scholarly journals Cleaning up Western blot signals from immunoprecipitated samples using alternative detection methods

BioTechniques ◽  
2014 ◽  
Vol 56 (3) ◽  
Author(s):  
Deborah L. Grainger ◽  
Ban Hudong ◽  
Du Chang ◽  
Ping Lan
Keyword(s):  
Western Blot ◽  
Detection Methods ◽  
Alternative Detection

scholarly journals Laboratory Confirmation of Lyme Disease

1991 ◽  
Vol 2 (2) ◽  
pp. 64-69 ◽  
Author(s):  
Tom G Schwan ◽  
Warren J Simpson ◽  
Patricia A Rosa
Keyword(s):  
Lyme Disease ◽  
Immunofluorescence Assay ◽  
Detection Methods ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serological Tests ◽  
Specificity And Sensitivity ◽  
Laboratory Confirmation ◽  
Staining Methods ◽  
Alternative Detection ◽  
Species Specific

Lyme disease can be confirmed in the laboratory by isolation or detection of its causative agent, a tick-borne spirocheteBorrelia burgdorferi,or by a diagnostic change in the titre of antibodies specific to the agent.B burgdorferican be isolated and cultivated in Barbour-Stoenner-Kelly II medium. It can be detected by light microscopy in tissue sections or, rarely, in blood smears using various staining methods. There is interest in the development of alternative detection methods, including identification of specific antigens ofB burgdorferiin the urine of suspected cases and demonstration of the presence of species-specific DNA using polymerase chain reaction assays. Currently, serological tests (indirect immunofluorescence assay, enzyme-linked immunosorbent assay and Western immunoblot) are the most practical and available methods for confirming Lyme disease. The quest to improve the specificity and sensitivity of serological tests – for example, through the use of specific recombinant antigens – continues.

Extended Enrichment Procedures Can Be Used To Define False-Negative Probabilities for Cultural Gold Standard Methods for Salmonella Detection, Facilitating Comparisons between Gold Standard and Alternative Methods

2020 ◽  
Vol 83 (6) ◽  
pp. 1030-1037
Author(s):  
GENEVIEVE SULLIVAN ◽  
XIAODONG GUO ◽  
JEFFREY I. TOKMAN ◽  
SHERRY ROOF ◽  
ALJOSA TRMCIC ◽  
...  
Keyword(s):  
Enzyme Immunoassay ◽  
Water Activity ◽  
Gold Standard ◽  
False Negative ◽  
Alternative Methods ◽  
Detection Methods ◽  
Pet Food ◽  
Probable Number ◽  
Alternative Detection ◽  
Contamination Levels

ABSTRACT Evaluation of alternative detection methods for foodborne pathogens typically involves comparisons against a “gold standard” culture method, which may produce false-negative (FN) results, particularly under worst-case scenarios such as low contamination levels, difficult-to-detect strains, and challenging food matrices (e.g., matrices with a water activity of <0.6). We used extended enrichment times (up to 72 h for both primary and secondary enrichments) to evaluate a gold standard method for Salmonella detection (the U.S. Food and Drug Administration Bacteriological Analytical Manual [BAM] method) in two low-water-activity foods (dry pet food and chocolate) inoculated at low contamination levels (most probable number ca. 1/25 g) with five Salmonella strains. Strains were selected to include those with a poor ability to grow in enrichment media. Among the 100 pet food and 100 chocolate samples tested, 53 and 50, respectively, were positive with the standard BAM method, and 57 and 59, respectively, were positive with the extended BAM method. Thus, the FN probabilities for the standard BAM method were 7% for pet food and 15% for chocolate. An alternative enzyme immunoassay method for detection of Salmonella in chocolate produced FN probabilities of 6 and 20% when compared against the standard and extended BAM methods, respectively. Detection of Salmonella Mississippi was significantly reduced with the alternative method (P = 0.023) compared with the extended BAM method. We calculated a composite reference standard to further define FN probabilities based on variable results from multiple assays (the standard BAM, extended BAM, and alternative methods). Based on this standard, the enzyme immunoassay for Salmonella detection in chocolate had a 28% FN probability and the standard and extended BAM methods had 23 and 9% FN probabilities, respectively. These results provide a framework for how inclusion of extended enrichment times can facilitate evaluation of alternative detection methods. HIGHLIGHTS

scholarly journals Identifying and Prioritizing Diseases Important for Detection in Adult Hearing Health Care

2016 ◽  
Vol 25 (3) ◽  
pp. 224-231 ◽  
Author(s):  
Samantha J. Kleindienst ◽  
Sumitrajit Dhar ◽  
Donald W. Nielsen ◽  
James W. Griffith ◽  
Larry B. Lundy ◽  
...  
Keyword(s):  
Health Care ◽  
Health Care Delivery ◽  
Care Delivery ◽  
Hearing Aid ◽  
Delivery Systems ◽  
Detection Methods ◽  
Hearing Aid Fitting ◽  
Hearing Health ◽  
Alternative Detection ◽  
Health Care Delivery Systems

Purpose The purpose of this research note is to identify and prioritize diseases important for detection in adult hearing health care delivery systems. Method Through literature review and expert consultation, the authors identified 195 diseases likely to occur in adults complaining of hearing loss. Five neurotologists rated the importance of disease on 3 dimensions related to the necessity of detection prior to adult hearing aid fitting. Results Ratings of adverse health consequences, diagnostic difficulty, and presence of nonotologic symptoms associated with these diseases resulted in the identification of 104 diseases potentially important for detection prior to adult hearing aid fitting. Conclusions Current and evolving health care delivery systems, including direct-to-consumer sales, involve inconsistent means of disease detection vigilance prior to device fitting. The first steps in determining the safety of these different delivery methods are to identify and prioritize which diseases present the greatest risk for poor health outcomes and, thus, should be detected in hearing health care delivery systems. Here the authors have developed a novel multidimensional rating system to rank disease importance. The rankings can be used to evaluate the effectiveness of alternative detection methods and to inform public health policy. The authors are currently using this information to validate a consumer questionnaire designed to accurately identify when pre- fitting medical evaluations should be required for hearing aid patients.

scholarly journals Detection of the Disease-Associated Isoform of the Prion Protein in Formalin-Fixed Tissues by Western Blot

2007 ◽  
Vol 19 (5) ◽  
pp. 548-552 ◽  
Author(s):  
Eric M. Nicholson ◽  
Robert A. Kunkle ◽  
Amir N. Hamir ◽  
Semakaleng Lebepe-Mazur ◽  
Dennis Orcutt
Keyword(s):  
Western Blot ◽  
Prion Protein ◽  
Prion Disease ◽  
Clinical Signs ◽  
Infectious Agent ◽  
Disease Diagnosis ◽  
Detection Methods ◽  
Serological Tests ◽  
Fresh Tissue ◽  
Formalin Fixed

Clinical signs of prion disease are not specific and include a variety of differential diagnoses. Serological tests and nucleic acid-based detection methods are not applicable to prion-disease-agent detection because of the unusual nature of the infectious agent. Prion-disease diagnosis is primarily conducted by means of immunodetection of the infectious agent, typically by at least 2 distinct procedures with immunohisto-chemistry and Western blot being the most informative. These approaches differ in the need for formalin-fixed and frozen or fresh tissue respectively. This work describes a method for the detection of the disease-associated isoform of the prion protein by Western blot using formalin-fixed tissues. The approach requires only minimal modification of existing Western-blot procedures and could readily be incorporated into existing detection schemes for confirmatory purposes when fresh or frozen tissues are unavailable.

A rapid method to detect Cryptolestes ferrugineus (Coleoptera: Cucujidae) larvae in stored grain

2002 ◽  
Vol 82 (3) ◽  
pp. 591-597 ◽  
Author(s):  
J. M. Minkevich ◽  
C. J. Demianyk ◽  
N. D. G. White ◽  
D. S. Jayas ◽  
B. Timlick
Keyword(s):  
Extraction Efficiency ◽  
Survival Rates ◽  
Detection Methods ◽  
Heat Sources ◽  
Cryptolestes Ferrugineus ◽  
Stored Grain ◽  
Potential Alternative ◽  
Alternative Detection ◽  
Gradient Principle ◽  
Seed Coats

Modifications of three detection methods, based on the heat-gradient principle employed by the Berlese funnel method were investigated to extract larvae of the rusty grain beetle, Cryptolestes ferrugineus (Stephens), developing under the seed coats of infested kernels in grain samples. One-kilogram samples of wheat, barley and corn were artificially infested with rusty grain beetle eggs, resulting in survival rates (to larval stage) of 71.1 ± 14.4, 58.9 ± 14.3, and 24.7 ± 11.8%, respectively. Sets of 10 infested kernels containing different-aged larvae (10 individuals × 4 instars) were added to 1-kg samples of hydrated grain, then heated on screens beneath heat sources (lights) at several heights in three different containers (Berlese funnel, with a 7-cm-deep grain layer, or square and rectangular screened boxes with a grain layer several kernels deep). There were no significantly different extraction rates between the rectangular and square containers for all heating trials. A larval extraction rate of 31% was produced by 1-h trials with wheat (15% moisture content wet basis) 5.5 cm below the lamp bank with a thermostat set at 50°C. This matched the efficiency of the Berlese funnel method (36% extraction in 6 h), but in much less time. Similar results were found for barley, bu t for corn the square and rectangle gave significantly better extraction than the Berlese funnel, although extraction efficiency was half that of wheat and barley. Considerably lower extraction rates were obtained from trials that did not use a thermostat. The results from this experiment show that there is a potential alternative detection method with the thermostatically controlled heating of a thin layer of grain that should be faster than the conventional 6-h Berlese funnel method. Key words: Cryptolestes ferrugineus, grain, larval extraction, Berlese funnel, grain monolayer

scholarly journals Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation

2020 ◽  
Author(s):  
Chang Qi ◽  
Jian Zhang ◽  
Peng Luo
Keyword(s):  
Western Blot ◽  
Visual Observation ◽  
Detection Methods ◽  
Image Manipulation ◽  
Apparent Difference ◽  
Unique Identifier ◽  
Western Blots ◽  
Image Detection ◽  
Scientific Fraud

AbstractScientific fraud by image duplications and manipulations within western blot images is a rising problem. Currently, problematic western blot images are mainly detected by checking repeated bands or through visual observation. However, the completeness of the above methods in detecting problematic images has not been demonstrated. Here we show that Generative Adversarial Nets (GANs) can generate realistic western blot images that indistinguishable from real western blots. The overall accuracy of researchers for identifying synthetic western blot images is 0.52, which almost equal to blind guess (0.5). We found that GANs can generate western blot images with bands of the expected lengths, widths, and angles in desired positions that can fool researchers. For the case study, we find that the accuracy of detecting the synthetic western blot images is related to years of researchers performed studies relevant to western blots, but there was no apparent difference in accuracy among researchers with different academic degrees. Our results demonstrate that GANs can generate fake western blot images to fool existing problematic image detection methods. Therefore, more information is needed to ensure that the western blots appearing in scientific articles are real. We argue to require every western blot image to be uploaded along with a unique identifier generated by the laboratory machine and to peer review these images along with the corresponding submitted articles, which may reduce the incidence of scientific fraud.

scholarly journals svpluscnv: analysis and visualization of complex structural variation data

2020 ◽  
Author(s):  
Gonzalo Lopez ◽  
Laura E Egolf ◽  
Federico M Giorgi ◽  
Sharon J Diskin ◽  
Adam A Margolin
Keyword(s):  
Hot Spot ◽  
Copy Number Variant ◽  
R Package ◽  
Detection Methods ◽  
Supplementary Information ◽  
Structural Variations ◽  
Complex Structural Variation ◽  
Complex Structural ◽  
Alternative Detection ◽  
Genomic Regions

Abstract Motivation Despite widespread prevalence of somatic structural variations (SVs) across most tumor types, understanding of their molecular implications often remains poor. SVs are extremely heterogeneous in size and complexity, hindering the interpretation of their pathogenic role. Tools integrating large SV datasets across platforms are required to fully characterize the cancer’s somatic landscape. Results svpluscnv R package is a swiss army knife for the integration and interpretation of orthogonal datasets including copy number variant segmentation profiles and sequencing-based structural variant calls. The package implements analysis and visualization tools to evaluate chromosomal instability and ploidy, identify genes harboring recurrent SVs and detects complex rearrangements such as chromothripsis and chromoplexia. Further, it allows systematic identification of hot-spot shattered genomic regions, showing reproducibility across alternative detection methods and datasets. Availability and implementation https://github.com/ccbiolab/svpluscnv. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

A Bispectral Analysis of the Radio Emissions of Pulsar J0437-4715

2020 ◽  
Vol 09 (04) ◽  
pp. 2050018
Author(s):  
Alexander Faustmann ◽  
Jacki Gilmore ◽  
Vereese van Tonder ◽  
Maciej Serylak
Keyword(s):  
Signal To Noise Ratio ◽  
Gaussian Model ◽  
Higher Order ◽  
Detection Methods ◽  
High Signal ◽  
Signal To Noise ◽  
Noise Ratio ◽  
Alternative Detection ◽  
Higher Order Spectra

A combination of the very low signal-to-noise ratio and the very large parameter space spanned by pulsar emissions makes pulsar detection a challenging task. Currently, brute force parameter searches are often used for pulsar detection and a cyclostationary Gaussian model is assumed for pulsar emissions. Higher-Order spectra offer high signal-to-noise ratio domains in problems where the desired signal is polluted by Gaussian noise. The presence of nonzero higher-order spectral components in pulsar bursts may offer alternative detection methods. This work presents a review of higher-order statistics and offers a motivation for their use in the characterization of pulsar bursts. A dish from the MeerKAT telescope was used to acquire recorded radio bursts from pulsar J0437-4715. These bursts were found to contain nonzero bispectral components that were dispersed in the same way as the components of the power spectrum.

scholarly journals Distribution of Neuronal Apoptosis Inhibitory Protein in Human Tissues

2007 ◽  
Vol 55 (9) ◽  
pp. 911-923 ◽  
Author(s):  
Johannes K. X. Maier ◽  
Sylvia Balabanian ◽  
Cynthia R. Coffill ◽  
Alexandra Stewart ◽  
Louise Pelletier ◽  
...  
Keyword(s):  
Western Blot ◽  
Neuronal Apoptosis ◽  
Muscular Atrophy ◽  
Detection Methods ◽  
Inhibitory Protein ◽  
Neuronal Apoptosis Inhibitory Protein ◽  
Recognition Protein ◽  
Intestinal Pathogen ◽  
The Central Nervous System ◽  
Naip Gene

The neuronal apoptosis inhibitory protein (NAIP) gene, also known as the baculovirus inhibitor of apoptosis repeat-containing protein 1 (BIRC1) gene, is a member of the inhibitors of apoptosis (IAP) family and was first characterized as a candidate gene for spinal muscular atrophy (SMA). The expression of NAIP has been thoroughly studied in the central nervous system and overlaps the pattern of neurodegeneration in SMA. Recent studies have pointed to a role for NAIP in non-neuronal cells. We report here the production of a specific anti-NAIP antibody and the profile of NAIP expression in human adult tissues by Western blot and immunohistochemical detection methods. NAIP was detected in a number of tissues by Western blot analysis, but immunohistochemistry revealed that NAIP's presence in certain tissues, such as liver, lung, and spleen, is most likely due to macrophage infiltration. In the small intestine, the expression of NAIP coincides with the expression of p21WAF1. This observation, coupled with findings from other groups, suggests a role for NAIP in increasing the survival of cells undergoing terminal differentiation as well as the possibility that the protein serves as an intestinal pathogen recognition protein. This manuscript contains online supplemental material at http://www.jhc.org . Please visit this article online to view these materials.

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