common fluorescence detection methods, such as 96 well plate readers, are not sufficiently sensitive for low concentra...

Direct detection of various pathogens by loop-mediated isothermal amplification assays on bacterial culture and bacterial colony.

PubMed

Yan, Muxia; Li, Weidong; Zhou, Zhenwen; Peng, Hongxia; Luo, Ziyan; Xu, Ling

2017-01-01

In this work, loop-mediated isothermal amplification based detection assay using bacterial culture and bacterial colony for various common pathogens direct detection had been established, evaluated and further applied. A total of five species of common pathogens and nine detection targets (tlh, tdh and trh for V. Parahaemolyticus, rfbE, stx1 and stx2 for E. coli, oprI for P. aeruginosa, invA for Salmonella and hylA for L. monocytogenes) were performed on bacterial culture and bacterial colony LAMP. To evaluate and optimize this assay, a total of 116 standard strains were included. Then, for each detected targets, 20 random selected strains were applied. Results were determined through both visual observation of the changed color by naked eye and electrophoresis, which increased the accuracy of survey. The minimum adding quantity of each primer had been confirmed, and the optimal amplification was obtained under 65 °C for 45 min with 25 μl reaction volume. The detection limit of bacterial culture LAMP and PCR assay were determined to be 10 2 and 10 4 or 10 5  CFU/reaction, respectively. No false positive amplification was observed when subjecting the bacterial -LAMP assay to 116 reference strains. This was the first report of colony-LAMP and culture-LAMP assay, which had been demonstrated to be a fast, reliable, cost-effective and simple method on detection of various common pathogens. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of polymorphic states in energetic samples of 1,3,5-trinitro-1,3,5-triazine (RDX) fabricated using drop-on-demand inkjet technology.

PubMed

Emmons, Erik D; Farrell, Mikella E; Holthoff, Ellen L; Tripathi, Ashish; Green, Norman; Moon, Raphael P; Guicheteau, Jason A; Christesen, Steven D; Pellegrino, Paul M; Fountain, Augustus W

2012-06-01

The United States Army and the first responder community are evaluating optical detection systems for the trace detection of hazardous energetic materials. Fielded detection systems must be evaluated with the appropriate material concentrations to accurately identify the residue in theater. Trace levels of energetic materials have been observed in mutable polymorphic phases and, therefore, the systems being evaluated must be able to detect and accurately identify variant sample phases observed in spectral data. In this work, we report on the novel application of drop-on-demand technology for the fabrication of standardized trace 1,3,5-trinitro-1,3,5-triazine (RDX) samples. The drop-on-demand sample fabrication technique is compared both visually and spectrally to the more commonly used drop-and-dry technique. As the drop-on-demand technique allows for the fabrication of trace level hazard materials, concerted efforts focused on characterization of the polymorphic phase changes observed with low concentrations of RDX commonly used in drop-on-demand processing. This information is important when evaluating optical detection technologies using samples prepared with a drop-on-demand inkjet system, as the technology may be "trained" to detect the common bulk α phase of the explosive based on its spectral features but fall short in positively detecting a trace quantity of RDX (β-phase). We report the polymorphic shifts observed between α- and β-phases of this energetic material and discuss the conditions leading to the favoring of one phase over the other.

A new method of time difference measurement: The time difference method by dual phase coincidence points detection

NASA Technical Reports Server (NTRS)

Zhou, Wei

1993-01-01

In the high accurate measurement of periodic signals, the greatest common factor frequency and its characteristics have special functions. A method of time difference measurement - the time difference method by dual 'phase coincidence points' detection is described. This method utilizes the characteristics of the greatest common factor frequency to measure time or phase difference between periodic signals. It can suit a very wide frequency range. Measurement precision and potential accuracy of several picoseconds were demonstrated with this new method. The instrument based on this method is very simple, and the demand for the common oscillator is low. This method and instrument can be used widely.

Probing plasmodesmata function with biochemical inhibitors.

PubMed

White, Rosemary G

2015-01-01

To investigate plasmodesmata (PD) function, a useful technique is to monitor the effect on cell-to-cell transport of applying an inhibitor of a physiological process, protein, or other cell component of interest. Changes in PD transport can then be monitored in one of several ways, most commonly by measuring the cell-to-cell movement of fluorescent tracer dyes or of free fluorescent proteins. Effects on PD structure can be detected in thin sections of embedded tissue observed using an electron microscope, most commonly a Transmission Electron Microscope (TEM). This chapter outlines commonly used inhibitors, methods for treating different tissues, how to detect altered cell-to-cell transport and PD structure, and important caveats.

Single-trial detection of visual evoked potentials by common spatial patterns and wavelet filtering for brain-computer interface.

PubMed

Tu, Yiheng; Huang, Gan; Hung, Yeung Sam; Hu, Li; Hu, Yong; Zhang, Zhiguo

2013-01-01

Event-related potentials (ERPs) are widely used in brain-computer interface (BCI) systems as input signals conveying a subject's intention. A fast and reliable single-trial ERP detection method can be used to develop a BCI system with both high speed and high accuracy. However, most of single-trial ERP detection methods are developed for offline EEG analysis and thus have a high computational complexity and need manual operations. Therefore, they are not applicable to practical BCI systems, which require a low-complexity and automatic ERP detection method. This work presents a joint spatial-time-frequency filter that combines common spatial patterns (CSP) and wavelet filtering (WF) for improving the signal-to-noise (SNR) of visual evoked potentials (VEP), which can lead to a single-trial ERP-based BCI.

Protein detection through different platforms of immuno-loop-mediated isothermal amplification

NASA Astrophysics Data System (ADS)

Pourhassan-Moghaddam, Mohammad; Rahmati-Yamchi, Mohammad; Akbarzadeh, Abolfazl; Daraee, Hadis; Nejati-Koshki, Kazem; Hanifehpour, Younes; Joo, Sang Woo

2013-11-01

Different immunoassay-based methods have been devised to detect protein targets. These methods have some challenges that make them inefficient for assaying ultra-low-amounted proteins. ELISA, iPCR, iRCA, and iNASBA are the common immunoassay-based methods of protein detection, each of which has specific and common technical challenges making it necessary to introduce a novel method in order to avoid their problems for detection of target proteins. Here we propose a new method nominated as `immuno-loop-mediated isothermal amplification' or `iLAMP'. This new method is free from the problems of the previous methods and has significant advantages over them. In this paper we also offer various configurations in order to improve the applicability of this method in real-world sample analyses. Important potential applications of this method are stated as well.

Common Diseases and Some Demographic Characteristics among Saudi Women

ERIC Educational Resources Information Center

Al-Haramlah, Ahmed Abdulrahman; Al-Bakr, Fawziah; Merza, Haniah

2015-01-01

This study aimed to detect the common diseases among Saudi women and their relationship with the level of physical activity and some variables. This study was applied to 1233 Saudi woman in different regions of the Kingdom, and adopted to explore the common diseases: obesity, hypertension, diabetes, cholesterol and asthma. The study results showed…

Real-Time Adaptation of Decision Thresholds in Sensor Networks for Detection of Moving Targets (PREPRINT)

DTIC Science & Technology

2010-01-01

target kinematics for multiple sensor detections is referred to as the track - before - detect strategy, and is commonly adopted in multi-sensor surveillance...of moving targets. Wettergren [4] presented an application of track - before - detect strategies to undersea distributed sensor networks. In de- signing...the deployment of a distributed passive sensor network that employs this track - before - detect procedure, it is impera- tive that the placement of

Volatile organic compounds in ground water from rural private wells, 1986 to 1999

USGS Publications Warehouse

Moran, M.J.; Lapham, W.W.; Rowe, B.L.; Zogorski, J.S.

2004-01-01

The U.S. Geological Survey (USGS) collected or compiled data on volatile organic compounds (VOCs) in samples of untreated ground water from 1,926 rural private wells during 1986 to 1999. At least one VOC was detected in 12 percent of samples from rural private wells. Individual VOCs were not commonly detected with the seven most frequently detected compounds found in only 1 to 5 percent of samples at or above a concentration of 0.2 microgram per liter (??g/l). An assessment level of 0.2 ??g/l was selected so that comparisons of detection frequencies between VOCs could be made. The seven most frequently detected VOCs were: trichloromethane, methyl tert-butyl ether, tetrachloroethene, dichlorodifluoromethane, methylbenzene, 1,1,1-trichloroethane, and 1,2-dibromo-3-chloropropane. Solvents and trihalomethanes were the most frequently detected VOC groups in private wells. The distributions of detections of gasoline oxygenates and fumigants seemed to be related to the use patterns of compounds in these groups. Mixtures were a common mode of occurrence of VOCs with one-quarter of all samples with detections including two or more VOCs. The concentrations of most detected VOCs were relatively small and only 1.4 percent of samples had one or more VOC concentrations that exceeded a federally established drinking water standard or health criterion.

Detection and molecular characterization of Giardia and Cryptosporidium in common dolphins (Delphinus delphis) stranded along the Galician coast (Northwest Spain).

PubMed

Reboredo-Fernández, A; Gómez-Couso, H; Martínez-Cedeira, J A; Cacciò, S M; Ares-Mazás, E

2014-05-28

The ubiquitous protozoan parasites Giardia and Cryptosporidium have been detected from many species of captive and free-living wildlife, representing most mammalian orders. Twenty species of marine mammals have been reported to inhabit Galician waters and the region has one of the highest rates of stranding in Europe. Evidence from stranding, reported by-catches and sightings, suggests that the common dolphin (Delphinus delphis) is the most abundant cetacean on the Galician coast (Northwest Spain). The objective of this study was to detect and molecularly characterize isolates of Giardia and Cryptosporidium obtained from common dolphins stranded in this area. Between 2005 and 2012, sections of large intestine from 133 common dolphins stranded along the Galician coast were collected by the personnel of the Galician Stranding Network (Coordinadora para o Estudo dos Mamíferos Mariños, CEMMA). Using direct immunofluorescence antibody test (IFAT) and PCR amplification and sequencing of the SSU-rDNA, β-giardin genes and the ITS1-5.8S-ITS2 region, Giardia and Cryptosporidium were detected in 8 (6.0%) and 12 samples (9.0%), respectively. In two samples, co-infection by both parasites was observed. The molecular characterization revealed the presence of Giardia duodenalis assemblages A (genotypes A1 and A2) and B and Cryptosporidium parvum in these samples. This constitutes the first study in which the presence of Giardia and Cryptosporidium has been investigated in common dolphins on the European Atlantic coast, and it is also the first report of C. parvum in this host. Our findings indicate that these animals could act as reservoir of these waterborne parasites or could be victims of the contamination originated by anthropogenic activities. Copyright © 2014 Elsevier B.V. All rights reserved.

Accuracy of CNV Detection from GWAS Data.

PubMed

Zhang, Dandan; Qian, Yudong; Akula, Nirmala; Alliey-Rodriguez, Ney; Tang, Jinsong; Gershon, Elliot S; Liu, Chunyu

2011-01-13

Several computer programs are available for detecting copy number variants (CNVs) using genome-wide SNP arrays. We evaluated the performance of four CNV detection software suites--Birdsuite, Partek, HelixTree, and PennCNV-Affy--in the identification of both rare and common CNVs. Each program's performance was assessed in two ways. The first was its recovery rate, i.e., its ability to call 893 CNVs previously identified in eight HapMap samples by paired-end sequencing of whole-genome fosmid clones, and 51,440 CNVs identified by array Comparative Genome Hybridization (aCGH) followed by validation procedures, in 90 HapMap CEU samples. The second evaluation was program performance calling rare and common CNVs in the Bipolar Genome Study (BiGS) data set (1001 bipolar cases and 1033 controls, all of European ancestry) as measured by the Affymetrix SNP 6.0 array. Accuracy in calling rare CNVs was assessed by positive predictive value, based on the proportion of rare CNVs validated by quantitative real-time PCR (qPCR), while accuracy in calling common CNVs was assessed by false positive/false negative rates based on qPCR validation results from a subset of common CNVs. Birdsuite recovered the highest percentages of known HapMap CNVs containing >20 markers in two reference CNV datasets. The recovery rate increased with decreased CNV frequency. In the tested rare CNV data, Birdsuite and Partek had higher positive predictive values than the other software suites. In a test of three common CNVs in the BiGS dataset, Birdsuite's call was 98.8% consistent with qPCR quantification in one CNV region, but the other two regions showed an unacceptable degree of accuracy. We found relatively poor consistency between the two "gold standards," the sequence data of Kidd et al., and aCGH data of Conrad et al. Algorithms for calling CNVs especially common ones need substantial improvement, and a "gold standard" for detection of CNVs remains to be established.

Clinical, ultrasonographic, and laboratory findings in 12 llamas and 12 alpacas with malignant round cell tumors

PubMed Central

Martin, Jeanne M.; Valentine, Beth A.; Cebra, Christopher K.

2010-01-01

Clinical signs, duration of illness, clinicopathologic findings, and ultrasonographic findings were evaluated in 12 llamas and 12 alpacas with malignant round cell tumors (MRCT). All but 1 animal died or was euthanized. Common clinical findings were anorexia, recumbency or weakness, and weight loss or poor growth. Peripheral lymphadenomegaly occurred in only 7 animals and was detected more often at necropsy than during physical examination. Common clinicopathologic abnormalities were hypoalbuminemia, acidosis, azotemia, anemia, hyperglycemia, and neutrophilia. Ultrasonography detected tumors in 4/6 animals. Cytologic evaluation of fluid or tissue aspirates or histopathology of biopsy tissue was diagnostic in 5/6 cases. A clinical course of 2 wk or less prior to death or euthanasia was more common in animals ≤ 2 y of age (9/11) than in older animals (6/13). Regular examination of camelids to include clinical pathology and evaluation of peripheral lymph nodes may result in early detection of MCRT. PMID:21358931

78 FR 15952 - Agency Information Collection Activities; Submission for Office of Management and Budget Review...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-13

... Request; Guidance on Reagents for Detection of Specific Novel Influenza A Viruses AGENCY: Food and Drug... review and clearance. Guidance on Reagents for Detection of Specific Novel Influenza A Viruses--(OMB... for detection of influenza subtype H5 (Asian lineage), commonly known as avian flu. FDA concluded that...

Novel vehicle detection system based on stacked DoG kernel and AdaBoost

PubMed Central

Kang, Hyun Ho; Lee, Seo Won; You, Sung Hyun

2018-01-01

This paper proposes a novel vehicle detection system that can overcome some limitations of typical vehicle detection systems using AdaBoost-based methods. The performance of the AdaBoost-based vehicle detection system is dependent on its training data. Thus, its performance decreases when the shape of a target differs from its training data, or the pattern of a preceding vehicle is not visible in the image due to the light conditions. A stacked Difference of Gaussian (DoG)–based feature extraction algorithm is proposed to address this issue by recognizing common characteristics, such as the shadow and rear wheels beneath vehicles—of vehicles under various conditions. The common characteristics of vehicles are extracted by applying the stacked DoG shaped kernel obtained from the 3D plot of an image through a convolution method and investigating only certain regions that have a similar patterns. A new vehicle detection system is constructed by combining the novel stacked DoG feature extraction algorithm with the AdaBoost method. Experiments are provided to demonstrate the effectiveness of the proposed vehicle detection system under different conditions. PMID:29513727

Study of concentration of HPV DNA probe immobilization for cervical cancer detection based IDE biosensor

NASA Astrophysics Data System (ADS)

Roshila, M. L.; Hashim, U.; Azizah, N.

2016-07-01

This paper mainly illustrates regarding the detection process of Human Papillomavirus (HPV) DNA probe. HPV is the most common virus that infected to human by a sexually transmitted virus. The most common high-risk HPV are 16 and 18. Interdigitated electrode (IDE) device used as based of Titanium Dioxide (TiO2) acts as inorganic surface, where by using APTES as a linker between inorganic surface and organic surface. A strategy of rapid and sensitive for the HPV detection was proposed by integrating simple DNA extraction with a gene of DNA. The extraction of the gene of DNA will make an efficiency of the detection process. It will depend on the sequence of the capture probes and the way to support their attached. The fabrication, surface modification, immobilization and hybridization processes are characterized by current voltage (I-V) measurement by using KEITHLEY 6487. This strategy will perform a good sensitivity of HPV detection.

Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination

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

Hewitson, Laura; Thissen, James B.; Gardner, Shea N.

In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV). Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA), was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR) was conducted. The LLMDA technologymore » was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae , Bacteroidaceae , and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations.« less

Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination

DOE PAGES

Hewitson, Laura; Thissen, James B.; Gardner, Shea N.; ...

2014-01-01

In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV). Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA), was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR) was conducted. The LLMDA technologymore » was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae , Bacteroidaceae , and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations.« less

Commonality of drug-associated adverse events detected by 4 commonly used data mining algorithms.

PubMed

Sakaeda, Toshiyuki; Kadoyama, Kaori; Minami, Keiko; Okuno, Yasushi

2014-01-01

Data mining algorithms have been developed for the quantitative detection of drug-associated adverse events (signals) from a large database on spontaneously reported adverse events. In the present study, the commonality of signals detected by 4 commonly used data mining algorithms was examined. A total of 2,231,029 reports were retrieved from the public release of the US Food and Drug Administration Adverse Event Reporting System database between 2004 and 2009. The deletion of duplicated submissions and revision of arbitrary drug names resulted in a reduction in the number of reports to 1,644,220. Associations with adverse events were analyzed for 16 unrelated drugs, using the proportional reporting ratio (PRR), reporting odds ratio (ROR), information component (IC), and empirical Bayes geometric mean (EBGM). All EBGM-based signals were included in the PRR-based signals as well as IC- or ROR-based ones, and PRR- and IC-based signals were included in ROR-based ones. The PRR scores of PRR-based signals were significantly larger for 15 of 16 drugs when adverse events were also detected as signals by the EBGM method, as were the IC scores of IC-based signals for all drugs; however, no such effect was observed in the ROR scores of ROR-based signals. The EBGM method was the most conservative among the 4 methods examined, which suggested its better suitability for pharmacoepidemiological studies. Further examinations should be performed on the reproducibility of clinical observations, especially for EBGM-based signals.

Research on IPv6 intrusion detection system Snort-based

NASA Astrophysics Data System (ADS)

Shen, Zihao; Wang, Hui

2010-07-01

This paper introduces the common intrusion detection technologies, discusses the work flow of Snort intrusion detection system, and analyzes IPv6 data packet encapsulation and protocol decoding technology. We propose the expanding Snort architecture to support IPv6 intrusion detection in accordance with CIDF standard combined with protocol analysis technology and pattern matching technology, and present its composition. The research indicates that the expanding Snort system can effectively detect various intrusion attacks; it is high in detection efficiency and detection accuracy and reduces false alarm and omission report, which effectively solves the problem of IPv6 intrusion detection.

Single nucleotide polymorphisms in common bean: their discovery and genotyping using a multiplex detection system

USDA-ARS?s Scientific Manuscript database

Single-nucleotide Polymorphism (SNP) markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean comparing sequences from coding and non-coding regions obtained from Genbank and genomic DNA and to compare sequencing resu...

Spectrum of prenatally detected central nervous system malformations: Neural tube defects continue to be the leading foetal malformation.

PubMed

Siddesh, Anjurani; Gupta, Geetika; Sharan, Ram; Agarwal, Meenal; Phadke, Shubha R

2017-04-01

Prenatal diagnosis of malformations is an important method of prevention and control of congenital anomalies with poor prognosis. Central nervous system (CNS) malformations amongst these are the most common. The information about the prevalence and spectrum of prenatally detected malformations is crucial for genetic counselling and policymaking for population-based preventive programmes. The objective of this study was to study the spectrum of prenatally detected CNS malformations and their association with chromosomal abnormalities and autopsy findings. This retrospective study was conducted in a tertiary care hospital in north India from January 2007 to December 2013. The details of cases with prenatally detected CNS malformations were collected and were related with the foetal chromosomal analysis and autopsy findings. Amongst 6044 prenatal ultrasonographic examinations performed; 768 (12.7%) had structural malformations and 243 (31.6%) had CNS malformations. Neural tube defects (NTDs) accounted for 52.3 per cent of CNS malformations and 16.5 per cent of all malformations. The other major groups of prenatally detected CNS malformations were ventriculomegaly and midline anomalies. Chromosomal abnormalities were detected in 8.2 per cent of the 73 cases studied. Foetal autopsy findings were available for 48 foetuses. Foetal autopsy identified additional findings in eight foetuses and the aetiological diagnosis changed in two of them (4.2%). Amongst prenatally detected malformations, CNS malformations were common. NTD, which largely is a preventable anomaly, continued to be the most common group. Moreover, 60 per cent of malformations were diagnosed after 20 weeks, posing legal issues. Chromosomal analysis and foetal autopsy are essential for genetic counselling based on aetiological diagnosis.

Evaluating a switch from meconium to umbilical cord tissue for newborn drug testing: A retrospective study at an academic medical center.

PubMed

Palmer, Kendra L; Wood, Kelly E; Krasowski, Matthew D

2017-04-01

The objective of this study was to compare detection rates of newborn drug exposure at an academic medical center transitioning from meconium to umbilical cord tissue toxicology testing. We performed an Institutional Review Board-approved retrospective chart review on all newborns (n=2072) for whom newborn drug testing was ordered at our academic medical center between June 2012 and August 2015 (in August 2013, umbilical cord tissue became the preferred specimen). Meconium toxicology testing was positive for at least one compound in 221 cases (21.3% of 1037 total specimens), with non-medical drug use identified in 85 cases (8.2%). Umbilical cord tissue toxicology testing was positive for at least one compound in 302 cases (29.2%), with non-medical drug use identified in 107 cases (10.3%). Of the cases involving non-medical drug use, the most common compounds detected were tetrahydrocannabinol and amphetamines. Non-medical drug use did not differ significantly between meconium and umbilical cord tissue, either as a total or for classes of drugs such as amphetamines, cannabinoids, and opiates. Maternal non-medical use of tramadol (not tested for in meconium) was identified in 5 cases (0.4%). There were significant differences in rate of detection of iatrogenic medications. Specifically, morphine, lorazepam, phenobarbital, and codeine were more commonly detected in meconium, while oxycodone was more commonly detected in umbilical cord tissue. Umbilical cord tissue toxicology testing yielded a similar detection rate compared to meconium testing. The use of umbilical cord tissue avoids detection of medications given to the neonate prior to meconium collection. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Detection of Viral and Bacterial Pathogens in Hospitalized Children With Acute Respiratory Illnesses, Chongqing, 2009–2013

PubMed Central

Wei, Lan; Liu, Wei; Zhang, Xiao-Ai; Liu, En-Mei; Wo, Yin; Cowling, Benjamin J.; Cao, Wu-Chun

2015-01-01

Abstract Acute respiratory infections (ARIs) cause large disease burden each year. The codetection of viral and bacterial pathogens is quite common; however, the significance for clinical severity remains controversial. We aimed to identify viruses and bacteria in hospitalized children with ARI and the impact of mixed detections. Hospitalized children with ARI aged ≤16 were recruited from 2009 to 2013 at the Children's Hospital of Chongqing Medical University, Chongqing, China. Nasopharyngeal aspirates (NPAs) were collected for detection of common respiratory viruses by reverse transcription polymerase chain reaction (RT-PCR) or PCR. Bacteria were isolated from NPAs by routine culture methods. Detection and codetection frequencies and clinical features and severity were compared. Of the 3181 hospitalized children, 2375 (74.7%) were detected with ≥1 virus and 707 (22.2%) with ≥1 bacteria, 901 (28.3%) with ≥2 viruses, 57 (1.8%) with ≥2 bacteria, and 542 (17.0%) with both virus and bacteria. The most frequently detected were Streptococcus pneumoniae, respiratory syncytial virus, parainfluenza virus, and influenza virus. Clinical characteristics were similar among different pathogen infections for older group (≥6 years old), with some significant difference for the younger. Cases with any codetection were more likely to present with fever; those with ≥2 virus detections had higher prevalence of cough; cases with virus and bacteria codetection were more likely to have cough and sputum. No significant difference in the risk of pneumonia, severe pneumonia, and intensive care unit admission were found for any codetection than monodetection. There was a high codetection rate of common respiratory pathogens among hospitalized pediatric ARI cases, with fever as a significant predictor. Cases with codetection showed no significant difference in severity than those with single pathogens. PMID:25906103

Rapid detection of pathological mutations and deletions of the haemoglobin beta gene (HBB) by High Resolution Melting (HRM) analysis and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR).

PubMed

Turner, Andrew; Sasse, Jurgen; Varadi, Aniko

2016-10-19

Inherited disorders of haemoglobin are the world's most common genetic diseases, resulting in significant morbidity and mortality. The large number of mutations associated with the haemoglobin beta gene (HBB) makes gene scanning by High Resolution Melting (HRM) PCR an attractive diagnostic approach. However, existing HRM-PCR assays are not able to detect all common point mutations and have only a very limited ability to detect larger gene rearrangements. The aim of the current study was to develop a HBB assay, which can be used as a screening test in highly heterogeneous populations, for detection of both point mutations and larger gene rearrangements. The assay is based on a combination of conventional HRM-PCR and a novel Gene Ratio Analysis Copy Enumeration (GRACE) PCR method. HRM-PCR was extensively optimised, which included the use of an unlabelled probe and incorporation of universal bases into primers to prevent interference from common non-pathological polymorphisms. GRACE-PCR was employed to determine HBB gene copy numbers relative to a reference gene using melt curve analysis to detect rearrangements in the HBB gene. The performance of the assay was evaluated by analysing 410 samples. A total of 44 distinct pathological genotypes were detected. In comparison with reference methods, the assay has a sensitivity of 100 % and a specificity of 98 %. We have developed an assay that detects both point mutations and larger rearrangements of the HBB gene. This assay is quick, sensitive, specific and cost effective making it suitable as an initial screening test that can be used for highly heterogeneous cohorts.

[Review on characteristics and detecting assay of bacterial endotoxin contamination in water environment].

PubMed

Zhang, Can; Liu, Wen-Jun; Zhang, Ming-Lu; Tian, Fang; Yang, Yi; An, Dai-Zhi

2014-04-01

Endotoxins, also known as lipopolysaccharide complexes, are anchored in the outer membrane cell wall of most Gram-negative bacteria and some cyanobacteria. They are continuously released to environment during cell decay. Being common pyrogens and highly immunogenic molecules, endotoxins are related to many human diseases. Due to the tolerances and thermo-stability of endotoxin molecules, they were hard to be removed by common methods. The health risk caused by the endotoxin contamination in drinking water and water environment by various exposure pathways have attracted more and more attention in recent years. In this paper, the physical and chemical properties, biological activities and detection assay of the endotoxin contamination were reviewed, and interfere factors of the main assay, the LAL/TAL (Limulus amebocyte lysate/Tachypleus amebocyte lysate) assay, for detecting endotoxin in water sample were investigated, and the development tendency of the endotoxin detection assay was analyzed.

Korean Guidelines for Colorectal Cancer Screening and Polyp Detection

PubMed Central

Lee, Bo-In; Hong, Sung Pil; Kim, Seong-Eun; Kim, Se Hyung; Hong, Sung Noh; Yang, Dong-Hoon; Shin, Sung Jae; Lee, Suck-Ho; Park, Dong Il; Kim, Young-Ho; Kim, Hyun Jung; Yang, Suk-Kyun; Kim, Hyo Jong; Jeon, Hae Jeong

2012-01-01

Now colorectal cancer is the second most common cancer in males and the fourth most common cancer in females in Korea. Since most of colorectal cancers occur after the prolonged transformation of adenomas into carcinomas, early detection and removal of colorectal adenomas are one of the most effective methods to prevent colorectal cancer. Considering the increasing incidence of colorectal cancer and polyps in Korea, it is very important to establish Korean guideline for colorectal cancer screening and polyp detection. The guideline was developed by the Korean Multi-Society Take Force and we tried to establish the guideline by evidence-based methods. Parts of the statements were draw by systematic reviews and meta-analyses. Herein we discussed epidemiology of colorectal cancers and adenomas in Korea and optimal methods for screening of colorectal cancer and detection of adenomas including fecal occult blood tests, radiologic tests, and endoscopic examinations. PMID:22741131

Artemisinin-Luminol Chemiluminescence for Forensic Bloodstain Detection Using a Smart Phone as a Detector.

PubMed

Gao, Wenyue; Wang, Chao; Muzyka, Kateryna; Kitte, Shimeles Addisu; Li, Jianping; Zhang, Wei; Xu, Guobao

2017-06-06

Forensic luminol chemiluminescence test is one of the most sensitive and popular methods for the determination of latent bloodstains. It mainly uses hydrogen peroxide or sodium perborate as coreactants. The easy decomposition of hydrogen peroxide and sodium perborate in the presence of many ions significantly affects the selectivity. Artemisinin is a natural peroxide that is quite stable in the presence of common ions. In the present study, artemisinin has been exploited for the forensic bloodstain chemiluminescence detection for the first time. Using smart phone as cost-effective portable detector, the visual detection of bloodstains has been achieved with a dilution factor of blood up to 100 000. Moreover, this system shows excellent selectivity against many common species. It can well differentiate bloodstains from other stains, such as coffee, brown sugar, and black tea. Both favorable sensitivity and selectivity makes the present method promising in forensic detection.

Development of a loop-mediated isothermal amplification (LAMP) assay for rapid and specific detection of common genetically modified organisms (GMOs).

PubMed

Feng, Jiawang; Tang, Shiming; Liu, Lideng; Kuang, Xiaoshan; Wang, Xiaoyu; Hu, Songnan; You, Shuzhu

2015-03-01

Here, we developed a loop-mediated isothermal amplification (LAMP) assay for 11 common transgenic target DNA in GMOs. Six sets of LAMP primer candidates for each target were designed and their specificity, sensitivity, and reproductivity were evaluated. With the optimized LAMP primers, this LAMP assay was simply run within 45-60 min to detect all these targets in GMOs tested. The sensitivity, specificity, and reproductivity of the LAMP assay were further analyzed in comparison with those of Real-Time PCR. In consistent with real-time PCR, detection of 0.5% GMOs in equivalent background DNA was possible using this LAMP assay for all targets. In comparison with real-time PCR, the LAMP assay showed the same results with simple instruments. Hence, the LAMP assay developed can provide a rapid and simple approach for routine screening as well as specific events detection of many GMOs.

Vascular Variations Associated with Intracranial Aneurysms.

PubMed

Orakdogen, Metin; Emon, Selin Tural; Somay, Hakan; Engin, Taner; Is, Merih; Hakan, Tayfun

2017-01-01

To investigate the vascular variations in patients with intracranial aneurysm in circle of Willis. We used the data on 128 consecutive intracranial aneurysm cases. Cerebral angiography images were analyzed retrospectively. Arteries were grouped as anterior cerebral arterial system (ACS), posterior cerebral arterial system (PCS) and middle cerebral arterial system (MCS) for grouping vascular variations. Lateralization, being single/multiple, gender; and also any connection with accompanying aneurysms" number, localization, dimension, whether bleeding/incidental aneurysm has been inspected. Variations were demonstrated in 57.8% of the cases. The most common variation was A1 variation (34.4%). The rate of variations was 36.7%, 24.2% and 10.2% respectively in ACS, PCS and MCS. MCS variations were significantly higher in males. Anterior communicating artery (ACoA) aneurysm observance rates were significantly higher and posterior communicating artery (PCoA) aneurysm and middle cerebral artery (MCA) aneurysm observance rates were significantly lower when compared to "no ACS variation detected" cases. In "PCS variation detected" cases, PCoA aneurysm observance rates and coexistence of multiple variations were significantly higher. The rate of vascular variations in patients with aneurysms was 57.8%. Arterial hypoplasia and aplasia were the most common variations. ACS was the most common region that variations were located in; they were mostly detected on the right side. Coexistence of ACoA aneurysm was higher than PCoA and MCA aneurysms. In the PCS variations group, PCoA aneurysms were the most common aneurysms that accompanying the variation and multiple variations were more common than in the other two groups. The variations in MCS were most common in males.

Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Roman, Monserrate C.; Jones, Kathy U.; Oubre, Cherie M.; Castro, Victoria; Ott, Mark C.; Birmele, Michele; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.

2013-01-01

Current methods for microbial detection: a) Labor & time intensive cultivation-based approaches that can fail to detect or characterize all cells present. b) Requires collection of samples on orbit and transportation back to ground for analysis. Disadvantages to current detection methods: a) Unable to perform quick and reliable detection on orbit. b) Lengthy sampling intervals. c) No microbe identification.

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.

Collision-free motion of two robot arms in a common workspace

NASA Technical Reports Server (NTRS)

Basta, Robert A.; Mehrotra, Rajiv; Varanasi, Murali R.

1987-01-01

Collision-free motion of two robot arms in a common workspace is investigated. A collision-free motion is obtained by detecting collisions along the preplanned trajectories using a sphere model for the wrist of each robot and then modifying the paths and/or trajectories of one or both robots to avoid the collision. Detecting and avoiding collisions are based on the premise that: preplanned trajectories of the robots follow a straight line; collisions are restricted to between the wrists of the two robots (which corresponds to the upper three links of PUMA manipulators); and collisions never occur between the beginning points or end points on the straight line paths. The collision detection algorithm is described and some approaches to collision avoidance are discussed.

Sampling little fish in big rivers: Larval fish detection probabilities in two Lake Erie tributaries and implications for sampling effort and abundance indices

USGS Publications Warehouse

Pritt, Jeremy J.; DuFour, Mark R.; Mayer, Christine M.; Roseman, Edward F.; DeBruyne, Robin L.

2014-01-01

Larval fish are frequently sampled in coastal tributaries to determine factors affecting recruitment, evaluate spawning success, and estimate production from spawning habitats. Imperfect detection of larvae is common, because larval fish are small and unevenly distributed in space and time, and coastal tributaries are often large and heterogeneous. We estimated detection probabilities of larval fish from several taxa in the Maumee and Detroit rivers, the two largest tributaries of Lake Erie. We then demonstrated how accounting for imperfect detection influenced (1) the probability of observing taxa as present relative to sampling effort and (2) abundance indices for larval fish of two Detroit River species. We found that detection probabilities ranged from 0.09 to 0.91 but were always less than 1.0, indicating that imperfect detection is common among taxa and between systems. In general, taxa with high fecundities, small larval length at hatching, and no nesting behaviors had the highest detection probabilities. Also, detection probabilities were higher in the Maumee River than in the Detroit River. Accounting for imperfect detection produced up to fourfold increases in abundance indices for Lake Whitefish Coregonus clupeaformis and Gizzard Shad Dorosoma cepedianum. The effect of accounting for imperfect detection in abundance indices was greatest during periods of low abundance for both species. Detection information can be used to determine the appropriate level of sampling effort for larval fishes and may improve management and conservation decisions based on larval fish data.

Material-specific detection and classification of single nanoparticles

PubMed Central

Person, Steven; Deutsch, Bradley; Mitra, Anirban; Novotny, Lukas

2010-01-01

Detection and classification of nanoparticles is important for environmental monitoring, contamination mitigation, biological label tracking, and bio-defense. Detection techniques involve a trade-off between sensitivity, discrimination, and speed. This paper presents a material-specific dual-color common-path interferometric detection system. Two wavelengths are simultaneously used to discriminate between 60 nm silver and 80 nm diameter gold particles in solution with a detection time of τ ≈ 1 ms. The detection technique is applicable to situations where both particle size and material are of interest. PMID:21142033

Detection of NH1N1 influenza virus in nonrespiratory sites among children.

PubMed

Wootton, Susan H; Aguilera, Elizabeth A; Wanger, Audrey; Jewell, Alan; Patel, Kirtida; Murphy, James R; Piedra, Pedro A

2014-01-01

Among 20 children admitted with laboratory-confirmed influenza, viral RNA was detected in respiratory secretion, stool and blood in 19, 5 and 1 children, respectively. Gastrointestinal symptoms were common but were not associated with viral RNA in stool. nH1N1 viremia was detected, for the first time, in an immunocompetent child.

The Trace Analysis of DEET in Water using an On-line Preconcentration Column and Liquid Chromatography with UV Photodiode Array Detection

EPA Science Inventory

A method for the detection of trace levels of N,N-diethyl-m-toluamide (DEET) in water is discussed. The method utilizes an on-line preconcentration column in series with high performance liquid chromatography (HPLC) and UV photodiode array detection. DEET, a common insect repel...

Peptide nucleic acid probe-based fluorescence melting curve analysis for rapid screening of common JAK2, MPL, and CALR mutations.

PubMed

Park, Joonhong; Song, Minsik; Jang, Woori; Chae, Hyojin; Lee, Gun Dong; Kim, KyungTak; Park, Heekyung; Kim, Myungshin; Kim, Yonggoo

2017-02-01

We developed and evaluated the feasibility of peptide nucleic acid (PNA)-based fluorescence melting curve analysis (FMCA) to detect common mutations in myeloproliferative neoplasms (MPNs). We have set up two separate reactions of PNA-based FMCA: JAK2 V617F &CALR p.Leu367fs*46 (set A) and MPL W515L/K &CALR p.Lys385fs*47 (set B). Clinical usefulness was validated with allele-specific real-time PCR, fragment analysis, Sanger sequencing in 57 BCR-ABL1-negative MPNs. The limit of detection (LOD) of PNA-based FMCA was approximately 10% for each mutation and interference reactions using mixtures of different mutations were not observed. Non-specific amplification was not observed in normal control. PNA-based FMCA was able to detect all JAK2 V617F (n=20), CALR p.Leu367fs*46 (n=10) and p.Lys385fs*47 (n=8). Three of six MPL mutations were detected except three samples with low mutant concentration in out of LOD. JAK2 exon 12 mutations (n=7) were negative without influencing V617F results. Among six variant CALR exon 9 mutations, two were detected by this method owing to invading of probe binding site. PNA-based FMCA for detecting common JAK2, MPL, and CALR mutations is a rapid, simple, and sensitive technique in BCR-ABL1-negative MPNs with >10% mutant allele at the time of initial diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Simple Common Plane contact detection algorithm for FE/FD methods

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

Vorobiev, O

2006-07-19

Common-plane (CP) algorithm is widely used in Discrete Element Method (DEM) to model contact forces between interacting particles or blocks. A new simple contact detection algorithm is proposed to model contacts in FE/FD methods which is similar to the CP algorithm. The CP is defined as a plane separating interacting faces of FE/FD mesh instead of blocks or particles in the original CP method. The method does not require iterations. It is very robust and easy to implement both in 2D and 3D case.

Ground-water quality in the western part of the Cambrian-Ordovician aquifer in the Western Lake Michigan Drainages, Wisconsin and Michigan

USGS Publications Warehouse

Saad, D.A.

1996-01-01

Seven pesticides or metabolites were detected in ground-water samples, and at least one pesticide was detected in samples from 24 percent (7 of 29) of wells. Most of the pesticides were detected at low concentrations and were from wells in the regionally unconfined, agricultural, southwest part of the study area. Atrazine was the most commonly detected pesticide and was typically detected in samples from wells that produced modern water.

Error-Detecting Identification Codes for Algebra Students.

ERIC Educational Resources Information Center

Sutherland, David C.

1990-01-01

Discusses common error-detecting identification codes using linear algebra terminology to provide an interesting application of algebra. Presents examples from the International Standard Book Number, the Universal Product Code, bank identification numbers, and the ZIP code bar code. (YP)

Analogies Among Current and Future Life Detection Missions and the Pharmaceutical/Biomedical Industries

NASA Astrophysics Data System (ADS)

Wainwright, N. R.; Steele, A.; Monaco, L.; Fries, M.

2017-02-01

Life detection goals and technologies are remarkably similar between several types of NASA missions and the pharmaceutical and biotechnology industries. Needs for sensitivity, specificity, speed have driven techniques and equipment to common ends.

Organochlorine contaminants in eggs of common terns from the Canadian Great Lakes 1981

USGS Publications Warehouse

Weseloh, D.V.; Custer, T.W.; Braune, B.M.

1989-01-01

To determine if contaminant levels in common terns had changed over the last decade, we collected and analyzed eggs from four nesting colonies on the three lower Great lakes during 1981. DDE and PCBs were detected in every egg from the four colonies. Dieldrin, mirex and trans-nonachlor were detected in more than 45% of the eggs. Seven other organochlorine contaminants (DDD, DDT, hexachlorobenzene, oxychlordane, cis-chlordane, cis-nonachlor and toxaphene) were detected in less than 25% of the eggs. Eggs from the Lake Ontario colony were generally the most heavily contaminated. Comparisons of DDE and PCB data with earlier studies of common terns indicated that contaminant levels in eggs from the four sampled colonies, or nearby sites, have decreased by up to 80-90% from 1969-73 to 1981. Interspecies comparisons showed that common tern eggs have lower organochlorine residue levels than eggs of caspian terns or herring gulls. Dietary variation and migratory status are possible explanations for the differences in residue levels among species. Eggshell thickness, log-PCBs, and log-DDE were not significantly intercorrelated. Elevated contaminant levels in the early 1970s might be at least partly responsible for the decline of the Great Lakes Common Tern population over the past decade. Stabilization of population numbers during the early 1980s suggests that organochlorine pollution levels have been reduced to a point where they are no longer an important factor in the population dynamics of this species on the Great Lakes.

To Control False Positives in Gene-Gene Interaction Analysis: Two Novel Conditional Entropy-Based Approaches

PubMed Central

Lin, Meihua; Li, Haoli; Zhao, Xiaolei; Qin, Jiheng

2013-01-01

Genome-wide analysis of gene-gene interactions has been recognized as a powerful avenue to identify the missing genetic components that can not be detected by using current single-point association analysis. Recently, several model-free methods (e.g. the commonly used information based metrics and several logistic regression-based metrics) were developed for detecting non-linear dependence between genetic loci, but they are potentially at the risk of inflated false positive error, in particular when the main effects at one or both loci are salient. In this study, we proposed two conditional entropy-based metrics to challenge this limitation. Extensive simulations demonstrated that the two proposed metrics, provided the disease is rare, could maintain consistently correct false positive rate. In the scenarios for a common disease, our proposed metrics achieved better or comparable control of false positive error, compared to four previously proposed model-free metrics. In terms of power, our methods outperformed several competing metrics in a range of common disease models. Furthermore, in real data analyses, both metrics succeeded in detecting interactions and were competitive with the originally reported results or the logistic regression approaches. In conclusion, the proposed conditional entropy-based metrics are promising as alternatives to current model-based approaches for detecting genuine epistatic effects. PMID:24339984

A new method for differentiating adducts of common drinking water DBPs from higher molecular weight DBPs in electrospray ionization-mass spectrometry analysis.

PubMed

Zhai, Hongyan; Zhang, Xiangru

2009-05-01

With the presence of bromide in source waters, numerous brominated disinfection byproducts (DBPs) are formed during chlorination. Many of them are polar/highly polar DBPs and thus hard to be detected by gas chromatography mass spectrometry. Electrospray ionization triple quadrupole mass spectrometry (ESI-MS/MS) is reported to be an effective method in finding polar brominated DBPs by setting precursor ion scans of m/z 79 and 81. But as a soft ionization technique, ESI could form adducts of common DBPs, which may complicate ESI-MS/MS spectra and hinder the efforts in finding new brominated DBPs. In this paper, a new method was developed for differentiating adducts of common DBPs from higher molecular weight DBPs. This method was based on the ESI-MS/MS precursor ion scans of the fragments that correspond to the molecular ions of common DBPs. Adducts of common DBPs were selectively detected in the ESI-MS/MS spectra of a simulated drinking water sample. Moreover, the structures of several new brominated DBPs in the sample were tentatively proposed.

Detection and discrimination of herpes simplex viruses, Haemophilus ducreyi, Treponema pallidum, and Calymmatobacterium (Klebsiella) granulomatis from genital ulcers.

PubMed

Mackay, Ian M; Harnett, Gerry; Jeoffreys, Neisha; Bastian, Ivan; Sriprakash, Kadaba S; Siebert, David; Sloots, Theo P

2006-05-15

Genital ulcer disease (GUD) is commonly caused by pathogens for which suitable therapies exist, but clinical and laboratory diagnoses may be problematic. This collaborative project was undertaken to address the need for a rapid, economical, and sensitive approach to the detection and diagnosis of GUD using noninvasive techniques to sample genital ulcers. The genital ulcer disease multiplex polymerase chain reaction (GUMP) was developed as an inhouse nucleic acid amplification technique targeting serious causes of GUD, namely, herpes simplex viruses (HSVs), H. ducreyi, Treponema pallidum, and Klebsiella species. In addition, the GUMP assay included an endogenous internal control. Amplification products from GUMP were detected by enzyme linked amplicon hybridization assay (ELAHA). GUMP-ELAHA was sensitive and specific in detecting a target microbe in 34.3% of specimens, including 1 detection of HSV-1, three detections of HSV-2, and 18 detections of T. pallidum. No H. ducreyi has been detected in Australia since 1998, and none was detected here. No Calymmatobacterium (Klebsiella) granulomatis was detected in the study, but there were 3 detections during ongoing diagnostic use of GUMP-ELAHA in 2004 and 2005. The presence of C. granulomatis was confirmed by restriction enzyme digestion and nucleotide sequencing of the 16S rRNA gene for phylogenetic analysis. GUMP-ELAHA permitted comprehensive detection of common and rare causes of GUD and incorporated noninvasive sampling techniques. Data obtained by using GUMP-ELAHA will aid specific treatment of GUD and better define the prevalence of each microbe among at-risk populations with a view to the eradication of chancroid and donovanosis in Australia.

Enhancement of drug detection and identification by use of various derivatizing reagents on GC-FTIR analysis.

DOT National Transportation Integrated Search

1992-07-01

Phenylpropanolamine (PPA) is a relatively common non-prescription sympathomimetic amine. As such, it is frequently detected during forensic analysis. The presence of phenylpropanolamine can be confirmed by using Gas Chromatograph-Fourier Transform In...

Estuarine Macroinvertebrate Pollution Indicator Species in the Virginian Biogeographic Province

EPA Science Inventory

Macroinvertebrates are commonly used as biomonitors to detect pollution impacts in estuaries. In this study we identified estuarine benthic invertebrates that could be used to detect presence or absence of pollution in the Virginian Biogeographic Province using available monitor...

Outcome Analyses of 15,189 Screenings Via Colonoscopy.

PubMed

Liu, Lan; Gao, Hongwei; Yu, Weihua; Zhang, Shanyan; Guo, Jianqiang; Zhu, Kongxi

2017-10-01

This study investigated the detection rates of common colorectal diseases during colonoscopy procedures to provide reference for clinical diagnoses in China. A total of 15,189 participants, who underwent total colonoscopy, were studied. We analyzed the detection rates of common colorectal diseases in different sex, age, and decade groups. The most common indication for colonoscopy is abdominal pain followed by change in bowel habits. Among the 15,189 participants, 5658 cases (37.25%) were normal. The most common positive finding was colorectal polyp (27.32%) followed by nonspecific colitis (12.06%), colorectal cancer (CRC) (7.71%), and ulcerative colitis (4.64%). The frequencies of polyp (31.56% vs. 21.99%; P=0.000) and CRC (8.28% vs. 7.00%; P=0.004) were higher in males than in females. By contrast, ischemic colitis (0.08% vs. 0.31%; P=0.001) and melanosis coli (1.15% vs. 1.87%; P=0.000) were more seen in females than in males. In addition, the detection rates for CRC (2.42% vs. 7.18% vs. 16.67%; P=0.000), colorectal polyp (17.65% vs. 32.27% vs. 34.73%; P=0.000), ischemic colitis (0.09% vs. 0.19% vs. 0.32%; P=0.033), and melanosis coli (0.71% vs. 1.09% vs. 3.21%; P=0.000) increased with age. The frequent positive findings were colorectal polyp, nonspecific colitis, and CRC. Patients showing alarming symptoms definitely require colonoscopy. The detection rates for colorectal polyp and melanosis coli were significantly higher in the later decade, so we should focus on these deseases.

Development and Validation of a Lateral Flow Immunoassay Test Kit for Dual Detection of Casein and β-Lactoglobulin Residues.

PubMed

Masiri, Jongkit; Barrios-Lopez, Brianda; Benoit, Lora; Tamayo, Joshua; Day, Jeffrey; Nadala, Cesar; Sung, Shao-Lei; Samadpour, Mansour

2016-03-01

Allergies to cow's milk are very common and can present as life-threatening anaphylaxis. Consequently, food labeling legislation mandates that foods containing milk residues, including casein and/or β-lactoglobulin, provide an indication of such on the product label. Because contamination with either component independent of the other can occur during food manufacturing, effective allergen management measures for containment of milk residues necessitates the use of dual screening methods. To assist the food industry in improving food safety practices, we have developed a rapid lateral flow immunoassay test kit that reliably reports both residues down to 0.01 μg per swab and 0.1 ppm of protein for foods. The assay utilizes both sandwich and competitive format test lines and is specific for bovine milk residues. Selectivity testing using a panel of matrices with potentially interfering substances, including commonly used sanitizing agents, indicated reduction in the limit of detection by one-to fourfold. With food, residues were easily detected in all cow's milk-based foods tested, but goat and sheep milk residues were not detected. Specificity analysis revealed no cross-reactivity with common commodities, with the exception of kidney beans when present at high concentrations (> 1%). The development of a highly sensitive and rapid test method capable of detecting trace amounts of casein and/or β-lactoglobulin should aid food manufacturers and regulatory agencies in monitoring for milk allergens in environmental and food samples.

Hermetic and Web Plagiarism Detection Systems for Student Essays--An Evaluation of the State-of-the-Art

ERIC Educational Resources Information Center

Kakkonen, Tuomo; Mozgovoy, Maxim

2010-01-01

Plagiarism has become a serious problem in education, and several plagiarism detection systems have been developed for dealing with this problem. This study provides an empirical evaluation of eight plagiarism detection systems for student essays. We present a categorical hierarchy of the most common types of plagiarism that are encountered in…

Determination of glucose and uric acid with bienzyme colorimetry on microfluidic paper-based analysis devices.

PubMed

Chen, Xi; Chen, Jin; Wang, Fubin; Xiang, Xia; Luo, Ming; Ji, Xinghu; He, Zhike

2012-05-15

In this work, we first employ a drying method combining with the bienzyme colorimetric detection of glucose and uric acid on microfluidic paper-based analysis devices (μPADs). The channels of 3D μPADs are also designed by us to get better results. The color results are recorded by both Gel Documentation systems and a common camera. By using Gel Documentation systems, the limits of detection (LOD) of glucose and uric acid are 3.81 × 10(-5)M and 4.31 × 10(-5)M, respectively one order of magnitude lower than that of the reported methods on μPADs. By using a common camera, the limits of detection (LOD) of glucose and uric acid are 2.13 × 10(-4)M and 2.87 × 10(-4)M, respectively. Furthermore, the effects of detection conditions have been investigated and discussed comprehensively. Human serum samples are detected with satisfactory results, which are comparable with the clinical testing results. A low-cost, simple and rapid colorimetric method for the simultaneous detection of glucose and uric acid on the μPADs has been developed with enhanced sensitivity. Copyright © 2012 Elsevier B.V. All rights reserved.

Geophysical and botanical monitoring of simulated graves in a tropical rainforest, Colombia, South America

NASA Astrophysics Data System (ADS)

Molina, Carlos Martin; Pringle, Jamie K.; Saumett, Miguel; Evans, Gethin T.

2016-12-01

In most Latin American countries there are significant numbers of missing people and forced disappearances, currently 80,000 only in Colombia. Successful detection of shallow buried human remains by forensic search teams is currently difficult in varying terrain and climates. Within this research we built four simulated clandestine burial styles in tropical rainforests, as this is a common scenario and depositional environment encountered in Latin America, to gain knowledge of optimum forensic geophysics detection techniques. The results of geophysically monitoring these burials using ground penetrating radar, magnetic susceptibility, bulk ground conductivity and electrical resistivity are presented from one to forty three weeks post-burial. Radar survey results with both the 250 MHz and 500 MHz frequency antennae showed good detection of modern simulated burials on 2D profiles and horizontal time slices but poor detection on the other simulated graves. Magnetic susceptibility, bulk ground conductivity and electrical resistivity results were generally poor at detecting the simulated targets. Observations of botanical variations on the test site show rapid regrowth of Malvaceae and Petiveria alliacea vegetation over all burials that are common in these forests, which can make detection more difficult.

Analysis of koi herpesvirus latency in wild common carp and ornamental koi in Oregon, USA.

PubMed

Xu, Jia-Rong; Bently, Jennifer; Beck, Linda; Reed, Aimee; Miller-Morgan, Tim; Heidel, Jerry R; Kent, Michael L; Rockey, Daniel D; Jin, Ling

2013-02-01

Koi herpesvirus (KHV) infection is associated with high mortalities in both common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi) worldwide. Although acute infection has been reported in both domestic and wild common carp, the status of KHV latent infection is largely unknown in wild common carp. To investigate whether KHV latency is present in wild common carp, the distribution of KHV latent infection was investigated in two geographically distinct populations of wild common carp in Oregon, as well as in koi from an Oregon-based commercial supplier. Latent KHV infection was demonstrated in white blood cells from each of these populations. Although KHV isolated from acute infections has two distinct genetic groups, Asian and European, KHV detected in wild carp has not been genetically characterized. DNA sequences from ORF 25 to 26 that are unique between Asian and European were investigated in this study. KHV from captive koi and some wild common carp were found to have ORF-25-26 sequences similar to KHV-J (Asian), while the majority of KHV DNA detected in wild common carp has similarity to KHV-U/-I (European). In addition, DNA sequences from IL-10, and TNFR were sequenced and compared with no differences found, which suggests immune suppressor genes of KHV are conserved between KHV in wild common carp and koi, and is consistent with KHV-U, -I, -J. Copyright © 2012 Elsevier B.V. All rights reserved.

Maximizing detection probability of Wetland-dependent birds during point-count surveys in northwestern Florida

USGS Publications Warehouse

Nadeau, C.P.; Conway, C.J.; Smith, B.S.; Lewis, T.E.

2008-01-01

We conducted 262 call-broadcast point-count surveys (1-6 replicate surveys on each of 62 points) using standardized North American Marsh Bird Monitoring Protocols between 31 May and 7 July 2006 on St. Vincent National Wildlife Refuge, an island off the northwest coast of Florida. We conducted double-blind multiple-observer surveys, paired morning and evening surveys, and paired morning and night surveys to examine the influence of call-broadcast and time of day on detection probability. Observer detection probability for all species pooled was 75% and was similar between passive (69%) and call-broadcast (65%) periods. Detection probability was higher on morning than evening (t = 3.0, P = 0.030) or night (t = 3.4, P = 0.042) surveys when we pooled all species. Detection probability was higher (but not significant for all species) on morning compared to evening or night surveys for all five focal species detected on surveys: Least Bittern (Ixobrychus exilis), Clapper Rail (Rallus longirostris), Purple Gallinule (Porphyrula martinica), Common Moorhen (Gallinula chloropus), and American Coot (Fulica americana). We detected more Least Bitterns (t = 2.4, P = 0.064) and Common Moorhens (t = 2.8, P = 0.026) on morning than evening surveys, and more Clapper Rails (t = 5.1, P = 0.014) on morning than night surveys.

Selective detection of trace nitroaromatic, nitramine, and nitrate ester explosive residues using a three-step fluorimetric sensing process: a tandem turn-off, turn-on sensor.

PubMed

Sanchez, Jason C; Toal, Sarah J; Wang, Zheng; Dugan, Regina E; Trogler, William C

2007-11-01

Detection of trace quantities of explosive residues plays a key role in military, civilian, and counter-terrorism applications. To advance explosives sensor technology, current methods will need to become cheaper and portable while maintaining sensitivity and selectivity. The detection of common explosives including trinitrotoluene (TNT), cyclotrimethylenetrinitramine, cyclotetramethylene-tetranitramine, pentaerythritol tetranitrate, 2,4,6-trinitrophenyl-N-methylnitramine, and trinitroglycerin may be carried out using a three-step process combining "turn-off" and "turn-on" fluorimetric sensing. This process first detects nitroaromatic explosives by their quenching of green luminescence of polymetalloles (lambda em approximately 400-510 nm). The second step places down a thin film of 2,3-diaminonaphthalene (DAN) while "erasing" the polymetallole luminescence. The final step completes the reaction of the nitramines and/or nitrate esters with DAN resulting in the formation of a blue luminescent traizole complex (lambda(em) = 450 nm) providing a "turn-on" response for nitramine and nitrate ester-based explosives. Detection limits as low as 2 ng are observed. Solid-state detection of production line explosives demonstrates the applicability of this method to real world situations. This method offers a sensitive and selective detection process for a diverse group of the most common high explosives used in military and terrorist applications today.

Comparison of detection techniques for capillary electrophoresis analysis of gold nanoparticles.

PubMed

Matczuk, Magdalena; Aleksenko, Svetlana S; Matysik, Frank-Michael; Jarosz, Maciej; Timerbaev, Andrei R

2015-05-01

As metallic nanoparticles are growing in importance as analytes in CE, increases an interest in appropriate detection methods for their quantification in various samples. For gold nanoparticles (AuNPs), the most common UV detection poses intricacy of inadequate sensitivity that hinders the applicability of CE. With the objective of resolving this challenge, UV detection was compared with C(4) D and ICP-MS as alternative modes of detection for AuNPs. A C(4) D detector, applied under pressure-driven conditions, exhibited better sensitivity than a UV detector. However, C(4) D turned to be unsatisfactory to differentiate the signal of AuNPs at common CE conditions despite varying the nature of BGE and detection conditions. Due to intrinsic sensitivity and low background levels typical to Au, ICP-MS greatly surpasses UV detection. After optimization trials, CE-ICP-MS gained the LOD of AuNPs as low as 2 × 10(-15) M, as well as an excellent performance in terms of signal stability and linearity. Also importantly, the optimized BGE appears to be well matched to explore the behavior of AuNPs in biologically relevant systems. This was demonstrated by probing the interaction between AuNPs and the main blood-transporting protein, HSA. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pelvic artery calcification detection on CT scans using convolutional neural networks

NASA Astrophysics Data System (ADS)

Liu, Jiamin; Lu, Le; Yao, Jianhua; Bagheri, Mohammadhadi; Summers, Ronald M.

2017-03-01

Artery calcification is observed commonly in elderly patients, especially in patients with chronic kidney disease, and may affect coronary, carotid and peripheral arteries. Vascular calcification has been associated with many clinical outcomes. Manual identification of calcification in CT scans requires substantial expert interaction, which makes it time-consuming and infeasible for large-scale studies. Many works have been proposed for coronary artery calcification detection in cardiac CT scans. In these works, coronary artery extraction is commonly required for calcification detection. However, there are few works about abdominal or pelvic artery calcification detection. In this work, we present a method for automatic pelvic artery calcification detection on CT scan. This method uses the recent advanced faster region-based convolutional neural network (R-CNN) to directly identify artery calcification without a need for artery extraction since pelvic artery extraction itself is challenging. Our method first generates category-independent region proposals for each slice of the input CT scan using region proposal networks (RPN). Then, each region proposal is jointly classified and refined by softmax classifier and bounding box regressor. We applied the detection method to 500 images from 20 CT scans of patients for evaluation. The detection system achieved a 77.4% average precision and a 85% sensitivity at 1 false positive per image.

The conclusiveness of less-invasive imaging techniques (computer tomography, X-ray) with regard to their identification of bone diseases in a primate model (Callithrix jacchus).

PubMed

Grohmann, J; Taetzner, S; Theuss, T; Kuehnel, F; Buchwald, U; Einspanier, A

2012-04-01

Although common marmosets seem to be appropriate animal models to examine bone diseases, no data about the conclusiveness of less-invasive techniques are available. Therefore, the aim was to combine different techniques to analyse changes in bone metabolism of common marmosets with bone diseases. Five monkeys were examined by X-ray, computer tomography (CT), histology and immunohistochemistry (IHC). Monkeys with lowest bone mineral density (BMD) showed increased bone marrow, decreased cancellous bone and decreased contrast in X-ray. Highest alkaline phosphatase (AP)-levels were detected in bones with low elastic modulus. Expression of osteopontin (OPN), osteocalcin (OC) and runt-related transcriptions factor 2 (RUNX 2) was detected in bones with high modulus. No expression was present in bones with lower modulus. Collagen type I and V were found in every bone. In conclusion, CT, X-ray and AP are useful techniques to detect bone diseases in common marmosets. These observations could be confirmed by IHC. © 2012 John Wiley & Sons A/S.

A DNA-Based Procedure for In Planta Detection of Fusarium oxysporum f. sp. phaseoli.

PubMed

Alves-Santos, Fernando M; Ramos, Brisa; García-Sánchez, M Asunción; Eslava, Arturo P; Díaz-Mínguez, José María

2002-03-01

ABSTRACT We have characterized strains of Fusarium oxysporum from common bean fields in Spain that were nonpathogenic on common bean, as well as F. oxysporum strains (F. oxysporum f. sp. phaseoli) pathogenic to common bean by random amplified polymorphic DNA (RAPD) analysis. We identified a RAPD marker (RAPD 4.12) specific for the highly virulent pathogenic strains of the seven races of F. oxysporum f. sp. phaseoli. Sequence analysis of RAPD 4.12 allowed the design of oligonucleotides that amplify a 609-bp sequence characterized amplified region (SCAR) marker (SCAR-B310A280). Under controlled environmental and greenhouse conditions, detection of the pathogen by polymerase chain reaction was 100% successful in root samples of infected but still symptomless plants and in stem samples of plants with disease severity of >/=4 in the Centro Internacional de Agricultura Tropical (CIAT; Cali, Colombia) scale. The diagnostic procedure can be completed in 5 h and allows the detection of all known races of the pathogen in plant samples at early stages of the disease with no visible symptoms.

[Detection of the introgression of genome elements of the Aegilops cylindrica host. into the Triticum aestivum L. genome by ISSR and SSR analysis].

PubMed

Galaev, A V; Babaiants, L T; Sivolap, Iu M

2004-12-01

To reveal sites of the donor genome in wheat crossed with Aegilops cylindrica, which acquired conferred resistance to fungal diseases, a comparative analysis of introgressive and parental forms was conducted. Two systems of PCR analysis, ISSR and SSR-PCR, were employed. Upon use of 7 ISSR primers in genotypes of 30 individual plants BC1 F9 belonging to lines 5/55-91 and 5/20-91, 19 ISSR loci were revealed and assigned to introgressive fragments of Aegilops cylindrica genome in Triticum aestivum. The 40 pairs of SSR primers allowed the detection of seven introgressive alleles; three of these alleles were located on common wheat chromosomes in the B genome, while four alleles, in the D genome. Based on data of microsatellite analysis, it was assumed that the telomeric region of the long arm of common wheat chromosome 6A also changed. ISSR and SSR methods were shown to be effective for detecting variability caused by introgression of foreign genetic material into the genome of common wheat.

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

Genome-wide meta-analysis of common variant differences between men and women

PubMed Central

Boraska, Vesna; Jerončić, Ana; Colonna, Vincenza; Southam, Lorraine; Nyholt, Dale R.; William Rayner, Nigel; Perry, John R.B.; Toniolo, Daniela; Albrecht, Eva; Ang, Wei; Bandinelli, Stefania; Barbalic, Maja; Barroso, Inês; Beckmann, Jacques S.; Biffar, Reiner; Boomsma, Dorret; Campbell, Harry; Corre, Tanguy; Erdmann, Jeanette; Esko, Tõnu; Fischer, Krista; Franceschini, Nora; Frayling, Timothy M.; Girotto, Giorgia; Gonzalez, Juan R.; Harris, Tamara B.; Heath, Andrew C.; Heid, Iris M.; Hoffmann, Wolfgang; Hofman, Albert; Horikoshi, Momoko; Hua Zhao, Jing; Jackson, Anne U.; Hottenga, Jouke-Jan; Jula, Antti; Kähönen, Mika; Khaw, Kay-Tee; Kiemeney, Lambertus A.; Klopp, Norman; Kutalik, Zoltán; Lagou, Vasiliki; Launer, Lenore J.; Lehtimäki, Terho; Lemire, Mathieu; Lokki, Marja-Liisa; Loley, Christina; Luan, Jian'an; Mangino, Massimo; Mateo Leach, Irene; Medland, Sarah E.; Mihailov, Evelin; Montgomery, Grant W.; Navis, Gerjan; Newnham, John; Nieminen, Markku S.; Palotie, Aarno; Panoutsopoulou, Kalliope; Peters, Annette; Pirastu, Nicola; Polašek, Ozren; Rehnström, Karola; Ripatti, Samuli; Ritchie, Graham R.S.; Rivadeneira, Fernando; Robino, Antonietta; Samani, Nilesh J.; Shin, So-Youn; Sinisalo, Juha; Smit, Johannes H.; Soranzo, Nicole; Stolk, Lisette; Swinkels, Dorine W.; Tanaka, Toshiko; Teumer, Alexander; Tönjes, Anke; Traglia, Michela; Tuomilehto, Jaakko; Valsesia, Armand; van Gilst, Wiek H.; van Meurs, Joyce B.J.; Smith, Albert Vernon; Viikari, Jorma; Vink, Jacqueline M.; Waeber, Gerard; Warrington, Nicole M.; Widen, Elisabeth; Willemsen, Gonneke; Wright, Alan F.; Zanke, Brent W.; Zgaga, Lina; Boehnke, Michael; d'Adamo, Adamo Pio; de Geus, Eco; Demerath, Ellen W.; den Heijer, Martin; Eriksson, Johan G.; Ferrucci, Luigi; Gieger, Christian; Gudnason, Vilmundur; Hayward, Caroline; Hengstenberg, Christian; Hudson, Thomas J.; Järvelin, Marjo-Riitta; Kogevinas, Manolis; Loos, Ruth J.F.; Martin, Nicholas G.; Metspalu, Andres; Pennell, Craig E.; Penninx, Brenda W.; Perola, Markus; Raitakari, Olli; Salomaa, Veikko; Schreiber, Stefan; Schunkert, Heribert; Spector, Tim D.; Stumvoll, Michael; Uitterlinden, André G.; Ulivi, Sheila; van der Harst, Pim; Vollenweider, Peter; Völzke, Henry; Wareham, Nicholas J.; Wichmann, H.-Erich; Wilson, James F.; Rudan, Igor; Xue, Yali; Zeggini, Eleftheria

2012-01-01

The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency >0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant (P < 5 × 10−8) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across ∼115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits. PMID:22843499

Survey and Experimental Infection of Enteropathogenic Escherichia coli in Common Marmosets (Callithrix jacchus).

PubMed

Hayashimoto, Nobuhito; Inoue, Takashi; Morita, Hanako; Yasuda, Masahiko; Ueno, Masami; Kawai, Kenji; Itoh, Toshio

2016-01-01

Common marmosets (Callithrix jacchus) are frequently used for biomedical research but can be afflicted with diarrhea-a serious and potentially lethal health problem. Enteropathogenic Escherichia coli (EPEC) is thought to be the causative pathogen of hemorrhagic typhlocolitis in common marmosets, but the actual incidence of the disease and the relationship between EPEC and hematochezia are unknown. This study investigated the prevalence of EPEC infection in common marmosets and the association between EPEC and hematochezia. A total of 230 stool or rectal swab samples were collected from 230 common marmosets (98 clinically healthy, 85 diarrhea, and 47 bloody stool samples) and tested by culture-based detection and PCR amplification of VT1, VT2, LT, ST, eae, and bfp genes. Healthy animals were divided into three groups (n = 4 each for high and low concentration groups and n = 2 as negative control), and those in the experimental groups were perorally inoculated with a 2-ml of suspension of EPEC R811 strain adjusted to 5 × 108 (high concentration) and 5 × 104 (low concentration) CFU/ ml. Two animals in each group were examined 3 and 14 days post-inoculation (DPI). EPEC was detected in 10 of 98 clinically healthy samples (10.2%), 17 of 85 diarrhea samples (20%), and all 47 bloody stool samples (100%), with a significant difference detected between presence of EPEC and sample status (P < 0.01). Acute hematochezia was observed in all animals of the high-concentration group but not in other groups at 1 or 2 DPI. A histopathological examination revealed the attachment of gram-negative bacilli to epithelial apical membranes and desquamated epithelial cells in the cecum of animals in the high-concentration group at 3 DPI. These findings suggest that EPEC is a causative agent of hemorrhagic typhlocolitis in common marmosets.

Comparison of a standardized procedure with current laboratory practices for the detection of lupus anticoagulant in France. Working Group on Hemostasis of the Société Française de Biologie Clinique.

PubMed

1993-11-15

A multicenter study involving 13 laboratories was designed to compare a common procedure for screening lupus anticoagulants (LA) to the different practices currently in use in these laboratories. The common procedure combined 3 phospholipid-dependent assays, including mixing studies and a phospholipid neutralizing test. Due to the heterogeneity of LA expression, an abnormal result in at least one of the tests was sufficient to classify a sample as positive for LA. Consecutive samples referred for LA diagnosis were evaluated in parallel by each participant and the data found using the common procedure were analyzed independently according to mutually agreed cut-offs and criteria for sample classification. Within a period of 3 months, 535 samples were included, of which 147 were judged LA positive, 29 undetermined and 359 negative by the respective laboratories using their current practice. When using the common procedure, 149 plasmas were said to be positive, 38 undetermined and 348 negative. Absolute concordance occurred for 81% of the specimen population and absolute discordance (positive versus negative) for 7%. The level of agreement between the common procedure and the current practices, assessed by kappa indexes, indicated noticeable variations in the rates of detection from laboratory to laboratory. Among the different tests used in the common procedure, regular APTT was the least sensitive (about 50% detection) but none of the other tests alone recognized more than 73% of specimens from the LA positive population. This yield increased to about 90% with any combination of 2 sensitive tests.(ABSTRACT TRUNCATED AT 250 WORDS)

Signal Detection and Monitoring Based on Longitudinal Healthcare Data

PubMed Central

Suling, Marc; Pigeot, Iris

2012-01-01

Post-marketing detection and surveillance of potential safety hazards are crucial tasks in pharmacovigilance. To uncover such safety risks, a wide set of techniques has been developed for spontaneous reporting data and, more recently, for longitudinal data. This paper gives a broad overview of the signal detection process and introduces some types of data sources typically used. The most commonly applied signal detection algorithms are presented, covering simple frequentistic methods like the proportional reporting rate or the reporting odds ratio, more advanced Bayesian techniques for spontaneous and longitudinal data, e.g., the Bayesian Confidence Propagation Neural Network or the Multi-item Gamma-Poisson Shrinker and methods developed for longitudinal data only, like the IC temporal pattern detection. Additionally, the problem of adjustment for underlying confounding is discussed and the most common strategies to automatically identify false-positive signals are addressed. A drug monitoring technique based on Wald’s sequential probability ratio test is presented. For each method, a real-life application is given, and a wide set of literature for further reading is referenced. PMID:24300373

Water-quality monitoring for a pilot piling removal field evaluation, Coal Creek Slough, Washington, 2008-09

USGS Publications Warehouse

Nilsen, Elena B.; Alvarez, David A.

2011-01-01

Significant Findings Water and sediment quality monitoring was conducted before and after the removal of a piling field located in Coal Creek Slough near Longview, Washington. Passive chemical samplers and continuous water-quality monitoring instruments were deployed at the piling removal site, Coal Creek Slough Site 1 (CCS1), and at a comparison site, Coal Creek Slough Site 2 (CCS2), before (2008) and after (2009) piling removal. Surface and subsurface (core) sediment samples were collected before and after piling removal and were analyzed for grain size, organic carbon content, and chemicals of concern. Significant findings from this study include: * Phenanthrene was the only compound detected in wood piling samples analyzed for a large suite of semivolatile organic compounds and polycyclic aromatic hydrocarbons (PAHs). Metals potentially associated with wood treatment were detected in the wood piling samples at low concentrations. * Organic carbon was slightly lower in core samples from CCS1 in pre-removal (2008) and post-removal (2009) samples than in surface samples from both sites in both years. * Grain-size class distributions were relatively uniform between sites and years. * Thirty-four out of 110 chemicals of concern were detected in sediments. Eight of those detected were anthropogenic waste indicator (AWI) compounds, 18 were PAHs, 4 were sterols, and 4 were metals potentially associated with wood treatment. * Nearly all reported concentrations of chemicals of concern in sediments are qualified as estimates, primarily due to interferences in extracts resulting from complex sample matrices. Indole, perylene, and fluoranthene are reported without qualification for some of the samples, and the metals are reported without qualification for all samples. * The highest frequency of detection of chemicals of concern was seen in the pre-removal surface samples at both sites. * AWI compounds were detected less frequently and at lower concentrations during the post-removal sampling compared to the pre-removal sampling. * Several PAHs were detected at relatively high concentrations in core samples, likely indicating historical sources. * Most commonly detected PAHs in sediments were 2,6-dimethylnaphthalene, fluoranthene, perylene, and pyrene. * Most commonly detected AWIs in sediments were 3-methyl-1h-indole (skatol), acetophenone, indole, phenol, and paracresol. * Sedimentary concentrations of perylene exceeded available sediment quality guidelines. Perylene is widespread in the environment and has large potential natural sources in addition to its anthropogenic sources. * Concentrations of metals did not exceed sediment quality guidelines. * Multiple organochlorine pesticides, both banned and currently used, were detected at each site using passive samplers. * Commonly detected pesticides included hexachlorobenzene, pentachloroanisole (a degradation product of pentachlorophenol), diazinon, cis-chlordane, endosulfan, DDD, and endosulfan sulfate. * PBDE concentrations detected in passive sampler extracts were less than the method detection limit at all sites with the exception of PBDE-99, detected at a concentration less than the reporting limit. * The fragrance galaxolide was detected at a concentration greater than the method detection limit. * Common PAHs, such as phenanthrene, fluoranthene, and pyrene, were detected in every passive sampler. * Dissolved oxygen concentration was slightly higher at site CCS1 compared to site CCS2 in both years. * Overall, there was no systematic increase in chemicals of concern at the restoration site during post-removal monitoring compared to conditions during pre-removal monitoring. Any immediate, short-duration effects of piling removal on water quality could not be determined because monitoring was not conducted during the removal.

Electrochemical characterization of an immunosensor for Salmonella spp. detection

USDA-ARS?s Scientific Manuscript database

Immunosensors represent a rapid alternative method for diagnosing Salmonella contamination. The objective of this study was to develop and evaluate the performance of an electrochemical immunosensor for the detection of Salmonella spp., the most common foodborne pathogen worldwide. In the immunosens...

CURRENT ISSUES IN HTE DETECTION OF HUMAN EXPOSURE TO THE CYANOBACTERIA TOXINS, MICROCYSTINS

EPA Science Inventory

Introduction: Toxic cyanobacteria are contaminants of surface waters worldwide. Microcystins are some of the most commonly detected toxins. Biological evidence of human exposure has been difficult to obtain due to technical, temporal, and biological limitations. However, evide...

Microbial biofilm detection on food contact surfaces by macro-scale fluorescence imaging

USDA-ARS?s Scientific Manuscript database

Hyperspectral fluorescence imaging methods were utilized to evaluate the potential of multispectral fluorescence methods for detection of pathogenic biofilm formations on four types of food contact surface materials: stainless steel, high density polyethylene (HDPE) commonly used for cutting boards,...

Novel ophthalmological OCT instrument design

NASA Astrophysics Data System (ADS)

Xu, Xiaonan; Gao, Jiansong; Guo, Jihua; Xue, Ping

2002-04-01

This paper presents a novel ophthamological optical coherence tomography detecting instrument, which we design, and introduces measuring arm emphatically. For glaucoma which is very common in the Orient, this system can achieve both the eyeground detection and the canthus detection. And it combines the cranny lamp's conventional detection with optical coherence tomography. Considering all the system, this design has a longitudinal resolution of 15 um, and a transverse resolution of 20 um at imaging velocity of 4 frames per second.

Leak detection by mass balance effective for Norman Wells line

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

Liou, J.C.P.

Mass-balance calculations for leak detection have been shown as effective as a leading software system, in a comparison based on a major Canadian crude-oil pipeline. The calculations and NovaCorp`s Leakstop software each detected 4% (approximately) or greater leaks on Interprovincial Pipe Line (IPL) Inc.`s Norman Wells pipeline. Insufficient data exist to assess performances of the two methods for leaks smaller than 4%. Pipeline leak detection using such software-based systems are common. Their effectiveness is measured by how small and how quickly a leak can be detected. Algorithms used and measurement uncertainties determine leak detectability.

Fog detection for interstate and state highways.

DOT National Transportation Integrated Search

2012-12-01

Fog is a common and recurrent phenomenon in West Virginia which is the cause of nearly 1.3% of all fatal crashes : occurring all over the state. All three types of fog are common in the state which results in lack visibility, limited : contrast, dist...

Common Bile Duct Stones Detected After Cholecystectomy:Advancement into the Duodenum via the Percutaneous Route

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

Ozcan, Nevzat, E-mail: nevzatcan@yahoo.com; Erdogan, Nuri; Baskol, Mevlut

2003-04-15

Purpose: To report our experience in the use of percutaneous extraction of common bile duct stones detected in the post-cholecystectomy period. Methods: Forty-two patients in whom endoscopic cannulation and/or sphincterotomy had failed or could not be done due to several reasons underwent balloon dilatation of the ampulla of Vater and subsequent advancement of the stones via the percutaneous transhepatic route or T-tube tract. Results: The procedure was successful in 42 cases. In three patients, stones were crushed in the common bile duct and pushed as fragments into the duodenum. In all cases transient adverse effects were observed. There were nomore » major complications. All cases were checked with ultrasonography for 6 months after the procedure. Conclusion: Percutaneous extraction of common bile duct stones is an effective method of treatment with a high success rate,low complication rate and shorter hospital stay. It may serve as an alternative method in cases where endoscopic removal of stones fails.« less

Identifying influential user communities on the social network

NASA Astrophysics Data System (ADS)

Hu, Weishu; Gong, Zhiguo; Hou U, Leong; Guo, Jingzhi

2015-10-01

Nowadays social network services have been popularly used in electronic commerce systems. Users on the social network can develop different relationships based on their common interests and activities. In order to promote the business, it is interesting to explore hidden relationships among users developed on the social network. Such knowledge can be used to locate target users for different advertisements and to provide effective product recommendations. In this paper, we define and study a novel community detection problem that is to discover the hidden community structure in large social networks based on their common interests. We observe that the users typically pay more attention to those users who share similar interests, which enable a way to partition the users into different communities according to their common interests. We propose two algorithms to detect influential communities using common interests in large social networks efficiently and effectively. We conduct our experimental evaluation using a data set from Epinions, which demonstrates that our method achieves 4-11.8% accuracy improvement over the state-of-the-art method.

Study on the Automatic Detection Method and System of Multifunctional Hydrocephalus Shunt

NASA Astrophysics Data System (ADS)

Sun, Xuan; Wang, Guangzhen; Dong, Quancheng; Li, Yuzhong

2017-07-01

Aiming to the difficulty of micro pressure detection and the difficulty of micro flow control in the testing process of hydrocephalus shunt, the principle of the shunt performance detection was analyzed.In this study, the author analyzed the principle of several items of shunt performance detection,and used advanced micro pressure sensor and micro flow peristaltic pump to overcome the micro pressure detection and micro flow control technology.At the same time,This study also puted many common experimental projects integrated, and successfully developed the automatic detection system for a shunt performance detection function, to achieve a test with high precision, high efficiency and automation.

Bartonella species detection in captive, stranded and free-ranging cetaceans.

PubMed

Harms, Craig A; Maggi, Ricardo G; Breitschwerdt, Edward B; Clemons-Chevis, Connie L; Solangi, Mobashir; Rotstein, David S; Fair, Patricia A; Hansen, Larry J; Hohn, Aleta A; Lovewell, Gretchen N; McLellan, William A; Pabst, D Ann; Rowles, Teri K; Schwacke, Lori H; Townsend, Forrest I; Wells, Randall S

2008-01-01

We present prevalence of Bartonella spp. for multiple cohorts of wild and captive cetaceans. One hundred and six cetaceans including 86 bottlenose dolphins (71 free-ranging, 14 captive in a facility with a dolphin experiencing debility of unknown origin, 1 stranded), 11 striped dolphins, 4 harbor porpoises, 3 Risso's dolphins, 1 dwarf sperm whale and 1 pygmy sperm whale (all stranded) were sampled. Whole blood (n = 95 live animals) and tissues (n = 15 freshly dead animals) were screened by PCR (n = 106 animals), PCR of enrichment cultures (n = 50 animals), and subcultures (n = 50 animals). Bartonella spp. were detected from 17 cetaceans, including 12 by direct extraction PCR of blood or tissues, 6 by PCR of enrichment cultures, and 4 by subculture isolation. Bartonella spp. were more commonly detected from the captive (6/14, 43%) than from free-ranging (2/71, 2.8%) bottlenose dolphins, and were commonly detected from the stranded animals (9/21, 43%; 3/11 striped dolphins, 3/4 harbor porpoises, 2/3 Risso's dolphins, 1/1 pygmy sperm whale, 0/1 dwarf sperm whale, 0/1 bottlenose dolphin). Sequencing identified a Bartonella spp. most similar to B. henselae San Antonio 2 in eight cases (4 bottlenose dolphins, 2 striped dolphins, 2 harbor porpoises), B. henselae Houston 1 in three cases (2 Risso's dolphins, 1 harbor porpoise), and untyped in six cases (4 bottlenose dolphins, 1 striped dolphin, 1 pygmy sperm whale). Although disease causation has not been established, Bartonella species were detected more commonly from cetaceans that were overtly debilitated or were cohabiting in captivity with a debilitated animal than from free-ranging animals. The detection of Bartonella spp. from cetaceans may be of pathophysiological concern.

Air Monitoring for Hazardous Gas Detection

NASA Technical Reports Server (NTRS)

Arkin, C. Richard; Griffin, Timothy P.; Adams, Frederick W.; Naylor, Guy; Haskell, William; Floyd, David; Curley, Charles; Follistein, Duke W.

2004-01-01

The Hazardous Gas Detection Lab (HGDL) at Kennedy Space Center is involved in the design and development of instrumentation that can detect and quantify various hazardous gases. Traditionally these systems are designed for leak detection of the cryogenic gases used for the propulsion of the Shuttle and other vehicles. Mass spectrometers are the basis of these systems, which provide excellent quantitation, sensitivity, selectivity, response times and detection limits. A Table lists common gases monitored for aerospace applications. The first five gases, hydrogen, helium, nitrogen, oxygen, and argon are historically the focus of the HGDL.

Anthropogenic organic compounds in source water of nine community water systems that withdraw from streams, 2002-05

USGS Publications Warehouse

Kingsbury, James A.; Delzer, Gregory C.; Hopple, Jessica A.

2008-01-01

Source water, herein defined as stream water collected at a water-system intake prior to water treatment, was sampled at nine community water systems, ranging in size from a system serving about 3,000 people to one that serves about 2 million people. As many as 17 source-water samples were collected at each site over about a 12-month period between 2002 and 2004 for analysis of 258 anthropogenic organic compounds. Most of these compounds are unregulated in drinking water, and the compounds analyzed include pesticides and selected pesticide degradates, gasoline hydrocarbons, personal-care and domestic-use compounds, and solvents. The laboratory analytical methods used in this study have relatively low detection levels - commonly 100 to 1,000 times lower than State and Federal standards and guidelines for protecting water quality. Detections, therefore, do not necessarily indicate a concern to human health but rather help to identify emerging issues and to track changes in occurrence and concentrations over time. About one-half (134) of the compounds were detected at least once in source-water samples. Forty-seven compounds were detected commonly (in 10 percent or more of the samples), and six compounds (chloroform, atrazine, simazine, metolachlor, deethylatrazine, and hexahydrohexamethylcyclopentabenzopyran (HHCB) were detected in more than one-half of the samples. Chloroform was the most commonly detected compound - in every sample (year round) at five sites. Findings for chloroform and the fragrances HHCB and acetyl hexamethyl tetrahydronaphthalene (AHTN) indicate an association between occurrence and the presence of large upstream wastewater discharges in the watersheds. The herbicides atrazine, simazine, and metolachlor also were among the most commonly detected compounds. Degradates of these herbicides, as well as those of a few other commonly occurring herbicides, generally were detected at concentrations similar to or greater than concentrations of the parent compound. Samples typically contained mixtures of two or more compounds. The total number of compounds and their total concentration in samples generally increased with the amount of urban and agricultural land use in a watershed. Annual mean concentrations of all compounds were less than human-health benchmarks. Single-sample concentrations of anthropogenic organic compounds in source water generally were less than 0.1 microgram per liter and less than established human-health benchmarks. Human-health benchmarks used for comparison were U.S. Environmental Protection Agency (USEPA) Maximum Contaminant Levels (MCLs) for regulated compounds and U.S. Geological Survey Health-Based Screening Levels for unregulated compounds. About one-half of all detected compounds do not have human-health benchmarks or adequate toxicity information for evaluating results in a human-health context. During a second sampling phase (2004-05), source water and finished water (water that has passed through all the treatment processes but prior to distribution) were sampled at eight of the nine community water systems. Water-treatment processes differ among the systems. Specifically, treatment at five of the systems is conventional, typically including steps of coagulation, flocculation, sedimentation, filtration, and disinfection. One water system uses slow sand filtration and disinfection, a second system uses ozone as a preliminary treatment step to conventional treatment, and a third system is a direct filtration treatment plant that uses many of the steps employed in conventional treatment. Most of these treatment steps are not designed specifically to remove the compounds monitored in this study. About two-thirds of the compounds detected commonly in source water were detected at similar frequencies in finished water. Although the water-treatment steps differ somewhat among the eight water systems, the amount of change in concentration of the compounds from source- to finish

Detection of Protein Interactions in T3S Systems Using Yeast Two-Hybrid Analysis.

PubMed

Nilles, Matthew L

2017-01-01

Two-hybrid systems, sometimes termed interaction traps, are genetic systems designed to find and analyze interactions between proteins. The most common systems are yeast based (commonly Saccharomyces cerevisae) and rely on the functional reconstitution of the GAL4 transcriptional activator. Reporter genes, such as the lacZ gene of Escherichia coli (encodes β-galactosidase), are placed under GAL4-dependent transcriptional control to provide quick and reliable detection of protein interactions. In this method the use of a yeast-based two-hybrid system is described to study protein interactions between components of type III secretion systems.

Physics Needs Philosophy. Philosophy Needs Physics

NASA Astrophysics Data System (ADS)

Rovelli, Carlo

2018-05-01

Contrary to claims about the irrelevance of philosophy for science, I argue that philosophy has had, and still has, far more influence on physics than is commonly assumed. I maintain that the current anti-philosophical ideology has had damaging effects on the fertility of science. I also suggest that recent important empirical results, such as the detection of the Higgs particle and gravitational waves, and the failure to detect supersymmetry where many expected to find it, question the validity of certain philosophical assumptions common among theoretical physicists, inviting us to engage in a clearer philosophical reflection on scientific method.

An acoustic survey of beaked whales at Cross Seamount near Hawaii.

PubMed

McDonald, Mark A; Hildebrand, John A; Wiggins, Sean M; Johnston, David W; Polovina, Jeffrey J

2009-02-01

An acoustic record from Cross Seamount, southwest of Hawaii, revealed sounds characteristic of beaked whale echolocation at the same relative abundance year-around (270 of 356 days), occurring almost entirely at night. The most common sound had a linear frequency upsweep from 35 to 100 kHz (the bandwidth of recording), an interpulse interval of 0.11 s, and duration of at least 932 mus. A less common upsweep sound with shorter interpulse interval and slower sweep rate was also present. Sounds matching Cuvier's beaked whale were not detected, and Blainville's beaked whale sounds were detected on only one occasion.

Pre-operative endoscopic ultrasonography can optimise the management of patients undergoing laparoscopic cholecystectomy with abnormal liver function tests as the sole risk factor for choledocholithiasis: a prospective study.

PubMed

Meroni, E; Bisagni, P; Bona, S; Fumagalli, U; Zago, M; Rosati, R; Malesci, A

2004-01-01

Pre-operative endosonography has been proposed as a cost-effective procedure in the management of patients who undergo laparoscopic cholecystectomy having an intermediate risk of common bile duct stones. We prospectively evaluated the impact of pre-operative endosonography on the management of patients facing laparoscopic cholecystectomy with abnormal liver function tests as the sole risk factor for choledocolithiasis. Among 587 consecutive patients scheduled for laparoscopic cholecystectomy, 47 (8%) patients having one or more abnormal liver function tests but a normal appearance of common bile duct at abdominal ultrasound, underwent pre-operative endosonography. In patients with endosonography-detected common bile duct stones, a pre-operative endoscopic retrograde cholangiography was performed, or an intra-operative endoscopic retrograde cholangiography was scheduled. In all endosonography-negative patients, an intra-operative trans-cystic cholangiography was performed. Endosonography detected common bile duct stones in nine patients (19%) but only in five of them stones were radiologically confirmed (PPV 0.55). Endosonography-detected stones were confirmed in four of four (100%) patients in whom cholangiography was performed within 1 week, but only in one of five (20%) patients in whom radiology was further delayed (P < 0.05). In three of four cases (75%), stones detected at endosonography but not confirmed at X-rays, were smaller than 2.0 mm. Among 38 patients with negative endosonography, common bile duct stones were found in two patients (NPV 0.95), whereas unplanned endoscopic stone extraction was needed only in one patient (NPV 0.97). Pre-operative endosonography can spare unnecessary pre-operative endoscopic retrograde cholangiography as well as inappropriate scheduling of intra-operative endoscopic retrograde cholangiography in patients undergoing laparoscopic cholecystectomy with abnormal liver function tests. To maximise the impact of endosonography on the management of these patients, the procedure should be performed immediately before laparoscopic cholecystectomy.

Factors affecting detectability of river otters during sign surveys

USGS Publications Warehouse

Jeffress, Mackenzie R.; Paukert, Craig P.; Sandercock, Brett K.; Gipson, Philip S.

2011-01-01

Sign surveys are commonly used to study and monitor wildlife species but may be flawed when surveys are conducted only once and cover short distances, which can lead to a lack of accountability for false absences. Multiple observers surveyed for river otter (Lontra canadensis) scat and tracks along stream and reservoir shorelines at 110 randomly selected sites in eastern Kansas from January to April 2008 and 2009 to determine if detection probability differed among substrates, sign types, observers, survey lengths, and near access points. We estimated detection probabilities (p) of river otters using occupancy models in Program PRESENCE. Mean detection probability for a 400-m survey was highest in mud substrates (p = 0.60) and lowest in snow (p = 0.18) and leaf litter substrates (p = 0.27). Scat had a higher detection probability (p = 0.53) than tracks (p = 0.18), and experienced observers had higher detection probabilities (p < 0.71) than novice observers (p < 0.55). Detection probabilities increased almost 3-fold as survey length increased from 200 m to 1,000 m, and otter sign was not concentrated near access points. After accounting for imperfect detection, our estimates of otter site occupancy based on a 400-m survey increased >3-fold, providing further evidence of the potential negative bias that can occur in estimates from sign surveys when imperfect detection is not addressed. Our study identifies areas for improvement in sign survey methodologies and results are applicable for sign surveys commonly used for many species across a range of habitats.

Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health

USGS Publications Warehouse

King, Dawn N.; Donohue, Maura J.; Vesper, Stephen J.; Villegas, Eric N.; Ware, Michael W.; Vogel, Megan E.; Furlong, Edward; Kolpin, Dana W.; Glassmeyer, Susan T.; Pfaller, Stacy

2016-01-01

An occurrence survey was conducted on selected pathogens in source and treated drinking water collected from 25 drinking water treatment plants (DWTPs) in the United States. Water samples were analyzed for the protozoa Giardia and Cryptosporidium (EPA Method 1623); the fungi Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus (quantitative PCR [qPCR]); and the bacteria Legionella pneumophila (qPCR), Mycobacterium avium, M. avium subspecies paratuberculosis, and Mycobacterium intracellulare (qPCR and culture). Cryptosporidium and Giardia were detected in 25% and in 46% of the source water samples, respectively (treated waters were not tested). Aspergillus fumigatus was the most commonly detected fungus in source waters (48%) but none of the three fungi were detected in treated water. Legionella pneumophila was detected in 25% of the source water samples but in only 4% of treated water samples. M. avium and M. intracellulare were both detected in 25% of source water, while all three mycobacteria were detected in 36% of treated water samples. Five species of mycobacteria, Mycobacterium mucogenicum, Mycobacterium phocaicum, Mycobacterium triplex, Mycobacterium fortuitum, and Mycobacterium lentiflavum were cultured from treated water samples. Although these DWTPs represent a fraction of those in the U.S., the results suggest that many of these pathogens are widespread in source waters but that treatment is generally effective in reducing them to below detection limits. The one exception is the mycobacteria, which were commonly detected in treated water, even when not detected in source waters.

Ability Of Optical Coherence Tomography To Detect Caries Beneath Commonly Used Dental Sealants

PubMed Central

Osann, Kathryn; Pharar, Jessica; Lee, Kenneth; Ahn, Yeh-chan; Tucker, Travis; Sabet, Sharareh; Chen, Zhongping; Gukasyan, Ripsik; Wilder-Smith, Petra

2010-01-01

Background and Objective The onset and progression of early tooth decay is often preventable with dental sealants. However, occasionally decay progresses underneath the sealant. Current technology does not permit monitoring of potential lesion progression or arrest. Dental sealants themselves mask the visual cues that identify early tooth decay, and radiographs are not sufficiently sensitive. Therefore clinicians can be reluctant to use dental sealant. The objective of this ex vivo study was to evaluate the ability of dentists to detect decay beneath commonly used dental sealants using Optical Coherence Tomography (OCT) imaging. Study Designs/Materials/Methods Forty extracted teeth were divided into equal groups of carious and non-carious teeth, as determined by visual inspection. After radiographs and OCT imaging, teeth were randomly assigned for sealant placement with one of four commonly purchased dental sealants: Clinpro™, Fuji Triage™, Embrace Wet Bond™, and Delton™. Following sealant placement, teeth were radiographed, imaged with OCT, sectioned, examined histologically, and scored as healthy/not healthy. OCT and radiographic images were scored separately. The gold standard was histopathological diagnosis from the serial sections. Cohen’s Kappa, sensitivity, negative predictive value and positive predictive value were computed for all measures. Results After 90 mins training, pre-standardized dentists were able to detect tooth decay more accurately using OCT than with visual or radiographic examination. Detection using OCT was somewhat better prior to sealant placement than afterwards. This effect varied in size depending on the type of sealant used. Radiographic diagnosis was also less accurate after sealant placement. Of the four dental sealants, Delton provided excellent positive predictive value and the best post-sealant negative predictive values. Conclusion In this ex vivo study, dentists were able to detect tooth decay beneath four commonly used dental sealants based on OCT images. Clinical investigations are now underway to determine the usefulness of this approach in vivo. PMID:20848554

Prevalence and Seasonal Distribution of Respiratory Viruses During the 2014 - 2015 Season in Istanbul

PubMed Central

Goktas, Safak; Sirin, Mumtaz Cem

2016-01-01

Background Acute respiratory tract infection (ARTI) is one of the most common infections worldwide, causing significant morbidity and mortality. Objectives This study was conducted to determine the prevalence and seasonal distribution of respiratory viruses in our region, in children and adults with a pre-diagnosis of ARTI. Methods A total of 845 nasopharyngeal swab specimens were analyzed with the RespiFinder Smart 22 kit (PathoFinder BV, Netherlands) and the Rotor-Gene 6000 real-time PCR system. Results At least one pathogen was detected in 612 (72.4%) of the specimens. Overall, 902 pathogens were detected; 821 (91%) were viruses and 81 (9%) were bacteria. The most commonly detected pathogens were influenza A virus (IFV-A) (n = 219), influenza B virus (IFV-B) (n=157), rhinovirus/enterovirus (n = 107), human bocavirus (HBoV) (n = 91), respiratory syncytial virus (RSV) A/B (n = 64), adenovirus (n = 56), human coronaviruses (n = 51), Mycoplasma pneumoniae (n = 49), parainfluenza viruses (n = 40), human metapneumovirus (n = 36), Bordetella pertussis (n = 15), Legionella pneumophila (n = 11), and Chlamydophila pneumoniae (n = 6), respectively. Among the 215 (25.4%) co-infected cases, IFV-A/HBoV and IFV-A/IFV-B were the most common co-infections. IFV-A was the most prevalent agent in all age groups except for children under 5 years of age, in whom RSV A/B was the most common pathogen. Approximately two thirds of the respiratory viruses were detected in early spring and winter, with peaks in January, March, and April. Conclusions With regard to the prevalence and seasonal distribution of respiratory viruses, our epidemiological data for the 2014 - 2015 season in Istanbul showed a predominance of IFV-A infections with a peak activity in early spring. Enhanced surveillance and early detection of respiratory viral pathogens can be useful in the diagnosis, treatment, and prevention of ARTIs, and for guiding the development of appropriate public health strategies. PMID:27800148

Devices Would Detect Drugs In Sweat

NASA Technical Reports Server (NTRS)

Mintz, Fredrick W.; Richards, Gil; Kidwell, David A.; Foster, Conrad; Kern, Roger G.; Nelson, Gregory A.

1996-01-01

Proposed devices worn on skin detect such substances as methamphetamine, morphine, tetrahydrocannabinol (THC), and cocaine in wearers' sweat and transmits radio signals in response to computer queries. Called Remote Biochemical Assay Telemetering System (R-BATS), commonly referred to as "drug badge," attached to wearer by use of adhesive wristband. Used for noninvasive monitoring of levels of prescribed medications in hospital and home-care settings and to detect overdoses quickly.

And along Came a Spider: An Attentional Bias for the Detection of Spiders in Young Children and Adults

ERIC Educational Resources Information Center

LoBue, Vanessa

2010-01-01

Spiders are among the most common targets of fears and phobias in the world. In visual search tasks, adults detect their presence more rapidly than other kinds of stimuli. Reported here is an investigation of whether young children share this attentional bias for the detection of spiders. In a series of experiments, preschoolers and adults were…

Exploring the role of wood waste landfills in early detection of non-native alien wood-boring beetles

Treesearch

Davide Rassati; Massimo Faccoli; Lorenzo Marini; Robert A. Haack; Andrea Battisti; Edoardo Petrucco Toffolo

2015-01-01

Non-native wood-boring beetles (Coleoptera) represent one of the most commonly intercepted groups of insects at ports worldwide. The development of early detection methods is a crucial step when implementing rapid response programs so that non-native wood-boring beetles can be quickly detected and a timely action plan can be produced. However, due to the limited...

Patient's Guide to Detecting and Treating Hypothyroidism Before, During, and After Pregnancy

MedlinePlus

Detecting and Treating Hypothyroidism Before, During, and After Pregnancy A Patient’s Guide Pregnancy causes major changes in the levels of hormones made by ... thyroid hormone, doctors call this underactive thyroid or hypothyroidism . Hypothyroidism during pregnancy is not common. However, the ...

A SIMPLE COLORIMETRIC METHOD TO DETECT BIOLOGICAL EVIDENCE OF HUMAN EXPOSURE TO MICROCYSTINS

EPA Science Inventory

Toxic cyanobacteria are contaminants of surface waters worldwide. Microcystins are some of the most commonly detected toxins. Biological evidence of human exposure may be difficult to obtain due to limitations associated with cost, laboratory capacity, analytic support, and exp...

DQE as detection probability of the radiation detectors

NASA Astrophysics Data System (ADS)

Zanella, Giovanni

2008-02-01

In this paper it is shown that quantum efficiency (DQE), as commonly defined for imaging detectors, can be extended to all radiation detectors with the meaning of detection probability, if Poisson statistics applies. This unified approach is possible in time-domain at zero spatial-frequency.

Linkage disequilibrium among commonly genotyped SNP and variants detected from bull sequence

USDA-ARS?s Scientific Manuscript database

Genomic prediction utilizing causal variants could increase selection accuracy above that achieved with SNP genotyped by commercial assays. A number of variants detected from sequencing influential sires are likely to be causal, but noticable improvements in prediction accuracy using imputed sequen...

Polarization speckle imaging as a potential technique for in vivo skin cancer detection.

PubMed

Tchvialeva, Lioudmila; Dhadwal, Gurbir; Lui, Harvey; Kalia, Sunil; Zeng, Haishan; McLean, David I; Lee, Tim K

2013-06-01

Skin cancer is the most common cancer in the Western world. In order to accurately detect the disease, especially malignant melanoma-the most fatal form of skin cancer-at an early stage when the prognosis is excellent, there is an urgent need to develop noninvasive early detection methods. We believe that polarization speckle patterns, defined as a spatial distribution of depolarization ratio of traditional speckle patterns, can be an important tool for skin cancer detection. To demonstrate our technique, we conduct a large in vivo clinical study of 214 skin lesions, and show that statistical moments of the polarization speckle pattern could differentiate different types of skin lesions, including three common types of skin cancers, malignant melanoma, squamous cell carcinoma, basal cell carcinoma, and two benign lesions, melanocytic nevus and seborrheic keratoses. In particular, the fourth order moment achieves better or similar sensitivity and specificity than many well-known and accepted optical techniques used to differentiate melanoma and seborrheic keratosis.

High-Performance Signal Detection for Adverse Drug Events using MapReduce Paradigm.

PubMed

Fan, Kai; Sun, Xingzhi; Tao, Ying; Xu, Linhao; Wang, Chen; Mao, Xianling; Peng, Bo; Pan, Yue

2010-11-13

Post-marketing pharmacovigilance is important for public health, as many Adverse Drug Events (ADEs) are unknown when those drugs were approved for marketing. However, due to the large number of reported drugs and drug combinations, detecting ADE signals by mining these reports is becoming a challenging task in terms of computational complexity. Recently, a parallel programming model, MapReduce has been introduced by Google to support large-scale data intensive applications. In this study, we proposed a MapReduce-based algorithm, for common ADE detection approach, Proportional Reporting Ratio (PRR), and tested it in mining spontaneous ADE reports from FDA. The purpose is to investigate the possibility of using MapReduce principle to speed up biomedical data mining tasks using this pharmacovigilance case as one specific example. The results demonstrated that MapReduce programming model could improve the performance of common signal detection algorithm for pharmacovigilance in a distributed computation environment at approximately liner speedup rates.

Polarization speckle imaging as a potential technique for in vivo skin cancer detection

NASA Astrophysics Data System (ADS)

Tchvialeva, Lioudmila; Dhadwal, Gurbir; Lui, Harvey; Kalia, Sunil; Zeng, Haishan; McLean, David I.; Lee, Tim K.

2013-06-01

Skin cancer is the most common cancer in the Western world. In order to accurately detect the disease, especially malignant melanoma-the most fatal form of skin cancer-at an early stage when the prognosis is excellent, there is an urgent need to develop noninvasive early detection methods. We believe that polarization speckle patterns, defined as a spatial distribution of depolarization ratio of traditional speckle patterns, can be an important tool for skin cancer detection. To demonstrate our technique, we conduct a large in vivo clinical study of 214 skin lesions, and show that statistical moments of the polarization speckle pattern could differentiate different types of skin lesions, including three common types of skin cancers, malignant melanoma, squamous cell carcinoma, basal cell carcinoma, and two benign lesions, melanocytic nevus and seborrheic keratoses. In particular, the fourth order moment achieves better or similar sensitivity and specificity than many well-known and accepted optical techniques used to differentiate melanoma and seborrheic keratosis.

Addressing alcohol-impaired driving : training physicians to detect and counsel their patients who drink heavily

DOT National Transportation Integrated Search

2000-07-01

Alcohol is the most common chronic disease in trauma patients, and one of the most common in patients treated in primary care. Studies have shown that brief counseling intervention in trauma centers and primary care clinics are efficient in reducing ...

Detecting free-mass common-mode motion induced by incident gravitational waves

NASA Astrophysics Data System (ADS)

Tobar, Michael Edmund; Suzuki, Toshikazu; Kuroda, Kazuaki

1999-05-01

In this paper we show that information on both the differential and common mode free-mass response to a gravitational wave can provide important information on discriminating the direction of the gravitational wave source and between different theories of gravitation. The conventional Michelson interferometer scheme only measures the differential free-mass response. By changing the orientation of the beam splitter, it is possible to configure the detector so it is sensitive to the common-mode of the free-mass motion. The proposed interferometer is an adaptation of the Fox-Smith interferometer. A major limitation to the new scheme is its enhanced sensitivity to laser frequency fluctuations over the conventional, and we propose a method of cancelling these fluctuations. The configuration could be used in parallel to the conventional differential detection scheme with a significant sensitivity and bandwidth.

A 2014 nationwide survey of the distribution of Soybean mosaic virus (SMV), Soybean yellow mottle mosaic virus (SYMMV) and Soybean yellow common mosaic virus (SYCMV) major viruses in South Korean soybean fields, and changes

USDA-ARS?s Scientific Manuscript database

In 2014 symptomatic soybean samples were collected throughout Korea, and were tested for the most important soybean viruses found in Korea, namely Soybean mosaic virus (SMV), Soybean yellow common mosaic virus (SYCMV), and Soybean yellow mottle mosaic virus (SYMMV). SYMMV was most commonly detected,...

High sensitivity leak detection method and apparatus

DOEpatents

Myneni, Ganapatic R.

1994-01-01

An improved leak detection method is provided that utilizes the cyclic adsorption and desorption of accumulated helium on a non-porous metallic surface. The method provides reliable leak detection at superfluid helium temperatures. The zero drift that is associated with residual gas analyzers in common leak detectors is virtually eliminated by utilizing a time integration technique. The sensitivity of the apparatus of this disclosure is capable of detecting leaks as small as 1.times.10.sup.-18 atm cc sec.sup.-1.

High sensitivity leak detection method and apparatus

DOEpatents

Myneni, G.R.

1994-09-06

An improved leak detection method is provided that utilizes the cyclic adsorption and desorption of accumulated helium on a non-porous metallic surface. The method provides reliable leak detection at superfluid helium temperatures. The zero drift that is associated with residual gas analyzers in common leak detectors is virtually eliminated by utilizing a time integration technique. The sensitivity of the apparatus of this disclosure is capable of detecting leaks as small as 1 [times] 10[sup [minus]18] atm cc sec[sup [minus]1]. 2 figs.

Prevalence and distribution of Wellfleet Bay virus exposure in the Common Eider (Somateria mollissima)

USGS Publications Warehouse

Ballard, Jennifer R.; Mickley, Randall M.; Gibbs, Samantha E.J.; Dwyer, Chris P.; Soos, Catherine; Harms, N. Jane; Gilchrist, H. Grant; Hall, Jeffrey S.; Franson, J. Christian; Milton, G. Randy; Parsons, Glen; Allen, Brad; Giroux, Jean-Francois; Lair, Stéphane; Mead, Daniel G.; Fischer, John R.

2017-01-01

Between 1998 and 2014, recurrent mortality events were reported in the Dresser's subspecies of the Common Eider (Somateria mollissima dresseri) on Cape Cod, Massachusetts, USA near Wellfleet Harbor. The early die-offs were attributed to parasitism and emaciation, but beginning in 2006 a suite of distinct lesions was observed concomitant with the isolation of a previously unknown RNA virus. This novel pathogen was identified as an orthomyxovirus in the genus Quaranjavirus and was named Wellfleet Bay virus (WFBV). To assess evidence of exposure to this virus in Common Eiders, we conducted a longitudinal study of the prevalence of WFBV antibodies at multiple locations from 2004–14; we collected 2,258 serum samples from six locations and analyzed each using a microneutralization assay. Results corroborate the emergence of WFBV in 2006 based on the first detection of antibodies in that year. Significantly higher prevalence was detected in Common Eiders sampled in Massachusetts compared to those in Maine, Nova Scotia, and Québec. For birds breeding and wintering in Massachusetss, viral exposure varied by age, sex, and season of sampling, and prevalence by season and sex were highly interrelated with greater numbers of antibody-positive males in the autumn and females in the spring. No evidence of viral exposure was detected in the Northern subspecies (Somateria mollissima borealis). Among the locations sampled, Massachusetts appears to be the epicenter of Common Eider exposure to WFBV. Further research is warranted to understand the factors controlling the epidemiology of WFBV in Massachussetts, including those that may be limiting geographic expansion of this virus.

Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.

PubMed

Dunbar, John; Eichorst, Stephanie A; Gallegos-Graves, La Verne; Silva, Shannon; Xie, Gary; Hengartner, N W; Evans, R David; Hungate, Bruce A; Jackson, Robert B; Megonigal, J Patrick; Schadt, Christopher W; Vilgalys, Rytas; Zak, Donald R; Kuske, Cheryl R

2012-05-01

Six terrestrial ecosystems in the USA were exposed to elevated atmospheric CO(2) in single or multifactorial experiments for more than a decade to assess potential impacts. We retrospectively assessed soil bacterial community responses in all six-field experiments and found ecosystem-specific and common patterns of soil bacterial community response to elevated CO(2) . Soil bacterial composition differed greatly across the six ecosystems. No common effect of elevated atmospheric CO(2) on bacterial biomass, richness and community composition across all of the ecosystems was identified, although significant responses were detected in individual ecosystems. The most striking common trend across the sites was a decrease of up to 3.5-fold in the relative abundance of Acidobacteria Group 1 bacteria in soils exposed to elevated CO(2) or other climate factors. The Acidobacteria Group 1 response observed in exploratory 16S rRNA gene clone library surveys was validated in one ecosystem by 100-fold deeper sequencing and semi-quantitative PCR assays. Collectively, the 16S rRNA gene sequencing approach revealed influences of elevated CO(2) on multiple ecosystems. Although few common trends across the ecosystems were detected in the small surveys, the trends may be harbingers of more substantive changes in less abundant, more sensitive taxa that can only be detected by deeper surveys. Representative bacterial 16S rRNA gene clone sequences were deposited in GenBank with Accession No. JQ366086–JQ387568. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Role of microbiological culture and polymerase chain reaction (PCR) of actinomyces in medication-related osteonecrosis of the jaw (MRONJ).

PubMed

Panya, Sappasith; Fliefel, Riham; Probst, Florian; Tröltzsch, Matthias; Ehrenfeld, Michael; Schubert, Sören; Otto, Sven

2017-03-01

We hypothesized that local infection plays a critical role in the pathogenesis of medication-related osteonecrosis of the jaw (MRONJ). Recent developments in molecular methods have revolutionized new approaches for the rapid detection of microorganisms including those difficult to culture. The aim of our study is to identify the bacterial profiles in MRONJ by microbiological culture and polymerase chain reactions (PCR). A retrospective analysis was performed on MRONJ patients from 2008 to 2014. The bacterial profile from MRONJ bone samples was determined using microbiological culture and PCR. Ninety five patients fulfilled the inclusion criteria with mean age of 69.85 ± 8.71 years. A female predilection was detected. The mandible was more commonly affected than maxilla. Tooth extraction was the frequent triggering factor. Breast cancer was the primary cause for administration and intravenous bisphosphonates were the most commonly administrated antiresorptive drugs. The majority of patients were classified as stage 2. Posterior teeth were most commonly affected. Based on bone culture results, the most common microorganism were both actinomyces and mixed flora. PCR confirmed the presence of actinomyces in 55 patients. Our data suggest that PCR might be an innovative method for detection of microorganisms difficult to culture using traditional microbiological techniques. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Optimization of biological and instrumental detection of explosives and ignitable liquid residues including canines, SPME/ITMS and GC/MSn

NASA Astrophysics Data System (ADS)

Furton, Kenneth G.; Harper, Ross J.; Perr, Jeannette M.; Almirall, Jose R.

2003-09-01

A comprehensive study and comparison is underway using biological detectors and instrumental methods for the rapid detection of ignitable liquid residues (ILR) and high explosives. Headspace solid phase microextraction (SPME) has been demonstrated to be an effective sampling method helping to identify active odor signature chemicals used by detector dogs to locate forensic specimens as well as a rapid pre-concentration technique prior to instrumental detection. Common ignitable liquids and common military and industrial explosives have been studied including trinitrotoluene, tetryl, RDX, HMX, EGDN, PETN and nitroglycerine. This study focuses on identifying volatile odor signature chemicals present, which can be used to enhance the level and reliability of detection of ILR and explosives by canines and instrumental methods. While most instrumental methods currently in use focus on particles and on parent organic compounds, which are often involatile, characteristic volatile organics are generally also present and can be exploited to enhance detection particularly for well-concealed devices. Specific examples include the volatile odor chemicals 2-ethyl-1-hexanol and cyclohexanone, which are readily available in the headspace of the high explosive composition C-4; whereas, the active chemical cyclo-1,3,5-trimethylene-2,4,6-trinitramine (RDX) is not. The analysis and identification of these headspace 'fingerprint' organics is followed by double-blind dog trials of the individual components using certified teams in an attempt to isolate and understand the target compounds to which dogs are sensitive. Studies to compare commonly used training aids with the actual target explosive have also been undertaken to determine their suitability and effectiveness. The optimization of solid phase microextraction (SPME) combined with ion trap mobility spectrometry (ITMS) and gas chromatography/mass spectrometry/mass spectrometry (GC/MSn) is detailed including interface development and comparisons of limits of detection. These instrumental methods are being optimized in order to detect the same target odor chemicals used by detector dogs to reliably locate explosives and ignitable liquids.

Pharmaceuticals, hormones, pesticides, and other bioactive contaminants in water, sediment, and tissue from Rocky Mountain National Park, 2012–2013

USGS Publications Warehouse

Battaglin, William A.; Bradley, Paul M.; Iwanowicz, Luke R.; Journey, Celeste A.; Walsh, Heather L.; Blazer, Vicki S.

2018-01-01

Pharmaceuticals, hormones, pesticides, and other bioactive contaminants (BCs) are commonly detected in surface water and bed sediment in urban and suburban areas, but these contaminants are understudied in remote locations. In Rocky Mountain National Park (RMNP), Colorado, USA, BCs may threaten the reproductive success and survival of native aquatic species, benthic communities, and pelagic food webs. In 2012–2013, 67 water, 57 sediment, 63 fish, 10 frog, and 12 quality-control samples (8 water and 4 sediment) were collected from 20 sites in RMNP. Samples were analyzed for 369 parameters including 149 pharmaceuticals, 22 hormones, 137 pesticides, and 61 other chemicals or conditions to provide a representative assessment of BC occurrence within RMNP. Results indicate that BCs were detected in water and/or sediment from both remote and more accessible locations in RMNP. The most commonly detected BCs in water were caffeine, camphor, para-cresol, and DEET; and the most commonly detected BCs in sediment were indole, 3-methyl-1H-indole, para-cresol, and 2,6-dimethyl-naphthalene. Some detected contaminants, including carbaryl, caffeine, and oxycodone, are clearly attributable to direct local human input, whereas others may be transported into the park atmospherically (e.g., atrazine) or have local natural sources (e.g., para-cresol). One or more pharmaceuticals were detected in at least 1 sample from 15 of 20 sites. Most of the 29 detected pharmaceuticals are excreted primarily in human urine, not feces. Elevated net estrogenicity was observed in 18% of water samples, and elevated vitellogenin in blood was observed in 12% of male trout, both evidence of potential endocrine disruption. Hormone concentrations in sediment tended to be greater than concentrations in water. Most BCs were observed at concentrations below those not expected to pose adverse effects to aquatic life. Results indicate that even in remote locations aquatic wildlife can be exposed to pharmaceuticals, hormones, pesticides, and other bioactive contaminants.

Corynebacterium Prosthetic Joint Infection

PubMed Central

Cazanave, Charles; Greenwood-Quaintance, Kerryl E.; Hanssen, Arlen D.

2012-01-01

Identification of Corynebacterium species may be challenging. Corynebacterium species are occasional causes of prosthetic joint infection (PJI), but few data are available on the subject. Based on the literature, C. amycolatum, C. aurimucosum, C. jeikeium, and C. striatum are the most common Corynebacterium species that cause PJI. We designed a rapid PCR assay to detect the most common human Corynebacterium species, with a specific focus on PJI. A polyphosphate kinase gene identified using whole-genome sequence was targeted. The assay differentiates the antibiotic-resistant species C. jeikeium and C. urealyticum from other species in a single assay. The assay was applied to a collection of human Corynebacterium isolates from multiple clinical sources, and clinically relevant species were detected. The assay was then tested on Corynebacterium isolates specifically associated with PJI; all were detected. We also describe the first case of C. simulans PJI. PMID:22337986

Terminology inaccuracies in the interpretation of imaging results in detection of cervical lymph node metastases in papillary thyroid cancer

PubMed Central

Mulla, Mubashir; Schulte, Klaus-Martin

2012-01-01

Cervical lymph nodes (CLNs) are the most common site of metastases in papillary thyroid cancer (PTC). Ultrasound scan (US) is the most commonly used imaging modality in the evaluation of CLNs in PTC. Computerised tomography (CT) and 18fluorodeoxyglucose positron emission tomography (18FDG PET–CT) are used less commonly. It is widely believed that the above imaging techniques should guide the surgical approach to the patient with PTC. Methods We performed a systematic review of imaging studies from the literature assessing the usefulness for the detection of metastatic CLNs in PTC. We evaluated the author's interpretation of their numeric findings specifically with regard to ‘sensitivity’ and ‘negative predictive value’ (NPV) by comparing their use against standard definitions of these terms in probabilistic statistics. Results A total of 16 studies used probabilistic terms to describe the value of US for the detection of LN metastases. Only 6 (37.5%) calculated sensitivity and NPV correctly. For CT, out of the eight studies, only 1 (12.5%) used correct terms to describe analytical results. One study looked at magnetic resonance imaging, while three assessed 18FDG PET–CT, none of which provided correct calculations for sensitivity and NPV. Conclusion Imaging provides high specificity for the detection of cervical metastases of PTC. However, sensitivity and NPV are low. The majority of studies reporting on a high sensitivity have not used key terms according to standard definitions of probabilistic statistics. Against common opinion, there is no current evidence that failure to find LN metastases on ultrasound or cross-sectional imaging can be used to guide surgical decision making. PMID:23781308

Foreign body ingestion in children

PubMed Central

Dereci, Selim; Koca, Tuğba; Serdaroğlu, Filiz; Akçam, Mustafa

2015-01-01

Aim: Foreign bodies ingested by the oral route enter into the gastrointestinal tract and are considered a significant health problem in the childhood. In this study, we evaluated the pediatric patients who presented to our hospital with the complaint of ingestion of foreign body. Material and Methods: The hospital records of all children who presented to our clinic because of ingestion of foreign body between January 2008 and January 2015 were examined retrospectively. The complaints at admission, the types of foreign bodies ingested, the localization of the foreign body in the gastrointestinal tract and the approaches and treatment methods used were examined. Results: Thirty-six (56%) of 64 patients included in the study were male and 28 (44%) were female and the mean age was 5.7±4.6 years (10 months–17 years). Thirty eight (59%) of 64 children who were included in the assessment were below the age of five years. The most common complaint at presentation was parental recognition of the ingested object and dysphagia. The most commonly ingested foreign bodies included coins, sewing pins, safety pins and hairclips. Nail clipper detected in the stomach, sewing pin which penetrated through the duodenal wall and stuck to hepatic parenchyma were the first pediatric cases in the literature. Upper esophagus was the most common location for foreign bodies. Endoscopic examinations were performed in 55 of 64 children. Conclusions: Early detection and treatment of ingested foreign bodies in the upper gastrointestinal system is important in terms of preventing possible complications. In our study, the most frequent foreign bodies detected in the upper digestive tract were coins and they were most frequently detected in the upper esophagus. Most of our patients were below the age of five years. Flexible endoscopic method was used commonly for treatment. PMID:26884693

Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell-free DNA from maternal plasma.

PubMed

Mazloom, Amin R; Džakula, Željko; Oeth, Paul; Wang, Huiquan; Jensen, Taylor; Tynan, John; McCullough, Ron; Saldivar, Juan-Sebastian; Ehrich, Mathias; van den Boom, Dirk; Bombard, Allan T; Maeder, Margo; McLennan, Graham; Meschino, Wendy; Palomaki, Glenn E; Canick, Jacob A; Deciu, Cosmin

2013-06-01

Whole-genome sequencing of circulating cell free (ccf) DNA from maternal plasma has enabled noninvasive prenatal testing for common autosomal aneuploidies. The purpose of this study was to extend the detection to include common sex chromosome aneuploidies (SCAs): [47,XXX], [45,X], [47,XXY], and [47,XYY] syndromes. Massively parallel sequencing was performed on ccf DNA isolated from the plasma of 1564 pregnant women with known fetal karyotype. A classification algorithm for SCA detection was constructed and trained on this cohort. Another study of 411 maternal samples from women with blinded-to-laboratory fetal karyotypes was then performed to determine the accuracy of the classification algorithm. In the training cohort, the new algorithm had a detection rate (DR) of 100% (95%CI: 82.3%, 100%), a false positive rate (FPR) of 0.1% (95%CI: 0%, 0.3%), and nonreportable rate of 6% (95%CI: 4.9%, 7.4%) for SCA determination. The blinded validation yielded similar results: DR of 96.2% (95%CI: 78.4%, 99.8%), FPR of 0.3% (95%CI: 0%, 1.8%), and nonreportable rate of 5% (95%CI: 3.2%, 7.7%) for SCA determination Noninvasive prenatal identification of the most common sex chromosome aneuploidies is possible using ccf DNA and massively parallel sequencing with a high DR and a low FPR. © 2013 John Wiley & Sons, Ltd.

Use of Whole-Cell Bioassays for Screening Quorum Signaling, Quorum Interference, and Biofilm Dispersion.

PubMed

Thornhill, Starla G; McLean, Robert J C

2018-01-01

In most bacteria, a global level of regulation, termed quorum sensing (QS), exists involving intercellular communication via the production and response to cell density-dependent signal molecules. QS has been associated with a number of important features in bacteria including virulence regulation and biofilm formation. Consequently, there is considerable interest in understanding, detecting, and inhibiting QS. N-acylated homoserine lactones (AHLs) are used as extracellular QS signals by a variety of Gram-negative bacteria. Chromobacterium violaceum, commonly found in soil and water, produces the characteristic purple pigment violacein, regulated by AHL-mediated QS. Based on this readily observed pigmentation phenotype, C. violaceum strains can be used to detect various aspects of AHL-mediated QS activity. In another commonly used bioassay organism, Agrobacterium tumefaciens, QS can be detected by the use of a reporter gene such as lacZ. Here, we describe several commonly used approaches incorporating C. violaceum and A. tumefaciens that can be used to detect AHL and QS inhibitors. Due to the inherent low susceptibility of biofilm bacteria to antimicrobial agents, biofilm dispersion, whereby bacteria reenter the planktonic community, is another increasingly important area of research. At least one signal, distinct from traditional QS, has been identified and there are a variety of other environmental factors that also trigger dispersion. We describe a microtiter-based experimental strategy whereby potential biofilm dispersion compounds can be screened.

Ternary Surface Monolayers for Ultrasensitive (Zeptomole) Amperometric Detection of Nucleic-Acid Hybridization without Signal Amplification

PubMed Central

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A.; Wang, Joseph

2010-01-01

A ternary surface monolayer, consisting of co-assembled thiolated capture probe (SHCP) mercaptohexanol (MCH) and dithiothreitol (DTT), is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers (SAMs). Remarkably low detection limits down to 40 zmole (in 4 μL samples) as well as only 1 CFU E. coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3′,5,5′-tetramethylbenzidine (HRP/TMB) system. Such dramatic improvements in the detection limits (compared to common binary alkanethiol interfaces and to most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to non-specific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration ‘backfillers’ that leads to a remarkably low background noise even in the presence of complex sample matrices. A wide range of surface compositions have been investigated and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety and forensic analysis. PMID:20883023

Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification.

PubMed

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A; Wang, Joseph

2010-11-01

A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.

Plagiarism in submitted manuscripts: incidence, characteristics and optimization of screening-case study in a major specialty medical journal.

PubMed

Higgins, Janet R; Lin, Feng-Chang; Evans, James P

2016-01-01

Plagiarism is common and threatens the integrity of the scientific literature. However, its detection is time consuming and difficult, presenting challenges to editors and publishers who are entrusted with ensuring the integrity of published literature. In this study, the extent of plagiarism in manuscripts submitted to a major specialty medical journal was documented. We manually curated submitted manuscripts and deemed an article contained plagiarism if one sentence had 80 % of the words copied from another published paper. Commercial plagiarism detection software was utilized and its use was optimized. In 400 consecutively submitted manuscripts, 17 % of submissions contained unacceptable levels of plagiarized material with 82 % of plagiarized manuscripts submitted from countries where English was not an official language. Using the most commonly employed commercial plagiarism detection software, sensitivity and specificity were studied with regard to the generated plagiarism score. The cutoff score maximizing both sensitivity and specificity was 15 % (sensitivity 84.8 % and specificity 80.5 %). Plagiarism was a common occurrence among manuscripts submitted for publication to a major American specialty medical journal and most manuscripts with plagiarized material were submitted from countries in which English was not an official language. The use of commercial plagiarism detection software can be optimized by selecting a cutoff score that reflects desired sensitivity and specificity.

A Method to Identify Estuarine Macroinvertebrate Pollution Indicator Species in the Virginian Biogeogarphic Province

EPA Science Inventory

Macroinvertebrates are commonly used as biomonitors to detect pollution impacts in estuaries. The goal of this research was to identify estuarine benthic invertebrates that could be used as indicator species to detect presence or absence of pollution in the Virginian Biogeograph...

An Adaptive Database Intrusion Detection System

ERIC Educational Resources Information Center

Barrios, Rita M.

2011-01-01

Intrusion detection is difficult to accomplish when attempting to employ current methodologies when considering the database and the authorized entity. It is a common understanding that current methodologies focus on the network architecture rather than the database, which is not an adequate solution when considering the insider threat. Recent…

Device for sampling and enriching impurities in hydrogen comprising hydrogen-permeable membrane

DOEpatents

Ahmed, Shabbir; Papadias, Dionissios D.; Lee, Sheldon D. H.; Kumar, Romesh

2017-01-31

Provided herein are methods and devices to enrich trace quantities of impurities in gaseous mixtures, such as hydrogen fuel. The methods and devices rely on concentration of impurities so as to allow the detection of the impurities using commonly-available detection methods.

Microbiological and mycological beach sand quality in a volcanic environment: Madeira archipelago, Portugal.

PubMed

Pereira, Elisabete; Figueira, Celso; Aguiar, Nuno; Vasconcelos, Rita; Vasconcelos, Sílvia; Calado, Graça; Brandão, João; Prada, Susana

2013-09-01

Madeira forms a mid-Atlantic volcanic archipelago, whose economy is largely dependent on tourism. There, one can encounter different types of sand beach: natural basaltic, natural calcareous and artificial calcareous. Microbiological and mycological quality of the sand was analyzed in two different years. Bacterial indicators were detected in higher number in 2010 (36.7% of the samples) than in 2011 (9.1%). Mycological indicators were detected in a similar percentage of samples in 2010 (68.3%) and 2011 (75%), even though the total number of colonies detected in 2010 was much higher (827 in 41 samples) than in 2011 (427 in 66 samples). Enterococci and potentially pathogenic and allergenic fungi (particularly Penicillium sp.) were the most common indicators detected in both years. Candida sp. yeast was also commonly detected in the samples. The analysis of the 3rd quartile and maximum numbers of all indicators in samples showed that artificial beaches tend to be more contaminated than the natural ones. However, a significant difference between the variables was lacking. More monitoring data (number of bathers, sea birds, radiation intensity variation, and a greater number of samples) should be collected in order to confirm if these differences are significant. In general, the sand quality in the archipelago's beaches was good. As the sand may be a vector of diseases, an international common set of indicators and values and a compatible methodologies for assessing sand contamination, should be defined, in order to provide the bather's with an indication of beach sand quality, rather than only the water. Copyright © 2013 Elsevier B.V. All rights reserved.

Beyond Multiple Regression: Using Commonality Analysis to Better Understand R[superscript 2] Results

ERIC Educational Resources Information Center

Warne, Russell T.

2011-01-01

Multiple regression is one of the most common statistical methods used in quantitative educational research. Despite the versatility and easy interpretability of multiple regression, it has some shortcomings in the detection of suppressor variables and for somewhat arbitrarily assigning values to the structure coefficients of correlated…

A rapid and cost effective method for soil carbon mineralization under static incubations

USDA-ARS?s Scientific Manuscript database

Soil incubations with subsequent determination of carbon dioxide (CO2) are common soil assays used to estimate C mineralization rates and active organic C pools. Two common methods used to detect CO2 in laboratory incubations are gas chromatography (GC) and alkali absorption followed by titration (...

A Common Parvovirus in Deer from California, USA.

PubMed

Li, Linlin; Woods, Leslie; Gerstenberg, Greg; Deng, Xutao; Delwart, Eric

2016-10-01

We characterize the genome of the first reported deer parvovirus, Ungulate tetraparvovirus 5, which we detected by PCR in multiple tissues from 2/9 California mule deer ( Odocoileus hemionus californicus) with hair loss syndrome (HLS) and in 4/12 deer without HLS, suggesting this common infection does not cause HLS.

Common and Innovative Visuals: A sparsity modeling framework for video.

PubMed

Abdolhosseini Moghadam, Abdolreza; Kumar, Mrityunjay; Radha, Hayder

2014-05-02

Efficient video representation models are critical for many video analysis and processing tasks. In this paper, we present a framework based on the concept of finding the sparsest solution to model video frames. To model the spatio-temporal information, frames from one scene are decomposed into two components: (i) a common frame, which describes the visual information common to all the frames in the scene/segment, and (ii) a set of innovative frames, which depicts the dynamic behaviour of the scene. The proposed approach exploits and builds on recent results in the field of compressed sensing to jointly estimate the common frame and the innovative frames for each video segment. We refer to the proposed modeling framework by CIV (Common and Innovative Visuals). We show how the proposed model can be utilized to find scene change boundaries and extend CIV to videos from multiple scenes. Furthermore, the proposed model is robust to noise and can be used for various video processing applications without relying on motion estimation and detection or image segmentation. Results for object tracking, video editing (object removal, inpainting) and scene change detection are presented to demonstrate the efficiency and the performance of the proposed model.

Evaluation of four endogenous reference genes and their real-time PCR assays for common wheat quantification in GMOs detection.

PubMed

Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao

2013-01-01

Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat.

Evaluation of Four Endogenous Reference Genes and Their Real-Time PCR Assays for Common Wheat Quantification in GMOs Detection

PubMed Central

Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao

2013-01-01

Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat. PMID:24098735

Islanding detection technique using wavelet energy in grid-connected PV system

NASA Astrophysics Data System (ADS)

Kim, Il Song

2016-08-01

This paper proposes a new islanding detection method using wavelet energy in a grid-connected photovoltaic system. The method detects spectral changes in the higher-frequency components of the point of common coupling voltage and obtains wavelet coefficients by multilevel wavelet analysis. The autocorrelation of the wavelet coefficients can clearly identify islanding detection, even in the variations of the grid voltage harmonics during normal operating conditions. The advantage of the proposed method is that it can detect islanding condition the conventional under voltage/over voltage/under frequency/over frequency methods fail to detect. The theoretical method to obtain wavelet energies is evolved and verified by the experimental result.

Toxin Detection by Surface Plasmon Resonance

PubMed Central

Hodnik, Vesna; Anderluh, Gregor

2009-01-01

Significant efforts have been invested in the past years for the development of analytical methods for fast toxin detection in food and water. Immunochemical methods like ELISA, spectroscopy and chromatography are the most used in toxin detection. Different methods have been linked, e.g. liquid chromatography and mass spectrometry (LC-MS), in order to detect as low concentrations as possible. Surface plasmon resonance (SPR) is one of the new biophysical methods which enables rapid toxin detection. Moreover, this method was already included in portable sensors for on-site determinations. In this paper we describe some of the most common methods for toxin detection, with an emphasis on SPR. PMID:22573957

First Indian study evaluating role of biochemical investigations and diagnostic tools in detection of adverse drug reactions.

PubMed

Tandon, Vishal R; Khajuria, Vijay; Raina, Kapila; Mahajan, Vivek; Sharma, Aman; Gillani, Zahid

2014-09-01

To evaluate the role of biochemical investigations (BI) and diagnostic tools (DT) in ADR detection. An observational prospective cross-sectional study was done using suspected ADR data collection form. A total of 2381 ADR related events were recorded in two years. Total number/percentage of biochemical abnormalities (BA) related ADR detection rate was 14.57% and of DT was 1.091% in contrast to 84.33% recorded with clinical presentation. Maximum cases were inward patients (87.13%), 67.02% were recorded by active surveillance. ADR detection rate at one point & detection on follow up was 56.31% Vs 46.38%. ADR detection rate of ECG, endoscopy, X-ray were 0.57%, 0.22%, 0.22% and of CT scan, MRI, DEXA scan, USG and biopsy was 0.04% each. Maximum ADRs were severe/serious, latent and Type-A in nature. Anemia (4.6%), followed by liver dysfunction (2.8%), renal dysfunction, electrolyte imbalance, hyperglycemia (1.1% each), abnormal coagulation profile (1%), decrease platelet count (0.8%), hypoglycemia (0.7%) were the most common BAs. Anti retroviral drugs (ART), tirofiban and methotrexate accounted for anemia, ART and anti tubercular drugs for liver & renal dysfunction, insulin for hypoglycemia, tirofiban, paclitaxel, capecipabine and ifosfamide for thrombocytopenia, hematuria by enoxaparin & dyslipidemia with ART were common ADRs. BI and DT can play very important role in ADR detection.

Detection of nitro-based and peroxide-based explosives by fast polarity-switchable ion mobility spectrometer with ion focusing in vicinity of Faraday detector.

PubMed

Zhou, Qinghua; Peng, Liying; Jiang, Dandan; Wang, Xin; Wang, Haiyan; Li, Haiyang

2015-05-29

Ion mobility spectrometer (IMS) has been widely deployed for on-site detection of explosives. The common nitro-based explosives are usually detected by negative IMS while the emerging peroxide-based explosives are better detected by positive IMS. In this study, a fast polarity-switchable IMS was constructed to detect these two explosive species in a single measurement. As the large traditional Faraday detector would cause a trailing reactant ion peak (RIP), a Faraday detector with ion focusing in vicinity was developed by reducing the detector radius to 3.3 mm and increasing the voltage difference between aperture grid and its front guard ring to 591 V, which could remove trailing peaks from RIP without loss of signal intensity. This fast polarity-switchable IMS with ion focusing in vicinity of Faraday detector was employed to detect a mixture of 10 ng 2,4,6-trinitrotoluene (TNT) and 50 ng hexamethylene triperoxide diamine (HMTD) by polarity-switching, and the result suggested that [TNT-H](-) and [HMTD+H](+) could be detected in a single measurement. Furthermore, the removal of trailing peaks from RIP by the Faraday detector with ion focusing in vicinity also promised the accurate identification of KClO4, KNO3 and S in common inorganic explosives, whose product ion peaks were fairly adjacent to RIP.

Rapid Detection of Cyprinid Herpesvirus 3 in Latently Infected Koi by Recombinase Polymerase Amplification.

PubMed

Prescott, Meagan A; Reed, Aimee N; Jin, Ling; Pastey, Manoj K

2016-09-01

Since the emergence of cyprinid herpesvirus 3 (CyHV-3), outbreaks have been devastating to Common Carp Cyprinus carpio and koi (a variant of Common Carp), leading to high economic losses. Current diagnostics for detecting CyHV-3 are limited in sensitivity and are further complicated by latency. Here we describe the detection of CyHV-3 by recombinase polymerase amplification (RPA). The RPA assay can detect as low as 10 copies of the CyHV-3 genome by an isothermal reaction and yields results in approximately 20 min. Using the RPA assay, the CyHV-3 genome can be detected in the total DNA of white blood cells isolated from koi latently infected with CyHV-3, while less than 10% of the latently infected koi can be detected by a real-time PCR assay in the total DNA of white blood cells. In addition, RPA products can be detected in a lateral flow device that is cheap and fast and can be used outside of the diagnostic lab. The RPA assay and lateral flow device provide for the rapid, sensitive, and specific amplification of CyHV-3 that with future modifications for field use and validation could lead to enhanced surveillance and early diagnosis of CyHV-3 in the laboratory and field. Received September 14, 2015; accepted April 9, 2016.

Cyber Security Audit and Attack Detection Toolkit

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

Peterson, Dale

2012-05-31

This goal of this project was to develop cyber security audit and attack detection tools for industrial control systems (ICS). Digital Bond developed and released a tool named Bandolier that audits ICS components commonly used in the energy sector against an optimal security configuration. The Portaledge Project developed a capability for the PI Historian, the most widely used Historian in the energy sector, to aggregate security events and detect cyber attacks.

Improving Cyber-Security of Smart Grid Systems via Anomaly Detection and Linguistic Domain Knowledge

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

Ondrej Linda; Todd Vollmer; Milos Manic

The planned large scale deployment of smart grid network devices will generate a large amount of information exchanged over various types of communication networks. The implementation of these critical systems will require appropriate cyber-security measures. A network anomaly detection solution is considered in this work. In common network architectures multiple communications streams are simultaneously present, making it difficult to build an anomaly detection solution for the entire system. In addition, common anomaly detection algorithms require specification of a sensitivity threshold, which inevitably leads to a tradeoff between false positives and false negatives rates. In order to alleviate these issues, thismore » paper proposes a novel anomaly detection architecture. The designed system applies the previously developed network security cyber-sensor method to individual selected communication streams allowing for learning accurate normal network behavior models. Furthermore, the developed system dynamically adjusts the sensitivity threshold of each anomaly detection algorithm based on domain knowledge about the specific network system. It is proposed to model this domain knowledge using Interval Type-2 Fuzzy Logic rules, which linguistically describe the relationship between various features of the network communication and the possibility of a cyber attack. The proposed method was tested on experimental smart grid system demonstrating enhanced cyber-security.« less

Biosensors for rapid and sensitive detection of Staphylococcus aureus in food.

PubMed

Rubab, Momna; Shahbaz, Hafiz Muhammad; Olaimat, Amin N; Oh, Deog-Hwan

2018-05-15

Foodborne illness outbreaks caused by the consumption of food contaminated with harmful bacteria has drastically increased in the past decades. Therefore, detection of harmful bacteria in the food has become an important factor for the recognition and prevention of problems associated with food safety and public health. Staphylococcus aureus is one of the most commonly isolated foodborne pathogen and it is considered as a major cause of foodborne illnesses worldwide. A number of different methods have been developed for the detection and identification of S. aureus in food samples. However, some of these methods are laborious and time-consuming and are not suitable for on-site applications. Therefore, it is highly important to develop rapid and more approachable detection methods. In the last decade, biosensors have gained popularity as an attractive alternative method and now considered as one of most rapid and on-site applicable methods. An overview of the biosensor based methods used for the detection of S. aureus is presented herein. This review focuses on the state-of-the-art biosensor methods towards the detection and quantification of S. aureus, and discusses the most commonly used biosensor methods based on the transducing mode, such as electrochemical, optical, and mass-based biosensors. Copyright © 2018 Elsevier B.V. All rights reserved.

Echogenicity based approach to detect, segment and track the common carotid artery in 2D ultrasound images.

PubMed

Narayan, Nikhil S; Marziliano, Pina

2015-08-01

Automatic detection and segmentation of the common carotid artery in transverse ultrasound (US) images of the thyroid gland play a vital role in the success of US guided intervention procedures. We propose in this paper a novel method to accurately detect, segment and track the carotid in 2D and 2D+t US images of the thyroid gland using concepts based on tissue echogenicity and ultrasound image formation. We first segment the hypoechoic anatomical regions of interest using local phase and energy in the input image. We then make use of a Hessian based blob like analysis to detect the carotid within the segmented hypoechoic regions. The carotid artery is segmented by making use of least squares ellipse fit for the edge points around the detected carotid candidate. Experiments performed on a multivendor dataset of 41 images show that the proposed algorithm can segment the carotid artery with high sensitivity (99.6 ±m 0.2%) and specificity (92.9 ±m 0.1%). Further experiments on a public database containing 971 images of the carotid artery showed that the proposed algorithm can achieve a detection accuracy of 95.2% with a 2% increase in performance when compared to the state-of-the-art method.

Fragment analysis represents a suitable approach for the detection of hotspot c.7541_7542delCT NOTCH1 mutation in chronic lymphocytic leukemia.

PubMed

Vavrova, Eva; Kantorova, Barbara; Vonkova, Barbara; Kabathova, Jitka; Skuhrova-Francova, Hana; Diviskova, Eva; Letocha, Ondrej; Kotaskova, Jana; Brychtova, Yvona; Doubek, Michael; Mayer, Jiri; Pospisilova, Sarka

2017-09-01

The hotspot c.7541_7542delCT NOTCH1 mutation has been proven to have a negative clinical impact in chronic lymphocytic leukemia (CLL). However, an optimal method for its detection has not yet been specified. The aim of our study was to examine the presence of the NOTCH1 mutation in CLL using three commonly used molecular methods. Sanger sequencing, fragment analysis and allele-specific PCR were compared in the detection of the c.7541_7542delCT NOTCH1 mutation in 201 CLL patients. In 7 patients with inconclusive mutational analysis results, the presence of the NOTCH1 mutation was also confirmed using ultra-deep next generation sequencing. The NOTCH1 mutation was detected in 15% (30/201) of examined patients. Only fragment analysis was able to identify all 30 NOTCH1-mutated patients. Sanger sequencing and allele-specific PCR showed a lower detection efficiency, determining 93% (28/30) and 80% (24/30) of the present NOTCH1 mutations, respectively. Considering these three most commonly used methodologies for c.7541_7542delCT NOTCH1 mutation screening in CLL, we defined fragment analysis as the most suitable approach for detecting the hotspot NOTCH1 mutation. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the Power and the Systematic Biases of the Detection of Chromosomal Inversions by Paired-End Genome Sequencing

PubMed Central

Lucas Lledó, José Ignacio; Cáceres, Mario

2013-01-01

One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with low coverage data. However, % of inversions located between segmental duplications are expected to go undetected by the most common sequencing strategies. In general, longer DNA libraries improve the detectability of inversions far better than increments of the coverage depth or the read length. Finally, we review the performance of three algorithms to detect inversions —SVDetect, GRIAL, and VariationHunter—, identify common pitfalls, and reveal important differences in their breakpoint precisions. These results stress the importance of the sequencing strategy for the detection of structural variants, especially inversions, and offer guidelines for the design of future genome sequencing projects. PMID:23637806

Highly Sensitive GMO Detection Using Real-Time PCR with a Large Amount of DNA Template: Single-Laboratory Validation.

PubMed

Mano, Junichi; Hatano, Shuko; Nagatomi, Yasuaki; Futo, Satoshi; Takabatake, Reona; Kitta, Kazumi

2018-03-01

Current genetically modified organism (GMO) detection methods allow for sensitive detection. However, a further increase in sensitivity will enable more efficient testing for large grain samples and reliable testing for processed foods. In this study, we investigated real-time PCR-based GMO detection methods using a large amount of DNA template. We selected target sequences that are commonly introduced into many kinds of GM crops, i.e., 35S promoter and nopaline synthase (NOS) terminator. This makes the newly developed method applicable to a wide range of GMOs, including some unauthorized ones. The estimated LOD of the new method was 0.005% of GM maize events; to the best of our knowledge, this method is the most sensitive among the GM maize detection methods for which the LOD was evaluated in terms of GMO content. A 10-fold increase in the DNA amount as compared with the amount used under common testing conditions gave an approximately 10-fold reduction in the LOD without PCR inhibition. Our method is applicable to various analytical samples, including processed foods. The use of other primers and fluorescence probes would permit highly sensitive detection of various recombinant DNA sequences besides the 35S promoter and NOS terminator.

Novel Hierarchical Fall Detection Algorithm Using a Multiphase Fall Model.

PubMed

Hsieh, Chia-Yeh; Liu, Kai-Chun; Huang, Chih-Ning; Chu, Woei-Chyn; Chan, Chia-Tai

2017-02-08

Falls are the primary cause of accidents for the elderly in the living environment. Reducing hazards in the living environment and performing exercises for training balance and muscles are the common strategies for fall prevention. However, falls cannot be avoided completely; fall detection provides an alarm that can decrease injuries or death caused by the lack of rescue. The automatic fall detection system has opportunities to provide real-time emergency alarms for improving the safety and quality of home healthcare services. Two common technical challenges are also tackled in order to provide a reliable fall detection algorithm, including variability and ambiguity. We propose a novel hierarchical fall detection algorithm involving threshold-based and knowledge-based approaches to detect a fall event. The threshold-based approach efficiently supports the detection and identification of fall events from continuous sensor data. A multiphase fall model is utilized, including free fall, impact, and rest phases for the knowledge-based approach, which identifies fall events and has the potential to deal with the aforementioned technical challenges of a fall detection system. Seven kinds of falls and seven types of daily activities arranged in an experiment are used to explore the performance of the proposed fall detection algorithm. The overall performances of the sensitivity, specificity, precision, and accuracy using a knowledge-based algorithm are 99.79%, 98.74%, 99.05% and 99.33%, respectively. The results show that the proposed novel hierarchical fall detection algorithm can cope with the variability and ambiguity of the technical challenges and fulfill the reliability, adaptability, and flexibility requirements of an automatic fall detection system with respect to the individual differences.

Novel Hierarchical Fall Detection Algorithm Using a Multiphase Fall Model

PubMed Central

Hsieh, Chia-Yeh; Liu, Kai-Chun; Huang, Chih-Ning; Chu, Woei-Chyn; Chan, Chia-Tai

2017-01-01

Falls are the primary cause of accidents for the elderly in the living environment. Reducing hazards in the living environment and performing exercises for training balance and muscles are the common strategies for fall prevention. However, falls cannot be avoided completely; fall detection provides an alarm that can decrease injuries or death caused by the lack of rescue. The automatic fall detection system has opportunities to provide real-time emergency alarms for improving the safety and quality of home healthcare services. Two common technical challenges are also tackled in order to provide a reliable fall detection algorithm, including variability and ambiguity. We propose a novel hierarchical fall detection algorithm involving threshold-based and knowledge-based approaches to detect a fall event. The threshold-based approach efficiently supports the detection and identification of fall events from continuous sensor data. A multiphase fall model is utilized, including free fall, impact, and rest phases for the knowledge-based approach, which identifies fall events and has the potential to deal with the aforementioned technical challenges of a fall detection system. Seven kinds of falls and seven types of daily activities arranged in an experiment are used to explore the performance of the proposed fall detection algorithm. The overall performances of the sensitivity, specificity, precision, and accuracy using a knowledge-based algorithm are 99.79%, 98.74%, 99.05% and 99.33%, respectively. The results show that the proposed novel hierarchical fall detection algorithm can cope with the variability and ambiguity of the technical challenges and fulfill the reliability, adaptability, and flexibility requirements of an automatic fall detection system with respect to the individual differences. PMID:28208694

Common dental and periodontal diseases: evaluation and management.

PubMed

Laudenbach, Joel M; Simon, Ziv

2014-11-01

Physicians may encounter patients with dental and periodontal diseases in the context of outpatient medical practice. It is important for physicians to be aware of common dental and periodontal conditions and be able to assess for the presence and severity of these diseases. This article reviews common dental and periodontal conditions, their cardinal signs and symptoms, outpatient-setting assessment techniques, as well as common methods of treatment. Physicians detecting gross abnormalities on clinical examination should refer the patient to a dentist for further evaluation and management. Copyright © 2014 Elsevier Inc. All rights reserved.

Family Medicine Residents' Performance with Detected Versus Undetected Simulated Patients Posing as Problem Drinkers.

PubMed

Kahan, Meldon; Liu, Eleanor; Borsoi, Diane; Wilson, Lynn; Brewster, Joan M; Sobell, Mark B; Sobell, Linda C

2004-12-01

Simulated patients are commonly used to evaluate medical trainees. Unannounced simulated patients provide an accurate measure of physician performance. To determine the effects of detection of SPs on physician performance, and identify factors leading to detection. Fixty-six family medicine residents were each visited by two unannounced simulated patients presenting with alcohol-induced hypertension or insomnia. Residents were then surveyed on their detection of SPs. SPs were detected on 45 out of 104 visits. Inner city clinics had higher detection rates than middle class clinics. Residents' checklist and global rating scores were substantially higher on detected than undetected visits, for both between-subject and within-subject comparisons. The most common reasons for detection concerned SP demographics and behaviour; the SP "did not act like a drinker" and was of a different social class than the typical clinic patient. Multi-clinic studies involving residents experienced with SPs should ensure that the SP role and behavior conform to physician expectations and the demographics of the clinic. SP station testing does not accurately reflect physicians' actual clinical behavior and should not be relied on as the primary method of evaluation. The study also suggests that physicians' poor performance in identifying and managing alcohol problems is not entirely due to lack of skill, as they demonstrated greater clinical skills when they became aware that they were being evaluated. Physicians' clinical priorities, sense of responsibility and other attitudinal determinants of their behavior should be addressed when training physicians on the management of alcohol problems.

Surface enhanced raman spectroscopy technique in rapid detection of live and dead salmonella cells

USDA-ARS?s Scientific Manuscript database

Many research proved that Surface Enhanced Raman Spectroscopy (SERS) can detect pathogens rapidly and accurately. In this study, a silver metal substrate was used for the selected common food pathogen Salmonella typhimurium bacteria. Nano silver rods were deposited on a thin titanium coating over t...

77 FR 23291 - Proposed Extension of Existing Information Collection; Notification of Methane Detected in...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-18

... Information Collection; Notification of Methane Detected in Underground Metal and Nonmetal Mine Atmospheres...); or 202-693-9441 (facsimile). SUPPLEMENTARY INFORMATION: I. Background Methane is a flammable gas commonly found in underground mines in the United States. Although methane is often associated with...

Validating an Asthma Case Detection Instrument in a Head Start Sample

ERIC Educational Resources Information Center

Bonner, Sebastian; Matte, Thomas; Rubin, Mitchell; Sheares, Beverley J.; Fagan, Joanne K.; Evans, David; Mellins, Robert B.

2006-01-01

Although specific tests screen children in preschool programs for vision, hearing, and dental conditions, there are no published validated instruments to detect preschool-age children with asthma, one of the most common pediatric chronic conditions affecting children in economically disadvantaged communities of color. As part of an asthma…

EVALUATION OF RAPID DNA EXTRACTION PROCEDURES FOR THE QUANTITATIVE DETECTION OF FUNGAL CELLS USING REAL TIME PCR ANALYSIS

EPA Science Inventory

The ease and rapidity of quantitative DNA sequence detection by real-time PCR instruments promises to make their use increasingly common for the microbial analysis many different types of environmental samples. To fully exploit the capabilities of these instruments, correspondin...

IMPROVED DETECTION OF HUMAN ENTERIC VIRUSES IN FOODS BY RT-PCR. (R826139)

EPA Science Inventory

Human enteric viruses (including hepatitis A virus (HAV) and Norwalk-like viruses (NLVs)) are now recognized as common causes of foodborne disease. While methods to detect these agents in clinical specimens have improved significantly over the last 10 years, applications to fo...

A SENSITIVE IMMUNOFLUORESCENCE ASSAY FOR DETECTION OF P53 PROTEIN ACCUMULATION IN SPUTUM

EPA Science Inventory

p53 mutations are common genetic alterations in lung cancers and usually result in p53 protein accumulation in tumor cells. Sputum is noninvasive to collect and ideal for screening p53 abnormalities. This study was to determine the feasibility of detecting p53 protein accumulatio...

Sensing the deadliest toxin: technologies for botulinum neurotoxin detection.

PubMed

Capek, Petr; Dickerson, Tobin J

2010-01-01

Sensitive and rapid detection of botulinum neurotoxins (BoNTs), the most poisonous substances known to date, is essential for studies of medical applications of BoNTs and detection of poisoned food, as well as for response to potential bioterrorist threats. Currently, the most common method of BoNT detection is the mouse bioassay. While this assay is sensitive, it is slow, quite expensive, has limited throughput and requires sacrificing animals. Herein, we discuss and compare recently developed alternative in vitro detection methods and assess their ability to supplement or replace the mouse bioassay in the analysis of complex matrix samples.

Automatically Detecting Failures in Natural Language Processing Tools for Online Community Text.

PubMed

Park, Albert; Hartzler, Andrea L; Huh, Jina; McDonald, David W; Pratt, Wanda

2015-08-31

The prevalence and value of patient-generated health text are increasing, but processing such text remains problematic. Although existing biomedical natural language processing (NLP) tools are appealing, most were developed to process clinician- or researcher-generated text, such as clinical notes or journal articles. In addition to being constructed for different types of text, other challenges of using existing NLP include constantly changing technologies, source vocabularies, and characteristics of text. These continuously evolving challenges warrant the need for applying low-cost systematic assessment. However, the primarily accepted evaluation method in NLP, manual annotation, requires tremendous effort and time. The primary objective of this study is to explore an alternative approach-using low-cost, automated methods to detect failures (eg, incorrect boundaries, missed terms, mismapped concepts) when processing patient-generated text with existing biomedical NLP tools. We first characterize common failures that NLP tools can make in processing online community text. We then demonstrate the feasibility of our automated approach in detecting these common failures using one of the most popular biomedical NLP tools, MetaMap. Using 9657 posts from an online cancer community, we explored our automated failure detection approach in two steps: (1) to characterize the failure types, we first manually reviewed MetaMap's commonly occurring failures, grouped the inaccurate mappings into failure types, and then identified causes of the failures through iterative rounds of manual review using open coding, and (2) to automatically detect these failure types, we then explored combinations of existing NLP techniques and dictionary-based matching for each failure cause. Finally, we manually evaluated the automatically detected failures. From our manual review, we characterized three types of failure: (1) boundary failures, (2) missed term failures, and (3) word ambiguity failures. Within these three failure types, we discovered 12 causes of inaccurate mappings of concepts. We used automated methods to detect almost half of 383,572 MetaMap's mappings as problematic. Word sense ambiguity failure was the most widely occurring, comprising 82.22% of failures. Boundary failure was the second most frequent, amounting to 15.90% of failures, while missed term failures were the least common, making up 1.88% of failures. The automated failure detection achieved precision, recall, accuracy, and F1 score of 83.00%, 92.57%, 88.17%, and 87.52%, respectively. We illustrate the challenges of processing patient-generated online health community text and characterize failures of NLP tools on this patient-generated health text, demonstrating the feasibility of our low-cost approach to automatically detect those failures. Our approach shows the potential for scalable and effective solutions to automatically assess the constantly evolving NLP tools and source vocabularies to process patient-generated text.

Anthropogenic constituents in shallow ground water in the Upper Illinois River Basin

USGS Publications Warehouse

Morrow, William S.

2003-01-01

The potential for anthropogenic effects on ground water is becoming of increasing concern as land throughout the Nation becomes more urbanized. The possible contamination of water resources by volatile organic compounds (VOCs), pesticides (including transformation products), and nitrate, from current urban land use and past agricultural land use, is of particular concern. As part of the U.S. Geological Survey's National Water-Quality Assessment program, water samples for analysis of VOCs, pesticides, and nitrate were collected from 43 wells in shallow (175 feet deep or less) ground water in glacial deposits overlying a major bedrock aquifer in recently urbanized areas in the Chicago, Ill. and Milwaukee, Wis. metropolitan counties.Constituents were reported using two reporting levels. For the laboratory reporting level, the risk of a false positive or false negative detection is less than or equal to 1 percent. For the information-rich method level, estimated concentrations are identified positively and are qualified to be present on the basis of quality-control criteria, but have a higher risk of false positive detections.VOCs were detected in 32 percent (12 of 38) of the well samples with 15 detections of 7 VOCs, based on laboratory reporting levels. Concentrations ranged from 0.03 (estimated) to 4.6 micrograms per liter (?g/L), with a median concentration of 0.13 ?g/L. Methyl tert-butyl ether (MTBE) and trichloromethane (chloroform) were the most common with detections in 10 percent (4 of 38) of the well samples. Using information-rich method reporting levels, VOCs were detected in 74 percent of the wells with 37 detections of 15 VOCs. Chloroform was most common with detections in 24 percent (9 of 38) of the well samples.Pesticides were detected in 62 percent (26 of 42) of the well samples with 83 detections of 20 pesticides, based on laboratory reporting levels for the respective constituent. Concentrations ranged from 0.003 (estimated) to 3.6 (estimated) ?g/L, with a median concentration of 0.06 ?g/L. Deethylatrazine was most common with detections in 43 percent (18 of 42) of the well samples. Using information-rich method reporting levels, pesticides were detected in 74 percent (31 of 42) of the well samples with 134 detections of 29 pesticides. Deethylatrazine was most common with detections in 45 percent (19 of 42) of the well samples.Nitrate concentrations ranged from less than 0.047 to 12.5 milligrams per liter (mg/L) with a median concentration of 0.068 mg/L. Nitrate concentrations were greater than 2 mg/L in 30 percent (13 of 43) of the wells sampled. Total VOC detections did not correlate well (less than Spearman Rank correlation value of plus or minus 0.10) with well depth, age, or dissolved oxygen. Total pesticide detections did correlate with dissolved oxygen and negatively correlated with well depth. Nitrate concentrations correlated with dissolved oxygen and apparent recharge date.No VOC or pesticide concentrations exceeded U.S. Environmental Protection Agency drinking-water standards and only one nitrate 2 Anthropogenic Constituents in Shallow Ground Water in the Upper Illinois River Basin detection exceeded the standards. However, of the 43 wells sampled for VOCs or pesticides using information-rich methods, or nitrate at laboratory reporting levels, 40 of 43 (93 percent) well samples had at least one detection of a VOC or pesticide, or a detection of nitrate above 2.0 mg/L. This result indicates that most of these wells are anthropogenically affected, but presently not at U.S. Environmental Protection Agency drinking-water regulation levels of concern. The wells sampled were not public drinking-water supplies; therefore, these wells were not subject to U.S. Environmental Protection Agency drinking-water regulations.

Multisensor configurations for early sniper detection

NASA Astrophysics Data System (ADS)

Lindgren, D.; Bank, D.; Carlsson, L.; Dulski, R.; Duval, Y.; Fournier, G.; Grasser, R.; Habberstad, H.; Jacquelard, C.; Kastek, M.; Otterlei, R.; Piau, G.-P.; Pierre, F.; Renhorn, I.; Sjöqvist, L.; Steinvall, O.; Trzaskawka, P.

2011-11-01

This contribution reports some of the fusion results from the EDA SNIPOD project, where different multisensor configurations for sniper detection and localization have been studied. A project aim has been to cover the whole time line from sniper transport and establishment to shot. To do so, different optical sensors with and without laser illumination have been tested, as well as acoustic arrays and solid state projectile radar. A sensor fusion node collects detections and background statistics from all sensors and employs hypothesis testing and multisensor estimation programs to produce unified and reliable sniper alarms and accurate sniper localizations. Operator interfaces that connect to the fusion node should be able to support both sniper countermeasures and the guidance of personnel to safety. Although the integrated platform has not been actually built, sensors have been evaluated at common field trials with military ammunitions in the caliber range 5.56 to 12.7 mm, and at sniper distances up to 900 m. It is concluded that integrating complementary sensors for pre- and postshot sniper detection in a common system with automatic detection and fusion will give superior performance, compared to stand alone sensors. A practical system is most likely designed with a cost effective subset of available complementary sensors.

Homozygosity mapping on a single patient: identification of homozygous regions of recent common ancestry by using population data.

PubMed

Zhang, Lu; Yang, Wanling; Ying, Dingge; Cherny, Stacey S; Hildebrandt, Friedhelm; Sham, Pak Chung; Lau, Yu Lung

2011-03-01

Homozygosity mapping has played an important role in detecting recessive mutations using families of consanguineous marriages. However, detection of regions identical and homozygosity by descent (HBD) when family data are not available, or when relationships are unknown, is still a challenge. Making use of population data from high-density SNP genotyping may allow detection of regions HBD from recent common founders in singleton patients without genealogy information. We report a novel algorithm that detects such regions by estimating the population haplotype frequencies (HF) for an entire homozygous region. We also developed a simulation method to evaluate the probability of HBD and linkage to disease for a homozygous region by examining the best regions in unaffected controls from the host population. The method can be applied to diseases of Mendelian inheritance but can also be extended to complex diseases to detect rare founder mutations that affect a very small number of patients using either multiplex families or sporadic cases. Testing of the method on both real cases (singleton affected) and simulated data demonstrated its superb sensitivity and robustness under genetic heterogeneity. © 2011 Wiley-Liss, Inc.

Comparison of PCR methods for the detection of genetic variants of carp edema virus.

PubMed

Adamek, Mikolaj; Matras, Marek; Jung-Schroers, Verena; Teitge, Felix; Heling, Max; Bergmann, Sven M; Reichert, Michal; Way, Keith; Stone, David M; Steinhagen, Dieter

2017-09-20

The infection of common carp and its ornamental variety, koi, with the carp edema virus (CEV) is often associated with the occurrence of a clinical disease called 'koi sleepy disease'. The disease may lead to high mortality in both koi and common carp populations. To prevent further spread of the infection and the disease, a reliable detection method for this virus is required. However, the high genetic variability of the CEV p4a gene used for PCR-based diagnostics could be a serious obstacle for successful and reliable detection of virus infection in field samples. By analysing 39 field samples from different geographical origins obtained from koi and farmed carp and from all 3 genogroups of CEV, using several recently available PCR protocols, we investigated which of the protocols would allow the detection of CEV from all known genogroups present in samples from Central European carp or koi populations. The comparison of 5 different PCR protocols showed that the PCR assays (both end-point and quantitative) developed in the Centre for Environment, Fisheries and Aquaculture Science exhibited the highest analytical inclusivity and diagnostic sensitivity. Currently, this makes them the most suitable protocols for detecting viruses from all known CEV genogroups.

Multi-Mycotoxin Screening Reveals the Occurrence of 139 Different Secondary Metabolites in Feed and Feed Ingredients

PubMed Central

Streit, Elisabeth; Schwab, Christina; Sulyok, Michael; Naehrer, Karin; Krska, Rudolf; Schatzmayr, Gerd

2013-01-01

The development of liquid chromatography-mass spectrometry (LC-MS)/mass spectrometry (MS) methods for the simultaneous detection and quantification of a broad spectrum of mycotoxins has facilitated the screening of a larger number of samples for contamination with a wide array of less well-known “emerging” mycotoxins and other metabolites. In this study, 83 samples of feed and feed raw materials were analysed. All of them were found to contain seven to 69 metabolites. The total number of detected metabolites amounts to 139. Fusarium mycotoxins were most common, but a number of Alternaria toxins also occurred very often. Furthermore, two so-called masked mycotoxins (i.e., mycotoxin conjugates), namely deoxynivalenol-3-glucoside (75% positives) and zearalenone-4-sulfate (49% positives), were frequently detected. Although the observed median concentrations of the individual analytes were generally in the low μg/kg range, evaluating the toxicological potential of a given sample is difficult. Toxicity data on less well-known mycotoxins and other detected metabolites are notoriously scarce, as an overview on the available information on the most commonly detected metabolites shows. Besides, the possible synergistic effects of co-occurring substances have to be considered. PMID:23529186

The CommonGround Visual Paradigm for Biosurveillance

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

Livnat, Yarden; Jurrus, Elizabeth R.; Gundlapalli, Adi V.

2013-06-14

Biosurveillance is a critical area in the intelligence community for real-time detection of disease outbreaks. Identifying epidemics enables analysts to detect and monitor disease outbreaks that might be spread from natural causes or from possible biological warfare attacks. Containing these events and disseminating alerts requires the ability to rapidly find, classify and track harmful biological signatures. In this paper, we describe a novel visual paradigm to conduct biosurveillance using an Infectious Disease Weather Map. Our system provides a visual common ground in which users can view, explore and discover emerging concepts and correlations such as symptoms, syndromes, pathogens, and geographicmore » locations.« less

Plasmodium falciparum spliceosomal RNAs: 3' and 5' end processing.

PubMed

Eliana, Calvo; Javier, Escobar; Moisés, Wasserman

2011-02-01

The major spliceosomal small nuclear ribonucleoproteins (snRNPs) consist of snRNA (U1, U2, U4 or U5) and several proteins which can be unique or common to each snRNP particle. The common proteins are known as Sm proteins; they are crucial for RNP assembly and nuclear import of spliceosomal RNPs. This paper reports detecting the interaction between Plasmodium falciparum snRNAs and Sm proteins, and the usual 5' trimethylated caps on the snRNAs, by immunoprecipitation with specific antibodies. Furthermore, an unusual poly(A) tail was detected on these non-coding RNAs. 2010 Elsevier B.V. All rights reserved.

Effects on Diagnostic Parameters After Removing Additional Synchronous Gear Meshes

NASA Technical Reports Server (NTRS)

Decker, Harry J.

2003-01-01

Gear cracks are typically difficult to diagnose with sufficient time before catastrophic damage occurs. Significant damage must be present before algorithms appear to be able to detect the damage. Frequently there are multiple gear meshes on a single shaft. Since they are all synchronous with the shaft frequency, the commonly used synchronous averaging technique is ineffective in removing other gear mesh effects. Carefully applying a filter to these extraneous gear mesh frequencies can reduce the overall vibration signal and increase the accuracy of commonly used vibration metrics. The vibration signals from three seeded fault tests were analyzed using this filtering procedure. Both the filtered and unfiltered vibration signals were then analyzed using commonly used fault detection metrics and compared. The tests were conducted on aerospace quality spur gears in a test rig. The tests were conducted at speeds ranging from 2500 to 5000 revolutions per minute and torques from 184 to 228 percent of design load. The inability to detect these cracks with high confidence results from the high loading which is causing fast fracture as opposed to stable crack growth. The results indicate that these techniques do not currently produce an indication of damage that significantly exceeds experimental scatter.

Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans.

PubMed

Kasalický, Vojtěch; Zeng, Yonghui; Piwosz, Kasia; Šimek, Karel; Kratochvilová, Hana; Koblížek, Michal

2018-01-01

The genus Limnohabitans ( Comamonadaceae , Betaproteobacteria ) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes pufLM and bchY in 28 of 46 strains from three Limnohabitans lineages. The pufM sequences obtained are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic Limnohabitans in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also among all potentially photosynthetic Betaproteobacteria strains. The expression of photosynthetic complexes was detected in a culture of Limnohabitans planktonicus II-D5 T using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent in situ hybridization. IMPORTANCE The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus Limnohabitans , indicating that they may have a novel role in freshwater habitats. Copyright © 2017 American Society for Microbiology.

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

Colotelo, Alison HA; Smokorowski, Karen; Haxton, Tim

Current methods of fish epithelial injury detection are limited to gross macroscopic examination that has a subjective bias as well as an inability to reliably quantify the degree of injury. Fluorescein, a presumptive test for blood, has been shown to have the capability to detect and quantify fish epithelial injury. However, there are several other presumptive tests for blood (Bluestar*, phenolphthalein, and HemastixH) that may have benefits over the use of fluorescein, particularly for field research on wild fish. This study investigated the capabilities of these four tests to detect and quantify a variety of injuries commonly encountered by fishmore » (abrasion, cuts, fin frays, and punctures) using the freshwater bluegill Lepomis macrochirus as a model. Fluorescein was consistently found to be the most reliable (i.e., detected the highest proportion of true positive results and rarely detected false positive reactions) of the four presumptive tests for blood compared. Further testing was conducted to examine the reliability of fluorescein. By 24 h after an injury was inflicted, the injury was no longer detectable by fluorescein, and when fluorescein was applied to an injured fish, the fluorescein was no longer detectable 3 h after application. In a comparison of two common anaesthetics used in fisheries research, there was no significant difference in the proportion of injury detected when 3- aminobenzoic acid ethyl ester methanesulfate (tricaine) was used compared with a clove oil and ethanol (1:9) solution. In summary, fluorescein was the most reliable presumptive test for blood examined in this study for the detection and quantification of recent (hours) fish epithelial injury.« less

Pesticides in streams in the Tar-Pamlico drainage basin, North Carolina, 1992-94

USGS Publications Warehouse

Woodside, Michael D.; Ruhl, Kelly E.

2001-01-01

From 1992 to 1994, 147 water samples were collected at 5 sites in the Tar-Pamlico drainage basin in North Carolina and analyzed for 46 herbicides, insecticides, and pesticide metabolites as part of the U.S. Geological Survey's National Water-Quality Assessment Program. Based on a common adjusted detection limit of 0.01 microgram per liter, the most frequently detected herbicides were metolachlor (84 percent), atrazine (78 percent), alachlor (72 percent), and prometon (57 percent). The insecticides detected most frequently were carbaryl (12 percent), carbofuran (7 percent), and diazinon (4 percent). Although the pesticides with the highest estimated uses generally were the compounds detected most frequently, there was not a strong correlation between estimated use and detection frequency. The development of statistical correlations between pesticide use and detection frequency was limited by the lack of information on pesticides commonly applied in urban and agricultural areas, such as prometon, chlorpyrifos, and diazinon, and the small number of basins included in this study. For example, prometon had the fourth highest detection frequency, but use information was not available. Nevertheless, the high detection frequency of prometon indicates that nonagricultural uses also contribute to pesticide levels in streams in the Tar-Pamlico drainage basin.Concentrations of the herbicides atrazine, alachlor, and trifluralin varied seasonally, with elevated concentrations generally occurring in the spring, during and immediately following application periods, and in the summer. Seasonal concentration patterns were less evident for prometon, diazinon, and chlorpyrifos. Alachlor is the only pesticide detected in concentrations that exceeded current (2000) drinking-water standards.

Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health.

PubMed

King, Dawn N; Donohue, Maura J; Vesper, Stephen J; Villegas, Eric N; Ware, Michael W; Vogel, Megan E; Furlong, Edward F; Kolpin, Dana W; Glassmeyer, Susan T; Pfaller, Stacy

2016-08-15

An occurrence survey was conducted on selected pathogens in source and treated drinking water collected from 25 drinking water treatment plants (DWTPs) in the United States. Water samples were analyzed for the protozoa Giardia and Cryptosporidium (EPA Method 1623); the fungi Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus (quantitative PCR [qPCR]); and the bacteria Legionella pneumophila (qPCR), Mycobacterium avium, M. avium subspecies paratuberculosis, and Mycobacterium intracellulare (qPCR and culture). Cryptosporidium and Giardia were detected in 25% and in 46% of the source water samples, respectively (treated waters were not tested). Aspergillus fumigatus was the most commonly detected fungus in source waters (48%) but none of the three fungi were detected in treated water. Legionella pneumophila was detected in 25% of the source water samples but in only 4% of treated water samples. M. avium and M. intracellulare were both detected in 25% of source water, while all three mycobacteria were detected in 36% of treated water samples. Five species of mycobacteria, Mycobacterium mucogenicum, Mycobacterium phocaicum, Mycobacterium triplex, Mycobacterium fortuitum, and Mycobacterium lentiflavum were cultured from treated water samples. Although these DWTPs represent a fraction of those in the U.S., the results suggest that many of these pathogens are widespread in source waters but that treatment is generally effective in reducing them to below detection limits. The one exception is the mycobacteria, which were commonly detected in treated water, even when not detected in source waters. Published by Elsevier B.V.

Screening or Symptoms? How Do We Detect Colorectal Cancer in an Equal Access Health Care System?

PubMed

Hatch, Quinton M; Kniery, Kevin R; Johnson, Eric K; Flores, Shelly A; Moeil, David L; Thompson, John J; Maykel, Justin A; Steele, Scott R

2016-02-01

Detection of colorectal cancer ideally occurs at an early stage through proper screening. We sought to establish methods by which colorectal cancers are diagnosed within an equal access military health care population and evaluate the correlation between TNM stage at colorectal cancer diagnosis and diagnostic modality (i.e., symptomatic detection vs screen detection). A retrospective chart review of all newly diagnosed colorectal cancer patients from January 2007 to August 2014 was conducted at the authors' equal access military institution. We evaluated TNM stage relative to diagnosis by screen detection (fecal occult blood test, flexible sigmoidoscopy, CT colonography, colonoscopy) or symptomatic evaluation (diagnostic colonoscopy or surgery). Of 197 colorectal cancers diagnosed (59 % male; mean age 62 years), 50 (25 %) had stage I, 47 (24 %) had stage II, 70 (36 %) had stage III, and 30 (15 %) had stage IV disease. Twenty-five percent of colorectal cancers were detected via screen detection (3 % by fecal occult blood testing (FOBT), 0.5 % by screening CT colonography, 17 % by screening colonoscopy, and 5 % by surveillance colonoscopy). One hundred forty-eight (75 %) were diagnosed after onset of signs or symptoms. The preponderance of these was advanced-stage disease (stages III-IV), although >50 % of stage I-II disease also had signs or symptoms at diagnosis. The most common symptoms were rectal bleeding (45 %), abdominal pain (35 %), and change in stool caliber (27 %). The most common overall sign was anemia (60 %). Screening FOBT (odds ratio (OR) 8.7, 95 % confidence interval (CI) 1.0-78.3; P = 0.05) independently predicted early diagnosis with stage I-II disease. Patient gender and ethnicity were not associated with cancer stage at diagnosis. Despite equal access to colorectal cancer screening, diagnosis after development of symptomatic cancer remains more common. Fecal occult blood screen detection is associated with early stage at colorectal cancer diagnosis and is the focus for future initiatives.

HIV/AIDS, HPV and Anal Cancer

PubMed Central

Wang, Chia-ching J.; Sparano, Joseph; Palefsky, Joel M.

2016-01-01

SYNOPSIS Anal cancer is an increasingly common non-AIDS-defining cancer among HIV-infected individuals. It is associated with human papillomavirus (HPV), the most common sexually transmitted infectious agent. The 14 oncogenic types of HPV are causally associated with 5–10% of all cancers, notably anogenital cancers. HPV16 is the most common genotype detected in about 70% of anal cancers. The HPV types detected in anal cancer are included in the 9-valent vaccine. HPV vaccines have demonstrated efficacy in reducing anal precancerous lesions in HIV-infected individuals. The standard treatment for anal cancer has been fluorouracil (5-FU) and mitomycin (or cisplatin) as chemotherapy agents plus radiation, which can also be effectively used for the HIV-infected patients. Continued studies will be needed to test new treatment strategies in HIV-infected patients with anal cancer to determine which treatment protocols provide the best therapeutic index. PMID:27889034

Water-quality assessment of the Connecticut, Housatonic, and Thames river basins study unit; analysis of available data on nutrients, suspended sediments, and pesticides, 1972-92

USGS Publications Warehouse

Zimmerman, Marc James; Grady, S.J.; Trench, E.C.; Flanagan, S.M.; Nielsen, M.G.

1996-01-01

This retrospective report examines available nutrient, suspended sediment, and pesticide data in surface and ground water in the Connecticut, Housatonic and Thames Rivers Study Unit of the National Water-Quality Assessment Program. The purpose of this study is to improve the under- standing of natural and anthropogenic factors affecting water quality in the study unit. Water-quality data were acquired from various sources, primarily, the U.S. Geological Survey and the U.S. Environmental Protection Agency. The report examines data for water years 1972-92, focusing on 1980-92, although it also includes additional data from as early as 1905. The study unit lies within the New England Physiographic Province and altitudes range from sea level in coastal Connecticut to 6,288 feet above sea level at Mount Washington, New Hampshire. Two major aquifer types underlie the study unit--unconsolidated glacial deposits and fractured bedrock. The climate generally is temperate and humid, with four distinct seasons. Average annual precipitation ranges from 34 to 65 inches. The study unit has a population of about 4.5 million, which is most highly concentrated in southwestern Connecticut and along the south-central region of the Connecticut River Valley. Surface-water-quality data were screened to provide information about sites with adequate numbers of analyses (50) over sufficiently long periods (1980-90) to enable valid statistical analyses. In order to compare effects of different types of land use on surface-water quality, examination of data required application of several statistical and graphical techniques, including mapping, histograms, boxplots, concentration-discharge plots, trend analysis, and load estimation. Spatial and temporal analysis of surface-water-quality data indicated that, with a single exception, only/stations in the Connecticut water-quality network had sufficient data collected over adequately long time periods to use in detailed analyses. Ground-water nutrient and pesticide data were compiled from several Federal and State agencies, primarily the U.S. Geological Survey, U.S. Environmental Protection Agency, and Connecticut Department of Health Services. Nutrient data were available for several thousand wells; nitrite plus nitrate as nitrogen was the most commonly reported constituent. Most wells with nutrient data are in Massachusetts and Connecticut. Relative to nutrient data in ground and surface water, pesticide data are less common. Pesticide data were available for slightly more than 200 surface-water sites and less than 500 wells; about 95 percent of the wells are completed in stratified-drift or till aquifers. Data for 81 pesticide compounds were available in various data bases. 2,4-D and silvex were the most commonly detected herbicides in surface water and dieldrin and diazinon were the most commonly detected insecticides. Most surface-water pesticide samples and detections are from bed sediment, but much of the data are not recent. Ethylene dibromide (EDB), a soil fumigant used in tobacco farming was detected in 268 well in a 50 square-mile area of north-central Connecticut; EDB contamination also was detected in wells in Massachusetts. Atrazine, an herbicide commonly used in corn farming, commonly was detected in wells installed in tilled agricultural fields. Corn herbicides were commonly detected in the northern par( of the study unit, although the sampling has been less frequent than in the southern part of the study unit. Pesticides were seldom detected in public-supply wells in Connecticut. Urban sites with relatively high population densities and high concentrations of dischargers were characterized by having the highest nutrient concentrations and loads when adjusted for differences in drainage area or population. Particularly, the Pequabuck, Naugatuck, and Quinnipiac River Basins were characterized by high nutrient concentrations--median total nitrogen concentrations ranged from 3.3 to 4.2 mg

Applied Graph-Mining Algorithms to Study Biomolecular Interaction Networks

PubMed Central

2014-01-01

Protein-protein interaction (PPI) networks carry vital information on the organization of molecular interactions in cellular systems. The identification of functionally relevant modules in PPI networks is one of the most important applications of biological network analysis. Computational analysis is becoming an indispensable tool to understand large-scale biomolecular interaction networks. Several types of computational methods have been developed and employed for the analysis of PPI networks. Of these computational methods, graph comparison and module detection are the two most commonly used strategies. This review summarizes current literature on graph kernel and graph alignment methods for graph comparison strategies, as well as module detection approaches including seed-and-extend, hierarchical clustering, optimization-based, probabilistic, and frequent subgraph methods. Herein, we provide a comprehensive review of the major algorithms employed under each theme, including our recently published frequent subgraph method, for detecting functional modules commonly shared across multiple cancer PPI networks. PMID:24800226

Current perspectives of herpesviral retinitis and choroiditis.

PubMed

Madhavan, H N; Priya, K; Biswas, J

2004-10-01

Vision-threatening viral retinitis are primarily caused by members of the herpesvirus family. The biology and molecular characterization of herpesviruses, clinical presentations of retinopathies, pathology and pathogenesis including the host responses, epidemiology and the laboratory methods of aetiological diagnosis of these diseases are described. Clinical syndromes are acute retinal necrosis (ARN), progressive outer retinal necrosis (PORN), cytomegalovirus (CMV) retinitis, multifocal choroiditis and serpiginous choroiditis besides other viral retinopathies. Herpes simplex virus (HSV) retinitis is more common in immunocompetent persons while varicella zoster virus (VZV) affects both immunocompetent and immunosuppressed patients equally. CMV retinitis is most common among patients with AIDS. The currently employed laboratory methods of antigen detection, virus isolation and antibody detection by enzyme linked immuno-sorbent assay (ELISA) have low sensitivity. Polymerase chain reaction (PCR) has increased the value of diagnosis due to its high clinical sensitivity and absolute specificity in detection of herpesviruses in intraocular specimens.

Short communication: culture-independent detection of lactic Acid bacteria bacteriocin genes in two traditional slovenian raw milk cheeses and their microbial consortia.

PubMed

Trmcić, A; Obermajer, T; Rogelj, I; Bogovic Matijasić, B

2008-12-01

Two Slovenian traditional raw milk cheeses, Tolminc (from cows' milk) and Kraski (from ewes' milk), were examined for the presence of 19 lactic acid bacteria bacteriocin genes by PCR analysis of total DNA extracts from 9 cheeses and from consortia of strains isolated from these cheeses. Eleven bacteriocin genes were detected in at least one cheese or consortium, or from both. Different cheeses or consortia contained 3 to 9 bacteriocin determinants. Plantaricin A gene determinants were found in all cheese and consortia DNA extracts. Genes for enterocins A, B, P, L50A, and L50B, and the bacteriocin cytolysin were commonly detected, as were genes for nisin. These results indicate that bacteriocinogenic strains of Lactobacillus, Enterococcus, and Lactococcus genera with protective potential are common members of indigenous microbiota of raw milk cheeses, which can be a good source of new protective strains.

Decreased sensitivity associated with an altered formulation of a commercially available kit for detection of protein carbonyls

PubMed Central

Wang, Ping; Powell, Saul R.

2010-01-01

Carbonylation is a commonly studied form of oxidative modification to proteins which can be conveniently detected using commercially available kits. The most common of these kits is the Oxyblot™ Protein Oxidation Detection Kit (Chemicon/Millipore). Over the past year we have observed severely diminished sensitivity of these kits which was shown to be a result of a change in the formulation of one of the components supplied in the kit. This component, the 10X 2,4-dinitrophenylhydrazine derivatization solution, which had previously been dissolved in 100% trifluoroacetic acid (TFA), was now dissolved in 2N hydrochloric acid, which according to our results is not acid enough. Further, we observed that upon storage even DNPH dissolved in TFA is subject to degradation. Based on these studies, we make recomendations that should improve the sensitivity and reproducibilty of this assay. PMID:20230891

Detection and genotyping of Toxoplasma gondii DNA in the blood and milk of naturally infected donkeys (Equus asinus).

PubMed

Mancianti, Francesca; Nardoni, Simona; Papini, Roberto; Mugnaini, Linda; Martini, Mina; Altomonte, Iolanda; Salari, Federica; D'Ascenzi, Carlo; Dubey, Jitender P

2014-04-03

Toxoplasma gondii is a worldwide zoonotic protozoan. Consumption of raw milk from infected animals is considered a risk factor for acquiring toxoplasmosis in humans. Recently, donkey milk has been indicated for therapeutic and nutritional purposes and T. gondii infection is common in donkeys. The purpose of the present paper was to detect the presence of parasite DNA in milk of T. gondii positive donkeys. Antibodies to T. gondii were found in 11 out of 44 healthy lactating donkeys by IFAT. T. gondii DNA was detected by PCR in blood of 6 and milk of 3 seropositive jennies. Results of limited RFLP-PCR genotyping indicated the presence of T. gondii genotype II or III, commonly found in Europe. The occurrence of T. gondii DNA in milk suggests that the consumption of raw milk from seropositive donkeys could be a potential source of human infection.

Shallow Reflection Method for Water-Filled Void Detection and Characterization

NASA Astrophysics Data System (ADS)

Zahari, M. N. H.; Madun, A.; Dahlan, S. H.; Joret, A.; Hazreek, Z. A. M.; Mohammad, A. H.; Izzaty, R. A.

2018-04-01

Shallow investigation is crucial in enhancing the characteristics of subsurface void commonly encountered in civil engineering, and one such technique commonly used is seismic-reflection technique. An assessment of the effectiveness of such an approach is critical to determine whether the quality of the works meets the prescribed requirements. Conventional quality testing suffers limitations including: limited coverage (both area and depth) and problems with resolution quality. Traditionally quality assurance measurements use laboratory and in-situ invasive and destructive tests. However geophysical approaches, which are typically non-invasive and non-destructive, offer a method by which improvement of detection can be measured in a cost-effective way. Of this seismic reflection have proved useful to assess void characteristic, this paper evaluates the application of shallow seismic-reflection method in characterizing the water-filled void properties at 0.34 m depth, specifically for detection and characterization of void measurement using 2-dimensional tomography.

A common-path optical coherence tomography based electrode for structural imaging of nerves and recording of action potentials

NASA Astrophysics Data System (ADS)

Islam, M. Shahidul; Haque, Md. Rezuanul; Oh, Christian M.; Wang, Yan; Park, B. Hyle

2013-03-01

Current technologies for monitoring neural activity either use different variety of electrodes (electrical recording) or require contrast agents introduced exogenously or through genetic modification (optical imaging). Here we demonstrate an optical method for non-contact and contrast agent free detection of nerve activity using phase-resolved optical coherence tomography (pr-OCT). A common-path variation of the pr-OCT is recently implemented and the developed system demonstrated the capability to detect rapid transient structural changes that accompany neural spike propagation. No averaging over multiple trials was required, indicating its capability of single-shot detection of individual impulses from functionally stimulated Limulus optic nerve. The strength of this OCT-based optical electrode is that it is a contactless method and does not require any exogenous contrast agent. With further improvements in accuracy and sensitivity, this optical electrode will play a complementary role to the existing recording technologies in future.

Troublesome Crystal Structures: Prevention, Detection, and Resolution

PubMed Central

Harlow, Richard L.

1996-01-01

A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures. PMID:27805169

Fast single run of vanilla fingerprint markers on microfluidic-electrochemistry chip for confirmation of common frauds.

PubMed

Avila, Mónica; Zougagh, Mohammed; Escarpa, Alberto; Ríos, Angel

2009-10-01

A new strategy based on the fast separation of the fingerprint markers of Vanilla planifolia extracts and vanilla-related samples on microfluidic-electrochemistry chip is proposed. This methodology allowed the detection of all required markers for confirmation of common frauds in this field. The elution order was strategically connected with sequential sample screening and analyte confirmation steps, where first ethyl vanillin was detected to distinguish natural from adultered samples; second, vanillin as prominent marker in V. planifolia, but frequently added in its synthetic form; and third, the final detection of the fingerprint markers (p-hydroxybenzaldehyde, vanillic acid, and p-hydroxybenzoic acid) of V. planifolia with confirmation purposes. The reliability of the proposed methodology was demonstrated in the confirmation the natural or non-natural origin of vanilla in samples using V. planifolia extracts and other selected food samples containing this flavor.

Selective identification and quantification of saccharin by liquid chromatography and fluorescence detection.

PubMed

Bruno, Sergio N F; Cardoso, Carlos R; Maciel, Márcia Mosca A; Vokac, Lidmila; da Silva Junior, Ademário I

2014-09-15

High-pressure liquid chromatography with ultra-violet detection (HPLC-UV) is one of the most commonly used methods to identify and quantify saccharin in non-alcoholic beverages. However, due to the wide variety of interfering UV spectra in saccharin-containing beverage matrices, the same method cannot be used to measure this analyte accurately. We have developed a new, highly effective method to identify and quantify saccharin using HPLC with fluorescence detection (HPLC-FLD). The excitation wavelength (250 nm) and emission wavelength (440 nm) chosen increased selectivity for all matrices and ensured few changes were required in the mobile phase or other parameters. The presence of saccharin in non-diet beverages - a fraud commonly used to replace more expensive sucrose - was confirmed by comparing coincident peaks as well as the emission spectra of standards and samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Using ion chromatography to monitor haloacetic acids in drinking water: a review of current technologies.

PubMed

Paull, Brett; Barron, Leon

2004-08-13

A review of the application of ion chromatography to the determination of haloacetic acids in drinking water is given. As it requires no sample derivatisation, ion chromatography in its various modes, such as ion-exchange, ion-interaction and ion-exclusion chromatography, is increasingly being investigated as a simpler alternative to gas chromatographic methods for the determination of polar disinfection by-products (DBPs) in drinking waters. Detection limits quoted for the regulated haloacetic acids (HAA5), are commonly in the mid to low microg/L range, however, in most cases analyte preconcentration is still necessary for detection at concentrations commonly found in actual drinking water samples. The coupling of ion chromatography to electrospray mass spectrometry provides a potential future direction, with improved sensitivity and selectivity compared to conductivity based detection, however associated cost and complexity for routine analysis is currently relatively high.

Detecting Motion from a Moving Platform; Phase 2: Lightweight, Low Power Robust Means of Removing Image Jitter

DTIC Science & Technology

2011-11-01

common housefly , Musca domestica. “Lightweight, Low Power Robust Means of Removing Image Jitter,” (AFRL-RX-TY-TR-2011-0096-02) develops an optimal...biological vision system of the common housefly , Musca domestica. Several variations of this sensor were designed, simulated extensively, and hardware

Isolated anomalous origin of the vertebral artery from the common carotid artery.

PubMed

Kesler, William W; Sabat, Shyamsunder B

2018-04-18

Anomalous origins of the vertebral arteries are uncommon and typically associated with other abnormalities of the great vessels. We present a case of an isolated origin of the right vertebral artery from the ipsilateral common carotid artery detected using magnetic resonance angiography. Such variants can significantly affect endovascular and surgical planning.

A rapid and cost effective method for soil carbon mineralization under static incubations

USDA-ARS?s Scientific Manuscript database

Soil incubations with subsequent measurement of carbon dioxide (CO2) evolved are common soil assays to estimate C mineralization rates and active organic C. Two common methods used to detect CO2 in laboratory incubations are gas chromatography (GC) and alkali absorption followed by titration (NaOH)...

Bioaccessibility of phenols in common beans (Phaseolus vulgaris L.) and iron (Fe) availability to Caco-2 cells

USDA-ARS?s Scientific Manuscript database

Samples of common and biofortified beans (Phaseolus vulgaris), both raw and cooked (autoclaved 120 deg C, 20 min) were analyzed for their polyphenol composition. Polyphenols were identified via HPLC-UV/diode array detection. Cooking favored the extraction of polyphenols without the need of a hydroly...

Wilt, crown, and root rot of common rose mallow (Hibiscus moscheutos) caused by a novel Fusarium sp

USDA-ARS?s Scientific Manuscript database

A new crown and root rot disease of landscape plantings of the malvaceous ornamental common rose mallow (Hibiscus moscheutos) was first detected in Washington State in 2012. The main objectives of this study were to complete Koch's postulates, document the disease sypmtoms photographically, and iden...

Predicting Boat-Generated Wave Heights: A Quantitative Analysis through Video Observations of Vessel Wakes

DTIC Science & Technology

2012-05-18

by the AWAC. It is a surface- penetrating device that measures continuous changes in the water elevations over time at much higher sampling rates of...background subtraction, a technique based on detecting change from a background scene. Their study highlights the difficulty in object detection and tracking...movements (Zhang et al. 2009) Alternatively, another common object detection method , known as Optical Flow Analysis , may be utilized for vessel

Previous conization on patient eligibility of sentinel lymph node detection for early invasive cervical cancer.

PubMed

Kato, Hidenori; Todo, Yukiharu; Minobe, Shin-Ichiro; Suzuki, Yoshihiro; Nakatani, Makiko; Ohba, Yoko; Yamashiro, Katsusige; Okamoto, Kazuhira

2011-11-01

Sentinel lymph node (SLN) detection has been accepted as a common strategy to preserve the quality of life of the patients with gynecologic cancers. However, the feasibility of SLN detection after conization is not yet clarified. Accuracy of SLN after conization was evaluated. Eighteen cases with prior conization (cone group) and 32 cases without conization (noncone group), all of which belonged to IB1 except 1 case in IA stage, underwent SLN detection. Systemic pelvic and para-aortic lymphadenectomy was coincidently performed for the estimation of negative and positive predictive values. Detection rate in which at least unilateral nodes were identified or bilaterally identified was 100% and 72.2% in the cone group, 90.6% and 71.9% in the noncone group, respectively. The average number of the detected SLN was 2.4 in the cone group and 2.1 in the noncone group. Negative and positive predictive value was 100% in both groups. On the distribution of sentinel node stations, most of the detected nodes were internal iliac and obturator node in both groups. Less frequent detection was observed in superficial common iliac node (5.4% in the cone group, 3.1% in the noncone group), external iliac node (2.7% and 9.5%), and parauterine artery node (5.4% and 1.6%).In both groups, no other lymph nodes were identified as SLN except 1 case in the cone group with the node in cardinal ligament. No significant difference was observed on detection rate, predictive value, and the distribution of sentinel node between the cone and noncone groups. Sentinel lymph node detection after conization can be performed with a certain reliability.

Sphincterotomy in patients with gallstones, elevated LFTs and a normal CBD on ERCP.

PubMed

Siddique, Iqbal; Mohan, Krishna; Khajah, Abdulkareem; Hasan, Fuad; Memon, Anjum; Kalaoui, Maher; al-Shamali, Mohammad; Patty, Istvan; al-Nakib, Basil

2003-01-01

To determine whether an endoscopic sphincterotomy affects outcome in patients with symptomatic gallstones, elevated liver function tests and a normal common bile duct on endoscopic retrograde cholangiopancreatogram. A total of 163 patients with symptomatic gallstones and elevated liver function tests, and found to have a normal common bile duct on endoscopic retrograde cholangiopancreatogram were included in the study. Endoscopic sphincterotomy was performed in 78 (47.8%) patients, while 85 (52.1%) patients did not have an endoscopic sphincterotomy. The two groups were compared for detection of small unseen common bile duct stones/debris, endoscopic retrograde cholangiopancreatogram related complications, and biliary complications after cholecystectomy. Small common bile duct stones/debris were recovered in 11/43 (25.5%) patients who had instrumentation of the common bile duct performed after endoscopic sphincterotomy. Common bile duct instrumentation was not performed in any of the patients without endoscopic sphincterotomy. No patient had any biliary complication after cholecystectomy, both in the immediate postoperative period and on a follow-up of 37.5 +/- 13.6 months (range 17-66). Endoscopic retrograde cholangiopancreatogram related complications occurred in 8 patients who had an endoscopic sphincterotomy and in 2 without endoscopic sphincterotomy (p < 0.05). Performing an endoscopic sphincterotomy in these patients increases the detection of small unseen common bile duct stones/debris without changing the clinical outcome after cholecystectomy. It also increases the endoscopic retrograde cholangiopancreatogram related complication rate, and therefore may not be necessary.

Detection of leaks in buried rural water pipelines using thermal infrared images

USGS Publications Warehouse

Eidenshink, Jeffery C.

1985-01-01

Leakage is a major problem in many pipelines. Minor leaks called 'seeper leaks', which generally range from 2 to 10 m3 per day, are common and are difficult to detect using conventional ground surveys. The objective of this research was to determine whether airborne thermal-infrared remote sensing could be used in detecting leaks and monitoring rural water pipelines. This study indicates that such leaks can be detected using low-altitude 8.7- to 11.5. micrometer wavelength, thermal infrared images collected under proper conditions.

Ventricular repolarization variability for hypoglycemia detection.

PubMed

Ling, Steve; Nguyen, H T

2011-01-01

Hypoglycemia is the most acute and common complication of Type 1 diabetes and is a limiting factor in a glycemic management of diabetes. In this paper, two main contributions are presented; firstly, ventricular repolarization variabilities are introduced for hypoglycemia detection, and secondly, a swarm-based support vector machine (SVM) algorithm with the inputs of the repolarization variabilities is developed to detect hypoglycemia. By using the algorithm and including several repolarization variabilities as inputs, the best hypoglycemia detection performance is found with sensitivity and specificity of 82.14% and 60.19%, respectively.

A signal detection theory analysis of an unconscious perception effect.

PubMed

Haase, S J; Theios, J; Jenison, R

1999-07-01

The independent observation model (Macmillan & Creelman, 1991) is fitted to detection-identification data collected under conditions of heavy masking. The model accurately predicts a quantitative relationship between stimulus detection and stimulus identification over a wide range of detection performance. This model can also be used to offer a signal detection interpretation of the common finding of above-chance identification following a missed signal. While our finding is not a new one, the stimuli used in this experiment (redundant three-letter strings) differ slightly from those used in traditional signal detection work. Also, the stimuli were presented very briefly and heavily masked, conditions typical in the study of unconscious perception effects.

Thyroidectomy: post-operative care and common complications.

PubMed

Furtado, L

Any surgical procedure involves risks. Thyroid surgery can cause potentially fatal complications during the early post-operative phase. It is essential that nurses have the knowledge and skills to detect early signs and symptoms of potential complications and take appropriate action. Early detection and rapid response are key to maintaining patient safety and minimising harm.

Rapid detection of E. coli on goat meat by electronic nose

USDA-ARS?s Scientific Manuscript database

Much attention has been paid on the foodborne illness of food, which is easily contaminated with bacterial or pathogens. Escherichia coli (E. coli) is one of these bacterial that commonly live in the contaminated animal meat. There is a growing need in the food industry for pathogen detection syst...

Detection of Catechol by Potentiometric-Flow Injection Analysis in the Presence of Interferents

ERIC Educational Resources Information Center

Lunsford, Suzanne K.; Widera, Justyna; Zhang, Hong

2007-01-01

This article describes an undergraduate analytical chemistry experiment developed to teach instrumental lab skills while incorporating common interferents encountered in the real-world analysis of catechol. The lab technique incorporates potentiometric-flow injection analysis on a dibenzo-18-crown-6 dual platinum electrode to detect catechol in…

75 FR 15357 - Airworthiness Directives; The Boeing Company Model 767 Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-29

... airplanes. This proposed AD would require repetitive inspections to detect fatigue cracking in the upper... this AD to detect and correct fatigue cracking in the upper wing skin at the fastener holes common to... October 28, 1999. Further Boeing analysis has determined the cracks to be a result of fatigue due to...

Detecting the fingerprints of complex land management practices in a tallgrass prairie site using phenocam and satellite images, and the eddy covariance technique

USDA-ARS?s Scientific Manuscript database

Burning, grazing, and baling (hay harvesting) are common management practices for tallgrass prairie. However, the impacts of these management practices on grassland phenology and carbon uptake are not well understood. Utilizing multiple observations to detect fingerprints of various management pract...

Histogram-based automatic thresholding for bruise detection of apples by structured-illumination reflectance imaging

USDA-ARS?s Scientific Manuscript database

Thresholding is an important step in the segmentation of image features, and the existing methods are not all effective when the image histogram exhibits a unimodal pattern, which is common in defect detection of fruit. This study was aimed at developing a general automatic thresholding methodology ...

Capacitively readout multi-element sensor array with common-mode cancellation

DOEpatents

Britton, Jr., Charles L.; Warmack, Robert J.; Bryan, William L.; Jones, Robert L.; Oden, Patrick Ian; Thundat, Thomas

2001-01-01

An improved multi-element apparatus for detecting the presence of at least one chemical, biological or physical component in a monitored area comprising an array or single set of the following elements: a capacitive transducer having at least one cantilever spring element secured thereto, the cantilever element having an area thereof coated with a chemical having an affinity for the component to be detected; a pick-up plate positioned adjacent to the cantilever element at a distance such that a capacitance between the cantilever element and the pick-up plate changes as the distance between the cantilever element and the pick-up plate varies, the change in capacitance being a measurable variation; a detection means for measuring the measurable variation in the capacitance between the cantilever element and the pick-up plate that forms a measurement channel signal; and at least one feedback cantilever spring element positioned apart from the coated cantilever element, the cantilever element substantially unaffected by the component being monitored and providing a reference channel signal to the detection means that achieves a common mode cancellation between the measurement channel signal and reference channel signal.

[VGKC-complex antibodies].

PubMed

Watanabe, Osamu

2013-04-01

Various antibodies are associated with voltage-gated potassium channels (VGKCs). Representative antibodies to VGKCs were first identified by radioimmunoassays using radioisotope-labeled alpha-dendrotoxin-VGKCs solubilized from rabbit brain. These antibodies were detected only in a proportion of patients with acquired neuromyotonia (Isaacs' syndrome). VGKC antibodies were also detected in patients with Morvan's syndrome and in those with a form of autoimmune limbic encephalitis. Recent studies indicated that the "VGKC" antibodies are mainly directed toward associated proteins (for example LGI-1 and CASPR-2) that complex with the VGKCs themselves. The "VGKC" antibodies are now commonly known as VGKC-complex antibodies. In general, LGI-1 antibodies are most commonly detected in patients with limbic encephalitis with syndrome of inappropriate secretion of antidiuretic hormone. CASPR-2 antibodies are present in the majority of patients with Morvan's syndrome. These patients develop combinations of CNS symptoms, autonomic dysfunction, and peripheral nerve hyperexcitability. Furthermore, VGKC-complex antibodies are tightly associated with chronic idiopathic pain. Hyperexcitability of nociceptive pathways has also been implicated. These antibodies may be detected in sera of some patients with neurodegenerative diseases (for example, amyotrophic lateral sclerosis and Creutzfeldt-Jakob disease).

Ground-based remote sensing of HDO/H2O ratio profiles: introduction and validation of an innovative retrieval approach

NASA Astrophysics Data System (ADS)

Schneider, M.; Hase, F.; Blumenstock, T.

2006-10-01

We propose an innovative approach for analysing ground-based FTIR spectra which allows us to detect variabilities of lower and middle/upper tropospheric HDO/H2O ratios. We show that the proposed method is superior to common approaches. We estimate that lower tropospheric HDO/H2O ratios can be detected with a noise to signal ratio of 15% and middle/upper tropospheric ratios with a noise to signal ratio of 50%. The method requires the inversion to be performed on a logarithmic scale and to introduce an inter-species constraint. While common methods calculate the isotope ratio posterior to an independent, optimal estimation of the HDO and H2O profile, the proposed approach is an optimal estimator for the ratio itself. We apply the innovative approach to spectra measured continuously during 15 months and present, for the first time, an annual cycle of tropospheric HDO/H2O ratio profiles as detected by ground-based measurements. Outliers in the detected middle/upper tropospheric ratios are interpreted by backward trajectories.

Ground-based remote sensing of HDO/H2O ratio profiles: introduction and validation of an innovative retrieval approach

NASA Astrophysics Data System (ADS)

Schneider, M.; Hase, F.; Blumenstock, T.

2006-06-01

We propose an innovative approach for analysing ground-based FTIR spectra which allows us to detect variabilities of lower and middle/upper tropospheric HDO/H2O ratios. We show that the proposed method is superior to common approaches. We estimate that lower tropospheric HDO/H2O ratios can be detected with a noise to signal ratio of 15% and middle/upper tropospheric ratios with a noise to signal ratio of 50%. The method requires the inversion to be performed on a logarithmic scale and to introduce an inter-species constraint. While common methods calculate the isotope ratio posterior to an independent, optimal estimation of the HDO and H2O profile, the proposed approach is an optimal estimator for the ratio itself. We apply the innovative approach to spectra measured continuously during 15 months and present, for the first time, an annual cycle of tropospheric HDO/H2O ratio profiles as detected by ground-based measurements. Outliers in the detected middle/upper tropospheric ratios are interpreted by backward trajectories.

Ion-exclusion/cation-exchange chromatography with dual detection of the conductivity and spectrophotometry for the simultaneous determination of common inorganic anionic species and cations in river and wastewater.

PubMed

Nakatani, Nobutake; Kozaki, Daisuke; Mori, Masanobu; Hasebe, Kiyoshi; Nakagoshi, Nobukazu; Tanaka, Kazuhiko

2011-01-01

Simultaneous determinations of common inorganic anionic species (SO(4)(2-), Cl(-), NO(3)(-), phosphate and silicate) and cations (Na(+), NH(4)(+), K(+), Mg(2+) and Ca(2+)) were conducted using an ion-chromatography system with dual detection of conductivity and spectrophotometry in tandem. The separation of ionic species on a weakly acidic cation-exchange resin was accomplished using a mixture of 100 mM ascorbic acid and 4 mM 18-crown-6 as an acidic eluent (pH 2.6), after which the ions were detected using a conductivity detector. Subsequently, phosphate and silicate were analyzed based on derivatization with molybdate and spectrophotometry at 700 nm. The detection limits at S/N = 3 ranged from 0.11 to 2.9 µM for analyte ionic species. This method was applied to practical river water and wastewater with acceptable criteria for the anion-cation balance and comparisons of the measured and calculated electrical conductivity, demonstrating the usefulness of the present method for water quality monitoring.

Development and validation of duplex, triplex, and pentaplex real-time PCR screening assays for the detection of genetically modified organisms in food and feed.

PubMed

Huber, Ingrid; Block, Annette; Sebah, Daniela; Debode, Frédéric; Morisset, Dany; Grohmann, Lutz; Berben, Gilbert; Stebih, Dejan; Milavec, Mojca; Zel, Jana; Busch, Ulrich

2013-10-30

Worldwide, qualitative methods based on PCR are most commonly used as screening tools for genetically modified material in food and feed. However, the increasing number and diversity of genetically modified organisms (GMO) require effective methods for simultaneously detecting several genetic elements marking the presence of transgenic events. Herein we describe the development and validation of a pentaplex, as well as complementary triplex and duplex real-time PCR assays, for the detection of the most common screening elements found in commercialized GMOs: P-35S, T-nos, ctp2-cp4-epsps, bar, and pat. The use of these screening assays allows the coverage of many GMO events globally approved for commercialization. Each multiplex real-time PCR assay shows high specificity and sensitivity with an absolute limit of detection below 20 copies for the targeted sequences. We demonstrate by intra- and interlaboratory tests that the assays are robust as well as cost- and time-effective for GMO screening if applied in routine GMO analysis.

Evaluation of antimicrobial susceptibilities and virulence factors of Staphylococcus aureus strains isolated from community-acquired and health-care associated pediatric infections.

PubMed

Karbuz, Adem; Karahan, Zeynep Ceren; Aldemir-Kocabaş, Bilge; Tekeli, Alper; Özdemir, Halil; Güriz, Haluk; Gökdemir, Refik; İnce, Erdal; Çiftçi, Ergin

2017-01-01

Karbuz A, Karahan ZC, Aldemir-Kocabaş B, Tekeli A, Özdemir H, Güriz H, Gökdemir R, İnce E, Çiftçi E. Evaluation of antimicrobial susceptibilities and virulence factors of Staphylococcus aureus strains isolated from community-acquired and health-care associated pediatric infections. Turk J Pediatr 2017; 59: 395-403. The aim of this study was to investigate the enterotoxins and Panton-Valentine leukocidin (PVL) gene as virulence factor, identification if antimicrobial sensitivity patterns, agr (accessory gene regulator) types and sequence types and in resistant cases to obtain SCCmec (staphylococcal cassette chromosome mec) gene types which will be helpful to decide empirical therapy and future health politics for S. aureus species. Total of 150 isolates of S. aureus were isolated from the cultures of the child patients in January 2011 and December 2012. In this study, the penicillin resistance was observed as 93.8%. PVL and mecA was detected positive in 8.7% and in 6% of all S. aureus strains, respectively. Two MRSA (methicillin resistant S.aureus) strains were detected as SCCmec type III and SCCmec type V and five MRSA strains were detected as SCCmec type IV. SET-I and SET-G were the most common detected enterotoxins. In both community-associated and healthcare-associated MRSA strains, agr type 1 was detected most commonly. The most common sequence types were ST737 in 13 patients than ST22 in eight patients and ST121 in six patients. This study highlights a necessity to review the cause of small changes in the structural genes in order to determine whether it is a cause or outcome; community-acquired and healthcare associated strains overlap.

Population-Based Genetic Study of β-Thalassemia Mutations in Mardan Division, Khyber Pakhtunkhwa Province, Pakistan.

PubMed

Muhammad, Raj; Shakeel, Muhammad; Rehman, Shoaib U; Lodhi, Muhammad A

2017-03-01

β-Thalassemia (β-thal) is the most prevalent hereditary blood disorder in Pakistan with a carrier rate of 5.0-8.0%. The homozygous affected children require frequent blood transfusions for their survival. This autosomal recessive disease can only be prevented through awareness programs, carrier screening, mutation detection, genetic counseling and prenatal diagnosis (PND). The present study aimed to determine the prevalence of various mutations causing β-thal and also to detect carriers of these mutations in families living in the Mardan Division, Khyber Pakhtunkhwa (KP) Province, Pakistan. The study was conducted at the Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan. Blood samples of β-thalassemic families were collected from various transfusion centers in Mardan Division. Using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique, all samples were analyzed for the six most common mutations causing β-thal in this area. Six different mutant primers for the detection of different mutations were used. The most common mutations detected in thalassemic patients were frameshift codons (FSC) 8/9 (+G) (HBB: c.27_28insG), codons 41/42 (-TTCT) (HBB: c.126_129delCTTT), and IVS-I-5 (G>C) (HBB: c.92+5G>C). The predominant mutation for carrying the mutant genes for β-thal were FSC 8/9, IVS-I-5, codons 41/42, IVS-I-1. It was also found that 66.7% of marriages were consanguineous. The FSC 8/9 mutation was found to be the most common β-thal mutation with a frequency of 44.4%. This research project provides a strong incentive for the establishment of large scale mutation detection and PND services in the Mardan Division.

Efficient, Validated Method for Detection of Mycobacterial Growth in Liquid Culture Media by Use of Bead Beating, Magnetic-Particle-Based Nucleic Acid Isolation, and Quantitative PCR

PubMed Central

Waldron, Anna M.; Begg, Douglas J.; de Silva, Kumudika; Purdie, Auriol C.; Whittington, Richard J.

2015-01-01

Pathogenic mycobacteria are difficult to culture, requiring specialized media and a long incubation time, and have complex and exceedingly robust cell walls. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease, a chronic wasting disease of ruminants, is a typical example. Culture of MAP from the feces and intestinal tissues is a commonly used test for confirmation of infection. Liquid medium offers greater sensitivity than solid medium for detection of MAP; however, support for the BD Bactec 460 system commonly used for this purpose has been discontinued. We previously developed a new liquid culture medium, M7H9C, to replace it, with confirmation of growth reliant on PCR. Here, we report an efficient DNA isolation and quantitative PCR methodology for the specific detection and confirmation of MAP growth in liquid culture media containing egg yolk. The analytical sensitivity was at least 104-fold higher than a commonly used method involving ethanol precipitation of DNA and conventional PCR; this may be partly due to the addition of a bead-beating step to manually disrupt the cell wall of the mycobacteria. The limit of detection, determined using pure cultures of two different MAP strains, was 100 to 1,000 MAP organisms/ml. The diagnostic accuracy was confirmed using a panel of cattle fecal (n = 54) and sheep fecal and tissue (n = 90) culture samples. This technique is directly relevant for diagnostic laboratories that perform MAP cultures but may also be applicable to the detection of other species, including M. avium and M. tuberculosis. PMID:25609725

Widespread detection of a brominated flame retardant, hexabromocyclododecane, in expanded polystyrene marine debris and microplastics from South Korea and the Asia-Pacific coastal region.

PubMed

Jang, Mi; Shim, Won Joon; Han, Gi Myung; Rani, Manviri; Song, Young Kyoung; Hong, Sang Hee

2017-12-01

The role of marine plastic debris and microplastics as a carrier of hazardous chemicals in the marine environment is an emerging issue. This study investigated expanded polystyrene (EPS, commonly known as styrofoam) debris, which is a common marine debris item worldwide, and its additive chemical, hexabromocyclododecane (HBCD). To obtain a better understanding of chemical dispersion via EPS pollution in the marine environment, intensive monitoring of HBCD levels in EPS debris and microplastics was conducted in South Korea, where EPS is the predominant marine debris originate mainly from fishing and aquaculture buoys. At the same time, EPS debris were collected from 12 other countries in the Asia-Pacific region, and HBCD concentrations were measured. HBCD was detected extensively in EPS buoy debris and EPS microplastics stranded along the Korean coasts, which might be related to the detection of a quantity of HBCD in non-flame-retardant EPS bead (raw material). The wide detection of the flame retardant in sea-floating buoys, and the recycling of high-HBCD-containing EPS waste inside large buoys highlight the need for proper guidelines for the production and use of EPS raw materials, and the recycling of EPS waste. HBCD was also abundantly detected in EPS debris collected from the Asia-Pacific coastal region, indicating that HBCD contamination via EPS debris is a common environmental issue worldwide. Suspected tsunami debris from Alaskan beaches indicated that EPS debris has the potential for long-range transport in the ocean, accompanying the movement of hazardous chemicals. The results of this study indicate that EPS debris can be a source of HBCD in marine environments and marine food web. Copyright © 2017 Elsevier Ltd. All rights reserved.

Economically motivated adulteration (EMA) of food: common characteristics of EMA incidents.

PubMed

Everstine, Karen; Spink, John; Kennedy, Shaun

2013-04-01

Economically motivated adulteration (EMA) of food, also known as food fraud, is the intentional adulteration of food for financial advantage. A common form of EMA, undeclared substitution with alternative ingredients, is usually a health concern because of allergen labeling requirements. As demonstrated by the nearly 300,000 illnesses in China from melamine adulteration of infant formula, EMA also has the potential to result in serious public health consequences. Furthermore, EMA incidents reveal gaps in quality assurance testing methodologies that could be exploited for intentional harm. In contrast to foodborne disease outbreaks, EMA incidents present a particular challenge to the food industry and regulators because they are deliberate acts that are intended to evade detection. Large-scale EMA incidents have been described in the scientific literature, but smaller incidents have been documented only in media sources. We reviewed journal articles and media reports of EMA since 1980. We identified 137 unique incidents in 11 food categories: fish and seafood (24 incidents), dairy products (15), fruit juices (12), oils and fats (12), grain products (11), honey and other natural sweeteners (10), spices and extracts (8), wine and other alcoholic beverages (7), infant formula (5), plant-based proteins (5), and other food products (28). We identified common characteristics among the incidents that may help us better evaluate and reduce the risk of EMA. These characteristics reflect the ways in which existing regulatory systems or testing methodologies were inadequate for detecting EMA and how novel detection methods and other deterrence strategies can be deployed. Prevention and detection of EMA cannot depend on traditional food safety strategies. Comprehensive food protection, as outlined by the Food Safety Modernization Act, will require innovative methods for detecting EMA and for targeting crucial resources toward the riskiest food products.

Efficient, validated method for detection of mycobacterial growth in liquid culture media by use of bead beating, magnetic-particle-based nucleic acid isolation, and quantitative PCR.

PubMed

Plain, Karren M; Waldron, Anna M; Begg, Douglas J; de Silva, Kumudika; Purdie, Auriol C; Whittington, Richard J

2015-04-01

Pathogenic mycobacteria are difficult to culture, requiring specialized media and a long incubation time, and have complex and exceedingly robust cell walls. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease, a chronic wasting disease of ruminants, is a typical example. Culture of MAP from the feces and intestinal tissues is a commonly used test for confirmation of infection. Liquid medium offers greater sensitivity than solid medium for detection of MAP; however, support for the BD Bactec 460 system commonly used for this purpose has been discontinued. We previously developed a new liquid culture medium, M7H9C, to replace it, with confirmation of growth reliant on PCR. Here, we report an efficient DNA isolation and quantitative PCR methodology for the specific detection and confirmation of MAP growth in liquid culture media containing egg yolk. The analytical sensitivity was at least 10(4)-fold higher than a commonly used method involving ethanol precipitation of DNA and conventional PCR; this may be partly due to the addition of a bead-beating step to manually disrupt the cell wall of the mycobacteria. The limit of detection, determined using pure cultures of two different MAP strains, was 100 to 1,000 MAP organisms/ml. The diagnostic accuracy was confirmed using a panel of cattle fecal (n=54) and sheep fecal and tissue (n=90) culture samples. This technique is directly relevant for diagnostic laboratories that perform MAP cultures but may also be applicable to the detection of other species, including M. avium and M. tuberculosis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Genome-wide detection of conservative site-specific recombination in bacteria

PubMed Central

Mathias Garrett, Elizabeth; Camilli, Andrew

2018-01-01

The ability of clonal bacterial populations to generate genomic and phenotypic heterogeneity is thought to be of great importance for many commensal and pathogenic bacteria. One common mechanism contributing to diversity formation relies on the inversion of small genomic DNA segments in a process commonly referred to as conservative site-specific recombination. This phenomenon is known to occur in several bacterial lineages, however it remains notoriously difficult to identify due to the lack of conserved features. Here, we report an easy-to-implement method based on high-throughput paired-end sequencing for genome-wide detection of conservative site-specific recombination on a single-nucleotide level. We demonstrate the effectiveness of the method by successfully detecting several novel inversion sites in an epidemic isolate of the enteric pathogen Clostridium difficile. Using an experimental approach, we validate the inversion potential of all detected sites in C. difficile and quantify their prevalence during exponential and stationary growth in vitro. In addition, we demonstrate that the master recombinase RecV is responsible for the inversion of some but not all invertible sites. Using a fluorescent gene-reporter system, we show that at least one gene from a two-component system located next to an invertible site is expressed in an on-off mode reminiscent of phase variation. We further demonstrate the applicability of our method by mining 209 publicly available sequencing datasets and show that conservative site-specific recombination is common in the bacterial realm but appears to be absent in some lineages. Finally, we show that the gene content associated with the inversion sites is diverse and goes beyond traditionally described surface components. Overall, our method provides a robust platform for detection of conservative site-specific recombination in bacteria and opens a new avenue for global exploration of this important phenomenon. PMID:29621238

An automated cross-correlation based event detection technique and its application to surface passive data set

USGS Publications Warehouse

Forghani-Arani, Farnoush; Behura, Jyoti; Haines, Seth S.; Batzle, Mike

2013-01-01

In studies on heavy oil, shale reservoirs, tight gas and enhanced geothermal systems, the use of surface passive seismic data to monitor induced microseismicity due to the fluid flow in the subsurface is becoming more common. However, in most studies passive seismic records contain days and months of data and manually analysing the data can be expensive and inaccurate. Moreover, in the presence of noise, detecting the arrival of weak microseismic events becomes challenging. Hence, the use of an automated, accurate and computationally fast technique for event detection in passive seismic data is essential. The conventional automatic event identification algorithm computes a running-window energy ratio of the short-term average to the long-term average of the passive seismic data for each trace. We show that for the common case of a low signal-to-noise ratio in surface passive records, the conventional method is not sufficiently effective at event identification. Here, we extend the conventional algorithm by introducing a technique that is based on the cross-correlation of the energy ratios computed by the conventional method. With our technique we can measure the similarities amongst the computed energy ratios at different traces. Our approach is successful at improving the detectability of events with a low signal-to-noise ratio that are not detectable with the conventional algorithm. Also, our algorithm has the advantage to identify if an event is common to all stations (a regional event) or to a limited number of stations (a local event). We provide examples of applying our technique to synthetic data and a field surface passive data set recorded at a geothermal site.

[Rabies in the common hamster (Cricetus cricetus) in Slovakia].

PubMed

Svrcek, S; Ondrejka, R; Mlynarcíková, K; Svec, J

1984-11-01

The trials were conducted within the full-scale research on the ecology of lyssa virus. In a period of the mass outbreak of common hamster population in the East Slovakian region, 283 hamsters were examined for rabies. Using the direct immunofluorescence method (DIFM), the rabies antigen was detected in the brain of five hamsters. Three virus strains (denoted as 3 O, 7 E, 9 E) were isolated by means of the inoculation test on sucking mice. On the basis of the detection of the nucleo-protein antigen by DIFM, or its inhibition, detection of the Babes-Negri bodies, determination of the neutralization index, titration on mice and determination of incubation time, the isolated strains were identified as the street strains of rabies virus. As determined by further detailed studies on biological characteristics (determination of the invasiveness index on animals with different susceptibility to rabies virus, determination of pathogenicity for different species of laboratory animals, different weight categories, with different methods of administration, invasiveness index), the "hamster" strains are included among those of intermediate virulence or reduced virulence. At intramuscular administration, the most virulent of the three "hamster" strains studied (3 O) induces a fatal course of rabies in common fox and cat; for wolves, dogs and rabbits it is apathogenic. This strain is also contained in the salivary glands of foxes and cats. In immunofluorescent detection of the rabies nucleoprotein antigen, the "hamster" strains formed a mixed picture of fluorescing particles, characteristic of street strains.

Thyroid disorders and the prevalence of antithyroid antibodies in Shiraz population.

PubMed

Karimi, Fariba; Kalantarhormozi, Mohammad Reza; Dabbaghmanesh, Mohammad Hossein; Ranjbar Omrani, Gholamhossein

2014-05-01

Thyroid dysfunction is a common health problem affecting millions of patients worldwide. Autoimmune thyroid disorders are among the most common autoimmune disorders. In this population-based study, we assessed the prevalence of abnormal thyroid function, antithyroid antibodies and the probable relationship between them in Shiraz, southern Iran. Serum thyrotropin (TSH) was determined in 981 subjects (66.8% female and 33.2% male; mean age: 39.1 ± 14.3 years), who were selected with stratified random sampling. Because of the preponderance of females over males, we performed the statistical analyses using sex-weighted data (50% for each sex). Also, antithyroid peroxidase antibodies (TPOAb), and antithyroglobulin antibodies (TgAb) were measured in two random subgroups of 376 and 537 patients respectively). Thyromegaly detected on physical examination. In this cross-sectional study, 8.1% of participants had elevated serum TSH level and 3.4% had low serum TSH level. A statistically significant relationship was found between gender and thyromegaly and TSH values. Positive TPOAb and positive TgAb were detected in 17% and 5.1% of participants respectively. In addition, a significant relationship was observed between elevated TSH levels and positive results for both antibodies. Detectable levels of thyroid antibodies correlated with female sex, while no correlation was observed between detectable levels of thyroid antibodies and thyromegaly. Thyroid disorders, especially elevated TSH level, are common. It seems that autoimmune mechanisms are strongly involved in the etiology of hypothyroidism in this area.

Gallium metal affinity capture tandem mass spectrometry for the selective detection of phosphopeptides in complex mixtures

PubMed Central

Blacken, Grady R.; Sadílek, Martin; Tureček, František

2008-01-01

Metal affinity capture tandem mass spectrometry (MAC-MSMS) is evaluated in a comparative study of a lysine-derived nitrilotriacetic acid (Nα, Nα-bis-(carboxymethyl)lysine, LysNTA) and an aspartic-acid-related iminodiacetic acid (N-(4-aminobutyl)aspartic acid, AspIDA) as selective phosphopeptide detection reagents. Both LysNTA and AspIDA spontaneously form ternary complexes with GaIII and phosphorylated amino acids and phosphopeptides upon mixing in solution. Collision-induced dissociation of positive complex ions produced by electrospray produces common fragments (LysNTA + H)+ or (AspIDA + H)+ at m/z 263 and 205, respectively. MSMS precursor scans using these fragments as reporter ions allow one to selectively detect multiple charge states of phosphopeptides in mixtures. It follows from this comparative study that LysNTA is superior to AspIDA in detecting phosphopeptides, possibly because of the higher coordination number and greater stability constant for GaIII – phosphopeptide complexation of the former reagent. In a continuing development of MAC-MSMS for proteomics applications, we demonstrate its utility in a post-column reaction format. Using a simple post-column-reaction ‘T’ and syringe pump to deliver our chelating reagents, α-casein tryptic phosphopeptides can be selectively analyzed from a solution containing a twofold molar excess of bovine serum albumin. The MAC-MSMS method is shown to be superior to the commonly used neutral loss scan for the common loss of phosphoric acid. PMID:18265438

Use of whole body CT to detect patterns of CPR-related injuries after sudden cardiac arrest.

PubMed

Dunham, Gregor M; Perez-Girbes, Alexandre; Bolster, Ferdia; Sheehan, Kellie; Linnau, Ken F

2017-11-09

We have recently implemented a dedicated sudden cardiac arrest (SCA) - whole-body computed tomography (WBCT) protocol to evaluate SCA patients with return of spontaneous circulation (ROSC) following cardiopulmonary resuscitation (CPR). The aim of this study is to evaluate the number and pattern of CPR-related injuries in ROSC patients with SCA-WBCT. Single-centre retrospective review of 39 patients (13 female; 20 male, mean age 51.8 years) with non-traumatic, out-of-hospital SCA and ROSC and evaluation with dedicated SCA-WBCT over a 10-month period. In-hospital mortality was 54%. CPR-related injuries were detected in 85% (33/39). Chest injuries were most common on WBCT: 85% (33) subjects had rib fractures (mean of 8.5 fractures/subject); 31% (12) sternal fractures; 13% (5) mediastinal haematoma; 10% (4) pneumothorax; 8% (3) pneumomediastinum and 3% (1) haemothorax. Three subjects (8%) had abdominal injuries on WBCT, including one hepatic haematoma with active haemorrhage. CPR-related injuries on WBCT after ROSC are common, with serial rib fractures detected most commonly. An unexpectedly high rate of abdominal injuries was detected on SCA-WBCT. Radiologists need to be attuned to the spectrum of CPR-related injuries in WBCT, including abdominal injuries and subtle rib fractures. • CPR frequently causes injuries. • Radiologists should be aware of the spectrum of CPR related injuries. • Rib fractures are frequent and radiologic findings often subtle. • Clinically unexpected abdominal injuries may be present.

Multiplex Ultrasensitive Genotyping of Patients with Non-Small Cell Lung Cancer for Epidermal Growth Factor Receptor (EGFR) Mutations by Means of Picodroplet Digital PCR.

PubMed

Watanabe, Masaru; Kawaguchi, Tomoya; Isa, Shun-Ichi; Ando, Masahiko; Tamiya, Akihiro; Kubo, Akihito; Saka, Hideo; Takeo, Sadanori; Adachi, Hirofumi; Tagawa, Tsutomu; Kawashima, Osamu; Yamashita, Motohiro; Kataoka, Kazuhiko; Ichinose, Yukito; Takeuchi, Yukiyasu; Watanabe, Katsuya; Matsumura, Akihide; Koh, Yasuhiro

2017-07-01

Epidermal growth factor receptor (EGFR) mutations have been used as the strongest predictor of effectiveness of treatment with EGFR tyrosine kinase inhibitors (TKIs). Three most common EGFR mutations (L858R, exon 19 deletion, and T790M) are known to be major selection markers for EGFR-TKIs therapy. Here, we developed a multiplex picodroplet digital PCR (ddPCR) assay to detect 3 common EGFR mutations in 1 reaction. Serial-dilution experiments with genomic DNA harboring EGFR mutations revealed linear performance, with analytical sensitivity ~0.01% for each mutation. All 33 EGFR-activating mutations detected in formalin-fixed paraffin-embedded (FFPE) tissue samples by the conventional method were also detected by this multiplex assay. Owing to the higher sensitivity, an additional mutation (T790M; including an ultra-low-level mutation, <0.1%) was detected in the same reaction. Regression analysis of the duplex assay and multiplex assay showed a correlation coefficient (R 2 ) of 0.9986 for L858R, 0.9844 for an exon 19 deletion, and 0.9959 for T790M. Using ddPCR, we designed a multiplex ultrasensitive genotyping platform for 3 common EGFR mutations. Results of this proof-of-principle study on clinical samples indicate clinical utility of multiplex ddPCR for screening for multiple EGFR mutations concurrently with an ultra-rare pretreatment mutation (T790M). Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Identification of methyl triclosan and halogenated analogues in male common carp (Cyprinus carpio) from Las Vegas Bay and semipermeable membrane devices from Las Vegas Wash, Nevada

USGS Publications Warehouse

Leiker, T.J.; Abney, S.R.; Goodbred, S.L.; Rosen, Michael R.

2009-01-01

Methyl triclosan and four halogenated analogues have been identified in extracts of individual whole-body male carp (Cyprinus carpio) tissue that were collected from Las Vegas Bay, Nevada, and Semipermeable Membrane Devices (SPMD) that were deployed in Las Vegas Wash, Nevada. Methyl triclosan is believed to be the microbially methylated product of the antibacterial agent triclosan (2, 4, 4'-trichloro-4-hydroxydiphenyl ether, Chemical Abstract Service Registry Number 3380-34-5, Irgasan DP300). The presence of methyl triclosan and four halogenated analogues was confirmed in SPMD extracts by comparing low- and high-resolution mass spectral data and Kovats retention indices of methyl triclosan with commercially obtained triclosan that was derivatized to the methyl ether with ethereal diazomethane. The four halogenated analogues of methyl triclosan detected in both whole-body tissue and SPMD extracts were tentatively identified by high resolution mass spectrometry. Methyl triclosan was detected in all 29 male common carp from Las Vegas Bay with a mean concentration of 596????g kg- 1 wet weight (ww) which is more than an order of magnitude higher than previously reported concentrations in the literature. The halogenated analogs were detected less frequently (21%-76%) and at much lower concentrations (< 51????g kg- 1 ww). None of these compounds were detected in common carp from a Lake Mead reference site in Overton Arm, Nevada.

Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses

USGS Publications Warehouse

Ramey, Andy M.; Reeves, Andrew; Teslaa, Joshua L.; Nashold, Sean W.; Donnelly, Tyrone F.; Bahl, Justin; Hall, Jeffrey S.

2016-01-01

Highly pathogenic clade 2.3.4.4 H5N8, H5N2, and H5N1 influenza A viruses were first detected in wild, captive, and domestic birds in North America in November–December 2014. In this study, we used wild waterbird samples collected in Alaska prior to the initial detection of clade 2.3.4.4 H5 influenza A viruses in North America to assess the evidence for: (1) dispersal of highly pathogenic influenza A viruses from East Asia to North America by migratory birds via Alaska and (2) ancestral origins of clade 2.3.4.4 H5 reassortant viruses in Beringia. Although we did not detect highly pathogenic influenza A viruses in our sample collection from western Alaska, we did identify viruses that contained gene segments sharing recent common ancestry with intercontinental reassortant H5N2 and H5N1 viruses. Results of phylogenetic analyses and estimates for times of most recent common ancestry support migratory birds sampled in Beringia as maintaining viral diversity closely related to novel highly pathogenic influenza A virus genotypes detected in North America. Although our results do not elucidate the route by which highly pathogenic influenza A viruses were introduced into North America, genetic evidence is consistent with the hypothesized trans-Beringian route of introduction via migratory birds.

Skin Rounds: A Quality Improvement Approach to Enhance Skin Care in the Neonatal Intensive Care Unit.

PubMed

Nist, Marliese Dion; Rodgers, Elizabeth A; Ruth, Brenda M; Bertoni, C Briana; Bartman, Thomas; Keller, Leah A; Dail, James W; Gardikes-Gingery, Renee; Shepherd, Edward G

2016-10-01

Skin injuries are common among neonatal intensive care unit (NICU) patients and may lead to significant complications. Standardized methods of preventing, detecting, and treating skin injuries are needed. The aim of this project was to standardize the assessment, documentation, and tracking of skin injuries among hospitalized neonatal patients and to determine the incidence of pressure ulcers in this patient population. (1) Creation of an interdisciplinary skin team to identify skin injuries through weekly skin rounds. (2) Assessment of all patients at least twice daily for the presence of skin injuries. Interventions were implemented upon identification of a skin injury. Pressure ulcers of Stage II or more were further assessed by wound/ostomy nurses. A total of 2299 NICU patients were hospitalized and assessed between July 2011 and December 2015. After the initiation of skin rounds, the baseline incidence of pressure ulcers increased from 0.49 per 1000 patient days to 4.6 per 1000 patient days, reflecting an improvement in detection and reporting. The most common skin injuries detected included erythema, skin tears, and ecchymosis; the most common cause of injuries was medical devices. A dedicated skin team can improve the detection and reporting of skin injuries among NICU patients. Determination of the incidence of pressure ulcers in this population is critical to develop targeted interventions. Further research is needed to determine the most effective interventions to prevent and treat skin injuries among hospitalized neonates.

Detection of chitinase activity by 2-aminobenzoic acid labeling of chito-oligosaccharides.

PubMed

Ghauharali-van der Vlugt, Karen; Bussink, Anton P; Groener, Johanna E M; Boot, Rolf G; Aerts, Johannes M F G

2009-01-01

Chitinases are hydrolases capable of hydrolyzing the abundant natural polysaccharide chitin. Next to artificial fluorescent substrates, more physiological chito-oligomers are commonly used in chitinase assays. Analysis of chito-oligosaccharides products is generally accomplished by UV detection. However, the relatively poor sensitivity poses a serious limitation. Here we report on a novel, much more sensitive assay for the detection of chito-oligosaccharide reaction products released by chitinases, based on fluorescent detection, following chemical labeling by 2-aminobenzoic acid. Comparison with existing UV-based assays, shows that the novel assay offers the same advantages yet allows detection of chito-oligosaccharides in the low picomolar range.

The ground truth about metadata and community detection in networks.

PubMed

Peel, Leto; Larremore, Daniel B; Clauset, Aaron

2017-05-01

Across many scientific domains, there is a common need to automatically extract a simplified view or coarse-graining of how a complex system's components interact. This general task is called community detection in networks and is analogous to searching for clusters in independent vector data. It is common to evaluate the performance of community detection algorithms by their ability to find so-called ground truth communities. This works well in synthetic networks with planted communities because these networks' links are formed explicitly based on those known communities. However, there are no planted communities in real-world networks. Instead, it is standard practice to treat some observed discrete-valued node attributes, or metadata, as ground truth. We show that metadata are not the same as ground truth and that treating them as such induces severe theoretical and practical problems. We prove that no algorithm can uniquely solve community detection, and we prove a general No Free Lunch theorem for community detection, which implies that there can be no algorithm that is optimal for all possible community detection tasks. However, community detection remains a powerful tool and node metadata still have value, so a careful exploration of their relationship with network structure can yield insights of genuine worth. We illustrate this point by introducing two statistical techniques that can quantify the relationship between metadata and community structure for a broad class of models. We demonstrate these techniques using both synthetic and real-world networks, and for multiple types of metadata and community structures.

A hybrid double-observer sightability model for aerial surveys

USGS Publications Warehouse

Griffin, Paul C.; Lubow, Bruce C.; Jenkins, Kurt J.; Vales, David J.; Moeller, Barbara J.; Reid, Mason; Happe, Patricia J.; Mccorquodale, Scott M.; Tirhi, Michelle J.; Schaberi, Jim P.; Beirne, Katherine

2013-01-01

Raw counts from aerial surveys make no correction for undetected animals and provide no estimate of precision with which to judge the utility of the counts. Sightability modeling and double-observer (DO) modeling are 2 commonly used approaches to account for detection bias and to estimate precision in aerial surveys. We developed a hybrid DO sightability model (model MH) that uses the strength of each approach to overcome the weakness in the other, for aerial surveys of elk (Cervus elaphus). The hybrid approach uses detection patterns of 2 independent observer pairs in a helicopter and telemetry-based detections of collared elk groups. Candidate MH models reflected hypotheses about effects of recorded covariates and unmodeled heterogeneity on the separate front-seat observer pair and back-seat observer pair detection probabilities. Group size and concealing vegetation cover strongly influenced detection probabilities. The pilot's previous experience participating in aerial surveys influenced detection by the front pair of observers if the elk group was on the pilot's side of the helicopter flight path. In 9 surveys in Mount Rainier National Park, the raw number of elk counted was approximately 80–93% of the abundance estimated by model MH. Uncorrected ratios of bulls per 100 cows generally were low compared to estimates adjusted for detection bias, but ratios of calves per 100 cows were comparable whether based on raw survey counts or adjusted estimates. The hybrid method was an improvement over commonly used alternatives, with improved precision compared to sightability modeling and reduced bias compared to DO modeling.

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

Ford, Eric C., E-mail: eford@uw.edu; Terezakis, Stephanie; Souranis, Annette

Purpose: To quantify the error-detection effectiveness of commonly used quality control (QC) measures. Methods: We analyzed incidents from 2007-2010 logged into a voluntary in-house, electronic incident learning systems at 2 academic radiation oncology clinics. None of the incidents resulted in patient harm. Each incident was graded for potential severity using the French Nuclear Safety Authority scoring scale; high potential severity incidents (score >3) were considered, along with a subset of 30 randomly chosen low severity incidents. Each report was evaluated to identify which of 15 common QC checks could have detected it. The effectiveness was calculated, defined as the percentagemore » of incidents that each QC measure could detect, both for individual QC checks and for combinations of checks. Results: In total, 4407 incidents were reported, 292 of which had high-potential severity. High- and low-severity incidents were detectable by 4.0 {+-} 2.3 (mean {+-} SD) and 2.6 {+-} 1.4 QC checks, respectively (P<.001). All individual checks were less than 50% sensitive with the exception of pretreatment plan review by a physicist (63%). An effectiveness of 97% was achieved with 7 checks used in combination and was not further improved with more checks. The combination of checks with the highest effectiveness includes physics plan review, physician plan review, Electronic Portal Imaging Device-based in vivo portal dosimetry, radiation therapist timeout, weekly physics chart check, the use of checklists, port films, and source-to-skin distance checks. Some commonly used QC checks such as pretreatment intensity modulated radiation therapy QA do not substantially add to the ability to detect errors in these data. Conclusions: The effectiveness of QC measures in radiation oncology depends sensitively on which checks are used and in which combinations. A small percentage of errors cannot be detected by any of the standard formal QC checks currently in broad use, suggesting that further improvements are needed. These data require confirmation with a broader incident-reporting database.« less

Influenza and other respiratory virus infections in outpatients with medically attended acute respiratory infection during the 2011-12 influenza season.

PubMed

Zimmerman, Richard K; Rinaldo, Charles R; Nowalk, Mary Patricia; Gk, Balasubramani; Thompson, Mark G; Moehling, Krissy K; Bullotta, Arlene; Wisniewski, Stephen

2014-07-01

Respiratory tract infections are a major cause of outpatient visits, yet only a portion is tested to determine the etiologic organism. Multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) assays for detection of multiple viruses are being used increasingly in clinical settings. During January-April 2012, outpatients with acute respiratory illness (≤ 7 days) were tested for influenza using singleplex RT-PCR (SRT-PCR). A subset was assayed for 18 viruses using MRT-PCR to compare detection of influenza and examine the distribution of viruses and characteristics of patients using multinomial logistic regression. Among 662 participants (6 months-82 years), detection of influenza was similar between the MRT-PCR and SRT-PCR (κ = 0.83). No virus was identified in 267 (40.3%) samples. Commonly detected viruses were human rhinovirus (HRV, 15.4%), coronavirus (CoV, 10.4%), respiratory syncytial virus (RSV, 8.4%), human metapneumovirus (hMPV, 8.3%), and influenza (6%). Co-detections were infrequent (6.9%) and most commonly occurred among those <18 years old. In regression analyses, compared with non-viral illnesses, RSV and hMPV were significantly more frequent in children and less frequent in 18- to 49-year-olds than in those ≥ 50 years (P = 0.01), fever was more common in hMPV and influenza infections (P = 0.008), nasal congestion was more frequent in CoV, HRV, hMPV, influenza and RSV infections (P = 0.001), and body mass index was higher among those with influenza (P = 0.036). Using MRT-PCR, a viral etiology was found in three-fifths of patients with medically attended outpatient visits for acute respiratory illness during the influenza season; co-detected viruses were infrequent. Symptoms varied by viral etiology. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

An inventory of terrestrial mammals at national parks in the Northeast Temperate Network and Sagamore Hill National Historic Site

USGS Publications Warehouse

Gilbert, Andrew T.; O'Connell, Allan F.; Annand, Elizabeth M.; Talancy, Neil W.; Sauer, John R.; Nichols, James D.

2008-01-01

An inventory of mammals was conducted during 2004 at nine national park sites in the Northeast Temperate Network (NETN): Acadia National Park (NP), Marsh-Billings-Rockefeller National Historical Park (NHP), Minute Man NHP, Morristown NHP, Roosevelt-Vanderbilt National Historic Site (NHS), Saint-Gaudens NHS, Saugus Iron Works NHS, Saratoga NHP, and Weir Farm NHS. Sagamore Hill NHS, part of the Northeast Coastal and Barrier Network (NCBN), was also surveyed. Each park except Acadia NP was sampled twice, once in the winter/spring and again in the summer/fall. During the winter/spring visit, indirect measure (IM) sampling arrays were employed at 2 to 16 stations and included sampling by remote cameras, cubby boxes (covered trackplates), and hair traps. IM stations were established and re-used during the summer/fall sampling period. Trapping was conducted at 2 to 12 stations at all parks except Acadia NP during the summer/fall period and consisted of arrays of small-mammal traps, squirrel-sized live traps, and some fox-sized live traps. We used estimation-based procedures and probabilistic sampling techniques to design this inventory. A total of 38 species was detected by IM sampling, trapping, and field observations. Species diversity (number of species) varied among parks, ranging from 8 to 24, with Minute Man NHP having the most species detected. Raccoon (Procyon lotor), Virginia Opossum (Didelphis virginiana), Fisher (Martes pennanti), and Domestic Cat (Felis silvestris) were the most common medium-sized mammals detected in this study and White-footed Mouse (Peromyscus leucopus), Northern Short-tailed Shrew (Blarina brevicauda), Deer Mouse (P. maniculatus), and Meadow Vole (Microtus pennsylvanicus) the most common small mammals detected. All species detected are considered fairly common throughout their range including the Fisher, which has been reintroduced in several New England states. We did not detect any state or federal endangered or threatened species.

Nothing more than a pair of curvatures: A common mechanism for the detection of both radial and non-radial frequency patterns.

PubMed

Schmidtmann, Gunnar; Kingdom, Frederick A A

2017-05-01

Radial frequency (RF) patterns, which are sinusoidal modulations of a radius in polar coordinates, are commonly used to study shape perception. Previous studies have argued that the detection of RF patterns is either achieved globally by a specialized global shape mechanism, or locally using as cue the maximum tangent orientation difference between the RF pattern and the circle. Here we challenge both ideas and suggest instead a model that accounts not only for the detection of RF patterns but also for line frequency patterns (LF), i.e. contours sinusoidally modulated around a straight line. The model has two features. The first is that the detection of both RF and LF patterns is based on curvature differences along the contour. The second is that this curvature metric is subject to what we term the Curve Frequency Sensitivity Function, or CFSF, which is characterized by a flat followed by declining response to curvature as a function of modulation frequency, analogous to the modulation transfer function of the eye. The evidence that curvature forms the basis for detection is that at very low modulation frequencies (1-3 cycles for the RF pattern) there is a dramatic difference in thresholds between the RF and LF patterns, a difference however that disappears at medium and high modulation frequencies. The CFSF feature on the other hand explains why thresholds, rather than continuously declining with modulation frequency, asymptote at medium and high modulation frequencies. In summary, our analysis suggests that the detection of shape modulations is processed by a common curvature-sensitive mechanism that is subject to a shape-frequency-dependent transfer function. This mechanism is independent of whether the modulation is applied to a circle or a straight line. Copyright © 2017 Elsevier Ltd. All rights reserved.

Detection of white matter lesions in cerebral small vessel disease

NASA Astrophysics Data System (ADS)

Riad, Medhat M.; Platel, Bram; de Leeuw, Frank-Erik; Karssemeijer, Nico

2013-02-01

White matter lesions (WML) are diffuse white matter abnormalities commonly found in older subjects and are important indicators of stroke, multiple sclerosis, dementia and other disorders. We present an automated WML detection method and evaluate it on a dataset of small vessel disease (SVD) patients. In early SVD, small WMLs are expected to be of importance for the prediction of disease progression. Commonly used WML segmentation methods tend to ignore small WMLs and are mostly validated on the basis of total lesion load or a Dice coefficient for all detected WMLs. Therefore, in this paper, we present a method that is designed to detect individual lesions, large or small, and we validate the detection performance of our system with FROC (free-response ROC) analysis. For the automated detection, we use supervised classification making use of multimodal voxel based features from different magnetic resonance imaging (MRI) sequences, including intensities, tissue probabilities, voxel locations and distances, neighborhood textures and others. After preprocessing, including co-registration, brain extraction, bias correction, intensity normalization, and nonlinear registration, ventricle segmentation is performed and features are calculated for each brain voxel. A gentle-boost classifier is trained using these features from 50 manually annotated subjects to give each voxel a probability of being a lesion voxel. We perform ROC analysis to illustrate the benefits of using additional features to the commonly used voxel intensities; significantly increasing the area under the curve (Az) from 0.81 to 0.96 (p<0.05). We perform the FROC analysis by testing our classifier on 50 previously unseen subjects and compare the results with manual annotations performed by two experts. Using the first annotator results as our reference, the second annotator performs at a sensitivity of 0.90 with an average of 41 false positives per subject while our automated method reached the same level of sensitivity at approximately 180 false positives per subject.

Isothermal Method of a Recombinase Polymerase Amplification Assay for the Detection of Most Common High-Risk Human Papillomavirus Type 16 and Type 18 DNA.

PubMed

Ma, Biao; Fang, Jiehong; Wang, Ye; He, Haizhen; Dai, Mingyan; Lin, Wei; Su, Wei; Zhang, Mingzhou

2017-01-01

Cervical cancer is a common gynecologic malignant tumor and has a great impact on women's health. Human papillomavirus (HPV) is implicated in cervical cancer and precancerous lesions and the two are possibly two stages of disease progression. With the technological development of molecular biology and epidemiology, detection and treatment of HPV has become an important means to prevent cervical cancer. Here we present a novel, rapid, sensitive and specific isothermal method of recombinase polymerase amplification (RPA), which is established to detect the two most common high-risk human papillomavirus type 16 and type 18 DNA. In this study, we evaluate the efficacy of the RPA assay, incubating clinical specimens of HPV16 and HPV18 using plasmids standard. It operates at constant low temperature without the thermal instrumentation for incubation. The products can be detected via agarose gel electrophoresis assay, reverse dot blot assay, and quantitative real-time assay with SYBR Green I. We assess the diagnostic performance of the RPA assay for detecting of HPV16 and HPV18 in 335 clinical samples from patients suspected of cervical cancer. The results revealed no cross-reaction with other HPV genotypes and the RPA assay achieve a sensitivity of 100 copies. Compared with TaqMan qPCR, the RPA technique achieves exponential amplification with no need for pretreatment of sample DNA at 37°C for 20 minutes, which reveals more satisfactory performance. The agreement between the RPA and qPCR assays was 97.6% (κ = 0.89) for HPV16 positivity and 98.5% (κ = 0.81) for HPV18 positivity, indicating very good correlation between both tests. Importantly, the RPA assay was demonstrated to be a useful and powerful method for detection of HPV virus, which therefore may serve as a valuable tool for rapid diagnosis of HPV infection in both commercial and clinical applications.

Two endornaviruses show differential infection patterns between gene pools of Phaseolus vulgaris.

PubMed

Khankhum, Surasak; Valverde, Rodrigo A; Pastor-Corrales, Marcial A; Osorno, Juan M; Sabanadzovic, Sead

2015-04-01

We investigated the occurrence of two plant endornaviruses, Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2, in breeding lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) collected from the two centers of common bean domestication: Mesoamerica and the Andes. The two endornaviruses were detected in many genotypes of Mesoamerican origin but rarely in genotypes of Andean origin. The results suggest that these two endornaviruses were introduced into the Mesoamerican modern genotypes during common bean domestication and provide more evidence for the existence of two divergent gene pools of common bean.

Detecting Lung and Colorectal Cancer Recurrence Using Structured Clinical/Administrative Data to Enable Outcomes Research and Population Health Management.

PubMed

Hassett, Michael J; Uno, Hajime; Cronin, Angel M; Carroll, Nikki M; Hornbrook, Mark C; Ritzwoller, Debra

2017-12-01

Recurrent cancer is common, costly, and lethal, yet we know little about it in community-based populations. Electronic health records and tumor registries contain vast amounts of data regarding community-based patients, but usually lack recurrence status. Existing algorithms that use structured data to detect recurrence have limitations. We developed algorithms to detect the presence and timing of recurrence after definitive therapy for stages I-III lung and colorectal cancer using 2 data sources that contain a widely available type of structured data (claims or electronic health record encounters) linked to gold-standard recurrence status: Medicare claims linked to the Cancer Care Outcomes Research and Surveillance study, and the Cancer Research Network Virtual Data Warehouse linked to registry data. Twelve potential indicators of recurrence were used to develop separate models for each cancer in each data source. Detection models maximized area under the ROC curve (AUC); timing models minimized average absolute error. Algorithms were compared by cancer type/data source, and contrasted with an existing binary detection rule. Detection model AUCs (>0.92) exceeded existing prediction rules. Timing models yielded absolute prediction errors that were small relative to follow-up time (<15%). Similar covariates were included in all detection and timing algorithms, though differences by cancer type and dataset challenged efforts to create 1 common algorithm for all scenarios. Valid and reliable detection of recurrence using big data is feasible. These tools will enable extensive, novel research on quality, effectiveness, and outcomes for lung and colorectal cancer patients and those who develop recurrence.

Sentinel lymph node biopsy in early-stage cervical cancer: utility of intraoperative versus postoperative assessment.

PubMed

Fader, A Nickles; Edwards, R P; Cost, M; Kanbour-Shakir, A; Kelley, J L; Schwartz, B; Sukumvanich, P; Comerci, J; Sumkin, J; Elishaev, E; Rohan, L Cencia

2008-10-01

To determine the diagnostic accuracy of sentinel lymph node (SLN) detection using lymphoscintigraphy, intraoperative blue dye, and radiocolloid in patients with early-stage cervical cancer. Intra-cervical injection of technetium-99 sulfur colloid and lymphoscintigraphy were performed preoperatively. Isosulfan blue was injected intra-cervically immediately prior to surgery. SLNs were excised and examined intraoperatively (imprint cytology and frozen section) and postoperatively (H and E histology and immunohistochemistry (IHC) for cytokeratin). Thirty eight patients were evaluable. Laparoscopy and laparotomy were performed in 28.9% and 71.1%, respectively. Subjects had squamous cell carcinoma (n=26), adenocarcinoma (n=10) or adenosquamous (n=2) histologies. 55.3% had cervical tumors <2 cm. The overall SLN detection rate was 92.1%. The external iliac region just distal to the common iliac bifurcation was the most common SLN location. A mean of 2.1 SLNs were detected per patient with bilateral SLNs observed in 47.4%. On final pathology, metastatic nodal disease was identified in 15.7% of patients. Of these, 83.3% were detected in the SLNs. Sensitivity of SLN detection of metastasis was 100% for patients with cervical tumors <2 cm. However intraoperative evaluation by imprint cytology and frozen section correctly identified lymph node metastasis in only 33.3%. SLN detection is feasible and accurately reflects pelvic nodal basin status when performed in early-stage cervical cancer patients. However, while current intraoperative pathology techniques for assessing nodal metastases reliably detect metastases larger than 2 mm, they lack sufficient sensitivity to detect micrometastasis and isolated tumor cells.

Sensitive detection of unlabeled oligonucleotides using a paired surface plasma waves biosensor.

PubMed

Li, Ying-Chang; Chiou, Chiuan-Chian; Luo, Ji-Dung; Chen, Wei-Ju; Su, Li-Chen; Chang, Ying-Feng; Chang, Yu-Sun; Lai, Chao-Sung; Lee, Cheng-Chung; Chou, Chien

2012-05-15

Detection of unlabeled oligonucleotides using surface plasmon resonance (SPR) is difficult because of the oligonucleotides' relatively lower molecular weight compared with proteins. In this paper, we describe a method for detecting unlabeled oligonucleotides at low concentration using a paired surface plasma waves biosensor (PSPWB). The biosensor uses a sensor chip with an immobilized probe to detect a target oligonucleotide via sequence-specific hybridization. PSPWB measures the demodulated amplitude of the heterodyne signal in real time. In the meantime, the ratio of the amplitudes between the detected output signal and reference can reduce the excess noise from the laser intensity fluctuation. Also, the common-path propagation of p and s waves cancels the common phase noise induced by temperature variation. Thus, a high signal-to-noise ratio (SNR) of the heterodyne signal is detected. The sequence specificity of oligonucleotide hybridization ensures that the platform is precisely discriminating between target and non-target oligonucleotides. Under optimized experimental conditions, the detected heterodyne signal increases linearly with the logarithm of the concentration of target oligonucleotide over the range 0.5-500 pM. The detection limit is 0.5 pM in this experiment. In addition, the non-target oligonucleotide at concentrations of 10 pM and 10nM generated signals only slightly higher than background, indicating the high selectivity and specificity of this method. Different length of perfectly matched oligonucleotide targets at 10-mer, 15-mer and 20-mer were identified at the concentration of 150 pM. Copyright © 2012 Elsevier B.V. All rights reserved.

Multienvironment Quantitative Trait Loci Analysis for Photosynthate Acquisition, Accumulation, and Remobilization Traits in Common Bean Under Drought Stress

PubMed Central

Asfaw, Asrat; Blair, Matthew W.; Struik, Paul C.

2012-01-01

Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance. PMID:22670228

Multienvironment quantitative trait Loci analysis for photosynthate acquisition, accumulation, and remobilization traits in common bean under drought stress.

PubMed

Asfaw, Asrat; Blair, Matthew W; Struik, Paul C

2012-05-01

Many of the world's common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers' field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance.

Proximal detection of chemical warfare agents using PMIRRAS

NASA Astrophysics Data System (ADS)

Petryk, Michael W. P.; Marenco, Armando J.

2010-04-01

Non-contact chemical warfare agent detection has been demonstrated on military painted surfaces using polarization modulation infrared reflection-absorption spectroscopy (PMIRRAS). Notably, VX has been detected on chemical agent resistance coating (CARC) paint at a distance of approximately 10 cm. PMIRRAS does not rely on the presence of chemical vapors and is not affected by many common battlefield interferants such as aerosolized dust, water and diesel vapors, etc., making it highly suitable for use in operational environments.

Triboelectrification-Enabled Self-Powered Detection and Removal of Heavy Metal Ions in Wastewater.

PubMed

Li, Zhaoling; Chen, Jun; Guo, Hengyu; Fan, Xing; Wen, Zhen; Yeh, Min-Hsin; Yu, Chongwen; Cao, Xia; Wang, Zhong Lin

2016-04-20

A fundamentally new working principle into the field of self-powered heavy-metal-ion detection and removal using the triboelectrification effect is introduced. The as-developed tribo-nanosensors can selectively detect common heavy metal ions. The water-driven triboelectric nanogenerator is taken as a sustainable power source for heavy-metal-ion removal by recycling the kinetic energy from flowing wastewater. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Detection of hypervelocity dust impacts on the Earth orbiting Cluster and MMS spacecraft and problems with signal interpretation

NASA Astrophysics Data System (ADS)

Vaverka, Jakub; Pellinen-Wannberg, Asta; Kero, Johan; Mann, Ingrid; De Spiegeleer, Alexandre; Hamrin, Maria; Norberg, Carol; Pitkänen, Timo

2017-04-01

Detection of hypervelocity dust impacts on a spacecraft body by electric field instruments have been reported by several missions such as Voyager, WIND, Cassini, STEREO. The mechanism of this detection is still not completely understood and is under intensive laboratory investigation. A commonly accepted theory is based on re-collection of plasma cloud particles generated by a hypervelocity dust impact by a spacecraft surface and an electric field antenna resulting in a fast change in the potential of the spacecraft body and antenna. These changes can be detected as a short pulse measured by the electric field instrument. We present the first detection of dust impacts on the Earth-orbiting MMS and Cluster satellites. Each of the four MMS spacecraft provide probe-to-spacecraft potential measurements for their respective the six electric field antennas. This gives a unique view on signals generated by dust impacts and allow their reliable identification which is not possible for example on the Cluster spacecraft. We discuss various instrumental effects and solitary waves, commonly present in the Earth's magnetosphere, which can be easily misinterpreted as dust impacts. We show the influence of local plasma environment on dust impact detection for satellites crossing various regions of the Earth's magnetosphere where the concentration and the temperature of plasma particles change significantly.

Development of a single-tube loop-mediated isothermal amplification assay for detection of four pathogens of bacterial meningitis.

PubMed

Huy, Nguyen Tien; Hang, Le Thi Thuy; Boamah, Daniel; Lan, Nguyen Thi Phuong; Van Thanh, Phan; Watanabe, Kiwao; Huong, Vu Thi Thu; Kikuchi, Mihoko; Ariyoshi, Koya; Morita, Kouichi; Hirayama, Kenji

2012-12-01

Several loop-mediated isothermal amplification (LAMP) assays have been developed to detect common causative pathogens of bacterial meningitis (BM). However, no LAMP assay is reported to detect Streptococcus agalactiae and Streptococcus suis, which are also among common pathogens of BM. Moreover, it is laborious and expensive by performing multiple reactions for each sample to detect bacterial pathogen. Thus, we aimed to design and develop a single-tube LAMP assay capable of detecting multiple bacterial species, based on the nucleotide sequences of the 16S rRNA genes of the bacteria. The nucleotide sequences of the 16S rRNA genes of main pathogens involved in BM were aligned to identify conserved regions, which were further used to design broad range specific LAMP assay primers. We successfully designed a set of broad range specific LAMP assay primers for simultaneous detection of four species including Staphylococcus aureus, Streptococcus pneumoniae, S. suis and S. agalactiae. The broad range LAMP assay was highly specific without cross-reactivity with other bacteria including Haemophilus influenzae, Neisseria meningitidis and Escherichia coli. The sensitivity of our LAMP assay was 100-1000 times higher compared with the conventional PCR assay. The bacterial species could be identified after digestion of the LAMP products with restriction endonuclease DdeI and HaeIII. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Identification of a self-paced hitting task in freely moving rats based on adaptive spike detection from multi-unit M1 cortical signals

PubMed Central

Hammad, Sofyan H. H.; Farina, Dario; Kamavuako, Ernest N.; Jensen, Winnie

2013-01-01

Invasive brain–computer interfaces (BCIs) may prove to be a useful rehabilitation tool for severely disabled patients. Although some systems have shown to work well in restricted laboratory settings, their usefulness must be tested in less controlled environments. Our objective was to investigate if a specific motor task could reliably be detected from multi-unit intra-cortical signals from freely moving animals. Four rats were trained to hit a retractable paddle (defined as a “hit”). Intra-cortical signals were obtained from electrodes placed in the primary motor cortex. First, the signal-to-noise ratio was increased by wavelet denoising. Action potentials were then detected using an adaptive threshold, counted in three consecutive time intervals and were used as features to classify either a “hit” or a “no-hit” (defined as an interval between two “hits”). We found that a “hit” could be detected with an accuracy of 75 ± 6% when wavelet denoising was applied whereas the accuracy dropped to 62 ± 5% without prior denoising. We compared our approach with the common daily practice in BCI that consists of using a fixed, manually selected threshold for spike detection without denoising. The results showed the feasibility of detecting a motor task in a less restricted environment than commonly applied within invasive BCI research. PMID:24298254

Computational analysis of gene-gene interactions using multifactor dimensionality reduction.

PubMed

Moore, Jason H

2004-11-01

Understanding the relationship between DNA sequence variations and biologic traits is expected to improve the diagnosis, prevention and treatment of common human diseases. Success in characterizing genetic architecture will depend on our ability to address nonlinearities in the genotype-to-phenotype mapping relationship as a result of gene-gene interactions, or epistasis. This review addresses the challenges associated with the detection and characterization of epistasis. A novel strategy known as multifactor dimensionality reduction that was specifically designed for the identification of multilocus genetic effects is presented. Several case studies that demonstrate the detection of gene-gene interactions in common diseases such as atrial fibrillation, Type II diabetes and essential hypertension are also discussed.

New Researches and Application Progress of Commonly Used Optical Molecular Imaging Technology

PubMed Central

Chen, Zhi-Yi; Yang, Feng; Lin, Yan; Zhou, Qiu-Lan; Liao, Yang-Ying

2014-01-01

Optical molecular imaging, a new medical imaging technique, is developed based on genomics, proteomics and modern optical imaging technique, characterized by non-invasiveness, non-radiativity, high cost-effectiveness, high resolution, high sensitivity and simple operation in comparison with conventional imaging modalities. Currently, it has become one of the most widely used molecular imaging techniques and has been applied in gene expression regulation and activity detection, biological development and cytological detection, drug research and development, pathogenesis research, pharmaceutical effect evaluation and therapeutic effect evaluation, and so forth, This paper will review the latest researches and application progresses of commonly used optical molecular imaging techniques such as bioluminescence imaging and fluorescence molecular imaging. PMID:24696850

Diagnostic and prognostic epigenetic biomarkers in cancer.

PubMed

Costa-Pinheiro, Pedro; Montezuma, Diana; Henrique, Rui; Jerónimo, Carmen

2015-01-01

Growing cancer incidence and mortality worldwide demands development of accurate biomarkers to perfect detection, diagnosis, prognostication and monitoring. Urologic (prostate, bladder, kidney), lung, breast and colorectal cancers are the most common and despite major advances in their characterization, this has seldom translated into biomarkers amenable for clinical practice. Epigenetic alterations are innovative cancer biomarkers owing to stability, frequency, reversibility and accessibility in body fluids, entailing great potential of assay development to assist in patient management. Several studies identified putative epigenetic cancer biomarkers, some of which have been commercialized. However, large multicenter validation studies are required to foster translation to the clinics. Herein we review the most promising epigenetic detection, diagnostic, prognostic and predictive biomarkers for the most common cancers.

The observational case for Jupiter being a typical massive planet.

PubMed

Lineweaver, Charles H; Grether, Daniel

2002-01-01

We identify a subsample of the recently detected extrasolar planets that is minimally affected by the selection effects of the Doppler detection method. With a simple analysis we quantify trends in the surface density of this subsample in the period-Msin(i) plane. A modest extrapolation of these trends puts Jupiter in the most densely occupied region of this parameter space, thus indicating that Jupiter is a typical massive planet rather than an outlier. Our analysis suggests that Jupiter is more typical than indicated by previous analyses. For example, instead of MJup mass exoplanets being twice as common as 2 MJup exoplanets, we find they are three times as common.

Detecting Motion from a Moving Platform; Phase 3: Unification of Control and Sensing for More Advanced Situational Awareness

DTIC Science & Technology

2011-11-01

RX-TY-TR-2011-0096-01) develops a novel computer vision sensor based upon the biological vision system of the common housefly , Musca domestica...01 summarizes the development of a novel computer vision sensor based upon the biological vision system of the common housefly , Musca domestica

Selection for Spontaneous "Escherichia coli" Streptomycin Mutants Using Basic Fuchsin.

ERIC Educational Resources Information Center

Walkosz, Ronald

1991-01-01

An exercise that uses a common bacterium, E. coli, in great numbers, to detect a demonstrable change in the ability of some cells to become resistant to the common antibiotic streptomycin is presented. The procedure for preparing and pouring the gradient antibiotic plates is provided. The advantages of using the Basic Fuchsin in the agar are…

Detection and quantitation of HPV in genital and oral tissues and fluids by real time PCR

PubMed Central

2010-01-01

Background Human papillomaviruses (HPVs) remain a serious world health problem due to their association with anogenital/oral cancers and warts. While over 100 HPV types have been identified, a subset is associated with malignancy. HPV16 and 18 are the most prevalent oncogenic types, while HPV6 and 11 are most commonly responsible for anogenital warts. While other quantitative PCR (qPCR) assays detect oncogenic HPV, there is no single tube assay distinguishing the most frequent oncogenic types and the most common types found in warts. Results A Sybr Green-based qPCR assay was developed utilizing degenerate primers to the highly conserved HPV E1 theoretically detecting any HPV type. A single tube multiplex qPCR assay was also developed using type-specific primer pairs and TaqMan probes that allowed for detection and quantitation of HPV6,11,16,18. Each HPV type was detected over a range from 2 × 101 to 2 × 106copies/reaction providing a reliable method of quantitating type-specific HPV in 140 anogenital/cutaneous/oral benign and malignant specimens. 35 oncogenic and low risk alpha genus HPV types were detected. Concordance was detected in previously typed specimens. Comparisons to the gold standard detected an overall sensitivity of 89% (95% CI: 77% - 96%) and specificity of 90% (95%CI: 52% - 98%). Conclusion There was good agreement between the ability of the qPCR assays described here to identify HPV types in malignancies previously typed using standard methods. These novel qPCR assays will allow rapid detection and quantitation of HPVs to assess their role in viral pathogenesis. PMID:20723234

Pesticides in streams of the United States : initial results from the National Water-Quality Assessment Program

USGS Publications Warehouse

Larson, Steven J.; Gilliom, Robert J.; Capel, Paul D.

1999-01-01

Water samples from 58 rivers and streams across the United States were analyzed for pesticides as part of the National Water-Quality Assessment Program of the U.S. Geological Survey. The sampling sites represent 37 diverse agricultural basins, 11 urban basins, and 10 basins with mixed land use. Forty-six pesticides and pesticide degradation products were analyzed in approximately 2,200 samples collected from 1992 to 1995. The target compounds account for approximately 70 percent of national agricultural use in terms of the mass of pesticides applied annually. All the target compounds were detected in one or more samples. Herbicides generally were detected more frequently and at higher concentrations than insecticides. Nationally, 11 herbicides, 1 herbicide degradation product, and 3 insecticides were detected in more than 10 percent of samples. The number of target compounds detected at each site ranged from 7 to 37. The herbicides atrazine, metolachlor, prometon, and simazine were detected most frequently; among the insecticides, carbaryl, chlorpyrifos, and diazinon were detected the most frequently. Distinct differences in pesticide occurrence were observed in streams draining the various agricultural settings. Relatively high levels of several herbicides occurred as seasonal pulses in corn-growing areas. Several insecticides were frequently detected in areas where the dominant crops consist of orchards and vegetables. The number of pesticides detected and their concentrations were lower in wheat-growing areas than in most other agricultural areas. In most urban areas, the herbicides prometon and simazine and the insecticides carbaryl, chlorpyrifos, diazinon, and malathion were commonly detected. Concentrations of pesticides rarely exceeded standards and criteria established for drinking water, but some pesticides commonly exceeded criteria established for the protection of aquatic life.

Detection and Diagnosis of Oral Neoplasia with Confocal Microscopy and Optical Coherence

DTIC Science & Technology

2003-08-01

In the United States, over 27,000 new cases and approximately 7,000 deaths attributable to oral cancer are expected in 2003. In some areas of the...world this malignancy is much more common; oral cancer is the most common cancer among men and the third most common cancer in women in India. Prognosis...for patients with oral cancer remains low with 5-year survival rates hovering in the 50th percentile. High resolution, in vivo optical imaging may

Detection of mass regions in mammograms by bilateral analysis adapted to breast density using similarity indexes and convolutional neural networks.

PubMed

Bandeira Diniz, João Otávio; Bandeira Diniz, Pedro Henrique; Azevedo Valente, Thales Levi; Corrêa Silva, Aristófanes; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-03-01

The processing of medical image is an important tool to assist in minimizing the degree of uncertainty of the specialist, while providing specialists with an additional source of detect and diagnosis information. Breast cancer is the most common type of cancer that affects the female population around the world. It is also the most deadly type of cancer among women. It is the second most common type of cancer among all others. The most common examination to diagnose breast cancer early is mammography. In the last decades, computational techniques have been developed with the purpose of automatically detecting structures that maybe associated with tumors in mammography examination. This work presents a computational methodology to automatically detection of mass regions in mammography by using a convolutional neural network. The materials used in this work is the DDSM database. The method proposed consists of two phases: training phase and test phase. The training phase has 2 main steps: (1) create a model to classify breast tissue into dense and non-dense (2) create a model to classify regions of breast into mass and non-mass. The test phase has 7 step: (1) preprocessing; (2) registration; (3) segmentation; (4) first reduction of false positives; (5) preprocessing of regions segmented; (6) density tissue classification (7) second reduction of false positives where regions will be classified into mass and non-mass. The proposed method achieved 95.6% of accuracy in classify non-dense breasts tissue and 97,72% accuracy in classify dense breasts. To detect regions of mass in non-dense breast, the method achieved a sensitivity value of 91.5%, and specificity value of 90.7%, with 91% accuracy. To detect regions in dense breasts, our method achieved 90.4% of sensitivity and 96.4% of specificity, with accuracy of 94.8%. According to the results achieved by CNN, we demonstrate the feasibility of using convolutional neural networks on medical image processing techniques for classification of breast tissue and mass detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Two stage algorithm vs commonly used approaches for the suspect screening of complex environmental samples analyzed via liquid chromatography high resolution time of flight mass spectroscopy: A test study.

PubMed

Samanipour, Saer; Baz-Lomba, Jose A; Alygizakis, Nikiforos A; Reid, Malcolm J; Thomaidis, Nikolaos S; Thomas, Kevin V

2017-06-09

LC-HR-QTOF-MS recently has become a commonly used approach for the analysis of complex samples. However, identification of small organic molecules in complex samples with the highest level of confidence is a challenging task. Here we report on the implementation of a two stage algorithm for LC-HR-QTOF-MS datasets. We compared the performances of the two stage algorithm, implemented via NIVA_MZ_Analyzer™, with two commonly used approaches (i.e. feature detection and XIC peak picking, implemented via UNIFI by Waters and TASQ by Bruker, respectively) for the suspect analysis of four influent wastewater samples. We first evaluated the cross platform compatibility of LC-HR-QTOF-MS datasets generated via instruments from two different manufacturers (i.e. Waters and Bruker). Our data showed that with an appropriate spectral weighting function the spectra recorded by the two tested instruments are comparable for our analytes. As a consequence, we were able to perform full spectral comparison between the data generated via the two studied instruments. Four extracts of wastewater influent were analyzed for 89 analytes, thus 356 detection cases. The analytes were divided into 158 detection cases of artificial suspect analytes (i.e. verified by target analysis) and 198 true suspects. The two stage algorithm resulted in a zero rate of false positive detection, based on the artificial suspect analytes while producing a rate of false negative detection of 0.12. For the conventional approaches, the rates of false positive detection varied between 0.06 for UNIFI and 0.15 for TASQ. The rates of false negative detection for these methods ranged between 0.07 for TASQ and 0.09 for UNIFI. The effect of background signal complexity on the two stage algorithm was evaluated through the generation of a synthetic signal. We further discuss the boundaries of applicability of the two stage algorithm. The importance of background knowledge and experience in evaluating the reliability of results during the suspect screening was evaluated. Copyright © 2017 Elsevier B.V. All rights reserved.

Recommended survey designs for occupancy modelling using motion-activated cameras: insights from empirical wildlife data

PubMed Central

Lewis, Jesse S.; Gerber, Brian D.

2014-01-01

Motion-activated cameras are a versatile tool that wildlife biologists can use for sampling wild animal populations to estimate species occurrence. Occupancy modelling provides a flexible framework for the analysis of these data; explicitly recognizing that given a species occupies an area the probability of detecting it is often less than one. Despite the number of studies using camera data in an occupancy framework, there is only limited guidance from the scientific literature about survey design trade-offs when using motion-activated cameras. A fuller understanding of these trade-offs will allow researchers to maximise available resources and determine whether the objectives of a monitoring program or research study are achievable. We use an empirical dataset collected from 40 cameras deployed across 160 km2 of the Western Slope of Colorado, USA to explore how survey effort (number of cameras deployed and the length of sampling period) affects the accuracy and precision (i.e., error) of the occupancy estimate for ten mammal and three virtual species. We do this using a simulation approach where species occupancy and detection parameters were informed by empirical data from motion-activated cameras. A total of 54 survey designs were considered by varying combinations of sites (10–120 cameras) and occasions (20–120 survey days). Our findings demonstrate that increasing total sampling effort generally decreases error associated with the occupancy estimate, but changing the number of sites or sampling duration can have very different results, depending on whether a species is spatially common or rare (occupancy = ψ) and easy or hard to detect when available (detection probability = p). For rare species with a low probability of detection (i.e., raccoon and spotted skunk) the required survey effort includes maximizing the number of sites and the number of survey days, often to a level that may be logistically unrealistic for many studies. For common species with low detection (i.e., bobcat and coyote) the most efficient sampling approach was to increase the number of occasions (survey days). However, for common species that are moderately detectable (i.e., cottontail rabbit and mule deer), occupancy could reliably be estimated with comparatively low numbers of cameras over a short sampling period. We provide general guidelines for reliably estimating occupancy across a range of terrestrial species (rare to common: ψ = 0.175–0.970, and low to moderate detectability: p = 0.003–0.200) using motion-activated cameras. Wildlife researchers/managers with limited knowledge of the relative abundance and likelihood of detection of a particular species can apply these guidelines regardless of location. We emphasize the importance of prior biological knowledge, defined objectives and detailed planning (e.g., simulating different study-design scenarios) for designing effective monitoring programs and research studies. PMID:25210658

Cryptosporidium source tracking in the Potomac River watershed.

PubMed

Yang, Wenli; Chen, Plato; Villegas, Eric N; Landy, Ronald B; Kanetsky, Charles; Cama, Vitaliano; Dearen, Theresa; Schultz, Cherie L; Orndorff, Kenneth G; Prelewicz, Gregory J; Brown, Miranda H; Young, Kim Roy; Xiao, Lihua

2008-11-01

To better characterize Cryptosporidium in the Potomac River watershed, a PCR-based genotyping tool was used to analyze 64 base flow and 28 storm flow samples from five sites in the watershed. These sites included two water treatment plant intakes, as well as three upstream sites, each associated with a different type of land use. The uses, including urban wastewater, agricultural (cattle) wastewater, and wildlife, posed different risks in terms of the potential contribution of Cryptosporidium oocysts to the source water. Cryptosporidium was detected in 27 base flow water samples and 23 storm flow water samples. The most frequently detected species was C. andersoni (detected in 41 samples), while 14 other species or genotypes, almost all wildlife associated, were occasionally detected. The two common human-pathogenic species, C. hominis and C. parvum, were not detected. Although C. andersoni was common at all four sites influenced by agriculture, it was largely absent at the urban wastewater site. There were very few positive samples as determined by Environmental Protection Agency method 1623 at any site; only 8 of 90 samples analyzed (9%) were positive for Cryptosporidium as determined by microscopy. The genotyping results suggest that many of the Cryptosporidium oocysts in the water treatment plant source waters were from old calves and adult cattle and might not pose a significant risk to human health.

The non-contact detection and identification of blood stained fingerprints using visible wavelength reflectance hyperspectral imaging: Part 1.

PubMed

Cadd, Samuel; Li, Bo; Beveridge, Peter; O'Hare, William T; Campbell, Andrew; Islam, Meez

2016-05-01

Blood is one of the most commonly encountered types of biological evidence found at scenes of violent crime and one of the most commonly observed fingerprint contaminants. Current visualisation methods rely on presumptive tests or chemical enhancement methods. Although these can successfully visualise ridge detail, they are destructive, do not confirm the presence of blood and can have a negative impact on DNA sampling. A novel application of visible wavelength reflectance hyperspectral imaging (HSI) has been used for the detection and positive identification of blood stained fingerprints in a non-contact and non-destructive manner on white ceramic tiles. The identification of blood was based on the unique visible absorption spectrum of haemoglobin between 400 and 500 nm. HSI has been used to successfully visualise ridge detail in blood stained fingerprints to the ninth depletion. Ridge detail was still detectable with diluted blood to 20-fold dilutions. Latent blood stains were detectable to 15,000-fold dilutions. Ridge detail was detectable for fingerprints up to 6 months old. HSI was also able to conclusively distinguish blood stained fingerprints from fingerprints in six paints and eleven other red/brown media with zero false positives. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

A Comparison of the Rasch Separate Calibration and Between-Fit Methods of Detecting Item Bias.

ERIC Educational Resources Information Center

Smith, Richard M.

1996-01-01

The separate calibration t-test approach of B. Wright and M. Stone (1979) and the common calibration between-fit approach of B. Wright, R. Mead, and R. Draba (1976) appeared to have similar Type I error rates and similar power to detect item bias within a Rasch framework. (SLD)

A comparison of automated crater detection methods

NASA Astrophysics Data System (ADS)

Bandeira, L.; Barreira, C.; Pina, P.; Saraiva, J.

2008-09-01

Abstract This work presents early results of a comparison between some common methodologies for automated crater detection. The three procedures considered were applied to images of the surface of Mars, thus illustrating some pros and cons of their use. We aim to establish the clear advantages in using this type of methods in the study of planetary surfaces.

A new immunoassay for detecting all subtypes of Shiga toxins produced by Shiga toxin-producing E. coli in ground beef

USDA-ARS?s Scientific Manuscript database

Background Shiga toxin (Stx) is a common virulence factor of all Shiga toxin producing E. coli (STEC) that cause a wide spectrum of disease, including hemorrhagic colitis and hemolytic uremic syndrome (HUS). Although several commercial kits are available for detection of Stx produced by STEC, none o...

Inter-observer variation in identifying mammals from their tracks at enclosed track plate stations

Treesearch

William J. Zielinski; Fredrick V. Schlexer

2009-01-01

Enclosed track plate stations are a common method to detect mammalian carnivores. Studies rely on these data to make inferences about geographic range, population status and detectability. Despite their popularity, there has been no effort to document inter-observer variation in identifying the species that leave their tracks. Four previous field crew leaders...

Freeze-thaw method improves the detection of volatile compounds in insects using Headspace Solid-Phase Microextraction (HS-SPME)

USDA-ARS?s Scientific Manuscript database

Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC-MS) is commonly used in analyzing insect volatiles. In order to improve the detection of volatiles in insects, a freeze-thaw method was applied to insect samples before the HS-SPME-GC-MS analysis. ...

Necrobiosis lipoidica associated with Hashimoto's thyroiditis and positive detection of ANA and ASMA autoantibodies.

PubMed

Borgia, Francesco; Russo, Giuseppina T; Villari, Provvidenza; Guarneri, Fabrizio; Cucinotta, Domenico; Cannavò, Serafinella P

2015-07-01

Necrobiosis lipoidica (NL) is a rare idiopathic cutaneous condition exceptionally associated with autoimmune thyroiditis. We describe the first case of NL, Hashimoto's thyroiditis and positive detection of autoantibodies. Appropriate screening for NL in patients with autoimmune thyroiditis may clarify its real incidence and the existence of a common pathogenetic pathway.

Sirex woodwasp - Sirex noctilio F. Hymenoptera: Siricidae)

Treesearch

Dennis Haugen; E. Richard Hoebeke

2005-01-01

Sirex woodwasp has been the most common species of exotic woodwasp detected at United States ports-of-entry associated with solid wood packing materials. Recent detections of sirex woodwasp outside of port areas in the United States have raised concerns because this insect has the potential to cause significant mortality of pines. Awareness of the symptoms and signs...

Process Model Improvement for Source Code Plagiarism Detection in Student Programming Assignments

ERIC Educational Resources Information Center

Kermek, Dragutin; Novak, Matija

2016-01-01

In programming courses there are various ways in which students attempt to cheat. The most commonly used method is copying source code from other students and making minimal changes in it, like renaming variable names. Several tools like Sherlock, JPlag and Moss have been devised to detect source code plagiarism. However, for larger student…

Acoustic impact testing and waveform analysis for damage detection in glued laminated timber

Treesearch

Feng Xu; Xiping Wang; Marko Teder; Yunfei Liu

2017-01-01

Delamination and decay are common structural defects in old glued laminated timber (glulam) buildings, which, if left undetected, could cause severe structural damage. This paper presents a new damage detection method for glulam inspection based on moment analysis and wavelet transform (WT) of impact acoustic signals. Acoustic signals were collected from a glulam arch...

UV gated Raman spectroscopy for standoff detection of explosives

NASA Astrophysics Data System (ADS)

Gaft, M.; Nagli, L.

2008-07-01

Real-time detection and identification of explosives at a standoff distance is a major issue in efforts to develop defense against so-called improvised explosive devices (IED). It is recognized that the only method, which is potentially capable to standoff detection of minimal amounts of explosives is laser-based spectroscopy. LDS technique belongs to trace detection, namely to its micro-particles variety. It is based on commonly held belief that surface contamination was very difficult to avoid and could be exploited for standoff detection. We have applied gated Raman spectroscopy for detection of main explosive materials, both factory and homemade. We developed and tested a Raman system for the field remote detection and identification of minimal amounts of explosives on relevant surfaces at a distance of up to 30 m.

Inability To Detect Cross-Reactive Memory T Cells Challenges the Frequency of Heterologous Immunity among Common Viruses.

PubMed

Rowntree, Louise C; Nguyen, Thi H O; Halim, Hanim; Purcell, Anthony W; Rossjohn, Jamie; Gras, Stephanie; Kotsimbos, Tom C; Mifsud, Nicole A

2018-06-15

Human memory T cells that cross-react with epitopes from unrelated viruses can potentially modulate immune responses to subsequent infections by a phenomenon termed heterologous immunity. However, it is unclear whether similarities in structure rather than sequence underpin heterologous T cell cross-reactivity. In this study, we aimed to explore the mechanism of heterologous immunity involving immunodominant epitopes derived from common viruses restricted to high-frequency HLA allotypes (HLA-A*02:01, -B*07:02, and -B*08:01). We examined EBV-specific memory T cells for their ability to cross-react with CMV or influenza A virus-derived epitopes. Following T cell immunoassays to determine phenotype and function, complemented with biophysical and structural investigations of peptide/HLA complexes, we did not detect cross-reactivity of EBV-specific memory T cells toward either CMV or influenza A virus epitopes presented by any of the selected HLA allomorphs. Thus, despite the ubiquitous nature of these human viruses and the dominant immune response directed toward the selected epitopes, heterologous virus-specific T cell cross-reactivity was not detected. This suggests that either heterologous immunity is not as common as previously reported, or that it requires a very specific biological context to develop and be clinically relevant. Copyright © 2018 by The American Association of Immunologists, Inc.

Characteristics of gunshot sound displays by North Atlantic right whales in the Bay of Fundy.

PubMed

Parks, Susan E; Hotchkin, Cara F; Cortopassi, Kathryn A; Clark, Christopher W

2012-04-01

North Atlantic right whales (Eubalaena glacialis) produce a loud, broadband signal referred to as the gunshot sound. These distinctive sounds may be suitable for passive acoustic monitoring and detection of right whales; however, little is known about the prevalence of these sounds in important right whale habitats, such as the Bay of Fundy. This study investigates the timing and distribution of gunshot sound production on the summer feeding grounds using an array of five marine acoustic recording units deployed in the Bay of Fundy, Canada in mid-summer 2004 and 2005. Gunshot sounds were common, detected on 37 of 38 recording days. Stereotyped gunshot bouts averaged 1.5 h, with some bouts exceeding 7 h in duration with up to seven individuals producing gunshots at any one time. Bouts were more commonly detected in the late afternoon and evening than during the morning hours. Locations of gunshots in bouts indicated that whales producing the sounds were either stationary or showed directional travel, suggesting gunshots have different communication functions depending on behavioral context. These results indicate that gunshots are a common right whale sound produced during the summer months and are an important component in the acoustic communication system of this endangered species.

Effects of scale of movement, detection probability, and true population density on common methods of estimating population density

DOE PAGES

Keiter, David A.; Davis, Amy J.; Rhodes, Olin E.; ...

2017-08-25

Knowledge of population density is necessary for effective management and conservation of wildlife, yet rarely are estimators compared in their robustness to effects of ecological and observational processes, which can greatly influence accuracy and precision of density estimates. For this study, we simulate biological and observational processes using empirical data to assess effects of animal scale of movement, true population density, and probability of detection on common density estimators. We also apply common data collection and analytical techniques in the field and evaluate their ability to estimate density of a globally widespread species. We find that animal scale of movementmore » had the greatest impact on accuracy of estimators, although all estimators suffered reduced performance when detection probability was low, and we provide recommendations as to when each field and analytical technique is most appropriately employed. The large influence of scale of movement on estimator accuracy emphasizes the importance of effective post-hoc calculation of area sampled or use of methods that implicitly account for spatial variation. In particular, scale of movement impacted estimators substantially, such that area covered and spacing of detectors (e.g. cameras, traps, etc.) must reflect movement characteristics of the focal species to reduce bias in estimates of movement and thus density.« less

Effects of scale of movement, detection probability, and true population density on common methods of estimating population density

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

Keiter, David A.; Davis, Amy J.; Rhodes, Olin E.

Knowledge of population density is necessary for effective management and conservation of wildlife, yet rarely are estimators compared in their robustness to effects of ecological and observational processes, which can greatly influence accuracy and precision of density estimates. For this study, we simulate biological and observational processes using empirical data to assess effects of animal scale of movement, true population density, and probability of detection on common density estimators. We also apply common data collection and analytical techniques in the field and evaluate their ability to estimate density of a globally widespread species. We find that animal scale of movementmore » had the greatest impact on accuracy of estimators, although all estimators suffered reduced performance when detection probability was low, and we provide recommendations as to when each field and analytical technique is most appropriately employed. The large influence of scale of movement on estimator accuracy emphasizes the importance of effective post-hoc calculation of area sampled or use of methods that implicitly account for spatial variation. In particular, scale of movement impacted estimators substantially, such that area covered and spacing of detectors (e.g. cameras, traps, etc.) must reflect movement characteristics of the focal species to reduce bias in estimates of movement and thus density.« less

Detection of Secondary Causes and Coexisting Diseases in Hypertensive Patients: OSA and PA Are the Common Causes Associated with Hypertension.

PubMed

Wang, Lei; Li, Nanfang; Yao, Xiaoguang; Chang, Guijuan; Zhang, Delian; Heizhati, Mulalibieke; Wang, Menghui; Luo, Qin; Kong, Jianqiong

2017-01-01

Since the control rate of blood pressure is lower in mainland China, the aim of this study is to investigate the proportion of secondary causes and coexisting diseases of hypertension in hypertensive patients. Data on consecutive patients with hypertension who visited the Hypertension Center. Diseases were detected using an established strict screening protocol. Detection rate of secondary causes and coexisting diseases of hypertension was 39.5% among 3003 hypertensive patients. Obstructive sleep apnea (OSA) was the most common, accounting for 24.7% of patients, followed by primary aldosteronism (PA) (5.8%) and PA + OSA (4.9%). Endocrine hypertension accounted for 12.1% of patients, including 10.7% of patients with PA, 1.1% with hypothyroidism, 0.1% with pheochromocytoma, 0.1% with Cushing's syndrome, and 0.1% with hyperthyroidism, respectively. Those who smoke, those who are obese, and those who have diabetes accounted for 31.3%, 27.5%, and 16.6% of total patients, respectively. There were overlapping conditions in secondary causes and coexisting diseases of hypertension. OSA was the most common in each age- and BMI-stratified group. Findings from the current study suggest an increasing frequency of secondary forms of hypertension, highlighting the burden of OSA and PA in hypertensive patients.

Detection of Secondary Causes and Coexisting Diseases in Hypertensive Patients: OSA and PA Are the Common Causes Associated with Hypertension

PubMed Central

Wang, Lei; Yao, Xiaoguang; Chang, Guijuan; Zhang, Delian; Heizhati, Mulalibieke; Wang, Menghui; Luo, Qin; Kong, Jianqiong

2017-01-01

Background Since the control rate of blood pressure is lower in mainland China, the aim of this study is to investigate the proportion of secondary causes and coexisting diseases of hypertension in hypertensive patients. Methods Data on consecutive patients with hypertension who visited the Hypertension Center. Diseases were detected using an established strict screening protocol. Results Detection rate of secondary causes and coexisting diseases of hypertension was 39.5% among 3003 hypertensive patients. Obstructive sleep apnea (OSA) was the most common, accounting for 24.7% of patients, followed by primary aldosteronism (PA) (5.8%) and PA + OSA (4.9%). Endocrine hypertension accounted for 12.1% of patients, including 10.7% of patients with PA, 1.1% with hypothyroidism, 0.1% with pheochromocytoma, 0.1% with Cushing's syndrome, and 0.1% with hyperthyroidism, respectively. Those who smoke, those who are obese, and those who have diabetes accounted for 31.3%, 27.5%, and 16.6% of total patients, respectively. There were overlapping conditions in secondary causes and coexisting diseases of hypertension. OSA was the most common in each age- and BMI-stratified group. Conclusion Findings from the current study suggest an increasing frequency of secondary forms of hypertension, highlighting the burden of OSA and PA in hypertensive patients. PMID:28691036

A model for anomaly classification in intrusion detection systems

NASA Astrophysics Data System (ADS)

Ferreira, V. O.; Galhardi, V. V.; Gonçalves, L. B. L.; Silva, R. C.; Cansian, A. M.

2015-09-01

Intrusion Detection Systems (IDS) are traditionally divided into two types according to the detection methods they employ, namely (i) misuse detection and (ii) anomaly detection. Anomaly detection has been widely used and its main advantage is the ability to detect new attacks. However, the analysis of anomalies generated can become expensive, since they often have no clear information about the malicious events they represent. In this context, this paper presents a model for automated classification of alerts generated by an anomaly based IDS. The main goal is either the classification of the detected anomalies in well-defined taxonomies of attacks or to identify whether it is a false positive misclassified by the IDS. Some common attacks to computer networks were considered and we achieved important results that can equip security analysts with best resources for their analyses.

Advances in Anthrax Detection: Overview of Bioprobes and Biosensors.

PubMed

Kim, Joungmok; Gedi, Vinayakumar; Lee, Sang-Choon; Cho, Jun-Haeng; Moon, Ji-Young; Yoon, Moon-Young

2015-06-01

Anthrax is an infectious disease caused by Bacillus anthracis. Although anthrax commonly affects domestic and wild animals, it causes a rare but lethal infection in humans. A variety of techniques have been introduced and evaluated to detect anthrax using cultures, polymerase chain reaction, and immunoassays to address the potential threat of anthrax being used as a bioweapon. The high-potential harm of anthrax in bioterrorism requires sensitive and specific detection systems that are rapid, field-ready, and real-time monitoring. Here, we provide a systematic overview of anthrax detection probes with their potential applications in various ultra-sensitive diagnostic systems.

Molecular analysis of beta-globin gene mutations among Thai beta-thalassemia children: results from a single center study

PubMed Central

Boonyawat, Boonchai; Monsereenusorn, Chalinee; Traivaree, Chanchai

2014-01-01

Background Beta-thalassemia is one of the most common genetic disorders in Thailand. Clinical phenotype ranges from silent carrier to clinically manifested conditions including severe beta-thalassemia major and mild beta-thalassemia intermedia. Objective This study aimed to characterize the spectrum of beta-globin gene mutations in pediatric patients who were followed-up in Phramongkutklao Hospital. Patients and methods Eighty unrelated beta-thalassemia patients were enrolled in this study including 57 with beta-thalassemia/hemoglobin E, eight with homozygous beta-thalassemia, and 15 with heterozygous beta-thalassemia. Mutation analysis was performed by multiplex amplification refractory mutation system (M-ARMS), direct DNA sequencing of beta-globin gene, and gap polymerase chain reaction for 3.4 kb deletion detection, respectively. Results A total of 13 different beta-thalassemia mutations were identified among 88 alleles. The most common mutation was codon 41/42 (-TCTT) (37.5%), followed by codon 17 (A>T) (26.1%), IVS-I-5 (G>C) (8%), IVS-II-654 (C>T) (6.8%), IVS-I-1 (G>T) (4.5%), and codon 71/72 (+A) (2.3%), and all these six common mutations (85.2%) were detected by M-ARMS. Six uncommon mutations (10.2%) were identified by DNA sequencing including 4.5% for codon 35 (C>A) and 1.1% initiation codon mutation (ATG>AGG), codon 15 (G>A), codon 19 (A>G), codon 27/28 (+C), and codon 123/124/125 (-ACCCCACC), respectively. The 3.4 kb deletion was detected at 4.5%. The most common genotype of beta-thalassemia major patients was codon 41/42 (-TCTT)/codon 26 (G>A) or betaE accounting for 40%. Conclusion All of the beta-thalassemia alleles have been characterized by a combination of techniques including M-ARMS, DNA sequencing, and gap polymerase chain reaction for 3.4 kb deletion detection. Thirteen mutations account for 100% of the beta-thalassemia genes among the pediatric patients in our study. PMID:25525381

The Most Common Detected Bacteria in Sputum of Patients with Community Acquired Pneumonia (CAP) Treated In Hospital

PubMed Central

Cukic, Vesna; Hadzic, Armin

2016-01-01

Introduction: Community acquired pneumonia (CAP) is the most common infective pulmonary disease. Objective: To show the most common detected bacteria in bacterial culture of sputum in patients with CAP hospitalized in Clinic for Pulmonary Diseases and TB “Podhrastovi” in four-year period: from 2012 to 2015. Material and methods: This is the retrospective analysis. Each patient gave sputum 3 days in a row when admitted to hospital. Sputum has been examined: bacterial culture with antibiotics sensitivity, Gram stain, Mycobacterium tuberculosis; in cases with high temperature blood cultures were done; when we were suspicious about bronchial carcinoma bronchoscopy with BAL (bronchoalveolar lavage) was done. We show analyzed patients according to age, sex, whether they had pneumonia or bronchopneumonia, bacteria isolated in sputum and in BAL. Results: 360 patients with CAP were treated in four-year period (247 males and 113 females). 167 or 43, 39 % had pneumonia (119 males and 48 females). Number of males was significantly bigger (χ2 = 30,186; p<0,001). 193 or 53, 61 % had bronchopneumonia (128 males and 65 females). Number of males was significantly bigger (χ2 = 20,556; p<0,001). Number of patients with negative bacterial culture of sputum (131–78, 44%) was significantly bigger than number of patients with positive culture (36–21, 56%) (χ2 = 50,042; p<0,001) in pneumonia. Number of patients with negative bacterial culture of sputum (154- 79, 79%) was significantly bigger than number of patients with positive culture (39- 20, 21%) (χ2 = 68,523; p<0,001) in bronchopneumonia. Streptococcus pneumoniae was significantly most common detected bacterium compared with the number of other isolated bacteria; in pneumonia (χ2 =33,222; p<0,001) and in bronchopneumonia (χ2 =51,231; p<0,001). Conclusion: It is very important to detect the bacterial cause of CAP to administrate the targeted antibiotic therapy. PMID:27994296

Reviving common standards in point-count surveys for broad inference across studies

USGS Publications Warehouse

Matsuoka, Steven M.; Mahon, C. Lisa; Handel, Colleen M.; Solymos, Peter; Bayne, Erin M.; Fontaine, Patricia C.; Ralph, C.J.

2014-01-01

We revisit the common standards recommended by Ralph et al. (1993, 1995a) for conducting point-count surveys to assess the relative abundance of landbirds breeding in North America. The standards originated from discussions among ornithologists in 1991 and were developed so that point-count survey data could be broadly compared and jointly analyzed by national data centers with the goals of monitoring populations and managing habitat. Twenty years later, we revisit these standards because (1) they have not been universally followed and (2) new methods allow estimation of absolute abundance from point counts, but these methods generally require data beyond the original standards to account for imperfect detection. Lack of standardization and the complications it introduces for analysis become apparent from aggregated data. For example, only 3% of 196,000 point counts conducted during the period 1992-2011 across Alaska and Canada followed the standards recommended for the count period and count radius. Ten-minute, unlimited-count-radius surveys increased the number of birds detected by >300% over 3-minute, 50-m-radius surveys. This effect size, which could be eliminated by standardized sampling, was ≥10 times the published effect sizes of observers, time of day, and date of the surveys. We suggest that the recommendations by Ralph et al. (1995a) continue to form the common standards when conducting point counts. This protocol is inexpensive and easy to follow but still allows the surveys to be adjusted for detection probabilities. Investigators might optionally collect additional information so that they can analyze their data with more flexible forms of removal and time-of-detection models, distance sampling, multiple-observer methods, repeated counts, or combinations of these methods. Maintaining the common standards as a base protocol, even as these study-specific modifications are added, will maximize the value of point-count data, allowing compilation and analysis by regional and national data centers.

DNA Extraction Method Affects the Detection of a Fungal Pathogen in Formalin-Fixed Specimens Using qPCR.

PubMed

Adams, Andrea J; LaBonte, John P; Ball, Morgan L; Richards-Hrdlicka, Kathryn L; Toothman, Mary H; Briggs, Cheryl J

2015-01-01

Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80-90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.

Occurrence, distribution, loads, and yields of selected pesticides in the Little River basin, Kentucky, 2003-04

USGS Publications Warehouse

Crain, Angela S.

2006-01-01

Water resources in the Little River Basin are potentially vulnerable to applications of pesticides associated with both agricultural and nonagricultural activities, because much of the basin is characterized by karst topography. Concerns about water quality resulting from pesticide use in karst areas and lack of data on concentrations of pesticides in surface water led to further investigation of water quality in the Little River Basin, which includes about 600 square miles in Christian and Trigg Counties and a portion of Caldwell County in western Kentucky. Water samples were collected in streams in the Little River Basin, Kentucky during 2003-04 as part of a study conducted in cooperation with the Kentucky Department of Agriculture. The objectives of the study were to assess the occurrence and distribution of pesticides, to evaluate the spatial and seasonal variability of pesticides, and to evaluate loads and yields of selected pesticides in the basin. A total of 91 water samples was collected at 4 fixed-network sites from March through November 2003 and from February through November 2004. An additional 20 samples were collected at 5 synoptic-network sites within the same period. Twenty-four pesticides were detected of the 127 pesticides analyzed in the stream samples. Of the 24 detected pesticides, 15 were herbicides, 7 were insecticides, and 2 were fungicides. The most commonly detected pesticides-atrazine, simazine, metolachlor, and acetochlor-were those most heavily used on crops during the study. Atrazine and simazine were detected in 100 percent of all surface-water samples, and metolachlor and acetochlor were detected in more than 45 percent. The pesticide degradate, deethylatrazine, was detected in 100 percent of the samples. Only one nonagricultural herbicide, prometon, was detected in more than 50 percent of the samples. Diazinon, the most commonly detected insecticide, was found in 25 percent of all samples and was found at all sites except Casey Creek. Metalaxyl was the most commonly detected fungicide (14 percent); most detections were in samples from the Sinking Fork subbasin. Concentrations of herbicides were highest following application in the spring (March-May). In contrast, insecticides typically were present during the summer (June-August). The most commonly detected pesticides in the Little River Basin were found at low concentrations in streams year-round. Atrazine and simazine (row-crop herbicides) had the highest measured concentrations (22 and 6.1 micrograms per liter (?g/L), respectively) and were the most heavily applied herbicides in the basin. Metolachlor also was heavily applied in the basin, but measured concentrations did not exceed 0.32 ?g/L. The insecticide, Malathion, was only detected in 4 percent of the samples, although it was heavily applied in the basin during 2003-04. Most detections of pesticides were at low concentrations in relation to drinking-water standards and guidelines established for the protection of aquatic life. Only two pesticide compounds--atrazine and simazine--exceeded the U.S. Environmental Protection Agency (USEPA) standards for drinking water. Atrazine exceeded the USEPA's maximum contaminant level (MCL) 19 times in 111 detections; simazine exceeded the established MCL 2 times in 111 detections. These exceedences occurred in the spring. Concentrations of atrazine also exceeded the established aquatic-life criterion (1.8 ?g/L) in 32 samples collected from all sites. Concentrations of deethylatrazine, an herbicide-transformation compound, tended to follow the same monthly concentration pattern as its parent compound (atrazine), but concentrations of deethylatrazine were lower than those of atrazine. Atrazine may have been present in the soil much longer at these sites, which might have allowed microbial populations to transform atrazine into deethylatrazine. A statistical comparison of concentrations of selected pesticides among four fixed-network sites

Kullback-Leibler divergence for detection of rare haplotype common disease association.

PubMed

Lin, Shili

2015-11-01

Rare haplotypes may tag rare causal variants of common diseases; hence, detection of such rare haplotypes may also contribute to our understanding of complex disease etiology. Because rare haplotypes frequently result from common single-nucleotide polymorphisms (SNPs), focusing on rare haplotypes is much more economical compared with using rare single-nucleotide variants (SNVs) from sequencing, as SNPs are available and 'free' from already amassed genome-wide studies. Further, associated haplotypes may shed light on the underlying disease causal mechanism, a feat unmatched by SNV-based collapsing methods. In recent years, data mining approaches have been adapted to detect rare haplotype association. However, as they rely on an assumed underlying disease model and require the specification of a null haplotype, results can be erroneous if such assumptions are violated. In this paper, we present a haplotype association method based on Kullback-Leibler divergence (hapKL) for case-control samples. The idea is to compare haplotype frequencies for the cases versus the controls by computing symmetrical divergence measures. An important property of such measures is that both the frequencies and logarithms of the frequencies contribute in parallel, thus balancing the contributions from rare and common, and accommodating both deleterious and protective, haplotypes. A simulation study under various scenarios shows that hapKL has well-controlled type I error rates and good power compared with existing data mining methods. Application of hapKL to age-related macular degeneration (AMD) shows a strong association of the complement factor H (CFH) gene with AMD, identifying several individual rare haplotypes with strong signals.

Statistically rigorous calculations do not support common input and long-term synchronization of motor-unit firings

PubMed Central

Kline, Joshua C.

2014-01-01

Over the past four decades, various methods have been implemented to measure synchronization of motor-unit firings. In this work, we provide evidence that prior reports of the existence of universal common inputs to all motoneurons and the presence of long-term synchronization are misleading, because they did not use sufficiently rigorous statistical tests to detect synchronization. We developed a statistically based method (SigMax) for computing synchronization and tested it with data from 17,736 motor-unit pairs containing 1,035,225 firing instances from the first dorsal interosseous and vastus lateralis muscles—a data set one order of magnitude greater than that reported in previous studies. Only firing data, obtained from surface electromyographic signal decomposition with >95% accuracy, were used in the study. The data were not subjectively selected in any manner. Because of the size of our data set and the statistical rigor inherent to SigMax, we have confidence that the synchronization values that we calculated provide an improved estimate of physiologically driven synchronization. Compared with three other commonly used techniques, ours revealed three types of discrepancies that result from failing to use sufficient statistical tests necessary to detect synchronization. 1) On average, the z-score method falsely detected synchronization at 16 separate latencies in each motor-unit pair. 2) The cumulative sum method missed one out of every four synchronization identifications found by SigMax. 3) The common input assumption method identified synchronization from 100% of motor-unit pairs studied. SigMax revealed that only 50% of motor-unit pairs actually manifested synchronization. PMID:25210152

Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array.

PubMed

Aydin, Muhsin; Carter-Conger, Jacqueline; Gao, Ning; Gilmore, David F; Ricke, Steven C; Ahn, Soohyoun

2018-04-01

Salmonella is one of major foodborne pathogens and the leading cause of foodborne illness-related hospitalizations and deaths. It is critical to develop a sensitive and rapid detection assay that can identify Salmonella to ensure food safety. In this study, a DNA sensor-based suspension array system of high multiplexing ability was developed to identify eight Salmonella serovars commonly associated with foodborne outbreaks to the serotype level. Each DNA sensor was prepared by activating pre-encoded microspheres with oligonucleotide probes that are targeting virulence genes and serovar-specific regions. The mixture of 12 different types of DNA sensors were loaded into a 96-well microplate and used as a 12-plex DNA sensor array platform. DNA isolated from Salmonella was amplified by multiplex polymerase chain reaction (mPCR), and the presence of Salmonella was determined by reading fluorescent signals from hybridization between probes on DNA sensors and fluorescently labeled target DNA using the Bio-Plex® system. The developed multiplex array was able to detect synthetic DNA at the concentration as low as 100 fM and various Salmonella serovars as low as 100 CFU/mL within 1 h post-PCR. Sensitivity of this assay was further improved to 1 CFU/mL with 6-h enrichment. The array system also correctly and specifically identified serotype of tested Salmonella strains without any cross-reactivity with other common foodborne pathogens. Our results indicate the developed DNA sensor suspension array can be a rapid and reliable high-throughput method for simultaneous detection and molecular identification of common Salmonella serotypes.

Characterization of Adverse Events Detected in a Large Health Care Delivery System Using an Enhanced Global Trigger Tool over a Five-Year Interval

PubMed Central

Kennerly, Donald A; Kudyakov, Rustam; da Graca, Briget; Saldaña, Margaret; Compton, Jan; Nicewander, David; Gilder, Richard

2014-01-01

Objective To report 5 years of adverse events (AEs) identified using an enhanced Global Trigger Tool (GTT) in a large health care system. Study Setting Records from monthly random samples of adults admitted to eight acute care hospitals from 2007 to 2011 with lengths of stay ≥3 days were reviewed. Study Design We examined AE incidence overall and by presence on admission, severity, stemming from care provided versus omitted, preventability, and category; and the overlap with commonly used AE-detection systems. Data Collection Professional nurse reviewers abstracted 9,017 records using the enhanced GTT, recording triggers and AEs. Medical record/account numbers were matched to identify overlapping voluntary reports or AHRQ Patient Safety Indicators (PSIs). Principal Findings Estimated AE rates were as follows: 61.4 AEs/1,000 patient-days, 38.1 AEs/100 discharges, and 32.1 percent of patients with ≥1 AE. Of 1,300 present-on-admission AEs (37.9 percent of total), 78.5 percent showed NCC-MERP level F harm and 87.6 percent were “preventable/possibly preventable.” Of 2,129 hospital-acquired AEs, 63.3 percent had level E harm, 70.8 percent were “preventable/possibly preventable”; the most common category was “surgical/procedural” (40.5 percent). Voluntary reports and PSIs captured <5 percent of encounters with hospital-acquired AEs. Conclusions AEs are common and potentially amenable to prevention. GTT-identified AEs are seldom caught by commonly used AE-detection systems. PMID:24628436

Antimicrobial resistance and its genetic determinants in aeromonads isolated in ornamental (koi) carp (Cyprinus carpio koi) and common carp (Cyprinus carpio).

PubMed

Cízek, Alois; Dolejská, Monika; Sochorová, Radana; Strachotová, Katerina; Piacková, Veronika; Veselý, Tomás

2010-05-19

The aim of this study was to evaluate antimicrobial susceptibility of Aeromonas spp. isolates from common carp and koi carp coming from randomly chosen farms. The isolates were tested for susceptibility to 8 antimicrobial agents using the standard agar dilution susceptibility test. In all isolates, PCR was used to detect the presence of tet(A-E) genes, integrase genes, and gene cassettes. From the total 72 isolates of motile aeromonads sampled from koi carp, 36 isolates (50%) were resistant to oxytetracycline, 18 (25%) to ciprofloxacin, 5 (7%) to chloramphenicol, 5 (7%) to florfenicol, and 11 (15%) to trimethoprim. Among 49 isolates of motile aeromonads collected from common carp, 20 (41%) were resistant to oxytetracycline, 3 (6%) to chloramphenicol, and 3 (6%) to florfenicol. The resistance of aeromonads isolated from koi carp was significantly higher to ciprofloxacin (P=0.00024). The presence of class 1 integrons was detected in these isolates only (P=0.00024). Tet genes were detected in 40% (48/121) of isolates, with tet(E) being the most dominant. Our results demonstrated a significant difference in the incidence of resistant isolates collected from koi carp and common carp (P=0.00042). This difference can be ascribed to a distinct antibiotic policy established on consumer fish farms versus ornamental fish farms. The potential risk for resistant bacteria to spread and transmit infection to humans should be considered in cases of technological crossover between the two types of fish farms. Copyright 2009 Elsevier B.V. All rights reserved.

Multiple and substitute addictions involving prescription drugs misuse among 12th graders: gateway theory revisited with Market Basket Analysis.

PubMed

Jayawardene, Wasantha Parakrama; YoussefAgha, Ahmed Hassan

2014-01-01

This study aimed to identify the sequential patterns of drug use initiation, which included prescription drugs misuse (PDM), among 12th-grade students in Indiana. The study also tested the suitability of the data mining method Market Basket Analysis (MBA) to detect common drug use initiation sequences in large-scale surveys. Data from 2007 to 2009 Annual Surveys of Alcohol, Tobacco, and Other Drug Use by Indiana Children and Adolescents were used for this study. A close-ended, self-administered questionnaire was used to ask adolescents about the use of 21 substance categories and the age of first use. "Support%" and "confidence%" statistics of Market Basket Analysis detected multiple and substitute addictions, respectively. The lifetime prevalence of using any addictive substance was 73.3%, and it has been decreasing during past few years. Although the lifetime prevalence of PDM was 19.2%, it has been increasing. Males and whites were more likely to use drugs and engage in multiple addictions. Market Basket Analysis identified common drug use initiation sequences that involved 11 drugs. High levels of support existed for associations among alcohol, cigarettes, and marijuana, whereas associations that included prescription drugs had medium levels of support. Market Basket Analysis is useful for the detection of common substance use initiation sequences in large-scale surveys. Before initiation of prescription drugs, physicians should consider the adolescents' risk of addiction. Prevention programs should address multiple addictions, substitute addictions, common sequences in drug use initiation, sex and racial differences in PDM, and normative beliefs of parents and adolescents in relation to PDM.

Bio-ALIRT biosurveillance detection algorithm evaluation.

PubMed

Siegrist, David; Pavlin, J

2004-09-24

Early detection of disease outbreaks by a medical biosurveillance system relies on two major components: 1) the contribution of early and reliable data sources and 2) the sensitivity, specificity, and timeliness of biosurveillance detection algorithms. This paper describes an effort to assess leading detection algorithms by arranging a common challenge problem and providing a common data set. The objectives of this study were to determine whether automated detection algorithms can reliably and quickly identify the onset of natural disease outbreaks that are surrogates for possible terrorist pathogen releases, and do so at acceptable false-alert rates (e.g., once every 2-6 weeks). Historic de-identified data were obtained from five metropolitan areas over 23 months; these data included International Classification of Diseases, Ninth Revision (ICD-9) codes related to respiratory and gastrointestinal illness syndromes. An outbreak detection group identified and labeled two natural disease outbreaks in these data and provided them to analysts for training of detection algorithms. All outbreaks in the remaining test data were identified but not revealed to the detection groups until after their analyses. The algorithms established a probability of outbreak for each day's counts. The probability of outbreak was assessed as an "actual" alert for different false-alert rates. The best algorithms were able to detect all of the outbreaks at false-alert rates of one every 2-6 weeks. They were often able to detect for the same day human investigators had identified as the true start of the outbreak. Because minimal data exists for an actual biologic attack, determining how quickly an algorithm might detect such an attack is difficult. However, application of these algorithms in combination with other data-analysis methods to historic outbreak data indicates that biosurveillance techniques for analyzing syndrome counts can rapidly detect seasonal respiratory and gastrointestinal illness outbreaks. Further research is needed to assess the value of electronic data sources for predictive detection. In addition, simulations need to be developed and implemented to better characterize the size and type of biologic attack that can be detected by current methods by challenging them under different projected operational conditions.

Detection of chronic bee paralysis virus and acute bee paralysis virus in Uruguayan honeybees.

PubMed

Antúnez, Karina; D' Alessandro, Bruno; Corbella, Eduardo; Zunino, Pablo

2005-09-01

Chronic bee paralysis virus (CBPV) causes a disease characterized by trembling, flightless, and crawling bees, while Acute bee paralysis virus (ABPV) is commonly detected in apparently healthy colonies, usually associated to Varroa destructor. Both viruses had been detected in most regions of the world, except in South America. In this work, we detected CBPV and ABPV in samples of Uruguayan honeybees by RT-PCR. The detection of both viruses in different provinces and the fact that most of the analyzed samples were infected, suggest that, they are widely spread in the region. This is the first record of the presence of CBPV and ABPV in Uruguay and South America.

Feasibility of using ground-penetrating radar to quantify root mass in Florida's intensively managed pine plantations

Treesearch

John Butnor; Brian Roth; Kurt Johnsen

2005-01-01

Tree root systems are commonly evaluated via labor intensive, destructive, time-consuming excavations. Ground-penetrating radar (GPR) can be used to detect and monitor roots if there is sufficient electromagnetic contrast with the surrounding soil matrix. This methodology is commonly used in civil engineering for non-destructive testing of concrete as well as road and...

Hydrogeology and ground-water quality of Valley Forge National Historical Park, Montgomery County, Pennsylvania

USGS Publications Warehouse

Sloto, Ronald A.; McManus, B. Craig

1996-01-01

Valley Forge National Historical Park is just southwest of the Commodore Semiconductor Group (CSG) National Priorities List (Superfund) Site, a source of volatile organic compounds (VOC's) in ground water. The 7.5-square-mile study area includes the part of the park in Lower Providence and West Norriton Townships in Montgomery County, Pa., and surrounding vicinity. The park is underlain by sedimentary rocks of the Upper Triassic age stockton Formation. A potentiometric-surface map constructed from water levels measured in 59 wells shows a cone of depression, approximately 0.5 mile in diameter, centered near the CSG Site. The cone of depression is caused by the pumping of six public supply wells. A ground-water divide between the cone of depression and Valley Forge National Historical Park provides a hydraulic barrier to the flow of ground water and contaminants from the CSG Site to the park. If pumping in the cone of depression was to cease, water levels would recover, and the ground-water divide would shift to the north. A hydraulic gradient between the CSG Site and the Schuylkill River would be established, causing contaminated ground water to flow to the park.Water samples were collected from 12 wells within the park boundary and 9 wells between the park boundary and the ground-water divide to the north of the park. All water samples were analyzed for physical properties (field determinations), nutrients, common ions, metals and other trace constituents, and VOC's. Water samples from the 12 wells inside the park boundary also were analyzed for pesticides. Concentrations of inorganic constituents in the water samples did not exceed U.S. Environmental Protection Agency maximum contaminant levels. Very low concentrations of organic compounds were detected in some of the water samples. VOC's were detected in water from 76 percent of the wells sampled; the maximum concentration detected was 5.8 micrograms per liter of chloroform. The most commonly detected VOC was chloroform. The second most commonly detected compound was methyl tert-butyl ether (MTBE), which was detected in water from 24 percent of wells sampled. Several pesticides were detected in water samples collected from within the park boundaries.: chlordane, DDD, dieldrin, endrin, heptachlor epoxide, and simazine. Concentrations of the detected pesticides were 0.1 micrograms per liter or less and did not exceed U.S. Environmental Protection Agency maximum contaminant levels.

The polyphenolic profiles of common bean (Phaseolus vulgaris L.).

PubMed

Lin, Long-Ze; Harnly, James M; Pastor-Corrales, Marcial S; Luthria, Devanand L

2008-03-01

Based on the phenolic profiles obtained by high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-DAD-ESI/MS), 24 common bean samples, representing 17 varieties and 7 generic off-the-shelf items, belonging to ten US commercial market classes can be organized into six different groups. All of them contained the same hydroxycinnaminic acids, but the flavonoid components showed distinct differences. Black beans contained primarily the 3- O -glucosides of delphinidin, petunidin and malvidin, while pinto beans contained kaempferol and its 3- O -glycosides. Light red kidney bean contained traces of quercetin 3- O -glucoside and its malonates, but pink and dark red kidney beans contained the diglycosides of quercetin and kaempferol. Small red beans contained kaempferol 3- O -glucoside and pelargonidin 3- O -glucoside, while no flavonoids were detected in alubia, cranberry, great northern, and navy beans. This is the first report of the tentative identification of quercetin 3- O -pentosylhexoside and flavonoid glucoside malonates, and the first detailed detection of hydroxycinnamates, in common beans.

Wetland occupancy of pond-breeding amphibians in Yosemite National Park, USA

USGS Publications Warehouse

Fellers, Gary M.; Kleeman, Patrick M.; Miller, David A.W.

2015-01-01

We estimated wetland occupancy and population trends for three species of pond-breeding anurans in Yosemite National Park from 2007-2011. We used a double survey technique in which two observers independently surveyed each site on the same day. Double surveys allowed us to calculate detectability for the three most common anurans within the park: Rana sierrae, Anaxyrus canorus, and Pseudacris regilla. Annual estimates of detectability were generally high; mean detectability ranged from 73.7% + 0.6 (SE) for any life history stage of A. canorus to 86.7% + 0.7 for sites with P. regilla reproduction (eggs or larvae present). Detectability was most variable for Anaxyrus canorus, which ranged from 45.9% to 99.7%. The probability of occupancy for R. sierrae was highest in larger, low-elevation wetlands that lacked fish. Anaxyrus canorus were more common in shallow high-elevation ponds; their occurrence was minimally impacted by the presence of fish. Finally, occurrence of P. regilla was largely unrelated to wetland size and elevation, but like R. sierrae, they were less likely to occupy sites with fi sh. Occupancy showed no trend over the five years of our study for R. sierrae or A. canorus when considering either sites with any life stage or only sites with reproduction. However, P. regilla showed a modest downward trend for sites with any life stage and sites with reproduction. Our results for R. sierrae run counter to expectations given recent concern about the decline of this species, while our findings for P. regilla raise concerns for this widespread and generally common species.

The subgingival microbiota of Papillon-Lefèvre syndrome.

PubMed

Albandar, Jasim M; Khattab, Razan; Monem, Fawza; Barbuto, Sara M; Paster, Bruce J

2012-07-01

There is little information about the microbiologic profiles of periodontal lesions in Papillon-Lefèvre syndrome (PLS) and the significance of bacteria in the pathogenesis of periodontitis in these patients. This comprehensive analysis of the subgingival microbiota in patients with PLS used 16S ribosomal RNA (rRNA) clonal analysis and the 16S rRNA-based Human Oral Microbe Identification Microarray (HOMIM). Thirteen patients with PLS from seven unrelated families volunteered for this microbiologic study. Subgingival plaque was collected with sterile paper points from multiple sites with ≥5 mm probing depth, and whole genomic DNA was extracted. The 16S rRNA genes were amplified, cloned, and sequenced. The samples were then probed for ≈300 predominant oral bacterial species using the HOMIM. The most commonly detected phylotypes in the clonal analysis were Gemella morbillorum, Gemella haemolysans, Granulicatella adiacens, Lachnospiraceae OT 100 (EI074), Parvimonas micra, Selenomonas noxia, and Veillonella parvula. As a group, streptococci were commonly detected in these individuals. In the HOMIM analysis, a total of 170 bacterial species/phylotypes were detected, with a range of 40 to 80 species per patient with PLS. Of these, 12 bacterial species were detected in medium to high levels in ≥50% of the individuals. The high-frequency strains were clustered into eight groups: Aggregatibacter actinomycetemcomitans, Campylobacter spp., Capnocytophaga granulosa, G. morbillorum, P. micra, Porphyromonas endodontalis, Streptococcus spp., and Tannerella forsythia. The subgingival microbiota in PLS is diverse. Periodontal pathogens commonly associated with chronic and aggressive periodontitis and opportunistic pathogens may be associated with the development of severe periodontitis in patients with PLS.

Technological advances in diagnostic testing for von Willebrand disease: new approaches and challenges.

PubMed

Hayward, C P M; Moffat, K A; Graf, L

2014-06-01

Diagnostic tests for von Willebrand disease (VWD) are important for the assessment of VWD, which is a commonly encountered bleeding disorder worldwide. Technical innovations have been applied to improve the precision and lower limit of detection of von Willebrand factor (VWF) assays, including the ristocetin cofactor activity assay (VWF:RCo) that uses the antibiotic ristocetin to induce plasma VWF binding to glycoprotein (GP) IbIXV on target platelets. VWF-collagen-binding assays, depending on the type of collagen used, can improve the detection of forms of VWD with high molecular weight VWF multimer loss, although the best method is debatable. A number of innovations have been applied to VWF:RCo (which is commonly performed on an aggregometer), including replacing the target platelets with immobilized GPIbα, and quantification by an enzyme-linked immunosorbent assay (ELISA), immunoturbidimetric, or chemiluminescent end-point. Some common polymorphisms in the VWF gene that do not cause bleeding are associated with falsely low VWF activity by ristocetin-dependent methods. To overcome the need for ristocetin, some new VWF activity assays use gain-of-function GPIbα mutants that bind VWF without the need for ristocetin, with an improved precision and lower limit of detection than measuring VWF:RCo by aggregometry. ELISA of VWF binding to mutated GPIbα shows promise as a method to identify gain-of-function defects from type 2B VWD. The performance characteristics of many new VWF activity assays suggest that the detection of VWD, and monitoring of VWD therapy, by clinical laboratories could be improved through adopting newer generation VWF assays. © 2014 John Wiley & Sons Ltd.

Rapid on-site detection of ephedrine and its analogues used as adulterants in slimming dietary supplements by TLC-SERS.

PubMed

Lv, Diya; Cao, Yan; Lou, Ziyang; Li, Shujin; Chen, Xiaofei; Chai, Yifeng; Lu, Feng

2015-02-01

Ephedrine and its analogues are in the list of prohibited substance in adulteration to botanical dietary supplements (BDS) for their uncontrollable stimulating side effects. However, they were always adulterated illegally in BDS to promote losing weight. In order to avoid detection, various kinds of ephedrine analogues were added rather than ephedrine itself. This has brought about great difficulties in authentication of BDS. In this study, we put forward for the first time a method which combined thin-layer chromatography (TLC) and surface-enhanced Raman scattering (SERS) to directly identify trace adulterant. Ephedrine, pseudoephedrine, methylephedrine, and norephedrine were mixed and used in this method to develop an analytical model. As a result, the four analogues were separated efficiently in TLC analysis, and trace-components and low-background SERS detection was realized. The limit of detection (LOD) of the four analogues was 0.01 mg/mL. Eight common Raman peaks (△υ = 620, 1003, 1030, 1159, 1181, 1205, 1454, 1603 cm(-1)) were extracted experimentally and statistically to characterize the common feature of ephedrine analogues. A TLC-SERS method coupled with common-peak model was adopted to examine nine practical samples, two of which were found to be adulterated with ephedrine analogues. Identification results were then confirmed by UPLC-QTOF/MS analysis. The proposed method was simple, rapid, and accurate and can also be employed to trace adulterant identification even when there are no available reference derivatives on-site or unknown types of ephedrine analogues are adulterated.

Two-stage Keypoint Detection Scheme for Region Duplication Forgery Detection in Digital Images.

PubMed

Emam, Mahmoud; Han, Qi; Zhang, Hongli

2018-01-01

In digital image forensics, copy-move or region duplication forgery detection became a vital research topic recently. Most of the existing keypoint-based forgery detection methods fail to detect the forgery in the smooth regions, rather than its sensitivity to geometric changes. To solve these problems and detect points which cover all the regions, we proposed two steps for keypoint detection. First, we employed the scale-invariant feature operator to detect the spatially distributed keypoints from the textured regions. Second, the keypoints from the missing regions are detected using Harris corner detector with nonmaximal suppression to evenly distribute the detected keypoints. To improve the matching performance, local feature points are described using Multi-support Region Order-based Gradient Histogram descriptor. Based on precision-recall rates and commonly tested dataset, comprehensive performance evaluation is performed. The results demonstrated that the proposed scheme has better detection and robustness against some geometric transformation attacks compared with state-of-the-art methods. © 2017 American Academy of Forensic Sciences.

A novel functional class 2 integron in clinical Proteus mirabilis isolates.

PubMed

Wei, Quhao; Hu, Qingfeng; Li, Shanshan; Lu, Huoyang; Chen, Guoqiang; Shen, Beiqiong; Zhang, Ping; Zhou, Yonglie

2014-04-01

To describe a novel functional class 2 integron that was found in clinical Proteus mirabilis isolates. Class 1 and 2 integrons were screened by PCR in 153 clinical Proteus isolates. The variable regions of class 1 and 2 integrons were determined by restriction analysis and sequencing. The mutations of internal stop codons in class 2 integrons and their common promoters were also determined by sequencing. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used to analyse the phylogenetic relations of class 2 integron-positive P. mirabilis isolates. Class 1 integrons were detected in 96 (63%) of 153 Proteus isolates: eight different gene cassette arrays were detected, including dfrA32-ereA1-aadA2, which was detected for the first time in P. mirabilis. Class 2 integrons were detected in 101 (66%) of 153 Proteus isolates: four different gene cassette arrays were detected, including dfrA1-catB2-sat2-aadA1, which was detected for the first time in a class 2 integron. A novel functional class 2 integron was detected in 38 P. mirabilis isolates with a common promoter (-35 TTTAAT|16 bp|-10 TAAAGT). The variable region of this functional class 2 integron contained dfrA14 and three novel open reading frames with unknown functions. Very similar ERIC-PCR fingerprinting patterns were detected in these 38 P. mirabilis isolates and were different from other class 2 integron-positive isolates. A novel functional class 2 integron was found for the first time in P. mirabilis. These functional class 2 integron-harbouring P. mirabilis isolates were likely to be clonally spread in our hospital.

Evaluation of a statewide foodborne illness complaint surveillance system in Minnesota, 2000 through 2006.

PubMed

Li, John; Smith, Kirk; Kaehler, Dawn; Everstine, Karen; Rounds, Josh; Hedberg, Craig

2010-11-01

Foodborne outbreaks are detected by recognition of similar illnesses among persons with a common exposure or by identification of case clusters through pathogen-specific surveillance. PulseNet USA has created a national framework for pathogen-specific surveillance, but no comparable effort has been made to improve surveillance of consumer complaints of suspected foodborne illness. The purpose of this study was to characterize the complaint surveillance system in Minnesota and to evaluate its use for detecting outbreaks. Minnesota Department of Health foodborne illness surveillance data from 2000 through 2006 were analyzed for this study. During this period, consumer complaint surveillance led to detection of 79% of confirmed foodborne outbreaks. Most norovirus infection outbreaks were detected through complaints. Complaint surveillance also directly led or contributed to detection of 25% of salmonellosis outbreaks. Eighty-one percent of complainants did not seek medical attention. The number of ill persons in a complainant's party was significantly associated with a complaint ultimately resulting in identification of a foodborne outbreak. Outbreak confirmation was related to a complainant's ability to identify a common exposure and was likely related to the process by which the Minnesota Department of Health chooses complaints to investigate. A significant difference (P < 0.001) was found in incubation periods between complaints that were outbreak associated (median, 27 h) and those that were not outbreak associated (median, 6 h). Complaint systems can be used to detect outbreaks caused by a variety of pathogens. Case detection for foodborne disease surveillance in Minnesota happens through a multitude of mechanisms. The ability to integrate these mechanisms and carry out rapid investigations leads to improved outbreak detection.

Towards a Video Passive Content Fingerprinting Method for Partial-Copy Detection Robust against Non-Simulated Attacks

PubMed Central

2016-01-01

Passive content fingerprinting is widely used for video content identification and monitoring. However, many challenges remain unsolved especially for partial-copies detection. The main challenge is to find the right balance between the computational cost of fingerprint extraction and fingerprint dimension, without compromising detection performance against various attacks (robustness). Fast video detection performance is desirable in several modern applications, for instance, in those where video detection involves the use of large video databases or in applications requiring real-time video detection of partial copies, a process whose difficulty increases when videos suffer severe transformations. In this context, conventional fingerprinting methods are not fully suitable to cope with the attacks and transformations mentioned before, either because the robustness of these methods is not enough or because their execution time is very high, where the time bottleneck is commonly found in the fingerprint extraction and matching operations. Motivated by these issues, in this work we propose a content fingerprinting method based on the extraction of a set of independent binary global and local fingerprints. Although these features are robust against common video transformations, their combination is more discriminant against severe video transformations such as signal processing attacks, geometric transformations and temporal and spatial desynchronization. Additionally, we use an efficient multilevel filtering system accelerating the processes of fingerprint extraction and matching. This multilevel filtering system helps to rapidly identify potential similar video copies upon which the fingerprint process is carried out only, thus saving computational time. We tested with datasets of real copied videos, and the results show how our method outperforms state-of-the-art methods regarding detection scores. Furthermore, the granularity of our method makes it suitable for partial-copy detection; that is, by processing only short segments of 1 second length. PMID:27861492

[Trend survey of ocular infections with bacteria at Toyama University Hospital over the past six years--from the standpoint of laboratory examination].

PubMed

Kubota, Tomomi; Hayashi, Shirou; Niimi, Hideki; Kitajima, Isao

2012-07-01

Specimens of bacterial ocular infections are frequently received in the clinical laboratory. However, a comprehensive trend survey of ocular infections with bacteria is very rare. Our objective is to understand the current tendency of ocular infections with bacteria in patients at Toyama University Hospital from the standpoint of laboratory examination. We studied 263 cases of ocular infection with bacteria diagnosed at Toyama University Hospital from January 2006 to December 2011. 123 were male and 140 were female, with a mean age of 61.2(0-98) years. Specimens were subjected to direct microscopy and culture. Cultures were positive in 174(66.2%) patients. The most common bacterial isolate was Staphylococcus (28.1%), followed by Corynebacterium (19.3%), Streptococcus (9.3%), and Propionibacterium (8.6%). MRSA accounted for 18.8% of all S. aureus isolates, and has increased in recent years. The number of bacteria detected was larger in March, June, July, August, and October. Age distribution indicated that around 70% of bacterial isolates were detected from patients over 60 years old. The most common specimen of ocular infections with bacteria was eye discharge (detection rate; 87.8%), followed by corneal scraping(41%), aqueous humor (19%), and vitreous body (27%). Nearly 80% of bacterial isolates were detected from patients with keratitis, endophthalmitis, dacryocystitis, and conjunctivitis. As for the disease specific detection rate, endophthalmitis was very low (38.3%). The detection rate by years indicated that the way doctors pick up the specimens greatly affects the detection rate. Based on this survey, we need close cooperation with medical doctors concerning laboratory examination in ocular infection with bacteria, and we must improve the detection sensitivity of specimens from patients with endophthalmitis.

The ground truth about metadata and community detection in networks

PubMed Central

Peel, Leto; Larremore, Daniel B.; Clauset, Aaron

2017-01-01

Across many scientific domains, there is a common need to automatically extract a simplified view or coarse-graining of how a complex system’s components interact. This general task is called community detection in networks and is analogous to searching for clusters in independent vector data. It is common to evaluate the performance of community detection algorithms by their ability to find so-called ground truth communities. This works well in synthetic networks with planted communities because these networks’ links are formed explicitly based on those known communities. However, there are no planted communities in real-world networks. Instead, it is standard practice to treat some observed discrete-valued node attributes, or metadata, as ground truth. We show that metadata are not the same as ground truth and that treating them as such induces severe theoretical and practical problems. We prove that no algorithm can uniquely solve community detection, and we prove a general No Free Lunch theorem for community detection, which implies that there can be no algorithm that is optimal for all possible community detection tasks. However, community detection remains a powerful tool and node metadata still have value, so a careful exploration of their relationship with network structure can yield insights of genuine worth. We illustrate this point by introducing two statistical techniques that can quantify the relationship between metadata and community structure for a broad class of models. We demonstrate these techniques using both synthetic and real-world networks, and for multiple types of metadata and community structures. PMID:28508065

Portable ceria nanoparticle-based assay for rapid detection of food antioxidants (NanoCerac)

PubMed Central

Sharpe, Erica; Frasco, Thalia; Andreescu, Daniel; Andreescu, Silvana

2012-01-01

With increased awareness of nutrition and the advocacy for healthier food choices, there exists a great demand for a simple, easy-to-use test that can reliably measure the antioxidant capacity of dietary products. We report development and characterization of a portable nanoparticle based-assay, similar to a small sensor patch, for rapid and sensitive detection of food antioxidants. The assay is based on the use of immobilized ceria nanoparticles, which change color after interaction with antioxidants by means of redox and surface chemistry reactions. Monitoring corresponding optical changes enables sensitive detection of antioxidants in which the nanoceria provides an optical ‘signature’ of antioxidant power, while the antioxidants act as reducing agents. The sensor has been tested for the detection of common antioxidant compounds including ascorbic acid, gallic acid, vanilic acid, quercetin, caffeic acid, and epigallocatechin gallate and its function has been successfully applied for the assessment of antioxidant activity in real samples (teas and medicinal mushrooms). The colorimetric response was concentration dependent, with detection limits ranging from 20–400 μM depending on the antioxidant involved. Steady-state color intensity was achieved within seconds upon addition of antioxidants. The results are presented in terms of Gallic Acid Equivalents (GAE). The sensor performed favorably when compared with commonly used antioxidant detection methods. This assay is particularly appealing for remote sensing applications, where specialized equipment is not available, and also for high throughput analysis of a large number of samples. Potential applications for antioxidant detection in remote locations are envisioned. PMID:23139929

A Short Interspersed Nuclear Element (SINE)-Based Real-Time PCR Approach to Detect and Quantify Porcine Component in Meat Products.

PubMed

Zhang, Chi; Fang, Xin; Qiu, Haopu; Li, Ning

2015-01-01

Real-time PCR amplification of mitochondria gene could not be used for DNA quantification, and that of single copy DNA did not allow an ideal sensitivity. Moreover, cross-reactions among similar species were commonly observed in the published methods amplifying repetitive sequence, which hindered their further application. The purpose of this study was to establish a short interspersed nuclear element (SINE)-based real-time PCR approach having high specificity for species detection that could be used in DNA quantification. After massive screening of candidate Sus scrofa SINEs, one optimal combination of primers and probe was selected, which had no cross-reaction with other common meat species. LOD of the method was 44 fg DNA/reaction. Further, quantification tests showed this approach was practical in DNA estimation without tissue variance. Thus, this study provided a new tool for qualitative detection of porcine component, which could be promising in the QC of meat products.

Measurement technology of RF interference current in high current system

NASA Astrophysics Data System (ADS)

Zhao, Zhihua; Li, Jianxuan; Zhang, Xiangming; Zhang, Lei

2018-06-01

Current probe is a detection method commonly used in electromagnetic compatibility. With the development of power electronics technology, the power level of power conversion devices is constantly increasing, and the power current of the electric energy conversion device in the electromagnetic launch system can reach 10kA. Current probe conventionally used in EMC (electromagnetic compatibility) detection cannot meet the test requirements on high current system due to the magnetic saturation problem. The conventional high current sensor is also not suitable for the RF (Radio Frequency) interference current measurement in high current power device due to the high noise level in the output of active amplifier. In this paper, a passive flexible current probe based on Rogowski coil and matching resistance is proposed that can withstand high current and has low noise level, to solve the measurement problems of interference current in high current power converter. And both differential mode and common mode current detection can be easily carried out with the proposed probe because of the probe's flexible structure.

Memory and the Moses illusion: failures to detect contradictions with stored knowledge yield negative memorial consequences.

PubMed

Bottoms, Hayden C; Eslick, Andrea N; Marsh, Elizabeth J

2010-08-01

Although contradictions with stored knowledge are common in daily life, people often fail to notice them. For example, in the Moses illusion, participants fail to notice errors in questions such as "How many animals of each kind did Moses take on the Ark?" despite later showing knowledge that the Biblical reference is to Noah, not Moses. We examined whether error prevalence affected participants' ability to detect distortions in questions, and whether this in turn had memorial consequences. Many of the errors were overlooked, but participants were better able to catch them when they were more common. More generally, the failure to detect errors had negative memorial consequences, increasing the likelihood that the errors were used to answer later general knowledge questions. Methodological implications of this finding are discussed, as it suggests that typical analyses likely underestimate the size of the Moses illusion. Overall, answering distorted questions can yield errors in the knowledge base; most importantly, prior knowledge does not protect against these negative memorial consequences.

The Role of 3 Tesla MRA in the Detection of Intracranial Aneurysms

PubMed Central

Kapsalaki, Eftychia Z.; Rountas, Christos D.; Fountas, Kostas N.

2012-01-01

Intracranial aneurysms constitute a common pathological entity, affecting approximately 1–8% of the general population. Their early detection is essential for their prompt treatment. Digital subtraction angiography is considered the imaging method of choice. However, other noninvasive methodologies such as CTA and MRA have been employed in the investigation of patients with suspected aneurysms. MRA is a noninvasive angiographic modality requiring no radiation exposure. However, its sensitivity and diagnostic accuracy were initially inadequate. Several MRA techniques have been developed for overcoming all these drawbacks and for improving its sensitivity. 3D TOF MRA and contrast-enhanced MRA are the most commonly employed techniques. The introduction of 3 T magnetic field further increased MRA's sensitivity, allowing detection of aneurysms smaller than 3 mm. The development of newer MRA techniques may provide valuable information regarding the flow characteristics of an aneurysm. Meticulous knowledge of MRA's limitations and pitfalls is of paramount importance for avoiding any erroneous interpretation of its findings. PMID:22292121

Detection of capacity imbalance in vanadium electrolyte and its electrochemical regeneration for all-vanadium redox-flow batteries

NASA Astrophysics Data System (ADS)

Roznyatovskaya, Nataliya; Herr, Tatjana; Küttinger, Michael; Fühl, Matthias; Noack, Jens; Pinkwart, Karsten; Tübke, Jens

2016-01-01

A vanadium electrolyte for redox-flow batteries (VRFB) with different VIII and VIV mole fractions has been studied by UV-vis spectroscopy. Spectrophotometric detection enables a rough estimate of the VIV and VIII content, which can be used to detect an electrolyte capacity imbalance, i.e. a deviation in the mole fraction of VIV or VIII away from 50%. The isosbestic point at 600 nm can be used as a reference point in the analysis of common VRFB electrolyte batches. The VRFB electrolyte is observed to have an imbalance after prolonged storage (a couple of years) in a tank under ambient conditions. A regeneration procedure, which involves pre-charging the unbalanced electrolyte and mixing part of it with a portion of initial unbalanced electrolyte, has been tested. The resulting rebalanced electrolyte has been compared with a common electrolyte in a charge-discharge cell test and is shown to be suitable for cell operation.

Individual differences in rate of encoding predict estimates of visual short-term memory capacity (K).

PubMed

Jannati, Ali; McDonald, John J; Di Lollo, Vincent

2015-06-01

The capacity of visual short-term memory (VSTM) is commonly estimated by K scores obtained with a change-detection task. Contrary to common belief, K may be influenced not only by capacity but also by the rate at which stimuli are encoded into VSTM. Experiment 1 showed that, contrary to earlier conclusions, estimates of VSTM capacity obtained with a change-detection task are constrained by temporal limitations. In Experiment 2, we used change-detection and backward-masking tasks to obtain separate within-subject estimates of K and of rate of encoding, respectively. A median split based on rate of encoding revealed significantly higher K estimates for fast encoders. Moreover, a significant correlation was found between K and the estimated rate of encoding. The present findings raise the prospect that the reported relationships between K and such cognitive concepts as fluid intelligence may be mediated not only by VSTM capacity but also by rate of encoding. (c) 2015 APA, all rights reserved).

Machine Learning for Detecting Gene-Gene Interactions

PubMed Central

McKinney, Brett A.; Reif, David M.; Ritchie, Marylyn D.; Moore, Jason H.

2011-01-01

Complex interactions among genes and environmental factors are known to play a role in common human disease aetiology. There is a growing body of evidence to suggest that complex interactions are ‘the norm’ and, rather than amounting to a small perturbation to classical Mendelian genetics, interactions may be the predominant effect. Traditional statistical methods are not well suited for detecting such interactions, especially when the data are high dimensional (many attributes or independent variables) or when interactions occur between more than two polymorphisms. In this review, we discuss machine-learning models and algorithms for identifying and characterising susceptibility genes in common, complex, multifactorial human diseases. We focus on the following machine-learning methods that have been used to detect gene-gene interactions: neural networks, cellular automata, random forests, and multifactor dimensionality reduction. We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics. PMID:16722772

Detection and Heterogeneity of Herpesviruses Causing Pacheco's Disease in Parrots

PubMed Central

Tomaszewski, Elizabeth; Wilson, Van G.; Wigle, William L.; Phalen, David N.

2001-01-01

Pacheco's disease (PD) is a common, often fatal, disease of parrots. We cloned a virus isolate from a parrot that had characteristic lesions of PD. Three viral clones were partially sequenced, demonstrating that this virus was an alphaherpesvirus most closely related to the gallid herpesvirus 1. Five primer sets were developed from these sequences. The primer sets were used with PCR to screen tissues or tissue culture media suspected to contain viruses from 54 outbreaks of PD. The primer sets amplified DNA from all but one sample. Ten amplification patterns were detected, indicating that PD is caused by a genetically heterogeneous population of viruses. A single genetic variant (psittacid herpesvirus variant 1) amplified with all primer sets and was the most common virus variant (62.7%). A single primer set (23F) amplified DNA from all of the positive samples, suggesting that PCR could be used as a rapid postmortem assay for these viruses. PCR was found to be significantly more sensitive than tissue culture for the detection of psittacid herpesviruses. PMID:11158102

Proteomic Characterization and Comparison of Malaysian Tropidolaemus wagleri and Cryptelytrops purpureomaculatus Venom Using Shotgun-Proteomics.

PubMed

Zainal Abidin, Syafiq Asnawi; Rajadurai, Pathmanathan; Chowdhury, Md Ezharul Hoque; Ahmad Rusmili, Muhamad Rusdi; Othman, Iekhsan; Naidu, Rakesh

2016-10-18

Tropidolaemus wagleri and Cryptelytrops purpureomaculatus are venomous pit viper species commonly found in Malaysia. Tandem mass spectrometry analysis of the crude venoms has detected different proteins in T. wagleri and C. purpureomaculatus . They were classified into 13 venom protein families consisting of enzymatic and nonenzymatic proteins. Enzymatic families detected in T. wagleri and C. purpureomaculatus venom were snake venom metalloproteinase, phospholipase A₂, ʟ-amino acid oxidase, serine proteases, 5'-nucleotidase, phosphodiesterase, and phospholipase B. In addition, glutaminyl cyclotransferase was detected in C. purpureomaculatus . C-type lectin-like proteins were common nonenzymatic components in both species. Waglerin was present and unique to T. wagleri -it was not in C. purpureomaculatus venom. In contrast, cysteine-rich secretory protein, bradykinin-potentiating peptide, and C-type natriuretic peptide were present in C. purpureomaculatus venom. Composition of the venom proteome of T. wagleri and C. purpureomaculatus provides useful information to guide production of effective antivenom and identification of proteins with potential therapeutic applications.

Proteomic Characterization and Comparison of Malaysian Tropidolaemus wagleri and Cryptelytrops purpureomaculatus Venom Using Shotgun-Proteomics

PubMed Central

Zainal Abidin, Syafiq Asnawi; Rajadurai, Pathmanathan; Chowdhury, Md Ezharul Hoque; Ahmad Rusmili, Muhamad Rusdi; Othman, Iekhsan; Naidu, Rakesh

2016-01-01

Tropidolaemus wagleri and Cryptelytrops purpureomaculatus are venomous pit viper species commonly found in Malaysia. Tandem mass spectrometry analysis of the crude venoms has detected different proteins in T. wagleri and C. purpureomaculatus. They were classified into 13 venom protein families consisting of enzymatic and nonenzymatic proteins. Enzymatic families detected in T. wagleri and C. purpureomaculatus venom were snake venom metalloproteinase, phospholipase A2, l-amino acid oxidase, serine proteases, 5′-nucleotidase, phosphodiesterase, and phospholipase B. In addition, glutaminyl cyclotransferase was detected in C. purpureomaculatus. C-type lectin-like proteins were common nonenzymatic components in both species. Waglerin was present and unique to T. wagleri—it was not in C. purpureomaculatus venom. In contrast, cysteine-rich secretory protein, bradykinin-potentiating peptide, and C-type natriuretic peptide were present in C. purpureomaculatus venom. Composition of the venom proteome of T. wagleri and C. purpureomaculatus provides useful information to guide production of effective antivenom and identification of proteins with potential therapeutic applications. PMID:27763534

Visual attention distracter insertion for improved EEG rapid serial visual presentation (RSVP) target stimuli detection

NASA Astrophysics Data System (ADS)

Khosla, Deepak; Huber, David J.; Martin, Kevin

2017-05-01

This paper† describes a technique in which we improve upon the prior performance of the Rapid Serial Visual Presentation (RSVP) EEG paradigm for image classification though the insertion of visual attention distracters and overall sequence reordering based upon the expected ratio of rare to common "events" in the environment and operational context. Inserting distracter images maintains the ratio of common events to rare events at an ideal level, maximizing the rare event detection via P300 EEG response to the RSVP stimuli. The method has two steps: first, we compute the optimal number of distracters needed for an RSVP stimuli based on the desired sequence length and expected number of targets and insert the distracters into the RSVP sequence, and then we reorder the RSVP sequence to maximize P300 detection. We show that by reducing the ratio of target events to nontarget events using this method, we can allow RSVP sequences with more targets without sacrificing area under the ROC curve (azimuth).

Acquired resistance and clonal evolution in melanoma during BRAF inhibitor therapy

PubMed Central

Kong, Xiangju; Hong, Aayoung; Koya, Richard C.; Moriceau, Gatien; Chodon, Thinle; Guo, Rongqing; Johnson, Douglas B.; Dahlman, Kimberly B.; Kelley, Mark C.; Kefford, Richard F.; Chmielowski, Bartosz; Glaspy, John A.; Sosman, Jeffrey A.; van Baren, Nicolas; Long, Georgina V.; Ribas, Antoni; Lo, Roger S.

2013-01-01

BRAF inhibitors elicit rapid anti-tumor responses in the majority of patients with V600BRAF mutant melanoma, but acquired drug resistance is almost universal. We sought to identify the core resistance pathways and the extent of tumor heterogeneity during disease progression. We show that MAPK reactivation mechanisms were detected among 70% of disease-progressive tissues, with RAS mutations, mutant BRAF amplification and alternative splicing being most common. We also detected PI3K-PTEN-AKT-upregulating genetic alterations among 22% of progressive melanomas. Distinct molecular lesions, in both core drug escape pathways, were commonly detected concurrently in the same tumor or among multiple tumors from the same patient. Beyond harboring extensively heterogeneous resistance mechanisms, melanoma re-growth emerging from BRAF inhibitor selection displayed branched evolution marked by altered mutational spectra/signatures and increased fitness. Thus, melanoma genomic heterogeneity contributes significantly to BRAF inhibitor treatment failure, implying upfront, co-targeting of two core pathways as an essential strategy for durable responses. PMID:24265155

Artificial neural networks in mammography interpretation and diagnostic decision making.

PubMed

Ayer, Turgay; Chen, Qiushi; Burnside, Elizabeth S

2013-01-01

Screening mammography is the most effective means for early detection of breast cancer. Although general rules for discriminating malignant and benign lesions exist, radiologists are unable to perfectly detect and classify all lesions as malignant and benign, for many reasons which include, but are not limited to, overlap of features that distinguish malignancy, difficulty in estimating disease risk, and variability in recommended management. When predictive variables are numerous and interact, ad hoc decision making strategies based on experience and memory may lead to systematic errors and variability in practice. The integration of computer models to help radiologists increase the accuracy of mammography examinations in diagnostic decision making has gained increasing attention in the last two decades. In this study, we provide an overview of one of the most commonly used models, artificial neural networks (ANNs), in mammography interpretation and diagnostic decision making and discuss important features in mammography interpretation. We conclude by discussing several common limitations of existing research on ANN-based detection and diagnostic models and provide possible future research directions.

Light without substrate amendment: the bacterial luciferase gene cassette as a mammalian bioreporter

NASA Astrophysics Data System (ADS)

Close, Dan M.; Xu, Tingting; Smartt, Abby E.; Jegier, Pat; Ripp, Steven A.; Sayler, Gary S.

2011-06-01

Bioluminescent production represents a facile method for bioreporter detection in mammalian tissues. The lack of endogenous bioluminescent reactions in these tissues allows for high signal to noise ratios even at low signal strength compared to fluorescent signal detection. While the luciferase enzymes commonly employed for bioluminescent detection are those from class Insecta (firefly and click beetle luciferases), these are handicapped in that they require concurrent administration of a luciferin compound to elicit a bioluminescent signal. The bacterial luciferase (lux) gene cassette offers the advantages common to other bioluminescent proteins, but is simultaneously capable of synthesizing its own luciferin substrates using endogenously available cellular compounds. The longstanding shortcoming of the lux cassette has been its recalcitrance to function in the mammalian cellular environment. This paper will present an overview of the work completed to date to overcome this limitation and provide examples of mammalian lux-based bioreporter technologies that could provide the framework for advanced, biomedically relevant real-time sensor development.

Radiation resistance of biological reagents for in situ life detection.

PubMed

Carr, Christopher E; Rowedder, Holli; Vafadari, Cyrus; Lui, Clarissa S; Cascio, Ethan; Zuber, Maria T; Ruvkun, Gary

2013-01-01

Life on Mars, if it exists, may share a common ancestry with life on Earth derived from meteoritic transfer of microbes between the planets. One means to test this hypothesis is to isolate, detect, and sequence nucleic acids in situ on Mars, then search for similarities to known common features of life on Earth. Such an instrument would require biological and chemical components, such as polymerase and fluorescent dye molecules. We show that reagents necessary for detection and sequencing of DNA survive several analogues of the radiation expected during a 2-year mission to Mars, including proton (H-1), heavy ion (Fe-56, O-18), and neutron bombardment. Some reagents have reduced performance or fail at higher doses. Overall, our findings suggest it is feasible to utilize space instruments with biological components, particularly for mission durations of up to several years in environments without large accumulations of charged particles, such as the surface of Mars, and have implications for the meteoritic transfer of microbes between planets.

Fabricating data: How substituting values for nondetects can ruin results, and what can be done about it

USGS Publications Warehouse

Helsel, D.R.

2006-01-01

The most commonly used method in environmental chemistry to deal with values below detection limits is to substitute a fraction of the detection limit for each nondetect. Two decades of research has shown that this fabrication of values produces poor estimates of statistics, and commonly obscures patterns and trends in the data. Papers using substitution may conclude that significant differences, correlations, and regression relationships do not exist, when in fact they do. The reverse may also be true. Fortunately, good alternative methods for dealing with nondetects already exist, and are summarized here with references to original sources. Substituting values for nondetects should be used rarely, and should generally be considered unacceptable in scientific research. There are better ways.

Advances in soil gas geochemical exploration for natural resources: Some current examples and practices

NASA Astrophysics Data System (ADS)

McCarthy, J. Howard, Jr.; Reimer, G. Michael

1986-11-01

Field studies have demonstrated that gas anomalies are found over buried mineral deposits. Abnormally high concentrations of sulfur gases and carbon dioxide and abnormally low concentrations of oxygen are commonly found over sulfide ore deposits. Helium anomalies are commonly associated with uranium deposits and geothermal areas. Helium and hydrocarbon gas anomalies have been detected over oil and gas deposits. Gases are sampled by extracting them from the pore space of soil, by degassing soil or rock, or by adsorbing them on artificial collectors. The two most widely used techniques for gas analysis are gas chromatography and mass spectrometry. The detection of gas anomalies at or near the surface may be an effective method to locate buried mineral deposits.

Sports-related injury of the pediatric spine.

PubMed

Maxfield, Bradley A

2010-11-01

Acute spinal injuries are fortunately rare in pediatric sports but can be catastrophic. Imaging is integral to the diagnosis and care of spinal trauma. Plain radiographs and CT are critical for detecting vertebral fracture, and MR imaging is an essential adjunct for evaluating muscular, ligamentous, and spinal cord injury. Back pain is a common complaint among athletes of all ages. The growing spine has unique weaknesses that result in a higher rate of detectable radiologic abnormalities. Disk pathology is less common in children, and is often uniquely associated with fracture of the ring apophyses. Spondylolysis is far more prevalent in youth athletes than in their adult counterparts, requiring a different approach to imaging for assessment of adolescent back pain. Copyright © 2010 Elsevier Inc. All rights reserved.

Detection of Intestinal Protozoa in the Clinical Laboratory

PubMed Central

McHardy, Ian H.; Wu, Max; Shimizu-Cohen, Robyn; Couturier, Marc Roger

2014-01-01

Despite recent advances in diagnostic technology, microscopic examination of stool specimens remains central to the diagnosis of most pathogenic intestinal protozoa. Microscopy is, however, labor-intensive and requires a skilled technologist. New, highly sensitive diagnostic methods have been developed for protozoa endemic to developed countries, including Giardia lamblia (syn. G. intestinalis/G. duodenalis) and Cryptosporidium spp., using technologies that, if expanded, could effectively complement or even replace microscopic approaches. To date, the scope of such novel technologies is limited and may not include common protozoa such as Dientamoeba fragilis, Entamoeba histolytica, or Cyclospora cayetanensis. This minireview describes canonical approaches for the detection of pathogenic intestinal protozoa, while highlighting recent developments and FDA-approved tools for clinical diagnosis of common intestinal protozoa. PMID:24197877

Sensing Parts per Million Level Ammonia and Parts per Billion Level Acetic Acid in the Gas Phase by Common Black Film with a Fluorescent pH Probe.

PubMed

Fu, Jingni; Zhang, Luning

2018-01-16

Relying on the nanometer-thick water core and large surface area-to-volume ratio (∼2 × 10 8 m -1 ) of common black film (CBF), we are able to use a pH-sensitive dye (carboxy-seminaphthorhodafluor-1, SNARF-1) to detect ammonia and acetic acid gas adsorption into the CBF, with the limit of detection reaching 0.8 ppm for NH 3 gas and 3 ppb for CH 3 COOH gas in the air. Data analysis reveals that fluorescence signal change is linearly proportional to the gas concentration up to 15 ppm and 65 ppb for NH 3 and CH 3 COOH, respectively.

Comparison of the calculation QRS angle for bundle branch block detection

NASA Astrophysics Data System (ADS)

Goeirmanto, L.; Mengko, R.; Rajab, T. L.

2016-04-01

QRS angle represent condition of blood circulation in the heart. Normally QRS angle is between -30 until 90 degree. Left Axis Defiation (LAD) and Right Axis Defiation (RAD) are abnormality conditions that lead to Bundle Branch Block. QRS angle is calculated using common method from physicians and compared to mathematical method using difference amplitudos and difference areas. We analyzed the standard 12 lead electrocardiogram data from MITBIH physiobank database. All methods using lead I and lead avF produce similar QRS angle and right QRS axis quadrant. QRS angle from mathematical method using difference areas is close to common method from physician. Mathematical method using difference areas can be used as a trigger for detecting heart condition.

Detection of intestinal protozoa in the clinical laboratory.

PubMed

McHardy, Ian H; Wu, Max; Shimizu-Cohen, Robyn; Couturier, Marc Roger; Humphries, Romney M

2014-03-01

Despite recent advances in diagnostic technology, microscopic examination of stool specimens remains central to the diagnosis of most pathogenic intestinal protozoa. Microscopy is, however, labor-intensive and requires a skilled technologist. New, highly sensitive diagnostic methods have been developed for protozoa endemic to developed countries, including Giardia lamblia (syn. G. intestinalis/G. duodenalis) and Cryptosporidium spp., using technologies that, if expanded, could effectively complement or even replace microscopic approaches. To date, the scope of such novel technologies is limited and may not include common protozoa such as Dientamoeba fragilis, Entamoeba histolytica, or Cyclospora cayetanensis. This minireview describes canonical approaches for the detection of pathogenic intestinal protozoa, while highlighting recent developments and FDA-approved tools for clinical diagnosis of common intestinal protozoa.

False Detection of Dangerous and Netural Substances in Commonly Used Materials by Means of the Standard THz Time Domain Spectroscopy

NASA Astrophysics Data System (ADS)

Trofimov, V. A.; Varentsova, S. A.

2016-04-01

Essential limitations of the standard THz Time Domain Spectroscopy (TDS), which lead to false detection of dangerous and neutral substances in commonly used materials, are demonstrated using the physical experiment with chocolate under real conditions as well as with semiconductors under laboratory conditions. To overcome this disadvantage, we propose using the time-dependent spectrum of the THz pulse, transmitted through or reflected from a substance. For quality assessment of the standard substance absorption frequency presence in the signal under analysis, we use time-dependent integral correlation criteria. The influence of aperture placed in front of the sample on spectral properties of silicon wafers with different resistivity is demonstrated as well.

Effects of Sampling Strategy, Detection Probability, and Independence of Counts on the Use of Point Counts

Treesearch

Grey W. Pendleton

1995-01-01

Many factors affect the use of point counts for monitoring bird populations, including sampling strategies, variation in detection rates, and independence of sample points. The most commonly used sampling plans are stratified sampling, cluster sampling, and systematic sampling. Each of these might be most useful for different objectives or field situations. Variation...

Comparison of Factor Simplicity Indices for Dichotomous Data: DETECT R, Bentler's Simplicity Index, and the Loading Simplicity Index

ERIC Educational Resources Information Center

Finch, Holmes; Stage, Alan Kirk; Monahan, Patrick

2008-01-01

A primary assumption underlying several of the common methods for modeling item response data is unidimensionality, that is, test items tap into only one latent trait. This assumption can be assessed several ways, using nonlinear factor analysis and DETECT, a method based on the item conditional covariances. When multidimensionality is identified,…

The Detection and Influence of Problematic Item Content in Ability Tests: An Examination of Sensitivity Review Practices for Personnel Selection Test Development

ERIC Educational Resources Information Center

Grand, James A.; Golubovich, Juliya; Ryan, Ann Marie; Schmitt, Neal

2013-01-01

In organizational and educational practices, sensitivity reviews are commonly advocated techniques for reducing test bias and enhancing fairness. In the present paper, results from two studies are reported which investigate how effective individuals are at detecting problematic test content and the influence such content has on important testing…

Monitoring forests at the speed of light.

Treesearch

Valerie Rapp

2005-01-01

Airborne laser scanning is a technology developed in the last 15 years. Commonly referred to as light detection and ranging, or LIDAR, these systems can map ground with up to a 6-inch elevation accuracy in open, flat terrain. LIDAR is being rapidly adopted for topographical and flood-plain mapping and the detection of earthquake faults hidden by vegetation, among other...

Detection of fecal bacteria and source tracking identifiers in environmental waters using rRNA-based RT-qPCR and rDNA-based qPCR assays

EPA Science Inventory

The identification of fecal pollution sources is commonly performed using DNA-based methods. However, there is evidence that DNA can be associated with dead cells or present as “naked DNA” in the environment. To this end, we compared the detection frequency of host specific marke...

Differential Item Functioning Detection with the Mantel-Haenszel Procedure: The Effects of Matching Types and Other Factors

ERIC Educational Resources Information Center

Socha, Alan; DeMars, Christine E.; Zilberberg, Anna; Phan, Ha

2015-01-01

The Mantel-Haenszel (MH) procedure is commonly used to detect items that function differentially for groups of examinees from various demographic and linguistic backgrounds--for example, in international assessments. As in some other DIF methods, the total score is used to match examinees on ability. In thin matching, each of the total score…

Lovell, Alfred Charles Bernard [Sir Bernard] (1913-)

NASA Astrophysics Data System (ADS)

Murdin, P.

2000-11-01

Physicist and astronomer, born in Oldland Common, Gloucestershire, England. Worked on cosmic rays at Manchester, researched radar in the Second World War, and afterwards with J S HEY procured an ex-army mobile radar unit used to detect V-2 rockets and attempted to detect cosmic ray showers with it. Interference from the electric trams at Manchester displaced the work to the university's botanical...

[Control of hypertension in nursing homes].

PubMed

Thomas, J M; Alvarez, W; Mulaj, M; De Breucker, S; Leeman, M; Pepersack, T

2006-09-01

In a cross sectional study we determined prevalence of hypertension among institutionalized old subjects. Prevalence of hypertension was 69%. Among detected hypertensive patients, 76% received an antihypertensive drug treatment. 61% of the declared hypertensive patients and 80% of the treated hypertensive patients had their blood pressure controlled. The general practitioners should better detect and treat this common geriatric problem associated with a high comorbidity.

Serological Cross-Reactions Between the Hemagglutinin Subunits of H0N1 and H1N1 Influenza Viruses Detected with “Monospecific” Antisera

PubMed Central

Baker, Nicola; Stone, H. O.; Webster, R. G.

1973-01-01

“Monospecific” antisera to the “fragile” hemaglutinnis of H0N1 (PR8) and H1N1 (FM1) influenza viruses detected an asymmetrical cross-reaction between these two strains that could not be explained by a common neuraminidase. Images PMID:4630797

Repurposing environmental DNA samples: Detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Treesearch

Joseph C. Dysthe; Torrey Rodgers; Thomas W. Franklin; Kellie J. Carim; Michael K. Young; Kevin S. McKelvey; Karen E. Mock; Michael K. Schwartz

2018-01-01

Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high-profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection...

Incidence and taxonomic richness of mosquitoes in the diets of little brown and big brown bats

Treesearch

Amy K Wray; Michelle A Jusino; Mark T Banik; Jonathan M Palmer; Heather Kaarakka; J Paul White; Daniel L Lindner; Claudio Gratton; M Zachariah Peery

2018-01-01

Bats have been portrayed as important consumers of mosquitoes, but evidence supporting this claim is surprisingly scant. We collected the fecal material of 2 common North American bats at 22 sites in Wisconsin, United States and screened samples for mosquitoes using a recently improved molecular method for detecting arthropod DNA. Overall, we detected 17 discrete...

Detection Monitoring of Crown Condition in South Carolina: A Case Study

Treesearch

William A. Bechtold; John W. Coulston

2005-01-01

This article presents a case study of how indicators of forest health can be adjusted for natural factors, standardized to a common basis, and subjected to spatial analysis for the purpose of detecting potential problems related to forest health. Two of five Forest Inventory and Analysis inventory panels in South Carolina and surrounding States were completed in 2000...

Efficient IDUA Gene Mutation Detection with Combined Use of dHPLC and Dried Blood Samples

PubMed Central

Duarte, Ana Joana; Vieira, Luis

2013-01-01

Objectives. Development of a simple mutation directed method in order to allow lowering the cost of mutation testing using an easily obtainable biological material. Assessment of the feasibility of such method was tested using a GC-rich amplicon. Design and Methods. A method of denaturing high-performance liquid chromatography (dHPLC) was improved and implemented as a technique for the detection of variants in exon 9 of the IDUA gene. The optimized method was tested in 500 genomic DNA samples obtained from dried blood spots (DBS). Results. With this dHPLC approach it was possible to detect different variants, including the common p.Trp402Ter mutation in the IDUA gene. The high GC content did not interfere with the resolution and reliability of this technique, and discrimination of G-C transversions was also achieved. Conclusion. This PCR-based dHPLC method is proved to be a rapid, a sensitive, and an excellent option for screening numerous samples obtained from DBS. Furthermore, it resulted in the consistent detection of clearly distinguishable profiles of the common p.Trp402Ter IDUA mutation with an advantageous balance of cost and technical requirements. PMID:27335677

Human Odorant Reception in the Common Bed Bug, Cimex lectularius.

PubMed

Liu, Feng; Liu, Nannan

2015-11-02

The common bed bug Cimex lectularius is a temporary ectoparasite on humans and currently resurgent in many developed countries. The ability of bed bugs to detect human odorants in the environment is critical for their host-seeking behavior. This study deciphered the chemical basis of host detection by investigating the neuronal response of olfactory sensilla to 104 human odorants using single sensillum recording and characterized the electro-physiological responses of bed bug odorant receptors to human odorants with the Xenopus expression system. The results showed that the D type of olfactory sensilla play a predominant role in detecting the human odorants tested. Different human odorants elicited different neuronal responses with different firing frequencies and temporal dynamics. Particularly, aldehydes and alcohols are the most effective stimuli in triggering strong response while none of the carboxylic acids showed a strong stimulation. Functional characterization of two bed bug odorant receptors and co-receptors in response to human odorants revealed their specific responses to the aldehyde human odorants. Taken together, the findings of this study not only provide exciting new insights into the human odorant detection of bed bugs, but also offer valuable information for developing new reagents (attractants or repellents) for the bed bug control.

Urinary tract infections in women with urogynaecological symptoms.

PubMed

Lakeman, Marielle M E; Roovers, Jan-Paul W R

2016-02-01

Urinary tract infections are common in the field of urogynaecology. Women with persistent urinary symptoms seem more likely to have bacteriuria despite negative cultures. In this review, we will give an overview of the recent insights on the relationship between urinary tract infection and persistent urinary symptoms and possible new therapeutic options. Recently published articles evaluated the prevalence of low-count bacteriuria (≥10 CFU/ml) or intracellular bacterial communities in women with overactive bladder symptoms (OAB). Differences in urinary microbioma observed in women with and without OAB symptoms were evaluated. In the light of these findings, current screening strategies were discussed and alternative screening methods for bacteriuria developed. Low-count bacteriuria (≥10 CFU/ml) seems to be more prevalent in women with OAB. Also intracellular bacterial communities are more commonly detected in these women. The microbioma found in women with urinary symptoms appeared to differ from healthy controls. The current screening methods might be insufficient as they are targeted at detecting uropathogenic Escherichia coli, mostly using a detection threshold of at least 10 CFU/ml and failing to detect intracellular bacterial communities. Studies evaluating the efficacy of treating women with low-count bacteriuria are limited but promising.

Human Odorant Reception in the Common Bed Bug, Cimex lectularius

PubMed Central

Liu, Feng; Liu, Nannan

2015-01-01

The common bed bug Cimex lectularius is a temporary ectoparasite on humans and currently resurgent in many developed countries. The ability of bed bugs to detect human odorants in the environment is critical for their host-seeking behavior. This study deciphered the chemical basis of host detection by investigating the neuronal response of olfactory sensilla to 104 human odorants using single sensillum recording and characterized the electro-physiological responses of bed bug odorant receptors to human odorants with the Xenopus expression system. The results showed that the D type of olfactory sensilla play a predominant role in detecting the human odorants tested. Different human odorants elicited different neuronal responses with different firing frequencies and temporal dynamics. Particularly, aldehydes and alcohols are the most effective stimuli in triggering strong response while none of the carboxylic acids showed a strong stimulation. Functional characterization of two bed bug odorant receptors and co-receptors in response to human odorants revealed their specific responses to the aldehyde human odorants. Taken together, the findings of this study not only provide exciting new insights into the human odorant detection of bed bugs, but also offer valuable information for developing new reagents (attractants or repellents) for the bed bug control. PMID:26522967

Differences in Movement Pattern and Detectability between Males and Females Influence How Common Sampling Methods Estimate Sex Ratio.

PubMed

Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco

2016-01-01

Sampling the biodiversity is an essential step for conservation, and understanding the efficiency of sampling methods allows us to estimate the quality of our biodiversity data. Sex ratio is an important population characteristic, but until now, no study has evaluated how efficient are the sampling methods commonly used in biodiversity surveys in estimating the sex ratio of populations. We used a virtual ecologist approach to investigate whether active and passive capture methods are able to accurately sample a population's sex ratio and whether differences in movement pattern and detectability between males and females produce biased estimates of sex-ratios when using these methods. Our simulation allowed the recognition of individuals, similar to mark-recapture studies. We found that differences in both movement patterns and detectability between males and females produce biased estimates of sex ratios. However, increasing the sampling effort or the number of sampling days improves the ability of passive or active capture methods to properly sample sex ratio. Thus, prior knowledge regarding movement patterns and detectability for species is important information to guide field studies aiming to understand sex ratio related patterns.

Digital fringe projection for hand surface coordinate variation analysis caused by osteoarthritis

NASA Astrophysics Data System (ADS)

Nor Haimi, Wan Mokhdzani Wan; Hau Tan, Cheek; Retnasamy, Vithyacharan; Vairavan, Rajendaran; Sauli, Zaliman; Roshidah Yusof, Nor; Hambali, Nor Azura Malini Ahmad; Aziz, Muhammad Hafiz Ab; Bakhit, Ahmad Syahir Ahmad

2017-11-01

Hand osteoarthritis is one of the most common forms of arthritis which impact millions of people worldwide. The disabling problem occurs when the protective cartilage on the boundaries of bones wear off over time. Currently, in order to identify hand osteoarthritis, special instruments namely X-ray scanning and MRI are used for the detection but it also has its limitations such as radiation exposure and can be quite costly. In this work, an optical metrology system based on digital fringe projection which comprises of an LCD projector, CCD camera and a personal computer has been developed to anticipate abnormal growth or deformation on the joints of the hand which are common symptoms of osteoarthritis. The main concept of this optical metrology system is to apply structured light as imaging source for surface change detection. The imaging source utilizes fringe patterns generated by C++ programming and is shifted by 3 phase shifts based on the 3 steps 2 shifts method. Phase wrapping technique and analysis were applied in order to detect the deformation of live subjects. The result has demonstrated a successful method of hand deformation detection based on the pixel tracking differences of a normal and deformed state.

Differences in Movement Pattern and Detectability between Males and Females Influence How Common Sampling Methods Estimate Sex Ratio

PubMed Central

Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco

2016-01-01

Sampling the biodiversity is an essential step for conservation, and understanding the efficiency of sampling methods allows us to estimate the quality of our biodiversity data. Sex ratio is an important population characteristic, but until now, no study has evaluated how efficient are the sampling methods commonly used in biodiversity surveys in estimating the sex ratio of populations. We used a virtual ecologist approach to investigate whether active and passive capture methods are able to accurately sample a population’s sex ratio and whether differences in movement pattern and detectability between males and females produce biased estimates of sex-ratios when using these methods. Our simulation allowed the recognition of individuals, similar to mark-recapture studies. We found that differences in both movement patterns and detectability between males and females produce biased estimates of sex ratios. However, increasing the sampling effort or the number of sampling days improves the ability of passive or active capture methods to properly sample sex ratio. Thus, prior knowledge regarding movement patterns and detectability for species is important information to guide field studies aiming to understand sex ratio related patterns. PMID:27441554

Common-path conoscopic interferometry for enhanced picosecond ultrasound detection

NASA Astrophysics Data System (ADS)

Liu, Liwang; Guillet, Yannick; Audoin, Bertrand

2018-05-01

We report on a common-path implementation of conoscopic interferometry in picosecond pump-probe reflectometry for simple and efficient detection of picosecond ultrasounds. The interferometric configuration proposed here is greatly simplified, involving only the insertion of a birefringent crystal in a standard reflectometry setup. Our approach is demonstrated by the optical detection of coherent acoustic phonons propagating through thin metal films under two representative geometries, one a particular case where the crystal slab is part of a sample as substrate of a metal film, and the other a more general case where the crystal slab is independent of the sample as part of the detection system. We first illustrate the former with a 300 nm thin film of polycrystalline titanium, deposited by physical vapor deposition on top of a 1 mm-thick uniaxial (0001) sapphire crystal. A signal-to-noise ratio (SNR) enhancement of more than 15 dB is achieved compared to conventional reflectometry. Next, the general case is demonstrated with a 900 nm-tungsten film sputtered on a silicon wafer substrate. More echoes can be discriminated by using the reported approach compared to standard reflectometry, which confirms the improvement in SNR and suggests broad applications for the reported method.

Highly sensitive detection of dipicolinic acid with a water-dispersible terbium-metal organic framework.

PubMed

Bhardwaj, Neha; Bhardwaj, Sanjeev; Mehta, Jyotsana; Kim, Ki-Hyun; Deep, Akash

2016-12-15

The sensitive detection of dipicolinic acid (DPA) is strongly associated with the sensing of bacterial organisms in food and many types of environmental samples. To date, the demand for a sensitive detection method for bacterial toxicity has increased remarkably. Herein, we investigated the DPA detection potential of a water-dispersible terbium-metal organic framework (Tb-MOF) based on the fluorescence quenching mechanism. The Tb-MOF showed a highly sensitive ability to detect DPA at a limit of detection of 0.04nM (linear range of detection: 1nM to 5µM) and also offered enhanced selectivity from other commonly associated organic molecules. The present study provides a basis for the application of Tb-MOF for direct, convenient, highly sensitive, and specific detection of DPA in the actual samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Monitoring of Total Type II Pyrethroid Pesticides in Citrus Oils and Water by Converting to a Common Product 3-Phenoxybenzoic Acid

PubMed Central

McCoy, Mark R.; Yang, Zheng; Fu, Xun; Ahn, Ki Chang; Gee, Shirley J.; Bom, David C.; Zhong, Ping; Chang, Dan; Hammock, Bruce D.

2012-01-01

Pyrethroids are a class of insecticides that are becoming increasingly popular in agricultural and home use applications. Sensitive assays for pyrethroid insecticides in complex matrices are difficult both with instrumental and immunochemical methods. Environmental analysis of the pyrethroids by immunoassay requires either knowing which pyrethroids contaminate the source or the use of non-specific antibodies with cross reactivities to a class of compounds. We describe an alternative method that converts the type-II-pyrethroids to a common chemical product, 3-phenoxybenzoic acid (3-PBA), prior to analysis. This method is much more sensitive than detecting the parent compound, and it is much easier to detect a single compound rather than an entire class of compounds. This is useful in screening for pyrethroids as a class or in situations where a single type of pyrethroid is used. We demonstrated this technique in both citrus oils and environmental water samples with conversion rates of the pyrethroid to 3-PBA that range from 45%-75% and methods that require no extraction steps for either the immunoassay or LC-MS/MS techniques. Limits of detection for this technique applied to orange oil are 5 nM, 2 μM, and 0.8 μM when detected by LC-MS/MS, GC-MS, and immunoassay respectively. The limit of detection for pyrethroids in water when detected by immunoassay was 2 nM. PMID:22486225

Comparison of traditional culture and molecular qPCR for detection of simultaneous carriage of multiple pneumococcal serotypes in African children.

PubMed

Olwagen, Courtney P; Adrian, Peter V; Madhi, Shabir A

2017-07-05

S. pneumoniae is a common colonizer of the human nasopharynx in high income and low-middle income countries. Due to limitations of standard culture methods, the prevalence of concurrent colonization with multiple serotypes is unclear. We evaluated the use of multiplex quantitative PCR (qPCR) to detect multiple pneumococcal serotypes/group colonization in archived nasopharyngeal swabs of pneumococcal conjugate vaccine naive children who had previously been investigated by traditional culture methods. Overall the detection of pneumococcal colonization was higher by qPCR (82%) compared to standard culture (71%; p < 0.001), with a high concordance (kappa = 0.73) of serotypes/groups identified by culture also being identified by qPCR. Also, qPCR was more sensitive in detecting multiple serotype/groups among colonized cases (28.7%) compared to culture (4.5%; p < 0.001). Of the additional serotypes detected only by qPCR, the majority were of lower density (<10 4 CFU/ml) than the dominant colonizing serotype, with serotype/group 6A/B, 19B/F and 23F being the highest density colonizers, followed by serotype 5 and serogroup 9A/L/N/V being the most common second and third colonizers respectively. The ability of qPCR to detect multiple pneumococcal serotypes at a low carriage density might provide better insight into underlying mechanism for changes in serotype colonization in PCV vaccinated children.

THE SCREENING AND RANKING ALGORITHM FOR CHANGE-POINTS DETECTION IN MULTIPLE SAMPLES

PubMed Central

Song, Chi; Min, Xiaoyi; Zhang, Heping

2016-01-01

The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based. Only a few multiple sample methods have been proposed using scan statistics that are computationally intensive and designed toward either common or rare change-points detection. In this paper, we propose a novel multiple sample method by adaptively combining the scan statistic of the screening and ranking algorithm (SaRa), which is computationally efficient and is able to detect both common and rare change-points. We prove that asymptotically this method can find the true change-points with almost certainty and show in theory that multiple sample methods are superior to single sample methods when shared change-points are of interest. Additionally, we report extensive simulation studies to examine the performance of our proposed method. Finally, using our proposed method as well as two competing approaches, we attempt to detect CNVs in the data from the Primary Open-Angle Glaucoma Genes and Environment study, and conclude that our method is faster and requires less information while our ability to detect the CNVs is comparable or better. PMID:28090239

Noninvasive Imaging of the Biliary System Relevant to Percutaneous Interventions

PubMed Central

Thomas, Stephen; Jahangir, Kayleen

2016-01-01

Clinical data such as history, physical examination, and laboratory tests are useful in identifying patients with biliary obstruction and biliary sources of infection. However, if intervention is planned, noninvasive imaging is needed to confirm the presence, location, and extent of the disease process. Currently, the most commonly available and used noninvasive modalities are ultrasound (US), computed tomography (CT), magnetic resonance (MR), and nuclear medicine hepatobiliary scintigraphy (HIDA). US is quick, portable, readily available, and is commonly the first imaging modality used when biliary pathology is suspected. It is excellent in the detection of cholelithiasis and acute cholecystitis but is limited in detecting choledocholithiasis. CT is excellent at detecting infected postoperative fluid collections, bilomas, biliary obstruction, and biliary infection but is limited in the detection of cholelithiasis. Therefore, US may be more useful than CT for the initial screening of acute biliary disease. MR has inherent advantages over CT, as it does not use ionizing radiation, can be done without intravenous contrast, and its detection of cholelithiasis is not affected by the internal composition of the stone. Magnetic resonance cholangiopancreatography can be used to determine the cause and location of biliary obstruction but is limited in the detection of small stones and the evaluation of the biliary tract near the ampulla. HIDA is used to evaluate for cholecystitis, biliary obstruction, and bile leaks. The main limitation is its lack of anatomical detail, and it is therefore frequently performed in conjunction with other described modalities. PMID:27904246

Changes in the Response Properties of Inferior Colliculus Neurons Relating to Tinnitus

PubMed Central

Berger, Joel I.; Coomber, Ben; Wells, Tobias T.; Wallace, Mark N.; Palmer, Alan R.

2014-01-01

Tinnitus is often identified in animal models by using the gap prepulse inhibition of acoustic startle. Impaired gap detection following acoustic over-exposure (AOE) is thought to be caused by tinnitus “filling in” the gap, thus, reducing its salience. This presumably involves altered perception, and could conceivably be caused by changes at the level of the neocortex, i.e., cortical reorganization. Alternatively, reduced gap detection ability might reflect poorer temporal processing in the brainstem, caused by AOE; in which case, impaired gap detection would not be a reliable indicator of tinnitus. We tested the latter hypothesis by examining gap detection in inferior colliculus (IC) neurons following AOE. Seven of nine unilaterally noise-exposed guinea pigs exhibited behavioral evidence of tinnitus. In these tinnitus animals, neural gap detection thresholds (GDTs) in the IC significantly increased in response to broadband noise stimuli, but not to pure tones or narrow-band noise. In addition, when IC neurons were sub-divided according to temporal response profile (onset vs. sustained firing patterns), we found a significant increase in the proportion of onset-type responses after AOE. Importantly, however, GDTs were still considerably shorter than gap durations commonly used in objective behavioral tests for tinnitus. These data indicate that the neural changes observed in the IC are insufficient to explain deficits in behavioral gap detection that are commonly attributed to tinnitus. The subtle changes in IC neuron response profiles following AOE warrant further investigation. PMID:25346722

The clinical performance evaluation of novel protein chips for eleven biomarkers detection and the diagnostic model study.

PubMed

Luo, Yuan; Zhu, Xu; Zhang, Pengjun; Shen, Qian; Wang, Zi; Wen, Xinyu; Wang, Ling; Gao, Jing; Dong, Jin; Yang, Caie; Wu, Tangming; Zhu, Zheng; Tian, Yaping

2015-01-01

We aimed to develop and validate two novel protein chips, which are based on microarray chemiluminescence immunoassay and can simultaneously detected 11 biomarkers, and then to evaluate their clinical diagnostic value by comparing with the traditional methods. Protein chips were evaluated for limit of detection, specificity, common interferences, linearity, precision and accuracy. 11 biomarkers were simultaneously detected by traditional methods and protein chips in 3683 samples, which included 1723 cancer patients, 1798 benign diseases patients and 162 healthy controls. After assay validation, protein chips demonstrated high sensitivity, high specificity, good linearity, low imprecision and were free of common interferences. Compared with the traditional methods, protein chips have good correlation in the detection of all the 13 kinds of biomarkers (r≥0.935, P<0.001). For specific cancer detection, there were no statistically significant differences between the traditional method and novel protein chips, except that male protein chip showed significantly better diagnostic value on NSE detection (P=0.004) but significantly worse value on pro-GRP detection (P=0.012), female chip showed significantly better diagnostic value on pro-GRP detection (P=0.005). Furthermore, both male and female multivariate diagnostic models had significantly better diagnostic value than single detection of PGI, PG II, pro-GRP, NSE and CA125 (P<0.05). In addition, male models had significantly better diagnostic value than single CA199 and free-PSA (P<0.05), while female models observed significantly better diagnostic value than single CA724 and β-HCG (P<0.05). For total disease or cancer detection, the AUC of multivariate logistic regression for the male and female disease detection was 0.981 (95% CI: 0.975-0.987) and 0.836 (95% CI: 0.798-0.874), respectively. While, that for total cancer detection was 0.691 (95% CI: 0.666-0.717) and 0.753 (95% CI: 0.731-0.775), respectively. The new designed protein chips are simple, multiplex and reliable clinical assays and the multi-parameter diagnostic models based on them could significantly improve their clinical performance.

The clinical performance evaluation of novel protein chips for eleven biomarkers detection and the diagnostic model study

PubMed Central

Luo, Yuan; Zhu, Xu; Zhang, Pengjun; Shen, Qian; Wang, Zi; Wen, Xinyu; Wang, Ling; Gao, Jing; Dong, Jin; Yang, Caie; Wu, Tangming; Zhu, Zheng; Tian, Yaping

2015-01-01

We aimed to develop and validate two novel protein chips, which are based on microarray chemiluminescence immunoassay and can simultaneously detected 11 biomarkers, and then to evaluate their clinical diagnostic value by comparing with the traditional methods. Protein chips were evaluated for limit of detection, specificity, common interferences, linearity, precision and accuracy. 11 biomarkers were simultaneously detected by traditional methods and protein chips in 3683 samples, which included 1723 cancer patients, 1798 benign diseases patients and 162 healthy controls. After assay validation, protein chips demonstrated high sensitivity, high specificity, good linearity, low imprecision and were free of common interferences. Compared with the traditional methods, protein chips have good correlation in the detection of all the 13 kinds of biomarkers (r≥0.935, P<0.001). For specific cancer detection, there were no statistically significant differences between the traditional method and novel protein chips, except that male protein chip showed significantly better diagnostic value on NSE detection (P=0.004) but significantly worse value on pro-GRP detection (P=0.012), female chip showed significantly better diagnostic value on pro-GRP detection (P=0.005). Furthermore, both male and female multivariate diagnostic models had significantly better diagnostic value than single detection of PGI, PG II, pro-GRP, NSE and CA125 (P<0.05). In addition, male models had significantly better diagnostic value than single CA199 and free-PSA (P<0.05), while female models observed significantly better diagnostic value than single CA724 and β-HCG (P<0.05). For total disease or cancer detection, the AUC of multivariate logistic regression for the male and female disease detection was 0.981 (95% CI: 0.975-0.987) and 0.836 (95% CI: 0.798-0.874), respectively. While, that for total cancer detection was 0.691 (95% CI: 0.666-0.717) and 0.753 (95% CI: 0.731-0.775), respectively. The new designed protein chips are simple, multiplex and reliable clinical assays and the multi-parameter diagnostic models based on them could significantly improve their clinical performance. PMID:26884957

Detection of In Vivo Foot and Ankle Implants by Walkthrough Metal Detectors.

PubMed

Chan, Jeremy Y; Mani, Sriniwasan B; Williams, Phillip N; O'Malley, Martin J; Levine, David S; Roberts, Matthew M; Ellis, Scott J

2014-08-01

Heightened security concerns have made metal detectors a standard security measure in many locations. While prior studies have investigated the detection rates of various hip and knee implants, none have looked specifically at the detection of foot and ankle implants in an in vivo model. Our goals were to identify which commonly used foot and ankle implants would be detected by walkthrough metal detectors both in vivo and ex vivo. Over a 7-month period, 153 weightbearing patients with foot and ankle hardware were recruited to walk through a standard airport metal detector at 3 different program settings (buildings, airports, and airports enhanced) with a base sensitivity of 165 (arbitrary units), as currently used by the Transportation Security Administration. The number of implants, location and type, as well as the presence of concomitant hardware outside of the foot and ankle were recorded. To determine the detection rate of common foot and ankle implants ex vivo, different hardware sets were walked through the detector at all 3 program settings. Seventeen patients were found to have detectable hardware at the buildings, airports, and airports enhanced settings. An additional 3 patients had hardware only detected at the airports enhanced setting. All 20 of these patients had concomitant metal implants outside of the foot and ankle from other orthopaedic procedures. All patients with foot and ankle implants alone passed through undetected. Seven hardware sets were detected ex vivo at the airports enhanced setting. Our results indicate that patients with foot and ankle implants alone are unlikely to be detected by walkthrough metal detectors at standard airport settings. When additional hardware is present from orthopaedic procedures outside of the foot and ankle, metal detection rates were higher. We believe that these results are important for surgeons in order to educate patients on how they might be affected when walking through a metal detector such as while traveling. Level II, prospective comparative study. © The Author(s) 2014.

Fatal Diesel Poisoning: A Case Report and Brief Review of Literature.

PubMed

Srinivasa Murthy, Abilash; Das, Siddhartha; Bheemanathi Hanuman, Srinivas

2018-06-01

Hydrocarbons are volatile substances that are used in routine life activities for cooking or as automobile fuel. Diesel is one of the commonly used automobile fuels obtained from crude oil. Death due to poisoning by diesel is rarely reported. Most commonly affected is the respiratory system either after aspiration or ingestion. The most common presentation is chemical pneumonitis or aspiration pneumonitis from which patient usually recovers. Gas chromatography techniques help in the detection of volatile substances like diesel. Here, we report a rare case of fatal pediatric accidental diesel poisoning.

Carbapenemase-Producing Enterobacteriaceae in Yunnan Province, China.

PubMed

Rui, Zheng; Dehua, Liu; Hua, Niu; Yue, Feng; Yunmin, Xu; Jianhua, Li; Xueshan, Xia

2016-11-22

Among 144 carbapenem-resistant Enterobacteriaceae strains isolated from 4 hospitals in Yunnan province, 113 were identified as carbapenemase-producing Enterobacteriaceae (CPE). Bla KPC-2 (99/113, 87.6%) was the most common carbapenemase gene and Klebsiella pneumoniae (100/113, 88.5%) was the most common species. Bla NDM-1 (11/113, 9.7%), bla IMP-4 (10/113, 8.8%), and bla IMP-1 (1/113, 0.9%) genes were also detected. Extended-spectrum β-lactamase genes were common in CPE, and the SHV- and CTX-M-types were predominant.

A strategy for the identification of plants in illegal pharmaceutical preparations and food supplements using chromatographic fingerprints.

PubMed

Deconinck, E; De Leersnijder, C; Custers, D; Courselle, P; De Beer, J O

2013-03-01

The detection of regulated and forbidden herbs in pharmaceutical preparations and nutritional supplements is a growing problem for laboratories charged with the analysis of illegal pharmaceutical preparations and counterfeit medicines. This article presents a feasibility study of the use of chromatographic fingerprints for the detection of plants in pharmaceutical preparations. Fingerprints were developed for three non-regulated common herbal products--Rhamnus purshiana, Passiflora incarnata L. and Crataegus monogyna--and this was done by combining three different types of detection: diode-array detection, evaporative light scattering detection and mass spectrometry. It is shown that these plants could be detected in respective triturations of the dry extracts with lactose and three different herbal matrices as well as in commercial preparations purchased on the open market.

Use of the Box-Cox Transformation in Detecting Changepoints in Daily Precipitation Data Series

NASA Astrophysics Data System (ADS)

Wang, X. L.; Chen, H.; Wu, Y.; Pu, Q.

2009-04-01

This study integrates a Box-Cox power transformation procedure into two statistical tests for detecting changepoints in Gaussian data series, to make the changepoint detection methods applicable to non-Gaussian data series, such as daily precipitation amounts. The detection power aspects of transformed methods in a common trend two-phase regression setting are assessed by Monte Carlo simulations for data of a log-normal or Gamma distribution. The results show that the transformed methods have increased the power of detection, in comparison with the corresponding original (untransformed) methods. The transformed data much better approximate to a Gaussian distribution. As an example of application, the new methods are applied to a series of daily precipitation amounts recorded at a station in Canada, showing satisfactory detection power.