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Sample records for identifies strain-specific diagnostic

  1. Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii

    PubMed Central

    Song, Carl; Chiasson, Melissa A; Nursimulu, Nirvana; Hung, Stacy S; Wasmuth, James; Grigg, Michael E; Parkinson, John

    2013-01-01

    Increasingly, metabolic potential is proving to be a critical determinant governing a pathogen's virulence as well as its capacity to expand its host range. To understand the potential contribution of metabolism to strain-specific infectivity differences, we present a constraint-based metabolic model of the opportunistic parasite, Toxoplasma gondii. Dominated by three clonal strains (Type I, II, and III demonstrating distinct virulence profiles), T. gondii exhibits a remarkably broad host range. Integrating functional genomic data, our model (which we term as iCS382) reveals that observed strain-specific differences in growth rates are driven by altered capacities for energy production. We further predict strain-specific differences in drug susceptibilities and validate one of these predictions in a drug-based assay, with a Type I strain demonstrating resistance to inhibitors that are effective against a Type II strain. We propose that these observed differences reflect an evolutionary strategy that allows the parasite to extend its host range, as well as result in a subsequent partitioning into discrete strains that display altered virulence profiles across different hosts, different organs, and even cell types. PMID:24247825

  2. Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns*

    PubMed Central

    Jhingan, Gagan Deep; Kumari, Sangeeta; Jamwal, Shilpa V.; Kalam, Haroon; Arora, Divya; Jain, Neharika; Kumaar, Lakshmi Krishna; Samal, Areejit; Rao, Kanury V. S.; Kumar, Dhiraj; Nandicoori, Vinay Kumar

    2016-01-01

    Mycobacterium tuberculosis is an adaptable intracellular pathogen, existing in both dormant as well as active disease-causing states. Here, we report systematic proteomic analyses of four strains, H37Ra, H37Rv, and clinical isolates BND and JAL, to determine the differences in protein expression patterns that contribute to their virulence and drug resistance. Resolution of lysates of the four strains by liquid chromatography, coupled to mass spectrometry analysis, identified a total of 2161 protein groups covering ∼54% of the predicted M. tuberculosis proteome. Label-free quantification analysis of the data revealed 257 differentially expressed protein groups. The differentially expressed protein groups could be classified into seven K-means cluster bins, which broadly delineated strain-specific variations. Analysis of the data for possible mechanisms responsible for drug resistance phenotype of JAL suggested that it could be due to a combination of overexpression of proteins implicated in drug resistance and the other factors. Expression pattern analyses of transcription factors and their downstream targets demonstrated substantial differential modulation in JAL, suggesting a complex regulatory mechanism. Results showed distinct variations in the protein expression patterns of Esx and mce1 operon proteins in JAL and BND strains, respectively. Abrogating higher levels of ESAT6, an important Esx protein known to be critical for virulence, in the JAL strain diminished its virulence, although it had marginal impact on the other strains. Taken together, this study reveals that strain-specific variations in protein expression patterns have a meaningful impact on the biology of the pathogen. PMID:27151218

  3. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

    PubMed Central

    Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K.; Fondi, Marco; Nizet, Victor; Palsson, Bernhard Ø.

    2016-01-01

    Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus. These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world. PMID:27286824

  4. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.

    PubMed

    Bosi, Emanuele; Monk, Jonathan M; Aziz, Ramy K; Fondi, Marco; Nizet, Victor; Palsson, Bernhard Ø

    2016-06-28

    Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world.

  5. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.

    PubMed

    Bosi, Emanuele; Monk, Jonathan M; Aziz, Ramy K; Fondi, Marco; Nizet, Victor; Palsson, Bernhard Ø

    2016-06-28

    Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world. PMID:27286824

  6. Diagnostics Tools Identify Faults Prior to Failure

    NASA Technical Reports Server (NTRS)

    2013-01-01

    Through the SBIR program, Rochester, New York-based Impact Technologies LLC collaborated with Ames Research Center to commercialize the Center s Hybrid Diagnostic Engine, or HyDE, software. The fault detecting program is now incorporated into a software suite that identifies potential faults early in the design phase of systems ranging from printers to vehicles and robots, saving time and money.

  7. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies

    PubMed Central

    2015-01-01

    Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas. PMID:26307380

  8. STRAIN-SPECIFIC MODIFIER GENES GOVERNING CRANIOFACIAL PHENOTYPES

    PubMed Central

    Mukhopadhyay, Partha; Brock, Guy; Webb, Cynthia; Pisano, M. Michele; Greene, Robert M

    2012-01-01

    BACKGROUND The presence of strain-specific modifier genes is known to modulate the phenotype and pathophysiology of mice harboring genetically engineered mutations. Thus, identification of genetic modifier genes is requisite to understanding control of phenotypic expression. c-Ski is a transcriptional regulator. Ski−/− mice on a C57BL6J (B6) background exhibit facial clefting, while Ski−/− mice on a 129P3 (129) background present with exencephaly. METHODS In the present study, oligonucleotide-based gene expression profiling was utilized to identify potential strain-specific modifier gene candidates present in wild-type mice of B6 and 129 genetic backgrounds. Changes in gene expression were verified by TaqMan quantitative real-time PCR. RESULTS Steady-state levels of 89 genes demonstrated a significantly higher level of expression, and those of 68 genes demonstrated a significantly lower level of expression in the developing neural tubes from E8.5, B6 embryos when compared to expression levels in neural tubes derived from E8.5, 129 embryos. CONCLUSIONS Based on the results from the current comparative microarray study, and taking into consideration a number of relevant published reports, several potential strain-specific gene candidates, likely to modify the craniofacial phenotypes in various knockout mouse models have been identified. PMID:22371338

  9. Strain-specific variations in Toxoplasma gondii GRA1, GRA5, GRA6, GRA8, and GRA14

    NASA Astrophysics Data System (ADS)

    Haryati, S.; Sari, Y.; Prasetyo, A. A.; Sariyatun, R.

    2016-02-01

    Diagnosis and identification of the genetic group of T. gondii (Toxoplasma gondii) are important to control better the T. gondii infection, particularly in immunocompromised people as HIV patients. This study aimed to identify strain-specific variations in T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 in order to help design such diagnostic tool to detect and characterize the parasite. Forty-three T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 sequences deposited in GenBank were aligned. A number of positions in the gene sequences were highly conserved. All GRA sequences had strain-specific positions, however, only GRA1, GRA5, and GRA6, which contained specific variations for each T. gondii lineage. In conclusion, T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 are predicted to contain highly conserved regions and positions with strain-specific variation, which might be useful for the design of diagnostic tools detecting and distinguishing T. gondiistrains.

  10. A Review and Comparison of Diagnostic Instruments to Identify Students' Misconceptions in Science

    ERIC Educational Resources Information Center

    Gurel, Derya Kaltakci; Eryilmaz, Ali; McDermott, Lillian Christie

    2015-01-01

    Different diagnostic tools have been developed and used by researchers to identify students' conceptions. The present study aimed to provide an overview of the common diagnostic instruments in science to assess students' misconceptions. Also the study provides a brief comparison of these common diagnostic instruments with their strengths and…

  11. Statistical Diagnostics to Identify Galactic Foregrounds in B -Mode Maps

    NASA Astrophysics Data System (ADS)

    Kamionkowski, Marc; Kovetz, Ely D.

    2014-11-01

    Recent developments in the search for inflationary gravitational waves in the cosmic microwave background polarization motivate the search for new diagnostics to distinguish the Galactic foreground contribution to B modes from the cosmic signal. We show that B modes from these foregrounds should exhibit a local hexadecapolar departure in power from statistical isotropy (SI). We present a simple algorithm to search for a uniform SI violation of this sort, as may arise in a sufficiently small patch of sky. We then show how to search for these effects if the orientation of the SI violation varies across the survey region, as is more likely to occur in surveys with more sky coverage. If detected, these departures from Gaussianity would indicate some level of Galactic foreground contamination in the B -mode maps. Given uncertainties about foreground properties, though, caution should be exercised in attributing a null detection to an absence of foregrounds.

  12. Strategies to develop strain-specific PCR based assays for probiotics.

    PubMed

    Treven, P

    2015-01-01

    Since health benefits conferred by probiotics are strain-specific, identification to the strain level is mandatory to allow the monitoring of the presence and the abundance of specific probiotic in a product or in a gastrointestinal tract. Compared to standard plate counts, the reduced duration of the assays and higher specificity makes PCR-based methods (standard PCR and quantitative PCR) very appropriate for detection or quantification of probiotics. Development of strain-specific assay consists of 4 main stages: (1) strain-specific marker identification; (2) construction of potential strain-specific primers; (3) validation on DNA from pure cultures of target and related strains; and (4) validation on spiked samples. The most important and also the most challenging step is the identification of strain-specific sequences, which can be subsequently targeted by specific primers or probes. Such regions can be identified on sequences derived from 16S-23S internally transcribed spacers, randomly amplified polymorphic DNA, representational difference analysis and suppression subtractive hybridisation. Already known phenotypic or genotypic characteristics of the target strain can also be used to develop the strain-specific assay. However, the initial stage of strain-specific assay development can be replaced by comparative genomics analysis of target genome with related genomes in public databases. Advances in whole genome sequencing (WGS) have resulted in a cost reduction for bacterial genome sequencing and consequently have made this approach available to most laboratories. In the present paper I reviewed the available literature on PCR and qPCR assays developed for detection of a specific probiotic strain and discussed future WGS and comparative genomics-based approaches.

  13. Identifying Differences in Diagnostic Skills between Physics Students: Students' Self-Diagnostic Performance Given Alternative Scaffolding

    NASA Astrophysics Data System (ADS)

    Cohen, E.; Mason, A.; Singh, C.; Yerushalmi, E.

    2008-10-01

    "Self-diagnosis tasks" aim at fostering diagnostic behavior by explicitly requiring students to present diagnosis as part of the activity of reviewing their problem solutions. We have been investigating the extent to which introductory physics students can diagnose their own mistakes when explicitly asked to do so with different levels of scaffolding support provided to them. In our study in an introductory physics class with more than 200 students, the recitation classes were split into three different experimental groups in which different levels of guidance were provided for performing the self-diagnosis activities. We present our findings that students' performance was far from perfect. However, differences in the scaffolding in the three experimental groups (i.e. providing a correct solution and a self-diagnosis rubric) noticeably affected the resulting diagnosis.

  14. A homozygous mutation in PEX16 identified by whole-exome sequencing ending a diagnostic odyssey

    PubMed Central

    Bacino, Carlos A.; Chao, Yu-Hsin; Seto, Elaine; Lotze, Tim; Xia, Fan; Jones, Richard O.; Moser, Ann; Wangler, Michael F.

    2015-01-01

    We present a patient with a unique neurological phenotype with a progressive neurodegenerative. An 18-year diagnostic odyssey for the patient ended when exome sequencing identified a homozygous PEX16 mutation suggesting an atypical peroxisomal biogenesis disorder (PBD). Interestingly, the patient's peroxisomal biochemical abnormalities were subtle, such that plasma very-long-chain fatty acids initially failed to provide a diagnosis. This case suggests that next-generation sequencing may be diagnostic in some atypical peroxisomal biogenesis disorders. PMID:26644994

  15. Mapping and modeling of a strain-specific epitope in the Norwalk virus capsid inner shell.

    PubMed

    Parra, Gabriel I; Sosnovtsev, Stanislav V; Abente, Eugenio J; Sandoval-Jaime, Carlos; Bok, Karin; Dolan, Michael A; Green, Kim Y

    2016-05-01

    Noroviruses are diverse positive-strand RNA viruses associated with acute gastroenteritis. Cross-reactive epitopes have been mapped primarily to conserved sequences in the capsid VP1 Shell (S) domain, and strain-specific epitopes to the highly variable Protruding (P) domain. In this work, we investigated a strain-specific linear epitope defined by MAb NV10 that was raised against prototype (Genogroup I.1) strain Norwalk virus (NV). Using peptide scanning and mutagenesis, the epitope was mapped to amino acids 21-32 (LVPEVNASDPLA) of the NV S domain, and its specificity was verified by epitope transfer and reactivity with a recombinant MAb NV10 single-chain variable fragment (scFv). Comparative structural modeling of the NV10 strain-specific and the broadly cross-reactive TV20 epitopes identified two internal non-overlapping sites in the NV shell, corresponding to variable and conserved amino acid sequences among strains, respectively. The S domain, like the P domain, contains strain-specific epitopes that contribute to the antigenic diversity among the noroviruses. PMID:26971245

  16. Comparison between diagnostic instruments for identifying high-functioning children with autism.

    PubMed

    Yirmiya, N; Sigman, M; Freeman, B J

    1994-06-01

    Two instruments for identifying autism in children and adolescents with intellectual abilities in the normal range were compared. Diagnostic tools consisted of the Autism Behavior Checklist (ABC) and the Autism Diagnostic Interview (ADI). The sample was composed of 18 children who were all diagnosed as having either infantile autism or infantile autism, residual state based on DSM-III criteria by a clinical team using observations, parental interviews, and interactions with the children. Only 4 of the children met diagnostic cutoffs for autism on the current ABC but all met criteria for diagnosis on the ABC using parental recall of the child's behavior at 3-5 years of age. The ADI had somewhat greater specificity in that 3 children did not meet criteria for diagnosis although 2 of these children also received ABC scores based on parental recollection that were in the borderline range. PMID:8050982

  17. Quantification of Azospirillum brasilense FP2 Bacteria in Wheat Roots by Strain-Specific Quantitative PCR.

    PubMed

    Stets, Maria Isabel; Alqueres, Sylvia Maria Campbell; Souza, Emanuel Maltempi; Pedrosa, Fábio de Oliveira; Schmid, Michael; Hartmann, Anton; Cruz, Leonardo Magalhães

    2015-10-01

    Azospirillum is a rhizobacterial genus containing plant growth-promoting species associated with different crops worldwide. Azospirillum brasilense strains exhibit a growth-promoting effect by means of phytohormone production and possibly by N2 fixation. However, one of the most important factors for achieving an increase in crop yield by plant growth-promoting rhizobacteria is the survival of the inoculant in the rhizosphere, which is not always achieved. The objective of this study was to develop quantitative PCR protocols for the strain-specific quantification of A. brasilense FP2. A novel approach was applied to identify strain-specific DNA sequences based on a comparison of the genomic sequences within the same species. The draft genome sequences of A. brasilense FP2 and Sp245 were aligned, and FP2-specific regions were filtered and checked for other possible matches in public databases. Strain-specific regions were then selected to design and evaluate strain-specific primer pairs. The primer pairs AzoR2.1, AzoR2.2, AzoR5.1, AzoR5.2, and AzoR5.3 were specific for the A. brasilense FP2 strain. These primer pairs were used to monitor quantitatively the population of A. brasilense in wheat roots under sterile and nonsterile growth conditions. In addition, coinoculations with other plant growth-promoting bacteria in wheat were performed under nonsterile conditions. The results showed that A. brasilense FP2 inoculated into wheat roots is highly competitive and achieves high cell numbers (∼10(7) CFU/g [fresh weight] of root) in the rhizosphere even under nonsterile conditions and when coinoculated with other rhizobacteria, maintaining the population at rather stable levels for at least up to 13 days after inoculation. The strategy used here can be applied to other organisms whose genome sequences are available.

  18. Quantification of Azospirillum brasilense FP2 Bacteria in Wheat Roots by Strain-Specific Quantitative PCR

    PubMed Central

    Stets, Maria Isabel; Alqueres, Sylvia Maria Campbell; Souza, Emanuel Maltempi; Pedrosa, Fábio de Oliveira; Schmid, Michael; Hartmann, Anton

    2015-01-01

    Azospirillum is a rhizobacterial genus containing plant growth-promoting species associated with different crops worldwide. Azospirillum brasilense strains exhibit a growth-promoting effect by means of phytohormone production and possibly by N2 fixation. However, one of the most important factors for achieving an increase in crop yield by plant growth-promoting rhizobacteria is the survival of the inoculant in the rhizosphere, which is not always achieved. The objective of this study was to develop quantitative PCR protocols for the strain-specific quantification of A. brasilense FP2. A novel approach was applied to identify strain-specific DNA sequences based on a comparison of the genomic sequences within the same species. The draft genome sequences of A. brasilense FP2 and Sp245 were aligned, and FP2-specific regions were filtered and checked for other possible matches in public databases. Strain-specific regions were then selected to design and evaluate strain-specific primer pairs. The primer pairs AzoR2.1, AzoR2.2, AzoR5.1, AzoR5.2, and AzoR5.3 were specific for the A. brasilense FP2 strain. These primer pairs were used to monitor quantitatively the population of A. brasilense in wheat roots under sterile and nonsterile growth conditions. In addition, coinoculations with other plant growth-promoting bacteria in wheat were performed under nonsterile conditions. The results showed that A. brasilense FP2 inoculated into wheat roots is highly competitive and achieves high cell numbers (∼107 CFU/g [fresh weight] of root) in the rhizosphere even under nonsterile conditions and when coinoculated with other rhizobacteria, maintaining the population at rather stable levels for at least up to 13 days after inoculation. The strategy used here can be applied to other organisms whose genome sequences are available. PMID:26187960

  19. Carrier and prenatal diagnostic strategy and newly identified mutations in Hungarian haemophilia A and B families.

    PubMed

    Bors, András; Andrikovics, Hajnalka; Illés, Zsuzsanna; Jáger, Rita; Kardos, Mária; Marosi, Anikó; Nemes, László; Tordai, Attila

    2015-03-01

    Deficiencies of blood coagulation factors VIII and IX (haemophilia A and haemophilia B) represent the most common inherited bleeding disorders with a wide range of causative mutations. Carrier and prenatal diagnostics are preferably performed by direct mutation detection; however, in certain situations, indirect family studies may also be useful. We aimed to utilize a combination of direct and indirect techniques for carrier and prenatal diagnostics in both haemophilias in a single national centre. Two hundred and eleven haemophilia A families were investigated by screening for inversions of introns 1 and 22, and by family studies using polymorphic markers. Twenty-eight haemophilia A and 39 haemophilia B families were investigated by Sanger-sequencing of the coding regions. Among severe haemophilia A families, frequencies of intron 22 and 1 inversions were 82 out of 145 (57%) and two out of 145 (1.4%). Sequencing of the entire coding region of the respective factor gene was performed and 12 (haemophilia A) and 5 (haemophilia B) previously unpublished disease-causing mutations were identified. For genetic markers used for haemophilia A indirect family testing, heterozygosity rates varied between 137 out of 327 [42% intragenic BclI restriction fragment length polymorphism (RFLP], 168 out of 254 (66% intragenic F8Civs13CA) and 202 out of 261 (77% extragenic DXS15CA) with a combined rate of 92% (intragenic markers) and 97% (all three markers). For male fetuses, prenatal diagnostics was provided to 43 haemophilia A families (n = 22 with direct mutation detection and n = 21 by indirect family testing) and to three haemophilia B families. The combination of direct and indirect molecular genetics approaches is a successful and cost-effective approach to provide carrier and prenatal diagnostics and risk assessment for inhibitor formation.

  20. Diagnostic accuracy of clinical examination features for identifying large rotator cuff tears in primary health care

    PubMed Central

    Cadogan, Angela; McNair, Peter; Laslett, Mark; Hing, Wayne; Taylor, Stephen

    2013-01-01

    Objectives: Rotator cuff tears are a common and disabling complaint. The early diagnosis of medium and large size rotator cuff tears can enhance the prognosis of the patient. The aim of this study was to identify clinical features with the strongest ability to accurately predict the presence of a medium, large or multitendon (MLM) rotator cuff tear in a primary care cohort. Methods: Participants were consecutively recruited from primary health care practices (n = 203). All participants underwent a standardized history and physical examination, followed by a standardized X-ray series and diagnostic ultrasound scan. Clinical features associated with the presence of a MLM rotator cuff tear were identified (P<0.200), a logistic multiple regression model was derived for identifying a MLM rotator cuff tear and thereafter diagnostic accuracy was calculated. Results: A MLM rotator cuff tear was identified in 24 participants (11.8%). Constant pain and a painful arc in abduction were the strongest predictors of a MLM tear (adjusted odds ratio 3.04 and 13.97 respectively). Combinations of ten history and physical examination variables demonstrated highest levels of sensitivity when five or fewer were positive [100%, 95% confidence interval (CI): 0.86–1.00; negative likelihood ratio: 0.00, 95% CI: 0.00–0.28], and highest specificity when eight or more were positive (0.91, 95% CI: 0.86–0.95; positive likelihood ratio 4.66, 95% CI: 2.34–8.74). Discussion: Combinations of patient history and physical examination findings were able to accurately detect the presence of a MLM rotator cuff tear. These findings may aid the primary care clinician in more efficient and accurate identification of rotator cuff tears that may require further investigation or orthopedic consultation. PMID:24421626

  1. Multiple Serum Cytokine Profiling to Identify Combinational Diagnostic Biomarkers in Attacks of Familial Mediterranean Fever.

    PubMed

    Koga, Tomohiro; Migita, Kiyoshi; Sato, Shuntaro; Umeda, Masataka; Nonaka, Fumiaki; Kawashiri, Shin-Ya; Iwamoto, Naoki; Ichinose, Kunihiro; Tamai, Mami; Nakamura, Hideki; Origuchi, Tomoki; Ueki, Yukitaka; Masumoto, Junya; Agematsu, Kazunaga; Yachie, Akihiro; Yoshiura, Koh-Ichiro; Eguchi, Katsumi; Kawakami, Atsushi

    2016-04-01

    The precise cytokine networks in the serum of individuals with familial Mediterranean fever (FMF) that are associated with its pathogenesis have been unknown. Here, we attempted to identify specific biomarkers to diagnose or assess disease activity in FMF patients. We measured serum levels of 45 cytokines in 75 FMF patients and 40 age-matched controls by multisuspension cytokine array. FMF in "attack" or "remission" was classified by Japan College of Rheumatology-certified rheumatologists according to the Tel Hashomer criteria. Cytokines were ranked by their importance by a multivariate classification algorithm. We performed a logistic regression analysis to determine specific biomarkers for discriminating FMF patients in attack. To identify specific molecular networks, we performed a cluster analysis of each cytokine. Twenty-nine of the 45 cytokines were available for further analyses. Eight cytokines' serum levels were significantly elevated in the FMF attack versus healthy control group. Nine cytokines were increased in FMF attack compared to FMF remission. Multivariate classification algorithms followed by a logistic regression analysis revealed that the combined measurement of IL-6, IL-18, and IL-17 distinguished FMF patients in attack from the controls with the highest accuracy (sensitivity 89.2%, specificity 100%, and accuracy 95.5%). Among the FMF patients, the combined measurement of IL-6, G-CSF, IL-10, and IL-12p40 discriminated febrile attack periods from remission periods with the highest accuracy (sensitivity 75.0%, specificity 87.9%, and accuracy 84.0%). Our data identified combinational diagnostic biomarkers in FMF patients based on the measurement of multiple cytokines. These findings help to improve the diagnostic performance of FMF in daily practice and extend our understanding of the activation of the inflammasome leading to enhanced cytokine networks. PMID:27100444

  2. Strain-Specific Ureolytic Microbial Calcium Carbonate Precipitation

    PubMed Central

    Hammes, Frederik; Boon, Nico; de Villiers, Johan; Verstraete, Willy; Siciliano, Steven Douglas

    2003-01-01

    During a study of ureolytic microbial calcium carbonate (CaCO3) precipitation by bacterial isolates collected from different environmental samples, morphological differences were observed in the large CaCO3 crystal aggregates precipitated within bacterial colonies grown on agar. Based on these differences, 12 isolates were selected for further study. We hypothesized that the striking differences in crystal morphology were the result of different microbial species or, alternatively, differences in the functional attributes of the isolates selected. Sequencing of 16S rRNA genes showed that all of the isolates were phylogenetically closely related to the Bacillus sphaericus group. Urease gene diversity among the isolates was examined by using a novel application of PCR-denaturing gradient gel electrophoresis (DGGE). This approach revealed significant differences between the isolates. Moreover, for several isolates, multiple bands appeared on the DGGE gels, suggesting the apparent presence of different urease genes in these isolates. The substrate affinities (Km) and maximum hydrolysis rates (Vmax) of crude enzyme extracts differed considerably for the different strains. For certain isolates, the urease activity increased up to 10-fold in the presence of 30 mM calcium, and apparently this contributed to the characteristic crystal formation by these isolates. We show that strain-specific calcification occurred during ureolytic microbial carbonate precipitation. The specificity was mainly due to differences in urease expression and the response to calcium. PMID:12902285

  3. Strain-specific morphologies of yeast prion amyloid fibrils

    PubMed Central

    Diaz-Avalos, Ruben; King, Chih-Yen; Wall, Joseph; Simon, Martha; Caspar, Donald L. D.

    2005-01-01

    Mass per length (mpl) measurements on single amyloid fibrils that specifically propagate the [VH], [VK], and [VL] strains of the yeast prion [PSI] reveal unanticipated differences in their structures. Many fibrils have ≈1.0 prion molecule per 4.7-Å cross-β repeat period, which is consistent with a self-replicating model built by parallel β-sheet hydrogen-bonding of like prion peptide segments, but other fibrils are definitely heavier. The predominantly straight fibrils of the dominant [VH] strain have a bimodal mpl distribution, corresponding to components with ≈1.0 and 1.2 prions per repeat. Fibrils of the weaker [VK] strain, which are almost all wavy, have a monodisperse mpl distribution with a mean of 1.15 prions per repeat. The recessive [VL] strain sample has ≈1.05 prions per repeat in single fibrils and includes ≈10% double fibrils, which are rare in the duplicate [VH] and [VK] samples. All of these samples were assembled from purified recombinant Sup35 prion protein by seeded growth on nuclei extracted from yeast bearing the three [PSI] strains. Infectious and noninfectious spontaneously assembled fibrils of the recombinant prion protein also display different heterogeneous morphologies. The strain-specific morphological differences we have observed directly confirm the structural prediction of the protein-only prion theory but do not have an obvious molecular explanation. PMID:16006506

  4. Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid.

    PubMed

    Liang, Li; Juarez, Silvia; Nga, Tran Vu Thieu; Dunstan, Sarah; Nakajima-Sasaki, Rie; Davies, D Huw; McSorley, Stephen; Baker, Stephen; Felgner, Philip L

    2013-01-01

    Current serological diagnostic assays for typhoid fever are based on detecting antibodies against Salmonella LPS or flagellum, resulting in a high false-positive rate. Here we used a protein microarray containing 2,724 Salmonella enterica serovar Typhi antigens (>63% of proteome) and identified antibodies against 16 IgG antigens and 77 IgM antigens that were differentially reactive among acute typhoid patients and healthy controls. The IgG target antigens produced a sensitivity of 97% and specificity of 80%, whereas the IgM target antigens produced 97% and 91% sensitivity and specificity, respectively. Our analyses indicated certain features such as membrane association, secretion, and protein expression were significant enriching features of the reactive antigens. About 72% of the serodiagnostic antigens were within the top 25% of the ranked antigen list using a Naïve bayes classifier. These data provide an important resource for improved diagnostics, therapeutics and vaccine development against an important human pathogen. PMID:23304434

  5. Strain-Specific Inhibition of nod Gene Induction in Bradyrhizobium japonicum by Flavonoid Compounds

    PubMed Central

    Kosslak, Renee M.; Joshi, Rita S.; Bowen, Benjamin A.; Paaren, Herbert E.; Appelbaum, Edward R.

    1990-01-01

    A broad-host-range plasmid, pEA2-21, containing a Bradyrhizobium japonicum nodABC'-'lacZ translational fusion was used to identify strain-specific inhibitors of the genes required for soybean nodulation, the common nod genes. The responses of type strains of B. japonicum serogroups USDA 110, USDA 123, USDA 127, USDA 129, USDA 122, and USDA 138 to nod gene inhibitors were compared. Few compounds inhibited nod gene expression in B. japonicum USDA 110. In contrast, nod gene expression in strains belonging to several other serogroups was inhibited by most of the flavonoids tested. However, the application of two of these strain-specific compounds, chrysin and naringenin, had little effect on the pattern of competition between indigenous and inoculum strains of B. japonicum in greenhouse and field trials. Preliminary studies with radiolabeled chrysin and naringenin suggest that the different responses to nod gene inhibitors may be partly due to the degree to which plant flavonoids can be metabolized by each strain. PMID:16348186

  6. On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions

    PubMed Central

    Hurlbert, Allen H.; Stegen, James C.

    2014-01-01

    We use a simulation model to examine four of the most common hypotheses for the latitudinal richness gradient and identify patterns that might be diagnostic of those four hypotheses. The hypotheses examined include (1) tropical niche conservatism, or the idea that the tropics are more diverse because a tropical clade origin has allowed more time for diversification in the tropics and has resulted in few species adapted to extra-tropical climates. (2) The ecological limits hypothesis suggests that species richness is limited by the amount of biologically available energy in a region. (3) The speciation rates hypothesis suggests that the latitudinal gradient arises from a gradient in speciation rates. (4) Finally, the tropical stability hypothesis argues that climatic fluctuations and glacial cycles in extratropical regions have led to greater extinction rates and less opportunity for specialization relative to the tropics. We found that tropical niche conservatism can be distinguished from the other three scenarios by phylogenies which are more balanced than expected, no relationship between mean root distance (MRD) and richness across regions, and a homogeneous rate of speciation across clades and through time. The energy gradient, speciation gradient, and disturbance gradient scenarios all produced phylogenies which were more imbalanced than expected, showed a negative relationship between MRD and richness, and diversity-dependence of speciation rate estimates through time. We found that the relationship between speciation rates and latitude could distinguish among these three scenarios, with no relation expected under the ecological limits hypothesis, a negative relationship expected under the speciation rates hypothesis, and a positive relationship expected under the tropical stability hypothesis. We emphasize the importance of considering multiple hypotheses and focusing on diagnostic predictions instead of predictions that are consistent with multiple

  7. Non-invasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer

    PubMed Central

    Mathé, Ewy A.; Patterson, Andrew D.; Haznadar, Majda; Manna, Soumen K.; Krausz, Kristopher W.; Bowman, Elise D.; Shields, Peter G.; Idle, Jeffrey R.; Smith, Philip B.; Anami, Katsuhiro; Kazandjian, Dickran G.; Hatzakis, Emmanuel; Gonzalez, Frank J.; Harris, Curtis C.

    2014-01-01

    Lung cancer remains the most common cause of cancer deaths worldwide, yet there is currently a lack of diagnostic noninvasive biomarkers that could guide treatment decisions. Small molecules (<1500 Da) were measured in urine collected from 469 lung cancer patients and 536 population controls using unbiased liquid chromatography-mass spectrometry. Clinical putative diagnostic and prognostic biomarkers were validated by quantitation and normalized to creatinine levels at two different time points and further validated in an independent sample set, which comprises 80 cases and 78 population controls, with similar demographic and clinical characteristics when compared to the training set. Creatine riboside (IUPAC name: 2-{2-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-oxolan-2-yl]-1-methylcarbamimidamido}acetic acid), a novel molecule identified in this study, and N-acetylneuraminic acid (NANA), were each significantly (P <0.00001) elevated in non–small cell lung cancer (NSCLC) and associated with worse prognosis (hazard ratio (HR) =1.81 [P =0.0002], and 1.54 [P =0.025], respectively). Creatine riboside was the strongest classifier of lung cancer status in all and stage I–II cases, important for early detection, and also associated with worse prognosis in stage I–II lung cancer (HR =1.71, P =0.048). All measurements were highly reproducible with intraclass correlation coefficients ranging from 0.82 – 0.99. Both metabolites were significantly (P <0.03) enriched in tumor tissue compared to adjacent non-tumor tissue (N =48), thus revealing their direct association with tumor metabolism. Creatine riboside and NANA may be robust urinary clinical metabolomic markers that are elevated in tumor tissue and associated with early lung cancer diagnosis and worse prognosis. PMID:24736543

  8. On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions

    SciTech Connect

    Hurlbert, Allen H.; Stegen, James C.

    2014-12-02

    Many processes have been put forward to explain the latitudinal gradient in species richness. Here, we use a simulation model to examine four of the most common hypotheses and identify patterns that might be diagnostic of those four hypotheses. The hypotheses examined include (1) tropical niche conservatism, or the idea that the tropics are more diverse because a tropical clade origin has allowed more time for diversification in the tropics and has resulted in few species adapted to extra-tropical climates. (2) The productivity, or energetic constraints, hypothesis suggests that species richness is limited by the amount of biologically available energy in a region. (3) The tropical stability hypothesis argues that major climatic fluctuations and glacial cycles in extratropical regions have led to greater extinction rates and less opportunity for specialization relative to the tropics. (4) Finally, the speciation rates hypothesis suggests that the latitudinal richness gradient arises from a parallel gradient in rates of speciation. We found that tropical niche conservatism can be distinguished from the other three scenarios by phylogenies which are more balanced than expected, no relationship between mean root distance and richness across regions, and a homogeneous rate of speciation across clades and through time. The energy gradient, speciation gradient, and disturbance gradient scenarios all exhibited phylogenies which were more imbalanced than expected, showed a negative relationship between mean root distance and richness, and diversity-dependence of speciation rate estimates through time. Using Bayesian Analysis of Macroevolutionary Mixtures on the simulated phylogenies, we found that the relationship between speciation rates and latitude could distinguish among these three scenarios. We emphasize the importance of considering multiple hypotheses and focusing on diagnostic predictions instead of predictions that are consistent with more than one hypothesis.

  9. A Novel Malaria Pf/Pv Ab Rapid Diagnostic Test Using a Differential Diagnostic Marker Identified by Network Biology.

    PubMed

    Cho, Sung Jin; Lee, Jihoo; Lee, Hyun Jae; Jo, Hyun-Young; Sinniah, Mangalam; Kim, Hak-Yong; Chong, Chom-Kyu; Song, Hyun-Ok

    2016-01-01

    Rapid diagnostic tests (RDTs) can detect anti-malaria antibodies in human blood. As they can detect parasite infection at the low parasite density, they are useful in endemic areas where light infection and/or re-infection of parasites are common. Thus, malaria antibody tests can be used for screening bloods in blood banks to prevent transfusion-transmitted malaria (TTM), an emerging problem in malaria endemic areas. However, only a few malaria antibody tests are available in the microwell-based assay format and these are not suitable for field application. A novel malaria antibody (Ab)-based RDT using a differential diagnostic marker for falciparum and vivax malaria was developed as a suitable high-throughput assay that is sensitive and practical for blood screening. The marker, merozoite surface protein 1 (MSP1) was discovered by generation of a Plasmodium-specific network and the hierarchical organization of modularity in the network. Clinical evaluation revealed that the novel Malaria Pf/Pv Ab RDT shows improved sensitivity (98%) and specificity (99.7%) compared with the performance of a commercial kit, SD BioLine Malaria P.f/P.v (95.1% sensitivity and 99.1% specificity). The novel Malaria Pf/Pv Ab RDT has potential for use as a cost-effective blood-screening tool for malaria and in turn, reduces TTM risk in endemic areas. PMID:27313496

  10. A Novel Malaria Pf/Pv Ab Rapid Diagnostic Test Using a Differential Diagnostic Marker Identified by Network Biology

    PubMed Central

    Cho, Sung Jin; Lee, Jihoo; Lee, Hyun Jae; Jo, Hyun-Young; Sinniah, Mangalam; Kim, Hak-Yong; Chong, Chom-Kyu; Song, Hyun-Ok

    2016-01-01

    Rapid diagnostic tests (RDTs) can detect anti-malaria antibodies in human blood. As they can detect parasite infection at the low parasite density, they are useful in endemic areas where light infection and/or re-infection of parasites are common. Thus, malaria antibody tests can be used for screening bloods in blood banks to prevent transfusion-transmitted malaria (TTM), an emerging problem in malaria endemic areas. However, only a few malaria antibody tests are available in the microwell-based assay format and these are not suitable for field application. A novel malaria antibody (Ab)-based RDT using a differential diagnostic marker for falciparum and vivax malaria was developed as a suitable high-throughput assay that is sensitive and practical for blood screening. The marker, merozoite surface protein 1 (MSP1) was discovered by generation of a Plasmodium-specific network and the hierarchical organization of modularity in the network. Clinical evaluation revealed that the novel Malaria Pf/Pv Ab RDT shows improved sensitivity (98%) and specificity (99.7%) compared with the performance of a commercial kit, SD BioLine Malaria P.f/P.v (95.1% sensitivity and 99.1% specificity). The novel Malaria Pf/Pv Ab RDT has potential for use as a cost-effective blood-screening tool for malaria and in turn, reduces TTM risk in endemic areas. PMID:27313496

  11. [Usefulness of clinical data and rapid diagnostic tests to identify bacterial etiology in adult respiratory infections].

    PubMed

    Toledano-Sierra, Pilar; Arriola-Hernández, Maite; Orueta-Sánchez, Ramón

    2015-01-19

    Respiratory tract infections are a common complaint and most of them, such as common cold and laryngitis, are viral in origin, so antibiotic use should be exceptional. However, there are other respiratory tract infections (sinusitis, pharyngitis, lower respiratory tract infections, and exacerbations of chronic obstructive pulmonary disease) where a bacterial etiology is responsible for a non-negligible percentage, and antibiotics are often empirically indicated. The aim of the study is to identify the strength of the data obtained from the symptoms, physical examination and rapid diagnostic methods in respiratory infections in which antibiotic use is frequently proposed in order to improve diagnosis and influence the decision to prescribe these drugs. The review concludes that history, physical examination and rapid tests are useful to guide the need for antibiotic treatment in diseases such as acute sinusitis, acute pharyngitis, exacerbation of lower respiratory tract infection and chronic obstructive pulmonary disease. However, no isolated data is accurate enough by itself to confirm or rule out the need for antibiotics. Therefore, clinical prediction rules bring together history and physical examination, thereby improving the accuracy of the decision to indicate or not antibiotics.

  12. The use of cellular diagnostics for identifying sub-lethal stress in reef corals.

    PubMed

    Downs, Craig A; Ostrander, Gary K; Rougee, Luc; Rongo, Teina; Knutson, Sean; Williams, David E; Mendiola, Wendy; Holbrook, Jackalyn; Richmond, Robert H

    2012-04-01

    Coral reefs throughout the world are exhibiting documented declines in coral cover and species diversity, which have been linked to anthropogenic stressors including land-based sources of pollution. Reductions in coastal water and substratum quality are affecting coral survivorship, reproduction and recruitment, and hence, the persistence of coral reefs. One major obstacle in effectively addressing these declines is the lack of tools that can identify cause-and-effect relationships between stressors and specific coral reef losses, while a second problem is the inability to measure the efficacy of mitigation efforts in a timely fashion. We examined corals from six coral reefs on Guam, Mariana Islands, which were being affected by different environmental stressors (e.g. PAH's, pesticides, PCB's and sedimentation). Cellular diagnostic analysis differentiated the cellular-physiological condition of these corals. Examination of protein expression provided insight into their homeostatic responses to chemical and physical stressors in exposed corals prior to outright mortality, providing improved opportunities for developing locally-based management responses. This approach adds critically needed tools for addressing the effects of multiple stressors on corals and will allow researchers to move beyond present assessment and monitoring techniques that simply document the loss of coral abundance and diversity.

  13. A search strategy to identify studies on the prognosis of work disability: a diagnostic test framework

    PubMed Central

    Kok, Rob; Verbeek, Jos A H M; Faber, Babs; van Dijk, Frank J H; Hoving, Jan L

    2015-01-01

    Objective Searching the medical literature for evidence on prognosis is an important aspect of evidence-based disability evaluation. To facilitate this, we aimed to develop and evaluate a comprehensive and efficient search strategy in PubMed, to be used by either researchers or practitioners and that will identify articles on the prognosis of work disability. Methods We used a diagnostic test analytic framework. First, we created a reference set of 225 articles on the prognosis of work disability by screening a total of 65 692 titles and abstracts from10 journals in the period 2000–2009. Included studies had a minimum follow-up of 6 months, participants in the age of 18–64 with a minimum sick leave of 4 weeks or longer or having serious activity limitations in 50% of the cases and outcome measures that reflect impairments, activity limitations or participation restrictions. Using text mining methods, we extracted search terms from the reference set and, according to sensitivity and relative frequency, we combined these into search strings. Results Both the research and the practice search filter outperformed existing filters in occupational health, all combined with the Yale-prognostic filter. The Work Disability Prognosis filter for Research showed a comprehensiveness of 90% (95% CI 86 to 94) and efficiency expressed more user-friendly as Number Needed to Read=20 (95% CI 17 to 34). Conclusions The Work Disability Prognosis filter will help practitioners and researchers who want to find prognostic evidence in the area of work disability evaluation. However, further refining of this filter is possible and needed, especially for the practitioner for whom efficiency is especially important. PMID:25991444

  14. There is need for antigen-based rapid diagnostic tests to identify common acute tropical illnesses.

    PubMed

    Wilde, Henry; Suankratay, Chusana

    2007-01-01

    Enteric fever, typhus, leptospirosis, dengue, melioidosis, and tuberculous meningitis present urgent diagnostic problems that require experience and clinical judgment to make early evidence-based management decisions. Basic and applied research dealing with reliable antigen-based diagnostics has been published and confirmed for several of these infections. This should have initiated commercial production but has not. Established international firms see little profit in such diagnostic kits since they would be used in poor countries with little prospects for return of investment capital. We attempt to illustrate this issue, using common causes of acute febrile illnesses in the Southeast Asian region. We believe that rapid diagnostic technology could prevent significant delay in starting appropriate therapy, reduce hospital expenses, and even save lives.

  15. Genetic assessment of strain-specific sources of lake trout recruitment in the Great Lakes

    USGS Publications Warehouse

    Page, Kevin S.; Scribner, Kim T.; Bennett, Kristine R.; Garzel, Laura M.; Burnham-Curtis, Mary K.

    2003-01-01

    Populations of wild lake trout Salvelinus namaycush have been extirpated from nearly all their historical habitats across the Great Lakes. Efforts to restore self-sustaining lake trout populations in U.S. waters have emphasized the stocking of coded-wire-tagged juveniles from six hatchery strains (Seneca Lake, Lewis Lake, Green Lake, Apostle Islands, Isle Royale, and Marquette) into vacant habitats. Strain-specific stocking success has historically been based on estimates of the survival and catch rates of coded-wire-tagged adults returning to spawning sites. However, traditional marking methods and estimates of relative strain abundance provide no means of assessing strain fitness (i.e., the realized contributions to natural recruitment) except by assuming that young-of-the-year production is proportional to adult spawner abundance. We used microsatellite genetic data collected from six hatchery strains with likelihood-based individual assignment tests (IA) and mixed-stock analysis (MSA) to identify the strain composition of young of the year recruited each year. We show that strain classifications based on IA and MSA were concordant and that the accuracy of both methods varied based on strain composition. Analyses of young-of-the-year lake trout samples from Little Traverse Bay (Lake Michigan) and Six Fathom Bank (Lake Huron) revealed that strain contributions differed significantly from estimates of the strain composition of adults returning to spawning reefs. The Seneca Lake strain contributed the majority of juveniles produced on Six Fathom Bank and more young of the year than expected within Little Traverse Bay. Microsatellite markers provided a method for accurately classifying the lake trout hatchery strains used for restoration efforts in the Great Lakes and for assessment of strain-specific reproductive success.

  16. Development and Assessment of a Diagnostic Tool to Identify Organic Chemistry Students' Alternative Conceptions Related to Acid Strength

    ERIC Educational Resources Information Center

    McClary, LaKeisha M.; Bretz, Stacey Lowery

    2012-01-01

    The central goal of this study was to create a new diagnostic tool to identify organic chemistry students' alternative conceptions related to acid strength. Twenty years of research on secondary and college students' conceptions about acids and bases has shown that these important concepts are difficult for students to apply to qualitative problem…

  17. The use of Diagnostic Imaging for Identifying Abnormal Gas Accumulations in Cetaceans and Pinnipeds.

    PubMed

    Dennison, Sophie; Fahlman, Andreas; Moore, Michael

    2012-01-01

    Recent dogma suggested that marine mammals are not at risk of decompression sickness due to a number of evolutionary adaptations. Several proposed adaptations exist. Lung compression and alveolar collapse that terminate gas-exchange before a depth is reached where supersaturation is significant and bradycardia with peripheral vasoconstriction affecting the distribution, and dynamics of blood and tissue nitrogen levels. Published accounts of gas and fat emboli and dysbaric osteonecrosis in marine mammals and theoretical modeling have challenged this view-point, suggesting that decompression-like symptoms may occur under certain circumstances, contrary to common belief. Diagnostic imaging modalities are invaluable tools for the non-invasive examination of animals for evidence of gas and have been used to demonstrate the presence of incidental decompression-related renal gas accumulations in some stranded cetaceans. Diagnostic imaging has also contributed to the recognition of clinically significant gas accumulations in live and dead cetaceans and pinnipeds. Understanding the appropriate application and limitations of the available imaging modalities is important for accurate interpretation of results. The presence of gas may be asymptomatic and must be interpreted cautiously alongside all other available data including clinical examination, clinical laboratory testing, gas analysis, necropsy examination, and histology results.

  18. The use of Diagnostic Imaging for Identifying Abnormal Gas Accumulations in Cetaceans and Pinnipeds.

    PubMed

    Dennison, Sophie; Fahlman, Andreas; Moore, Michael

    2012-01-01

    Recent dogma suggested that marine mammals are not at risk of decompression sickness due to a number of evolutionary adaptations. Several proposed adaptations exist. Lung compression and alveolar collapse that terminate gas-exchange before a depth is reached where supersaturation is significant and bradycardia with peripheral vasoconstriction affecting the distribution, and dynamics of blood and tissue nitrogen levels. Published accounts of gas and fat emboli and dysbaric osteonecrosis in marine mammals and theoretical modeling have challenged this view-point, suggesting that decompression-like symptoms may occur under certain circumstances, contrary to common belief. Diagnostic imaging modalities are invaluable tools for the non-invasive examination of animals for evidence of gas and have been used to demonstrate the presence of incidental decompression-related renal gas accumulations in some stranded cetaceans. Diagnostic imaging has also contributed to the recognition of clinically significant gas accumulations in live and dead cetaceans and pinnipeds. Understanding the appropriate application and limitations of the available imaging modalities is important for accurate interpretation of results. The presence of gas may be asymptomatic and must be interpreted cautiously alongside all other available data including clinical examination, clinical laboratory testing, gas analysis, necropsy examination, and histology results. PMID:22685439

  19. The use of Diagnostic Imaging for Identifying Abnormal Gas Accumulations in Cetaceans and Pinnipeds

    PubMed Central

    Dennison, Sophie; Fahlman, Andreas; Moore, Michael

    2012-01-01

    Recent dogma suggested that marine mammals are not at risk of decompression sickness due to a number of evolutionary adaptations. Several proposed adaptations exist. Lung compression and alveolar collapse that terminate gas-exchange before a depth is reached where supersaturation is significant and bradycardia with peripheral vasoconstriction affecting the distribution, and dynamics of blood and tissue nitrogen levels. Published accounts of gas and fat emboli and dysbaric osteonecrosis in marine mammals and theoretical modeling have challenged this view-point, suggesting that decompression-like symptoms may occur under certain circumstances, contrary to common belief. Diagnostic imaging modalities are invaluable tools for the non-invasive examination of animals for evidence of gas and have been used to demonstrate the presence of incidental decompression-related renal gas accumulations in some stranded cetaceans. Diagnostic imaging has also contributed to the recognition of clinically significant gas accumulations in live and dead cetaceans and pinnipeds. Understanding the appropriate application and limitations of the available imaging modalities is important for accurate interpretation of results. The presence of gas may be asymptomatic and must be interpreted cautiously alongside all other available data including clinical examination, clinical laboratory testing, gas analysis, necropsy examination, and histology results. PMID:22685439

  20. DNA diagnostics to identify internal feeders (Lepidoptera: Tortricidae) of pome fruits of quarantine importance.

    PubMed

    Barcenas, N M; Unruh, T R; Neven, L G

    2005-04-01

    A diagnostic polymerase chain reaction (PCR) method is presented for differentiating among the North American internal apple-feeding pests codling moth, Cydia pomonella (L.); oriental fruit moth, Grapholita molesta (Busck); lesser appleworm, Grapholita prunivora (Walsh); and cherry fruitworm, Grapholita packardi Zeller. An approximately 470-bp fragment of mitochondrial cytochrome oxidase subunit I (COI) was sequenced in three to six specimens of each species. Consistent and diagnostic differences were observed among the species in two regions of COI from which forward and reverse primers were designed to amplify a 112-116-bp segment of the gene. The primer sets were used to selectively amplify DNA from specimens of diverse geographic origin for each corresponding target species. Protocols were adapted for conventional and quantitative PCR, the latter being substantially faster. The method was validated as a decision-making tool for quarantine identifications for Mexico by representatives of their phytosanitary agency (Sanidad Vegetal). The method can facilitate identification of intercepted internal feeding Lepidoptera in apple and pear for many other importing nations.

  1. Identifying Differences In Diagnostic Skills Between Physics Students: Developing A Rubric

    NASA Astrophysics Data System (ADS)

    Mason, A.; Cohen, E.; Yerushalmi, E.; Singh, C.

    2008-10-01

    Expert problem solvers are characterized by continuous evaluation of their progress towards a solution. One characteristic of expertise is self-diagnosis directed towards elaboration of the solvers' conceptual understanding, knowledge organization or strategic approach. "Self-diagnosis tasks" aim at fostering diagnostic behavior by explicitly requiring students to present diagnosis as part of the activity of reviewing their problem solutions. We have been investigating how introductory physics students perform in such tasks. Developing a robust rubric is essential for objective evaluation of students' self-diagnosis skills. We discuss the development of a grading rubric that takes into account introductory physics students' content knowledge as well as analysis, planning and presentation skills. Using this rubric, we have found the inter-rater reliability to be better than 80%. The rubric can easily be adapted to other problems, as will be discussed in a companion paper.

  2. Statistical diagnostics to identify galactic foregrounds in B-mode maps.

    PubMed

    Kamionkowski, Marc; Kovetz, Ely D

    2014-11-01

    Recent developments in the search for inflationary gravitational waves in the cosmic microwave background polarization motivate the search for new diagnostics to distinguish the Galactic foreground contribution to B modes from the cosmic signal. We show that B modes from these foregrounds should exhibit a local hexadecapolar departure in power from statistical isotropy (SI). We present a simple algorithm to search for a uniform SI violation of this sort, as may arise in a sufficiently small patch of sky. We then show how to search for these effects if the orientation of the SI violation varies across the survey region, as is more likely to occur in surveys with more sky coverage. If detected, these departures from Gaussianity would indicate some level of Galactic foreground contamination in the B-mode maps. Given uncertainties about foreground properties, though, caution should be exercised in attributing a null detection to an absence of foregrounds. PMID:25415897

  3. Identifying Strategy Use in Category Learning Tasks: A Case for More Diagnostic Data and Models

    ERIC Educational Resources Information Center

    Donkin, Chris; Newell, Ben R.; Kalish, Mike; Dunn, John C.; Nosofsky, Robert M.

    2015-01-01

    The strength of conclusions about the adoption of different categorization strategies--and their implications for theories about the cognitive and neural bases of category learning--depend heavily on the techniques for identifying strategy use. We examine performance in an often-used "information-integration" category structure and…

  4. Strain-Specific Survival of Salmonella enterica in Peanut Oil, Peanut Shell, and Chia Seeds.

    PubMed

    Fong, Karen; Wang, Siyun

    2016-03-01

    In North America, outbreaks of Salmonella have been linked to low-water activity (aw) foods, such as nuts and seeds. These outbreaks have implicated an assortment of Salmonella serotypes. Some Salmonella serotypes (e.g., Enteritidis and Typhimurium) cause high proportions of salmonellosis. Nevertheless, there has recently been an emergence of uncommon Salmonella serotypes and strains (e.g., Tennessee, Hartford, and Thompson) in low-aw foods. The aim of this study was to evaluate the survival characteristics of Salmonella serotypes Enteritidis, Typhimurium, Tennessee, Hartford, and Thompson in three low-aw food ingredients with varying aw: peanut oil (aw = 0.521 ± 0.003), peanut shell (aw = 0.321 ± 0.20), and chia seeds (aw = 0.585 ± 0.003). The survival of individual Salmonella strains on each food matrix was monitored for a maximum of 150 days by spreading the bacterial cells onto Luria-Bertani and/or xylose lysine deoxycholate agar. Overall, Salmonella survived for the longest periods of time in peanut oil (96 ± 8 days), followed by chia seeds (94 ± 46 days). The survival period was substantially reduced on the surface of peanut shell (42 ± 49 h), although PCR after 70 days of incubation revealed the presence of Salmonella cells. In addition, Salmonella exhibited a strain-specific response in the three low-aw foods tested. Salmonella Hartford was identified as highly persistent in all low-aw food matrices, whereas Salmonella Typhimurium was the least persistent. The current research emphasizes the adaptable nature of Salmonella to low-aw food ingredients. This may pose additional problems owing to the downstream production of various end products. Additionally, unique survival characteristics among Salmonella strains highlight the need for tailored mitigation strategies regarding high-risk Salmonella strains in the food industry. PMID:26939645

  5. Strain-Specific Survival of Salmonella enterica in Peanut Oil, Peanut Shell, and Chia Seeds.

    PubMed

    Fong, Karen; Wang, Siyun

    2016-03-01

    In North America, outbreaks of Salmonella have been linked to low-water activity (aw) foods, such as nuts and seeds. These outbreaks have implicated an assortment of Salmonella serotypes. Some Salmonella serotypes (e.g., Enteritidis and Typhimurium) cause high proportions of salmonellosis. Nevertheless, there has recently been an emergence of uncommon Salmonella serotypes and strains (e.g., Tennessee, Hartford, and Thompson) in low-aw foods. The aim of this study was to evaluate the survival characteristics of Salmonella serotypes Enteritidis, Typhimurium, Tennessee, Hartford, and Thompson in three low-aw food ingredients with varying aw: peanut oil (aw = 0.521 ± 0.003), peanut shell (aw = 0.321 ± 0.20), and chia seeds (aw = 0.585 ± 0.003). The survival of individual Salmonella strains on each food matrix was monitored for a maximum of 150 days by spreading the bacterial cells onto Luria-Bertani and/or xylose lysine deoxycholate agar. Overall, Salmonella survived for the longest periods of time in peanut oil (96 ± 8 days), followed by chia seeds (94 ± 46 days). The survival period was substantially reduced on the surface of peanut shell (42 ± 49 h), although PCR after 70 days of incubation revealed the presence of Salmonella cells. In addition, Salmonella exhibited a strain-specific response in the three low-aw foods tested. Salmonella Hartford was identified as highly persistent in all low-aw food matrices, whereas Salmonella Typhimurium was the least persistent. The current research emphasizes the adaptable nature of Salmonella to low-aw food ingredients. This may pose additional problems owing to the downstream production of various end products. Additionally, unique survival characteristics among Salmonella strains highlight the need for tailored mitigation strategies regarding high-risk Salmonella strains in the food industry.

  6. Diagnostic accuracy of existing methods for identifying diabetic foot ulcers from inpatient and outpatient datasets

    PubMed Central

    2010-01-01

    Background As the number of persons with diabetes is projected to double in the next 25 years in the US, an accurate method of identifying diabetic foot ulcers in population-based data sources are ever more important for disease surveillance and public health purposes. The objectives of this study are to evaluate the accuracy of existing methods and to propose a new method. Methods Four existing methods were used to identify all patients diagnosed with a foot ulcer in a Department of Veterans Affairs (VA) hospital from the inpatient and outpatient datasets for 2003. Their electronic medical records were reviewed to verify whether the medical records positively indicate presence of a diabetic foot ulcer in diagnoses, medical assessments, or consults. For each method, five measures of accuracy and agreement were evaluated using data from medical records as the gold standard. Results Our medical record reviews show that all methods had sensitivity > 92% but their specificity varied substantially between 74% and 91%. A method used in Harrington et al. (2004) was the most accurate with 94% sensitivity and 91% specificity and produced an annual prevalence of 3.3% among VA users with diabetes nationwide. A new and simpler method consisting of two codes (707.1× and 707.9) shows an equally good accuracy with 93% sensitivity and 91% specificity and 3.1% prevalence. Conclusions Our results indicate that the Harrington and New methods are highly comparable and accurate. We recommend the Harrington method for its accuracy and the New method for its simplicity and comparable accuracy. PMID:21106076

  7. Identifying prescription opioid use disorder in primary care: diagnostic characteristics of the Current Opioid Misuse Measure (COMM).

    PubMed

    Meltzer, Ellen C; Rybin, Denis; Saitz, Richard; Samet, Jeffrey H; Schwartz, Sonia L; Butler, Stephen F; Liebschutz, Jane M

    2011-02-01

    The Current Opioid Misuse Measure (COMM), a self-report assessment of past-month aberrant medication-related behaviors, has been validated in specialty pain management patients. The performance characteristics of the COMM were evaluated in primary care (PC) patients with chronic pain. It was hypothesized that the COMM could identify patients with prescription drug use disorder (PDD). English-speaking adults awaiting PC visits at an urban, safety-net hospital, who had chronic pain and had received any opioid analgesic prescription in the past year, were administered the COMM. The Composite International Diagnostic Interview served as the "gold standard," using DSM-IV criteria for PDD and other substance use disorders (SUDs). A receiver operating characteristic (ROC) curve demonstrated the COMM's diagnostic test characteristics. Of the 238 participants, 27 (11%) met DSM-IV PDD criteria, whereas 17 (7%) had other SUDs, and 194 (82%) had no disorder. The mean COMM score was higher in those with PDD than among all others (ie, those with other SUDs or no disorder, mean 20.4 [SD 10.8] vs 8.4 [SD 7.5], P<.0001). A COMM score of⩾13 had a sensitivity of 77% and a specificity of 77% for identifying patients with PDD. The area under the ROC curve was 0.84. For chronic pain patients prescribed opioids, the development of PDD is an undesirable complication. Among PC patients with chronic pain-prescribed prescription opioids, the COMM is a promising tool for identifying those with PDD. Among primary care patients with chronic pain-prescribed opioids, the validated Current Opioid Misuse Measure (COMM) is a promising tool for identifying patients with prescription opioid use disorder.

  8. Structural basis for epitope masking and strain specificity of a conserved epitope in an intrinsically disordered malaria vaccine candidate

    PubMed Central

    Morales, Rodrigo A. V.; MacRaild, Christopher A.; Seow, Jeffrey; Krishnarjuna, Bankala; Drinkwater, Nyssa; Rouet, Romain; Anders, Robin F.; Christ, Daniel; McGowan, Sheena; Norton, Raymond S.

    2015-01-01

    Merozoite surface protein 2 (MSP2) is an intrinsically disordered, membrane-anchored antigen of the malaria parasite Plasmodium falciparum. MSP2 can elicit a protective, albeit strain-specific, antibody response in humans. Antibodies are generated to the conserved N- and C-terminal regions but many of these react poorly with the native antigen on the parasite surface. Here we demonstrate that recognition of a conserved N-terminal epitope by mAb 6D8 is incompatible with the membrane-bound conformation of that region, suggesting a mechanism by which native MSP2 escapes antibody recognition. Furthermore, crystal structures and NMR spectroscopy identify transient, strain-specific interactions between the 6D8 antibody and regions of MSP2 beyond the conserved epitope. These interactions account for the differential affinity of 6D8 for the two allelic families of MSP2, even though 6D8 binds to a fully conserved epitope. These results highlight unappreciated mechanisms that may modulate the specificity and efficacy of immune responses towards disordered antigens. PMID:25965408

  9. A diagnostic protocol to identify water buffaloes (Bubalus bubalis) vaccinated with Brucella abortus strain RB51 vaccine.

    PubMed

    Tittarelli, Manuela; Atzeni, Marcello; Calistri, Paolo; Di Giannatale, Elisabetta; Ferri, Nicola; Marchi, Enrico; Martucciello, Alessandra; De Massis, Fabrizio

    2015-01-01

    The use of live vaccine strain RB51 for vaccination of domestic water buffaloes (Bubalus bubalis) at risk of infection with Brucella abortus is permitted notwithstanding the plans for the eradication and only under strict veterinary control. The antibodies induced by RB51 vaccination are not detectable using conventional diagnostic techniques; therefore, it is necessary to have a specific diagnostic tool able to discriminate vaccinated from unvaccinated animals. The combination of a complement fixation test (CFT) with specific RB51 antigen (RB51-CFT) and a brucellin skin test has been demonstrated to be a reliable diagnostic system to identify single cattle (Bos taurus) vaccinated with RB51. So far, no data are available in the international scientific literature regarding the use of this test association in water buffalo. For this reason the suitability of this test combination has been evaluated in a water buffalo herd. One hundred twenty-seven animals farmed in a herd of Salerno province (Campania, Southern Italy), in the context of a presumptive unauthorized use of RB51 vaccine were chosen for this study. All tested animals resulted negative to Rose Bengal test (RBT) and complement fixation test (CFT) used for the detection of specific antibodies against Brucella field strains. Seventy-one animals (56%) developed RB51 antigen-specific CFT (RB51-CFT) antibodies against RB51 vaccine in a first sampling, while 104 animals (82%) gave positive result to a second serum sampling conducted 11 days after the intradermal inoculation of the RB51 brucellin. One hundred and seven animals (84%) showed a positive reaction to the RB51-CFT in at least 1 sampling, while 111 animals (87%) resulted positive to the RB51 brucellin skin test. Thus, analysing the results of the 3 testing in parallel, 119 animals (94%) were positive to at least 1 of the performed tests. The results suggest that the use in parallel of the RB51 brucellin skin test with RB51-CFT may represent a reliable

  10. Strain-Specific Changes in Locomotor Behavior in Larval Zebrafish Elicited by Cholinergic Challenge

    EPA Science Inventory

    Some studies have compared the baseline behavior of different strains of larval zebrafish (Danio rerio), but there is sparse information on strain-specific responses to chemical challenges. The following study examines both the basal activity and response to a pharmacological cha...

  11. Strain-Specific Protective Effect of the Immunity Induced by Live Malarial Sporozoites under Chloroquine Cover

    PubMed Central

    Wijayalath, Wathsala; Cheesman, Sandra; Tanabe, Kazuyuki; Handunnetti, Shiroma; Carter, Richard; Pathirana, Sisira

    2012-01-01

    The efficacy of a whole-sporozoite malaria vaccine would partly be determined by the strain-specificity of the protective responses against malarial sporozoites and liver-stage parasites. Evidence from previous reports were inconsistent, where some studies have shown that the protective immunity induced by irradiated or live sporozoites in rodents or humans were cross-protective and in others strain-specific. In the present work, we have studied the strain-specificity of live sporozoite-induced immunity using two genetically and immunologically different strains of Plasmodium cynomolgi, Pc746 and PcCeylon, in toque monkeys. Two groups of monkeys were immunized against live sporozoites of either the Pc746 (n = 5), or the PcCeylon (n = 4) strain, by the bites of 2–4 sporozoite-infected Anopheles tessellates mosquitoes per monkey under concurrent treatments with chloroquine and primaquine to abrogate detectable blood infections. Subsequently, a group of non-immunized monkeys (n = 4), and the two groups of immunized monkeys were challenged with a mixture of sporozoites of the two strains by the bites of 2–5 infective mosquitoes from each strain per monkey. In order to determine the strain-specificity of the protective immunity, the proportions of parasites of the two strains in the challenge infections were quantified using an allele quantification assay, Pyrosequencing™, based on a single nucleotide polymorphism (SNP) in the parasites’ circumsporozoite protein gene. The Pyrosequencing™ data showed that a significant reduction of parasites of the immunizing strain in each group of strain-specifically immunized monkeys had occurred, indicating a stronger killing effect on parasites of the immunizing strain. Thus, the protective immunity developed following a single, live sporozoite/chloroquine immunization, acted specifically against the immunizing strain and was, therefore, strain-specific. As our experiment does not allow us to determine the

  12. Diagnostic Strategy for Identifying Avian Pathogenic Escherichia coli Based on Four Patterns of Virulence Genes

    PubMed Central

    Schaeffer, Brigitte; Brée, Annie; Mora, Azucena; Dahbi, Ghizlane; Biet, François; Oswald, Eric; Mainil, Jacques; Blanco, Jorge; Moulin-Schouleur, Maryvonne

    2012-01-01

    In order to improve the identification of avian pathogenic Escherichia coli (APEC) strains, an extensive characterization of 1,491 E. coli isolates was conducted, based on serotyping, virulence genotyping, and experimental pathogenicity for chickens. The isolates originated from lesions of avian colibacillosis (n = 1,307) or from the intestines of healthy animals (n = 184) from France, Spain, and Belgium. A subset (460 isolates) of this collection was defined according to their virulence for chicks. Six serogroups (O1, O2, O5, O8, O18, and O78) accounted for 56.5% of the APEC isolates and 22.5% of the nonpathogenic isolates. Thirteen virulence genes were more frequently present in APEC isolates than in nonpathogenic isolates but, individually, none of them could allow the identification of an isolate as an APEC strain. In order to take into account the diversity of APEC strains, a statistical analysis based on a tree-modeling method was therefore conducted on the sample of 460 pathogenic and nonpathogenic isolates. This resulted in the identification of four different associations of virulence genes that enables the identification of 70.2% of the pathogenic strains. Pathogenic strains were identified with an error margin of 4.3%. The reliability of the link between these four virulence patterns and pathogenicity for chickens was validated on a sample of 395 E. coli isolates from the collection. The genotyping method described here allowed the identification of more APEC isolates with greater reliability than the classical serotyping methods currently used in veterinary laboratories. PMID:22378905

  13. Bioorthogonal labeling cell-surface proteins expressed in pancreatic cancer cells to identify potential diagnostic/therapeutic biomarkers

    PubMed Central

    Haun, Randy S; Quick, Charles M; Siegel, Eric R; Raju, Ilangovan; Mackintosh, Samuel G; Tackett, Alan J

    2015-01-01

    To develop new diagnostic and therapeutic tools to specifically target pancreatic tumors, it is necessary to identify cell-surface proteins that may serve as potential tumor-specific targets. In this study we used an azido-labeled bioorthogonal chemical reporter to metabolically label N-linked glycoproteins on the surface of pancreatic cancer cell lines to identify potential targets that may be exploited for detection and/or treatment of pancreatic cancer. Labeled glycoproteins were tagged with biotin using click chemistry, purified by streptavidin-coupled magnetic beads, separated by gel electrophoresis, and identified by liquid chromatography-tandem mass spectrometry (MS). MS/MS analysis of peptides from 3 cell lines revealed 954 unique proteins enriched in the azido sugar samples relative to control sugar samples. A comparison of the proteins identified in each sample indicated 20% of these proteins were present in 2 cell lines (193 of 954) and 17 of the proteins were found in all 3 cell lines. Five of the 17 proteins identified in all 3 cell lines have not been previously reported to be expressed in pancreatic cancer; thus indicating that novel cell-surface proteins can be revealed through glycoprotein profiling. Western analysis of one of these glycoproteins, ecto-5′-nucleotidase (NT5E), revealed it is expressed in 8 out of 8 pancreatic cancer cell lines examined. Further, immunohistochemical analysis of human pancreatic tissues indicates NT5E is significantly overexpressed in pancreatic tumors compared to normal pancreas. Thus, we have demonstrated that metabolic labeling with bioorthogonal chemical reporters can be used to selectively enrich and identify novel cell-surface glycoproteins expressed in pancreatic ductal adenocarcinomas. PMID:26176765

  14. Peripheral Blood Cell Gene Expression Diagnostic for Identifying Symptomatic Transthyretin Amyloidosis Patients: Male and Female Specific Signatures

    PubMed Central

    Kurian, Sunil M.; Novais, Marta; Whisenant, Thomas; Gelbart, Terri; Buxbaum, Joel N.; Kelly, Jeffery W.; Coelho, Teresa; Salomon, Daniel R.

    2016-01-01

    Background: Early diagnosis of familial transthyretin (TTR) amyloid diseases remains challenging because of variable disease penetrance. Currently, patients must have an amyloid positive tissue biopsy to be eligible for disease-modifying therapies. Endomyocardial biopsies are typically amyloid positive when cardiomyopathy is suspected, but this disease manifestation is generally diagnosed late. Early diagnosis is often difficult because patients exhibit apparent symptoms of polyneuropathy, but have a negative amyloid biopsy. Thus, there is a pressing need for an additional early diagnostic strategy for TTR-aggregation-associated polyneuropathy and cardiomyopathy. Methods and Findings: Global peripheral blood cell mRNA expression profiles from 263 tafamidis-treated and untreated V30M Familiar Amyloid Neuropathy patients, asymptomatic V30M carriers, and healthy, age- and sex-matched controls without TTR mutations were used to differentiate symptomatic from asymptomatic patients. We demonstrate that blood cell gene expression patterns reveal sex-independent, as well as male- and female-specific inflammatory signatures in symptomatic FAP patients, but not in asymptomatic carriers. These signatures differentiated symptomatic patients from asymptomatic V30M carriers with >80% accuracy. There was a global downregulation of the eIF2 pathway and its associated genes in all symptomatic FAP patients. We also demonstrated that the molecular scores based on these signatures significantly trended toward normalized values in an independent cohort of 46 FAP patients after only 3 months of tafamidis treatment. Conclusions: This study identifies novel molecular signatures that differentiate symptomatic FAP patients from asymptomatic V30M carriers as well as affected males and females. We envision using this approach, initially in parallel with amyloid biopsies, to identify individuals who are asymptomatic gene carriers that may convert to FAP patients. Upon further validation

  15. Use of Randomly Amplified Polymorphic DNA as a Means of Developing Genus- and Strain-Specific Streptomyces DNA Probes

    PubMed Central

    Roberts, Mark A.; Crawford, Don L.

    2000-01-01

    We have analyzed 20 randomly amplified polymorphic DNA (RAPD) primers against 36 Streptomyces strains, including 17 taxonomically undefined strains, 25 nonstreptomycete actinomycetes, and 12 outgroups consisting of gram-positive and -negative species. Most of the primers were useful in identifying unique DNA polymorphisms of all strains tested. We have used RAPD techniques to develop a genus-specific probe, one not necessarily targeting the ribosomal gene, for Streptomyces, and a strain-specific probe for the biological control agent Streptomyces lydicus WYEC108. In the course of these investigations, small-scale DNA isolations were also developed for efficiently isolating actinomycete DNA. Various modifications of isolation procedures for soil DNA were compared, and the reliability and specificity of the RAPD methodology were tested by specifically detecting the S. lydicus WYEC108 in DNA isolated from soil. PMID:10831438

  16. Modular microfluidic system fabricated in thermoplastics for the strain-specific detection of bacterial pathogens.

    PubMed

    Chen, Yi-Wen; Wang, Hong; Hupert, Mateusz; Witek, Makgorzata; Dharmasiri, Udara; Pingle, Maneesh R; Barany, Francis; Soper, Steven A

    2012-09-21

    The recent outbreaks of a lethal E. coli strain in Germany have aroused renewed interest in developing rapid, specific and accurate systems for detecting and characterizing bacterial pathogens in suspected contaminated food and/or water supplies. To address this need, we have designed, fabricated and tested an integrated modular-based microfluidic system and the accompanying assay for the strain-specific identification of bacterial pathogens. The system can carry out the entire molecular processing pipeline in a single disposable fluidic cartridge and detect single nucleotide variations in selected genes to allow for the identification of the bacterial species, even its strain with high specificity. The unique aspect of this fluidic cartridge is its modular format with task-specific modules interconnected to a fluidic motherboard to permit the selection of the target material. In addition, to minimize the amount of finishing steps for assembling the fluidic cartridge, many of the functional components were produced during the polymer molding step used to create the fluidic network. The operation of the cartridge was provided by electronic, mechanical, optical and hydraulic controls located off-chip and packaged into a small footprint instrument (1 ft(3)). The fluidic cartridge was capable of performing cell enrichment, cell lysis, solid-phase extraction (SPE) of genomic DNA, continuous flow (CF) PCR, CF ligase detection reaction (LDR) and universal DNA array readout. The cartridge was comprised of modules situated on a fluidic motherboard; the motherboard was made from polycarbonate, PC, and used for cell lysis, SPE, CF PCR and CF LDR. The modules were task-specific units and performed universal zip-code array readout or affinity enrichment of the target cells with both made from poly(methylmethacrylate), PMMA. Two genes, uidA and sipB/C, were used to discriminate between E. coli and Salmonella, and evaluated as a model system. Results showed that the fluidic

  17. Modular microfluidic system fabricated in thermoplastics for the strain-specific detection of bacterial pathogens.

    PubMed

    Chen, Yi-Wen; Wang, Hong; Hupert, Mateusz; Witek, Makgorzata; Dharmasiri, Udara; Pingle, Maneesh R; Barany, Francis; Soper, Steven A

    2012-09-21

    The recent outbreaks of a lethal E. coli strain in Germany have aroused renewed interest in developing rapid, specific and accurate systems for detecting and characterizing bacterial pathogens in suspected contaminated food and/or water supplies. To address this need, we have designed, fabricated and tested an integrated modular-based microfluidic system and the accompanying assay for the strain-specific identification of bacterial pathogens. The system can carry out the entire molecular processing pipeline in a single disposable fluidic cartridge and detect single nucleotide variations in selected genes to allow for the identification of the bacterial species, even its strain with high specificity. The unique aspect of this fluidic cartridge is its modular format with task-specific modules interconnected to a fluidic motherboard to permit the selection of the target material. In addition, to minimize the amount of finishing steps for assembling the fluidic cartridge, many of the functional components were produced during the polymer molding step used to create the fluidic network. The operation of the cartridge was provided by electronic, mechanical, optical and hydraulic controls located off-chip and packaged into a small footprint instrument (1 ft(3)). The fluidic cartridge was capable of performing cell enrichment, cell lysis, solid-phase extraction (SPE) of genomic DNA, continuous flow (CF) PCR, CF ligase detection reaction (LDR) and universal DNA array readout. The cartridge was comprised of modules situated on a fluidic motherboard; the motherboard was made from polycarbonate, PC, and used for cell lysis, SPE, CF PCR and CF LDR. The modules were task-specific units and performed universal zip-code array readout or affinity enrichment of the target cells with both made from poly(methylmethacrylate), PMMA. Two genes, uidA and sipB/C, were used to discriminate between E. coli and Salmonella, and evaluated as a model system. Results showed that the fluidic

  18. Modular microfluidic system fabricated in thermoplastics for the strain-specific detection of bacterial pathogens†

    PubMed Central

    Chen, Yi-Wen; Wang, Hong; Hupert, Mateusz; Witek, Makgorzata; Dharmasiri, Udara; Pingle, Maneesh R.; Barany, Francis

    2015-01-01

    The recent outbreaks of a lethal E. coli strain in Germany have aroused renewed interest in developing rapid, specific and accurate systems for detecting and characterizing bacterial pathogens in suspected contaminated food and/or water supplies. To address this need, we have designed, fabricated and tested an integrated modular-based microfluidic system and the accompanying assay for the strain-specific identification of bacterial pathogens. The system can carry out the entire molecular processing pipeline in a single disposable fluidic cartridge and detect single nucleotide variations in selected genes to allow for the identification of the bacterial species, even its strain with high specificity. The unique aspect of this fluidic cartridge is its modular format with task-specific modules interconnected to a fluidic motherboard to permit the selection of the target material. In addition, to minimize the amount of finishing steps for assembling the fluidic cartridge, many of the functional components were produced during the polymer molding step used to create the fluidic network. The operation of the cartridge was provided by electronic, mechanical, optical and hydraulic controls located off-chip and packaged into a small footprint instrument (1 ft3). The fluidic cartridge was capable of performing cell enrichment, cell lysis, solid-phase extraction (SPE) of genomic DNA, continuous flow (CF) PCR, CF ligase detection reaction (LDR) and universal DNA array readout. The cartridge was comprised of modules situated on a fluidic motherboard; the motherboard was made from polycarbonate, PC, and used for cell lysis, SPE, CF PCR and CF LDR. The modules were task-specific units and performed universal zip-code array readout or affinity enrichment of the target cells with both made from poly(methylmethacrylate), PMMA. Two genes, uidA and sipB/C, were used to discriminate between E. coli and Salmonella, and evaluated as a model system. Results showed that the fluidic system

  19. Tracking a Tuberculosis Outbreak Over 21 Years: Strain-Specific Single-Nucleotide Polymorphism Typing Combined With Targeted Whole-Genome Sequencing

    PubMed Central

    Stucki, David; Ballif, Marie; Bodmer, Thomas; Coscolla, Mireia; Maurer, Anne-Marie; Droz, Sara; Butz, Christa; Borrell, Sonia; Längle, Christel; Feldmann, Julia; Furrer, Hansjakob; Mordasini, Carlo; Helbling, Peter; Rieder, Hans L.; Egger, Matthias; Gagneux, Sébastien; Fenner, Lukas

    2015-01-01

    Background. Whole-genome sequencing (WGS) is increasingly used in molecular-epidemiological investigations of bacterial pathogens, despite cost- and time-intensive analyses. We combined strain-specific single-nucleotide polymorphism (SNP) typing and targeted WGS to investigate a tuberculosis cluster spanning 21 years in Bern, Switzerland. Methods. On the basis of genome sequences of 3 historical outbreak Mycobacterium tuberculosis isolates, we developed a strain-specific SNP-typing assay to identify further cases. We screened 1642 patient isolates and performed WGS on all identified cluster isolates. We extracted SNPs to construct genomic networks. Clinical and social data were retrospectively collected. Results. We identified 68 patients associated with the outbreak strain. Most received a tuberculosis diagnosis in 1991–1995, but cases were observed until 2011. Two thirds were homeless and/or substance abusers. Targeted WGS revealed 133 variable SNP positions among outbreak isolates. Genomic network analyses suggested a single origin of the outbreak, with subsequent division into 3 subclusters. Isolates from patients with confirmed epidemiological links differed by 0–11 SNPs. Conclusions. Strain-specific SNP genotyping allowed rapid and inexpensive identification of M. tuberculosis outbreak isolates in a population-based strain collection. Subsequent targeted WGS provided detailed insights into transmission dynamics. This combined approach could be applied to track bacterial pathogens in real time and at high resolution. PMID:25362193

  20. Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells.

    PubMed

    Mvubu, Nontobeko Eunice; Pillay, Balakrishna; Gamieldien, Junaid; Bishai, William; Pillay, Manormoney

    2016-12-01

    Although pulmonary epithelial cells are integral to innate and adaptive immune responses during Mycobacterium tuberculosis infection, global transcriptomic changes in these cells remain largely unknown. Changes in gene expression induced in pulmonary epithelial cells infected with M. tuberculosis F15/LAM4/KZN, F11, F28, Beijing and Unique genotypes were investigated by RNA sequencing (RNA-Seq). The Illumina HiSeq 2000 platform generated 50 bp reads that were mapped to the human genome (Hg19) using Tophat (2.0.10). Differential gene expression induced by the different strains in infected relative to the uninfected cells was quantified and compared using Cufflinks (2.1.0) and MeV (4.0.9), respectively. Gene expression varied among the strains with the total number of genes as follows: F15/LAM4/KZN (1187), Beijing (1252), F11 (1639), F28 (870), Unique (886) and H37Rv (1179). A subset of 292 genes was commonly induced by all strains, where 52 genes were down-regulated while 240 genes were up-regulated. Differentially expressed genes were compared among the strains and the number of induced strain-specific gene signatures were as follows: F15/LAM4/KZN (138), Beijing (52), F11 (255), F28 (55), Unique (186) and H37Rv (125). Strain-specific molecular gene signatures associated with functional pathways were observed only for the Unique and H37Rv strains while certain biological functions may be associated with other strain signatures. This study demonstrated that strains of M. tuberculosis induce differential gene expression and strain-specific molecular signatures in pulmonary epithelial cells. Specific signatures induced by clinical strains of M. tuberculosis can be further explored for novel host-associated biomarkers and adjunctive immunotherapies. PMID:27497873

  1. Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells.

    PubMed

    Mvubu, Nontobeko Eunice; Pillay, Balakrishna; Gamieldien, Junaid; Bishai, William; Pillay, Manormoney

    2016-12-01

    Although pulmonary epithelial cells are integral to innate and adaptive immune responses during Mycobacterium tuberculosis infection, global transcriptomic changes in these cells remain largely unknown. Changes in gene expression induced in pulmonary epithelial cells infected with M. tuberculosis F15/LAM4/KZN, F11, F28, Beijing and Unique genotypes were investigated by RNA sequencing (RNA-Seq). The Illumina HiSeq 2000 platform generated 50 bp reads that were mapped to the human genome (Hg19) using Tophat (2.0.10). Differential gene expression induced by the different strains in infected relative to the uninfected cells was quantified and compared using Cufflinks (2.1.0) and MeV (4.0.9), respectively. Gene expression varied among the strains with the total number of genes as follows: F15/LAM4/KZN (1187), Beijing (1252), F11 (1639), F28 (870), Unique (886) and H37Rv (1179). A subset of 292 genes was commonly induced by all strains, where 52 genes were down-regulated while 240 genes were up-regulated. Differentially expressed genes were compared among the strains and the number of induced strain-specific gene signatures were as follows: F15/LAM4/KZN (138), Beijing (52), F11 (255), F28 (55), Unique (186) and H37Rv (125). Strain-specific molecular gene signatures associated with functional pathways were observed only for the Unique and H37Rv strains while certain biological functions may be associated with other strain signatures. This study demonstrated that strains of M. tuberculosis induce differential gene expression and strain-specific molecular signatures in pulmonary epithelial cells. Specific signatures induced by clinical strains of M. tuberculosis can be further explored for novel host-associated biomarkers and adjunctive immunotherapies.

  2. Gender-related traits in gay men, lesbian women, and heterosexual men and women: the virtual identify of homosexual-heterosexual diagnosticity and gender diagnosticity.

    PubMed

    Lippa, R A

    2000-10-01

    Three studies investigated the relationship between gender-related traits and sexual orientation. Study 1 showed that gay men and lesbians in an unselected sample of 721 college students differed from same-sex heterosexuals most strongly on gender diagnosticity (GD) measures, which assess male- versus female-typicality of interests (effect sizes of 2.70 for men and .96 for women) and least strongly on measures of instrumentality (I) and expressiveness (E). In Study 2, GD measures showed large differences between 95 gay and 136 heterosexual men (effect sizes of 1.61 and 1.83) and between 46 lesbian and 225 heterosexual women (effect sizes of .98 and 1.28), whereas I and E showed much smaller differences. In Study 3, GD showed large differences between 90 gay and 81 heterosexual men (effect sizes of 1.76 and 1.97) and between 82 lesbians and 108 heterosexual women (effect sizes 1.67 and 1.70). whereas I and E showed much smaller differences. Using data from Studies 2 and 3, "gay-heterosexual diagnosticity" measures were computed for men and "lesbian-heterosexual diagnosticity" measures for women, based on occupational and hobby preferences. These measures correlated very strongly with GD measures.

  3. Borrelia burgdorferi strain-specific Osp C-mediated immunity in mice.

    PubMed Central

    Bockenstedt, L K; Hodzic, E; Feng, S; Bourrel, K W; de Silva, A; Montgomery, R R; Fikrig, E; Radolf, J D; Barthold, S W

    1997-01-01

    Antibodies to the outer surface proteins (Osps) A, B, and C of the spirochete Borrelia burgdorferi can prevent infection in animal models of Lyme borreliosis. We have previously demonstrated that immune serum from mice infected with B. burgdorferi N40 can also prevent challenge infection and induce disease regression in infected mice. The antigens targeted by protective and disease-modulating antibodies are presently unknown, but they do not include Osp A or Osp B. Because Osp C antibodies are present in immune mouse serum, we investigated the ability of hyperimmune serum to recombinant Osp C (N40) to protect mice against challenge infection with N40 spirochetes. In both active and passive immunization studies, Osp C (N40) antiserum failed to protect mice from challenge infection with cultured organisms. Mice actively immunized with recombinant Osp C (N40) were susceptible to tick-borne challenge infection, and nymphal ticks remained infected after feeding on Osp C-hyperimmunized mice. In contrast, similar immunization studies performed with Osp C (PKo) antiserum prevented challenge infection of mice with a clone of PKo spirochetes pathogenic for mice. Both Osp C (N40) and Osp C (PKo) antisera showed minimal in vitro borreliacidal activity, and immunofluorescence studies localized Osp C beneath the outer membrane of both N40 and PKo spirochetes. We conclude that Osp C antibody-mediated immunity is strain specific and propose that differences in Osp C surface expression by spirochetes in vivo may account for strain-specific immunity. PMID:9353047

  4. Spontaneous voiding by mice reveals strain-specific lower urinary tract function to be a quantitative genetic trait.

    PubMed

    Yu, Weiqun; Ackert-Bicknell, Cheryl; Larigakis, John D; MacIver, Bryce; Steers, William D; Churchill, Gary A; Hill, Warren G; Zeidel, Mark L

    2014-06-01

    Lower urinary tract (LUT) symptoms become prevalent with aging and affect millions; however, therapy is often ineffective because the etiology is unknown. Existing assays of LUT function in animal models are often invasive; however, a noninvasive assay is required to study symptom progression and determine genetic correlates. Here, we present a spontaneous voiding assay that is simple, reproducible, quantitative, and noninvasive. Young female mice from eight inbred mouse strains (129S1/SvImJ, A/J, C57BL/6J, NOD/ShiLtJ, NZO/H1LtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ) were tested for urination patterns on filter paper. Repeat testing at different times of the day showed minimal within-individual and within-strain variations, but all parameters (spot number, total volume, percent area in primary void, corner voiding, and center voiding) exhibited significant variations between strains. Calculation of the intraclass correlation coefficient, an estimate of broad-sense heritability, for each time of day and for each voiding parameter revealed highly significant heritability [spot number: 61%, percent urine in primary void: 90%, and total volume: 94% (afternoon data)]. Cystometrograms confirmed strong strain-specific urodynamic characteristics. Behavior-voiding correlation analysis showed no correlation with anxiety phenotypes. Diagnostically, the assay revealed LUT symptoms in several systems, including a demonstration of voiding abnormalities in older C57BL/6J mice (18-24 mo), in a model of protamine sulfate-induced urothelial damage and in a model of sucrose-induced diuresis. This assay may be used to derive pathophysiological LUT readouts from mouse models. Voiding characteristics are heritable traits, opening the way for genetic studies of LUT symptoms using outbred mouse populations. PMID:24717733

  5. Stability of transgene methylation patterns in mice: position effects, strain specificity and cellular mosaicism.

    PubMed

    Koetsier, P A; Mangel, L; Schmitz, B; Doerfler, W

    1996-07-01

    The methylation status of a transgene, which carried the adenovirus type 2 E2A late promoter linked to the chloramphenicol acetyltransferase gene, was studied in three transgenic mouse lines (5-8, 7-1 and 8-1). These lines were analysed over a large number of offspring generations beyond the founder animal. In mating experiments, the influence of the parent-of-origin and strain-specific backgrounds on the transgene methylation patterns were assessed and found to have no effect on the pre-established methylation patterns in mouse lines 5-8 and 8-1. The founder animal 7-1 carried two groups of a total of ten transgenes, which were located on two different chromosomes. These arrays of transgenes could be segregated into separate mouse lines 7-1A and 7-1B. The transgenes of 7-1A animals exhibited cellular mosaic methylation patterns that were demethylated in approximately 10% of the offspring in a mixed genetic background. Upon further transmission of these transgenes in a mixed genetic background, the grandparental methylation patterns were reestablished in most progeny. Mating to inbred DBA/2 mice resulted in maintenance of the demethylated pattern or in further demethylation of the transgenes in approximately 50% of the offspring. In contrast, an equal number of transgenic siblings from matings to C57BL/6 mice showed a return to the original methylation pattern. The mosaic methylation status of this locus was apparently controlled by mouse-strain-specific factors. The methylation patterns of the 7-1B transgenes were not cellular mosaic and remained stable in all offspring, as with lines 5-8 and 8-1. Hence, the strain-dependent and cellular mosaic transgene methylation patterns of 7-1A animals were probably a consequence of the chromosomal integration site of the transgenes (position effect).

  6. Strain-specific antiviral activity of iminosugars against human influenza A viruses

    PubMed Central

    Hussain, S.; Miller, J. L.; Harvey, D. J.; Gu, Y.; Rosenthal, P. B.; Zitzmann, N.; McCauley, J. W.

    2015-01-01

    Objectives Drugs that target host cell processes can be employed to complement drugs that specifically target viruses, and iminosugar compounds that inhibit host α-glucosidases have been reported to show antiviral activity against multiple viruses. Here the effect and mechanism of two iminosugar α-glucosidase inhibitors, N-butyl-deoxynojirimycin (NB-DNJ) and N-nonyl-deoxynojirimycin (NN-DNJ), on human influenza A viruses was examined. Methods The viruses examined were a recently circulating seasonal influenza A(H3N2) virus strain A/Brisbane/10/2007, an older H3N2 strain A/Udorn/307/72, and A/Lviv/N6/2009, a strain representative of the currently circulating pandemic influenza A(H1N1)pdm09 virus. Results The inhibitors had the strongest effect on Brisbane/10 and NN-DNJ was more potent than NB-DNJ. Both compounds showed antiviral activity in cell culture against three human influenza A viruses in a strain-specific manner. Consistent with its action as an α-glucosidase inhibitor, NN-DNJ treatment resulted in an altered glycan processing of influenza haemagglutinin (HA) and neuraminidase (NA), confirmed by MS. NN-DNJ treatment was found to reduce the cell surface expression of the H3 subtype HA. The level of sialidase activity of NA was reduced in infected cells, but the addition of exogenous sialidase to the cells did not complement the NN-DNJ-mediated inhibition of virus replication. Using reassortant viruses, the drug susceptibility profile was determined to correlate with the origin of the HA. Conclusions NN-DNJ inhibits influenza A virus replication in a strain-specific manner that is dependent on the HA. PMID:25223974

  7. The establishment of sub-strain specific WHO Reference Reagents for BCG vaccine

    PubMed Central

    Dagg, Belinda; Hockley, Jason; Rigsby, Peter; Ho, Mei M.

    2014-01-01

    As the latest addition to the sub-strain specific WHO Reference Reagents of BCG vaccine, an international collaborative study was completed to evaluate the suitability of a candidate BCG Moreau-RJ sub-strain as a WHO Reference Reagent of BCG vaccine. This follows the recent replacement of the WHO 1st International Reference Preparation for BCG vaccine, by three sub-strain specific WHO Reference Reagents of BCG vaccine (Danish 1331, Tokyo 172-1 and Russian BCG-I) in order to complete the coverage of most predominant sub-strains used for BCG vaccine production and distribution for use worldwide. The study used cultural viable count and modified ATP assays to quantify the preparation and multiplex PCR to confirm the identity of the sub-strain. The establishment of this WHO Reference Reagent of BCG vaccine of Moreau-RJ sub-strain was approved by the WHO Expert Committee on Biological Standardization meeting in October 2012. This preparation is available for distribution by NIBSC-MHRA, UK. The data from real-time stability monitoring demonstrated that these Reference Reagents of BCG vaccine are very stable in storage condition at −20 °C. They serve as the valuable source of BCG Reference Reagents for use as comparators (1) for viability assays (such as cultural viable count and modified ATP assays); (2) for in vivo assays (such as the absence of virulent mycobacteria, dermal reactivity and protection assays) in the evaluation of candidate TB vaccines in non-clinical models; (3) for identity assays using molecular biology techniques. PMID:25312272

  8. Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed mutagenesis study

    SciTech Connect

    Tan Ming |; Xia Ming; Cao Sheng; Huang Pengwei; Farkas, Tibor |; Meller, Jarek |; Hegde, Rashmi S. |; Li Xuemei; Rao Zihe; Jiang Xi |

    2008-09-30

    Noroviruses interact with histo-blood group antigen (HBGA) receptors in a strain-specific manner probably detecting subtle structural differences in the carbohydrate receptors. The specific recognition of types A and B antigens by various norovirus strains is a typical example. The only difference between the types A and B antigens is the acetamide linked to the terminal galactose of the A but not to the B antigen. The crystal structure of the P dimer of a GII-4 norovirus (VA387) bound to types A and B trisaccharides has elucidated the A/B binding site on the capsid but did not explain the binding specificity of the two antigens. In this study, using site-directed mutagenesis, we have identified three residues on the VA387 capsid that are sterically close to the acetamide and are required for binding to A but not B antigens, indicating that the acetamide determines the binding specificity between the A and B antigens. Further mutational analysis showed that a nearby open cavity may also be involved in binding specificity to HBGAs. In addition, a systematic mutational analysis of residues in and around the binding interface has identified a group of amino acids that are required for binding but do not have direct contact with the carbohydrate antigens, implying that these residues may be involved in the structural integrity of the receptor binding interface. Taken together, our study provides new insights into the carbohydrate/capsid interactions which are a valuable complement to the atomic structures in understanding the virus/host interaction and in the future design of antiviral agents.

  9. Evaluation of strain-specific primers for identification of Lactobacillus rhamnosus GG.

    PubMed

    Endo, Akihito; Aakko, Juhani; Salminen, Seppo

    2012-12-01

    Lactobacillus rhamnosus strain GG (ATCC 53103) is one of the most widely studied and commercialized probiotic strains, and thus strain-specific identification for the strain is highly valuable. In this study, two published PCR-based identification methods for strain GG, a transposase gene-targeting system and a phage-related gene-targeting system, were evaluated. The former produced amplicons from eight of the 41 strains tested and the phage-related system from five of the tested strains, including the strain GG. Fingerprinting analysis indicated that the strains LMG 18025, LMG 18030, and LMG 18038, which had an amplicon by the former system but none by the latter, were genetically distinguishable from L. rhamnosus GG at strain level. Strains LMG 23320, LMG 23325, LMG 23534, and LMG 25859 showed profiles very similar to that of the strain GG, suggesting that these strains might be identical to GG or derivative strains of it. The results here indicated that the phage-related gene-targeting system is a good tool for accurate identification of L. rhamnosus GG. This system would be able to detect both the original L. rhamnosus GG and its derivative strains.

  10. Strain-specific antibodies reduce co-feeding transmission of the Lyme disease pathogen, Borrelia afzelii.

    PubMed

    Jacquet, Maxime; Durand, Jonas; Rais, Olivier; Voordouw, Maarten J

    2016-03-01

    Vector-borne pathogens use a diversity of strategies to evade the vertebrate immune system. Co-feeding transmission is a potential immune evasion strategy because the vector-borne pathogen minimizes the time spent in the vertebrate host. We tested whether the Lyme disease pathogen, Borrelia afzelii, can use co-feeding transmission to escape the acquired immune response in the vertebrate host. We induced a strain-specific, protective antibody response by immunizing mice with one of two variants of OspC (A3 and A10), the highly variable outer surface protein C of Borrelia pathogens. Immunized mice were challenged via tick bite with B. afzelii strains A3 or A10 and infested with larval ticks at days 2 and 34 post-infection to measure co-feeding and systemic transmission respectively. Antibodies against a particular OspC variant significantly reduced co-feeding transmission of the targeted (homologous) strain but not the non-targeted (heterologous) strain. Cross-immunity between OspC antigens had no effect in co-feeding ticks but reduced the spirochaete load twofold in ticks infected via systemic transmission. In summary, OspC-specific antibodies reduced co-feeding transmission of a homologous but not a heterologous strain of B. afzelii. Co-feeding transmission allowed B. afzelii to evade the negative consequences of cross-immunity on the tick spirochaete load.

  11. Strain-specific regulation of intracellular Wolbachia density in multiply infected insects.

    PubMed

    Mouton, L; Henri, H; Bouletreau, M; Vavre, F

    2003-12-01

    Vertically transmitted symbionts suffer a severe reduction in numbers when they pass through host generations, resulting in genetic homogeneity or even clonality of their populations. Wolbachia endosymbionts that induce cytoplasmic incompatibility in their hosts depart from this rule, because cytoplasmic incompatibility actively maintains multiple infection within hosts. Hosts and symbionts are thus probably under peculiar selective pressures that must shape the way intracellular bacterial populations are regulated. We studied the density and location of Wolbachia within adult Leptopilina heterotoma, a haplodiploid wasp that is parasitic on Drosophila and that is naturally infected with three Wolbachia strains, but for which we also obtained one simply infected and two doubly infected lines. Comparison of these four lines by quantitative polymerase chain reaction using a real-time detection system showed that total Wolbachia density varies according to the infection status of individuals, while the specific density of each Wolbachia strain remains constant regardless of the presence of other strains. This suggests that Wolbachia strains do not compete with one another within the same host individual, and that a strain-specific regulatory mechanism is operating. We discuss the regulatory mechanisms that are involved, and how this process might have evolved as a response to selective pressures acting on both partners. PMID:14629360

  12. Isolation of Rhizobium loti Strain-Specific DNA Sequences by Subtraction Hybridization

    PubMed Central

    Bjourson, A. J.; Cooper, J. E.

    1988-01-01

    Mixed-phase (heterogeneous) and single-phase (homogeneous) DNA subtraction-hybridization methods were used to isolate specific DNA probes for closely related Rhizobium loti strains. In the heterogeneous method, DNA from the prospective probe strain was repeatedly hybridized to a mixture of DNA from cross-hybridizing strains (subtracter DNA) which was immobilized on an epoxy-activated cellulose matrix. Probe strain sequences which shared homology with the matrix-bound subtracter DNA hybridized to it, leaving unique probe strain sequences in the mobile phase. In the homogeneous method, probe strain sequences were hybridized in solution to biotinylated, mercurated subtracter DNA. Biotinylated, mercurated subtracer DNA and probe strain sequences hybridized to it were removed by two-step affinity chromatography on streptavidin-agarose and thiol-Sepharose. The specificity of the sequences remaining after subtraction hybridization by both methods was assessed and compared by colony hybridization with R. loti strains. Both methods allowed the rapid isolation of strain-specific DNA fragments which were suitable for use as probes. Images PMID:16347782

  13. Strain-specific probiotics properties of Lactobacillus fermentum, Lactobacillus plantarum and Lactobacillus brevis isolates from Brazilian food products.

    PubMed

    Ramos, Cíntia Lacerda; Thorsen, Line; Schwan, Rosane Freitas; Jespersen, Lene

    2013-10-01

    A total of 234 LAB isolates from Brazilian food products were initially screened for their ability to survive at pH 2.0. Fifty one of the isolates survived and were selected. They were characterized by phenotypic methods, rep-PCR and identified using 16S rRNA gene sequencing as Lactobacillus fermentum (34 isolates), Lactobacillus plantarum (10) and Lactobacillus brevis (7). Based on being either highly tolerant to bile, showing an ability for auto-aggregation and/or hydrophobic properties, one L. fermentum (CH58), three L. plantarum (CH3, CH41 and SAU96) and two L. brevis (SAU105 and FFC199) were selected. The highest co-aggregation ability with Escherichia coli was observed to L. plantarum CH41. L. brevis SAU105 and FFC199 and L. fermentum CH58 exhibited antagonistic activity towards the pathogens Listeria monocytogenes and Staphylococcus aureus. L. plantarum CH3 and CH41 and L. brevis FFC199 showed adhesion ability to Caco-2 cells (1.6, 1.1 and 0.9%, respectively) similar to the commercial probiotic, Lactobacillus rhamnosus GG (1.5%). They were able to increase the transepithelial electrical resistance (TEER) of Caco-2 cells over 24 h (p < 0.05). The present work showed that the probiotic characteristics were strain-specific and that the isolates L. plantarum CH3 and CH41 (cocoa) and L. brevis FFC199 (cauim) exhibited potential probiotics properties.

  14. Strain-specific colonization patterns and serum modulation of multi-species oral biofilm development.

    PubMed

    Biyikoğlu, Basak; Ricker, Austin; Diaz, Patricia I

    2012-08-01

    Periodontitis results from an ecological shift in the composition of subgingival biofilms. Subgingival community maturation is modulated by inter-organismal interactions and the relationship of communities with the host. In an effort to better understand this process, we evaluated biofilm formation, with oral commensal species, by three strains of the subgingivally prevalent microorganism Fusobacterium nucleatum and four strains of the periodontopathogen Porphyromonas gingivalis. We also tested the effect of serum, which resembles gingival exudates, on subgingival biofilms. Biofilms were allowed to develop in flow cells using salivary medium. We found that although not all strains of F. nucleatum were able to grow in mono-species biofilms, forming a community with health-associated partners Actinomyces oris and Veillonella parvula promoted biofilm growth of all F. nucleatum strains. Strains of P. gingivalis also showed variable ability to form mono-species biofilms. P. gingivalis W50 and W83 did not form biofilms, while ATCC 33277 and 381 formed biofilm structures, but only strain ATCC 33277 grew over time. Unlike the enhanced growth of F. nucleatum with the two health-associated species, no strain of P. gingivalis grew in three-species communities with A. oris and V. parvula. However, addition of F. nucleatum facilitated growth of P. gingivalis ATCC 33277 with health-associated partners. Importantly, serum negatively affected the adhesion of F. nucleatum, while it favored biofilm growth by P. gingivalis. This work highlights strain specificity in subgingival biofilm formation. Environmental factors such as serum alter the colonization patterns of oral microorganisms and could impact subgingival biofilms by selectively promoting pathogenic species.

  15. Strain-Specific Interactions of Listeria monocytogenes with the Autophagy System in Host Cells

    PubMed Central

    Stöckli, Martina; Higgins, Darren E.; Brumell, John H.

    2015-01-01

    Listeria monocytogenes is an intracellular bacterial pathogen that can replicate in the cytosol of host cells. These bacteria undergo actin-based motility in the cytosol via expression of ActA, which recruits host actin-regulatory proteins to the bacterial surface. L. monocytogenes is thought to evade killing by autophagy using ActA-dependent mechanisms. ActA-independent mechanisms of autophagy evasion have also been proposed, but remain poorly understood. Here we examined autophagy of non-motile (ΔactA) mutants of L. monocytogenes strains 10403S and EGD-e, two commonly studied strains of this pathogen. The ΔactA mutants displayed accumulation of ubiquitinated proteins and p62/SQSTM1 on their surface. However, only strain EGD-e ΔactA displayed colocalization with the autophagy marker LC3 at 8 hours post infection. A bacteriostatic agent (chloramphenicol) was required for LC3 recruitment to 10403S ΔactA, suggesting that these bacteria produce a factor for autophagy evasion. Internalin K was proposed to block autophagy of L. monocytogenes in the cytosol of host cells. However, deletion of inlK in either the wild-type or ΔactA background of strain 10403S had no impact on autophagy evasion by bacteria, indicating it does not play an essential role in evading autophagy. Replication of ΔactA mutants of strain EGD-e and 10403S was comparable to their parent wild-type strain in macrophages. Thus, ΔactA mutants of L. monocytogenes can block killing by autophagy at a step downstream of protein ubiquitination and, in the case of strain EGD-e, downstream of LC3 recruitment to bacteria. Our findings highlight the strain-specific differences in the mechanisms that L. monocytogenes uses to evade killing by autophagy in host cells. PMID:25970638

  16. Pneumocystis Elicits a STAT6-Dependent, Strain-Specific Innate Immune Response and Airway Hyperresponsiveness

    PubMed Central

    Meissner, Nicole N.; Siemsen, Dan W.; McInnerney, Kate; Harmsen, Allen G.

    2012-01-01

    It is widely held that exposure to pathogens such as fungi can be an agent of comorbidity, such as exacerbation of asthma or chronic obstructive pulmonary disease. Although many studies have examined allergic responses to fungi and their effects on pulmonary function, the possible pathologic implications of the early innate responses to fungal pathogens have not been explored. We examined early responses to the atypical fungus Pneumocystis in two common strains of mice in terms of overall immunological response and related pathology, such as cell damage and airway hyperresponsiveness (AHR). We found a strong strain-specific response in BALB/c mice that included recruitment of neutrophils, NK, NKT, and CD4 T cells. This response was accompanied by elevated indicators of lung damage (bronchoalveolar lavage fluid albumin and LDH) and profound AHR. This early response was absent in C57BL/6 mice, although both strains exhibited a later response associated with the clearance of Pneumocystis. We found that this AHR could not be attributed exclusively to the presence of recruited neutrophils, NKT, NK, or CD4 cells or to the actions of IFN-γ or IL-4. However, in the absence of STAT6 signaling, AHR and inflammatory cell recruitment were virtually absent. Gene expression analysis indicated that this early response included activation of several transcription factors that could be involved in pulmonary remodeling. These results show that exposure to a fungus such as Pneumocystis can elicit pulmonary responses that may contribute to morbidity, even without prior sensitization, in the context of certain genetic backgrounds. PMID:21960549

  17. Generation of a Novel Bacteriophage Library Displaying scFv Antibody Fragments from the Natural Buffalo Host to Identify Antigens from Adult Schistosoma japonicum for Diagnostic Development.

    PubMed

    Hosking, Christopher G; McWilliam, Hamish E G; Driguez, Patrick; Piedrafita, David; Li, Yuesheng; McManus, Donald P; Ilag, Leodevico L; Meeusen, Els N T; Veer, Michael J de

    2015-12-01

    The development of effective diagnostic tools will be essential in the continuing fight to reduce schistosome infection; however, the diagnostic tests available to date are generally laborious and difficult to implement in current parasite control strategies. We generated a series of single-chain antibody Fv domain (scFv) phage display libraries from the portal lymph node of field exposed water buffaloes, Bubalus bubalis, 11-12 days post challenge with Schistosoma japonicum cercariae. The selected scFv-phages showed clear enrichment towards adult schistosomes and excretory-secretory (ES) proteins by immunofluorescence, ELISA and western blot analysis. The enriched libraries were used to probe a schistosome specific protein microarray resulting in the recognition of a number of proteins, five of which were specific to schistosomes, with RNA expression predominantly in the adult life-stage based on interrogation of schistosome expressed sequence tags (EST). As the libraries were enriched by panning against ES products, these antigens may be excreted or secreted into the host vasculature and hence may make good targets for a diagnostic assay. Further selection of the scFv library against infected mouse sera identified five soluble scFv clones that could selectively recognise soluble whole adult preparations (SWAP) relative to an irrelevant protein control (ovalbumin). Furthermore, two of the identified scFv clones also selectively recognised SWAP proteins when spiked into naïve mouse sera. These host B-cell derived scFvs that specifically bind to schistosome protein preparations will be valuable reagents for further development of a cost effective point-of-care diagnostic test. PMID:26684756

  18. Generation of a Novel Bacteriophage Library Displaying scFv Antibody Fragments from the Natural Buffalo Host to Identify Antigens from Adult Schistosoma japonicum for Diagnostic Development

    PubMed Central

    Hosking, Christopher G.; McWilliam, Hamish E. G.; Driguez, Patrick; Piedrafita, David; Li, Yuesheng; McManus, Donald P.; Ilag, Leodevico L.; Meeusen, Els N. T.; de Veer, Michael J.

    2015-01-01

    The development of effective diagnostic tools will be essential in the continuing fight to reduce schistosome infection; however, the diagnostic tests available to date are generally laborious and difficult to implement in current parasite control strategies. We generated a series of single-chain antibody Fv domain (scFv) phage display libraries from the portal lymph node of field exposed water buffaloes, Bubalus bubalis, 11–12 days post challenge with Schistosoma japonicum cercariae. The selected scFv-phages showed clear enrichment towards adult schistosomes and excretory-secretory (ES) proteins by immunofluorescence, ELISA and western blot analysis. The enriched libraries were used to probe a schistosome specific protein microarray resulting in the recognition of a number of proteins, five of which were specific to schistosomes, with RNA expression predominantly in the adult life-stage based on interrogation of schistosome expressed sequence tags (EST). As the libraries were enriched by panning against ES products, these antigens may be excreted or secreted into the host vasculature and hence may make good targets for a diagnostic assay. Further selection of the scFv library against infected mouse sera identified five soluble scFv clones that could selectively recognise soluble whole adult preparations (SWAP) relative to an irrelevant protein control (ovalbumin). Furthermore, two of the identified scFv clones also selectively recognised SWAP proteins when spiked into naïve mouse sera. These host B-cell derived scFvs that specifically bind to schistosome protein preparations will be valuable reagents for further development of a cost effective point-of-care diagnostic test. PMID:26684756

  19. Generation of a Novel Bacteriophage Library Displaying scFv Antibody Fragments from the Natural Buffalo Host to Identify Antigens from Adult Schistosoma japonicum for Diagnostic Development.

    PubMed

    Hosking, Christopher G; McWilliam, Hamish E G; Driguez, Patrick; Piedrafita, David; Li, Yuesheng; McManus, Donald P; Ilag, Leodevico L; Meeusen, Els N T; Veer, Michael J de

    2015-12-01

    The development of effective diagnostic tools will be essential in the continuing fight to reduce schistosome infection; however, the diagnostic tests available to date are generally laborious and difficult to implement in current parasite control strategies. We generated a series of single-chain antibody Fv domain (scFv) phage display libraries from the portal lymph node of field exposed water buffaloes, Bubalus bubalis, 11-12 days post challenge with Schistosoma japonicum cercariae. The selected scFv-phages showed clear enrichment towards adult schistosomes and excretory-secretory (ES) proteins by immunofluorescence, ELISA and western blot analysis. The enriched libraries were used to probe a schistosome specific protein microarray resulting in the recognition of a number of proteins, five of which were specific to schistosomes, with RNA expression predominantly in the adult life-stage based on interrogation of schistosome expressed sequence tags (EST). As the libraries were enriched by panning against ES products, these antigens may be excreted or secreted into the host vasculature and hence may make good targets for a diagnostic assay. Further selection of the scFv library against infected mouse sera identified five soluble scFv clones that could selectively recognise soluble whole adult preparations (SWAP) relative to an irrelevant protein control (ovalbumin). Furthermore, two of the identified scFv clones also selectively recognised SWAP proteins when spiked into naïve mouse sera. These host B-cell derived scFvs that specifically bind to schistosome protein preparations will be valuable reagents for further development of a cost effective point-of-care diagnostic test.

  20. Diagnostic Utility of the Posttraumatic Stress Disorder (PTSD) Checklist for Identifying Full and Partial PTSD in Active-Duty Military.

    PubMed

    Dickstein, Benjamin D; Weathers, Frank W; Angkaw, Abigail C; Nievergelt, Caroline M; Yurgil, Kate; Nash, William P; Baker, Dewleen G; Litz, Brett T

    2015-06-01

    The aim of this study was to determine optimally efficient cutoff scores on the Posttraumatic Stress Disorder Checklist (PCL) for identifying full posttraumatic stress disorder (PTSD) and partial PTSD (P-PTSD) in active-duty Marines and Sailors. Participants were 1,016 Marines and Sailors who were administered the PCL and Clinician-Administered PTSD Scale (CAPS) 3 months after returning from Operations Iraqi and Enduring Freedom. PCL cutoffs were tested against three CAPS-based classifications: full PTSD, stringent P-PTSD, and lenient P-PTSD. A PCL score of 39 was found to be optimally efficient for identifying full PTSD. Scores of 38 and 33 were found to be optimally efficient for identifying stringent and lenient P-PTSD, respectively. Findings suggest that the PCL cutoff that is optimally efficient for detecting PTSD in active-duty Marines and Sailors is substantially lower than the score of 50 commonly used by researchers. In addition, findings provide scores useful for identifying P-PTSD in returning service members.

  1. Cost-effectiveness of diagnostic strategies using quantitative real-time PCR and bacterial culture to identify contagious mastitis cases in large dairy herds.

    PubMed

    Murai, Kiyokazu; Lehenbauer, Terry W; Champagne, John D; Glenn, Kathy; Aly, Sharif S

    2014-03-01

    the 3 pathogens. A stochastic model was used to assess the effect of prevalence or herd size on the cost-effectiveness of diagnostic strategies. In the current study, increasing the prevalence of mastitis did not alter the ranking of strategies by cost-effectiveness. However, larger herds could benefit from testing larger pools such as 50 or 100 samples to improve cost-effectiveness. Several diagnostic strategy options exist to identify contagious mastitis in herds, decisions should be based on cost and sensitivity of the strategies available. PMID:24485275

  2. The Diagnostic Value of Serum C-Reactive Protein for Identifying Pneumonia in Hospitalized Patients with Acute Respiratory Symptoms

    PubMed Central

    Utrillo, Laia; Bielsa, Silvia; Falguera, Miquel; Porcel, José M.

    2016-01-01

    Background. The clinical diagnosis of pneumonia is sometimes difficult since chest radiographs are often indeterminate. In this study, we aimed to assess whether serum C-reactive protein (CRP) could assist in identifying patients with pneumonia. Methods. For one winter, all consecutive patients with acute respiratory symptoms admitted to the emergency ward of a single center were prospectively enrolled. In addition to chest radiographs, basic laboratory tests, and microbiology, serum levels of CRP were measured at entry. Results. A total of 923 (62.3%) of 1473 patients hospitalized for acute respiratory symptoms were included. Subjects with a final diagnosis of pneumonia had higher serum CRP levels (median 187 mg/L) than those with exacerbations of chronic obstructive pulmonary disease (63 mg/L) or acute bronchitis (54 mg/L, p < 0.01). CRP was accurate in identifying pneumonia (area under the curve 0.84, 95% CI 0.82–0.87). The multilevel likelihood ratio (LR) for intervals of CRP provided useful information on the posttest probability of having pneumonia. CRP intervals above 200 mg/L were associated with LR+ > 5, for which pneumonia is likely, whereas CRP intervals below 75 mg/L were associated with LR < 0.2, for which pneumonia is unlikely. Conclusion. Serum CRP may be a useful addition for diagnosing pneumonia in hospitalized patients with acute respiratory symptoms.

  3. The Diagnostic Value of Serum C-Reactive Protein for Identifying Pneumonia in Hospitalized Patients with Acute Respiratory Symptoms

    PubMed Central

    Utrillo, Laia; Bielsa, Silvia; Falguera, Miquel; Porcel, José M.

    2016-01-01

    Background. The clinical diagnosis of pneumonia is sometimes difficult since chest radiographs are often indeterminate. In this study, we aimed to assess whether serum C-reactive protein (CRP) could assist in identifying patients with pneumonia. Methods. For one winter, all consecutive patients with acute respiratory symptoms admitted to the emergency ward of a single center were prospectively enrolled. In addition to chest radiographs, basic laboratory tests, and microbiology, serum levels of CRP were measured at entry. Results. A total of 923 (62.3%) of 1473 patients hospitalized for acute respiratory symptoms were included. Subjects with a final diagnosis of pneumonia had higher serum CRP levels (median 187 mg/L) than those with exacerbations of chronic obstructive pulmonary disease (63 mg/L) or acute bronchitis (54 mg/L, p < 0.01). CRP was accurate in identifying pneumonia (area under the curve 0.84, 95% CI 0.82–0.87). The multilevel likelihood ratio (LR) for intervals of CRP provided useful information on the posttest probability of having pneumonia. CRP intervals above 200 mg/L were associated with LR+ > 5, for which pneumonia is likely, whereas CRP intervals below 75 mg/L were associated with LR < 0.2, for which pneumonia is unlikely. Conclusion. Serum CRP may be a useful addition for diagnosing pneumonia in hospitalized patients with acute respiratory symptoms. PMID:27610265

  4. The Diagnostic Value of Serum C-Reactive Protein for Identifying Pneumonia in Hospitalized Patients with Acute Respiratory Symptoms.

    PubMed

    Ruiz-González, Agustín; Utrillo, Laia; Bielsa, Silvia; Falguera, Miquel; Porcel, José M

    2016-01-01

    Background. The clinical diagnosis of pneumonia is sometimes difficult since chest radiographs are often indeterminate. In this study, we aimed to assess whether serum C-reactive protein (CRP) could assist in identifying patients with pneumonia. Methods. For one winter, all consecutive patients with acute respiratory symptoms admitted to the emergency ward of a single center were prospectively enrolled. In addition to chest radiographs, basic laboratory tests, and microbiology, serum levels of CRP were measured at entry. Results. A total of 923 (62.3%) of 1473 patients hospitalized for acute respiratory symptoms were included. Subjects with a final diagnosis of pneumonia had higher serum CRP levels (median 187 mg/L) than those with exacerbations of chronic obstructive pulmonary disease (63 mg/L) or acute bronchitis (54 mg/L, p < 0.01). CRP was accurate in identifying pneumonia (area under the curve 0.84, 95% CI 0.82-0.87). The multilevel likelihood ratio (LR) for intervals of CRP provided useful information on the posttest probability of having pneumonia. CRP intervals above 200 mg/L were associated with LR+ > 5, for which pneumonia is likely, whereas CRP intervals below 75 mg/L were associated with LR < 0.2, for which pneumonia is unlikely. Conclusion. Serum CRP may be a useful addition for diagnosing pneumonia in hospitalized patients with acute respiratory symptoms. PMID:27610265

  5. The sensitivity and specificity of four questions (HARK) to identify intimate partner violence: a diagnostic accuracy study in general practice

    PubMed Central

    Sohal, Hardip; Eldridge, Sandra; Feder, Gene

    2007-01-01

    Background Intimate partner violence (IPV) including physical, sexual and emotional violence, causes short and long term ill-health. Brief questions that reliably identify women experiencing IPV who present in clinical settings are a pre-requisite for an appropriate response from health services to this substantial public health problem. We estimated the sensitivity and specificity of four questions (HARK) developed from the Abuse Assessment screen, compared to a 30-item abuse questionnaire, the Composite Abuse Scale (CAS). Methods We administered the four HARK questions and the CAS to women approached by two researchers in general practice waiting rooms in Newham, east London. Inclusions: women aged more than 17 years waiting to see a doctor or nurse, who had been in an intimate relationship in the last year. Exclusions: women who were accompanied by children over four years of age or another adult, too unwell to complete the questionnaires, unable to understand English or unable to give informed consent. Results Two hundred and thirty two women were recruited. The response rate was 54%. The prevalence of current intimate partner violence, within the last 12 months, using the CAS cut off score of ≥3, was 23% (95% C.I. 17% to 28%) with pre-test odds of 0.3 (95% C.I. 0.2 to 0.4). The receiver operator characteristic curve demonstrated that a HARK cut off score of ≥1 maximises the true positives whilst minimising the false positives. The sensitivity of the optimal HARK cut-off score of ≥1 was 81% (95% C.I. 69% to 90%), specificity 95% (95% C.I. 91% to 98%), positive predictive value 83% (95% C.I. 70% to 91%), negative predictive value 94% (95% C.I. 90% to 97%), likelihood ratio 16 (95% C.I. 8 to 31) and post-test odds 5. Conclusion The four HARK questions accurately identify women experiencing IPV in the past year and may help women disclose abuse in general practice. The HARK questions could be incorporated into the electronic medical record in primary care to

  6. Diagnostic Exome Sequencing Identifies a Novel Gene, EMILIN1, Associated with Autosomal‐Dominant Hereditary Connective Tissue Disease

    PubMed Central

    Capuano, Alessandra; Bucciotti, Francesco; Farwell, Kelly D.; Tippin Davis, Brigette; Mroske, Cameron; Hulick, Peter J.; Weissman, Scott M.; Gao, Qingshen; Spessotto, Paola; Doliana, Roberto

    2015-01-01

    ABSTRACT Heritable connective tissue diseases are a highly heterogeneous family of over 200 disorders that affect the extracellular matrix. While the genetic basis of several disorders is established, the etiology has not been discovered for a large portion of patients, likely due to rare yet undiscovered disease genes. By performing trio‐exome sequencing of a 55‐year‐old male proband presenting with multiple symptoms indicative of a connective disorder, we identified a heterozygous missense alteration in exon 1 of the Elastin Microfibril Interfacer 1 (EMILIN1) gene, c.64G>A (p.A22T). The proband presented with ascending and descending aortic aneurysms, bilateral lower leg and foot sensorimotor peripheral neuropathy, arthropathy, and increased skin elasticity. Sanger sequencing confirmed that the EMILIN1 alteration, which maps around the signal peptide cleavage site, segregated with disease in the affected proband, mother, and son. The impaired secretion of EMILIN‐1 in cells transfected with the mutant p.A22T coincided with abnormal protein accumulation within the endoplasmic reticulum. In skin biopsy of the proband, we detected less EMILIN‐1 with disorganized and abnormal coarse fibrils, aggregated deposits underneath the epidermis basal lamina, and dermal cells apoptosis. These findings collectively suggest that EMILIN1 may represent a new disease gene associated with an autosomal‐dominant connective tissue disorder. PMID:26462740

  7. Diagnostic Exome Sequencing Identifies a Novel Gene, EMILIN1, Associated with Autosomal-Dominant Hereditary Connective Tissue Disease.

    PubMed

    Capuano, Alessandra; Bucciotti, Francesco; Farwell, Kelly D; Tippin Davis, Brigette; Mroske, Cameron; Hulick, Peter J; Weissman, Scott M; Gao, Qingshen; Spessotto, Paola; Colombatti, Alfonso; Doliana, Roberto

    2016-01-01

    Heritable connective tissue diseases are a highly heterogeneous family of over 200 disorders that affect the extracellular matrix. While the genetic basis of several disorders is established, the etiology has not been discovered for a large portion of patients, likely due to rare yet undiscovered disease genes. By performing trio-exome sequencing of a 55-year-old male proband presenting with multiple symptoms indicative of a connective disorder, we identified a heterozygous missense alteration in exon 1 of the Elastin Microfibril Interfacer 1 (EMILIN1) gene, c.64G>A (p.A22T). The proband presented with ascending and descending aortic aneurysms, bilateral lower leg and foot sensorimotor peripheral neuropathy, arthropathy, and increased skin elasticity. Sanger sequencing confirmed that the EMILIN1 alteration, which maps around the signal peptide cleavage site, segregated with disease in the affected proband, mother, and son. The impaired secretion of EMILIN-1 in cells transfected with the mutant p.A22T coincided with abnormal protein accumulation within the endoplasmic reticulum. In skin biopsy of the proband, we detected less EMILIN-1 with disorganized and abnormal coarse fibrils, aggregated deposits underneath the epidermis basal lamina, and dermal cells apoptosis. These findings collectively suggest that EMILIN1 may represent a new disease gene associated with an autosomal-dominant connective tissue disorder.

  8. Temperature diagnostic to identify high risk areas and optimize Legionella pneumophila surveillance in hot water distribution systems.

    PubMed

    Bédard, Emilie; Fey, Stéphanie; Charron, Dominique; Lalancette, Cindy; Cantin, Philippe; Dolcé, Patrick; Laferrière, Céline; Déziel, Eric; Prévost, Michèle

    2015-03-15

    Legionella pneumophila is frequently detected in hot water distribution systems and thermal control is a common measure implemented by health care facilities. A risk assessment based on water temperature profiling and temperature distribution within the network is proposed, to guide effective monitoring strategies and allow the identification of high risk areas. Temperature and heat loss at control points (water heater, recirculation, representative points-of-use) were monitored in various sections of five health care facilities hot water distribution systems and results used to develop a temperature-based risk assessment tool. Detailed investigations show that defective return valves in faucets can cause widespread temperature losses because of hot and cold water mixing. Systems in which water temperature coming out of the water heaters was kept consistently above 60 °C and maintained above 55 °C across the network were negative for Legionella by culture or qPCR. For systems not meeting these temperature criteria, risk areas for L. pneumophila were identified using temperature profiling and system's characterization; higher risk was confirmed by more frequent microbiological detection by culture and qPCR. Results confirmed that maintaining sufficiently high temperatures within hot water distribution systems suppressed L. pneumophila culturability. However, the risk remains as shown by the persistence of L. pneumophila by qPCR.

  9. Temperature diagnostic to identify high risk areas and optimize Legionella pneumophila surveillance in hot water distribution systems.

    PubMed

    Bédard, Emilie; Fey, Stéphanie; Charron, Dominique; Lalancette, Cindy; Cantin, Philippe; Dolcé, Patrick; Laferrière, Céline; Déziel, Eric; Prévost, Michèle

    2015-03-15

    Legionella pneumophila is frequently detected in hot water distribution systems and thermal control is a common measure implemented by health care facilities. A risk assessment based on water temperature profiling and temperature distribution within the network is proposed, to guide effective monitoring strategies and allow the identification of high risk areas. Temperature and heat loss at control points (water heater, recirculation, representative points-of-use) were monitored in various sections of five health care facilities hot water distribution systems and results used to develop a temperature-based risk assessment tool. Detailed investigations show that defective return valves in faucets can cause widespread temperature losses because of hot and cold water mixing. Systems in which water temperature coming out of the water heaters was kept consistently above 60 °C and maintained above 55 °C across the network were negative for Legionella by culture or qPCR. For systems not meeting these temperature criteria, risk areas for L. pneumophila were identified using temperature profiling and system's characterization; higher risk was confirmed by more frequent microbiological detection by culture and qPCR. Results confirmed that maintaining sufficiently high temperatures within hot water distribution systems suppressed L. pneumophila culturability. However, the risk remains as shown by the persistence of L. pneumophila by qPCR. PMID:25622002

  10. Microsatellites for disentangling underground networks: strain-specific identification of Glomus intraradices, an arbuscular mycorrhizal fungus.

    PubMed

    Mathimaran, Natarajan; Falquet, Laurent; Ineichen, Kurt; Picard, Cyril; Redecker, Dirk; Boller, Thomas; Wiemken, Andres

    2008-06-01

    The underground network of arbuscular mycorrhizal (AM) fungi is decisive for the above-ground diversity of many plant ecosystems, but tools to investigate the population structure of AM fungi are sorely lacking. Here, we present a bioinformatics approach to identify microsatellite markers in the AM fungus Glomus intraradices. Based on 1958 contigs of this fungus, assembled from public databases, we identified 842 microsatellites. One hundred of them were subjected to closer scrutiny by designing flanking primers and performing an extensive screen to identify polymorphic loci. We obtained 18 polymorphic microsatellite markers, and we found that seven out of eight individual single-spore cultures of G. intraradices could readily be identified by at least five allelic differences, as compared to all other strains. Two single-spore cultures, however, nominally originating from completely different locations, displayed identity at all 18 loci, suggesting with 99.999999% probability that they represent a single clone.

  11. Molecular epidemiology and strain-specific characteristics of Streptococcus agalactiae at the herd and cow level.

    PubMed

    Mahmmod, Y S; Klaas, I C; Katholm, J; Lutton, M; Zadoks, R N

    2015-10-01

    Host-adaptation of Streptococcus agalactiae subpopulations has been described whereby strains that are commonly associated with asymptomatic carriage or disease in people differ phenotypically and genotypically from those causing mastitis in dairy cattle. Based on multilocus sequence typing (MLST), the most common strains in dairy herds in Denmark belong to sequence types (ST) that are also frequently found in people. The aim of this study was to describe epidemiological and diagnostic characteristics of such strains in relation to bovine mastitis. Among 1,199 cattle from 6 herds, cow-level prevalence of S. agalactiae was estimated to be 27.4% based on PCR and 7.8% based on bacteriological culture. Quarter-level prevalence was estimated at 2.8% based on bacteriological culture. Per herd, between 2 and 26 isolates were characterized by pulsed-field gel electrophoresis (PFGE) and MLST. Within each herd, a single PFGE type and ST predominated, consistent with a contagious mode of transmission or point source infection within herds. Evidence of within-herd evolution of S. agalactiae was detected with both typing methods, although ST belonged to a single clonal complex (CC) per herd. Detection of CC23 (3 herds) was associated with significantly lower approximate count (colony-forming units) at the quarter level and significantly lower cycle threshold value at the cow level than detection of CC1 (2 herds) or CC19 (1 herd), indicating a lower bacterial load in CC23 infections. Median values for the number of infected quarters and somatic cell count (SCC) were numerically but not significantly lower for cows infected with CC23 than for cows with CC1 or CC19. For all CC, an SCC threshold of 200,000 cells/mL was an unreliable indicator of infection status, and prescreening of animals based on SCC as part of S. agalactiae detection and eradication campaigns should be discouraged. PMID:26233443

  12. Diagnostic Performance of Endoscopic and Microscopic Procedures for Identifying Different Middle Ear Structures and Remaining Disease in Patients with Chronic Otitis Media: A Prospective Cohort Study

    PubMed Central

    Farahani, Farhad; Shariatpanahi, Elnaz; Jahanshahi, Javane; Poorolajal, Jalal

    2015-01-01

    Background The diagnostic performance of endoscopic and microscopic procedures for detecting diseases of the middle ear in patients with chronic otitis media (COM) has rarely been investigated. This study was conducted to compare the performance of these procedures for identifying middle ear structures and their associated diseases in COM patients. Methods In this prospective cohort study, 58 patients with chronic COM, who were candidates for tympanoplasty with or without a mastoidectomy, were enrolled. Before the surgical intervention, the middle ear was examined via an operating microscope and then through an endoscope to identify the middle ear structures as well as diseases associated with the middle ear. Results The patients were 15 years of age or older. The anatomical parts of the middle ear – the epitympanic, posterior mesotympanic, and hypotympanic structures – were more visible through an endoscope than through a microscope. In addition, the various segments of the mesotympanum, oval window, round window, and Eustachian tube were more visible via endoscopy. The post-operative endoscopic reevaluation of the middle ear revealed that a cholesteatoma had remained in four of 13 patients after surgery. Conclusion According to the results of this study, in cases in which there is poor visibility with the operating microscope or the surgeon suspects remaining disease within the middle ear, endoscopy could be utilized to improve the evaluation of more hidden middle ear pits and structures, particularly if there is a potentially recrudescent pathology. PMID:26167935

  13. Ossification of the Medial Clavicular Epiphysis on Chest Radiographs: Utility and Diagnostic Accuracy in Identifying Korean Adolescents and Young Adults under the Age of Majority

    PubMed Central

    2016-01-01

    The aim of our study was to evaluate the utility and diagnostic accuracy of the ossification grade of medial clavicular epiphysis on chest radiographs for identifying Korean adolescents and young adults under the age of majority. Overall, 1,151 patients (age, 16-30) without any systemic disease and who underwent chest radiography were included for ossification grading. Two radiologists independently classified the ossification of the medial clavicular epiphysis from chest radiographs into five grades. The age distribution and inter-observer agreement on the ossification grade were assessed. The diagnostic accuracy of the averaged ossification grades for determining whether the patient is under the age of majority was analyzed by using receiver operating characteristic (ROC) curves. Two separate inexperienced radiologists assessed the ossification grade in a subgroup of the patients after reviewing the detailed descriptions and image atlases developed for ossification grading. The median value of the ossification grades increased with increasing age (from 16 to 30 years), and the trend was best fitted by a quadratic function (R-square, 0.978). The inter-observer agreements on the ossification grade were 0.420 (right) and 0.404 (left). The area under the ROC curve (AUC) was 0.922 (95% CI, 0.902-0.942). The averaged ossification scores of 2.62 and 4.37 provided 95% specificity for a person < 19 years of age and a person ≥ 19 years of age, respectively. A preliminary assessment by inexperienced radiologists resulted in an AUC of 0.860 (95% CI, 0.740-0.981). The age of majority in Korean adolescents and young adults can be estimated using chest radiographs. PMID:27550480

  14. Ossification of the Medial Clavicular Epiphysis on Chest Radiographs: Utility and Diagnostic Accuracy in Identifying Korean Adolescents and Young Adults under the Age of Majority.

    PubMed

    Yoon, Soon Ho; Yoo, Hye Jin; Yoo, Roh Eul; Lim, Hyun Ju; Yoon, Jeong Hwa; Park, Chang Min; Lee, Sang Seob; Yoo, Seong Ho

    2016-10-01

    The aim of our study was to evaluate the utility and diagnostic accuracy of the ossification grade of medial clavicular epiphysis on chest radiographs for identifying Korean adolescents and young adults under the age of majority. Overall, 1,151 patients (age, 16-30) without any systemic disease and who underwent chest radiography were included for ossification grading. Two radiologists independently classified the ossification of the medial clavicular epiphysis from chest radiographs into five grades. The age distribution and inter-observer agreement on the ossification grade were assessed. The diagnostic accuracy of the averaged ossification grades for determining whether the patient is under the age of majority was analyzed by using receiver operating characteristic (ROC) curves. Two separate inexperienced radiologists assessed the ossification grade in a subgroup of the patients after reviewing the detailed descriptions and image atlases developed for ossification grading. The median value of the ossification grades increased with increasing age (from 16 to 30 years), and the trend was best fitted by a quadratic function (R-square, 0.978). The inter-observer agreements on the ossification grade were 0.420 (right) and 0.404 (left). The area under the ROC curve (AUC) was 0.922 (95% CI, 0.902-0.942). The averaged ossification scores of 2.62 and 4.37 provided 95% specificity for a person < 19 years of age and a person ≥ 19 years of age, respectively. A preliminary assessment by inexperienced radiologists resulted in an AUC of 0.860 (95% CI, 0.740-0.981). The age of majority in Korean adolescents and young adults can be estimated using chest radiographs.

  15. Ossification of the Medial Clavicular Epiphysis on Chest Radiographs: Utility and Diagnostic Accuracy in Identifying Korean Adolescents and Young Adults under the Age of Majority.

    PubMed

    Yoon, Soon Ho; Yoo, Hye Jin; Yoo, Roh Eul; Lim, Hyun Ju; Yoon, Jeong Hwa; Park, Chang Min; Lee, Sang Seob; Yoo, Seong Ho

    2016-10-01

    The aim of our study was to evaluate the utility and diagnostic accuracy of the ossification grade of medial clavicular epiphysis on chest radiographs for identifying Korean adolescents and young adults under the age of majority. Overall, 1,151 patients (age, 16-30) without any systemic disease and who underwent chest radiography were included for ossification grading. Two radiologists independently classified the ossification of the medial clavicular epiphysis from chest radiographs into five grades. The age distribution and inter-observer agreement on the ossification grade were assessed. The diagnostic accuracy of the averaged ossification grades for determining whether the patient is under the age of majority was analyzed by using receiver operating characteristic (ROC) curves. Two separate inexperienced radiologists assessed the ossification grade in a subgroup of the patients after reviewing the detailed descriptions and image atlases developed for ossification grading. The median value of the ossification grades increased with increasing age (from 16 to 30 years), and the trend was best fitted by a quadratic function (R-square, 0.978). The inter-observer agreements on the ossification grade were 0.420 (right) and 0.404 (left). The area under the ROC curve (AUC) was 0.922 (95% CI, 0.902-0.942). The averaged ossification scores of 2.62 and 4.37 provided 95% specificity for a person < 19 years of age and a person ≥ 19 years of age, respectively. A preliminary assessment by inexperienced radiologists resulted in an AUC of 0.860 (95% CI, 0.740-0.981). The age of majority in Korean adolescents and young adults can be estimated using chest radiographs. PMID:27550480

  16. Transcriptome Analysis Reveals Strain-Specific and Conserved Stemness Genes in Schmidtea mediterranea

    PubMed Central

    Lu, Yi-Chien; Horowitz, Michael; Graveley, Brenton R.

    2012-01-01

    The planarian Schmidtea mediterranea is a powerful model organism for studying stem cell biology due to its extraordinary regenerative ability mediated by neoblasts, a population of adult somatic stem cells. Elucidation of the S. mediterranea transcriptome and the dynamics of transcript expression will increase our understanding of the gene regulatory programs that regulate stem cell function and differentiation. Here, we have used RNA-Seq to characterize the S. mediterranea transcriptome in sexual and asexual animals and in purified neoblast and differentiated cell populations. Our analysis identified many uncharacterized genes, transcripts, and alternatively spliced isoforms that are differentially expressed in a strain or cell type-specific manner. Transcriptome profiling of purified neoblasts and differentiated cells identified neoblast-enriched transcripts, many of which likely play important roles in regeneration and stem cell function. Strikingly, many of the neoblast-enriched genes are orthologs of genes whose expression is enriched in human embryonic stem cells, suggesting that a core set of genes that regulate stem cell function are conserved across metazoan species. PMID:22496805

  17. Strain specific genotype-environment interactions and evolutionary potential for body mass in brook charr (Salvelinus fontinalis).

    PubMed

    Crespel, Amélie; Bernatchez, Louis; Audet, Céline; Garant, Dany

    2013-03-01

    Discriminating between genetic and environmental causes of phenotypic variation is an essential requirement for understanding the evolutionary potential of populations. However, the extent to which genetic variation differs among conspecific groups and environments during ontogeny has rarely been investigated. In this study, the genetic basis of body mass was measured in three divergent strains of brook charr (Salvelinus fontinalis) in different rearing environments and at different time periods. The results indicate that body mass was a heritable trait in all strains but that the level of heritability greatly differed among strains. Moreover, heritability estimates of each strain varied differently according to environmental rearing conditions, and cross-environments correlations were all significantly lower than unity, indicating strain-specific patterns of genotype-environment interactions. Heritability estimates also varied throughout ontogeny and decreased by 50% from 9 to 21 months of age. This study highlights the divergence in genetic architecture and evolutionary potential among these strains and emphasizes the importance of considering the strain-specific potential of the response to selection according to environmental variation.

  18. Structural conservation of prion strain specificities in recombinant prion protein fibrils in real-time quaking-induced conversion.

    PubMed

    Sano, Kazunori; Atarashi, Ryuichiro; Nishida, Noriyuki

    2015-01-01

    A major unsolved issue of prion biology is the existence of multiple strains with distinct phenotypes and this strain phenomenon is postulated to be associated with the conformational diversity of the abnormal prion protein (PrP(Sc)). Real-time quaking-induced conversion (RT-QUIC) assay that uses Escherichia coli-derived recombinant prion protein (rPrP) for the sensitive detection of PrP(Sc) results in the formation of rPrP-fibrils seeded with various strains. We demonstrated that there are differences in the secondary structures, especially in the β-sheets, and conformational stability between 2 rPrP-fibrils seeded with either Chandler or 22L strains in the first round of RT-QUIC. In particular, the differences in conformational properties of these 2 rPrP-fibrils were common to those of the original PrP(Sc). However, the strain specificities of rPrP-fibrils seen in the first round were lost in subsequent rounds. Instead, our findings suggest that nonspecific fibrils became the major species, probable owing to their selective growth advantage in the RT-QUIC. This study shows that at least some strain-specific conformational properties of the original PrP(Sc) can be transmitted to rPrP-fibrils in vitro, but further conservation appears to require unknown cofactors or environmental conditions or both.

  19. Individual and combined diagnostic accuracy of ultrasound diagnosis, ultrasound-guided fine-needle aspiration and polymerase chain reaction in identifying tuberculous lymph nodes in the neck.

    PubMed

    Kim, Dong Wook; Jung, Soo Jin; Ha, Tae Kwun; Park, Ha Kyoung

    2013-12-01

    The aim of this study was to assess the efficacy of, both individually and in combination, ultrasound (US) diagnosis, US-guided fine-needle aspiration (US-FNA) and polymerase chain reaction (PCR) in diagnosing tuberculous lymph nodes in the neck (i.e., tuberculous cervical lymph nodes [TCLs]). Eighty-two patients who underwent US diagnosis, US-FNA and PCR for clinical suspicion of TCLs were enrolled. Of the 82 patients, 31 were confirmed as having TCLs. The sensitivity, specificity, positive and negative predictive values and accuracy of US diagnosis, US-FNA and PCR were 93.5%, 76.5%, 70.7%, 95.1% and 82.9%; 64.5%, 98.0%, 95.2%, 82.0% and 85.4%; and 100%, 96.1%, 93.9%, 100% and 97.6%, respectively. The diagnostic values of PCR alone and in combination with US-FNA were found to be higher than those of other methods. No US feature with high sensitivity and specificity was identified.

  20. Strain-specific salt tolerance and osmoregulatory mechanisms in Azospirillum brasilense.

    PubMed

    Chowdhury, Soumitra Paul; Nagarajan, Thirunavukkarasu; Tripathi, Rachna; Mishra, Mukti Nath; Le Rudulier, Daniel; Tripathi, Anil Kumar

    2007-02-01

    Salinity stress inhibits the growth and nitrogen fixation ability of the plant growth-promoting rhizobacterium Azospirillum brasilense. Five strains of A. brasilense were isolated from the rhizosphere of Indian cereals and grasses and identified on the basis of their phenotypic features and 16S rRNA gene sequence. The five Indian isolates and two standard strains of A. brasilense, Sp7 and Cd, showed notable differences in growth, acetylene-reducing activity under salt stress, and ability to take up and use glycine betaine for the restoration of growth and acetylene-reducing activity under salt stress. Salt stress also enhanced the production of exopolysaccharides and cell aggregates, the extent of which varied in different strains of A. brasilense at different carbon to nitrogen ratios in the culture medium. It can be concluded that the production of exopolysaccharides and cell aggregates is a more consistent physiological response of A. brasilense to salt stress than is the uptake and osmoprotection by glycine betaine. PMID:17156127

  1. Strain-Specific Battery of Tests for Domains of Mania: Effects of Valproate, Lithium and Imipramine

    PubMed Central

    Flaisher-Grinberg, Shlomit; Einat, Haim

    2010-01-01

    The lack of efficient animal models for bipolar disorder (BPD), especially for the manic pole, is a major factor hindering the research of its pathophysiology and the development of improved drug treatments. The present study was designed to identify an appropriate mouse strain for modeling some behavioral domains of mania and to evaluate the effects of drugs using this strain. The study compared the behavior of four strains: Black Swiss, C57Bl/6, CBA/J and A/J mice in a battery of tests that included spontaneous activity; sweet solution preference; light/dark box; resident-intruder; forced-swim and amphetamine-induced hyperactivity. Based on the ‘manic-like’ behavior demonstrated by the Black Swiss strain, the study evaluated the effects of the mood stabilizers valproate and lithium and of the antidepressant imipramine in the same tests using this strain. Results indicated that lithium and valproate attenuate the ‘manic-like’ behavior of Black Swiss mice whereas imipramine had no effects. These findings suggest that Black Swiss mice might be a good choice for modeling several domains of mania and distinguishing the effects of drugs on these specific domains. However, the relevance of the behavioral phenotype of Black Swiss mice to the biology of BPD is unknown at this time and future studies will investigate molecular differences between Black Swiss mice and other strains and asess the interaction between strain and mood stabilizing treatment. PMID:21423422

  2. Strain-specific salt tolerance and osmoregulatory mechanisms in Azospirillum brasilense.

    PubMed

    Chowdhury, Soumitra Paul; Nagarajan, Thirunavukkarasu; Tripathi, Rachna; Mishra, Mukti Nath; Le Rudulier, Daniel; Tripathi, Anil Kumar

    2007-02-01

    Salinity stress inhibits the growth and nitrogen fixation ability of the plant growth-promoting rhizobacterium Azospirillum brasilense. Five strains of A. brasilense were isolated from the rhizosphere of Indian cereals and grasses and identified on the basis of their phenotypic features and 16S rRNA gene sequence. The five Indian isolates and two standard strains of A. brasilense, Sp7 and Cd, showed notable differences in growth, acetylene-reducing activity under salt stress, and ability to take up and use glycine betaine for the restoration of growth and acetylene-reducing activity under salt stress. Salt stress also enhanced the production of exopolysaccharides and cell aggregates, the extent of which varied in different strains of A. brasilense at different carbon to nitrogen ratios in the culture medium. It can be concluded that the production of exopolysaccharides and cell aggregates is a more consistent physiological response of A. brasilense to salt stress than is the uptake and osmoprotection by glycine betaine.

  3. Diet, Helicobacter pylori strain-specific infection, and gastric cancer risk among Chinese men.

    PubMed

    Epplein, Meira; Zheng, Wei; Li, Honglan; Peek, Richard M; Correa, Pelayo; Gao, Jing; Michel, Angelika; Pawlita, Michael; Cai, Qiuyin; Xiang, Yong-Bing; Shu, Xiao-Ou

    2014-01-01

    Evidence for the association of diet and gastric cancer is equivocal, and the majority of previous studies have not evaluated the interaction of diet and infection with Helicobacter pylori, the leading risk factor for gastric cancer. We examined these associations among 226 cases and 451 controls nested within a prospective cohort. Dietary intakes were calculated from validated food frequency questionnaires. Blood levels of 15 antibodies to Helicobacter pylori proteins were assessed using multiplex serology. Odds ratios (ORs) were calculated using logistic regression. Among individuals infected with high-risk Helicobacter pylori (sero-positivity to 5-6 virulent H. pylori proteins), increasing intake of red meat, heme iron, and sodium increased risk (comparing highest tertile to lowest: ORs [95% confidence interval {CI}]: 1.85 [1.01-3.40]; 1.95 [1.06-3.57]; and 1.76 [0.91-3.43], respectively) while increasing intake of fruit decreased gastric cancer risk (comparing highest tertile of intake to lowest: OR [95% CI]: 0.52 [0.28-0.94]). No associations of diet with risk were found among individuals infected with low-risk H. pylori (P for interaction for red meat and sodium: 0.02 and 0.01, respectively). In this population with over 90% prevalence of CagA-positive H. pylori infection, categorizing individuals using H. pylori multiplex serology may identify individuals for whom a diet intervention may be effective. PMID:24666234

  4. Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers: a diagnostic approach based on cluster analysis.

    PubMed

    Egsgaard, Line Lindhardt; Eskehave, Thomas Navndrup; Bay-Jensen, Anne C; Hoeck, Hans Christian; Arendt-Nielsen, Lars

    2015-01-01

    Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary.

  5. Strain-Specific Virolysis Patterns of Human Noroviruses in Response to Alcohols.

    PubMed

    Park, Geun Woo; Collins, Nikail; Barclay, Leslie; Hu, Liya; Prasad, B V Venkataram; Lopman, Benjamin A; Vinjé, Jan

    2016-01-01

    Alcohol-based hand sanitizers are widely used to disinfect hands to prevent the spread of pathogens including noroviruses. Alcohols inactivate norovirus by destruction of the viral capsid, resulting in the leakage of viral RNA (virolysis). Since conflicting results have been reported on the susceptibility of human noroviruses against alcohols, we exposed a panel of 30 human norovirus strains (14 GI and 16 GII strains) to different concentrations (50%, 70%, 90%) of ethanol and isopropanol and tested the viral RNA titer by RT-qPCR. Viral RNA titers of 10 (71.4%), 14 (100%), 3 (21.4%) and 7 (50%) of the 14 GI strains were reduced by > 1 log10 RNA copies/ml after exposure to 70% and 90% ethanol, and 70% and 90% isopropanol, respectively. RNA titers of 6 of the 7 non-GII 4 strains remained unaffected after alcohol exposure. Compared to GII strains, GI strains were more susceptible to ethanol than to isopropanol. At 90%, both alcohols reduced RNA titers of 8 of the 9 GII.4 strains by ≥ 1 log10 RNA copies/ml. After exposure to 70% ethanol, RNA titers of GII.4 Den Haag and Sydney strains decreased by ≥ 1.9 log10, whereas RNA reductions for GII.4 New Orleans strains were < 0.5 log10. To explain these differences, we sequenced the complete capsid gene of the 9 GII.4 strains and identified 17 amino acid substitutions in the P2 region among the 3 GII.4 variant viruses. When comparing with an additional set of 200 GII.4 VP1 sequences, only S310 and P396 were present in all GII.4 New Orleans viruses but not in the ethanol-sensitive GII.4 Sydney and GII.4 Den Haag viruses Our data demonstrate that alcohol susceptibility patterns between different norovirus genotypes vary widely and that virolysis data for a single strain or genotype are not representative for all noroviruses. PMID:27337036

  6. Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids

    PubMed Central

    Drini, Sima; Criscuolo, Alexis; Lechat, Pierre; Imamura, Hideo; Skalický, Tomáš; Rachidi, Najma; Lukeš, Julius; Dujardin, Jean-Claude; Späth, Gerald F.

    2016-01-01

    All eukaryotic genomes encode multiple members of the heat shock protein 70 (HSP70) family, which evolved distinctive structural and functional features in response to specific environmental constraints. Phylogenetic analysis of this protein family thus can inform on genetic and molecular mechanisms that drive species-specific environmental adaptation. Here we use the eukaryotic pathogen Leishmania spp. as a model system to investigate the evolution of the HSP70 protein family in an early-branching eukaryote that is prone to gene amplification and adapts to cytotoxic host environments by stress-induced and chaperone-dependent stage differentiation. Combining phylogenetic and comparative analyses of trypanosomatid genomes, draft genome of Paratrypanosoma and recently published genome sequences of 204 L. donovani field isolates, we gained unique insight into the evolutionary dynamics of the Leishmania HSP70 protein family. We provide evidence for (i) significant evolutionary expansion of this protein family in Leishmania through gene amplification and functional specialization of highly conserved canonical HSP70 members, (ii) evolution of trypanosomatid-specific, non-canonical family members that likely gained ATPase-independent functions, and (iii) loss of one atypical HSP70 member in the Trypanosoma genus. Finally, we reveal considerable copy number variation of canonical cytoplasmic HSP70 in highly related L. donovani field isolates, thus identifying this locus as a potential hot spot of environment–genotype interaction. Our data draw a complex picture of the genetic history of HSP70 in trypanosomatids that is driven by the remarkable plasticity of the Leishmania genome to undergo massive intra-chromosomal gene amplification to compensate for the absence of regulated transcriptional control in these parasites. PMID:27371955

  7. Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids.

    PubMed

    Drini, Sima; Criscuolo, Alexis; Lechat, Pierre; Imamura, Hideo; Skalický, Tomáš; Rachidi, Najma; Lukeš, Julius; Dujardin, Jean-Claude; Späth, Gerald F

    2016-01-01

    All eukaryotic genomes encode multiple members of the heat shock protein 70 (HSP70) family, which evolved distinctive structural and functional features in response to specific environmental constraints. Phylogenetic analysis of this protein family thus can inform on genetic and molecular mechanisms that drive species-specific environmental adaptation. Here we use the eukaryotic pathogen Leishmania spp. as a model system to investigate the evolution of the HSP70 protein family in an early-branching eukaryote that is prone to gene amplification and adapts to cytotoxic host environments by stress-induced and chaperone-dependent stage differentiation. Combining phylogenetic and comparative analyses of trypanosomatid genomes, draft genome of Paratrypanosoma and recently published genome sequences of 204 L. donovani field isolates, we gained unique insight into the evolutionary dynamics of the Leishmania HSP70 protein family. We provide evidence for (i) significant evolutionary expansion of this protein family in Leishmania through gene amplification and functional specialization of highly conserved canonical HSP70 members, (ii) evolution of trypanosomatid-specific, non-canonical family members that likely gained ATPase-independent functions, and (iii) loss of one atypical HSP70 member in the Trypanosoma genus. Finally, we reveal considerable copy number variation of canonical cytoplasmic HSP70 in highly related L. donovani field isolates, thus identifying this locus as a potential hot spot of environment-genotype interaction. Our data draw a complex picture of the genetic history of HSP70 in trypanosomatids that is driven by the remarkable plasticity of the Leishmania genome to undergo massive intra-chromosomal gene amplification to compensate for the absence of regulated transcriptional control in these parasites. PMID:27371955

  8. Strain-Specific Virolysis Patterns of Human Noroviruses in Response to Alcohols

    PubMed Central

    Park, Geun Woo; Collins, Nikail; Barclay, Leslie; Hu, Liya; Prasad, B. V. Venkataram; Lopman, Benjamin A.; Vinjé, Jan

    2016-01-01

    Alcohol-based hand sanitizers are widely used to disinfect hands to prevent the spread of pathogens including noroviruses. Alcohols inactivate norovirus by destruction of the viral capsid, resulting in the leakage of viral RNA (virolysis). Since conflicting results have been reported on the susceptibility of human noroviruses against alcohols, we exposed a panel of 30 human norovirus strains (14 GI and 16 GII strains) to different concentrations (50%, 70%, 90%) of ethanol and isopropanol and tested the viral RNA titer by RT-qPCR. Viral RNA titers of 10 (71.4%), 14 (100%), 3 (21.4%) and 7 (50%) of the 14 GI strains were reduced by > 1 log10 RNA copies/ml after exposure to 70% and 90% ethanol, and 70% and 90% isopropanol, respectively. RNA titers of 6 of the 7 non-GII 4 strains remained unaffected after alcohol exposure. Compared to GII strains, GI strains were more susceptible to ethanol than to isopropanol. At 90%, both alcohols reduced RNA titers of 8 of the 9 GII.4 strains by ≥ 1 log10 RNA copies/ml. After exposure to 70% ethanol, RNA titers of GII.4 Den Haag and Sydney strains decreased by ≥ 1.9 log10, whereas RNA reductions for GII.4 New Orleans strains were < 0.5 log10. To explain these differences, we sequenced the complete capsid gene of the 9 GII.4 strains and identified 17 amino acid substitutions in the P2 region among the 3 GII.4 variant viruses. When comparing with an additional set of 200 GII.4 VP1 sequences, only S310 and P396 were present in all GII.4 New Orleans viruses but not in the ethanol-sensitive GII.4 Sydney and GII.4 Den Haag viruses Our data demonstrate that alcohol susceptibility patterns between different norovirus genotypes vary widely and that virolysis data for a single strain or genotype are not representative for all noroviruses. PMID:27337036

  9. Comparative evaluation of three Lactobacilli with strain-specific activities for rats when supplied in drinking water.

    PubMed

    Guo, Xiao-Hua; Zhao, Zhi-Dan; Nam, Hyang-Mi; Kim, Jae-Myung

    2012-11-01

    To test the in vivo benefits of three lactobacilli and to compare their different efficacies based on strain-specific activities by using rats as an experimental model, a growth-promotion and a challenge trial were conducted. The three strains, Lactobacillus salivarius G1-1, Lactobacillus reuteri G22-2, and Lactobacillus reuteri G8-5 shared antimicrobial, bile-salt-hydrolase and amylolytic activities in vitro, respectively. In the 17 day growth-promotion trial, 48 rats were allotted to four treatments with 12 replicates per treatment: a control group, which received saline, as well as three experimental groups, which received 10(8) cells/ml of one of the three lactobacilli in saline suspension. The results showed that compared with the control group, L. reuteri G8-5 significantly improved feed efficiency and decreased fecal pH values on days 8 and 17, concomitant with reduced faecal coliform counts on d 17 (p < 0.05). All treatments with lactobacilli caused an increase in the moisture content of the faeces and a decrease in the serum total cholesterol and blood urea nitrogen levels. High-density lipoprotein cholesterol was only elevated for rats which received L. reuteri G22-2. In the Salmonella-challenge trial, 40 rats were allotted to five treatments (8 replicates per treatment) which consisted of a positive control (infected, no Lactobacillus pretreatment), a negative control (uninfected, no Lactobacillus pretreatment) and three Lactobacillus-pretreated groups (10(9) cells/ml in saline). The results showed that rats in all Lactobacillus pretreated groups were protected from infection with significantly higher weight gain, feed intake and feed efficiency compared with positive control rats (p < 0.05). Rats treated with L. salivarius G1-1 and L. reuteri G22-2 tended to exhibit higher weight gains than those pretreated with L. reuteri G8-5. Significantly lower Salmonella shedding in faeces, Salmonella numbers in the spleen and the relative weight of the spleen

  10. Identifying factors likely to influence compliance with diagnostic imaging guideline recommendations for spine disorders among chiropractors in North America: a focus group study using the Theoretical Domains Framework

    PubMed Central

    2012-01-01

    about capabilities); and guideline awareness and agreements ( knowledge). Conclusions Chiropractors’ use of diagnostic imaging appears to be influenced by a number of factors. Five key domains may be important considering the presence of conflicting beliefs, evidence of strong beliefs likely to impact the behavior of interest, and high frequency of beliefs. The results will inform the development of a theory-based survey to help identify potential targets for behavioral-change strategies. PMID:22938135

  11. The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific

    PubMed Central

    Aktas, Busra; De Wolfe, Travis J.; Safdar, Nasia; Darien, Benjamin J.; Steele, James L.

    2016-01-01

    The probiotic function to impact human health is thought to be related to their ability to alter the composition of the gut microbiota and modulate the human innate immune system. The ability to function as a probiotic is believed to be strain specific. Strains of Lactobacillus casei are commonly utilized as probiotics that when consumed alter the composition of the gut microbiota and modulate the host immune response. L. casei strains are known to differ significantly in gene content. The objective of this study was to investigate seven different L. casei strains for their ability to alter the murine gut microbiota and modulate the murine immune system. C57BL/6 mice were fed L. casei strains at a dose of 108 CFU/day/mouse for seven days and sacrificed 3.5h after the last administration. The cecal content and the ileum tissue were collected for microbiota analysis and immune profiling, respectively. While 5 of the L. casei strains altered the gut microbiota in a strain specific manner, two of the strains did not alter the overall cecal microbiota composition. The observed changes cluster into three groups containing between 1 and 2 strains. Two strains that did not affect the gut microbiota composition cluster together with the control in their impact on pattern recognition receptors (PRRs) expression, suggesting that the ability to alter the cecal microbiota correlates with the ability to alter PRR expression. They also cluster together in their impact on the expression of intestinal antimicrobial peptides (AMPs). This result suggests that a relationship exists between the capability of a L. casei strains to alter the composition of the gut microbiota, PRR regulation, and AMP regulation. PMID:27244133

  12. Strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the Polynucleobacter cluster.

    PubMed

    Boenigk, Jens; Stadler, Peter; Wiedlroither, Anneliese; Hahn, Martin W

    2004-10-01

    Ultramicrobacteria (cell volume < 0.1 microm(3)) are the numerically dominant organisms in the plankton of marine and freshwater habitats. Flagellates and other protists are assumed to be the most important predators of these ultramicrobacteria as well as of larger planktonic bacteria. However, due to controversial observations conducted previously, it is not clear as to whether fractions of the ultramicrobacteria are resistant to flagellate predation. Furthermore, it is not known if closely related bacteria vary significantly in their sensitivity to flagellate predation. We investigated the sensitivity of ultramicrobacteria affiliated with the cosmopolitan Polynucleobacter cluster to grazing by Spumella-like nanoflagellates. Laboratory grazing experiments with four closely related (> or =99.6% 16S rRNA gene sequence similarity) bacteria and three closely related (100% 18S rRNA gene sequence similarity) flagellates were performed. In comparison to larger bacteria, predation on the ultramicrobacterial Polynucleobacter strains was weak, and the growth of the predating flagellates was slow. Specific clearance rates ranged between 0.14 x 10(5) and 2.8 x 10(5) units of predator size h(-1). Feeding rates strongly depended on the flagellate and bacterial strain (P < 0.001). Grazing mortality rates of the three flagellate strains investigated varied for the same prey strain by up to almost fourfold. We conclude that (i) ultramicrobacteria affiliated with the Polynucleobacter cluster are not protected from grazing, (ii) strain-specific variations in grazing sensitivity even between closely related bacteria are high, and (iii) strain-specific differences in predator-prey interaction could be an important factor in the evolution and maintenance of microbial microdiversity.

  13. The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific.

    PubMed

    Aktas, Busra; De Wolfe, Travis J; Safdar, Nasia; Darien, Benjamin J; Steele, James L

    2016-01-01

    The probiotic function to impact human health is thought to be related to their ability to alter the composition of the gut microbiota and modulate the human innate immune system. The ability to function as a probiotic is believed to be strain specific. Strains of Lactobacillus casei are commonly utilized as probiotics that when consumed alter the composition of the gut microbiota and modulate the host immune response. L. casei strains are known to differ significantly in gene content. The objective of this study was to investigate seven different L. casei strains for their ability to alter the murine gut microbiota and modulate the murine immune system. C57BL/6 mice were fed L. casei strains at a dose of 108 CFU/day/mouse for seven days and sacrificed 3.5h after the last administration. The cecal content and the ileum tissue were collected for microbiota analysis and immune profiling, respectively. While 5 of the L. casei strains altered the gut microbiota in a strain specific manner, two of the strains did not alter the overall cecal microbiota composition. The observed changes cluster into three groups containing between 1 and 2 strains. Two strains that did not affect the gut microbiota composition cluster together with the control in their impact on pattern recognition receptors (PRRs) expression, suggesting that the ability to alter the cecal microbiota correlates with the ability to alter PRR expression. They also cluster together in their impact on the expression of intestinal antimicrobial peptides (AMPs). This result suggests that a relationship exists between the capability of a L. casei strains to alter the composition of the gut microbiota, PRR regulation, and AMP regulation. PMID:27244133

  14. Suppression subtractive hybridisation and real-time PCR for strain-specific quantification of the probiotic Bifidobacterium animalis BAN in broiler feed.

    PubMed

    Fibi, Silvia; Klose, Viviana; Mohnl, Michaela; Weber, Barbara; Haslberger, Alexander G; Sattler, Verity Ann

    2016-04-01

    To ensure quality management during the production processes of probiotics and for efficacy testing in vivo, accurate tools are needed for the identification and quantification of probiotic strains. In this study, a strain-specific qPCR assay based on Suppression Subtractive Hybridisation (SSH) for identifying unique sequences, was developed to quantify the strain Bifidobacterium animalis BAN in broiler feed. Seventy potential BAN specific sequences were obtained after SSH of the BAN genome, with a pool of closely related strain genomes and subsequent differential screening by dot blot hybridisation. Primers were designed for 30 sequences which showed no match with any sequence database entry, using BLAST and FASTA. Primer specificity was assessed by qPCR using 45 non-target strains and species in a stepwise approach. Primer T39_S2 was the only primer pair without any unspecific binding properties and it showed a PCR efficiency of 80% with a Cq value of 17.32 for 20 ng BAN DNA. Optimised feed-matrix dependent calibration curve for the quantification of BAN was generated, ranging from 6.28 × 10(3)cfu g(-1) to 1.61 × 10(6)cfu g(-1). Limit of detection of the qPCR assay was 2 × 10(1)cfu g(-1) BAN. Applicability of the strain-specific qPCR assay was confirmed in a spiking experiment which added BAN to the feed in two concentrations, 2 × 10(6)cfu g(-1) and 2 × 10(4)cfu g(-1). Results showed BAN mean recovery rates in feed of 1.44 × 10(6) ± 4.39 × 10(5)cfu g(-1) and 1.59 × 10(4) ± 1.69 × 10(4)cfu g(-1), respectively. The presented BAN-specific qPCR assay can be applied in animal feeding trials, in order to control the correct inclusion rates of the probiotic to the feed, and it could further be adapted, to monitor the uptake of the probiotic into the gastrointestinal tract of broiler chickens. PMID:26883620

  15. Suppression subtractive hybridisation and real-time PCR for strain-specific quantification of the probiotic Bifidobacterium animalis BAN in broiler feed.

    PubMed

    Fibi, Silvia; Klose, Viviana; Mohnl, Michaela; Weber, Barbara; Haslberger, Alexander G; Sattler, Verity Ann

    2016-04-01

    To ensure quality management during the production processes of probiotics and for efficacy testing in vivo, accurate tools are needed for the identification and quantification of probiotic strains. In this study, a strain-specific qPCR assay based on Suppression Subtractive Hybridisation (SSH) for identifying unique sequences, was developed to quantify the strain Bifidobacterium animalis BAN in broiler feed. Seventy potential BAN specific sequences were obtained after SSH of the BAN genome, with a pool of closely related strain genomes and subsequent differential screening by dot blot hybridisation. Primers were designed for 30 sequences which showed no match with any sequence database entry, using BLAST and FASTA. Primer specificity was assessed by qPCR using 45 non-target strains and species in a stepwise approach. Primer T39_S2 was the only primer pair without any unspecific binding properties and it showed a PCR efficiency of 80% with a Cq value of 17.32 for 20 ng BAN DNA. Optimised feed-matrix dependent calibration curve for the quantification of BAN was generated, ranging from 6.28 × 10(3)cfu g(-1) to 1.61 × 10(6)cfu g(-1). Limit of detection of the qPCR assay was 2 × 10(1)cfu g(-1) BAN. Applicability of the strain-specific qPCR assay was confirmed in a spiking experiment which added BAN to the feed in two concentrations, 2 × 10(6)cfu g(-1) and 2 × 10(4)cfu g(-1). Results showed BAN mean recovery rates in feed of 1.44 × 10(6) ± 4.39 × 10(5)cfu g(-1) and 1.59 × 10(4) ± 1.69 × 10(4)cfu g(-1), respectively. The presented BAN-specific qPCR assay can be applied in animal feeding trials, in order to control the correct inclusion rates of the probiotic to the feed, and it could further be adapted, to monitor the uptake of the probiotic into the gastrointestinal tract of broiler chickens.

  16. Strain specificity and binding affinity requirements of neutralizing monoclonal antibodies to the C4 domain of gp120 from human immunodeficiency virus type 1.

    PubMed Central

    Nakamura, G R; Byrn, R; Wilkes, D M; Fox, J A; Hobbs, M R; Hastings, R; Wessling, H C; Norcross, M A; Fendly, B M; Berman, P W

    1993-01-01

    The binding properties of seven CD4-blocking monoclonal antibodies raised against recombinant gp120 of human immunodeficiency virus type 1 strain MN (HIV-1MN) and two CD4-blocking monoclonal antibodies to recombinant envelope glycoproteins gp120 and gp160 of substrain IIIB of HIVLAI were analyzed. With a panel of recombinant gp120s from seven diverse HIV-1 isolates, eight of the nine antibodies were found to be strain specific and one was broadly cross-reactive. Epitope mapping revealed that all nine antibodies bound to epitopes located in the fourth conserved domain (C4) of gp120. Within this region, three distinct epitopes could be identified: two were polymorphic between HIV-1 strains, and one was highly conserved. Studies with synthetic peptides demonstrated that the conserved epitope, recognized by antibody 13H8, was located between residues 431 and 439. Site-directed mutagenesis of gp120 demonstrated that residue 429 and/or 432 was critical for the binding of the seven antibodies to gp120 from HIV-1MN. Similarly, residues 423 and 429 were essential for the binding of monoclonal antibody 5C2 raised against gp120 from HIV-1IIIB. The amino acids located at positions 423 and 429 were found to vary between strains of HIV-1 as well as between molecular clones derived from the MN and LAI isolates of HIV-1. Polymorphism at these positions prevented the binding of virus-neutralizing monoclonal antibodies and raised the possibility that HIV-1 neutralization serotypes may be defined on the basis of C4 domain sequences. Analysis of the binding characteristics of the CD4-blocking antibodies demonstrated that their virus-neutralizing activity was directly proportional to their gp120-binding affinity. These studies account for the strain specificity of antibodies to the C4 domain of gp120 and demonstrate for the first time that antibodies to this region can be as effective as those directed to the principal neutralizing determinant (V3 domain) in neutralizing HIV-1

  17. Strain-specific Plasmodium falciparum multifunctional CD4(+) T cell cytokine expression in Malian children immunized with the FMP2.1/AS02A vaccine candidate.

    PubMed

    Graves, Shawna F; Kouriba, Bourema; Diarra, Issa; Daou, Modibo; Niangaly, Amadou; Coulibaly, Drissa; Keita, Yamoussa; Laurens, Matthew B; Berry, Andrea A; Vekemans, Johan; Ripley Ballou, W; Lanar, David E; Dutta, Sheetij; Gray Heppner, D; Soisson, Lorraine; Diggs, Carter L; Thera, Mahamadou A; Doumbo, Ogobara K; Plowe, Christopher V; Sztein, Marcelo B; Lyke, Kirsten E

    2016-05-17

    Based on Plasmodium falciparum (Pf) apical membrane antigen 1 (AMA1) from strain 3D7, the malaria vaccine candidate FMP2.1/AS02A showed strain-specific efficacy in a Phase 2 clinical trial in 400 Malian children randomized to 3 doses of the AMA1 vaccine candidate or control rabies vaccine on days 0, 30 and 60. A subset of 10 Pf(-) (i.e., no clinical malaria episodes) AMA1 recipients, 11 Pf(+) (clinical malaria episodes with parasites with 3D7 or Fab9-type AMA1 cluster 1 loop [c1L]) AMA1 recipients, and 10 controls were randomly chosen for analysis. Peripheral blood mononuclear cells (PBMCs) isolated on days 0, 90 and 150 were stimulated with full-length 3D7 AMA1 and c1L from strains 3D7 (c3D7) and Fab9 (cFab9). Production of IFN-γ, TNF-α, IL-2, and/or IL-17A was analyzed by flow cytometry. Among AMA1 recipients, 18/21 evaluable samples stimulated with AMA1 demonstrated increased IFN-γ, TNF-α, and IL-2 derived from CD4(+) T cells by day 150 compared to 0/10 in the control group (p<0.0001). Among AMA1 vaccines, CD4(+) cells expressing both TNF-α and IL-2 were increased in Pf(-) children compared to Pf(+) children. When PBMCs were stimulated with c3D7 and cFab9 separately, 4/18 AMA1 recipients with an AMA1-specific CD4(+) response had a significant response to one or both c1L. This suggests that recognition of the AMA1 antigen is not dependent upon c1L alone. In summary, AMA1-specific T cell responses were notably increased in children immunized with an AMA1-based vaccine candidate. The role of CD4(+)TNF-α(+)IL-2(+)-expressing T cells in vaccine-induced strain-specific protection against clinical malaria requires further exploration. Clinicaltrials.gov Identifier: NCT00460525. PMID:27087149

  18. Fast and low-cost decentralized surveillance of transmission of tuberculosis based on strain-specific PCRs tailored from whole genome sequencing data: a pilot study.

    PubMed

    Pérez-Lago, L; Martínez Lirola, M; Herranz, M; Comas, I; Bouza, E; García-de-Viedma, D

    2015-03-01

    Molecular epidemiology has transformed our knowledge of how tuberculosis (TB) is transmitted. Whole genome sequencing (WGS) has reached unprecedented levels of accuracy. However, it has increased technical requirements and costs, and analysis of data delays results. Our objective was to find a way to reconcile speed and ease of implementation with the high resolution of WGS. The targeted regional allele-specific oligonucleotide PCR (TRAP) assay presented here is based on allele-specific PCR targeting strain-specific single nucleotide polymorphisms, identified from WGS, and makes it possible to track actively transmitted Mycobacterium tuberculosis strains. A TRAP assay was optimized to track the most actively transmitted strains in a population in Almería, Southeast Spain, with high rates of TB. TRAP was transferred to the local laboratory where transmission was occurring. It performed well from cultured isolates and directly from sputa, enabling new secondary cases of infection from the actively transmitted strains to be detected. TRAP constitutes a fast, simple and low-cost tool that could modify surveillance of TB transmission. This pilot study could help to define a new model to survey TB transmission based on a decentralized multinodal network of local laboratories applying fast and low-cost TRAPs, which are developed by central reference centres, tailored to the specific demands of transmission at each local node.

  19. Comparative Proteomics Reveals Strain-Specific β-TrCP Degradation via Rotavirus NSP1 Hijacking a Host Cullin-3-Rbx1 Complex

    PubMed Central

    Ding, Siyuan; Mooney, Nancie; Li, Bin; Kelly, Marcus R.; Feng, Ningguo; Loktev, Alexander V.; Sen, Adrish; Patton, John T.; Jackson, Peter K.; Greenberg, Harry B.

    2016-01-01

    Rotaviruses (RVs) are the leading cause of severe gastroenteritis in young children, accounting for half a million deaths annually worldwide. RV encodes non-structural protein 1 (NSP1), a well-characterized interferon (IFN) antagonist, which facilitates virus replication by mediating the degradation of host antiviral factors including IRF3 and β-TrCP. Here, we utilized six human and animal RV NSP1s as baits and performed tandem-affinity purification coupled with high-resolution mass spectrometry to comprehensively characterize NSP1-host protein interaction network. Multiple Cullin-RING ubiquitin ligase (CRL) complexes were identified. Importantly, inhibition of cullin-3 (Cul3) or RING-box protein 1 (Rbx1), by siRNA silencing or chemical perturbation, significantly impairs strain-specific NSP1-mediated β-TrCP degradation. Mechanistically, we demonstrate that NSP1 localizes to the Golgi with the host Cul3-Rbx1 CRL complex, which targets β-TrCP and NSP1 for co-destruction at the proteasome. Our study uncovers a novel mechanism that RV employs to promote β-TrCP turnover and provides molecular insights into virus-mediated innate immunity inhibition. PMID:27706223

  20. Fast and low-cost decentralized surveillance of transmission of tuberculosis based on strain-specific PCRs tailored from whole genome sequencing data: a pilot study.

    PubMed

    Pérez-Lago, L; Martínez Lirola, M; Herranz, M; Comas, I; Bouza, E; García-de-Viedma, D

    2015-03-01

    Molecular epidemiology has transformed our knowledge of how tuberculosis (TB) is transmitted. Whole genome sequencing (WGS) has reached unprecedented levels of accuracy. However, it has increased technical requirements and costs, and analysis of data delays results. Our objective was to find a way to reconcile speed and ease of implementation with the high resolution of WGS. The targeted regional allele-specific oligonucleotide PCR (TRAP) assay presented here is based on allele-specific PCR targeting strain-specific single nucleotide polymorphisms, identified from WGS, and makes it possible to track actively transmitted Mycobacterium tuberculosis strains. A TRAP assay was optimized to track the most actively transmitted strains in a population in Almería, Southeast Spain, with high rates of TB. TRAP was transferred to the local laboratory where transmission was occurring. It performed well from cultured isolates and directly from sputa, enabling new secondary cases of infection from the actively transmitted strains to be detected. TRAP constitutes a fast, simple and low-cost tool that could modify surveillance of TB transmission. This pilot study could help to define a new model to survey TB transmission based on a decentralized multinodal network of local laboratories applying fast and low-cost TRAPs, which are developed by central reference centres, tailored to the specific demands of transmission at each local node. PMID:25614157

  1. Complete Genome Sequence of the Biocontrol Strain Pseudomonas protegens Cab57 Discovered in Japan Reveals Strain-Specific Diversity of This Species

    PubMed Central

    Takeuchi, Kasumi; Noda, Naomi; Someya, Nobutaka

    2014-01-01

    The biocontrol strain Pseudomonas sp. Cab57 was isolated from the rhizosphere of shepherd’s purse growing in a field in Hokkaido by screening the antibiotic producers. The whole genome sequence of this strain was obtained by paired-end and whole-genome shotgun sequencing, and the gaps between the contigs were closed using gap-spanning PCR products. The P. sp. Cab57 genome is organized into a single circular chromosome with 6,827,892 bp, 63.3% G+C content, and 6,186 predicted protein-coding sequences. Based on 16S rRNA gene analysis and whole genome analysis, strain Cab57 was identified as P. protegens. As reported in P. protegens CHA0 and Pf-5, four gene clusters (phl, prn, plt, and hcn) encoding the typical antibiotic metabolites and the reported genes associated with Gac/Rsm signal transduction pathway of these strains are fully conserved in the Cab57 genome. Actually strain Cab57 exhibited typical Gac/Rsm activities and antibiotic production, and these activities were enhanced by knocking out the retS gene (for a sensor kinase acting as an antagonist of GacS). Two large segments (79 and 115 kb) lacking in the Cab57 genome, as compared with the Pf-5 genome, accounted for the majority of the difference (247 kb) between these genomes. One of these segments was the complete rhizoxin analog biosynthesis gene cluster (ca. 79 kb) and another one was the 115-kb mobile genomic island. A whole genome comparison of those relative strains revealed that each strain has unique gene clusters involved in metabolism such as nitrite/nitrate assimilation, which was identified in the Cab57 genome. These findings suggest that P. protegens is a ubiquitous bacterium that controls its biocontrol traits while building up strain-specific genomic repertoires for the biosynthesis of secondary metabolites and niche adaptation. PMID:24695768

  2. Inhibition of chlamydiae by primary alcohols correlates with the strain-specific complement of plasticity zone phospholipase D genes.

    PubMed

    Nelson, David E; Crane, Deborah D; Taylor, Lacey D; Dorward, David W; Goheen, Morgan M; Caldwell, Harlan D

    2006-01-01

    Members of the genus Chlamydia are obligate intracellular pathogens that have a unique biphasic developmental cycle and interactions with host cells. Many genes that dictate host infection tropism and, putatively, pathogenic manifestations of disease are clustered in a hypervariable region of the genome termed the plasticity zone (PZ). Comparative genomics studies have determined that an uncharacterized family of PZ genes encoding orthologs of eukaryotic and prokaryotic members of the phospholipase D (PLD) enzyme family varies among chlamydiae. Here, we show that the PZ PLD (pzPLD) of Chlamydia trachomatis are transcribed during both normal and persistent infection and that the corresponding PLD proteins are predominantly localized in reticulate bodies on the inner leaflet of the inclusion membrane. Further, we show that strains of chlamydiae encoding the pzPLD, but not a strain lacking these genes, are inhibited by primary alcohols, potent PLD inhibitors, during growth in HeLa 229 cells. This inhibitory effect is amplified approximately 5,000-fold during recovery from persistent infection. These findings suggest that the chlamydial pzPLD may be important, strain-specific, pathogenesis factors in vivo.

  3. Identification of a Universally Primed-PCR-Derived Sequence-Characterized Amplified Region Marker for an Antagonistic Strain of Clonostachys rosea and Development of a Strain-Specific PCR Detection Assay

    PubMed Central

    Bulat, Sergey A.; Lübeck, Mette; Alekhina, Irina A.; Jensen, Dan Funck; Knudsen, Inge M. B.; Lübeck, Peter Stephensen

    2000-01-01

    We developed a PCR detection method that selectively recognizes a single biological control agent and demonstrated that universally primed PCR (UP-PCR) can identify strain-specific markers. Antagonistic strains of Clonostachys rosea (syn. Gliocladium roseum) were screened by UP-PCR, and a strain-specific marker was identified for strain GR5. No significant sequence homology was found between this marker and any other sequences in the databases. Southern blot analysis of the PCR product revealed that the marker represented a single-copy sequence specific for strain GR5. The marker was converted into a sequence-characterized amplified region (SCAR), and a specific PCR primer pair was designed. Eighty-two strains, isolated primarily from Danish soils, and 31 soil samples, originating from different localities, were tested, and this specificity was confirmed. Two strains responded to the SCAR primers under suboptimal PCR conditions, and the amplified sequences from these strains were similar, but not identical, to the GR5 marker. Soil assays in which total DNA was extracted from GR5-infested and noninoculated field soils showed that the SCAR primers could detect GR5 in a pool of mixed DNA and that no other soil microorganisms present contained sequences amplified by the primers. The assay developed will be useful for monitoring biological control agents released into natural field soil. PMID:11055920

  4. Evaluation of Optical Coherence Tomography as a Means of Identifying Earlier Stage Basal Cell Carcinomas while Reducing the Use of Diagnostic Biopsy

    PubMed Central

    Schwartz, Michelle; Feldman, Eleanor; Bienenfeld, Amanda; Bieber, Amy K.; Ellis, Jeffery; Alapati, Usha; Lebwohl, Mark; Siegel, Daniel M.

    2015-01-01

    Objective: To determine the diagnostic accuracy of optical coherence tomography for basal cell carcinoma and the proportion of biopsies that could be avoided if optical coherence tomography is used to rule-in surgery. Design: Multicenter, prospective, observational study. Setting: Dermatology clinics. Participants: Consecutive patients with clinically challenging pink lesions suspicious for basal cell carcinoma. Measurements: Clinical, dermoscopic, and optical coherence tomography images were obtained for all subjects. At each stage, the clinician made a diagnosis (pathology + subtype if applicable), and assessed his/her own confidence in the diagnosis. Results: Optical coherence tomography significantly (p<0.01) improved sensitivity and specificity over clinical or dermoscopic evaluation. The percentage of correct diagnoses was 57.4 percent (clinical), 69.6 percent (dermoscopy), and 87.8 percent (optical coherence tomography). Optical coherence tomography significantly increased the certainty of diagnosis; clinicians indicated they were certain (>95% confident) in 17 percent of lesions examined clinically, in 38.6 percent examined with dermoscopy, and in 70 percent examined with optical coherence tomography. With the use of optical coherence tomography in the diagnosis of basal cell carcinoma, more than 1 in 3 patients could avoid a diagnostic biopsy. Conclusion: In a population of clinically challenging lesions, optical coherence tomography improved diagnostic certainty by a factor of four over clinical examination alone and improved diagnostic accuracy by 50 percent (57-88%). The addition of optical coherence tomography to other standard assessments can improve the false-positive rate and give a high degree of certainty for ruling in a positive diagnosis for basal cell carcinoma. A reduction of 36 percent in overall biopsies could be achieved by sending high certainty basal cell carcinoma positive optical coherence tomography diagnoses straight to surgery. PMID

  5. Strain-Specific Variation in Murine Natural Killer Gene Complex Contributes to Differences in Immunosurveillance for Urethane-Induced Lung Cancer

    PubMed Central

    Kreisel, Daniel; Gelman, Andrew E.; Higashikubo, Ryuji; Lin, Xue; Vikis, Haris G.; White, J. Michael; Toth, Kelsey A.; Deshpande, Charuhas; Carreno, Beatriz M.; You, Ming; Taffner, Samantha M.; Yokoyama, Wayne M.; Bui, Jack D.; Schreiber, Robert D.; Krupnick, Alexander S.

    2012-01-01

    Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide and results from a complex interaction between carcinogen exposure and inherent susceptibility. Despite its prevalence genetic factors that predispose to the development of lung cancer remain elusive. Inbred mouse models offer a unique and clinically relevant tool to study genetic factors that contribute to lung carcinogenesis due to the development of tumors that resemble human adenocarcinoma and broad strain-specific variation in cancer incidence after carcinogen administration. Here we set out to investigate whether strain-specific variability in tumor immunosurveillance contributes to differences in lung cancer. Using bone marrow transplantation we determined that hematopoietic cells from lung cancer-resistant mice could significantly impede the development of cancer in a susceptible strain. Furthermore, we show that this is not due to differences in tumor-promoting inflammatory changes or variability in immunosurveillance by the adaptive immune system, but results from strain-specific differences in natural killer cell (NK) cytotoxicity. Using a newly discovered congenic strain of mice we demonstrate a previously unrecognized role for strain-specific polymorphisms in the natural killer gene complex (NKC) in immunosurveillance for carcinogen-induced lung cancer. Since polymorphisms in the NKC are highly prevalent in man, our data may explain why certain individuals without obvious risk factors develop lung cancer while others remain resistant to the disease despite heavy environmental carcinogen exposure. PMID:22751136

  6. Neuropsychopharmacology and Neurogenetic Aspects of Executive Functioning: Should Reward Gene Polymorphisms Constitute a Diagnostic Tool to Identify Individuals at Risk for Impaired Judgment?

    PubMed Central

    Bowirrat, Abdalla; Chen, Thomas JH; Oscar-Berman, Marlene; Madigan, Margaret; Chen, Amanda LH; Bailey, John A.; Braverman, Eric R.; Kerner, Mallory; Giordano, John; Morse, Siohban; Downs, B. William; Waite, Roger L.; Fornari, Frank; Armaly, Zaher; Blum, Kenneth

    2013-01-01

    Executive functions are processes that act in harmony to control behaviors necessary for maintaining focus and achieving outcomes. Executive dysfunction in neuropsychiatric disorders is attributed to structural or functional pathology of brain networks involving prefrontal cortex (PFC) and its connections with other brain regions. The PFC receives innervations from different neurons associated with a number of neurotransmitters, especially dopamine (DA). Here we review findings on the contribution of PFC DA to higher-order cognitive and emotional behaviors. We suggest examination of multifactorial interactions of an individual’s genetic history, along with environmental risk factors, can assist in the characterization of executive functioning for that individual. Based upon the results of genetic studies we also propose genetic mapping as a probable diagnostic tool serving as a therapeutic adjunct for augmenting executive functioning capabilities. We conclude that preservation of the neurological underpinnings of executive functions requires the integrity of complex neural systems including the influence of specific genes and associated polymorphisms to provide adequate neurotransmission. PMID:22371275

  7. Neuropsychopharmacology and neurogenetic aspects of executive functioning: should reward gene polymorphisms constitute a diagnostic tool to identify individuals at risk for impaired judgment?

    PubMed

    Bowirrat, Abdalla; Chen, Thomas J H; Oscar-Berman, Marlene; Madigan, Margaret; Chen, Amanda Lh; Bailey, John A; Braverman, Eric R; Kerner, Mallory; Giordano, John; Morse, Siobhan; Downs, B William; Waite, Roger L; Fornari, Frank; Armaly, Zaher; Blum, Kenneth

    2012-04-01

    Executive functions are processes that act in harmony to control behaviors necessary for maintaining focus and achieving outcomes. Executive dysfunction in neuropsychiatric disorders is attributed to structural or functional pathology of brain networks involving prefrontal cortex (PFC) and its connections with other brain regions. The PFC receives innervations from different neurons associated with a number of neurotransmitters, especially dopamine (DA). Here we review findings on the contribution of PFC DA to higher-order cognitive and emotional behaviors. We suggest that examination of multifactorial interactions of an individual's genetic history, along with environmental risk factors, can assist in the characterization of executive functioning for that individual. Based upon the results of genetic studies, we also propose genetic mapping as a probable diagnostic tool serving as a therapeutic adjunct for augmenting executive functioning capabilities. We conclude that preservation of the neurological underpinnings of executive functions requires the integrity of complex neural systems including the influence of specific genes and associated polymorphisms to provide adequate neurotransmission.

  8. Immune pressure selects for Plasmodium falciparum parasites presenting distinct red blood cell surface antigens and inducing strain-specific protection in Saimiri sciureus monkeys

    PubMed Central

    1995-01-01

    The passive transfer of specific antibodies to a naive splenectomized Saimiri sciureus monkey infected with the Palo Alto FUP/SP strain of Plasmodium falciparum resulted in the emergence of parasites resistant to the transferred antibodies. Molecular typing indicated that the original and resistant parasites were isogenic. Saimiri monkeys primed with original parasites were fully susceptible to a challenge by the resistant ones, and vice versa. This absence of crossprotection indicates that strain-specific determinants would be the major targets of protective immunity developed in these monkeys. Phenotypic analysis showed that the surface of the infected red blood cells differed in both lines. Original parasites formed rosettes, autoagglutinated, presented characteristic knobs at the surface of the infected red blood cell, and did not agglutinate in the presence of a pool of human immune sera. In contrast, the resistant parasites did not form rosettes, did not spontaneously autoagglutinate, presented abnormal flattened knobs, and formed large aggregates in the presence of a pool of human immune sera. The presence of strain-specific determinants at the surface of the resistant parasites was confirmed by surface immunofluorescence and agglutination using homologous Saimiri serum. Neither the original nor the resistant parasites cytoadhered to an amelanotic melanoma cell line, suggesting that cytoadherence and agglutination can be dissociated. These results indicate that parasites that differ by the antigens exposed at the surface of the red blood cell induce strain- specific immunity. Furthermore they show that rosetting and nonrosetting parasites differ in their antigenic properties and do not crossprotect. PMID:7807008

  9. Development of a Sequence-Characterized Amplified Region Marker-Targeted Quantitative PCR Assay for Strain-Specific Detection of Oenococcus oeni during Wine Malolactic Fermentation▿

    PubMed Central

    Solieri, Lisa; Giudici, Paolo

    2010-01-01

    Control over malolactic fermentation (MLF) is a difficult goal in winemaking and needs rapid methods to monitor Oenococcus oeni malolactic starters (MLS) in a stressful environment such as wine. In this study, we describe a novel quantitative PCR (QPCR) assay enabling the detection of an O. oeni strain during MLF without culturing. O. oeni strain LB221 was used as a model to develop a strain-specific sequence-characterized amplified region (SCAR) marker derived from a discriminatory OPA20-based randomly amplified polymorphic DNA (RAPD) band. The 5′ and 3′ flanking regions and the copy number of the SCAR marker were characterized using inverse PCR and Southern blotting, respectively. Primer pairs targeting the SCAR sequence enabled strain-specific detection without cross amplification of other O. oeni strains or wine species of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeasts. The SCAR-QPCR assay was linear over a range of cell concentrations (7 log units) and detected as few as 2.2 × 102 CFU per ml of red wine with good quantification effectiveness, as shown by the correlation of QPCR and plate counting results. Therefore, the cultivation-independent monitoring of a single O. oeni strain in wine based on a SCAR marker represents a rapid and effective strain-specific approach. This strategy can be adopted to develop easy and rapid detection techniques for monitoring the implantation of inoculated O. oeni MLS on the indigenous LAB population, reducing the risk of unsuccessful MLF. PMID:20935116

  10. Rapid diagnostic test supply chain and consumption study in Cabo Delgado, Mozambique: estimating stock shortages and identifying drivers of stock-outs

    PubMed Central

    2014-01-01

    Background Malaria rapid diagnostic tests (RDTs) are particularly useful in low-resource settings where follow-through on traditional laboratory diagnosis is challenging or lacking. The availability of these tests depends on supply chain processes within the distribution system. In Mozambique, stock-outs of malaria RDTs are fairly common at health facilities. A longitudinal cross-sectional study was conducted to evaluate drivers of stock shortages in the Cabo Delgado province. Methods Data were collected from purposively sampled health facilities, using monthly cross-sectional surveys between October 2011 and May 2012. Estimates of lost consumption (consumption not met due to stock-outs) served as the primary quantitative indicator of stock shortages. This is a better measure of the magnitude of stock-outs than binary indicators that only measure frequency of stock-outs at a given facility. Using a case study based methodology, distribution system characteristics were qualitatively analysed to examine causes of stock-outs at the provincial, district and health centre levels. Results 15 health facilities were surveyed over 120 time points. Stock-out patterns varied by data source; average monthly proportions of 59%, 17% and 17% of health centres reported a stock-out on stock cards, laboratory and pharmacy forms, respectively. Estimates of lost consumption percentage were significantly high; ranging from 0% to 149%; with a weighted average of 78%. Each ten-unit increase in monthly-observed consumption was associated with a nine-unit increase in lost consumption percentage indicating that higher rates of stock-outs occurred at higher levels of observed consumption. Causes of stock-outs included inaccurate tracking of lost consumption, insufficient sophistication in inventory management and replenishment, and poor process compliance by facility workers, all arguably stemming from inadequate attention to the design and implementation of the distribution system

  11. European surveillance network for influenza in pigs: surveillance programs, diagnostic tools and Swine influenza virus subtypes identified in 14 European countries from 2010 to 2013.

    PubMed

    Simon, Gaëlle; Larsen, Lars E; Dürrwald, Ralf; Foni, Emanuela; Harder, Timm; Van Reeth, Kristien; Markowska-Daniel, Iwona; Reid, Scott M; Dan, Adam; Maldonado, Jaime; Huovilainen, Anita; Billinis, Charalambos; Davidson, Irit; Agüero, Montserrat; Vila, Thaïs; Hervé, Séverine; Breum, Solvej Østergaard; Chiapponi, Chiara; Urbaniak, Kinga; Kyriakis, Constantinos S; Brown, Ian H; Loeffen, Willie

    2014-01-01

    Swine influenza causes concern for global veterinary and public health officials. In continuing two previous networks that initiated the surveillance of swine influenza viruses (SIVs) circulating in European pigs between 2001 and 2008, a third European Surveillance Network for Influenza in Pigs (ESNIP3, 2010-2013) aimed to expand widely the knowledge of the epidemiology of European SIVs. ESNIP3 stimulated programs of harmonized SIV surveillance in European countries and supported the coordination of appropriate diagnostic tools and subtyping methods. Thus, an extensive virological monitoring, mainly conducted through passive surveillance programs, resulted in the examination of more than 9 000 herds in 17 countries. Influenza A viruses were detected in 31% of herds examined from which 1887 viruses were preliminary characterized. The dominating subtypes were the three European enzootic SIVs: avian-like swine H1N1 (53.6%), human-like reassortant swine H1N2 (13%) and human-like reassortant swine H3N2 (9.1%), as well as pandemic A/H1N1 2009 (H1N1pdm) virus (10.3%). Viruses from these four lineages co-circulated in several countries but with very different relative levels of incidence. For instance, the H3N2 subtype was not detected at all in some geographic areas whereas it was still prevalent in other parts of Europe. Interestingly, H3N2-free areas were those that exhibited highest frequencies of circulating H1N2 viruses. H1N1pdm viruses were isolated at an increasing incidence in some countries from 2010 to 2013, indicating that this subtype has become established in the European pig population. Finally, 13.9% of the viruses represented reassortants between these four lineages, especially between previous enzootic SIVs and H1N1pdm. These novel viruses were detected at the same time in several countries, with increasing prevalence. Some of them might become established in pig herds, causing implications for zoonotic infections.

  12. Proteome Profiling of Urinary Exosomes Identifies Alpha 1-Antitrypsin and H2B1K as Diagnostic and Prognostic Biomarkers for Urothelial Carcinoma

    PubMed Central

    Lin, Shih-Yi; Chang, Chao-Hsiang; Wu, His-Chin; Lin, Ching-Chan; Chang, Kai-Po; Yang, Chi-Rei; Huang, Chi-Ping; Hsu, Wu-Huei; Chang, Chiz-Tzung; Chen, Chao-Jung

    2016-01-01

    MALDI-TOF spectrometry has not been used for urinary exosome analysis. We used it for determining UC biomarkers. From 2012 to 2015, we enrolled 129 consecutive patients with UC and 62 participants without UC. Exosomes from their urine were isolated, and analyzed through MALDI-TOF spectrometry. Immunohistochemical (IHC) analysis of another 122 UC and 26 non-UC tissues was conducted to verify the discovered biomarkers. Two peaks at m/z 5593 (fragmented peptide of alpha-1-antitrypsin; sensitivity, 50.4%; specificity, 96.9%) and m/z 5947 (fragmented peptide of histone H2B1K sensitivity, 62.0%; specificity, 92.3%) were identified as UC diagnosis exosome biomarkers. UC patients with detectable histone H2B1K showed 2.29- and 3.11-fold increased risks of recurrence and progression, respectively, compared with those with nondetectable histone H2B1K. Verification results of IHC staining revealed significantly higher expression of alpha 1-antitrypsin (p = 0.038) and H2B1K (p = 0.005) in UC tissues than in normal tissues. The expression of alpha 1-antitrypsin and H2B1K in UC tissues was significantly correlated with UC grades (p < 0.05). Urinary exosome proteins alpha 1-antitrypsin and histone H2B1K, which are identified through MALDI-TOF analysis, could facilitate rapid diagnosis and prognosis of UC. PMID:27686150

  13. A comparative proteomic study of plasma in feline pancreatitis and pancreatic carcinoma using 2-dimensional gel electrophoresis to identify diagnostic biomarkers: A pilot study

    PubMed Central

    Meachem, Melissa D.; Snead, Elisabeth R.; Kidney, Beverly A.; Jackson, Marion L.; Dickinson, Ryan; Larson, Victoria; Simko, Elemir

    2015-01-01

    While pancreatitis is now recognized as a common ailment in cats, the diagnosis remains challenging due to discordant results and suboptimal sensitivity of ultrasound and specific feline pancreatic lipase (Spec fPL) assay. Pancreatitis also shares similar clinical features with pancreatic carcinoma, a rare but aggressive disease with a grave prognosis. The objective of this pilot study was to compare the plasma proteomes of normal healthy cats (n = 6), cats with pancreatitis (n = 6), and cats with pancreatic carcinoma (n = 6) in order to identify potential new biomarkers of feline pancreatic disease. After plasma protein separation by 2-dimensional gel electrophoresis, protein spots were detected by Coomassie Brilliant Blue G-250 staining and identified by mass spectrometry. Alpha-1-acid glycoprotein (AGP), apolipoprotein-A1 (Apo-A1), and apolipoprotein-A1 precursor (Pre Apo-A1) appeared to be differentially expressed, which suggests the presence of a systemic acute-phase response and alteration of lipid metabolism in cats with pancreatic disease. Future studies involving greater case numbers are needed in order to assess the utility of these proteins as potential biomarkers. More sensitive proteomic techniques may also be helpful in detecting significant but low-abundance proteins. PMID:26130850

  14. Microfluidic based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in sera of prostate cancer patients

    PubMed Central

    Moltzahn, Felix; Olshen, Adam B.; Baehner, Lauren; Peek, Andrew; Fong, Lawrence; Stöppler, Hubert; Simko, Jeffry; Hilton, Joan F.; Carroll, Peter; Blelloch, Robert

    2010-01-01

    Recent prostate specific antigen (PSA) based screening trials indicate an urgent need for novel and non-invasive biomarker identification strategies to improve the prediction of prostate cancer behavior. Non-coding microRNAs (miRNAs) in the serum and plasma have been shown to have potential as non-invasive markers for physiological and pathological conditions. To identify serum miRNAs that diagnose and correlate with prognosis of prostate cancer, we developed a multiplex quantitative reverse transcription PCR (qRT-PCR) method involving purification of multiplex PCR products followed by uniplex analysis on a microfluidics chip to evaluate 384 human miRNAs. Using Dgcr8 and Dicer knockout (small RNA - deficient) mouse ES cells (mESC) as the benchmark, we confirmed the validity of our technique, while uncovering a significant lack of accuracy in previously published methods. Profiling 48 sera from healthy men and untreated prostate cancer patients with differing CAPRA (Cancer of the Prostate Risk Assessment) scores, we identified miRNA signatures that allow to diagnose cancer patients and correlate with prognosis. These serum signatures include oncogenic and tumor suppressive miRNAs suggesting functional roles in prostate cancer progression. PMID:21098088

  15. Simultaneous use of camera and probe diagnostics to unambiguously identify and study the dynamics of multiple underlying instabilities during the route to plasma turbulence

    SciTech Connect

    Thakur, S. C. Tynan, G. R.; Brandt, C.; Cui, L.; Gosselin, J. J.; Light, A.

    2014-11-15

    We use multiple-tip Langmuir probes and fast imaging to unambiguously identify and study the dynamics of underlying instabilities during the controlled route to fully-developed plasma turbulence in a linear magnetized helicon plasma device. Langmuir probes measure radial profiles of electron temperature, plasma density and potential; from which we compute linear growth rates of instabilities, cross-phase between density and potential fluctuations, Reynold's stress, particle flux, vorticity, time-delay estimated velocity, etc. Fast imaging complements the 1D probe measurements by providing temporally and spatially resolved 2D details of plasma structures associated with the instabilities. We find that three radially separated plasma instabilities exist simultaneously. Density gradient driven resistive drift waves propagating in the electron diamagnetic drift direction separate the plasma into an edge region dominated by strong, velocity shear driven Kelvin-Helmholtz instabilities and a central core region which shows coherent Rayleigh-Taylor modes propagating in the ion diamagnetic drift direction. The simultaneous, complementary use of both probes and camera was crucial to identify the instabilities and understand the details of the very rich plasma dynamics.

  16. Simultaneous use of camera and probe diagnostics to unambiguously identify and study the dynamics of multiple underlying instabilities during the route to plasma turbulence.

    PubMed

    Thakur, S C; Brandt, C; Light, A; Cui, L; Gosselin, J J; Tynan, G R

    2014-11-01

    We use multiple-tip Langmuir probes and fast imaging to unambiguously identify and study the dynamics of underlying instabilities during the controlled route to fully-developed plasma turbulence in a linear magnetized helicon plasma device. Langmuir probes measure radial profiles of electron temperature, plasma density and potential; from which we compute linear growth rates of instabilities, cross-phase between density and potential fluctuations, Reynold's stress, particle flux, vorticity, time-delay estimated velocity, etc. Fast imaging complements the 1D probe measurements by providing temporally and spatially resolved 2D details of plasma structures associated with the instabilities. We find that three radially separated plasma instabilities exist simultaneously. Density gradient driven resistive drift waves propagating in the electron diamagnetic drift direction separate the plasma into an edge region dominated by strong, velocity shear driven Kelvin-Helmholtz instabilities and a central core region which shows coherent Rayleigh-Taylor modes propagating in the ion diamagnetic drift direction. The simultaneous, complementary use of both probes and camera was crucial to identify the instabilities and understand the details of the very rich plasma dynamics.

  17. Postnatal Identification of Trisomy 21: An Overview of 7,133 Postnatal Trisomy 21 Cases Identified in a Diagnostic Reference Laboratory in China.

    PubMed

    Zhao, Weiwei; Chen, Fan; Wu, Menghua; Jiang, Shuai; Wu, Binbin; Luo, Huali; Wen, Jingyi; Hu, Chaohui; Yu, Shihui

    2015-01-01

    This study describes the cytogenetic characteristics of 7,133 trisomy 21 (Tri21) identified from 247,818 consecutive postnatal cases karyotyped in a single reference laboratory in China for a period of 4 years. The average detection rate of Tri21 is 2.88% ranging from 3.39% in 2011 to 2.52% in 2014. The decreased detection rates over the years might reflect a possible impact of noninvasive prenatal testing applied rapidly in China and elective termination of affected pregnancies. 95.32% of the Tri21 karyotypes are standard Tri21, 4.53% are Robertsonian Tri21, and less than 1% are other Tri21 forms. There are more mosaic Tri21 in older children and adults, consistent with previous observations that clinical features in individuals with mosaic Tri21 are generally milder and easily missed during perinatal period. The male/female (M/F ratio) for the total 7,133 Tri21 cases and for the 6,671 cases with non-mosaic standard Tri21 are 1.50 and 1.53 respectively, significantly higher than the 0.93 for all the 247,818 cases we karyotyped, the 1.30 for the Down syndrome (DS) identified during perinatal period in China, and the 1.20 for the livebirth in Chinese population. In contrast, the mosaic standard Tri21 case has a significantly lower proportion of males when compared with the non-mosaic standard Tri21, indicating different underlying mechanisms leading to their formations. Opposite M/F ratios in different subtypes of ROB Tri21 were observed. A long list of rare or private karyotypes where Tri21 are concurrently present was identified. The large collection of Tri21 cases with a diversity of clinical findings and a wide age range allowed us to determine the frequency of the different karyotypes of Down syndrome in China, given the fact that this kind of national epidemiological data is lacking currently. PMID:26176847

  18. Postnatal Identification of Trisomy 21: An Overview of 7,133 Postnatal Trisomy 21 Cases Identified in a Diagnostic Reference Laboratory in China

    PubMed Central

    Wu, Menghua; Jiang, Shuai; Wu, Binbin; Luo, Huali; Wen, Jingyi; Hu, Chaohui; Yu, Shihui

    2015-01-01

    This study describes the cytogenetic characteristics of 7,133 trisomy 21 (Tri21) identified from 247,818 consecutive postnatal cases karyotyped in a single reference laboratory in China for a period of 4 years. The average detection rate of Tri21 is 2.88% ranging from 3.39% in 2011 to 2.52% in 2014. The decreased detection rates over the years might reflect a possible impact of noninvasive prenatal testing applied rapidly in China and elective termination of affected pregnancies. 95.32% of the Tri21 karyotypes are standard Tri21, 4.53% are Robertsonian Tri21, and less than 1% are other Tri21 forms. There are more mosaic Tri21 in older children and adults, consistent with previous observations that clinical features in individuals with mosaic Tri21 are generally milder and easily missed during perinatal period. The male/female (M/F ratio) for the total 7,133 Tri21 cases and for the 6,671 cases with non-mosaic standard Tri21 are 1.50 and 1.53 respectively, significantly higher than the 0.93 for all the 247,818 cases we karyotyped, the 1.30 for the Down syndrome (DS) identified during perinatal period in China, and the 1.20 for the livebirth in Chinese population. In contrast, the mosaic standard Tri21 case has a significantly lower proportion of males when compared with the non-mosaic standard Tri21, indicating different underlying mechanisms leading to their formations. Opposite M/F ratios in different subtypes of ROB Tri21 were observed. A long list of rare or private karyotypes where Tri21 are concurrently present was identified. The large collection of Tri21 cases with a diversity of clinical findings and a wide age range allowed us to determine the frequency of the different karyotypes of Down syndrome in China, given the fact that this kind of national epidemiological data is lacking currently. PMID:26176847

  19. Identifying diagnostically-relevant resting state brain functional connectivity in the ventral posterior complex via genetic data mining in autism spectrum disorder.

    PubMed

    Baldwin, Philip R; Curtis, Kaylah N; Patriquin, Michelle A; Wolf, Varina; Viswanath, Humsini; Shaw, Chad; Sakai, Yasunari; Salas, Ramiro

    2016-05-01

    Exome sequencing and copy number variation analyses continue to provide novel insight to the biological bases of autism spectrum disorder (ASD). The growing speed at which massive genetic data are produced causes serious lags in analysis and interpretation of the data. Thus, there is a need to develop systematic genetic data mining processes that facilitate efficient analysis of large datasets. We report a new genetic data mining system, ProcessGeneLists and integrated a list of ASD-related genes with currently available resources in gene expression and functional connectivity of the human brain. Our data-mining program successfully identified three primary regions of interest (ROIs) in the mouse brain: inferior colliculus, ventral posterior complex of the thalamus (VPC), and parafascicular nucleus (PFn). To understand its pathogenic relevance in ASD, we examined the resting state functional connectivity (RSFC) of the homologous ROIs in human brain with other brain regions that were previously implicated in the neuro-psychiatric features of ASD. Among them, the RSFC of the VPC with the medial frontal gyrus (MFG) was significantly more anticorrelated, whereas the RSFC of the PN with the globus pallidus was significantly increased in children with ASD compared with healthy children. Moreover, greater values of RSFC between VPC and MFG were correlated with severity index and repetitive behaviors in children with ASD. No significant RSFC differences were detected in adults with ASD. Together, these data demonstrate the utility of our data-mining program through identifying the aberrant connectivity of thalamo-cortical circuits in children with ASD. Autism Res 2016, 9: 553-562. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

  20. Multiple diagnostic tests to identify cattle with Bovine viral diarrhea virus and duration of positive test results in persistently infected cattle.

    PubMed

    Fulton, Robert W; Hessman, Bill E; Ridpath, Julia F; Johnson, Bill J; Burge, Lurinda J; Kapil, Sanjay; Braziel, Barbara; Kautz, Kira; Reck, Amy

    2009-04-01

    Several tests for Bovine viral diarrhea virus (BVDV) were applied to samples collected monthly from December 20, 2005, through November 27, 2006 (day 0 to day 342) from 12 persistently infected (PI) cattle with BVDV subtypes found in US cattle: BVDV-1a, BVDV-1b, and BVDV-2a. The samples included clotted blood for serum, nasal swabs, and fresh and formalin-fixed ear notches. The tests were as follows: titration of infectious virus in serum and nasal swabs; antigen-capture (AC) enzyme-linked immunosorbent assay (ELISA), or ACE, on serum, nasal swabs, and fresh ear notches; gel-based polymerase chain reaction (PCR) testing of serum, nasal swabs, and fresh ear notches; immunohistochemical (IHC) testing of formalin-fixed ear notches; and serologic testing for BVDV antibodies in serum. Of the 12 animals starting the study, 3 died with mucosal disease. The ACE and IHC tests on ear notches had positive results throughout the study, as did the ACE and PCR tests on serum. There was detectable virus in nasal swabs from all the cattle throughout the study except for a few samples that were toxic to cell cultures. The serum had a virus titer > or = log(10) 1.60 in all samples from all the cattle except for 3 collections from 1 animal. Although there were several equivocal results, the PCR test most often had positive results. The BVDV antibodies were due to vaccination or exposure to heterologous strains and did not appear to interfere with any BVDV test. These findings illustrate that PI cattle may be identified by several tests, but differentiation of PI cattle from cattle with acute BVDV infection requires additional testing, especially of blood samples and nasal swabs positive on initial testing. Also, calves PI with BVDV are continual shedders of infectious virus, as shown by the infectivity of nasal swabs over the 11-mo study.

  1. The first case of mitochondrial acetoacetyl-CoA thiolase deficiency identified by expanded newborn metabolic screening in Italy: the importance of an integrated diagnostic approach.

    PubMed

    Catanzano, Francesca; Ombrone, Daniela; Di Stefano, Cristina; Rossi, Anna; Nosari, Norberto; Scolamiero, Emanuela; Tandurella, Igor; Frisso, Giulia; Parenti, Giancarlo; Ruoppolo, Margherita; Andria, Generoso; Salvatore, Francesco

    2010-12-01

    A pilot expanded newborn screening programme to detect inherited metabolic disorders by means of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) began in the Campania region, southern Italy, in 2007. By October 2009, >8,800 dried blood samples on filter paper from 11 hospitals had been screened. Within this screening programme, we identified a case of mitochondrial acetoacetyl-coenzyme A (CoA) thiolase deficiency [β-ketothiolase (β-KT) deficiency] by analysing the acylcarnitine profile from a dried blood spot with LC-MS/MS. Gas chromatography coupled with mass spectrometry analysis of urinary organic acids and LC-MS/MS analysis of urinary acylcarnitines were in line with this disorder. In fact, concentrations were well beyond the cut-off values of tiglyl carnitine, 3-hydroxybutyrylcarnitine and 2-methyl-3-hydroxybutyrylcarnitine, 2-methyl-3-hydroxybutyric acid and tiglyl glycine. The absence of 2-methylacetoacetic acid in urine may be attributed to: (i) the instability of this β-ketoacid because it undergoes spontaneous decarboxylation to 2-butanone, which is highly volatile and thus difficult to detect, and (ii) the good health of the patient in the first days of life. β-KT deficiency was subsequently diagnosed in the patient's older sister, who showed increased levels of the same metabolites but also small amounts of 2-methylacetoacetic acid, which is considered a key marker for β-KT diagnosis. Genomic analysis revealed mutation c.1189C >G in exon 12 of the ACAT1 gene, which results in a severe defect because of the p.H397D amino acid change in both alleles of both patients.

  2. Multiple diagnostic tests to identify cattle with Bovine viral diarrhea virus and duration of positive test results in persistently infected cattle.

    PubMed

    Fulton, Robert W; Hessman, Bill E; Ridpath, Julia F; Johnson, Bill J; Burge, Lurinda J; Kapil, Sanjay; Braziel, Barbara; Kautz, Kira; Reck, Amy

    2009-04-01

    Several tests for Bovine viral diarrhea virus (BVDV) were applied to samples collected monthly from December 20, 2005, through November 27, 2006 (day 0 to day 342) from 12 persistently infected (PI) cattle with BVDV subtypes found in US cattle: BVDV-1a, BVDV-1b, and BVDV-2a. The samples included clotted blood for serum, nasal swabs, and fresh and formalin-fixed ear notches. The tests were as follows: titration of infectious virus in serum and nasal swabs; antigen-capture (AC) enzyme-linked immunosorbent assay (ELISA), or ACE, on serum, nasal swabs, and fresh ear notches; gel-based polymerase chain reaction (PCR) testing of serum, nasal swabs, and fresh ear notches; immunohistochemical (IHC) testing of formalin-fixed ear notches; and serologic testing for BVDV antibodies in serum. Of the 12 animals starting the study, 3 died with mucosal disease. The ACE and IHC tests on ear notches had positive results throughout the study, as did the ACE and PCR tests on serum. There was detectable virus in nasal swabs from all the cattle throughout the study except for a few samples that were toxic to cell cultures. The serum had a virus titer > or = log(10) 1.60 in all samples from all the cattle except for 3 collections from 1 animal. Although there were several equivocal results, the PCR test most often had positive results. The BVDV antibodies were due to vaccination or exposure to heterologous strains and did not appear to interfere with any BVDV test. These findings illustrate that PI cattle may be identified by several tests, but differentiation of PI cattle from cattle with acute BVDV infection requires additional testing, especially of blood samples and nasal swabs positive on initial testing. Also, calves PI with BVDV are continual shedders of infectious virus, as shown by the infectivity of nasal swabs over the 11-mo study. PMID:19436580

  3. The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics-Identifying biomarker signatures by multivariate data analysis.

    PubMed

    Melanie, Spornraft; Benedikt, Kirchner; Pfaffl, Michael W; Irmgard, Riedmaier

    2015-09-01

    Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, 'black sheep' among farmers might circumvent the detection methods used in routine controls, which highlights the need for an innovative and reliable detection method. Transcriptomics is a promising new approach in the discovery of veterinary medicine biomarkers and also a missing puzzle piece, as up to date, metabolomics and proteomics are paramount. Due to increased stability and easy sampling, circulating extracellular small RNAs (smexRNAs) in bovine plasma were small RNA-sequenced and their potential to serve as biomarker candidates was evaluated using multivariate data analysis tools. After running the data evaluation pipeline, the proportion of miRNAs (microRNAs) and piRNAs (PIWI-interacting small non-coding RNAs) on the total sequenced reads was calculated. Additionally, top 10 signatures were compared which revealed that the readcount data sets were highly affected by the most abundant miRNA and piRNA profiles. To evaluate the discriminative power of multivariate data analyses to identify animals after veterinary drug application on the basis of smexRNAs, OPLS-DA was performed. In summary, the quality of miRNA models using all mapped reads for both treatment groups (animals treated with steroid hormones or the β-agonist clenbuterol) is predominant to those generated with combined data sets or piRNAs alone. Using multivariate projection methodologies like OPLS-DA have proven the best potential to generate discriminative miRNA models, supported by small RNA-Seq data. Based on the presented comparative OPLS-DA, miRNAs are the favorable smexRNA biomarker candidates in the research field of veterinary drug abuse.

  4. Methods and procedures for use of complement-fixation technique in type- and strain-specific diagnosis of influenza*†

    PubMed Central

    Lief, Florence S.; Henle, Werner

    1959-01-01

    It is now well established that there are two kinds of complement-fixing antigens of influenza virus: the soluble, type-specific, antigens, found mainly in infected tissue but also within the virus particle; and the virus, strain-specific, antigens, closely linked with the haemagglutinating component. For true results in complement-fixation testing in influenza, antigens or antisera of the one kind must be free of the other kind. This paper describes in detail the preparation of reagents for such testing and a variety of basic aspects of test procedures. PMID:13651922

  5. Diagnosis of the Earliest Strain-Specific Interactions between Tobacco Mosaic Virus and Chloroplasts of Tobacco Leaves in Vivo by Means of Chlorophyll Fluorescence Imaging.

    PubMed Central

    Balachandran, S.; Osmond, C. B.; Daley, P. F.

    1994-01-01

    Fluorescence imaging was used to diagnose early stages of the strain-specific interactions between tobacco mosaic virus (strain PV230) and chloroplasts following infection of tobacco leaves (Nicotiana tabacum cv Xanthi). The earliest indication of interaction in tissues that ultimately become chlorotic was a reduction in chlorophyll fluorescence, and there was little fluorescence quenching compared with adjacent healthy tissues. Subsequently, fluorescence increased but remained unquenched. In the late stages fluorescence declined again in chlorotic regions as the chloroticmosaic symptoms developed. These in vivo data showing altered fluorescence yields confirm strain-specific interaction of virus coat protein with photosystem II (PSII) components in vitro, leading to photoinhibition and photooxidation of chlorophyll in infected cells and the development of visible chlorotic-mosaic symptoms. Although mechanisms leading to the low, unquenched fluorescence condition are not known, the intermediate high, unquenched fluorescence condition is consistent with impaired PSII electron transport as measured in vitro. Fluorescence lesions appear more rapidly and develop more extensively in high light, consistent with the faster and larger extent of symptom formation in high-light-grown leaves than in low-light-grown leaves. PMID:12232149

  6. X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses

    PubMed Central

    Kamiya, Mana; Kawase, Tomoyuki; Hayama, Kazuhide; Tsuchimochi, Makoto; Okuda, Kazuhiro; Yoshie, Hiromasa

    2015-01-01

    Abstract Radiation therapy for head and neck cancers often causes xerostomia (dry mouth) by acutely damaging the salivary glands through the induction of severe acute inflammation. By contrast, the mechanism underlying the X-ray-induced delayed salivary dysfunction is unknown and has attracted increasing attention. To identify and develop a mouse model that distinguishes the delayed from the acute effects, we examined three different mouse strains (C57BL/6, ICR, and ICR-nu/nu) that showed distinct T-cell activities to comparatively analyze their responses to X-ray irradiation. Three strains were irradiated with X-rays (25 Gy), and functional changes of the submandibular glands were examined by determining pilocarpine-induced saliva secretion. Structural changes were evaluated using histopathological and immunohistochemical examinations of CD3, cleaved poly (ADP-ribose) polymerase (PARP), and Bcl-xL. In C57BL/6 mice, the X-ray irradiation induced acute inflammation accompanied by severe inflammatory cell infiltration at 4 days postirradiation, causing substantial destruction and significant dysfunction at 2 weeks. Fibrotic repair was observed at 16 weeks. In ICR-nu/nu mice, the inflammation and organ destruction were much milder than in the other mice strains, but increased apoptotic cells and a significant reduction in salivary secretion were observed at 4 and 8 weeks and beyond, respectively. These results suggest that in C57BL/6 mice, X-ray-induced functional and structural damage to the salivary glands is caused mainly by acute inflammation. By contrast, although neither acute inflammation nor organ destruction was observed in ICR-nu/nu mice, apoptotic cell death preceded the dysfunction in salivary secretion in the later phase. These data suggest that the X-ray-irradiated ICR-nu/nu mouse may be a useful animal model for developing more specific therapeutic methods for the delayed dysfunction of salivary glands. PMID:26309806

  7. X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses.

    PubMed

    Kamiya, Mana; Kawase, Tomoyuki; Hayama, Kazuhide; Tsuchimochi, Makoto; Okuda, Kazuhiro; Yoshie, Hiromasa

    2015-01-01

    Radiation therapy for head and neck cancers often causes xerostomia (dry mouth) by acutely damaging the salivary glands through the induction of severe acute inflammation. By contrast, the mechanism underlying the X-ray-induced delayed salivary dysfunction is unknown and has attracted increasing attention. To identify and develop a mouse model that distinguishes the delayed from the acute effects, we examined three different mouse strains (C57BL/6, ICR, and ICR-nu/nu) that showed distinct T-cell activities to comparatively analyze their responses to X-ray irradiation. Three strains were irradiated with X-rays (25 Gy), and functional changes of the submandibular glands were examined by determining pilocarpine-induced saliva secretion. Structural changes were evaluated using histopathological and immunohistochemical examinations of CD3, cleaved poly (ADP-ribose) polymerase (PARP), and Bcl-xL. In C57BL/6 mice, the X-ray irradiation induced acute inflammation accompanied by severe inflammatory cell infiltration at 4 days postirradiation, causing substantial destruction and significant dysfunction at 2 weeks. Fibrotic repair was observed at 16 weeks. In ICR-nu/nu mice, the inflammation and organ destruction were much milder than in the other mice strains, but increased apoptotic cells and a significant reduction in salivary secretion were observed at 4 and 8 weeks and beyond, respectively. These results suggest that in C57BL/6 mice, X-ray-induced functional and structural damage to the salivary glands is caused mainly by acute inflammation. By contrast, although neither acute inflammation nor organ destruction was observed in ICR-nu/nu mice, apoptotic cell death preceded the dysfunction in salivary secretion in the later phase. These data suggest that the X-ray-irradiated ICR-nu/nu mouse may be a useful animal model for developing more specific therapeutic methods for the delayed dysfunction of salivary glands. PMID:26309806

  8. Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs

    PubMed Central

    2011-01-01

    Background Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of these intersubtype HIV-1 recombinants still require further investigation. All intersubtype HIV-1 recombinants are generated and evolve from initial dual infections, but are difficult to identify in the human population. In vitro studies provide the most practical system to study mechanisms, but the recombination rates are usually very low in dual infections with primary HIV-1 isolates. This study describes the use of HIV-1 isolate-specific siRNAs to enrich intersubtype HIV-1 recombinants and inhibit the parental HIV-1 isolates from a dual infection. Results Following a dual infection with subtype A and D primary HIV-1 isolates and two rounds of siRNA treatment, nearly 100% of replicative virus was resistant to a siRNA specific for an upstream target sequence in the subtype A envelope (env) gene as well as a siRNA specific for a downstream target sequence in the subtype D env gene. Only 20% (10/50) of the replicating virus had nucleotide substitutions in the siRNA-target sequence whereas the remaining 78% (39/50) harbored a recombination breakpoint that removed both siRNA target sequences, and rendered the intersubtype D/A recombinant virus resistant to the dual siRNA treatment. Since siRNAs target the newly transcribed HIV-1 mRNA, the siRNAs only enrich intersubtype env recombinants and do not influence the recombination process during reverse transcription. Using this system, a strong bias is selected for recombination breakpoints in the C2 region, whereas other HIV-1 env regions, most notably the hypervariable regions, were nearly devoid of intersubtype recombination breakpoints. Sequence conservation plays an important role in selecting for recombination breakpoints, but the lack of breakpoints in many conserved

  9. Strain-Specific Variation of the Decorin-Binding Adhesin DbpA Influences the Tissue Tropism of the Lyme Disease Spirochete

    PubMed Central

    Lin, Yi-Pin; Benoit, Vivian; Yang, Xiuli; Martínez-Herranz, Raúl; Pal, Utpal; Leong, John M.

    2014-01-01

    Lyme disease spirochetes demonstrate strain- and species-specific differences in tissue tropism. For example, the three major Lyme disease spirochete species, Borrelia burgdorferi sensu stricto, B. garinii, and B. afzelii, are each most commonly associated with overlapping but distinct spectra of clinical manifestations. Borrelia burgdorferi sensu stricto, the most common Lyme spirochete in the U.S., is closely associated with arthritis. The attachment of microbial pathogens to cells or to the extracellular matrix of target tissues may promote colonization and disease, and the Lyme disease spirochete encodes several surface proteins, including the decorin- and dermatan sulfate-binding adhesin DbpA, which vary among strains and have been postulated to contribute to strain-specific differences in tissue tropism. DbpA variants differ in their ability to bind to its host ligands and to cultured mammalian cells. To directly test whether variation in dbpA influences tissue tropism, we analyzed murine infection by isogenic B. burgdorferi strains that encode different dbpA alleles. Compared to dbpA alleles of B. afzelii strain VS461 or B. burgdorferi strain N40-D10/E9, dbpA of B. garinii strain PBr conferred the greatest decorin- and dermatan sulfate-binding activity, promoted the greatest colonization at the inoculation site and heart, and caused the most severe carditis. The dbpA of strain N40-D10/E9 conferred the weakest decorin- and GAG-binding activity, but the most robust joint colonization and was the only dbpA allele capable of conferring significant joint disease. Thus, dbpA mediates colonization and disease by the Lyme disease spirochete in an allele-dependent manner and may contribute to the etiology of distinct clinical manifestations associated with different Lyme disease strains. This study provides important support for the long-postulated model that strain-specific variations of Borrelia surface proteins influence tissue tropism. PMID:25079227

  10. Strain-specific variation of the decorin-binding adhesin DbpA influences the tissue tropism of the lyme disease spirochete.

    PubMed

    Lin, Yi-Pin; Benoit, Vivian; Yang, Xiuli; Martínez-Herranz, Raúl; Pal, Utpal; Leong, John M

    2014-07-01

    Lyme disease spirochetes demonstrate strain- and species-specific differences in tissue tropism. For example, the three major Lyme disease spirochete species, Borrelia burgdorferi sensu stricto, B. garinii, and B. afzelii, are each most commonly associated with overlapping but distinct spectra of clinical manifestations. Borrelia burgdorferi sensu stricto, the most common Lyme spirochete in the U.S., is closely associated with arthritis. The attachment of microbial pathogens to cells or to the extracellular matrix of target tissues may promote colonization and disease, and the Lyme disease spirochete encodes several surface proteins, including the decorin- and dermatan sulfate-binding adhesin DbpA, which vary among strains and have been postulated to contribute to strain-specific differences in tissue tropism. DbpA variants differ in their ability to bind to its host ligands and to cultured mammalian cells. To directly test whether variation in dbpA influences tissue tropism, we analyzed murine infection by isogenic B. burgdorferi strains that encode different dbpA alleles. Compared to dbpA alleles of B. afzelii strain VS461 or B. burgdorferi strain N40-D10/E9, dbpA of B. garinii strain PBr conferred the greatest decorin- and dermatan sulfate-binding activity, promoted the greatest colonization at the inoculation site and heart, and caused the most severe carditis. The dbpA of strain N40-D10/E9 conferred the weakest decorin- and GAG-binding activity, but the most robust joint colonization and was the only dbpA allele capable of conferring significant joint disease. Thus, dbpA mediates colonization and disease by the Lyme disease spirochete in an allele-dependent manner and may contribute to the etiology of distinct clinical manifestations associated with different Lyme disease strains. This study provides important support for the long-postulated model that strain-specific variations of Borrelia surface proteins influence tissue tropism.

  11. [Diagnostics in osteology].

    PubMed

    Jakob, F; Genest, F; Seefried, L; Tsourdi, E; Lapa, C; Hofbauer, L C

    2016-07-01

    Clinical diagnostics in metabolic bone diseases cover a broad spectrum of conventional and state of the art methods ranging from the medical history and clinical examination to molecular imaging. Patient treatment is carried out in an interdisciplinary team due to the multiple interactions of bone with other organ systems. Diagnosis of osteoporosis is supported by high level national guidelines. A paradigm shift concerning the clinical relevance of bone mineral density measurement renders this now to be a strong risk factor rather than a diagnostic parameter, while strengthening the value of other clinical factors for risk assessment. The impact of parameters for muscle mass, structure and function is steadily increasing in all age groups. In order to identify underlying diseases that influence bone metabolism a panel of general laboratory diagnostic parameters is recommended. Markers for bone formation and resorption and specific parameters for the regulation of calcium and phosphate metabolism should be evaluated by specialists because they require diligence in preanalytics and experience in interpretation. Genetic diagnosis is well established for rare bone diseases while diagnostic panels are not yet available for routine diagnostics in polygenetic diseases such as osteoporosis. Conventional radiology is still very important to identify, e. g. fractures, osteolytic and osteoblastic lesions and extraosseous calcifications; however tomography-based methods which combine, e. g. scintigraphy or positron emission technologies with anatomical imaging are of increasing significance. Clinical diagnostics in osteology require profound knowledge and are subject to a dynamic evolution. PMID:27307159

  12. Molecular Diagnostics

    PubMed Central

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid, polymerase chain reaction–based detection of bacterial genes, and metabolomic determination of responses to orthopaedic infection. PMID:25808967

  13. Direct contact transmission of three different foot-and-mouth disease virus strains in swine demonstrates important strain-specific differences.

    PubMed

    Pacheco, Juan M; Tucker, Meghan; Hartwig, Ethan; Bishop, Elizabeth; Arzt, Jonathan; Rodriguez, Luis L

    2012-08-01

    A novel direct contact transmission model for the study of foot-and-mouth disease virus (FMDV) infection of swine was utilized to investigate transmission characteristics of three FMDV strains belonging to serotypes A, O and Asia1. Each strain demonstrated distinct transmission characteristics and required different exposure times to achieve successful contact transmission. While a 4h exposure was sufficient for strain A24 Cruzeiro (A24Cru), both O1 Manisa and Asia1 Shamir transmission required 18 h or more. Viral excretion levels from donors (for all three strains) and virus present in room air (for A24Cru and O1 Manisa) were evaluated and associated with clinical signs and observed transmission pattern. Although all directly inoculated donor animals showed acute FMD, A24Cru had the highest levels of viral shedding in saliva and nasal swabs followed by O1 Manisa and Asia1 Shamir. Virus levels in room air were higher and were detected longer for A24Cru than for O1 Manisa. These results provide direct evidence for important strain-specific variation in transmission characteristics and emphasize the need for thorough evaluation of different FMDV viral strains using a well defined contact transmission methodology. This information is critical for vaccine and biotherapeutic efficacy testing, pathogenesis and disease modeling of FMDV transmission.

  14. Monitoring Lysobacter capsici AZ78 using strain specific qPCR reveals the importance of the formulation for its survival in vineyards.

    PubMed

    Segarra, Guillem; Puopolo, Gerardo; Porcel-Rodríguez, Elena; Giovannini, Oscar; Pertot, Ilaria

    2016-02-01

    Survival in the phyllosphere is a critical feature for biofungicides based on non-spore forming bacteria. Moreover, knowledge of their persistence on plants is important to design effective formulations and application techniques. With this scope, the aim of this work was to develop a specific method to monitor the fate in the environment of Lysobacter capsici AZ78, a biocontrol agent of Plasmopara viticola, and to evaluate the contribution of formulation in its persistence on grapevine leaves. A strain-specific primer pair derived from REP-PCR fingerprinting was used in quantitative PCR experiments to track the evolution of L. capsici AZ78 population in vineyards. The population reached between 5 and 6 log10 cells gram of leaf(-1) after application and decreased by more than 100 times in one week. Multiple regression analysis showed that unfavourable temperature was the main environmental factor correlating with the decrease of L. capsici AZ78 persistence on grapevine leaves. Importantly, the use of formulation additives protected L. capsici AZ78 against environmental factors and improved its persistence on the leaves by more than 10 times compared to nude cells. Formulation and the knowledge about the persistence of L. capsici AZ78 in vineyards will be useful to develop commercial biofungicides for foliar application. PMID:26691736

  15. Diagnosis of amebic dysentery by detection of Entamoeba histolytica fecal antigen by an invasive strain-specific, monoclonal antibody-based enzyme-linked immunosorbent assay.

    PubMed Central

    Gonzalez-Ruiz, A; Haque, R; Rehman, T; Aguirre, A; Hall, A; Guhl, F; Warhurst, D C; Miles, M A

    1994-01-01

    An invasive strain-specific monoclonal antibody against Entamoeba histolytica has been used in a capture enzyme-linked immunosorbent assay (ELISA) for the detection of invasive E. histolytica fecal antigen in clinical specimens and for the diagnosis of amebic dysentery in patients from Bangladesh. The fecal antigen capture ELISA (FAC-ELISA) did not cross-react with other parasite species in the clinical specimens or with noninvasive E. histolytica present in those specimens and in experimentally seeded stools. The limit of detection of the assay for invasive E. histolytica crude antigen diluted in phosphate-buffered saline or in stools was 0.58 and 3.9 micrograms/ml, respectively, which is the equivalent of approximately 72 and 487 E. histolytica trophozoites per well, respectively. The sensitivity, specificity, and efficiency of the FAC-ELISA were 87, 100, and 98%, respectively, for the detection of invasive E. histolytica antigens and 100, 100, and 100%, respectively, for the diagnosis of amebic dysentery. The FAC-ELISA is a potential alternative for the field diagnosis of amebic dysentery and for epidemiological studies to define the distribution of invasive E. histolytica. PMID:8027351

  16. Monitoring Lysobacter capsici AZ78 using strain specific qPCR reveals the importance of the formulation for its survival in vineyards.

    PubMed

    Segarra, Guillem; Puopolo, Gerardo; Porcel-Rodríguez, Elena; Giovannini, Oscar; Pertot, Ilaria

    2016-02-01

    Survival in the phyllosphere is a critical feature for biofungicides based on non-spore forming bacteria. Moreover, knowledge of their persistence on plants is important to design effective formulations and application techniques. With this scope, the aim of this work was to develop a specific method to monitor the fate in the environment of Lysobacter capsici AZ78, a biocontrol agent of Plasmopara viticola, and to evaluate the contribution of formulation in its persistence on grapevine leaves. A strain-specific primer pair derived from REP-PCR fingerprinting was used in quantitative PCR experiments to track the evolution of L. capsici AZ78 population in vineyards. The population reached between 5 and 6 log10 cells gram of leaf(-1) after application and decreased by more than 100 times in one week. Multiple regression analysis showed that unfavourable temperature was the main environmental factor correlating with the decrease of L. capsici AZ78 persistence on grapevine leaves. Importantly, the use of formulation additives protected L. capsici AZ78 against environmental factors and improved its persistence on the leaves by more than 10 times compared to nude cells. Formulation and the knowledge about the persistence of L. capsici AZ78 in vineyards will be useful to develop commercial biofungicides for foliar application.

  17. Fungal Diagnostics

    PubMed Central

    Kozel, Thomas R.; Wickes, Brian

    2014-01-01

    Early diagnosis of fungal infection is critical to effective treatment. There are many impediments to diagnosis such as a diminishing number of clinical mycologists, cost, time to result, and requirements for sensitivity and specificity. In addition, fungal diagnostics must meet the contrasting needs presented by the increasing diversity of fungi found in association with the use of immunosuppressive agents in countries with high levels of medical care and the need for diagnostics in resource-limited countries where large numbers of opportunistic infections occur in patients with AIDS. Traditional approaches to diagnosis include direct microscopic examination of clinical samples, histopathology, culture, and serology. Emerging technologies include molecular diagnostics and antigen detection in clinical samples. Innovative new technologies that use molecular and immunoassay platforms have the potential to meet the needs of both resource-rich and resource-limited clinical environments. PMID:24692193

  18. Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses.

    PubMed

    King, Thea; Lucchini, Sacha; Hinton, Jay C D; Gobius, Kari

    2010-10-01

    The food-borne pathogen Escherichia coli O157:H7 is commonly exposed to organic acid in processed and preserved foods, allowing adaptation and the development of tolerance to pH levels otherwise lethal. Since little is known about the molecular basis of adaptation of E. coli to organic acids, we studied K-12 MG1655 and O157:H7 Sakai during exposure to acetic, lactic, and hydrochloric acid at pH 5.5. This is the first analysis of the pH-dependent transcriptomic response of stationary-phase E. coli. Thirty-four genes and three intergenic regions were upregulated by both strains during exposure to all acids. This universal acid response included genes involved in oxidative, envelope, and cold stress resistance and iron and manganese uptake, as well as 10 genes of unknown function. Acidulant- and strain-specific responses were also revealed. The acidulant-specific response reflects differences in the modes of microbial inactivation, even between weak organic acids. The two strains exhibited similar responses to lactic and hydrochloric acid, while the response to acetic acid was distinct. Acidulant-dependent differences between the strains involved induction of genes involved in the heat shock response, osmoregulation, inorganic ion and nucleotide transport and metabolism, translation, and energy production. E. coli O157:H7-specific acid-inducible genes were identified, suggesting that the enterohemorrhagic E. coli strain possesses additional molecular mechanisms contributing to acid resistance that are absent in K-12. While E. coli K-12 was most resistant to lactic and hydrochloric acid, O157:H7 may have a greater ability to survive in more complex acidic environments, such as those encountered in the host and during food processing.

  19. Development of a strain-specific real-time PCR assay for enumeration of a probiotic Lactobacillus reuteri in chicken feed and intestine.

    PubMed

    Sattler, Verity Ann; Mohnl, Michaela; Klose, Viviana

    2014-01-01

    A strain-specific real-time PCR assay was developed for quantification of a probiotic Lactobacillus reuteri (DSM 16350) in poultry feed and intestine. The specific primers were designed based on a genomic sequence of the strain derived from suppression subtractive hybridization with the type strain L. reuteri DSM 20016. Specificity was tested using a set of non-target strains from several sources. Applicability of the real-time PCR assay was evaluated in a controlled broiler feeding trial by using standard curves specific for feed and intestinal matrices. The amount of the probiotic L. reuteri was determined in feed from three feeding phases and in intestinal samples of the jejunum, ileum, and caecum of three, 14, and 39 day old birds. L. reuteri DSM 16350 cells were enumerated in all feeds supplemented with the probiotic close to the inclusion rate of 7.0 × 10(3) cfu/g, however, were not detected in L. reuteri DSM 16350 free feed. In three day old birds L. reuteri DSM 16350 was only detected in intestinal samples from probiotic fed animals ranging from 8.2 ± 7.8 × 10(5) cfu/g in the jejunum, 1.0 ± 1.1×10(7) cfu/g in the ileum, and 2.5 ± 5.7 × 10(5) cfu/g in the caecum. Similar results were obtained for intestinal samples of older birds (14 and 39 days). With increasing age of the animals the amount of L. reuteri signals in the control animals, however, also increased, indicating the appearance of highly similar bacterial genomes in the gut microbiota. The L. reuteri DSM 16350 qPCR assay could be used in future for feeding trials to assure the accurate inclusion of the supplement to the feed and to monitor it's uptake into the GIT of young chicken.

  20. Sensitivity of the Green Alga Pediastrum duplex Meyen to Allelochemicals Is Strain-Specific and Not Related to Co-Occurrence with Allelopathic Macrophytes

    PubMed Central

    Eigemann, Falk; Vanormelingen, Pieter; Hilt, Sabine

    2013-01-01

    Interspecific differences in the response of microalgae to stress have numerous ecological implications. However, little is known of intraspecific sensitivities and the potential role of local genetic adaptation of populations. We compared the allelochemical sensitivity of 23 Pediastrum duplex Meyen strains, a common component of the freshwater phytoplankton. In order to test for local genetic adaptation, strains were isolated from water bodies with and without the allelopathically-active submerged macrophyte Myriophyllum. Strains were assigned to P. duplex on the basis of cell shape and colony morphology and only P. duplex strains that belonged to the same lineage in an ITS rDNA phylogeny were used. Inhibition of strain growth rates and maximum quantum yields of photosystem II were measured after exposure to tannic acid (TA) and co-culture with Myriophyllum spicatum. Growth rate inhibition varied over one order of magnitude between the P. duplex strains. There was no correlation between the presence of Myriophyllum in the source location and the sensitivity of the strains to TA or the presence of Myriophyllum, suggesting that at least strong unidirectional local adaptation to Myriophyllum had not taken place in the studied water bodies. The maximum quantum yield of photosystem II of TA exposed algae decreased, whereas the yield of algae exposed to M. spicatum was slightly higher than that of the controls. The ranking of P. duplex strain sensitivities differed between the types of exposure (single additions of TA versus co-existence with M. spicatum) and the parameter measured (growth rate versus maximum quantum yield), emphasizing the importance of measuring multiple traits when analysing strain-specific sensitivities towards allelochemicals. The observation that sensitivities to allelochemicals vary widely among strains of a single freshwater algal species should be taken into account if evaluating ecological consequences of allelopathic interactions. PMID

  1. Bifidobacterium longum CCM 7952 Promotes Epithelial Barrier Function and Prevents Acute DSS-Induced Colitis in Strictly Strain-Specific Manner

    PubMed Central

    Srutkova, Dagmar; Schwarzer, Martin; Hudcovic, Tomas; Zakostelska, Zuzana; Drab, Vladimir; Spanova, Alena; Rittich, Bohuslav; Kozakova, Hana; Schabussova, Irma

    2015-01-01

    Background Reduced microbial diversity has been associated with inflammatory bowel disease (IBD) and probiotic bacteria have been proposed for its prevention and/or treatment. Nevertheless, comparative studies of strains of the same subspecies for specific health benefits are scarce. Here we compared two Bifidobacterium longum ssp. longum strains for their capacity to prevent experimental colitis. Methods Immunomodulatory properties of nine probiotic bifidobacteria were assessed by stimulation of murine splenocytes. The immune responses to B. longum ssp. longum CCM 7952 (Bl 7952) and CCDM 372 (Bl 372) were further characterized by stimulation of bone marrow-derived dendritic cell, HEK293/TLR2 or HEK293/NOD2 cells. A mouse model of dextran sulphate sodium (DSS)-induced colitis was used to compare their beneficial effects in vivo. Results The nine bifidobacteria exhibited strain-specific abilities to induce cytokine production. Bl 372 induced higher levels of both pro- and anti-inflammatory cytokines in spleen and dendritic cell cultures compared to Bl 7952. Both strains engaged TLR2 and contain ligands for NOD2. In a mouse model of DSS-induced colitis, Bl 7952, but not Bl 372, reduced clinical symptoms and preserved expression of tight junction proteins. Importantly, Bl 7952 improved intestinal barrier function as demonstrated by reduced FITC-dextran levels in serum. Conclusions We have shown that Bl 7952, but not Bl 372, protected mice from the development of experimental colitis. Our data suggest that although some immunomodulatory properties might be widespread among the genus Bifidobacterium, others may be rare and characteristic only for a specific strain. Therefore, careful selection might be crucial in providing beneficial outcome in clinical trials with probiotics in IBD. PMID:26218526

  2. Diagnostic imaging.

    PubMed

    Morris, Peter; Perkins, Alan

    2012-04-21

    Physical techniques have always had a key role in medicine, and the second half of the 20th century in particular saw a revolution in medical diagnostic techniques with the development of key imaging instruments: x-ray imaging and emission tomography (nuclear imaging and PET), MRI, and ultrasound. These techniques use the full width of the electromagnetic spectrum, from gamma rays to radio waves, and sound. In most cases, the development of a medical imaging device was opportunistic; many scientists in physics laboratories were experimenting with simple x-ray images within the first year of the discovery of such rays, the development of the cyclotron and later nuclear reactors created the opportunity for nuclear medicine, and one of the co-inventors of MRI was initially attempting to develop an alternative to x-ray diffraction for the analysis of crystal structures. What all these techniques have in common is the brilliant insight of a few pioneering physical scientists and engineers who had the tenacity to develop their inventions, followed by a series of technical innovations that enabled the full diagnostic potential of these instruments to be realised. In this report, we focus on the key part played by these scientists and engineers and the new imaging instruments and diagnostic procedures that they developed. By bringing the key developments and applications together we hope to show the true legacy of physics and engineering in diagnostic medicine. PMID:22516558

  3. Diagnostic Imaging

    MedlinePlus

    Diagnostic imaging lets doctors look inside your body for clues about a medical condition. A variety of machines and techniques can create pictures of the structures and activities inside your body. The type of imaging your doctor uses depends on your symptoms and ...

  4. MJO Simulation Diagnostics

    SciTech Connect

    Waliser, D; Sperber, K; Hendon, H; Kim, D; Maloney, E; Wheeler, M; Weickmann, K; Zhang, C; Donner, L; Gottschalck, J; Higgins, W; Kang, I; Legler, D; Moncrieff, M; Schubert, S; Stern, W; Vitart, F; Wang, B; Wang, W; Woolnough, S

    2008-06-02

    The Madden-Julian Oscillation (MJO) interacts with, and influences, a wide range of weather and climate phenomena (e.g., monsoons, ENSO, tropical storms, mid-latitude weather), and represents an important, and as yet unexploited, source of predictability at the subseasonal time scale. Despite the important role of the MJO in our climate and weather systems, current global circulation models (GCMs) exhibit considerable shortcomings in representing this phenomenon. These shortcomings have been documented in a number of multi-model comparison studies over the last decade. However, diagnosis of model performance has been challenging, and model progress has been difficult to track, due to the lack of a coherent and standardized set of MJO diagnostics. One of the chief objectives of the US CLIVAR MJO Working Group is the development of observation-based diagnostics for objectively evaluating global model simulations of the MJO in a consistent framework. Motivation for this activity is reviewed, and the intent and justification for a set of diagnostics is provided, along with specification for their calculation, and illustrations of their application. The diagnostics range from relatively simple analyses of variance and correlation, to more sophisticated space-time spectral and empirical orthogonal function analyses. These diagnostic techniques are used to detect MJO signals, to construct composite life-cycles, to identify associations of MJO activity with the mean state, and to describe interannual variability of the MJO.

  5. Immunogenicity, reactogenicity, and safety of a P1.7b,4 strain-specific serogroup B meningococcal vaccine given to preteens.

    PubMed

    Hosking, Jamie; Rasanathan, Kumanan; Mow, Florina Chan; Jackson, Catherine; Martin, Diana; O'Hallahan, Jane; Oster, Philipp; Ypma, Ellen; Reid, Stewart; Aaberge, Ingeborg; Crengle, Sue; Stewart, Joanna; Lennon, Diana

    2007-11-01

    New Zealand (NZ) has experienced a Neisseria meningitidis serogroup B epidemic since 1991. MeNZB, a strain-specific outer membrane vesicle vaccine made using an NZ epidemic strain isolate, NZ98/254 (B:4:P1.7b,4), from two manufacturing sites, the Norwegian Institute of Public Health (NIPH) and Chiron Vaccines (CV; now Novartis), was evaluated for safety, immunogenicity, and reactogenicity in this observer-blind trial with 8- to 12-year-old children. In year 1, cohort A (n = 302) was randomized 4:1 for receipt of NIPH-MeNZB or MenBvac (Norwegian parent vaccine strain 44/76; B:15:P1.7,16). In year 2, cohort B (n = 313) was randomized 4:1 for receipt of CV-MeNZB or NIPH-MeNZB. Participants all received three vaccinations 6 weeks apart. Local and systemic reactions were monitored for 7 days. Seroresponse was defined as a fourfold or greater rise in the serum bactericidal antibody titer from the baseline titer as measured by a serum bactericidal assay. Those with baseline titers of <1:4 required titers of >/=1:8 to serorespond. Intention-to-treat (ITT) and per protocol (PP) analyses are presented. In cohort A, 74% (ITT) and 73% (PP) of NIPH-MeNZB recipients demonstrated seroresponses against NZ98/254 after three doses, versus 32% (ITT and PP) of MenBvac recipients. In cohort B, seroresponses against NZ98/254 after three doses occurred in 79% (ITT and PP) of CV-MeNZB versus 75% (ITT) and 76% (PP) of NIPH-MeNZB recipients. Vaccines were tolerable, with no vaccine-related serious adverse events. In conclusion, the NZ strain meningococcal B vaccine (MeNZB) from either manufacturing site was immunogenic against New Zealand epidemic vaccine strain meningococci with no safety concerns when given in three doses to these 8- to 12-year-old children.

  6. Immunogenicity, reactogenicity, and safety of a P1.7b,4 strain-specific serogroup B meningococcal vaccine given to preteens.

    PubMed

    Hosking, Jamie; Rasanathan, Kumanan; Mow, Florina Chan; Jackson, Catherine; Martin, Diana; O'Hallahan, Jane; Oster, Philipp; Ypma, Ellen; Reid, Stewart; Aaberge, Ingeborg; Crengle, Sue; Stewart, Joanna; Lennon, Diana

    2007-11-01

    New Zealand (NZ) has experienced a Neisseria meningitidis serogroup B epidemic since 1991. MeNZB, a strain-specific outer membrane vesicle vaccine made using an NZ epidemic strain isolate, NZ98/254 (B:4:P1.7b,4), from two manufacturing sites, the Norwegian Institute of Public Health (NIPH) and Chiron Vaccines (CV; now Novartis), was evaluated for safety, immunogenicity, and reactogenicity in this observer-blind trial with 8- to 12-year-old children. In year 1, cohort A (n = 302) was randomized 4:1 for receipt of NIPH-MeNZB or MenBvac (Norwegian parent vaccine strain 44/76; B:15:P1.7,16). In year 2, cohort B (n = 313) was randomized 4:1 for receipt of CV-MeNZB or NIPH-MeNZB. Participants all received three vaccinations 6 weeks apart. Local and systemic reactions were monitored for 7 days. Seroresponse was defined as a fourfold or greater rise in the serum bactericidal antibody titer from the baseline titer as measured by a serum bactericidal assay. Those with baseline titers of <1:4 required titers of >/=1:8 to serorespond. Intention-to-treat (ITT) and per protocol (PP) analyses are presented. In cohort A, 74% (ITT) and 73% (PP) of NIPH-MeNZB recipients demonstrated seroresponses against NZ98/254 after three doses, versus 32% (ITT and PP) of MenBvac recipients. In cohort B, seroresponses against NZ98/254 after three doses occurred in 79% (ITT and PP) of CV-MeNZB versus 75% (ITT) and 76% (PP) of NIPH-MeNZB recipients. Vaccines were tolerable, with no vaccine-related serious adverse events. In conclusion, the NZ strain meningococcal B vaccine (MeNZB) from either manufacturing site was immunogenic against New Zealand epidemic vaccine strain meningococci with no safety concerns when given in three doses to these 8- to 12-year-old children. PMID:17898183

  7. A new method for the characterization of strain-specific conformational stability of protease-sensitive and protease-resistant PrPSc.

    PubMed

    Pirisinu, Laura; Di Bari, Michele; Marcon, Stefano; Vaccari, Gabriele; D'Agostino, Claudia; Fazzi, Paola; Esposito, Elena; Galeno, Roberta; Langeveld, Jan; Agrimi, Umberto; Nonno, Romolo

    2010-09-14

    Although proteinacious in nature, prions exist as strains with specific self-perpetuating biological properties. Prion strains are thought to be associated with different conformers of PrP(Sc), a disease-associated isoform of the host-encoded cellular protein (PrP(C)). Molecular strain typing approaches have been developed which rely on the characterization of protease-resistant PrP(Sc). However, PrP(Sc) is composed not only of protease-resistant but also of protease-sensitive isoforms. The aim of this work was to develop a protocol for the molecular characterization of both, protease-resistant and protease-sensitive PrP(Sc) aggregates. We first set up experimental conditions which allowed the most advantageous separation of PrP(C) and PrP(Sc) by means of differential centrifugation. The conformational solubility and stability assay (CSSA) was then developed by measuring PrP(Sc) solubility as a function of increased exposure to GdnHCl. Brain homogenates from voles infected with human and sheep prion isolates were analysed by CSSA and showed strain-specific conformational stabilities, with mean [GdnHCl](1/2) values ranging from 1.6 M for MM2 sCJD to 2.1 for scrapie and to 2.8 M for MM1/MV1 sCJD and E200K gCJD. Interestingly, the rank order of [GdnHCl](1/2) values observed in the human and sheep isolates used as inocula closely matched those found following transmission in voles, being MM1 sCJD the most resistant (3.3 M), followed by sheep scrapie (2.2 M) and by MM2 sCJD (1.6 M). In order to test the ability of CSSA to characterise protease-sensitive PrP(Sc), we analysed sheep isolates of Nor98 and compared them to classical scrapie isolates. In Nor98, insoluble PrP(Sc) aggregates were mainly protease-sensitive and showed a conformational stability much lower than in classical scrapie. Our results show that CSSA is able to reveal strain-specified PrP(Sc) conformational stabilities of protease-resistant and protease-sensitive PrP(Sc) and that it is a valuable tool for

  8. A New Method for the Characterization of Strain-Specific Conformational Stability of Protease-Sensitive and Protease-Resistant PrPSc

    PubMed Central

    Pirisinu, Laura; Di Bari, Michele; Marcon, Stefano; Vaccari, Gabriele; D'Agostino, Claudia; Fazzi, Paola; Esposito, Elena; Galeno, Roberta; Langeveld, Jan; Agrimi, Umberto; Nonno, Romolo

    2010-01-01

    Although proteinacious in nature, prions exist as strains with specific self-perpetuating biological properties. Prion strains are thought to be associated with different conformers of PrPSc, a disease-associated isoform of the host-encoded cellular protein (PrPC). Molecular strain typing approaches have been developed which rely on the characterization of protease-resistant PrPSc. However, PrPSc is composed not only of protease-resistant but also of protease-sensitive isoforms. The aim of this work was to develop a protocol for the molecular characterization of both, protease-resistant and protease-sensitive PrPSc aggregates. We first set up experimental conditions which allowed the most advantageous separation of PrPC and PrPSc by means of differential centrifugation. The conformational solubility and stability assay (CSSA) was then developed by measuring PrPSc solubility as a function of increased exposure to GdnHCl. Brain homogenates from voles infected with human and sheep prion isolates were analysed by CSSA and showed strain-specific conformational stabilities, with mean [GdnHCl]1/2 values ranging from 1.6 M for MM2 sCJD to 2.1 for scrapie and to 2.8 M for MM1/MV1 sCJD and E200K gCJD. Interestingly, the rank order of [GdnHCl]1/2 values observed in the human and sheep isolates used as inocula closely matched those found following transmission in voles, being MM1 sCJD the most resistant (3.3 M), followed by sheep scrapie (2.2 M) and by MM2 sCJD (1.6 M). In order to test the ability of CSSA to characterise protease-sensitive PrPSc, we analysed sheep isolates of Nor98 and compared them to classical scrapie isolates. In Nor98, insoluble PrPSc aggregates were mainly protease-sensitive and showed a conformational stability much lower than in classical scrapie. Our results show that CSSA is able to reveal strain-specified PrPSc conformational stabilities of protease-resistant and protease-sensitive PrPSc and that it is a valuable tool for strain typing in natural

  9. The utilization of fluorescence to identify the components of lipofuscin by imaging mass spectrometry.

    PubMed

    Ablonczy, Zsolt; Smith, Noah; Anderson, David M; Grey, Angus C; Spraggins, Jeffrey; Koutalos, Yiannis; Schey, Kevin L; Crouch, Rosalie K

    2014-04-01

    Lipofuscin, an aging marker in the retinal pigment epithelium (RPE) associated with the development of age-related macular degeneration, is primarily characterized by its fluorescence. The most abundant component of RPE lipofuscin is N-retinylidene-N-retinylethanolamine (A2E) but its exact composition is not known due to the complexity of the RPE extract. In this study, we utilized MALDI imaging to find potential molecules responsible for lipofuscin fluorescence in RPE tissue from Abca4(-/-) , Sv129, and C57Bl6/J mice aged 2 and 6 months. To assert relationships, the individual images in the MALDI imaging datasets were correlated with lipofuscin fluorescence recorded from the same tissues following proper registration. Spatial correlation information, which is usually lost in bioanalytics, pinpointed a relatively small number of potential lipofuscin components. The comparison of four samples in each condition further limited the possibility of false positives and provided various new, age- and strain-specific targets. Validating the usefulness of the fluorescence-enhanced imaging strategy, many known adducts of A2E were identified in the short list of lipofuscin components. These results provided evidence that mass spectrometric imaging can be utilized as a tool to begin to identify the molecular substructure of clinically-relevant diagnostic information.

  10. Rotorcraft Diagnostics

    NASA Technical Reports Server (NTRS)

    Haste, Deepak; Azam, Mohammad; Ghoshal, Sudipto; Monte, James

    2012-01-01

    Health management (HM) in any engineering systems requires adequate understanding about the system s functioning; a sufficient amount of monitored data; the capability to extract, analyze, and collate information; and the capability to combine understanding and information for HM-related estimation and decision-making. Rotorcraft systems are, in general, highly complex. Obtaining adequate understanding about functioning of such systems is quite difficult, because of the proprietary (restricted access) nature of their designs and dynamic models. Development of an EIM (exact inverse map) solution for rotorcraft requires a process that can overcome the abovementioned difficulties and maximally utilize monitored information for HM facilitation via employing advanced analytic techniques. The goal was to develop a versatile HM solution for rotorcraft for facilitation of the Condition Based Maintenance Plus (CBM+) capabilities. The effort was geared towards developing analytic and reasoning techniques, and proving the ability to embed the required capabilities on a rotorcraft platform, paving the way for implementing the solution on an aircraft-level system for consolidation and reporting. The solution for rotorcraft can he used offboard or embedded directly onto a rotorcraft system. The envisioned solution utilizes available monitored and archived data for real-time fault detection and identification, failure precursor identification, and offline fault detection and diagnostics, health condition forecasting, optimal guided troubleshooting, and maintenance decision support. A variant of the onboard version is a self-contained hardware and software (HW+SW) package that can be embedded on rotorcraft systems. The HM solution comprises components that gather/ingest data and information, perform information/feature extraction, analyze information in conjunction with the dependency/diagnostic model of the target system, facilitate optimal guided troubleshooting, and offer

  11. Evaluation of the effects of long-term storage of bovine ear notch samples on the ability of 2 diagnostic assays to identify calves persistently infected with bovine viral diarrhoea virus.

    PubMed

    Khan, F; Vorster, J H; van Vuuren, M; Mapham, P

    2011-03-01

    Research aimed at optimising diagnostic laboratory procedures is central to the development of effective bovine viral diarrhoea virus (BVDV) control programmes. BVDV is a single-stranded RNA virus that crosses the placenta to infect foetuses, resulting in reproductive losses due to foetal death or persistently infected calves that die early in life. Persistently infected animals are widely accepted to be the primary reservoir of BVDV and the largest source of infection. This poses important challenges to overall animal/herd health and can cause major losses to the cattle industry. Long-term storage of bovine ear notch samples from calves persistently infected with BVDV may adversely affect the ability of diagnostic assays to detect the virus efficiently. In order to test this hypothesis, ear notch samples from 7 animals were divided into 2 groups. One set was subjected to prompt formalin fixation and the other set stored either as fresh samples without preservatives at -2 degrees C, or soaked overnight in phosphate buffered saline followed by freezing of the supernatant fluid at -2 degrees C. Frozen ear notches and ear notch supernatant yielded positive results with an antigen-capture, enzyme linked immunosorbent assay (AC-ELISA) for the duration of the study (6 months) and optical density (OD) values remained significantly within range. There was no significant difference between storing fresh ear notch samples or PBS at -2 degrees C. However, positive immunohistochemistry (IHC) staining on formalin fixed ear notches started to fade between Day 17 and Day 29 when stored at room temperature. It was concluded that fresh ear notches could safely be stored at -2 degrees C for a period of 6 months prior to testing for BVD viral antigens.

  12. Graphical presentation of diagnostic information

    PubMed Central

    Whiting, Penny F; Sterne, Jonathan AC; Westwood, Marie E; Bachmann, Lucas M; Harbord, Roger; Egger, Matthias; Deeks, Jonathan J

    2008-01-01

    Background Graphical displays of results allow researchers to summarise and communicate the key findings of their study. Diagnostic information should be presented in an easily interpretable way, which conveys both test characteristics (diagnostic accuracy) and the potential for use in clinical practice (predictive value). Methods We discuss the types of graphical display commonly encountered in primary diagnostic accuracy studies and systematic reviews of such studies, and systematically review the use of graphical displays in recent diagnostic primary studies and systematic reviews. Results We identified 57 primary studies and 49 systematic reviews. Fifty-six percent of primary studies and 53% of systematic reviews used graphical displays to present results. Dot-plot or box-and- whisker plots were the most commonly used graph in primary studies and were included in 22 (39%) studies. ROC plots were the most common type of plot included in systematic reviews and were included in 22 (45%) reviews. One primary study and five systematic reviews included a probability-modifying plot. Conclusion Graphical displays are currently underused in primary diagnostic accuracy studies and systematic reviews of such studies. Diagnostic accuracy studies need to include multiple types of graphic in order to provide both a detailed overview of the results (diagnostic accuracy) and to communicate information that can be used to inform clinical practice (predictive value). Work is required to improve graphical displays, to better communicate the utility of a test in clinical practice and the implications of test results for individual patients. PMID:18405357

  13. PML diagnostic criteria

    PubMed Central

    Aksamit, Allen J.; Clifford, David B.; Davis, Larry; Koralnik, Igor J.; Sejvar, James J.; Bartt, Russell; Major, Eugene O.; Nath, Avindra

    2013-01-01

    Objective: To establish criteria for the diagnosis of progressive multifocal leukoencephalopathy (PML). Methods: We reviewed available literature to identify various diagnostic criteria employed. Several search strategies employing the terms “progressive multifocal leukoencephalopathy” with or without “JC virus” were performed with PubMed, SCOPUS, and EMBASE search engines. The articles were reviewed by a committee of individuals with expertise in the disorder in order to determine the most useful applicable criteria. Results: A consensus statement was developed employing clinical, imaging, pathologic, and virologic evidence in support of the diagnosis of PML. Two separate pathways, histopathologic and clinical, for PML diagnosis are proposed. Diagnostic classification includes certain, probable, possible, and not PML. Conclusion: Definitive diagnosis of PML requires neuropathologic demonstration of the typical histopathologic triad (demyelination, bizarre astrocytes, and enlarged oligodendroglial nuclei) coupled with the techniques to show the presence of JC virus. The presence of clinical and imaging manifestations consistent with the diagnosis and not better explained by other disorders coupled with the demonstration of JC virus by PCR in CSF is also considered diagnostic. Algorithms for establishing the diagnosis have been recommended. PMID:23568998

  14. [Frontal mass: diagnostic challenges].

    PubMed

    Rubino, Gina; Correia, Alexandre; Rodrigues, Fernanda

    2012-01-01

    Capnocytophaga spp. are part of the oral flora of humans and animals, being responsible for skin and soft tissues infections and invasive infections. Microbiological identification can be difficult due to its slow growth. We present a case of infection caused by this bacteria in the form of an extracerebral intracranial abscess, presenting as a frontal mass that posed some diagnostic challenges. A surgical drainage was performed together with antibiotic therapy with favourable outcome. This microorganism was identified in the second week of treatment and then a careful history revealed a dog bite days prior to the initial symptoms. This could have been the site of entry to a posterior focalization. PMID:23069241

  15. Quantification of Propionibacterium acidipropionici P169 bacteria in environmental samples by use of strain-specific primers derived by suppressive subtractive hybridization.

    PubMed

    Peng, Min; Smith, Alexandra H; Rehberger, Thomas G

    2011-06-01

    A quantitative PCR (qPCR) assay targeting a gene identified by suppressive subtractive hybridization (SSH) was developed to detect Propionibacterium acidipropionici P169, with a threshold of 10(4) CFU/U of dairy feed or rumen fluid. The report is the first using a molecular marker generated by SSH to quantify a bacterial strain in environmental samples.

  16. Behavioral diagnostics.

    PubMed

    Bailey, J S; Pyles, D A

    1989-01-01

    The contemporary behavior analyst, to operate ethically and effectively, must be aware of many more factors affecting behavior than simple consequences. Although the literature demonstrating the effectiveness of active behavior management is impressive, a compelling argument can be made that a great number of behavior problem seen in individuals with developmental disabilities may be attributable to factors other than consequences. Our experience has been more often than not that physiological, organic, medication, or situational variables are the actual culprits in maladaptive behavior. Individuals with severe or profound retardation may respond to aversive features of their environment by displaying noncompliance, tantrums, aggression, or self-injurious behavior. These antecedents can affect their behavior just as powerfully as can the consequences of their behavior. Behavior analysts must become sensitive to these potential factors and be prepared to employ behavioral diagnostic strategies in the search for the causes of maladaptive behavior. Finally, they must be prepared to design rather unconventional passive behavior management treatment programs involving the manipulation of the antecedent environment. In the case of Carrie, from the example at the beginning of this paper, the analysis yielded the hypothesis that her face scratching was a reaction to sinus blockage caused by seasonal allergies. Her treatment involved daily dosages of antihistamines administered by our nurses and subsequent elimination of the scratching. Tom was found to be suffering from "wheelchair fatigue." When he was allowed to recline on other surfaces (e.g., bean bag chair, mat, bolster) on a regular basis, he did not attempt any form of self-injury. Melissa was found to have a severe case of Pre Menstrual Syndrome as well as seizure disorder, and was treated with the appropriate medications. Her headbanging was reduced to a few minor incidents per month. Walter's tantrums on closer

  17. Complementary Methodologies To Identify Specific Agrobacterium Strains †

    PubMed Central

    Bouzar, Hacene; Moore, Larry W.

    1987-01-01

    Serological techniques and restriction enzyme cleavage patterns of total DNA were used to differentiate strains of Agrobacterium spp. Forty-five wild-type and plasmid-cured Agrobacterium strains were tested by immunodiffusion and immunofluorescence against polyclonal antisera to a crude ribosome preparation from Agrobacterium strains K84, U11, B6, A323, NT1, and C58. In immunodiffusion gels, these antisera reacted only with water-phenol extracts of the homologous strain, producing a single, strain-specific precipitin line. In contrast, when the same antisera were used in immunofluorescence staining, cross-reactions occurred with a limited number of heterologous Agrobacterium strains. However, the cross-reacting heterologous cells fluoresced generally less brightly than the homologous cells. When the EcoRI-digested DNA profiles from the same Agrobacterium strains were compared, 34 distinct cleavage patterns were observed. The DNA profiles were the same for all strains sharing a common chromosomal background and correlated with the strain-specific serological reaction. The presence or absence of plasmid DNA did not alter the strain-specific serological reaction or the DNA cleavage patterns. Both the serological reaction and the restriction enzyme digestion of total DNA were complementary to each other. These methods were used successfully to identify A. radiobacter K84 strains which were recovered 6 months after being inoculated to young trees in the field. Images PMID:16347485

  18. Recombinant HA1 produced in E. coli forms functional oligomers and generates strain-specific SRID potency antibodies for pandemic influenza vaccines.

    PubMed

    Khurana, Surender; Larkin, Christopher; Verma, Swati; Joshi, Manju B; Fontana, Juan; Steven, Alasdair C; King, Lisa R; Manischewitz, Jody; McCormick, William; Gupta, Rajesh K; Golding, Hana

    2011-08-01

    Vaccine production and initiation of mass vaccination is a key factor in rapid response to new influenza pandemic. During the 2009-2010 H1N1 pandemic, several bottlenecks were identified, including the delayed availability of vaccine potency reagents. Currently, antisera for the single-radial immunodiffusion (SRID) potency assay are generated in sheep immunized repeatedly with HA released and purified after bromelain-treatment of influenza virus grown in eggs. This approach was a major bottleneck for pandemic H1N1 (H1N1pdm09) potency reagent development in 2009. Alternative approaches are needed to make HA immunogens for generation of SRID reagents in the shortest possible time. In this study, we found that properly folded recombinant HA1 globular domain (rHA1) from several type A viruses including H1N1pdm09 and two H5N1 viruses could be produced efficiently using a bacterial expression system and subsequent purification. The rHA1 proteins were shown to form functional oligomers of trimers, similar to virus derived HA, and elicited high titer of neutralizing antibodies in rabbits and sheep. Importantly, the immune sera formed precipitation rings with reference antigens in the SRID assay in a dose-dependent manner. The HA contents in multiple H1N1 vaccine products from different manufacturers (and in several lots) as determined with the rHA1-generated sheep sera were similar to the values obtained with a traditionally generated sheep serum from NIBSC. We conclude that bacterially expressed recombinant HA1 proteins can be produced rapidly and used to generate SRID potency reagents shortly after new influenza strains with pandemic potential are identified.

  19. Sensitivity to the seizure-inducing effects of nicotine is associated with strain-specific variants of the alpha 5 and alpha 7 nicotinic receptor subunit genes.

    PubMed

    Stitzel, J A; Blanchette, J M; Collins, A C

    1998-03-01

    Restriction fragment length polymorphisms (rflps) have been identified for the nicotinic ACh receptor subunit genes alpha 5 and alpha 7 between two mouse strains (C3H/2ibg and DBA/2ibg) that differ in sensitivity to the convulsant effects of nicotine. In the study reported here, F2 animals derived from these two parental stains were tested for their sensitivity to the convulsant effects of nicotine as measured by seizure frequency and overall sensitivity score. Subsequently, the animals were genotyped for the alpha 5 and alpha 7 rflps. In addition, levels of alpha-bungarotoxin (alpha-BTX) binding were measured in four brain regions (colliculi, hippocampus, hypothalamus and striatum) to determine whether there is a correlation among alpha-BTX binding levels, sensitivity to nicotine and nicotinic ACh receptor subunit genotype. A significant relationship was observed between alpha 5 and alpha 7 genotype and sensitivity to nicotine. In addition, the alpha 7 rflp significantly correlated with levels of alpha-BTX binding in hippocampus, colliculi and striatum. The alpha 5 rflp did not correlate with alpha-BTX binding levels in any brain region. Levels of alpha-BTX binding did not correlate with nicotine-induced seizure sensitivity or overall nicotine sensitivity score in any of the four brain regions examined.

  20. Cytotoxic T lymphocytes from cattle immunized against Theileria parva exhibit pronounced cross-reactivity among different strain-specific epitopes of the Tp1 antigen.

    PubMed

    Steinaa, L; Saya, R; Awino, E; Toye, P

    2012-02-15

    The protozoan parasite Theileria parva causes a usually fatal disease in cattle, known as East Coast fever. Cattle can be vaccinated by injecting live parasites simultaneously with long acting oxytetracycline (the infection and treatment method, ITM). The immunity induced by ITM is believed to be mediated by cytotoxic T lymphocytes (CTL). Although effective, the ITM vaccine has disadvantages such as the need for a liquid nitrogen cold chain and a complex production process, which may be overcome by the development of a subunit vaccine. However, the high level of antigenic polymorphism among different strains of T. parva may hinder the development of a subunit vaccine aimed at induction of a protective CTL response. In this study, the CTL cross-reactivity among T. parva strains was examined. The Tp1(214-224) epitope has previously been shown to be recognized by cattle of the A18 BoLA type. Three different variants of this epitope have been identified from different T. parva strains. Here, bulk CTL and CTL clones were generated from two animals using both the live sporozoite vaccine composed of three different strains and a Muguga strain for immunization. The cross-reactivity of these CTL with the three variant Tp1 epitopes was examined in interferon gamma ELISPOT assays and CTL killing assays. CD8(+) cells from both animals cross-reacted with the three variant CTL epitopes in interferon gamma ELISPOT assays, although the CD8(+) cells from the Muguga-immunized animal showed a more epitope restricted response. Clones from the vaccine immunized animal showed diverse response patterns with clones responding to each variant peptide. Although some variability in the cytotoxic response was observed, overall strong cross-reactivity among the variant Tp1 epitopes was seen in both animals. Such epitope polymorphism does not, in this case, serve as a potential challenge in a putative subunit vaccine as it would be sufficient to only include one of the variant epitopes.

  1. Thioaptamer Diagnostic System (TDS)

    NASA Technical Reports Server (NTRS)

    Yang, Xianbin

    2015-01-01

    AM Biotechnologies, LLC, in partnership with Sandia National Laboratories, has developed a diagnostic device that quickly detects sampled biomarkers. The TDS quickly quantifies clinically relevant biomarkers using only microliters of a single sample. The system combines ambient-stable, long shelf-life affinity assays with handheld, microfluidic gel electrophoresis affinity assay quantification technology. The TDS is easy to use, operates in microgravity, and permits simultaneous quantification of 32 biomarkers. In Phase I of the project, the partners demonstrated that a thioaptamer assay used in the microfluidic instrument could quantify a specific biomarker in serum in the low nanomolar range. The team also identified novel affinity agents to bone-specific alkaline phosphatase (BAP) and demonstrated their ability to detect BAP with the microfluidic instrument. In Phase II, AM Biotech expanded the number of ambient affinity agents and demonstrated a TDS prototype. In the long term, the clinical version of the TDS will provide a robust, flight-tested diagnostic capability for space exploration missions.

  2. The Diagnostic/Therapeutic Preabortion Interview.

    ERIC Educational Resources Information Center

    Boekelheide, Priscilla Day

    1978-01-01

    The therapeutic and diagnostic aspect of the preabortion interview are discussed with attention to specifics that will identify students with the greatest likelihood for psychological problems and/or repeat abortions. (JD)

  3. Combining Quantitative Genetic Footprinting and Trait Enrichment Analysis to Identify Fitness Determinants of a Bacterial Pathogen

    PubMed Central

    Wiles, Travis J.; Norton, J. Paul; Russell, Colin W.; Dalley, Brian K.; Fischer, Kael F.; Mulvey, Matthew A.

    2013-01-01

    Strains of Extraintestinal Pathogenic Escherichia c oli (ExPEC) exhibit an array of virulence strategies and are a major cause of urinary tract infections, sepsis and meningitis. Efforts to understand ExPEC pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates. Determining which virulence traits are widespread and which are strain-specific will greatly benefit the design of more effective therapies. Towards this goal, we utilized a quantitative genetic footprinting technique known as transposon insertion sequencing (Tn-seq) in conjunction with comparative pathogenomics to functionally dissect the genetic repertoire of a reference ExPEC isolate. Using Tn-seq and high-throughput zebrafish infection models, we tracked changes in the abundance of ExPEC variants within saturated transposon mutant libraries following selection within distinct host niches. Nine hundred and seventy bacterial genes (18% of the genome) were found to promote pathogen fitness in either a niche-dependent or independent manner. To identify genes with the highest therapeutic and diagnostic potential, a novel Trait Enrichment Analysis (TEA) algorithm was developed to ascertain the phylogenetic distribution of candidate genes. TEA revealed that a significant portion of the 970 genes identified by Tn-seq have homologues more often contained within the genomes of ExPEC and other known pathogens, which, as suggested by the first axiom of molecular Koch's postulates, is considered to be a key feature of true virulence determinants. Three of these Tn-seq-derived pathogen-associated genes—a transcriptional repressor, a putative metalloendopeptidase toxin and a hypothetical DNA binding protein—were deleted and shown to independently affect ExPEC fitness in zebrafish and mouse models of infection. Together, the approaches and observations reported herein provide a resource for future pathogenomics-based research and highlight the diversity of

  4. DIM and diagnostic placement for NIF experiments

    SciTech Connect

    Kalantar, D

    1999-09-14

    The input that has been provided on the NIF experiment setup sheets has allowed us to review the diagnostic and DIM placement as well as the baseline unconverted light management plan. We have done an iteration to identify common diagnostic lines of sight, and with additional requirements defined by specific experiments, we propose (1) a baseline plan for DIM placement requiring only five DIMs that may be moved between up to seven DIM ports, and (2) a modified baseline unconverted light management plan. We request additional input to identify primary vs. secondary diagnostics for each experiment definition.

  5. Diagnostics for ITER

    SciTech Connect

    Donne, A. J. H.; Hellermann, M. G. von; Barnsley, R.

    2008-10-22

    After an introduction into the specific challenges in the field of diagnostics for ITER (specifically high level of nuclear radiation, long pulses, high fluxes of particles to plasma facing components, need for reliability and robustness), an overview will be given of the spectroscopic diagnostics foreseen for ITER. The paper will describe both active neutral-beam based diagnostics as well as passive spectroscopic diagnostics operating in the visible, ultra-violet and x-ray spectral regions.

  6. Thymineless Death in Escherichia coli: Strain Specificity

    PubMed Central

    Cummings, Donald J.; Mondale, Lee

    1967-01-01

    Thymineless death of various ultraviolet (UV)-sensitive strains of Escherichia coli B and K-12 was investigated. It was found that E. coli B, Bs−12, K-12 rec-21, and possibly K-12 Lon−, all sensitive to UV, were also sensitive to thymine starvation. However, other UV-sensitive strains of E. coli were found to display the typical resistant-type kinetics of thymineless death. The correlation of these results with various other cellular processes suggested that the filament-forming ability of the bacteria might be involved in the mechanism of thymineless death. It was apparent from the present results that capacity for host-cell reactivation, recombination ability, thymine dimer excision, and probably induction of a defective prophage had little to do with determining sensitivity to thymine deprivation. Images PMID:5337772

  7. A Diagnostic Procedural Model for Identifying Real Educational Needs.

    ERIC Educational Resources Information Center

    Londoner, Carroll

    This study evaluated educational problems and needs in the administrative management council of Bloomington Hospital, Bloomington, Indiana, in order to help produce a more effective task group within the hospital's institutional framework. Over a seven week period, the investigator observed department heads in their weekly conferences by means of…

  8. Regulatory considerations for companion diagnostic devices.

    PubMed

    Lee, Eunice Y; Shen, Hsin-Chieh Jennifer

    2015-01-01

    The emergence of companion diagnostic devices has been spurred by drug discovery and development efforts towards targeted therapies, particularly in oncology. Companion diagnostics and their corresponding therapeutics are often codeveloped, or developed in parallel, to ensure the safe and effective use of the products. The regulatory framework for companion diagnostics has gradually evolved as a result of the essential role of diagnostic tests to identify the intended population for a corresponding treatment. Here, we describe the current regulatory model for companion diagnostics in the US and outline key strategies for a successful codevelopment program from the device perspective. We also discuss how technological advances and changes in clinical management may challenge the regulatory model in the future. PMID:25605456

  9. Diagnostic odor recognition

    PubMed

    Rosenblatt; Phan; Desandre; Lobon; Hsu

    2000-10-01

    Many diseases, toxic ingestions, and intoxications have characteristic odors. These odors may provide diagnostic clues that affect rapid treatment long before laboratory confirmation or clinical deterioration. Odor recognition skills, similar to auscultation and palpation skills, require teaching and practical exposure. Dr. Goldfrank and colleagues recognized the importance of teaching odor recognition to emergency service providers. They proposed the "sniffing bar" method for odor recognition training. OBJECTIVES: (1) To identify the recognition rates of medically important odors among emergency care providers. (2) To investigate the effectiveness of teaching odor recognition. Hypothesis: The recognition rates of medically important odors will increase after teaching exposure. METHODS: The study exposed emergency care providers to 11 tubes of odors. Identifications of each substance were recorded. After corrective feedback, subjects were re-tested on their ability to identify the odors. Analysis of odor recognition improvement after teaching was done via chi-square test. RESULTS: Improvement in identification after teaching was seen in all odors. However, the improvement was significant only in the lesscommon substances because their initial recognition was especially low. Significant changes may improve with a larger sample size. Subjects often confuse the odors of alcohol with acetone, and wintergreen with camphor. CONCLUSIONS: The recognition rates are higher for the more-common odors, and lower for the less-common odors. Teaching exposures to the less well-known odors are effective and can significantly improve the recognition rate of these substances. Because odor recognition may affect rapid diagnosis and treatment of certain medical emergencies such as toxic ingestion, future studies should investigate the correlation between odor recognition and the ability to identify corresponding medical emergencies.

  10. DIAGNOSTIC METHODS IN AYURVEDA

    PubMed Central

    Thakar, V. J.

    1982-01-01

    This is an analytical study of the Diagnostic methods Prescribes in Ayurveda. As in the case of disease and treatments the concept of diagnosis also is unique in Ayurveda. It goes to the Nidana of Doshicimbalance by studying the physical, physiological, psychic and behavoural aspects of the patient. The paper gives an insight into the various diagnostic methods enunciated in Sastras which turns out to be a fore-runner of any of modern diagnostic methods. PMID:22556480

  11. Plasma diagnostics for FED

    SciTech Connect

    Nelson, W.D.

    1981-01-01

    An overview of the plasma diagnostic instruments recommended for the Fusion Engineering Device (FED) is described. First the role and need for plasma diagnostics is discussed. This is followed by an identification of particles and radiation eminating from the plasma. Next some design considerations are presented for the overall set of diagnostic instruments. Finally, instruments used for control and for plasma performance measurements are included in separate lists.

  12. Diagnostic Development on NSTX

    SciTech Connect

    A.L. Roquemore; D. Johnson; R. Kaita; et al

    1999-12-16

    Diagnostics are described which are currently installed or under active development for the newly commissioned NSTX device. The low aspect ratio (R/a less than or equal to 1.3) and low toroidal field (0.1-0.3T) used in this device dictate adaptations in many standard diagnostic techniques. Technical summaries of each diagnostic are given, and adaptations, where significant, are highlighted.

  13. TFTR diagnostic vacuum controller

    SciTech Connect

    Olsen, D.; Persons, R.

    1981-01-01

    The TFTR diagnostic vacuum controller (DVC) provides in conjunction with the Central Instrumentation Control and Data Acquisition System (CICADA), control and monitoring for the pumps, valves and gauges associated with each individual diagnostic vacuum system. There will be approximately 50 systems on TFTR. Two standard versions of the controller (A and B) wil be provided in order to meet the requirements of two diagnostic manifold arrangements. All pump and valve sequencing, as well as protection features, will be implemented by the controller.

  14. How to appraise a diagnostic test.

    PubMed

    Manikandan, Ramanitharan; Dorairajan, Lalgudi N

    2011-10-01

    Urologists frequently encounter problems in making a clinical diagnosis whose resolution requires the use of diagnostic tests. With an ever increasing choice of investigations being available, the urologist often has to decide which diagnostic test(s) will best resolve the patient's diagnostic problem. In this article, we aim to help the urologist understand how to critically appraise studies on diagnostic tests and make a rational choice. This article presents the guiding principles in scientifically assessing studies on diagnostic tests by proposing a clinical scenario. The authors describe a standardized protocol to assess the validity of the test and its relevance to the clinical problem that can help the urologist in decision making. The three important issues to be considered when evaluating the validity of the study are to identify how the study population was chosen, how the test was performed and whether there is a comparison to the gold standard test so as to confirm or refute the diagnosis. Then, the urologist would need to know the probability of the test in providing the correct diagnosis in an individual patient in order to decide about its utility in solving the diagnostic dilemma. By performing the steps described in this article, the urologist would be able to critically appraise diagnostic studies and draw meaningful conclusions about the investigations in terms of validity, results and its applicability to the patient's problem. This would provide a scientific basis for using diagnostic tests for improving patient care.

  15. [Diagnostic Errors in Medicine].

    PubMed

    Buser, Claudia; Bankova, Andriyana

    2015-12-01

    The recognition of diagnostic errors in everyday practice can help improve patient safety. The most common diagnostic errors are the cognitive errors, followed by system-related errors and no fault errors. The cognitive errors often result from mental shortcuts, known as heuristics. The rate of cognitive errors can be reduced by a better understanding of heuristics and the use of checklists. The autopsy as a retrospective quality assessment of clinical diagnosis has a crucial role in learning from diagnostic errors. Diagnostic errors occur more often in primary care in comparison to hospital settings. On the other hand, the inpatient errors are more severe than the outpatient errors.

  16. [Diagnostic Errors in Medicine].

    PubMed

    Buser, Claudia; Bankova, Andriyana

    2015-12-01

    The recognition of diagnostic errors in everyday practice can help improve patient safety. The most common diagnostic errors are the cognitive errors, followed by system-related errors and no fault errors. The cognitive errors often result from mental shortcuts, known as heuristics. The rate of cognitive errors can be reduced by a better understanding of heuristics and the use of checklists. The autopsy as a retrospective quality assessment of clinical diagnosis has a crucial role in learning from diagnostic errors. Diagnostic errors occur more often in primary care in comparison to hospital settings. On the other hand, the inpatient errors are more severe than the outpatient errors. PMID:26649954

  17. Moving past serology: Diagnostic options without serum.

    PubMed

    Reichel, Michael P; Lanyon, Sasha R; Hill, Fraser I

    2016-09-01

    Detecting antibodies formed in serum in response to infection is the traditional function of serology. Diagnostic modalities have included complement fixation tests, agar gel immune-diffusion, radioimmunoassay, ELISA and immunofluorescence. More recent technology now allows for the direct detection of pathogens by PCR. This review details the options for diagnostic testing using specimen types other than serum, identifying the advantages and disadvantages of these options and providing evidence for more widespread use of these techniques and specimen types. PMID:27160006

  18. Turbofan engine core noise source diagnostics

    NASA Technical Reports Server (NTRS)

    Karchmer, Allen M.

    1987-01-01

    The paper describes a turbofan-engine measurement program utilizing a variety of diagnostic techniques to identify a source of core-generated noise which contributes to the overall external engine noise characteristics. Included in the turbofan engine diagnostics are data examination, time domain correlation, and frequency domain analysis. It is found that the turbulent pressure fluctuations within the combustor are a source for core noise which propagates through the nozzle and radiates to the far-field.

  19. Intelligent diagnostics systems

    NASA Technical Reports Server (NTRS)

    Mcquiston, Barbara M.; Dehoff, Ronald L.

    1992-01-01

    Intelligent systems have been applied to today's problems and could also be applied to space operations integrity. One of these systems is the XMAN tool designed for 'troubleshooting' jet engines. XMAN is the eXpert MAiNtenance tool developed to be an expert information analysis tool which stores trending and diagnostic data on Air Force engines. XMAN operates with a 'network topology' which follows a flow chart containing engine management information reports required by the governments technical order procedures. With XMAN technology, the user is able to identify engine problems by presenting the assertions of the fault isolation logic and attempting to satisfy individual assertions by referring to the databases created by an engine monitoring system. The troubleshooting process requires interaction between the technician and the computer to acquire new evidence form auxiliary maintenance tests corroboration of analytical results to accurately diagnose equipment malfunctions. This same technology will be required for systems which are functioning in space either with an onboard crew, or with an unmanned system. The technology and lessons learned developing this technology while suggesting definite applications for its use with developing space systems are addressed.

  20. Diagnostic Procedures of Itch.

    PubMed

    Reich, Adam; Szepietowski, Jacek C

    2016-01-01

    A complex and multifactorial pathogenesis of itch makes the proper diagnosis of underlying disease a difficult and challenging clinical problem. The examination of every patient with itch should be started by gathering an accurate history. During the anamnesis it is important to obtain data about the beginning of the appearance of symptoms, its location, diurnal variation, and the factors influencing itch perception. After careful anamnesis the patient should undergo a detailed physical examination, with particular attention to the skin in order to look for any signs of skin lesions. Special attention should be paid to distinguish the primary lesion from the changes resulting from scratching. In patients in whom the etiology of the itch cannot be identified on the basis of the medical examination, a panel of primary screen laboratory examination may be required, and if necessary, depending on the results of basic laboratory results and data from medical history, additional diagnostic tests should be considered. In patients in whom an organic cause of itching has not been established, itch is most likely of undetermined origin; however, psychogenic causes should also be suspected and ruled out. In conclusion, it could be stated that itch is a common symptom of many skin diseases, systemic of neurological diseases. Despite the complex etiology of the disease, an exact cause of itch should be searched for in each patient, as successful therapy is largely dependent on the determination of the cause of the itching. PMID:27578067

  1. Automotive Diagnostic Technologies.

    ERIC Educational Resources Information Center

    Columbus State Community Coll., OH.

    This document contains materials developed for and about the automotive diagnostic technologies tech prep program of the South-Western City Schools in Ohio. Part 1 begins with a map of the program, which begins with an automotive/diagnostic technologies program in grades 11 and 12 that leads to entry-level employment or a 2-year automotive…

  2. Rayleigh Scattering Diagnostics Workshop

    NASA Technical Reports Server (NTRS)

    Seasholtz, Richard (Compiler)

    1996-01-01

    The Rayleigh Scattering Diagnostics Workshop was held July 25-26, 1995 at the NASA Lewis Research Center in Cleveland, Ohio. The purpose of the workshop was to foster timely exchange of information and expertise acquired by researchers and users of laser based Rayleigh scattering diagnostics for aerospace flow facilities and other applications. This Conference Publication includes the 12 technical presentations and transcriptions of the two panel discussions. The first panel was made up of 'users' of optical diagnostics, mainly in aerospace test facilities, and its purpose was to assess areas of potential applications of Rayleigh scattering diagnostics. The second panel was made up of active researchers in Rayleigh scattering diagnostics, and its purpose was to discuss the direction of future work.

  3. A strain-specific catalase mutation and mutation of the metal-binding transporter gene mntC attenuate Neisseria gonorrhoeae in vivo but not by increasing susceptibility to oxidative killing by phagocytes.

    PubMed

    Wu, Hong; Soler-García, Angel A; Jerse, Ann E

    2009-03-01

    The hallmark of gonorrhea is an intense inflammatory response that is characterized by polymorphonuclear leukocytes (PMNs) with intracellular gonococci. A redundancy of defenses may protect Neisseria gonorrhoeae from phagocyte-derived reactive oxygen species. Here we showed that a gonococcal catalase (kat) mutant in strain MS11 was more sensitive to H(2)O(2) than mutants in cytochrome c peroxidase (ccp), methionine sulfoxide reductase (msrA), or the metal-binding protein (mntC) of the MntABC transporter. kat ccp and kat ccp mntC mutants were significantly more sensitive to H(2)O(2) than mutants in any single factor. None of the mutants showed increased susceptibility to murine PMNs. Recovery of the mntC and kat ccp mntC mutants from the lower genital tract of BALB/c mice, but not the kat or kat ccp mutants, was significantly reduced relative to wild-type bacteria. Interestingly, unlike the MS11 kat mutant, a kat mutant of strain FA1090 was attenuated during competitive infection with wild-type FA1090 bacteria. The FA1090 kat mutant and MS11 mntC mutant were also attenuated in mice that are unable to generate a phagocytic respiratory burst. We conclude that inactivation of three well-characterized antioxidant genes (kat, ccp, and mntC) does not increase gonococcal susceptibility to the phagocytic respiratory burst during infection and that gonococcal catalase and the MntC protein confer an unidentified advantage in vivo. In the case of catalase, this advantage is strain specific. Finally, we also showed that an msrA mutant of strain MS11 demonstrated delayed attenuation in BALB/c but not C57BL/6 mice. Therefore, MsrA/B also appears to play a role in infection that is dependent on host genetic background.

  4. The incidence of diagnostic error in medicine.

    PubMed

    Graber, Mark L

    2013-10-01

    A wide variety of research studies suggest that breakdowns in the diagnostic process result in a staggering toll of harm and patient deaths. These include autopsy studies, case reviews, surveys of patient and physicians, voluntary reporting systems, using standardised patients, second reviews, diagnostic testing audits and closed claims reviews. Although these different approaches provide important information and unique insights regarding diagnostic errors, each has limitations and none is well suited to establishing the incidence of diagnostic error in actual practice, or the aggregate rate of error and harm. We argue that being able to measure the incidence of diagnostic error is essential to enable research studies on diagnostic error, and to initiate quality improvement projects aimed at reducing the risk of error and harm. Three approaches appear most promising in this regard: (1) using 'trigger tools' to identify from electronic health records cases at high risk for diagnostic error; (2) using standardised patients (secret shoppers) to study the rate of error in practice; (3) encouraging both patients and physicians to voluntarily report errors they encounter, and facilitating this process. PMID:23771902

  5. Cable Diagnostic Focused Initiative

    SciTech Connect

    Hartlein, R.A.; Hampton, R.N.

    2010-12-30

    This report summarizes an extensive effort made to understand how to effectively use the various diagnostic technologies to establish the condition of medium voltage underground cable circuits. These circuits make up an extensive portion of the electric delivery infrastructure in the United States. Much of this infrastructure is old and experiencing unacceptable failure rates. By deploying efficient diagnostic testing programs, electric utilities can replace or repair circuits that are about to fail, providing an optimal approach to improving electric system reliability. This is an intrinsically complex topic. Underground cable systems are not homogeneous. Cable circuits often contain multiple branches with different cable designs and a range of insulation materials. In addition, each insulation material ages differently as a function of time, temperature and operating environment. To complicate matters further, there are a wide variety of diagnostic technologies available for assessing the condition of cable circuits with a diversity of claims about the effectiveness of each approach. As a result, the benefits of deploying cable diagnostic testing programs have been difficult to establish, leading many utilities to avoid the their use altogether. This project was designed to help address these issues. The information provided is the result of a collaborative effort between Georgia Tech NEETRAC staff, Georgia Tech academic faculty, electric utility industry participants, as well as cable system diagnostic testing service providers and test equipment providers. Report topics include: •How cable systems age and fail, •The various technologies available for detecting potential failure sites, •The advantages and disadvantages of different diagnostic technologies, •Different approaches for utilities to employ cable system diagnostics. The primary deliverables of this project are this report, a Cable Diagnostic Handbook (a subset of this report) and an online

  6. Melioidosis Diagnostic Workshop, 20131

    PubMed Central

    AuCoin, David; Baccam, Prasith; Baggett, Henry C.; Baird, Rob; Bhengsri, Saithip; Blaney, David D.; Brett, Paul J.; Brooks, Timothy J.G.; Brown, Katherine A.; Chantratita, Narisara; Cheng, Allen C.; Dance, David A.B.; Decuypere, Saskia; Defenbaugh, Dawn; Gee, Jay E.; Houghton, Raymond; Jorakate, Possawat; Lertmemongkolchai, Ganjana; Limmathurotsakul, Direk; Merlin, Toby L.; Mukhopadhyay, Chiranjay; Norton, Robert; Peacock, Sharon J.; Rolim, Dionne B.; Simpson, Andrew J.; Steinmetz, Ivo; Stoddard, Robyn A.; Stokes, Martha M.; Sue, David; Tuanyok, Apichai; Whistler, Toni; Wuthiekanun, Vanaporn; Walke, Henry T.

    2015-01-01

    Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions. PMID:25626057

  7. Plasma diagnostic reflectometry

    SciTech Connect

    Cohen, B.I.; Afeyan, B.B.; Garrison, J.C.; Kaiser, T.B.; Luhmann, N.C. Jr.; Domier, C.W.; Chou, A.E.; Baang, S.

    1996-02-26

    Theoretical and experimental studies of plasma diagnostic reflectometry have been undertaken as a collaborative research project between the Lawrence Livermore National Laboratory (LLNL) and the University of California Department of Applied Science Plasma Diagnostics Group under the auspices of the Laboratory Directed Research and Development Program at LLNL. Theoretical analyses have explored the basic principles of reflectometry to understand its limitations, to address specific gaps in the understanding of reflectometry measurements in laboratory experiments, and to explore extensions of reflectometry such as ultra-short-pulse reflectometry. The theory has supported basic laboratory reflectometry experiments where reflectometry measurements can be corroborated by independent diagnostic measurements.

  8. Sequencing Needs for Viral Diagnostics

    SciTech Connect

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  9. [Implant-associated infections - Diagnostics].

    PubMed

    Renz, N; Müller, M; Perka, C; Trampuz, A

    2016-10-01

    The diagnosis of implant-associated infections is challenging as chronic low-grade infections often only manifest as subtle clinical symptoms. Clinical evaluation, patient history, imaging, histopathological and microbiological examinations build the cornerstones of the diagnostics for implant-associated infections. New onset of pain at rest, local symptoms at the surgical site and early loosening of the prosthesis or pseudarthrosis should raise suspicion for an infection and prompt further evaluation. Percutaneous sinus tracts, purulent wound secretions and skin erosions with exposure of the implant are certain signs of implant-associated infections. Elevated C‑reactive protein levels in blood support the diagnosis of infection but are neither sufficient sensitive nor specific to confirm or exclude infection. Preoperative antibiotic therapy interferes with the diagnostic evaluation and should be avoided. In periprosthetic joint infections, joint aspiration with determination of the leukocyte count and microbiological examination is a crucial first diagnostic step. Through microbiological and histopathological examinations of intraoperative tissue samples, as well as sonication of explanted implants, the causative pathogen can be identified in most cases. In osteosynthesis-associated infections imaging plays a key role to detect non-union, infection callus, sequester, peri-implant osteolysis and extraosseous and intramedullary pathologies. In prosthetic joint infections imaging provides information about the position and stability of the prosthesis. In case of hematogenic infection seeding from a distant focus, blood cultures should be sampled, followed by a meticulous investigation of potential primary focus of infection, depending on the causative agent.

  10. Radioactive diagnostic agent

    SciTech Connect

    Shigematsu, A.; Aihara, M.; Matsuda, M.; Suzuki, A.; Tsuya, A.

    1984-02-07

    A radioactive diagnostic agent for renal cortex, adrenal cortex, myocardium, brain stem, spinal nerve, etc., which comprises as an essential component monoiodoacetic acid wherein the iodine atom is radioactive.

  11. Manual of diagnostic imaging

    SciTech Connect

    Gaylord, G.; Baker, S.; Davis, L.

    1988-01-01

    This book is on ordering and understanding the results of radiologic studies. Main sections are (I) Diagnostic Radiology serves as a basic introduction; (II) Diagnostic Modalities dedicates a chapter to each imaging modality in a clinical context, with a brief technical description and patient preparation guidelines; and (III) Organ System Imaging contains a chapter on each major organ system, covering the abilities and limitations of each modality to image a specific organ system and the significance of anatomic, physiologic, and general pathologic information.

  12. Diagnostics for pulmonary tuberculosis

    PubMed Central

    Cudahy, Patrick

    2016-01-01

    Tuberculosis (TB) remains a leading cause of human suffering and mortality despite decades of effective treatment being available. Accurate and timely diagnosis remains an unmet goal. The HIV epidemic has also led to new challenges in the diagnosis of TB. Several new developments in TB diagnostics have the potential to positively influence the global campaign against TB. We aim to review the performance of both established as well as new diagnostics for pulmonary TB in adults, and discuss the ongoing challenges. PMID:27005271

  13. Hemoptysis with diagnostic dilemma.

    PubMed

    Pramanik, Bimalendu

    2013-02-01

    Hemoptysis is a common symptom. Although initial diagnostic workup, including a chest radiograph, often gives a clue to the cause, it provides no diagnostic hints in 3.0-42.2% of episodes of hemoptysis. To describe those cases with no diagnostic hints at initial investigations, experts have used different terms, including unexplained hemoptysis, idiopathic hemoptysis, cryptogenic hemoptysis and hemoptysis with normal chest radiographs. As hemoptysis is a common symptom of bronchogenic carcinoma, there is a concern of having underlying malignancy. Physicians value high-resolution computed tomography and fiberoptic bronchoscopy as the next investigations to establish diagnosis. These investigations however are expensive and nonspecific results are common in those cases of hemoptysis where initial diagnostic workup gives no clues to the cause. As a result, controversies exist with regard to their use. In this article, the author has proposed diagnostic approaches to evaluate those cases of hemoptysis with no diagnostic hints at initial investigation, after extensive review of published articles related to the case scenario. PMID:23362818

  14. Neutron Diagnostics for NIF

    NASA Astrophysics Data System (ADS)

    Barnes, Cris W.; Berggren, R.; Caldwell, S.; Chrien, R. C.; Cverna, F.; Faulkner, J.; Mack, J. M.; Morgan, G. L.; Murphy, T. J.; Oertel, J. A.; Tegtmeier, J.; Walton, R.; Wilke, M.; Wilson, D. C.; Young, C. S.

    1999-11-01

    The National Ignition Facility (NIF) will be a pre-emminent facility for research on burning plasmas. Los Alamos National Laboratory is developing a focus area of coordinating fusion reaction product diagnostics on NIF and studying fusion burn. We will be developing ``core'' diagnostics for NIF including neutron time-of-flight and single-hit systems for ion temperature and neutron spectra, measurements of ``bang-time'' (time of fusion burn relative to start of laser pulse), and support for activation measurements for high-yield and radiochemical analysis. We are also developing advanced Phase 2 diagnostics including a gas Cerenkov burn history diagnostic and work on apertures and detectors for neutron imaging. This will include tests of these diagnostic systems on the OMEGA laser in the coming years. The measurement requirements and system descriptions of these NIF diagnostics will be described. This work was performed under the auspices of the U. S. Department of Energy by the Los Alamos National Laboratory under contract No. W-7405-Eng-36.

  15. International Consensus Diagnostic Criteria for Autoimmune Pancreatitis and Its Japanese Amendment Have Improved Diagnostic Ability over Existing Criteria

    PubMed Central

    Maruyama, Masahiro; Watanabe, Takayuki; Kanai, Keita; Oguchi, Takaya; Muraki, Takashi; Hamano, Hideaki; Arakura, Norikazu; Kawa, Shigeyuki

    2013-01-01

    Objectives. The recent International Consensus Diagnostic Criteria (ICDC) for autoimmune pancreatitis (AIP) and its Japanese amendment developed by the Japanese Pancreas Society (JPS 2011) may have overcome the drawbacks of earlier criteria and achieved a higher diagnostic ability for AIP. The aim of the present study is to evaluate this possibility and identify the underlying causes of this change. Methods. We compared the diagnostic abilities of the ICDC and JPS 2011 with those of the Japanese diagnostic criteria 2006 (JPS 2006), Korean diagnostic criteria (Korean), Asian diagnostic criteria (Asian), and HISORt diagnostic criteria in 110 patients with AIP and 31 patients with malignant pancreatic cancer. Results. The ICDC achieved the highest diagnostic ability in terms of accuracy (95.0%), followed by JPS 2011 (92.9%), Korean (92.2%), HISORt (88.7%), Asian (87.2%), and JPS 2006 (85.1%). Nearly all criteria systems exhibited a high specificity of 100%, indicating that the enhanced diagnostic ability of the ICDC and JPS 2011 likely stemmed from increased sensitivity brought about by inclusion of diagnostic items requiring no endoscopic retrograde pancreatography. The diagnostic ability of JPS 2011 was nearly equivalent to that of the ICDC. Conclusions. The ICDC and JPS 2011 have improved diagnostic ability as compared with earlier criteria sets because of an increase in sensitivity. PMID:24348535

  16. Strain-specific differences in cell proliferation and differentiation in the dentate gyrus of C57BL/6N and C3H/HeN mice fed a high fat diet.

    PubMed

    Hwang, In Koo; Kim, Il Yong; Kim, Dae Won; Yoo, Ki-Yeon; Kim, Yo Na; Yi, Sun Shin; Won, Moo-Ho; Lee, In Se; Yoon, Yeo Sung; Seong, Je Kyung

    2008-11-19

    The authors investigated strain-specific cell proliferation and differentiation differences in the dentate gyri of C57BL/6N (susceptible strain to obesity) and C3H/HeN (resistant strain to obesity) mice. In addition, the influences of a high fat diet (HD) on neuronal differentiation in C57BL/6N and C3H/HeN mice fed a low-fat diet (LD) or HD for 4 or 12 weeks were investigated. Body weight and body weight gains were significantly higher in HD-fed C57BL/6N and C3H/HeN mice than in LD-fed C57BL/6N and C3H/HeN mice. In particular, body weight gains were significantly higher in C57BL/6N mice than in C3H/HeN mice. In both of HD- and LD-fed C57BL/6N and C3H/HeN mice for 4 weeks, some Ki67 and many DCX immunoreactive cells were detected in the subgranular zone of the dentate gyrus. In HD-fed C57BL/6N and C3H/HeN mice, the number of Ki67 immunoreactive cells and DCX immunoreactivities in the dentate gyri were significantly lower than in LD-fed C57BL/6N and C3H/HeN mice. However, the number of Ki67 immunoreactive cells and DCX immunoreactivities in HD-fed C57BL/6N mice were significantly lower than in HD-fed C3H/HeN mice. These results suggest that C57BL/6N mice are more vulnerable to HD induced obesity than C3H/HeN mice. In addition, the feeding of HD was found to exacerbate reduced cell proliferation and differentiation in the dentate gyri of C57BL/6N mice as compared with that in C3H/HeN mice.

  17. Practical Diagnostics for Evaluating Residential Commissioning Metrics

    SciTech Connect

    Wray, Craig; Walker, Iain; Siegel, Jeff; Sherman, Max

    2002-06-11

    In this report, we identify and describe 24 practical diagnostics that are ready now to evaluate residential commissioning metrics, and that we expect to include in the commissioning guide. Our discussion in the main body of this report is limited to existing diagnostics in areas of particular concern with significant interactions: envelope and HVAC systems. These areas include insulation quality, windows, airtightness, envelope moisture, fan and duct system airflows, duct leakage, cooling equipment charge, and combustion appliance backdrafting with spillage. Appendix C describes the 83 other diagnostics that we have examined in the course of this project, but that are not ready or are inappropriate for residential commissioning. Combined with Appendix B, Table 1 in the main body of the report summarizes the advantages and disadvantages of all 107 diagnostics. We first describe what residential commissioning is, its characteristic elements, and how one might structure its process. Our intent in this discussion is to formulate and clarify these issues, but is largely preliminary because such a practice does not yet exist. Subsequent sections of the report describe metrics one can use in residential commissioning, along with the consolidated set of 24 practical diagnostics that the building industry can use now to evaluate them. Where possible, we also discuss the accuracy and usability of diagnostics, based on recent laboratory work and field studies by LBNL staff and others in more than 100 houses. These studies concentrate on evaluating diagnostics in the following four areas: the DeltaQ duct leakage test, air-handler airflow tests, supply and return grille airflow tests, and refrigerant charge tests. Appendix A describes those efforts in detail. In addition, where possible, we identify the costs to purchase diagnostic equipment and the amount of time required to conduct the diagnostics. Table 1 summarizes these data. Individual equipment costs for the 24

  18. Diagnostic 'omics' for active tuberculosis.

    PubMed

    Haas, Carolin T; Roe, Jennifer K; Pollara, Gabriele; Mehta, Meera; Noursadeghi, Mahdad

    2016-01-01

    The decision to treat active tuberculosis (TB) is dependent on microbiological tests for the organism or evidence of disease compatible with TB in people with a high demographic risk of exposure. The tuberculin skin test and peripheral blood interferon-γ release assays do not distinguish active TB from a cleared or latent infection. Microbiological culture of mycobacteria is slow. Moreover, the sensitivities of culture and microscopy for acid-fast bacilli and nucleic acid detection by PCR are often compromised by difficulty in obtaining samples from the site of disease. Consequently, we need sensitive and rapid tests for easily obtained clinical samples, which can be deployed to assess patients exposed to TB, discriminate TB from other infectious, inflammatory or autoimmune diseases, and to identify subclinical TB in HIV-1 infected patients prior to commencing antiretroviral therapy. We discuss the evaluation of peripheral blood transcriptomics, proteomics and metabolomics to develop the next generation of rapid diagnostics for active TB. We catalogue the studies published to date seeking to discriminate active TB from healthy volunteers, patients with latent infection and those with other diseases. We identify the limitations of these studies and the barriers to their adoption in clinical practice. In so doing, we aim to develop a framework to guide our approach to discovery and development of diagnostic biomarkers for active TB. PMID:27005907

  19. The use of diagnostic wax-ups in treatment planning.

    PubMed

    Garcia, Lily T; Bohnenkamp, David M

    2003-03-01

    The use of diagnostic wax-ups as diagnostic aids in treatment planning has been presented for use in various situations--from simple patient assessment to more extensive prosthodontic rehabilitation. Requesting a diagnostic wax-up from the dental technician may add to the expense of treatment planning for a patient because of the laboratory fee incurred for this service. The cost is negligible, considering the value of identifying potential treatment obstacles that could affect both treatment outcomes and patient satisfaction.

  20. A new classification system for lesbians: the Dyke Diagnostic Manual.

    PubMed

    Eliason, Michele J

    2010-01-01

    There has been a long-standing need for a diagnostic manual that documents the unique pathological behaviors of lesbians. The Dyke Diagnostic Manual (DDM) is meant to supplement mainstream classification systems used to identify problematic behaviors in heterosexuals. This article presents thirteen uniquely lesbian conditions that are nowhere to be found in heterosexist diagnostic systems. The DDM may help to reduce the pain and suffering found in many lesbian relationships where one or both partners are afflicted. PMID:20661801

  1. Better Tests, Better Care: Improved Diagnostics for Infectious Diseases

    PubMed Central

    Caliendo, Angela M.; Gilbert, David N.; Ginocchio, Christine C.; Hanson, Kimberly E.; May, Larissa; Quinn, Thomas C.; Tenover, Fred C.; Alland, David; Blaschke, Anne J.; Bonomo, Robert A.; Carroll, Karen C.; Ferraro, Mary Jane; Hirschhorn, Lisa R.; Joseph, W. Patrick; Karchmer, Tobi; MacIntyre, Ann T.; Reller, L. Barth; Jackson, Audrey F.

    2013-01-01

    In this IDSA policy paper, we review the current diagnostic landscape, including unmet needs and emerging technologies, and assess the challenges to the development and clinical integration of improved tests. To fulfill the promise of emerging diagnostics, IDSA presents recommendations that address a host of identified barriers. Achieving these goals will require the engagement and coordination of a number of stakeholders, including Congress, funding and regulatory bodies, public health agencies, the diagnostics industry, healthcare systems, professional societies, and individual clinicians. PMID:24200831

  2. [Diagnostic criteria in acute neuromyelitis].

    PubMed

    Panea, Cristina; Petrescu, Simona; Monica, Pop; Voinea, Liliana; Dascălu, Ana-Maria; Nicolae, Miruna; Ungureanu, E; Panca, Aida; Grădinaru, Sânziana

    2007-01-01

    Neuromyelitis optica, also known as Devic disease, was identified in the 19th century, is one of the inflammatory idiopathic demyelinating diseases of the central nervous system, often mistaken for severe multiple sclerosis. In 1999 it had been proposed diagnostic criteria for neuromyelitis optica, but in 2006 these criteria were revised by Dean Wingerchuck. These criteria are 99% sensitive and 90% specific for differentiating neuromyelitis optica from multiple sclerosis that present with optic neuritis or a myelitis syndrome. In the following article we present clinical, spinal and cerebral MR imaging, serological and aspects of cerebrospinal fluid examination features of neuromyelitis optica and the revised criteria of neuromyelitis optica established in 2006. The recently identified serum antibody biomarker: neuromyelitis optica immunoglobulin G (NMO Ig G), which target aquaporin 4 water channel, distinguish neuromyelitis optica from multiple sclerosis, is one of the revised criteria of neuromyelitis optica. PMID:18543687

  3. Development of Companion Diagnostics.

    PubMed

    Mankoff, David A; Edmonds, Christine E; Farwell, Michael D; Pryma, Daniel A

    2016-01-01

    The goal of individualized and targeted treatment and precision medicine requires the assessment of potential therapeutic targets to direct treatment selection. The biomarkers used to direct precision medicine, often termed companion diagnostics, for highly targeted drugs have thus far been almost entirely based on in vitro assay of biopsy material. Molecular imaging companion diagnostics offer a number of features complementary to those from in vitro assay, including the ability to measure the heterogeneity of each patient's cancer across the entire disease burden and to measure early changes in response to treatment. We discuss the use of molecular imaging methods as companion diagnostics for cancer therapy with the goal of predicting response to targeted therapy and measuring early (pharmacodynamic) response as an indication of whether the treatment has "hit" the target. We also discuss considerations for probe development for molecular imaging companion diagnostics, including both small-molecule probes and larger molecules such as labeled antibodies and related constructs. We then describe two examples where both predictive and pharmacodynamic molecular imaging markers have been tested in humans: endocrine therapy for breast cancer and human epidermal growth factor receptor type 2-targeted therapy. The review closes with a summary of the items needed to move molecular imaging companion diagnostics from early studies into multicenter trials and into the clinic.

  4. Development of Companion Diagnostics.

    PubMed

    Mankoff, David A; Edmonds, Christine E; Farwell, Michael D; Pryma, Daniel A

    2016-01-01

    The goal of individualized and targeted treatment and precision medicine requires the assessment of potential therapeutic targets to direct treatment selection. The biomarkers used to direct precision medicine, often termed companion diagnostics, for highly targeted drugs have thus far been almost entirely based on in vitro assay of biopsy material. Molecular imaging companion diagnostics offer a number of features complementary to those from in vitro assay, including the ability to measure the heterogeneity of each patient's cancer across the entire disease burden and to measure early changes in response to treatment. We discuss the use of molecular imaging methods as companion diagnostics for cancer therapy with the goal of predicting response to targeted therapy and measuring early (pharmacodynamic) response as an indication of whether the treatment has "hit" the target. We also discuss considerations for probe development for molecular imaging companion diagnostics, including both small-molecule probes and larger molecules such as labeled antibodies and related constructs. We then describe two examples where both predictive and pharmacodynamic molecular imaging markers have been tested in humans: endocrine therapy for breast cancer and human epidermal growth factor receptor type 2-targeted therapy. The review closes with a summary of the items needed to move molecular imaging companion diagnostics from early studies into multicenter trials and into the clinic. PMID:26687857

  5. Development of Companion Diagnostics

    PubMed Central

    Mankoff, David A.; Edmonds, Christine E.; Farwell, Michael D.; Pryma, Daniel A.

    2016-01-01

    The goal of individualized and targeted treatment and precision medicine requires the assessment of potential therapeutic targets to direct treatment selection. The biomarkers used to direct precision medicine, often termed companion diagnostics, for highly targeted drugs have thus far been almost entirely based on in vitro assay of biopsy material. Molecular imaging companion diagnostics offer a number of features complementary to those from in vitro assay, including the ability to measure the heterogeneity of each patient’s cancer across the entire disease burden and to measure early changes in response to treatment. We discuss the use of molecular imaging methods as companion diagnostics for cancer therapy with the goal of predicting response to targeted therapy and measuring early (pharmacodynamic) response as an indication of whether the treatment has “hit” the target. We also discuss considerations for probe development for molecular imaging companion diagnostics, including both small-molecule probes and larger molecules such as labeled antibodies and related constructs. We then describe two examples where both predictive and pharmacodynamic molecular imaging markers have been tested in humans: endocrine therapy for breast cancer and human epidermal growth factor receptor type 2–targeted therapy. The review closes with a summary of the items needed to move molecular imaging companion diagnostics from early studies into multicenter trials and into the clinic. PMID:26687857

  6. Diagnostic Hypothesis Generation and Human Judgment

    ERIC Educational Resources Information Center

    Thomas, Rick P.; Dougherty, Michael R.; Sprenger, Amber M.; Harbison, J. Isaiah

    2008-01-01

    Diagnostic hypothesis-generation processes are ubiquitous in human reasoning. For example, clinicians generate disease hypotheses to explain symptoms and help guide treatment, auditors generate hypotheses for identifying sources of accounting errors, and laypeople generate hypotheses to explain patterns of information (i.e., data) in the…

  7. The Popcorn Book: A Diagnostic Teaching Unit.

    ERIC Educational Resources Information Center

    Bock, Marjorie A.; Barger, Rita.

    1998-01-01

    Presents a diagnostic teaching unit designed to identify effective teaching strategies for fourth- or fifth-grade students with learning or behavior disorders. The unit uses "The Popcorn Book" (de Paola) for activities to evaluate the effectiveness of teaching strategies across the content areas of reading, writing, and mathematics. (CR)

  8. ORION laser target diagnostics.

    PubMed

    Bentley, C D; Edwards, R D; Andrew, J E; James, S F; Gardner, M D; Comley, A J; Vaughan, K; Horsfield, C J; Rubery, M S; Rothman, S D; Daykin, S; Masoero, S J; Palmer, J B; Meadowcroft, A L; Williams, B M; Gumbrell, E T; Fyrth, J D; Brown, C R D; Hill, M P; Oades, K; Wright, M J; Hood, B A; Kemshall, P

    2012-10-01

    The ORION laser facility is one of the UK's premier laser facilities which became operational at AWE in 2010. Its primary mission is one of stockpile stewardship, ORION will extend the UK's experimental plasma physics capability to the high temperature, high density regime relevant to Atomic Weapons Establishment's (AWE) program. The ORION laser combines ten laser beams operating in the ns regime with two sub ps short pulse chirped pulse amplification beams. This gives the UK a unique combined long pulse/short pulse laser capability which is not only available to AWE personnel but also gives access to our international partners and visiting UK academia. The ORION laser facility is equipped with a comprehensive suite of some 45 diagnostics covering optical, particle, and x-ray diagnostics all able to image the laser target interaction point. This paper focuses on a small selection of these diagnostics. PMID:23126904

  9. Beamlet laser diagnostics

    SciTech Connect

    Burkhart, S.C.; Behrendt, W.C.; Smith, I.

    1996-06-01

    Beamlet is instrumented extensively to monitor the performance of the overall laser system and many of its subsystems. Beam diagnostics, installed in key locations, are used to fully characterize the beam during its propagation through the multipass cavity and the laser`s output section. This article describes the diagnostics stations located on Beamlet and discusses the design, calibration, and performance of the Beamlet calorimeters. The authors used Nova`s diagnostics packages to develop the Beamlet design to determine beam energy, spatial profile, temporal profile, and other beam parameters. Technologic improvements within the last several years in controls, charge-coupled device (CCD) cameras, and fast oscilloscopes have allowed the authors to obtain more accurate measurements on the Beamlet laser system. They briefly cover some of these techniques, including a description of their LabVIEW based data acquisition system.

  10. ORION laser target diagnostics.

    PubMed

    Bentley, C D; Edwards, R D; Andrew, J E; James, S F; Gardner, M D; Comley, A J; Vaughan, K; Horsfield, C J; Rubery, M S; Rothman, S D; Daykin, S; Masoero, S J; Palmer, J B; Meadowcroft, A L; Williams, B M; Gumbrell, E T; Fyrth, J D; Brown, C R D; Hill, M P; Oades, K; Wright, M J; Hood, B A; Kemshall, P

    2012-10-01

    The ORION laser facility is one of the UK's premier laser facilities which became operational at AWE in 2010. Its primary mission is one of stockpile stewardship, ORION will extend the UK's experimental plasma physics capability to the high temperature, high density regime relevant to Atomic Weapons Establishment's (AWE) program. The ORION laser combines ten laser beams operating in the ns regime with two sub ps short pulse chirped pulse amplification beams. This gives the UK a unique combined long pulse/short pulse laser capability which is not only available to AWE personnel but also gives access to our international partners and visiting UK academia. The ORION laser facility is equipped with a comprehensive suite of some 45 diagnostics covering optical, particle, and x-ray diagnostics all able to image the laser target interaction point. This paper focuses on a small selection of these diagnostics.

  11. ORION laser target diagnostics

    SciTech Connect

    Bentley, C. D.; Edwards, R. D.; Andrew, J. E.; James, S. F.; Gardner, M. D.; Comley, A. J.; Vaughan, K.; Horsfield, C. J.; Rubery, M. S.; Rothman, S. D.; Daykin, S.; Masoero, S. J.; Palmer, J. B.; Meadowcroft, A. L.; Williams, B. M.; Gumbrell, E. T.; Fyrth, J. D.; Brown, C. R. D.; Hill, M. P.; Oades, K.; and others

    2012-10-15

    The ORION laser facility is one of the UK's premier laser facilities which became operational at AWE in 2010. Its primary mission is one of stockpile stewardship, ORION will extend the UK's experimental plasma physics capability to the high temperature, high density regime relevant to Atomic Weapons Establishment's (AWE) program. The ORION laser combines ten laser beams operating in the ns regime with two sub ps short pulse chirped pulse amplification beams. This gives the UK a unique combined long pulse/short pulse laser capability which is not only available to AWE personnel but also gives access to our international partners and visiting UK academia. The ORION laser facility is equipped with a comprehensive suite of some 45 diagnostics covering optical, particle, and x-ray diagnostics all able to image the laser target interaction point. This paper focuses on a small selection of these diagnostics.

  12. Reversed field pinch diagnostics

    SciTech Connect

    Weber, P.G.

    1986-01-01

    The Reversed Field Pinch (RFP) is a toroidal, axisymmetric magnetic confinement configuration characterized by a magnetic field configuration in which the toroidal magnetic field is of similar strength to the poloidal field, and is reversed at the edge compared to the center. The RFP routinely operates at high beta, and is a strong candidate for a compact fusion device. Relevant attributes of the configuration will be presented, together with an overview of present and planned experiments and their diagnostics. RFP diagnostics are in many ways similar to those of other magnetic confinement devices (such as tokamaks); these lectures will point out pertinent differences, and will present some diagnostics which provide special insights into unique attributes of the RFP.

  13. PDX diagnostic control system

    SciTech Connect

    Mika, R.

    1981-01-01

    This paper describes a computer-base diagnostic control system operating on the PDX Tokamak. The prime function of the system is to control mechanical positioning devices associated with various diagnostics including Thomson Scattering, X-Ray Pulse Height Analyzer, Rotating Scanning Monochromator, Fast Ion Detection Experiment, Bolometers and Plasma Limiters. The diagnostic control system consists of a PDP-11/34 computer, a CAMAC system partitioned between the PDX control room and the PDX machine area, and special electronic control modules developed at PPL. The special modules include a digital closed loop motor controller and user interface control panel for control and status display. A standard control panel was developed for interfacing each system user with the PDP-11/34 computer, through specially developed CAMAC modules.

  14. Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease

    PubMed Central

    Ellingford, Jamie M.; Barton, Stephanie; Bhaskar, Sanjeev; Williams, Simon G.; Sergouniotis, Panagiotis I.; O'Sullivan, James; Lamb, Janine A.; Perveen, Rahat; Hall, Georgina; Newman, William G.; Bishop, Paul N.; Roberts, Stephen A.; Leach, Rick; Tearle, Rick; Bayliss, Stuart; Ramsden, Simon C.; Nemeth, Andrea H.; Black, Graeme C.M.

    2016-01-01

    Purpose To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Design Case series. Participants A total of 562 patients diagnosed with IRD. Methods We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data. Main Outcome Measures Diagnostic yield of genomic testing. Results Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15–45) uplift in diagnostic yield. Conclusions We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS. PMID:26872967

  15. Psychoeducational Diagnostic Services for Learning Disabled Youths. Research Procedures.

    ERIC Educational Resources Information Center

    Barrows, Thomas S.; And Others

    A detailed explicit definition of learning disability (LD) is presented in terms of the diagnostic procedures and decision points used in identifying that category among a group of juvenile delinquent and control group adolescent males. The described procedures include a review of existing records, interviews, and diagnostic assessments.…

  16. Diagnostic Errors in Ambulatory Care: Dimensions and Preventive Strategies

    ERIC Educational Resources Information Center

    Singh, Hardeep; Weingart, Saul N.

    2009-01-01

    Despite an increasing focus on patient safety in ambulatory care, progress in understanding and reducing diagnostic errors in this setting lag behind many other safety concerns such as medication errors. To explore the extent and nature of diagnostic errors in ambulatory care, we identified five dimensions of ambulatory care from which errors may…

  17. [Diagnostic models. 2. Fabrication].

    PubMed

    Lefèvre, M; Vincent, G; L'Official-Vincent, M

    1989-09-01

    After describing in Part I the preparation of diagnostic cast, the authors describe the Wax Up preparation. Most of the definition of centric relation agree that the position of the mandible is slightly behind its position in centric occlusion. The Hinge axis position is used for mounting the cast on articulator. The final restauration must reconstruct both position and the occlusion should be established in front the centric occlusion. After equilibration anterior guidance is studied and restaured if necessary. After creating the different curve of occlusion, the final Wax Up is settled. The use of the diagnostic cast so obtained will be presented in Part III.

  18. Diagnostic hematology of reptiles.

    PubMed

    Stacy, Nicole I; Alleman, A Rick; Sayler, Katherine A

    2011-03-01

    The hematologic evaluation of reptiles is an indispensable diagnostic tool in exotic veterinary practice. The diversity of reptile species, their characteristic physiologic features, and effects of intrinsic and extrinsic factors present unique challenges for accurate interpretation of the hemogram. Combining the clinical presentation with hematologic findings provides valuable information in the diagnosis and monitoring of disease and helps guide the clinician toward therapy and further diagnostic testing. This article outlines the normal and pathologic morphology of blood cells of reptile species. The specific comparative aspects of reptiles are emphasized, and structural and functional abnormalities in the reptilian hemogram are described.

  19. Diagnostic workup for ARDS patients.

    PubMed

    Papazian, Laurent; Calfee, Carolyn S; Chiumello, Davide; Luyt, Charles-Edouard; Meyer, Nuala J; Sekiguchi, Hiroshi; Matthay, Michael A; Meduri, Gianfranco Umberto

    2016-05-01

    Acute respiratory distress syndrome (ARDS) is defined by the association of bilateral infiltrates and hypoxaemia following an initial insult. Although a new definition has been recently proposed (Berlin definition), there are various forms of ARDS with potential differences regarding their management (ventilator settings, prone positioning use, corticosteroids). ARDS can be caused by various aetiologies, and the adequate treatment of the responsible cause is crucial to improve the outcome. It is of paramount importance to characterize the mechanisms causing lung injury to optimize both the aetiological treatment and the symptomatic treatment. If there is no obvious cause of ARDS or if a direct lung injury is suspected, bronchoalveolar lavage (BAL) should be strongly considered to identify microorganisms responsible for pneumonia. Blood samples can also help to identify microorganisms and to evaluate biomarkers of infection. If there is no infectious cause of ARDS or no other apparent aetiology is found, second-line examinations should include markers of immunologic diseases. In selected cases, open lung biopsy remains useful to identify the cause of ARDS when all other examinations remain inconclusive. CT scan is fundamental when there is a suspicion of intra-abdominal sepsis and in some cases of pneumonia. Ultrasonography is important not only in evaluating biventricular function but also in identifying pleural effusions and pneumothorax. The definition of ARDS remains clinical and the main objective of the diagnostic workup should be to be focused on identification of its aetiology, especially a treatable infection. PMID:27007111

  20. Diagnostic Lessons as Assessment.

    ERIC Educational Resources Information Center

    Walker, Barbara J.

    Embedded in a sensitive instructional context rather than a stifling testing atmosphere, diagnostic lessons provide assessment that is reliable, practical, valid, and efficient. In this type of assessment, there are several determiners of instructional placement: (1) students' propensity to adapt strategies as a result of specified instruction,…

  1. Sexual Addiction: Diagnostic Problems

    ERIC Educational Resources Information Center

    Giugliano, John R.

    2009-01-01

    In recent years clinicians report a great deal of concern about definition, diagnostic assessment, and treatment modalities when dealing with what might be called out-of-control sexual behavior. Many terms have been used to describe the phenomenon of problematic sexual behavior. Many of these concepts overlap, some are no longer popular, and some…

  2. Diagnostic Testing Project.

    ERIC Educational Resources Information Center

    McArthur, David L.

    This paper presents an explanation of the program design of the three separate Pascal-language programs which comprise UCLA's Diagnostic Testing Package "DX." The three parts of the DX test package are three closely interrelated programs--Editest, Runtest, and Summary. Editest serves the following functions: (1) the creation of a suitable…

  3. Equivalent Diagnostic Classification Models

    ERIC Educational Resources Information Center

    Maris, Gunter; Bechger, Timo

    2009-01-01

    Rupp and Templin (2008) do a good job at describing the ever expanding landscape of Diagnostic Classification Models (DCM). In many ways, their review article clearly points to some of the questions that need to be answered before DCMs can become part of the psychometric practitioners toolkit. Apart from the issues mentioned in this article that…

  4. Heterodyne laser diagnostic system

    DOEpatents

    Globig, Michael A.; Johnson, Michael A.; Wyeth, Richard W.

    1990-01-01

    The heterodyne laser diagnostic system includes, in one embodiment, an average power pulsed laser optical spectrum analyzer for determining the average power of the pulsed laser. In another embodiment, the system includes a pulsed laser instantaneous optical frequency measurement for determining the instantaneous optical frequency of the pulsed laser.

  5. Diagnostics for induction accelerators

    SciTech Connect

    Fessenden, T.J.

    1996-04-01

    The induction accelerator was conceived by N. C. Christofilos and first realized as the Astron accelerator that operated at LLNL from the early 1960`s to the end of 1975. This accelerator generated electron beams at energies near 6 MeV with typical currents of 600 Amperes in 400 ns pulses. The Advanced Test Accelerator (ATA) built at Livermore`s Site 300 produced 10,000 Ampere beams with pulse widths of 70 ns at energies approaching 50 MeV. Several other electron and ion induction accelerators have been fabricated at LLNL and LBNL. This paper reviews the principal diagnostics developed through efforts by scientists at both laboratories for measuring the current, position, energy, and emittance of beams generated by these high current, short pulse accelerators. Many of these diagnostics are closely related to those developed for other accelerators. However, the very fast and intense current pulses often require special diagnostic techniques and considerations. The physics and design of the more unique diagnostics developed for electron induction accelerators are presented and discussed in detail.

  6. Beam Diagnostics for FACET

    SciTech Connect

    Li, S.Z.; Hogan, M.J.; /SLAC

    2011-08-19

    FACET, the Facility for Advanced Accelerator and Experimental Tests, is a new facility being constructed in sector 20 of the SLAC linac primarily to study beam driven plasma wakefield acceleration beginning in summer 2011. The nominal FACET parameters are 23GeV, 3nC electron bunches compressed to about 20 {micro}m long and focussed to about 10 {micro}m wide. Characterization of the beam-plasma interaction requires complete knowledge of the incoming beam parameters on a pulse-to-pulse basis. FACET diagnostics include Beam Position Monitors, Toroidal current monitors, X-ray and Cerenkov based energy spectrometers, optical transition radiation (OTR) profile monitors and coherent transition radiation (CTR) bunch length measurement systems. The compliment of beam diagnostics and their expected performance are reviewed. Beam diagnostic measurements not only provide valuable insights to the running and tuning of the accelerator but also are crucial for the PWFA experiments in particular. Beam diagnostic devices are being set up at FACET and will be ready for beam commissioning in summer 2011.

  7. microRNA: Diagnostic Perspective

    PubMed Central

    Faruq, Omar; Vecchione, Andrea

    2015-01-01

    Biomarkers are biological measures of a biological state. An ideal marker should be safe and easy to measure, cost efficient, modifiable with treatment, and consistent across gender and ethnic groups. To date, none of the available biomarkers satisfy all of these criteria. In addition, the major limitations of these markers are low specificity, sensitivity, and false positive results. Recently identified, microRNAs (miRNAs) are endogenous, evolutionarily conserved small non-coding RNA (about 22–25 nt long), also known as micro-coordinators of gene expression, which have been shown to be an effective tools to study the biology of diseases and to have great potential as novel diagnostic and prognostic biomarkers with high specificity and sensitivity. In fact, it has been demonstrated that miRNAs play a pivotal role in the regulation of a wide range of developmental and physiological processes and their deficiencies have been related to a number of disease. In addition, miRNAs are stable and can be easily isolated and measured from tissues and body fluids. In this review, we provide a perspective on emerging concepts and potential usefulness of miRNAs as diagnostic markers, emphasizing the involvement of specific miRNAs in particular tumor types, subtypes, cardiovascular diseases, diabetes, infectious diseases, and forensic test. PMID:26284247

  8. Tularemia without lesions in grey tree squirrels: A diagnostic challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fifteen cases of Francisella tularenesis infection (tularemia) were identified in western grey (Sciurus griseus) and eastern grey (Sciurus carolinesis) squirrels submitted to the Washington Animal Disease Diagnostic Laboratory between 2008 and 2011. All of the squirrels originated in Washington stat...

  9. Diagnostics for the Combustion Science Workbench

    SciTech Connect

    Grcar, J.F.; Day, M.S.; Bell, J.B.

    2007-02-21

    As the cost of computers declines relative to outfitting andmaintaining laser spectroscopy laboratories, computers will account foran increasing proportion of the research conducted in fundamentalcombustion science. W.C. Gardiner foresaw that progress will be limitedby the ability to understand the implications of what has been computedand to draw inferences about the elementary components of the combustionmodels. Yet the diagnostics that are routinely applied to computerexperiments have changed little from the sensitivity analyses includedwith the original chemkin software distribution. This paper describessome diagnostics capabilities that may be found on the virtual combustionscience workbench of the future. These diagnostics are illustrated bysome new results concerning which of the hydrogen/oxygen chain branchingreactions actually occur in flames, the increased formation of NOx inwrinkled flames versus flat flames, and the adequacy oftheoreticalpredictions of the effects of stretch. Several areas are identified wherework is needed, including the areas of combustion chemistry and laserdiagnostics, to make the virtual laboratory a reality.

  10. Automated diagnostics scoping study. Final report

    SciTech Connect

    Quadrel, R.W.; Lash, T.A.

    1994-06-01

    The objective of the Automated Diagnostics Scoping Study was to investigate the needs for diagnostics in building operation and to examine some of the current technologies in automated diagnostics that can address these needs. The study was conducted in two parts. In the needs analysis, the authors interviewed facility managers and engineers at five building sites. In the technology survey, they collected published information on automated diagnostic technologies in commercial and military applications as well as on technologies currently under research. The following describe key areas that the authors identify for the research, development, and deployment of automated diagnostic technologies: tools and techniques to aid diagnosis during building commissioning, especially those that address issues arising from integrating building systems and diagnosing multiple simultaneous faults; technologies to aid diagnosis for systems and components that are unmonitored or unalarmed; automated capabilities to assist cause-and-effect exploration during diagnosis; inexpensive, reliable sensors, especially those that expand the current range of sensory input; technologies that aid predictive diagnosis through trend analysis; integration of simulation and optimization tools with building automation systems to optimize control strategies and energy performance; integration of diagnostic, control, and preventive maintenance technologies. By relating existing technologies to perceived and actual needs, the authors reached some conclusions about the opportunities for automated diagnostics in building operation. Some of a building operator`s needs can be satisfied by off-the-shelf hardware and software. Other needs are not so easily satisfied, suggesting directions for future research. Their conclusions and suggestions are offered in the final section of this study.

  11. Diagnostic Tools of Pleural Effusion

    PubMed Central

    2014-01-01

    Pleural effusion is not a rare disease in Korea. The diagnosis of pleural effusion is very difficult, even though the patients often complain of typical symptoms indicating of pleural diseases. Pleural effusion is characterized by the pleural cavity filled with transudative or exudative pleural fluids, and it is developed by various etiologies. The presence of pleural effusion can be confirmed by radiological studies including simple chest radiography, ultrasonography, or computed tomography. Identifying the causes of pleural effusions by pleural fluid analysis is essential for proper treatments. This review article provides information on the diagnostic approaches of pleural effusions and further suggested ways to confirm their various etiologies, by using the most recent journals for references. PMID:24920946

  12. The diagnostics of colorectal cancer.

    PubMed

    Swiderska, Magdalena; Choromańska, Barbara; Dąbrowska, Ewelina; Konarzewska-Duchnowska, Emilia; Choromańska, Katarzyna; Szczurko, Grzegorz; Myśliwiec, Piotr; Dadan, Jacek; Ladny, Jerzy Robert; Zwierz, Krzysztof

    2014-01-01

    Colorectal cancer (CRC) is one of the most frequent human malignant neoplasms. CRC has an estimated incidence of more than 1,000,000 new cases annually worldwide. Approximately one out of three people who develop CRC dies from the disease. Furthermore, CRC often affects inhabitants of industrialized countries in comparison to less developed countries. Several markers of colon cancer, including CEA, CA-19-9, TPS, TAG-72 and lysosomal hydrolases, have been identified and are now being adopted in routine clinical practice. Increased values of these markers are often the first signal of recurrence or metastases, which is useful in prediction and prognosis of clinical outcome of patients with CRC. Determination of the activity of lysosomal exoglycosidases in body fluids may bring some hope of improving diagnosis of colorectal cancer. However, it has to be remembered that currently the most effective diagnostic method of CRC is endoscopy. PMID:24876814

  13. Culture-Independent Diagnostics for Health Security.

    PubMed

    Doggett, Norman A; Mukundan, Harshini; Lefkowitz, Elliot J; Slezak, Tom R; Chain, Patrick S; Morse, Stephen; Anderson, Kevin; Hodge, David R; Pillai, Segaran

    2016-01-01

    The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop.

  14. Culture-Independent Diagnostics for Health Security.

    PubMed

    Doggett, Norman A; Mukundan, Harshini; Lefkowitz, Elliot J; Slezak, Tom R; Chain, Patrick S; Morse, Stephen; Anderson, Kevin; Hodge, David R; Pillai, Segaran

    2016-01-01

    The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop. PMID:27314653

  15. Cardiovascular modeling and diagnostics

    SciTech Connect

    Kangas, L.J.; Keller, P.E.; Hashem, S.; Kouzes, R.T.

    1995-12-31

    In this paper, a novel approach to modeling and diagnosing the cardiovascular system is introduced. A model exhibits a subset of the dynamics of the cardiovascular behavior of an individual by using a recurrent artificial neural network. Potentially, a model will be incorporated into a cardiovascular diagnostic system. This approach is unique in that each cardiovascular model is developed from physiological measurements of an individual. Any differences between the modeled variables and the variables of an individual at a given time are used for diagnosis. This approach also exploits sensor fusion to optimize the utilization of biomedical sensors. The advantage of sensor fusion has been demonstrated in applications including control and diagnostics of mechanical and chemical processes.

  16. Blast wave energy diagnostic.

    PubMed

    Tierney, Thomas E; Tierney, Heidi E; Idzorek, George C; Watt, Robert G; Peterson, Robert R; Peterson, Darrell L; Fryer, Christopher L; Lopez, Mike R; Jones, Michael C; Sinars, Daniel; Rochau, Gregory A; Bailey, James E

    2008-10-01

    The distance radiation waves that supersonically propagate in optically thick, diffusive media are energy sensitive. A blast wave can form in a material when the initially diffusive, supersonic radiation wave becomes transonic. Under specific conditions, the blast wave is visible with radiography as a density perturbation. [Peterson et al., Phys. Plasmas 13, 056901 (2006)] showed that the time-integrated drive energy can be measured using blast wave positions with uncertainties less than 10% at the Z Facility. In some cases, direct measurements of energy loss through diagnostic holes are not possible with bolometric and x-ray radiometric diagnostics. Thus, radiography of high compression blast waves can serve as a complementary technique that provides time-integrated energy loss through apertures. In this paper, we use blast waves to characterize the energy emerging through a 2.4 mm aperture and show experimental results in comparison to simulations. PMID:19044574

  17. Nanodevices in diagnostics

    PubMed Central

    Hu, Ye; Fine, Daniel H.; Tasciotti, Ennio; Bouamrani, Ali; Ferrari, Mauro

    2010-01-01

    The real-time, personalized and highly sensitive early-stage diagnosis of disease remains an important challenge in modern medicine. With the ability to interact with matter at the nanoscale, the development of nanotechnology architectures and materials could potentially extend subcellular and molecular detection beyond the limits of conventional diagnostic modalities. At the very least, nanotechnology should be able to dramatically accelerate biomarker discovery, as well as facilitate disease monitoring, especially of maladies presenting a high degree of molecular and compositional heterogeneity. This article gives an overview of several of the most promising nanodevices and nanomaterials along with their applications in clinical practice. Significant work to adapt nanoscale materials and devices to clinical applications involving large interdisciplinary collaborations is already underway with the potential for nanotechnology to become an important enabling diagnostic technology. PMID:20229595

  18. DIAGNOSTICS OF BNL ERL

    SciTech Connect

    POZDEYEV,E.; BEN-ZVI, I.; CAMERON, P.; GASSNER, D.; KAYRAN, D.; ET AL.

    2007-06-25

    The ERL Prototype project is currently under development at the Brookhaven National Laboratory. The ERL is expected to demonstrate energy recovery of high-intensity beams with a current of up to a few hundred milliamps, while preserving the emittance of bunches with a charge of a few nanocoulombs produced by a high-current SRF gun. To successfully accomplish this task the machine will include beam diagnostics that will be used for accurate characterization of the three dimensional beam phase space at the injection and recirculation energies, transverse and longitudinal beam matching, orbit alignment, beam current measurement, and machine protection. This paper outlines requirements on the ERL diagnostics and describes its setup and modes of operation.

  19. Sonographic diagnostics in dermatology.

    PubMed

    Ulrich, Jens; Schwürzer-Voit, Markus; Jenderka, Klaus-Vitold; Voit, Christiane

    2014-12-01

    Ultrasonography non-invasively visualizes changes within the skin, skin appendages, subcutaneous tissue, subcutaneous (regional) lymph nodes and peripheral vessels. Thus it is an established diagnostic tool in dermatology. Compared to X-ray, MRI and PET, ultrasonography has some advantages; however, it is more dependent on the individual experience of the investigator. Therefore a structured education and continuous training are necessary. This review describes the physical and technical basics, the administrative requirements and the main indications in dermatology.

  20. Upgrading Diagnostic Diagrams

    NASA Astrophysics Data System (ADS)

    Proxauf, B.; Kimeswenger, S.; Öttl, S.

    2014-04-01

    Diagnostic diagrams of forbidden lines have been a useful tool for observers in astrophysics for many decades now. They are used to obtain information on the basic physical properties of thin gaseous nebulae. Moreover they are also the initial tool to derive thermodynamic properties of the plasma from observations to get ionization correction factors and thus to obtain proper abundances of the nebulae. Some diagnostic diagrams are in wavelengths domains which were difficult to take either due to missing wavelength coverage or low resolution of older spectrographs. Thus they were hardly used in the past. An upgrade of this useful tool is necessary because most of the diagrams were calculated using only the species involved as a single atom gas, although several are affected by well-known fluorescence mechanisms as well. Additionally the atomic data have improved up to the present time. The new diagnostic diagrams are calculated by using large grids of parameter space in the photoionization code CLOUDY. For a given basic parameter the input radiation field is varied to find the solutions with cooling-heating-equilibrium. Empirical numerical functions are fitted to provide formulas usable in e.g. data reduction pipelines. The resulting diagrams differ significantly from those used up to now and will improve the thermodynamic calculations.

  1. Diagnostics for Developing Countries.

    PubMed

    McNerney, Ruth

    2015-01-01

    Improving the availability of high quality diagnostic tests for infectious diseases is a global priority. Lack of access by people living in low income countries may deprive them of life saving treatment and reduces opportunities to prevent onward transmission and spread of the disease. Diagnostic laboratories are often poorly resourced in developing countries, and sparsely distributed. Improved access may be achieved by using tests that do not require laboratory support, including rapid tests for use at the point-of-care. Despite increased interest, few new in vitro diagnostic (IVD) products reach the majority populations in low income countries. Barriers to uptake include cost and lack of robustness, with reduced test performances due to environmental pressures such as high ambient temperatures or dust. In addition to environmental factors test developers must consider the local epidemiology. Confounding conditions such as immunosuppression or variations in antigen presentation or genotype can affect test performance. Barriers to product development include access to finance to establish manufacturing capacity and cover the costs of market entry for new devices. Costs and delays may be inflated by current regulatory preregistration processes to ensure product safety and quality, and more harmonized approaches are needed.

  2. ITER Diagnostic First Wal

    SciTech Connect

    G. Douglas Loesser, et. al.

    2012-09-21

    The ITER Diagnostic Division is responsible for designing and procuring the First Wall Blankets that are mounted on the vacuum vessel port plugs at both the upper and equatorial levels This paper will discuss the effects of the diagnostic aperture shape and configuration on the coolant circuit design. The DFW design is driven in large part by the need to conform the coolant arrangement to a wide variety of diagnostic apertures combined with the more severe heating conditions at the surface facing the plasma, the first wall. At the first wall, a radiant heat flux of 35W/cm2 combines with approximate peak volumetric heating rates of 8W/cm3 (equatorial ports) and 5W/cm3 (upper ports). Here at the FW, a fast thermal response is desirable and leads to a thin element between the heat flux and coolant. This requirement is opposed by the wish for a thicker FW element to accommodate surface erosion and other off-normal plasma events.

  3. Dosimetry in diagnostic radiology.

    PubMed

    Meghzifene, Ahmed; Dance, David R; McLean, Donald; Kramer, Hans-Michael

    2010-10-01

    Dosimetry is an area of increasing importance in diagnostic radiology. There is a realisation amongst health professionals that the radiation dose received by patients from modern X-ray examinations and procedures can be at a level of significance for the induction of cancer across a population, and in some unfortunate instances, in the acute damage to particular body organs such as skin and eyes. The formulation and measurement procedures for diagnostic radiology dosimetry have recently been standardised through an international code of practice which describes the methodologies necessary to address the diverging imaging modalities used in diagnostic radiology. Common to all dosimetry methodologies is the measurement of the air kerma from the X-ray device under defined conditions. To ensure the accuracy of the dosimetric determination, such measurements need to be made with appropriate instrumentation that has a calibration that is traceable to a standards laboratory. Dosimetric methods are used in radiology departments for a variety of purposes including the determination of patient dose levels to allow examinations to be optimized and to assist in decisions on the justification of examination choices. Patient dosimetry is important for special cases such as for X-ray examinations of children and pregnant patients. It is also a key component of the quality control of X-ray equipment and procedures. PMID:20655679

  4. [Acromegaly: reducing diagnostic delay].

    PubMed

    Giustina, Andrea

    2016-08-01

    Diagnostic delay of acromegaly is still very relevant (6-8 years on average) without substantial changes in last twenty years. Clinical impact of this diagnostic delay is significant: tumor growth (2/3 of the patients at diagnosis bear a pituitary macroadenoma), development of irreversible complications (arthropathy, sleep apnea) and in all increased mortality. Reasons for this delay are related to the disease itself (facial and acral changes are very slow and subtle) but also to medical unawareness. Simple tools based on a few sufficiently sensitive and specific signs and symptoms which can trigger the diagnostic suspect would be useful in clinical practice. Global evaluation during follow-up (tumor volume, signs and symptoms, complications, circulating levels of growth hormone and its peripheral mediator IGF-I) has become crucial for the therapeutic decision making. In this regard, tools like SAGIT are now under validation and are expected to improve management of acromegaly. In fact, in the last 30 years there has been a relevant growth of the medical options to treat acromegaly and in the near future there will be an expansion of the medical options. This will greatly help the needed personalization of treatment which necessarily should consider patient convenience and preference and control of complications such as diabetes mellitus. PMID:27571562

  5. Microsphere based saliva diagnostics

    NASA Astrophysics Data System (ADS)

    Rissin, David M.; DiCesare, Christopher; Hayman, Ryan B.; Blicharz, Timothy M.; Walt, David R.

    2005-11-01

    Saliva presents a minimally invasive alternative medium to blood for performing diagnostics1. Microsphere sensors for ions, small organic molecules, and proteins are currently being developed and optical microarrays containing thousands of these sensors will be used for simultaneous multi-analyte analysis. The fiber bundle platform in use is 1mm in diameter and contains approximately 50,000 individually addressable 3.1μm fibers, each with an etched well capable of housing a single 3.1μm microsphere sensor. Micron-sized bead-based chemistries are produced in house, followed by deposition onto a fiber-optic bundle platform, allowing for multiplexed analysis. The ultimate goal is to develop a universal diagnostic system using saliva as the diagnostic medium. This platform will permit multiplexed analysis of a sample by integrating microfluidics with the optical arrays loaded with sensors capable of detecting relevant biomarkers associated with a wide range of disease states. Disease states that are currently under investigation include end stage renal disease (ESRD) and Sjoegrens Syndrome (SS).

  6. Diagnostics for Developing Countries.

    PubMed

    McNerney, Ruth

    2015-01-01

    Improving the availability of high quality diagnostic tests for infectious diseases is a global priority. Lack of access by people living in low income countries may deprive them of life saving treatment and reduces opportunities to prevent onward transmission and spread of the disease. Diagnostic laboratories are often poorly resourced in developing countries, and sparsely distributed. Improved access may be achieved by using tests that do not require laboratory support, including rapid tests for use at the point-of-care. Despite increased interest, few new in vitro diagnostic (IVD) products reach the majority populations in low income countries. Barriers to uptake include cost and lack of robustness, with reduced test performances due to environmental pressures such as high ambient temperatures or dust. In addition to environmental factors test developers must consider the local epidemiology. Confounding conditions such as immunosuppression or variations in antigen presentation or genotype can affect test performance. Barriers to product development include access to finance to establish manufacturing capacity and cover the costs of market entry for new devices. Costs and delays may be inflated by current regulatory preregistration processes to ensure product safety and quality, and more harmonized approaches are needed. PMID:26854149

  7. Astigmatism and diagnostic procedures.

    PubMed

    Visnjić, Mirna Belovari; Zrinsćak, Ognjen; Barisić, Freja; Iveković, Renata; Laus, Katia Novak; Mandić, Zdravko

    2012-06-01

    Astigmatism represents an inability of the cornea and lens to provide a sharp image onto the retina. Correcting astigmatic errors, whether congenital, contact lens induced or surgically induced, is now an integral part of modern cataract and refractive procedures. Development of modern technology has enabled accurate diagnosis and perfect opportunities for correction; however, while cataract and keratorefractive surgery have come a long way in the last decade, the treatment and diagnosis of astigmatism continue to challenge ophthalmologists. There are several diagnostic procedures and tools available today, some standard and some contemporary that include keratometry, corneal topography, apparatus using wavefront or Scheimpflug analysis like Orbscan, Pentacam, Wavescan, etc. With the introduction of several new diagnostic tools, measurements of astigmatism have become less of an issue, but in some cases it is still difficult to obtain consistent results. What remains still unanswered is the question of the best diagnostic tool on the market. Further research is needed to evaluate both tools as well as their clinical application for optimal use. PMID:23115957

  8. Microgravity Combustion Diagnostics Workshop

    NASA Technical Reports Server (NTRS)

    Santoro, Gilbert J. (Editor); Greenberg, Paul S. (Editor); Piltch, Nancy D. (Editor)

    1988-01-01

    Through the Microgravity Science and Applications Division (MSAD) of the Office of Space Science and Applications (OSSA) at NASA Headquarters, a program entitled, Advanced Technology Development (ATD) was promulgated with the objective of providing advanced technologies that will enable the development of future microgravity science and applications experimental flight hardware. Among the ATD projects one, Microgravity Combustion Diagnostics (MCD), has the objective of developing advanced diagnostic techniques and technologies to provide nonperturbing measurements of combustion characteristics and parameters that will enhance the scientific integrity and quality of microgravity combustion experiments. As part of the approach to this project, a workshop was held on July 28 and 29, 1987, at the NASA Lewis Research Center. A small group of laser combustion diagnosticians met with a group of microgravity combustion experimenters to discuss the science requirements, the state-of-the-art of laser diagnostic technology, and plan the direction for near-, intermediate-, and long-term programs. This publication describes the proceedings of that workshop.

  9. Alpha Particle Diagnostic

    SciTech Connect

    Fisher, Ray, K.

    2009-05-13

    The study of burning plasmas is the next frontier in fusion energy research, and will be a major objective of the U.S. fusion program through U.S. collaboration with our international partners on the ITER Project. For DT magnetic fusion to be useful for energy production, it is essential that the energetic alpha particles produced by the fusion reactions be confined long enough to deposit a significant fraction of their initial ~3.5 MeV energy in the plasma before they are lost. Development of diagnostics to study the behavior of energetic confined alpha particles is a very important if not essential part of burning plasma research. Despite the clear need for these measurements, development of diagnostics to study confined the fast confined alphas to date has proven extremely difficult, and the available techniques remain for the most part unproven and with significant uncertainties. Research under this grant had the goal of developing diagnostics of fast confined alphas, primarily based on measurements of the neutron and ion tails resulting from alpha particle knock-on collisions with the plasma deuterium and tritium fuel ions. One of the strengths of this approach is the ability to measure the alphas in the hot plasma core where the interesting ignition physics will occur.

  10. Nuclear Diagnostics of ICF

    SciTech Connect

    Izumi, N; Ierche, R A; Moran, M J; Phillips, T W; Sangster, T C; Schmid, G J; Stoyer, M A; Disdier, L; Bourgade, J L; Rouyer, A; Fisher, R K; Gerggren, R R; Caldwen, S E; Faulkner, J R; Mack, J M; Oertel, J A; Young, C S; Glebov, V Y; Jaanimagi, P A; Meyerhofer, D D; Soures, J M; Stockel, C; Frenje, J A; Li, C K; Petrasso, R D

    2001-10-18

    In inertial confinement fusion (ICF), a high temperature and high density plasma is produced by the spherical implosion of a small capsule. A spherical target capsule is irradiated uniformly by a laser beam (direct irradiation) or x-rays from a high Z enclosure (hohlraum) that is irradiated by laser or ion beams (indirect irradiation). Then high-pressure ablation of the surface causes the fuel to be accelerated inward. Thermonuclear fusion reactions begin in the center region of the capsule as it is heated to sufficient temperature (10 keV) by the converging shocks (hot spot formation). During the stagnation of the imploded shell, the fuel in the shell region is compressed to high density ({approx} 10{sup 3} times solid density in fuel region). When these conditions are established, energy released by the initial nuclear reactions in center ''hot-spot'' region can heat up the cold ''fuel'' region and cause ignition. They are developing advanced nuclear diagnostics for imploding plasmas of the ignition campaign on the National Ignition Facility (NIF). The NIF is a 1.8MJ, 192-beam glass laser system that is under construction at Lawrence Livermore National Laboratory. One objective of the NIF is to demonstrate ignition and gain in an inertial confinement fusion plasma. Extreme physical conditions characterize the imploded plasmas on the NIF. First, the thickness of the plasma, expressed by areal density (plasma density times radius), is large, up to {approx} 1 g/cm{sup 2}. Highly penetrating probes such as energetic neutrons, hard x-rays, or {gamma} rays are required to see deep inside the plasma. Second, the implosion time is quite short. The implosion process takes {approx} 20 ns and the duration of the fusion reaction is on the order of 100 picoseconds. To observe the time history of the nuclear reactions, time resolution better than 10 ps is required. Third, the size of the imploded plasma is quite small ({approx} 100 {micro}m). To see the shape of burning region

  11. Diagnostic Assessment of Driver Problems: Volume 2. Assessment Techniques for Operational Users: Final Report.

    ERIC Educational Resources Information Center

    McBride, Robin S.; Stroad, Kenneth W., Jr.

    Volume 2 studies the operational feasibility of the diagnostic assessment of driver problems. Target groups for driver countermeasures are identified from research on diagnostic predictors and performance criteria. A diagnostic assessment model is presented which incorporates assessment techniques that were useful in an operational setting. The…

  12. Merits and Pitfalls of Currently Used Diagnostic Tools in Mycetoma

    PubMed Central

    van de Sande, Wendy W. J.; Fahal, Ahmed H.; Goodfellow, Michael; Mahgoub, El Sheikh; Welsh, Oliverio; Zijlstra, Ed E.

    2014-01-01

    Treatment of mycetoma depends on the causative organism and since many organisms, both actinomycetes (actinomycetoma) and fungi (eumycetoma), are capable of producing mycetoma, an accurate diagnosis is crucial. Currently, multiple diagnostic tools are used to determine the extent of infections and to identify the causative agents of mycetoma. These include various imaging, cytological, histopathological, serological, and culture techniques; phenotypic characterisation; and molecular diagnostics. In this review, we summarize these techniques and identify their merits and pitfalls in the identification of the causative agents of mycetoma and the extent of the disease. We also emphasize the fact that there is no ideal diagnostic tool available to identify the causative agents and that future research should focus on the development of new and reliable diagnostic tools. PMID:24992636

  13. Identification of factors associated with diagnostic error in primary care

    PubMed Central

    2014-01-01

    Background Missed, delayed or incorrect diagnoses are considered to be diagnostic errors. The aim of this paper is to describe the methodology of a study to analyse cognitive aspects of the process by which primary care (PC) physicians diagnose dyspnoea. It examines the possible links between the use of heuristics, suboptimal cognitive acts and diagnostic errors, using Reason’s taxonomy of human error (slips, lapses, mistakes and violations). The influence of situational factors (professional experience, perceived overwork and fatigue) is also analysed. Methods Cohort study of new episodes of dyspnoea in patients receiving care from family physicians and residents at PC centres in Granada (Spain). With an initial expected diagnostic error rate of 20%, and a sampling error of 3%, 384 episodes of dyspnoea are calculated to be required. In addition to filling out the electronic medical record of the patients attended, each physician fills out 2 specially designed questionnaires about the diagnostic process performed in each case of dyspnoea. The first questionnaire includes questions on the physician’s initial diagnostic impression, the 3 most likely diagnoses (in order of likelihood), and the diagnosis reached after the initial medical history and physical examination. It also includes items on the physicians’ perceived overwork and fatigue during patient care. The second questionnaire records the confirmed diagnosis once it is reached. The complete diagnostic process is peer-reviewed to identify and classify the diagnostic errors. The possible use of heuristics of representativeness, availability, and anchoring and adjustment in each diagnostic process is also analysed. Each audit is reviewed with the physician responsible for the diagnostic process. Finally, logistic regression models are used to determine if there are differences in the diagnostic error variables based on the heuristics identified. Discussion This work sets out a new approach to studying the

  14. Universal microbial diagnostics using random DNA probes

    PubMed Central

    Aghazadeh, Amirali; Lin, Adam Y.; Sheikh, Mona A.; Chen, Allen L.; Atkins, Lisa M.; Johnson, Coreen L.; Petrosino, Joseph F.; Drezek, Rebekah A.; Baraniuk, Richard G.

    2016-01-01

    Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal microbial diagnostics (UMD) platform to screen for microbial organisms in an infectious sample, using a small number of random DNA probes that are agnostic to the target DNA sequences. Our platform leverages the theory of sparse signal recovery (compressive sensing) to identify the composition of a microbial sample that potentially contains novel or mutant species. We validated the UMD platform in vitro using five random probes to recover 11 pathogenic bacteria. We further demonstrated in silico that UMD can be generalized to screen for common human pathogens in different taxonomy levels. UMD’s unorthodox sensing approach opens the door to more efficient and universal molecular diagnostics. PMID:27704040

  15. Planetary Transmission Diagnostics

    NASA Technical Reports Server (NTRS)

    Lewicki, David G. (Technical Monitor); Samuel, Paul D.; Conroy, Joseph K.; Pines, Darryll J.

    2004-01-01

    This report presents a methodology for detecting and diagnosing gear faults in the planetary stage of a helicopter transmission. This diagnostic technique is based on the constrained adaptive lifting algorithm. The lifting scheme, developed by Wim Sweldens of Bell Labs, is a time domain, prediction-error realization of the wavelet transform that allows for greater flexibility in the construction of wavelet bases. Classic lifting analyzes a given signal using wavelets derived from a single fundamental basis function. A number of researchers have proposed techniques for adding adaptivity to the lifting scheme, allowing the transform to choose from a set of fundamental bases the basis that best fits the signal. This characteristic is desirable for gear diagnostics as it allows the technique to tailor itself to a specific transmission by selecting a set of wavelets that best represent vibration signals obtained while the gearbox is operating under healthy-state conditions. However, constraints on certain basis characteristics are necessary to enhance the detection of local wave-form changes caused by certain types of gear damage. The proposed methodology analyzes individual tooth-mesh waveforms from a healthy-state gearbox vibration signal that was generated using the vibration separation (synchronous signal-averaging) algorithm. Each waveform is separated into analysis domains using zeros of its slope and curvature. The bases selected in each analysis domain are chosen to minimize the prediction error, and constrained to have the same-sign local slope and curvature as the original signal. The resulting set of bases is used to analyze future-state vibration signals and the lifting prediction error is inspected. The constraints allow the transform to effectively adapt to global amplitude changes, yielding small prediction errors. However, local wave-form changes associated with certain types of gear damage are poorly adapted, causing a significant change in the

  16. FASTBUS Snoop Diagnostic Module

    SciTech Connect

    Walz, H.V.; Downing, R.

    1980-11-01

    Development of the FASTBUS Snoop Module, undertaken as part of the prototype program for the new interlaboratory data bus standard, is described. The Snoop Module resides on a FASTBUS crate segment and provides diagnostic monitoring and testing capability. Communication with a remote host computer is handled independent of FASTBUS through a serial link. The module consists of a high-speed ECL front-end to monitor and single-step FASTBUS cycles, a master-slave interface, and a control microprocessor with serial communication ports. Design details and performance specifications of the prototype module are reported. 9 figures, 1 table.

  17. Diagnostics for hybrid reactors

    SciTech Connect

    Orsitto, Francesco Paolo

    2012-06-19

    The Hybrid Reactor(HR) can be considered an attractive actinide-burner or a fusion assisted transmutation for destruction of transuranic(TRU) nuclear waste. The hybrid reactor has two important subsystems: the tokamak neutron source and the blanket which includes a fuel zone where the TRU are placed and a tritium breeding zone. The diagnostic system for a HR must be as simple and robust as possible to monitor and control the plasma scenario, guarantee the protection of the machine and monitor the transmutation.

  18. Current developments in salivary diagnostics

    PubMed Central

    Foley, Joseph D; Bailey, Alison L; Campell, Charles L; Humphries, Roger L; Christodoulides, Nicolaos; Floriano, Pierre N; Simmons, Glennon; Bhagwandin, Bryon; Jacobson, James W; Redding, Spencer W; Ebersole, Jeffrey L; McDevitt, John T

    2010-01-01

    Salivary diagnostics is an emerging field that has progressed through several important developments in the past decade, including the publication of the human salivary proteome and the infusion of federal funds to integrate nanotechnologies and microfluidic engineering concepts into developing compact point-of-care devices for rapid analysis of this secretion. In this article, we discuss some of these developments and their relevance to the prognosis, diagnosis and management of periodontitis, as an oral target, and cardiovascular disease, as a systemic example for the potential of these biodiagnostics. Our findings suggest that several biomarkers are associated with distinct biological stages of these diseases and demonstrate promise as practical biomarkers in identifying and managing periodontal disease, and acute myocardial infarction. The majority of these studies have progressed through biomarker discovery, with the identified molecules requiring more robust clinical studies to enable substantive validation for disease diagnosis. It is predicted that with continued advances in this field the use of a combination of biomarkers in multiplex panels is likely to yield accurate screening tools for these diagnoses in the near future. PMID:20387312

  19. Instrumentation and diagnostics

    SciTech Connect

    Nakaishi, C.V.; Bedick, R.C.

    1990-12-01

    This Technology Status Report describes research and accomplishments for the Instrumentation and Diagnostics (I D) Projects within the Advanced Research and Technology Development (AR TD) Program of the United States Department of Energy (DOE) Office of Fossil Energy (FE). Process understanding and control can be improved through the development of advanced instrumentation and diagnostics. The thrust of the I D Projects is to further develop existing measurement and control techniques for application to advanced coal-based technologies. Project highlights are: an inductively coupled plasma (ICP) instrument has been developed to analyze trace elements in gasification and combustion process streams. An in situ two-color Mie scattering technique with LSS can simultaneously measure the size, velocity, and elemental composition of coal particles during combustion. A high-temperature, fluorescence thermometry technique has accurately measured gas temperatures during field testing in combustion and gasification environments. Expert systems have been developed to improve the control of advanced coal-based processes. Capacitance flowmeters were developed to determine the mass flowrate, solid volume fraction, and particle velocities of coal slurries. 32 refs., 9 figs.

  20. Molecular diagnostics in tuberculosis.

    PubMed

    Cheng, V C C; Yew, W W; Yuen, K Y

    2005-11-01

    Molecular diagnostics in tuberculosis has enabled rapid detection of Mycobacterium tuberculosis complex in clinical specimens, identification of mycobacterial species, detection of drug resistance, and typing for epidemiological investigation. In the laboratory diagnosis of tuberculosis, the nucleic acid amplification (NAA) test is rapid and specific but not as sensitive as culture of mycobacteria. The primary determinant of successful NAA testing for tuberculosis depends on the shedding of mycobacterial DNA in secretions from caseating granulomas and its dissemination into sterile body fluids or tissue biopsies. In multibacillary diseases with a high mycobacterial load, a positive Ziehl-Neelsen smear with a positive NAA test is diagnostic of active tuberculosis, whereas a positive Ziehl-Neelsen smear with a negative NAA test in the absence of inhibitors would indicate nontuberculous mycobacterial disease. The role of the NAA test is more important in paucibacillary diseases with low mycobacterial loads. The presence of polymerase chain reaction (PCR) inhibitors, however, especially in extrapulmonary specimens, may produce false-negative results. Although this problem can be overcome to some extent by extra extraction steps, the additional processing invariably leads to the loss of mycobacterial DNA. To circumvent this problem, a brief culture augmentation step is carried out before the NAA test is performed, which can enhance the mycobacterial load while concomitantly diluting inhibitors, thereby maintaining the sensitivity of the test without excessively increasing turnaround time.

  1. Radiation hardening of diagnostics

    SciTech Connect

    Siemon, R.E.

    1991-01-01

    The world fusion program has advanced to the stage where it is appropriate to construct a number of devices for the purpose of burning DT fuel. In these next-generation experiments, the expected flux and fluence of 14 MeV neutrons and associated gamma rays will pose a significant challenge to the operation and diagnostics of the fusion device. Radiation effects include structural damage to materials such as vacuum windows and seals, modifications to electrical properties such as electrical conductivity and dielectric strength and impaired optical properties such as reduced transparency and luminescence of windows and fiber optics during irradiation. In preparation for construction and operation of these new facilities, the fusion diagnostics community needs to work with materials scientists to develop a better understanding of radiation effects, and to undertake a testing program aimed at developing workable solutions for this multi-faceted problem. A unique facility to help in this regard is the Los Alamos Spallation Radiation Effects Facility, a neutron source located at the beam stop of the world's most powerful accelerator, the Los Alamos Meson Physics Facility (LAMPF). The LAMPF proton beam generates 10{sup 16} neutrons per second because of spallation'' reactions when the protons collide with the copper nuclei in the beam stop.

  2. Diagnostic Technologies in Practice

    PubMed Central

    Steinberg, Malcolm; Kwag, Michael; Chown, Sarah A.; Doupe, Glenn; Trussler, Terry; Rekart, Michael; Gilbert, Mark

    2015-01-01

    Diagnosing HIV-positive gay men through enhanced testing technologies that detect acute HIV infection (AHI) or recent HIV infection provides opportunities for individual and population health benefits. We recruited 25 men in British Columbia who received an acute (n = 13) or recent (n = 12) HIV diagnosis to engage in a longitudinal multiple-methods study over one year or longer. Our thematic analysis of baseline qualitative interviews revealed insights within men’s accounts of technologically mediated processes of HIV discovery and diagnosis. Our analysis illuminated the dialectic of new HIV technologies in practice by considering the relationship between advances in diagnostics (e.g., nucleic acid amplification tests) and the users of these medical technologies in clinical settings (e.g., clients and practitioners). Technological innovations and testing protocols have shifted experiences of learning of one’s HIV-positive status; these innovations have created new diagnostic categories that require successful interpretation and translation to be rendered meaningful, to alleviate uncertainty, and to support public health objectives. PMID:25201583

  3. NIO1 diagnostics

    SciTech Connect

    Zaniol, B. Barbisan, M.; Pasqualotto, R.; Serianni, G.; Cavenago, M.; De Muri, M.; Mimo, A.

    2015-04-08

    The radio frequency ion source NIO1, jointly developed by Consorzio RFX and INFN-LNL, will generate a 60kV-135mA hydrogen negative ion beam, composed of 9 beamlets over an area of about 40 × 40 mm{sup 2}. This experiment will operate in continuous mode and in conditions similar to those foreseen for the larger ion sources of the Neutral Beam Injectors for ITER. The modular design of NIO1 is convenient to address the several still open important issues related to beam extraction, optics, and performance optimization. To this purpose a set of diagnostics is being implemented. Electric and water cooling plant related measurements will allow monitoring current, pressure, flow, and temperature. The plasma in the source will be characterized by emission spectroscopy, cavity ring-down and laser absorption spectroscopy. The accelerated beam will be analyzed with a fast emittance scanner, its intensity profile and divergence with beam emission spectroscopy and visible tomography. The power distribution of the beam on the calorimeter will be monitored by thermocouples and by an infrared camera. This contribution presents the implementation and initial operation of some of these diagnostics in the commissioning phase of the experiment, in particular the cooling water calorimetry and emission spectroscopy.

  4. [Hemophagocytic syndrome: diagnostic problems].

    PubMed

    Czogała, Małgorzata; Czogała, Wojciech; Balwierz, Walentyna

    2006-01-01

    Hemophagocytic syndrome (HS) is a rare but life-threatening disease caused by inappropriate activation of T-lymphocytes and histiocytes, hipercytokinemia and hemophagocytosis. The most common symptoms are fever, hepatosplenomegaly, unspecific neurological abnormalities, pancytopenia, coagulopathy, hiperferritinemia and lipid abnormalities. HS is classified into two forms: primary, inherited (Familial Hamophagocytic Lymphohistiocytosis--FHL) and secondary (associated with infection, malignancy, autoimmune disease). In spite of the fact that diagnostic guidelines are available it often remains unrecognised. Prognosis of HS depends on the form of disease and in case of secondary HS on the underlying disease. Development of the treatment protocols (HLH-94, HLH-2004) which combine immunochemiotherapy with hematopoietic stem cell transplantation has strongly improved prognosis in HS especially in the primary form. Three-year overall survival for children with HS is now over 50%. Early diagnosis and appropriate therapy is crucial for effectiveness of the treatment. Popularisation of the knowledge about the syndrome, diagnostic guidelines and treatment protocols can contribute to more frequent appropriate recognition of HS and to improvement of the treatment results. PMID:16892901

  5. Aircraft Engine Gas Path Diagnostic Methods: Public Benchmarking Results

    NASA Technical Reports Server (NTRS)

    Simon, Donald L.; Borguet, Sebastien; Leonard, Olivier; Zhang, Xiaodong (Frank)

    2013-01-01

    Recent technology reviews have identified the need for objective assessments of aircraft engine health management (EHM) technologies. To help address this issue, a gas path diagnostic benchmark problem has been created and made publicly available. This software tool, referred to as the Propulsion Diagnostic Method Evaluation Strategy (ProDiMES), has been constructed based on feedback provided by the aircraft EHM community. It provides a standard benchmark problem enabling users to develop, evaluate and compare diagnostic methods. This paper will present an overview of ProDiMES along with a description of four gas path diagnostic methods developed and applied to the problem. These methods, which include analytical and empirical diagnostic techniques, will be described and associated blind-test-case metric results will be presented and compared. Lessons learned along with recommendations for improving the public benchmarking processes will also be presented and discussed.

  6. Boosting medical diagnostics by pooling independent judgments

    PubMed Central

    Kurvers, Ralf H. J. M.; Herzog, Stefan M.; Hertwig, Ralph; Krause, Jens; Carney, Patricia A.; Bogart, Andy; Argenziano, Giuseppe; Zalaudek, Iris; Wolf, Max

    2016-01-01

    Collective intelligence refers to the ability of groups to outperform individual decision makers when solving complex cognitive problems. Despite its potential to revolutionize decision making in a wide range of domains, including medical, economic, and political decision making, at present, little is known about the conditions underlying collective intelligence in real-world contexts. We here focus on two key areas of medical diagnostics, breast and skin cancer detection. Using a simulation study that draws on large real-world datasets, involving more than 140 doctors making more than 20,000 diagnoses, we investigate when combining the independent judgments of multiple doctors outperforms the best doctor in a group. We find that similarity in diagnostic accuracy is a key condition for collective intelligence: Aggregating the independent judgments of doctors outperforms the best doctor in a group whenever the diagnostic accuracy of doctors is relatively similar, but not when doctors’ diagnostic accuracy differs too much. This intriguingly simple result is highly robust and holds across different group sizes, performance levels of the best doctor, and collective intelligence rules. The enabling role of similarity, in turn, is explained by its systematic effects on the number of correct and incorrect decisions of the best doctor that are overruled by the collective. By identifying a key factor underlying collective intelligence in two important real-world contexts, our findings pave the way for innovative and more effective approaches to complex real-world decision making, and to the scientific analyses of those approaches. PMID:27432950

  7. Boosting medical diagnostics by pooling independent judgments.

    PubMed

    Kurvers, Ralf H J M; Herzog, Stefan M; Hertwig, Ralph; Krause, Jens; Carney, Patricia A; Bogart, Andy; Argenziano, Giuseppe; Zalaudek, Iris; Wolf, Max

    2016-08-01

    Collective intelligence refers to the ability of groups to outperform individual decision makers when solving complex cognitive problems. Despite its potential to revolutionize decision making in a wide range of domains, including medical, economic, and political decision making, at present, little is known about the conditions underlying collective intelligence in real-world contexts. We here focus on two key areas of medical diagnostics, breast and skin cancer detection. Using a simulation study that draws on large real-world datasets, involving more than 140 doctors making more than 20,000 diagnoses, we investigate when combining the independent judgments of multiple doctors outperforms the best doctor in a group. We find that similarity in diagnostic accuracy is a key condition for collective intelligence: Aggregating the independent judgments of doctors outperforms the best doctor in a group whenever the diagnostic accuracy of doctors is relatively similar, but not when doctors' diagnostic accuracy differs too much. This intriguingly simple result is highly robust and holds across different group sizes, performance levels of the best doctor, and collective intelligence rules. The enabling role of similarity, in turn, is explained by its systematic effects on the number of correct and incorrect decisions of the best doctor that are overruled by the collective. By identifying a key factor underlying collective intelligence in two important real-world contexts, our findings pave the way for innovative and more effective approaches to complex real-world decision making, and to the scientific analyses of those approaches.

  8. Boosting medical diagnostics by pooling independent judgments.

    PubMed

    Kurvers, Ralf H J M; Herzog, Stefan M; Hertwig, Ralph; Krause, Jens; Carney, Patricia A; Bogart, Andy; Argenziano, Giuseppe; Zalaudek, Iris; Wolf, Max

    2016-08-01

    Collective intelligence refers to the ability of groups to outperform individual decision makers when solving complex cognitive problems. Despite its potential to revolutionize decision making in a wide range of domains, including medical, economic, and political decision making, at present, little is known about the conditions underlying collective intelligence in real-world contexts. We here focus on two key areas of medical diagnostics, breast and skin cancer detection. Using a simulation study that draws on large real-world datasets, involving more than 140 doctors making more than 20,000 diagnoses, we investigate when combining the independent judgments of multiple doctors outperforms the best doctor in a group. We find that similarity in diagnostic accuracy is a key condition for collective intelligence: Aggregating the independent judgments of doctors outperforms the best doctor in a group whenever the diagnostic accuracy of doctors is relatively similar, but not when doctors' diagnostic accuracy differs too much. This intriguingly simple result is highly robust and holds across different group sizes, performance levels of the best doctor, and collective intelligence rules. The enabling role of similarity, in turn, is explained by its systematic effects on the number of correct and incorrect decisions of the best doctor that are overruled by the collective. By identifying a key factor underlying collective intelligence in two important real-world contexts, our findings pave the way for innovative and more effective approaches to complex real-world decision making, and to the scientific analyses of those approaches. PMID:27432950

  9. PCR-based diagnostics for anaerobic infections.

    PubMed

    Song, Yuli

    2005-01-01

    Conventional methods to identify anaerobic bacteria have often relied on unique clinical findings, isolation of organisms, and laboratory identification by morphology and biochemical tests (phenotypic tests). Although these methods are still fundamental, there is an increasing move toward molecular diagnostics of anaerobes. In this review, some of the molecular approaches to anaerobic diagnostics based on the polymerase chain reaction (PCR) are discussed. This includes several technological advances in PCR-based methods for the detection, identification, and quantitation of anaerobes including real-time PCR which has been successfully used to provide rapid, quantitative data on anaerobic species on clinical samples. Since its introduction in the mid-1980s, PCR has provided many molecular diagnostic tools, some of which are discussed within this review. With the advances in micro-array technology and real-time PCR methods, the future is bright for the development of accurate, quantitative diagnostic tools that can provide information not only on individual anaerobic species but also on whole communities.

  10. Fungal molecular diagnostics: a mini review.

    PubMed

    Atkins, Simon D; Clark, Ian M

    2004-01-01

    Conventional methods to identify fungi have often relied on identification of disease symptoms, isolation and culturing of environmental organisms, and laboratory identification by morphology and biochemical tests. Although these methods are still fundamental there is an increasing move towards molecular diagnostics of fungi in all fields. In this review, some of the molecular approaches to fungal diagnostics based on polymerase chain reaction (PCR) and DNA/RNA probe technology are discussed. This includes several technological advances in PCR-based methods for the detection, identification and quantification of fungi including real-time PCR which has been successfully used to provide rapid, quantitative data on fungal species from environmental samples. PCR and probe based methods have provided new tools for the enumeration of fungal species, but it is still necessary to combine the new technology with more conventional methods to gain a fuller understanding of interactions occurring in the environment. Since its introduction in the mid 1980's PCR has provided many molecular diagnostic tools, some of which are discussed within this review, and with the advances in micro-array technology and real-time PCR methods the future is bright for the development of accurate, quantitative diagnostic tools that can provide information not only on individual fungal species but also on whole communities.

  11. Region of interest identification and diagnostic agreement in breast pathology.

    PubMed

    Nagarkar, Dilip B; Mercan, Ezgi; Weaver, Donald L; Brunyé, Tad T; Carney, Patricia A; Rendi, Mara H; Beck, Andrew H; Frederick, Paul D; Shapiro, Linda G; Elmore, Joann G

    2016-09-01

    A pathologist's accurate interpretation relies on identifying relevant histopathological features. Little is known about the precise relationship between feature identification and diagnostic decision making. We hypothesized that greater overlap between a pathologist's selected diagnostic region of interest (ROI) and a consensus derived ROI is associated with higher diagnostic accuracy. We developed breast biopsy test cases that included atypical ductal hyperplasia (n=80); ductal carcinoma in situ (n=78); and invasive breast cancer (n=22). Benign cases were excluded due to the absence of specific abnormalities. Three experienced breast pathologists conducted an independent review of the 180 digital whole slide images, established a reference consensus diagnosis and marked one or more diagnostic ROIs for each case. Forty-four participating pathologists independently diagnosed and marked ROIs on the images. Participant diagnoses and ROI were compared with consensus reference diagnoses and ROI. Regression models tested whether percent overlap between participant ROI and consensus reference ROI predicted diagnostic accuracy. Each of the 44 participants interpreted 39-50 cases for a total of 1972 individual diagnoses. Percent ROI overlap with the expert reference ROI was higher in pathologists who self-reported academic affiliation (69 vs 65%, P=0.002). Percent overlap between participants' ROI and consensus reference ROI was then classified into ordinal categories: 0, 1-33, 34-65, 66-99 and 100% overlap. For each incremental change in the ordinal percent ROI overlap, diagnostic agreement increased by 60% (OR 1.6, 95% CI (1.5-1.7), P<0.001) and the association remained significant even after adjustment for other covariates. The magnitude of the association between ROI overlap and diagnostic agreement increased with increasing diagnostic severity. The findings indicate that pathologists are more likely to converge with an expert reference diagnosis when they identify an

  12. Diagnostics and Microelectronics

    SciTech Connect

    Balch, J.W.

    1993-03-01

    This report discusses activities of the Diagnostics and Microelectronics thrust area which conducts activities in semiconductor devices and semiconductor fabrication technology for programs at Lawrence Livermore National Laboratory. Our multidisciplinary engineering and scientific staff use modern computational tools and semi-conductor microfabrication equipment to develop high-performance devices. Our work concentrates on three broad technologies of semiconductor microdevices: (1) silicon on III-V semiconductor microeletronics, (2) lithium niobate-based and III-V semiconductor-based photonics, and (3) silicon-based micromaching for application to microstructures and microinstruments. In FY-92, we worked on projects in seven areas, described in this report: novel photonic detectors; a wideband phase modulator; an optoelectronic terahertz beam system; the fabrication of microelectrode electrochemical sensors; diamond heatsinks; advanced micromachining technologies; and electrophoresis using silicon microchannels.

  13. Diagnostic evaluation of rhabdomyolysis.

    PubMed

    Nance, Jessica R; Mammen, Andrew L

    2015-06-01

    Rhabdomyolysis is characterized by severe acute muscle injury resulting in muscle pain, weakness, and/or swelling with release of myofiber contents into the bloodstream. Symptoms develop over hours to days after an inciting factor and may be associated with dark pigmentation of the urine. Serum creatine kinase and urine myoglobin levels are markedly elevated. Clinical examination, history, laboratory studies, muscle biopsy, and genetic testing are useful tools for diagnosis of rhabdomyolysis, and they can help differentiate acquired from inherited causes of rhabdomyolysis. Acquired causes include substance abuse, medication or toxic exposures, electrolyte abnormalities, endocrine disturbances, and autoimmune myopathies. Inherited predisposition to rhabdomyolysis can occur with disorders of glycogen metabolism, fatty acid β-oxidation, and mitochondrial oxidative phosphorylation. Less common inherited causes of rhabdomyolysis include structural myopathies, channelopathies, and sickle-cell disease. This review focuses on the differentiation of acquired and inherited causes of rhabdomyolysis and proposes a practical diagnostic algorithm. Muscle Nerve 51: 793-810, 2015. PMID:25678154

  14. Rig Diagnostic Tools

    NASA Technical Reports Server (NTRS)

    Soileau, Kerry M.; Baicy, John W.

    2008-01-01

    Rig Diagnostic Tools is a suite of applications designed to allow an operator to monitor the status and health of complex networked systems using a unique interface between Java applications and UNIX scripts. The suite consists of Java applications, C scripts, Vx- Works applications, UNIX utilities, C programs, and configuration files. The UNIX scripts retrieve data from the system and write them to a certain set of files. The Java side monitors these files and presents the data in user-friendly formats for operators to use in making troubleshooting decisions. This design allows for rapid prototyping and expansion of higher-level displays without affecting the basic data-gathering applications. The suite is designed to be extensible, with the ability to add new system components in building block fashion without affecting existing system applications. This allows for monitoring of complex systems for which unplanned shutdown time comes at a prohibitive cost.

  15. Peritoneal tuberculosis: diagnostic options.

    PubMed Central

    Lal, N; Soto-Wright, V

    1999-01-01

    BACKGROUND: Extrapulmonary tuberculosis has vague symptoms and few signs. It is essential to recognize and diagnose this curable disease prior to performing definitive surgery. Newer tests such as DNA or RNA amplification allow for early diagnosis but have limitations. CASE: We report a case of peritoneal tuberculosis in an immigrant woman. She had vague symptoms of low-grade fever, mild abdominal pain, obstipation, and bloating. Diagnostic laparoscopy was performed to establish the diagnosis. Tuberculosis was confirmed by DNA extraction from the frozen section specimen with subsequent analysis using polymerase chain reaction. CONCLUSION: Peritoneal tuberculosis is a disease that often simulates malignancies. With the increasing prevalence of human immunodeficiency virus in developed countries, tuberculosis is also on the rise and should be considered in the differential diagnosis of a patient with an abdominal/pelvic mass and ascites. PMID:10524670

  16. Diagnostic Evaluation of Rhabdomyolysis

    PubMed Central

    Nance, Jessica R.; Mammen, Andrew L.

    2015-01-01

    Rhabdomyolysis is characterized by severe acute muscle injury resulting in muscle pain, weakness, and/or swelling with release of myofiber contents into the bloodstream. Symptoms develop over hours to days following an inciting factor and may be associated with dark pigmentation of the urine. Serum creatine kinase and urine myoglobin levels are markedly elevated. The clinical examination, history, laboratory studies, muscle biopsy, and genetic testing are useful tools for diagnosis of rhabdomyolysis, and they can help differentiate acquired from inherited causes of rhabdomyolysis. Acquired causes include substance abuse, medication or toxic exposures, electrolyte abnormalities, endocrine disturbance, and autoimmune myopathies. Inherited predisposition to rhabdomyolysis can occur with disorders of glycogen metabolism, fatty acid beta-oxidation, and mitochondrial oxidative phosphorylation. Less common inherited causes of rhabdomyolysis include structural myopathies, channelopathies, and sickle cell disease. This review focuses on the differentiation of acquired and inherited causes of rhabdomyolysis and proposes a practical diagnostic algorithm. PMID:25678154

  17. Balloon gondola diagnostics package

    NASA Technical Reports Server (NTRS)

    Cantor, K. M.

    1986-01-01

    In order to define a new gondola structural specification and to quantify the balloon termination environment, NASA developed a balloon gondola diagnostics package (GDP). This addition to the balloon flight train is comprised of a large array of electronic sensors employed to define the forces and accelerations imposed on a gondola during the termination event. These sensors include the following: a load cell, a three-axis accelerometer, two three-axis rate gyros, two magnetometers, and a two axis inclinometer. A transceiver couple allows the data to be telemetered across any in-line rotator to the gondola-mounted memory system. The GDP is commanded 'ON' just prior to parachute deployment in order to record the entire event.

  18. Diagnostic and vaccine chapter.

    PubMed

    Wolfram, J H; Kokanov, S K; Verkhovsky, O A

    2010-10-01

    The first report in this chapter describes the development of a killed composite vaccine. This killed vaccine is non-infectious to humans, other animals, and the environment. The vaccine has low reactivity, is non-abortive, and does not induce pathomorphological alterations to the organs of vaccinated animals. The second report of this chapter describes the diagnostic value of a competitive enzyme-linked immunosorbent assay for detecting Brucella-specific antibodies and its ability to discriminate vaccinated cattle from infected cattle. The results indicated that the competitive enzyme-linked immunosorbent assay is more sensitive than traditional tests for detecting antibodies to Brucella abortus in naturally and experimentally infected cattle. PMID:20850688

  19. Diagnostic and forensic toxicology.

    PubMed

    Galey, F D

    1995-12-01

    In most competent veterinary diagnostic laboratories, analytical findings are interpreted by the veterinary toxicologist to determine the significance of the finding in view of historic, clinical, and pathologic findings. A veterinary toxicologist also will provide consultation about possible toxic rule-outs for a case, treatment of affected animals, and prevention of additional cases. Once all of the information is available, a complete summary of the findings can be provided to the client. When the procedures outlined are followed, including a systematic approach to collecting all the evidence (historic, clinical, pathologic, and analytic), proper sampling techniques, and good communication between the clinician and the client and laboratory, the usefulness of the toxicology investigation will be maximized.

  20. Oral vs. salivary diagnostics

    NASA Astrophysics Data System (ADS)

    Marques, Joana; Corby, Patricia M.; Barber, Cheryl A.; Abrams, William R.; Malamud, Daniel

    2015-05-01

    The field of "salivary diagnostics" includes studies utilizing samples obtained from a variety of sources within the oral cavity. These samples include; whole unstimulated saliva, stimulated whole saliva, duct saliva collected directly from the parotid, submandibular/sublingual glands or minor salivary glands, swabs of the buccal mucosa, tongue or tonsils, and gingival crevicular fluid. Many publications state "we collected saliva from subjects" without fully describing the process or source of the oral fluid. Factors that need to be documented in any study include the time of day of the collection, the method used to stimulate and collect the fluid, and how much fluid is being collected and for how long. The handling of the oral fluid during and post-collection is also critical and may include addition of protease or nuclease inhibitors, centrifugation, and cold or frozen storage prior to assay. In an effort to create a standard protocol for determining a biomarker's origin we carried out a pilot study collecting oral fluid from 5 different sites in the mouth and monitoring the concentrations of pro- and anti-inflammatory cytokines detected using MesoScaleDiscovery (MSD) electrochemiluminesence assays. Our data suggested that 3 of the cytokines are primarily derived from the submandibular gland, while 7 of the cytokines come from a source other than the major salivary glands such as the minor salivary glands or cells in the oral mucosae. Here we review the literature on monitoring biomarkers in oral samples and stress the need for determining the blood/saliva ratio when a quantitative determination is needed and suggest that the term oral diagnostic be used if the source of an analyte in the oral cavity is unknown.

  1. Optical Diagnostics in Medicine

    NASA Astrophysics Data System (ADS)

    Iftimia, Nicusor

    2003-03-01

    Light has a unique potential for non-invasive tissue diagnosis. The relatively short wavelength of light allows imaging of tissue at the resolution of histopathology. While strong multiple scattering of light in tissue makes attainment of this resolution difficult for thick tissues, most pathology emanates from epithelial surfaces. Therefore, high-resolution diagnosis of many important diseases may be achieved by transmitting light to the surface of interest. The recent fiber-optic implementation of technologies that reject multiple scattering, such as confocal microscopy and optical low coherence interferometry, have brought us one step closer to realizing non-invasive imaging of architectural and cellular features of tissue. Optical coherence tomography (OCT) can produce high-resolution cross-sectional images of biological structures. Clinical OCT studies conducted in the gastrointestinal tract and cardiovascular system have shown that OCT is capable of providing images of the architectural (> 20 µm) microanatomy of a variety of epithelial tissues, including the layered structure of squamous epithelium and arterial vessels. Fine Needle Aspiration- Low Coherence Interferometry (FNA-LCI) is another optical diagnostics technique, which is a suitable solution to increase the effectiveness of the FNA procedures. LCI is capable of measuring depth resolved (axial, z) tissue structure, birefringence, flow (Doppler shift), and spectra at a resolution of several microns. Since LCI systems are fiber-optic based, LCI probes may easily fit within the bore of a fine gauge needle, allowing diagnostic information to be obtained directly from the FNA biopsy site. Fiber optic spectrally encoded confocal microscopy (SECM) is a new confocal microscopy method, which eliminates the need for rapid beam scanning within the optical probe. This advance enables confocal microscopy to be performed through small diameter probes and will allow assessment of internal human tissues in vivo at

  2. Chronic pancreatitis: A diagnostic dilemma

    PubMed Central

    Duggan, Sinead N; Ní Chonchubhair, Hazel M; Lawal, Oladapo; O’Connor, Donal B; Conlon, Kevin C

    2016-01-01

    Typical clinical symptoms of chronic pancreatitis are vague and non-specific and therefore diagnostic tests are required, none of which provide absolute diagnostic certainly, especially in the early stages of disease. Recently-published guidelines bring much needed structure to the diagnostic work-up of patients with suspected chronic pancreatitis. In addition, novel diagnostic modalities bring promise for the future. The assessment and diagnosis of pancreatic exocrine insufficiency remains challenging and this review contests the accepted perspective that steatorrhea only occurs with > 90% destruction of the gland. PMID:26900292

  3. Progress on US ITER Diagnostics

    NASA Astrophysics Data System (ADS)

    Johnson, David; Feder, Russ

    2010-11-01

    There have been significant advances in the design concepts for the 8 ITER diagnostic systems being provided by the US. Concepts for integration of the diagnostics into the port plugs have also evolved. A prerequisite for the signoff of the procurement arrangements for these each diagnostic is a Conceptual Design Review organized by the ITER Organization. US experts under contract with the USIPO have been assisting the IO to prepare for these Reviews. In addition, a design team at PPPL has been working with these experts and designers from other ITER parties to package diagnostic front-ends into the 5 US plugs. Modular diagnostic shield modules are now being considered in order to simplify the interfaces between the diagnostics within each plug. Diagnostic first wall elements are envisioned to be integral with these shield modules. This simplifies the remote handling of the diagnostics and provides flexibility for future removal of one diagnostic minimally affecting others. Front-end configurations will be presented, along with lists of issues needing resolution prior to the start of preliminary design.

  4. Diagnostics development plan for ZR.

    SciTech Connect

    Hanson, David Lester

    2003-09-01

    The Z Refurbishment (ZR) Project is a program to upgrade the Z machine at SNL with modern durable pulsed power technology, providing additional shot capacity and improved reliability as well as advanced capabilities for both pulsed x-ray production and high pressure generation. The development of enhanced diagnostic capabilities is an essential requirement for ZR to meet critical mission needs. This report presents a comprehensive plan for diagnostic instrument and infrastructure development for the first few years of ZR operation. The focus of the plan is on: (1) developing diagnostic instruments with high spatial and temporal resolution, capable of low noise operation and survival in the severe EMP, bremsstrahlung, and blast environments of ZR; and (2) providing diagnostic infrastructure improvements, including reduced diagnostic trigger signal jitter, more and flexible diagnostic line-of-sight access, and the capability for efficient exchange of diagnostics with other laboratories. This diagnostic plan is the first step in an extended process to provide enhanced diagnostic capabilities for ZR to meet the diverse programmatic needs of a broad range of defense, energy, and general science programs of an international user community into the next decade.

  5. Variola Virus-Specific Diagnostic Assays: Characterization, Sensitivity, and Specificity

    PubMed Central

    Kondas, Ashley V.; Olson, Victoria A.; Li, Yu; Abel, Jason; Laker, Miriam; Rose, Laura; Wilkins, Kimberly; Turner, Jonathan; Kline, Richard

    2015-01-01

    A public health response relies upon rapid and reliable confirmation of disease by diagnostic assays. Here, we detail the design and validation of two variola virus-specific real-time PCR assays, since previous assays cross-reacted with newly identified cowpox viruses. The assay specificity must continually be reassessed as other closely related viruses are identified. PMID:25673790

  6. Variola virus-specific diagnostic assays: characterization, sensitivity, and specificity.

    PubMed

    Kondas, Ashley V; Olson, Victoria A; Li, Yu; Abel, Jason; Laker, Miriam; Rose, Laura; Wilkins, Kimberly; Turner, Jonathan; Kline, Richard; Damon, Inger K

    2015-04-01

    A public health response relies upon rapid and reliable confirmation of disease by diagnostic assays. Here, we detail the design and validation of two variola virus-specific real-time PCR assays, since previous assays cross-reacted with newly identified cowpox viruses. The assay specificity must continually be reassessed as other closely related viruses are identified.

  7. Hair: A Diagnostic Tool to Complement Blood Serum and Urine.

    ERIC Educational Resources Information Center

    Maugh, Thomas H., II

    1978-01-01

    Trace elements and some drugs can be identified in hair and it seems likely that other organic chemicals will be identifiable in the future. Since hair is so easily collected, stored, and analyzed it promises to be an ideal complement to serum and urine analysis as a diagnostic tool. (BB)

  8. [Genetic diagnostic testing in inherited retinal dystrophies].

    PubMed

    Kohl, S; Biskup, S

    2013-03-01

    Inherited retinal dystrophies are clinically and genetically highly heterogeneous. They can be divided according to the clinical phenotype and course of the disease, as well as the underlying mode of inheritance. Isolated retinal dystrophies (i.e., retinitis pigmentosa, Leber's congenital amaurosis, cone and cone-rod dystrophy, macular dystrophy, achromatopsia, congenital stationary nightblindness) and syndromal forms (i.e., Usher syndrome, Bardet-Biedl syndrome) can be differentiated. To date almost 180 genes and thousands of distinct mutations have been identified that are responsible for the different forms of these blinding illnesses. Until recently, there was no adequate diagnostic genetic testing available. With the development of the next generation sequencing technologies, a comprehensive genetic screening analysis for all known genes for inherited retinal dystrophies has been established at reasonable costs and in appropriate turn-around times. Depending on the primary clinical diagnosis and the presumed mode of inheritance, different diagnostic panels can be chosen for genetic testing. Statistics show that in 55-80 % of the cases the genetic defect of the inherited retinal dystrophy can be identified with this approach, depending on the initial clinical diagnosis. The aim of any genetic diagnostics is to define the genetic cause of a given illness within the affected patient and family and thereby i) confirm the clinical diagnosis, ii) provide targeted genetic testing in family members, iii) enable therapeutic intervention, iv) give a prognosis on disease course and progression and v) in the long run provide the basis for novel therapeutic approaches and personalised medicine.

  9. Strain-specific SCAR markers for the detection of Trichoderma harzianum AS12-2, a biological control agent against Rhizoctonia solani, the causal agent of rice sheath blight.

    PubMed

    Naeimi, S; Kocsubé, S; Antal, Zsuzsanna; Okhovvat, S M; Javan-Nikkhah, M; Vágvölgyi, C; Kredics, L

    2011-03-01

    In order to identify a specific marker for T. harzianum AS12-2, a strain capable of controlling rice sheath blight caused by Rhizoctonia solani, UP-PCR was performed using five universal primers (UP) both separately and in pairwise combinations. The application of two UP primers resulted in the amplification of unique fragments from the genomic DNA of T. harzianum AS12-2, clearly distinguishing it from other Trichoderma strains. The unique fragments had no significant sequence homology with any other known sequence available in databases. Based on the sequences of the unique fragments, 14 oligonucleotide primers were designed. Two primer sets amplified a fragment of expected size from the DNA of strain T. harzianum AS12-2 but not from any other examined strains belonging to T. harzianum, to other Trichoderma species assayed, or to other common fungi present in paddy fields of Mazandaran province, Iran. In conclusion, SCAR (sequence characterized amplified regions) markers were successfully identified and rapid, reliable tools were provided for the detection of an effective biocontrol Trichoderma strain, which can facilitate studies of its population dynamics and establishment after release into the natural environment.

  10. [Diagnostic imaging of "body packers"].

    PubMed

    Ichikawa, K; Tajima, N; Tajima, H; Murakami, R; Okada, S; Hosaka, J; Ito, K; Yamamoto, K; Kumazaki, T; Masuno, T; Yokota, H; Makino, T

    1997-02-01

    Drug smuggling by intra-abdominal concealment, so called "body packing," has recently increased, even in Japan. Because of fatal drug intoxication and other adverse side effects, it is important to make a radiological diagnosis of body packers as soon as possible. A retrospective analysis of the images of plain abdominal radiography, computed tomography (CT) and ultrasound (US) was performed in twenty-three body packers to evaluate the imaging characteristics of three drugs (cannabis, cocaine and heroin). Cannabis (16 patients) and cocaine (5 patients) packages were demonstrated as well-demarcated rectangular-shaped high-density shadows surrounded by gas halo ("double condom sign") in abdominal plain radiographs and CT. Heroin packages (2 patients) were demonstrated as obscure shadows and were difficult to identify on plain radiographs, because they resembled stool masses. US was performed in one cannabis patient because of the refusal of radiological examination, and packages were demonstrated as round echogenic structures with dorsal echo extinctions. In conclusion, abdominal plain radiography, CT and US represent valuable diagnostic modalities in the assessment of body packers.

  11. Optimizing Patient-centered Communication and Multidisciplinary Care Coordination in Emergency Diagnostic Imaging: A Research Agenda.

    PubMed

    Sabbatini, Amber K; Merck, Lisa H; Froemming, Adam T; Vaughan, William; Brown, Michael D; Hess, Erik P; Applegate, Kimberly E; Comfere, Nneka I

    2015-12-01

    Patient-centered emergency diagnostic imaging relies on efficient communication and multispecialty care coordination to ensure optimal imaging utilization. The construct of the emergency diagnostic imaging care coordination cycle with three main phases (pretest, test, and posttest) provides a useful framework to evaluate care coordination in patient-centered emergency diagnostic imaging. This article summarizes findings reached during the patient-centered outcomes session of the 2015 Academic Emergency Medicine consensus conference "Diagnostic Imaging in the Emergency Department: A Research Agenda to Optimize Utilization." The primary objective was to develop a research agenda focused on 1) defining component parts of the emergency diagnostic imaging care coordination process, 2) identifying gaps in communication that affect emergency diagnostic imaging, and 3) defining optimal methods of communication and multidisciplinary care coordination that ensure patient-centered emergency diagnostic imaging. Prioritized research questions provided the framework to define a research agenda for multidisciplinary care coordination in emergency diagnostic imaging.

  12. Towards diagnostic markers for the psychoses.

    PubMed

    Lawrie, Stephen M; O'Donovan, Michael C; Saks, Elyn; Burns, Tom; Lieberman, Jeffrey A

    2016-04-01

    Psychotic disorders are currently grouped under broad phenomenological diagnostic rubrics. Researchers hope that progress in identifying aetiological mechanisms will ultimately enable more precise division of heterogeneous diagnoses into specific and valid subgroups. This goal has been an aim of psychiatry since the 19th century, when patients with general paresis were thought to have "insanity" similar to dementia praecox and manic depressive illness. Nowadays, the constructs of organic-induced and substance-induced psychotic disorder show that our diagnostic classification system already reflects, in part, aetiological factors. Most recently, gene copy number variation and autoimmunity have been associated with schizophrenia. We suggest how, on the basis of recent scientific advances, we can progress the identification of further putative subgroups and make the most of currently available interventions. Prompt diagnosis and treatment, and a more routine search for causes, could preserve function and improve outcome, and therefore be more acceptable to patients and carers.

  13. Epidemiology of and Diagnostic Strategies for Toxoplasmosis

    PubMed Central

    Dardé, Marie-Laure

    2012-01-01

    Summary: The apicomplexan parasite Toxoplasma gondii was discovered a little over 100 years ago, but knowledge of its biological life cycle and its medical importance has grown in the last 40 years. This obligate intracellular parasite was identified early as a pathogen responsible for congenital infection, but its clinical expression and the importance of reactivations of infections in immunocompromised patients were recognized later, in the era of organ transplantation and HIV infection. Recent knowledge of host cell-parasite interactions and of parasite virulence has brought new insights into the comprehension of the pathophysiology of infection. In this review, we focus on epidemiological and diagnostic aspects, putting them in perspective with current knowledge of parasite genotypes. In particular, we provide critical information on diagnostic methods according to the patient's background and discuss the implementation of screening tools for congenital toxoplasmosis according to health policies. PMID:22491772

  14. Towards diagnostic markers for the psychoses.

    PubMed

    Lawrie, Stephen M; O'Donovan, Michael C; Saks, Elyn; Burns, Tom; Lieberman, Jeffrey A

    2016-04-01

    Psychotic disorders are currently grouped under broad phenomenological diagnostic rubrics. Researchers hope that progress in identifying aetiological mechanisms will ultimately enable more precise division of heterogeneous diagnoses into specific and valid subgroups. This goal has been an aim of psychiatry since the 19th century, when patients with general paresis were thought to have "insanity" similar to dementia praecox and manic depressive illness. Nowadays, the constructs of organic-induced and substance-induced psychotic disorder show that our diagnostic classification system already reflects, in part, aetiological factors. Most recently, gene copy number variation and autoimmunity have been associated with schizophrenia. We suggest how, on the basis of recent scientific advances, we can progress the identification of further putative subgroups and make the most of currently available interventions. Prompt diagnosis and treatment, and a more routine search for causes, could preserve function and improve outcome, and therefore be more acceptable to patients and carers. PMID:27063388

  15. Dual Processing and Diagnostic Errors

    ERIC Educational Resources Information Center

    Norman, Geoff

    2009-01-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. "Dual Process" theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be made with either a fast, unconscious, contextual process called System 1 or a slow, analytical,…

  16. Saliva as a diagnostic fluid.

    PubMed

    Streckfus, C F; Bigler, L R

    2002-03-01

    In the last 10 years, the use of saliva as a diagnostic fluid has become somewhat of a translational research success story. Technologies are now available enabling saliva to be used to diagnose disease and predict disease progression. This review describes some important recent advances in salivary diagnostics and barriers to application and advancement. This review will also stimulate future research activity.

  17. Student Interpretations of Diagnostic Feedback

    ERIC Educational Resources Information Center

    Doe, Christine

    2015-01-01

    Diagnostic assessment is increasingly being recognized as a potentially beneficial tool for teaching and learning (Jang, 2012). There have been calls in the research literature for students to receive diagnostic feedback and for researchers to investigate how such feedback is used by students. Therefore, this study examined how students…

  18. Real-time PCR analysis of candidate imprinted genes on mouse chromosome 11 shows balanced expression from the maternal and paternal chromosomes and strain-specific variation in expression levels.

    PubMed

    Tuskan, Robert G; Tsang, Shirley; Sun, Zhonghe; Baer, Jessica; Rozenblum, Ester; Wu, Xiaolin; Munroe, David J; Reilly, Karlyne M

    2008-01-01

    Imprinted genes are monoallelically expressed from either the maternal or paternal genome. Because cancer develops through genetic and epigenetic alterations, imprinted genes affect tumorigenesis depending on which parental allele undergoes alteration. We have shown previously in a mouse model of neurofibromatosis type 1 (NF1) that inheriting mutant alleles of Nf1 and Trp53 on chromosome 11 from the mother or father dramatically changes the tumor spectrum of mutant progeny, likely due to alteration in an imprinted gene(s) linked to Nf1 and Trp53. In order to identify imprinted genes on chromosome 11 that are responsible for differences in susceptibility, we tested candidate imprinted genes predicted by a bioinformatics approach and an experimental approach. We have tested 30 candidate genes (Havcr2, Camk2b, Ccdc85a, Cntnap1, Ikzf1, 5730522E02Rik, Gria1, Zfp39, Sgcd, Jup, Nxph3, Spnb2, Asb3, Rasd1, Map2k3, Map2k4, Trp53, Serpinf1, Crk, Rasl10b, Itga3, Hoxb5, Cbx1, Pparbp, Igfbp4, Smarce1, Stat3, Atp6v0a1, Nbr1 and Meox1), two known imprinted genes (Grb10 and Impact) and Nf1, which has not been previously identified as an imprinted gene. Although we confirmed the imprinting of Grb10 and Impact, we found no other genes imprinted in the brain. We did, however, find strain-biased expression of Camk2b, 5730522E02Rik, Havcr2, Map2k3, Serpinf1, Rasl10b, Itga3, Asb3, Trp53, Nf1, Smarce1, Stat3, Cbx1, Pparbp and Cntnap1. These results suggest that the prediction of imprinted genes is complicated and must be individually validated. This manuscript includes supplementary data listing primer sequences for Taqman assays and Ct values for Taqman PCR. PMID:18188004

  19. 42 CFR 410.32 - Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 2 2014-10-01 2014-10-01 false Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions. 410.32 Section 410.32 Public Health CENTERS FOR MEDICARE... (SMI) BENEFITS Medical and Other Health Services § 410.32 Diagnostic x-ray tests, diagnostic...

  20. 42 CFR 410.32 - Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 2 2013-10-01 2013-10-01 false Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions. 410.32 Section 410.32 Public Health CENTERS FOR MEDICARE... (SMI) BENEFITS Medical and Other Health Services § 410.32 Diagnostic x-ray tests, diagnostic...

  1. The tissue diagnostic instrument.

    PubMed

    Hansma, Paul; Yu, Hongmei; Schultz, David; Rodriguez, Azucena; Yurtsev, Eugene A; Orr, Jessica; Tang, Simon; Miller, Jon; Wallace, Joseph; Zok, Frank; Li, Cheng; Souza, Richard; Proctor, Alexander; Brimer, Davis; Nogues-Solan, Xavier; Mellbovsky, Leonardo; Peña, M Jesus; Diez-Ferrer, Oriol; Mathews, Phillip; Randall, Connor; Kuo, Alfred; Chen, Carol; Peters, Mathilde; Kohn, David; Buckley, Jenni; Li, Xiaojuan; Pruitt, Lisa; Diez-Perez, Adolfo; Alliston, Tamara; Weaver, Valerie; Lotz, Jeffrey

    2009-05-01

    Tissue mechanical properties reflect extracellular matrix composition and organization, and as such, their changes can be a signature of disease. Examples of such diseases include intervertebral disk degeneration, cancer, atherosclerosis, osteoarthritis, osteoporosis, and tooth decay. Here we introduce the tissue diagnostic instrument (TDI), a device designed to probe the mechanical properties of normal and diseased soft and hard tissues not only in the laboratory but also in patients. The TDI can distinguish between the nucleus and the annulus of spinal disks, between young and degenerated cartilage, and between normal and cancerous mammary glands. It can quantify the elastic modulus and hardness of the wet dentin left in a cavity after excavation. It can perform an indentation test of bone tissue, quantifying the indentation depth increase and other mechanical parameters. With local anesthesia and disposable, sterile, probe assemblies, there has been neither pain nor complications in tests on patients. We anticipate that this unique device will facilitate research on many tissue systems in living organisms, including plants, leading to new insights into disease mechanisms and methods for their early detection.

  2. [Diagnostic imaging of lying].

    PubMed

    Lass, Piotr; Sławek, Jarosław; Sitek, Emilia; Szurowska, Edyta; Zimmermann, Agnieszka

    2013-01-01

    Functional diagnostic imaging has been applied in neuropsychology for more than two decades. Nowadays, the functional magnetic resonance (fMRI) seems to be the most important technique. Brain imaging in lying has been performed and discussed since 2001. There are postulates to use fMRI for forensic purposes, as well as commercially, e.g. testing the loyalty of employees, especially because of the limitations of traditional polygraph in some cases. In USA fMRI is performed in truthfulness/lying assessment by at least two commercial companies. Those applications are a matter of heated debate of practitioners, lawyers and specialists of ethics. The opponents of fMRI use for forensic purposes indicate the lack of common agreement on it and the lack of wide recognition and insufficient standardisation. Therefore it cannot serve as a forensic proof, yet. However, considering the development of MRI and a high failure rate of traditional polygraphy, forensic applications of MRI seem to be highly probable in future. PMID:23888745

  3. The tissue diagnostic instrument

    PubMed Central

    Hansma, Paul; Yu, Hongmei; Schultz, David; Rodriguez, Azucena; Yurtsev, Eugene A.; Orr, Jessica; Tang, Simon; Miller, Jon; Wallace, Joseph; Zok, Frank; Li, Cheng; Souza, Richard; Proctor, Alexander; Brimer, Davis; Nogues-Solan, Xavier; Mellbovsky, Leonardo; Peña, M. Jesus; Diez-Ferrer, Oriol; Mathews, Phillip; Randall, Connor; Kuo, Alfred; Chen, Carol; Peters, Mathilde; Kohn, David; Buckley, Jenni; Li, Xiaojuan; Pruitt, Lisa; Diez-Perez, Adolfo; Alliston, Tamara; Weaver, Valerie; Lotz, Jeffrey

    2009-01-01

    Tissue mechanical properties reflect extracellular matrix composition and organization, and as such, their changes can be a signature of disease. Examples of such diseases include intervertebral disk degeneration, cancer, atherosclerosis, osteoarthritis, osteoporosis, and tooth decay. Here we introduce the tissue diagnostic instrument (TDI), a device designed to probe the mechanical properties of normal and diseased soft and hard tissues not only in the laboratory but also in patients. The TDI can distinguish between the nucleus and the annulus of spinal disks, between young and degenerated cartilage, and between normal and cancerous mammary glands. It can quantify the elastic modulus and hardness of the wet dentin left in a cavity after excavation. It can perform an indentation test of bone tissue, quantifying the indentation depth increase and other mechanical parameters. With local anesthesia and disposable, sterile, probe assemblies, there has been neither pain nor complications in tests on patients. We anticipate that this unique device will facilitate research on many tissue systems in living organisms, including plants, leading to new insights into disease mechanisms and methods for their early detection. PMID:19485522

  4. Gonorrhoea diagnostics: An update.

    PubMed

    Verma, R; Sood, S

    2016-01-01

    Diagnosis of gonorrhoea is an ongoing challenge. The organism is fastidious requiring meticulous collection and transport for successful cultivation. Asymptomatic infections are common which go undetected by conventional methods thereby leading to continued transmission and the risk of complications. The nucleic acid amplification tests, now increasingly used in developed countries, offer improved sensitivity compared to bacterial culture. However, these continue to suffer sequence related problems leading to false positive and false negative results. Further, these cannot be used for generation of data on antibiotic susceptibility because genetic markers of antibiotic resistance to recommended therapies have not been fully characterised. They are unaffordable in a setting like ours where reliance is placed on syndromic approach for sexually transmitted infection (STI) management. The use of syndromic approach has resulted in a considerable decline in the number of Neisseria gonorrhoeae isolates that have been cultured for diagnostic purposes. Many laboratories formerly doing so are no longer performing culture for gonococci, and the basic skills have been lost. There is a need to not only revive this skill but also adopt newer technologies that can aid in accurate diagnosis in a cost-effective manner. There is room for innovation that can facilitate the development of a point-of-care test for this bacterial STI. PMID:27080763

  5. The tissue diagnostic instrument

    NASA Astrophysics Data System (ADS)

    Hansma, Paul; Yu, Hongmei; Schultz, David; Rodriguez, Azucena; Yurtsev, Eugene A.; Orr, Jessica; Tang, Simon; Miller, Jon; Wallace, Joseph; Zok, Frank; Li, Cheng; Souza, Richard; Proctor, Alexander; Brimer, Davis; Nogues-Solan, Xavier; Mellbovsky, Leonardo; Peña, M. Jesus; Diez-Ferrer, Oriol; Mathews, Phillip; Randall, Connor; Kuo, Alfred; Chen, Carol; Peters, Mathilde; Kohn, David; Buckley, Jenni; Li, Xiaojuan; Pruitt, Lisa; Diez-Perez, Adolfo; Alliston, Tamara; Weaver, Valerie; Lotz, Jeffrey

    2009-05-01

    Tissue mechanical properties reflect extracellular matrix composition and organization, and as such, their changes can be a signature of disease. Examples of such diseases include intervertebral disk degeneration, cancer, atherosclerosis, osteoarthritis, osteoporosis, and tooth decay. Here we introduce the tissue diagnostic instrument (TDI), a device designed to probe the mechanical properties of normal and diseased soft and hard tissues not only in the laboratory but also in patients. The TDI can distinguish between the nucleus and the annulus of spinal disks, between young and degenerated cartilage, and between normal and cancerous mammary glands. It can quantify the elastic modulus and hardness of the wet dentin left in a cavity after excavation. It can perform an indentation test of bone tissue, quantifying the indentation depth increase and other mechanical parameters. With local anesthesia and disposable, sterile, probe assemblies, there has been neither pain nor complications in tests on patients. We anticipate that this unique device will facilitate research on many tissue systems in living organisms, including plants, leading to new insights into disease mechanisms and methods for their early detection.

  6. Molecular diagnostics in genodermatoses.

    PubMed

    Schaffer, Julie V

    2012-12-01

    In recent years, there has been tremendous progress in elucidating the molecular bases of genodermatoses. The interface between genetics and dermatology has broadened with the identification of "new" heritable disorders, improved recognition of phenotypic spectrums, and integration of molecular and clinical data to simplify disease categorization and highlight relationships between conditions. With the advent of next-generation sequencing and other technological advances, dermatologists have promising new tools for diagnosis of genodermatoses. This article first addresses phenotypic characterization and classification with the use of online databases, considering concepts of clinical and genetic heterogeneity. Indications for genetic testing related to medical care and patient/family decision making are discussed. Standard genetic testing is reviewed, including resources for finding specialized laboratories, methods of gene analysis, and patient/family counseling. The benefits and challenges associated with multigene panels, array-based analysis (eg, copy number variation, linkage, and homozygosity), and whole-exome or whole-genome sequencing are then examined. Specific issues relating to molecular analysis of mosaic skin conditions and prenatal/preimplantation diagnosis are also presented. Use of the modern molecular diagnostics described herein enhance our ability to counsel, monitor, and treat patients and families affected by genodermatoses, with broader benefits of providing insights into cutaneous physiology and multifactorial skin disorders.

  7. Gang Identifiers and Terminology.

    ERIC Educational Resources Information Center

    Cantrell, Mary Lynn

    1992-01-01

    Provides lists of gang identifiers and terminology. Suggests that, to find out names and associated identifiers of local gangs, readers should talk to their local police. Included in listing are descriptions of gang-related symbols, physical signals, graffiti, slogans, right-left rules, colors, clothing, jewelry, hair styles, and fingernails. Also…

  8. Neurogenic thoracic outlet syndrome: current diagnostic criteria and advances in MRI diagnostics.

    PubMed

    Magill, Stephen T; Brus-Ramer, Marcel; Weinstein, Philip R; Chin, Cynthia T; Jacques, Line

    2015-09-01

    Neurogenic thoracic outlet syndrome (nTOS) is caused by compression of the brachial plexus as it traverses from the thoracic outlet to the axilla. Diagnosing nTOS can be difficult because of overlap with other complex pain and entrapment syndromes. An nTOS diagnosis is made based on patient history, physical exam, electrodiagnostic studies, and, more recently, interpretation of MR neurograms with tractography. Advances in high-resolution MRI and tractography can confirm an nTOS diagnosis and identify the location of nerve compression, allowing tailored surgical decompression. In this report, the authors review the current diagnostic criteria, present an update on advances in MRI, and provide case examples demonstrating how MR neurography (MRN) can aid in diagnosing nTOS. The authors conclude that improved high-resolution MRN and tractography are valuable tools for identifying the source of nerve compression in patients with nTOS and can augment current diagnostic modalities for this syndrome.

  9. Development of a New Diagnostic System for Human Liver Diseases Based on Conventional Ultrasonic Diagnostic Equipment

    NASA Astrophysics Data System (ADS)

    Kikuchi, Tsuneo; Nakazawa, Toshihiro; Harada, Akimitsu; Sato, Hiroaki; Maruyama, Yukio; Sato, Sojun

    2001-05-01

    In this paper, the authors present the experimental results of using a quantitative ultrasonic diagnosis technique for human liver diseases using the fractal dimension (FD) of the shape of the power spectra (PS) of RF signals. We have developed an experimental system based on a conventional ultrasonic diagnostic system. As a result, we show that normal livers, fatty livers and liver cirrhosis can be identified using the FD values.

  10. Identifying methamphetamine exposure in children

    PubMed Central

    Castaneto, Marisol S.; Barnes, Allan J.; Scheidweiler, Karl B.; Schaffer, Michael; Rogers, Kristen K.; Stewart, Deborah; Huestis, Marilyn A.

    2013-01-01

    Introduction Methamphetamine (MAMP) use, distribution and manufacture remain a serious public health and safety problem in the United States, and children environmentally exposed to MAMP face a myriad of developmental, social and health risks, including severe abuse and neglect necessitating child protection involvement. It is recommended that drug-endangered children receive medical evaluation and care with documentation of overall physical and mental conditions and have urine drug testing.1 The primary aim of this study was to determine the best biological matrix to detect MAMP, amphetamine (AMP), methylenedioxymethamphetamine (MDMA), methylenedioxyamphetamine (MDA) and methylenedioxyethylamphetamine (MDEA) in environmentally exposed children. Method 91 children, environmentally exposed to household MAMP intake, were medically evaluated at the Child and Adolescent Abuse Resource and Evaluation (CAARE) Diagnostic and Treatment Center at the University of California, Davis (UCD) Children's Hospital. MAMP, AMP, MDMA, MDA and MDEA were quantified in urine and oral fluid (OF) by gas chromatography mass spectrometry (GCMS) and in hair by liquid chromatography tandem mass spectrometry (LCMSMS). Results Overall drug detection rates in OF, urine and hair were 6.9%, 22.1% and 77.8%, respectively. Seventy children (79%) tested positive for 1 or more drugs in 1 or more matrices. MAMP was the primary analyte detected in all 3 biological matrices. All positive OF (n=5) and 18 of 19 positive urine specimens also had a positive hair test. Conclusion Hair analysis offered a more sensitive tool for identifying MAMP, AMP and MDMA environmental exposure in children than urine or OF testing. A negative urine, or hair test does not exclude the possibility of drug exposure, but hair testing provided the greatest sensitivity for identifying drug-exposed children. PMID:24263642

  11. Diagnostics for slapper detonator systems

    SciTech Connect

    Boberg, R.E.; Lee, R.E.; Lee, R.S.; Von Holle, W.

    1989-03-28

    This report discusses diagnostics which have been used to evaluate CDU characteristics and performance, slapper characteristics and performance and the response of a HE detonator output pellet to a slapper stimulus. Many of the diagnostics discussed are appropriate for development and production testing. These include CVR current measurements, voltage probe measurements, time-of-flight measurements, threshold measurements, function time measurements, use of steel witness plates and determination of design margin. Some of the more-sophisticated, expensive diagnostics discussed have yielded very useful information, but are not required for development and production testing. 8 refs., 9 figs., 1 tab.

  12. Knowledge based jet engine diagnostics

    NASA Technical Reports Server (NTRS)

    Jellison, Timothy G.; Dehoff, Ronald L.

    1987-01-01

    A fielded expert system automates equipment fault isolation and recommends corrective maintenance action for Air Force jet engines. The knowledge based diagnostics tool was developed as an expert system interface to the Comprehensive Engine Management System, Increment IV (CEMS IV), the standard Air Force base level maintenance decision support system. XMAM (trademark), the Expert Maintenance Tool, automates procedures for troubleshooting equipment faults, provides a facility for interactive user training, and fits within a diagnostics information feedback loop to improve the troubleshooting and equipment maintenance processes. The application of expert diagnostics to the Air Force A-10A aircraft TF-34 engine equipped with the Turbine Engine Monitoring System (TEMS) is presented.

  13. Next-generation confirmatory disease diagnostics

    NASA Astrophysics Data System (ADS)

    Lin, Robert; Gerver, Rachel; Karns, Kelly; Apori, Akwasi A.; Denisin, Aleksandra K.; Herr, Amy E.

    2014-06-01

    Microfluidic tools are advancing capabilities in screening diagnostics for use in near-patient settings. Here, we review three case studies to illustrate the flexibility and analytical power offered by microanalytical tools. We first overview a near-patient tool for detection of protein markers found in cerebrospinal fluid (CSF), as a means to identify the presence of cerebrospinal fluid in nasal mucous - an indication that CSF is leaking into the nasal cavity. Microfluidic design allowed integration of several up-stream preparatory steps and rapid, specific completion of the human CSF protein assay. Second, we overview a tear fluid based assay for lactoferrin, a protein produced in the lacrimal gland, then secreted into tear fluid. Tear Lf is a putative biomarker for primary SS. A critical contribution of this and related work being measurement of Lf, even in light of well-known and significant matrix interactions and losses during the tear fluid collection and preparation. Lastly, we review a microfluidic barcode platform that enables rapid measurement of multiple infectious disease biomarkers in human sera. The assay presents a new approach to multiplexed biomarker detection, yet in a simple straight microchannel - thus providing a streamlined, simplified microanalytical platform, as is relevant to robust operation in diagnostic settings. We view microfluidic design and analytical chemistry as the basis for emerging, sophisticated assays that will advance not just screening diagnostic technology, but confirmatory assays, sample preparation and handling, and thus introduction and utilization of new biomarkers and assay formats.

  14. PAH diagnostic ratios for the identification of pollution emission sources.

    PubMed

    Tobiszewski, Marek; Namieśnik, Jacek

    2012-03-01

    Polycyclic aromatic hydrocarbon (PAH) diagnostic ratios have recently come into common use as a tool for identifying and assessing pollution emission sources. Some diagnostic ratios are based on parent PAHs, others on the proportions of alkyl-substituted to non-substituted molecules. The ratios are applicable to PAHs determined in different environmental media: air (gas + particle phase), water, sediment, soil, as well as biomonitor organisms such as leaves or coniferous needles, and mussels. These ratios distinguish PAH pollution originating from petroleum products, petroleum combustion and biomass or coal burning. The compounds involved in each ratio have the same molar mass, so it is assumed they have similar physicochemical properties. Numerous studies show that diagnostic ratios change in value to different extents during phase transfers and environmental degradation. The paper reviews applications of diagnostic ratios, comments on their use and specifies their limitations.

  15. Alzheimer's disease dementia guidelines for diagnostic testing: a systematic review.

    PubMed

    Arevalo-Rodriguez, Ingrid; Pedraza, Olga L; Rodríguez, Andrea; Sánchez, Erick; Gich, Ignasi; Solà, Ivan; Bonfill, Xavier; Alonso-Coello, Pablo

    2013-03-01

    Alzheimer's disease dementia (AD dementia) is one of the most common neurodegenerative diseases worldwide, with a growing incidence during the last decades. Clinical diagnosis of cognitive impairment and presence of AD biomarkers have become important issues for early and adequate treatment. We performed a systematic literature search and quality appraisal of AD dementia guidelines, published between 2005 and 2011, which contained diagnostic recommendations on AD dementia. We also analyzed diagnostic recommendations related to the use of brief cognitive tests, neuropsychological evaluation, and AD biomarkers. Of the 537 retrieved references, 15 met the selection criteria. We found that Appraisal of Guidelines Research and Evaluation (AGREE)-II domains such as applicability and editorial independence had the lowest scores. The wide variability on assessment of quality of evidence and strength of recommendations were the main concerns identified regarding diagnostic testing. Although the appropriate methodology for clinical practice guideline development is well known, the quality of diagnostic AD dementia guidelines can be significantly improved. PMID:23288575

  16. Measurements and Diagnostics of Diamond Films and Coatings

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa; Wu, Richard L. C.

    1999-01-01

    The commercial potential of chemical-vapor-deposited (CVD) diamond films has been established and a number of applications have been identified through university, industry, and government research studies. This paper discusses the methodologies used for property measurement and diagnostic of CVD diamond films and coatings. Measurement and diagnostic techniques studied include scanning electron microscopy, transmission electron microscopy, atomic force microscopy, stylus profilometry, x-ray diffraction, electron diffraction, Raman spectroscopy, Rutherford backscattering, elastic recoil spectroscopy, and friction examination. Each measurement and diagnostic technique provides unique information. A combination of techniques can provide the technical information required to understand the quality and properties of CVD diamond films, which are important to their application in specific component systems and environments. In this study the combination of measurement and diagnostic techniques was successfully applied to correlate deposition parameters and resultant diamond film composition, crystallinity, grain size, surface roughness, and coefficient of friction.

  17. Diagnostics for the National Compact Stellarator Experiment

    SciTech Connect

    B.C. Stratton; D. Johnson; R. Feder; E. Fredrickson; H. Neilson; H. Takahashi; M. Zarnstorf; M. Cole; P. Goranson; E. Lazarus; B. Nelson

    2003-09-16

    The status of planning of the National Compact Stellarator Experiment (NCSX) diagnostics is presented, with the emphasis on resolution of diagnostics access issues and on diagnostics required for the early phases of operation.

  18. Embedded diagnostics in microprocessor based CAMAC controller

    SciTech Connect

    Calvo, O.A.; Kraft, G.D.

    1989-02-01

    The objective of this paper is to describe the embedded diagnostics incorporated in Fermilab's Smart CAMAC Controller (SCC). This software was created to assist technical personnel during the production and maintenance of SCCs. It also allows the user to identify faulty components in the experiment controlled and monitored by the CAMAC system. The software consists of a set of routines residing in EPROM that have been appended to an existing monitor, the SCCBug. Depending on the severity of the failure, different levels of tests are provided.

  19. [Hereditary ichthyosis: A diagnostic and therapeutic challenge].

    PubMed

    Vega Almendra, Nadia; Aranibar Duran, Ligia

    2016-01-01

    Hereditary ichthyoses are a group of genetic disorders of cornification, which are characterised by hyperkeratosis and scaling. The new classification identifies 36 types of ichthyosis, which are subdivided according to their frequency, pattern of inheritance and extracutaneous involvement. The diagnosis is mainly based on clinical features, since genetic studies are not available in our setting. Treatment is symptomatic and management should be performed by a multidisciplinary team. In this article, the diagnostic and therapeutic aspects of different types of ichthyosis are reviewed, taking into account the nomenclature and modifications presented in the new classification.

  20. Immunohistochemical diagnostic and prognostic markers for melanoma.

    PubMed

    Nosrati, Mehdi; Kashani-Sabet, Mohammed

    2014-01-01

    Recent studies in our laboratory have identified novel molecular diagnostic and prognostic markers based on analyses in large cohorts of melanoma patients. These markers were initially derived from gene expression profiling analyses of distinct stages of melanoma progression. Immunohistochemical analyses confirmed the differential expression of these markers, and immunohistochemistry-based multimarker assays were developed to assess melanoma diagnosis and prognosis at the molecular level. In this chapter we review the development of these assays and the methodologies used to assess marker expression in both nevi and primary melanomas. PMID:24258983

  1. Spectroscopic diagnostics for bacteria in biologic sample

    DOEpatents

    El-Sayed, Mostafa A.; El-Sayed, Ivan H.

    2002-01-01

    A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

  2. [Hereditary ichthyosis: A diagnostic and therapeutic challenge].

    PubMed

    Vega Almendra, Nadia; Aranibar Duran, Ligia

    2016-01-01

    Hereditary ichthyoses are a group of genetic disorders of cornification, which are characterised by hyperkeratosis and scaling. The new classification identifies 36 types of ichthyosis, which are subdivided according to their frequency, pattern of inheritance and extracutaneous involvement. The diagnosis is mainly based on clinical features, since genetic studies are not available in our setting. Treatment is symptomatic and management should be performed by a multidisciplinary team. In this article, the diagnostic and therapeutic aspects of different types of ichthyosis are reviewed, taking into account the nomenclature and modifications presented in the new classification. PMID:26471314

  3. [The rational diagnostic of cholangiocarcinoma].

    PubMed

    Rydlo, Martin; Dvořáčková, Jana; Kupka, Tomáš; Klvaňa, Pavel; Havelka, Jaroslav; Uvírová, Magdalena; Geryk, Edvard; Czerný, Daniel; Jonszta, Tomáš; Bojková, Martina; Hrabovský, Vladimír; Jelínková, Veronika; Martínek, Arnošt; Dítě, Petr

    2016-02-01

    Cholangiocarcinoma (CC) is a rare malignant tumour arising from cholangiocytes, and its prognosis is usually unfavourable, mostly as a result of late diagnosis of the tumour. The current incidence of cholangiocarcinoma in the Czech Republic is 1.4/100,000 inhabitants per year; in less than 30 % of patients with CC, one of the known risk factors can be identified, most frequently, primary sclerosing cholangitis. Only patients with early diagnosed and surgically amenable cholangiocarcinoma are likely to have a longer survival time; in their case, survival for more than five years has been achieved in 20 % to 40 %. From the perspective of the need for early diagnosis of CC, a significant part is played by imaging and histopathologic evaluation; the early diagnostic significance of oncomarkers is limited. The rational early diagnosis of CC consists in effective use of differentiated advantages of different imaging modalities - MRI with DSA appears to be the optimal method, endosonography is a sensitive method for the identification of malignancy in the hepatic hilum or distal common bile duct, MRCP (magnetic resonance cholangiopancreatography) is used to display pathological changes in the biliary tree, ERCP (endoscopic retrograde cholangiopancreatography) allows material removal for histopathological examination. Other new approaches are also beneficial, such as IDUS - intraductal ultrasonography of biliary tract or SPY-GLASS, enabling examination of the bile ducts by direct view with the possibility of taking targeted biopsies. Sensitivity and specificity of histology and cytology can be increased by using the molecular cytogenetic FISH method, i.e. fluorescence in situ by hybridization, with a specificity of 97 %. PMID:27172439

  4. Immunochromatographic diagnostic test analysis using Google Glass.

    PubMed

    Feng, Steve; Caire, Romain; Cortazar, Bingen; Turan, Mehmet; Wong, Andrew; Ozcan, Aydogan

    2014-03-25

    We demonstrate a Google Glass-based rapid diagnostic test (RDT) reader platform capable of qualitative and quantitative measurements of various lateral flow immunochromatographic assays and similar biomedical diagnostics tests. Using a custom-written Glass application and without any external hardware attachments, one or more RDTs labeled with Quick Response (QR) code identifiers are simultaneously imaged using the built-in camera of the Google Glass that is based on a hands-free and voice-controlled interface and digitally transmitted to a server for digital processing. The acquired JPEG images are automatically processed to locate all the RDTs and, for each RDT, to produce a quantitative diagnostic result, which is returned to the Google Glass (i.e., the user) and also stored on a central server along with the RDT image, QR code, and other related information (e.g., demographic data). The same server also provides a dynamic spatiotemporal map and real-time statistics for uploaded RDT results accessible through Internet browsers. We tested this Google Glass-based diagnostic platform using qualitative (i.e., yes/no) human immunodeficiency virus (HIV) and quantitative prostate-specific antigen (PSA) tests. For the quantitative RDTs, we measured activated tests at various concentrations ranging from 0 to 200 ng/mL for free and total PSA. This wearable RDT reader platform running on Google Glass combines a hands-free sensing and image capture interface with powerful servers running our custom image processing codes, and it can be quite useful for real-time spatiotemporal tracking of various diseases and personal medical conditions, providing a valuable tool for epidemiology and mobile health.

  5. Immunochromatographic Diagnostic Test Analysis Using Google Glass

    PubMed Central

    2014-01-01

    We demonstrate a Google Glass-based rapid diagnostic test (RDT) reader platform capable of qualitative and quantitative measurements of various lateral flow immunochromatographic assays and similar biomedical diagnostics tests. Using a custom-written Glass application and without any external hardware attachments, one or more RDTs labeled with Quick Response (QR) code identifiers are simultaneously imaged using the built-in camera of the Google Glass that is based on a hands-free and voice-controlled interface and digitally transmitted to a server for digital processing. The acquired JPEG images are automatically processed to locate all the RDTs and, for each RDT, to produce a quantitative diagnostic result, which is returned to the Google Glass (i.e., the user) and also stored on a central server along with the RDT image, QR code, and other related information (e.g., demographic data). The same server also provides a dynamic spatiotemporal map and real-time statistics for uploaded RDT results accessible through Internet browsers. We tested this Google Glass-based diagnostic platform using qualitative (i.e., yes/no) human immunodeficiency virus (HIV) and quantitative prostate-specific antigen (PSA) tests. For the quantitative RDTs, we measured activated tests at various concentrations ranging from 0 to 200 ng/mL for free and total PSA. This wearable RDT reader platform running on Google Glass combines a hands-free sensing and image capture interface with powerful servers running our custom image processing codes, and it can be quite useful for real-time spatiotemporal tracking of various diseases and personal medical conditions, providing a valuable tool for epidemiology and mobile health. PMID:24571349

  6. Saliva Preservative for Diagnostic Purposes

    NASA Technical Reports Server (NTRS)

    Pierson, Duane L.; Mehta, Satish K.

    2012-01-01

    Saliva is an important body fluid for diagnostic purposes. Glycoproteins, glucose, steroids, DNA, and other molecules of diagnostic value are found in saliva. It is easier to collect as compared to blood or urine. Unfortunately, saliva also contains large numbers of bacteria that can release enzymes, which can degrade proteins and nucleic acids. These degradative enzymes destroy or reduce saliva s diagnostic value. This innovation describes the formulation of a chemical preservative that prevents microbial growth and inactivates the degradative enzymes. This extends the time that saliva can be stored or transported without losing its diagnostic value. Multiple samples of saliva can be collected if needed without causing discomfort to the subject and it does not require any special facilities to handle after it is collected.

  7. FEL-accelerator related diagnostics

    SciTech Connect

    Kevin Jordan; David Douglas; Stephen V. Benson; Pavel Evtuschenko

    2007-08-02

    Free Electron Lasers (FEL) present a unique set of beam parameters to the diagnostics suite. The FEL requires characterization of the full six dimensional phase space of the electron beam at the wiggler and accurate alignment of the electron beam to the optical mode of the laser. In addition to the FEL requirements on the diagnostics suite, the Jefferson Lab FEL is operated as an Energy Recovered Linac (ERL) which imposes additional requirements on the diagnostics. The ERL aspect of the Jefferson Lab FEL requires that diagnostics operate over a unique dynamic range and operate with simultaneous transport of the accelerated and energy recovered beams. This talk will present how these challenges are addressed at the Jefferson Lab FEL.

  8. Rapid diagnostic tests for malaria.

    PubMed

    Visser, Theodoor; Daily, Jennifer; Hotte, Nora; Dolkart, Caitlin; Cunningham, Jane; Yadav, Prashant

    2015-12-01

    Maintaining quality, competitiveness and innovation in global health technology is a constant challenge for manufacturers, while affordability, access and equity are challenges for governments and international agencies. In this paper we discuss these issues with reference to rapid diagnostic tests for malaria. Strategies to control and eliminate malaria depend on early and accurate diagnosis. Rapid diagnostic tests for malaria require little training and equipment and can be performed by non-specialists in remote settings. Use of these tests has expanded significantly over the last few years, following recommendations to test all suspected malaria cases before treatment and the implementation of an evaluation programme to assess the performance of the malaria rapid diagnostic tests. Despite these gains, challenges exist that, if not addressed, could jeopardize the progress made to date. We discuss recent developments in rapid diagnostic tests for malaria, highlight some of the challenges and provide suggestions to address them.

  9. Rapid diagnostic tests for malaria

    PubMed Central

    Daily, Jennifer; Hotte, Nora; Dolkart, Caitlin; Cunningham, Jane; Yadav, Prashant

    2015-01-01

    Abstract Maintaining quality, competitiveness and innovation in global health technology is a constant challenge for manufacturers, while affordability, access and equity are challenges for governments and international agencies. In this paper we discuss these issues with reference to rapid diagnostic tests for malaria. Strategies to control and eliminate malaria depend on early and accurate diagnosis. Rapid diagnostic tests for malaria require little training and equipment and can be performed by non-specialists in remote settings. Use of these tests has expanded significantly over the last few years, following recommendations to test all suspected malaria cases before treatment and the implementation of an evaluation programme to assess the performance of the malaria rapid diagnostic tests. Despite these gains, challenges exist that, if not addressed, could jeopardize the progress made to date. We discuss recent developments in rapid diagnostic tests for malaria, highlight some of the challenges and provide suggestions to address them. PMID:26668438

  10. Diagnostic Studies With GLA Fields

    NASA Technical Reports Server (NTRS)

    Salstein, David A.

    1997-01-01

    Assessments of the NASA Goddard Earth Observing System-1 Data Assimilation System (GEOS-1 DAS) regarding heating rates, energetics and angular momentum quantities were made. These diagnostics can be viewed as measures of climate variability. Comparisons with the NOAA/NCEP reanalysis system of momentum and energetics diagnostics are included. Water vapor and angular momentum are diagnosed in many models, including those of NASA, as part of the Atmospheric Model Intercomparison Project. Relevant preprints are included herein.

  11. Saliva as a diagnostic fluid.

    PubMed

    Malamud, Daniel

    2011-01-01

    Salivary diagnostics is a dynamic and emerging field utilizing nanotechnology and molecular diagnostics to aid in the diagnosis of oral and systemic diseases. In this article the author critically reviews the latest advances using oral biomarkers for disease detection. The use of oral fluids is broadening perspectives in clinical diagnosis, disease monitoring, and decision making for patient care. Important elements determining the future possibilities and challenges in this field are also discussed.

  12. Salivary Diagnostics: A Brief Review

    PubMed Central

    Malathi, Narasimhan; Mythili, Sabesan; Vasanthi, Hannah R.

    2014-01-01

    Early detection of disease plays a crucial role for treatment planning and prognosis. Saliva has great potential as a diagnostic fluid and offers advantage over serum and other biological fluids by an economic and noninvasive collection method for monitoring of systemic health and disease progression. The plethora of components in this fluid can act as biomarkers for diagnosis of various systemic and local diseases. In this review paper, we have emphasized the role of salivary biomarkers as diagnostic tools. PMID:24616813

  13. Metal alloy identifier

    DOEpatents

    Riley, William D.; Brown, Jr., Robert D.

    1987-01-01

    To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

  14. Identifying and Managing Risk.

    ERIC Educational Resources Information Center

    Abraham, Janice M.

    1999-01-01

    The role of the college or university chief financial officer in institutional risk management is (1) to identify risk (physical, casualty, fiscal, business, reputational, workplace safety, legal liability, employment practices, general liability), (2) to develop a campus plan to reduce and control risk, (3) to transfer risk, and (4) to track and…

  15. 42 CFR 410.32 - Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Service Act, as implemented by 21 CFR part 900, subpart B. (d) Diagnostic laboratory tests—(1) Who may... 42 Public Health 2 2011-10-01 2011-10-01 false Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions. 410.32 Section 410.32 Public Health CENTERS FOR...

  16. 42 CFR 410.32 - Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Service Act, as implemented by 21 CFR part 900, subpart B. (d) Diagnostic laboratory tests—(1) Who may... 42 Public Health 2 2012-10-01 2012-10-01 false Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions. 410.32 Section 410.32 Public Health CENTERS FOR...

  17. 42 CFR 410.32 - Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... implemented by 21 CFR part 900, subpart B. (d) Diagnostic laboratory tests—(1) Who may furnish services... 42 Public Health 2 2010-10-01 2010-10-01 false Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions. 410.32 Section 410.32 Public Health CENTERS FOR...

  18. Far infrared fusion plasma diagnostics

    SciTech Connect

    Luhmann, N.C. Jr.; Peebles, W.A.

    1990-01-01

    Over the last several years, reflectometry has grown in importance as a diagnostic for both steady-state density Profiles as well as for the investigation of density fluctuations and turbulence. As a diagnostic for density profile measurement, it is generally believed to be well understood in the tokamak environment. However, its use as a fluctuation diagnostic is hampered by a lack of quantitative experimental understanding of its wavenumber sensitivity and spatial resolution. Several researchers, have theoretically investigated these questions. However, prior to the UCLA laboratory investigation, no group has experimentally investigated these questions. Because of the reflectometer's importance to the world effort in understanding plasma turbulence and transport, UCLA has, over the last year, made its primary Task IIIA effort the resolution of these questions. UCLA has taken the lead in a quantitative experimental understanding of reflectometer data as applied to the measurement of density fluctuations. In addition to this, work has proceeded on the design, construction, and installation of a reflectometer system on UCLA's CCT tokamak. This effort will allow a comparison between the improved confinement regimes (H-mode) observed on both the DIII-D and CCT machines with the goal of achieving a physics understanding of the phenomena. Preliminary investigation of a new diagnostic technique to measure density profiles as a function of time has been initiated at UCLA. The technique promises to be a valuable addition to the range of available plasma diagnostics. Work on advanced holographic reflectometry technique as applied to fluctuation diagnostics has awaited a better understanding of the reflectometer signal itself as discussed above. Efforts to ensure the transfer of the diagnostic developments have continued with particular attention devoted to the preliminary design of a multichannel FIR interferometer for MST.

  19. Guide to good practices for teamwork training and diagnostic skills development

    SciTech Connect

    1997-06-01

    This guide provides assistance in the development, implementation, and improvement of training on teamwork and diagnostics. DOE and contractor representatives identified the need for teamwork and diagnostics training guidance. This need was based on the increasing emphasis of properly applying knowledge and skills to complete assigned tasks. Teamwork and diagnostic skills have become a focal point because of the impact they have on effective facility operation and safety.

  20. Identifying Marine Phytoplankton

    NASA Astrophysics Data System (ADS)

    Hargraves, Paul E.

    Until recently, anyone who needed to accurately identify marine phytoplankton had one of four choices: use the outdated Englishlanguage volumes by E. E. Cupp and N. I. Hendey plus the more recent book by J. Dodge, acquire a working knowledge of German and use the old volumes by Schiller and Hustedt, spend huge amounts of time in an exceedingly well-equipped marine science library trying in vain to keep up with the rapidly evolving field of phytoplankton systematics and taxonomy, or track down one of the rarest of endangered species—a phytoplankton taxonomist—and beg for help.To these unfortunate choices is added one considerably more hopeful: Identifying Marine Phytoplankton. This volume, which has seven contributing authors, contains most of the taxonomic groups that make up the planktonic autotrophs and some heterotrophs of the seas, coasts, and estuaries of the world (missing are cyanobacteria and some of the picoplankton groups).

  1. Strain Specific Factors Control Effector Gene Silencing in Phytophthora sojae.

    PubMed

    Shrestha, Sirjana Devi; Chapman, Patrick; Zhang, Yun; Gijzen, Mark

    2016-01-01

    The Phytophthora sojae avirulence gene Avr3a encodes an effector that is capable of triggering immunity on soybean plants carrying the resistance gene Rps3a. P. sojae strains that express Avr3a are avirulent to Rps3a plants, while strains that do not are virulent. To study the inheritance of Avr3a expression and virulence towards Rps3a, genetic crosses and self-fertilizations were performed. A cross between P. sojae strains ACR10 X P7076 causes transgenerational gene silencing of Avr3a allele, and this effect is meiotically stable up to the F5 generation. However, test-crosses of F1 progeny (ACR10 X P7076) with strain P6497 result in the release of silencing of Avr3a. Expression of Avr3a in the progeny is variable and correlates with the phenotypic penetrance of the avirulence trait. The F1 progeny from a direct cross of P6497 X ACR10 segregate for inheritance for Avr3a expression, a result that could not be explained by parental imprinting or heterozygosity. Analysis of small RNA arising from the Avr3a gene sequence in the parental strains and hybrid progeny suggests that the presence of small RNA is necessary but not sufficient for gene silencing. Overall, we conclude that inheritance of the Avr3a gene silenced phenotype relies on factors that are variable among P. sojae strains.

  2. Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns.

    PubMed

    Sánchez, Flora; Manrique, Pilar; Mansilla, Carmen; Lunello, Pablo; Wang, Xiaowu; Rodrigo, Guillermo; López-González, Silvia; Jenner, Carol; González-Melendi, Pablo; Elena, Santiago F; Walsh, John; Ponz, Fernando

    2015-12-01

    Turnip mosaic virus (TuMV) infections affect many Arabidopsis developmental traits. This paper analyzes, at different levels, the development-related differential alterations induced by different strains of TuMV, represented by isolates UK 1 and JPN 1. The genomic sequence of JPN 1 TuMV isolate revealed highest divergence in the P1 and P3 viral cistrons, upon comparison with the UK 1 sequence. Infectious viral chimeras covering the whole viral genome uncovered the P3 cistron as a major viral determinant of development alterations, excluding the involvement of the PIPO open reading frame. However, constitutive transgenic expression of P3 in Arabidopsis did not induce developmental alterations nor modulate the strong effects induced by the transgenic RNA silencing suppressor HC-Pro from either strain. This highlights the importance of studying viral determinants within the context of actual viral infections. Transcriptomic and interactomic analyses at different stages of plant development revealed large differences in the number of genes affected by the different infections at medium infection times but no significant differences at very early times. Biological functions affected by UK 1 (the most severe strain) included mainly stress response and transport. Most cellular components affected cell-wall transport or metabolism. Hubs in the interactome were affected upon infection. PMID:26646245

  3. Strain Specific Factors Control Effector Gene Silencing in Phytophthora sojae.

    PubMed

    Shrestha, Sirjana Devi; Chapman, Patrick; Zhang, Yun; Gijzen, Mark

    2016-01-01

    The Phytophthora sojae avirulence gene Avr3a encodes an effector that is capable of triggering immunity on soybean plants carrying the resistance gene Rps3a. P. sojae strains that express Avr3a are avirulent to Rps3a plants, while strains that do not are virulent. To study the inheritance of Avr3a expression and virulence towards Rps3a, genetic crosses and self-fertilizations were performed. A cross between P. sojae strains ACR10 X P7076 causes transgenerational gene silencing of Avr3a allele, and this effect is meiotically stable up to the F5 generation. However, test-crosses of F1 progeny (ACR10 X P7076) with strain P6497 result in the release of silencing of Avr3a. Expression of Avr3a in the progeny is variable and correlates with the phenotypic penetrance of the avirulence trait. The F1 progeny from a direct cross of P6497 X ACR10 segregate for inheritance for Avr3a expression, a result that could not be explained by parental imprinting or heterozygosity. Analysis of small RNA arising from the Avr3a gene sequence in the parental strains and hybrid progeny suggests that the presence of small RNA is necessary but not sufficient for gene silencing. Overall, we conclude that inheritance of the Avr3a gene silenced phenotype relies on factors that are variable among P. sojae strains. PMID:26930612

  4. Prion recognition elements govern nucleation, strain specificity and species barriers

    PubMed Central

    Tessier, Peter M.; Lindquist, Susan

    2007-01-01

    Prions are proteins that can switch to self-perpetuating, infectious conformations. The abilities of prions to replicate, form structurally distinct strains, and to establish and overcome transmission barriers between species are poorly understood. We exploit surface-bound peptides to overcome complexities of investigating such problems in solution. For the yeast prion Sup35, we find that the switch to the prion state is controlled with exquisite specificity by small elements of primary sequence. Strikingly, these same sequence elements govern the formation of distinct self-perpetuating conformations (prion strains) and determine species-specific seeding activities. A Sup35 chimera that traverses the transmission barrier between two yeast species possesses the critical sequence elements from both. Using this chimera, we show that the influence of environment and mutations on the formation of species-specific strains is driven by selective recognition of one or the other sequence element. Thus, critical aspects of prion conversion are enciphered by subtle differences between small, highly-specific recognition elements. PMID:17495929

  5. Comparison of Experimental Diagnostic Signals with Numerical Predictions

    NASA Astrophysics Data System (ADS)

    Comer, K.; Turnbull, A. D.

    1997-11-01

    A new code has been written to compare experimental diagnostic signals with those predicted by stability code output and experimental equilibrium diagnostic signals such as SXR, ECE, BSE, and reflectometry. Comparison of expected and actual diagnostic signals will help distinguish or identify modes by the signals they produce, and will also help validate stability codes. Predicted diagnostic signals are obtained by taking the total time derivative of S, the signal amplitude, and assuming steady state conditions so that the partial time derivative can be set to zero. Multiplying by delta-time (Dt) results in δ S = tilde\\underlineξ \\cdot \\underlinenablaS, where δ S is the predicted diagnostic signal, tilde\\underlineξ is the plasma displacement predicted by various equilibrium codes (such as GATO or MARS), and \\underlinenablaS is the gradient of the equilibrium diagnostic signal. \\underlinenablaS may be obtained from an experimental equilibrium signal amplitude profile, or from a functional dependence of the signal amplitude on equilibrium temperature and density. Comparisons of predicted and actual signals from linear ideal and resistive codes show reasonable agreement with the measured signals in some cases, but there are also some significant discrepancies.

  6. Viral diagnostics: will new technology save the day?

    PubMed

    Spackman, Erica

    2012-01-01

    Technology for infectious agent detection continues to evolve, particularly molecular methods that first emerged in the mid-1970s. The goals of new technology in diagnostics, whether in humans or in animals, including poultry, are to achieve the highest sensitivity and specificity possible to accurately identify the infection status of an individual or flock in the shortest time possible. Ease of use, low cost and increased information from a single test (e.g. multiplexing) are also critical areas frequently targeted for improvement. New tests and modifications of current tests are reported often, and diagnostic tests are now commonly developed by commercial companies. As one would expect, most advances in diagnostic technology are applied first to human health, and then may be adapted to animal health if practical. In the present review the trends and novel innovative technologies in primarily viral diagnostics are reviewed and the practicality of these methods and application for poultry health are discussed briefly. Also, influenza will seem to be over-represented in viral diagnostics since it is frequently used as a proof-of-concept target for novel technology due to its importance for animal and public health. Finally, the review is intended to be a brief survey of some of the innovative diagnostic technologies reported in recent years. It is not entirely comprehensive of all technology and the author makes no claims or endorsements of any of the technology or products mentioned.

  7. PICADAR: a diagnostic predictive tool for primary ciliary dyskinesia

    PubMed Central

    Behan, Laura; Dimitrov, Borislav D.; Kuehni, Claudia E.; Hogg, Claire; Carroll, Mary; Evans, Hazel J.; Goutaki, Myrofora; Harris, Amanda; Packham, Samantha; Walker, Woolf T.

    2016-01-01

    Symptoms of primary ciliary dyskinesia (PCD) are nonspecific and guidance on whom to refer for testing is limited. Diagnostic tests for PCD are highly specialised, requiring expensive equipment and experienced PCD scientists. This study aims to develop a practical clinical diagnostic tool to identify patients requiring testing. Patients consecutively referred for testing were studied. Information readily obtained from patient history was correlated with diagnostic outcome. Using logistic regression, the predictive performance of the best model was tested by receiver operating characteristic curve analyses. The model was simplified into a practical tool (PICADAR) and externally validated in a second diagnostic centre. Of 641 referrals with a definitive diagnostic outcome, 75 (12%) were positive. PICADAR applies to patients with persistent wet cough and has seven predictive parameters: full-term gestation, neonatal chest symptoms, neonatal intensive care admittance, chronic rhinitis, ear symptoms, situs inversus and congenital cardiac defect. Sensitivity and specificity of the tool were 0.90 and 0.75 for a cut-off score of 5 points. Area under the curve for the internally and externally validated tool was 0.91 and 0.87, respectively. PICADAR represents a simple diagnostic clinical prediction rule with good accuracy and validity, ready for testing in respiratory centres referring to PCD centres. PMID:26917608

  8. Diagnostic Accuracy of Procalcitonin in Bacterial Meningitis Versus Nonbacterial Meningitis

    PubMed Central

    Wei, Ting-Ting; Hu, Zhi-De; Qin, Bao-Dong; Ma, Ning; Tang, Qing-Qin; Wang, Li-Li; Zhou, Lin; Zhong, Ren-Qian

    2016-01-01

    Abstract Several studies have investigated the diagnostic accuracy of procalcitonin (PCT) levels in blood or cerebrospinal fluid (CSF) in bacterial meningitis (BM), but the results were heterogeneous. The aim of the present study was to ascertain the diagnostic accuracy of PCT as a marker for BM detection. A systematic search of the EMBASE, Scopus, Web of Science, and PubMed databases was performed to identify studies published before December 7, 2015 investigating the diagnostic accuracy of PCT for BM. The quality of the eligible studies was assessed using the revised Quality Assessment for Studies of Diagnostic Accuracy method. The overall diagnostic accuracy of PCT detection in CSF or blood was pooled using the bivariate model. Twenty-two studies involving 2058 subjects were included in this systematic review and meta-analysis. The overall specificities and sensitivities were 0.86 and 0.80 for CSF PCT, and 0.97 and 0.95 for blood PCT, respectively. Areas under the summary receiver operating characteristic curves were 0.90 and 0.98 for CSF PCT and blood PCT, respectively. The major limitation of this systematic review and meta-analysis was the small number of studies included and the heterogeneous diagnostic thresholds adopted by eligible studies. Our meta-analysis shows that PCT is a useful biomarker for BM diagnosis. PMID:26986140

  9. Tomographic diagnostics of nonthermal plasmas

    NASA Astrophysics Data System (ADS)

    Denisova, Natalia

    2009-10-01

    In the previous work [1], we discussed a ``technology'' of tomographic method and relations between the tomographic diagnostics in thermal (equilibrium) and nonthermal (nonequilibrium) plasma sources. The conclusion has been made that tomographic reconstruction in thermal plasma sources is the standard procedure at present, which can provide much useful information on the plasma structure and its evolution in time, while the tomographic reconstruction of nonthermal plasma has a great potential at making a contribution to understanding the fundamental problem of substance behavior in strongly nonequilibrium conditions. Using medical terminology, one could say, that tomographic diagnostics of the equilibrium plasma sources studies their ``anatomic'' structure, while reconstruction of the nonequilibrium plasma is similar to the ``physiological'' examination: it is directed to study the physical mechanisms and processes. The present work is focused on nonthermal plasma research. The tomographic diagnostics is directed to study spatial structures formed in the gas discharge plasmas under the influence of electrical and gravitational fields. The ways of plasma ``self-organization'' in changing and extreme conditions are analyzed. The analysis has been made using some examples from our practical tomographic diagnostics of nonthermal plasma sources, such as low-pressure capacitive and inductive discharges. [0pt] [1] Denisova N. Plasma diagnostics using computed tomography method // IEEE Trans. Plasma Sci. 2009 37 4 502.

  10. New diagnostic tools in schistosomiasis.

    PubMed

    Utzinger, J; Becker, S L; van Lieshout, L; van Dam, G J; Knopp, S

    2015-06-01

    Schistosomiasis is a water-based parasitic disease that affects over 250 million people. Control efforts have long been in vain, which is one reason why schistosomiasis is considered a neglected tropical disease. However, since the new millennium, interventions against schistosomiasis are escalating. The initial impetus stems from a 2001 World Health Assembly resolution, urging member states to scale-up deworming of school-aged children with the anthelminthic drug praziquantel. Because praziquantel is safe, efficacious and inexpensive when delivered through the school platform, diagnosis before drug intervention was deemed unnecessary and not cost-effective. Hence, there was little interest in research and development of novel diagnostic tools. With the recent publication of the World Health Organization (WHO) Roadmap to overcome the impact of neglected tropical diseases in 2020, we have entered a new era. Elimination of schistosomiasis has become the buzzword and this has important ramifications for diagnostic tools. Indeed, measuring progress towards the WHO Roadmap and whether local elimination has been achieved requires highly accurate diagnostic assays. Here, we introduce target product profiles for diagnostic tools that are required for different stages of a schistosomiasis control programme. We provide an update of the latest developments in schistosomiasis diagnosis, including microscopic techniques, rapid diagnostic tests for antigen detection, polymerase chain reaction (PCR) assays and proxy markers for morbidity assessments. Particular emphasis is placed on challenges and solutions for new technologies to enter clinical practice.

  11. Diagnostic vitrectomy for infectious uveitis

    PubMed Central

    Jeroudi, Abdallah; Yeh, Steven

    2014-01-01

    The identification of an infectious or noninfectious uveitis syndrome is important to determine the range of therapeutic and prognostic implications of that disease entity. Diagnostic dilemmas arise with atypical history, atypical clinical presentations, inconclusive diagnostic workup, and persistent or worsened inflammation despite appropriate immunosuppression. More invasive intraocular testing is indicated in these situations particularly in infectious uveitis where a delay in treatment may result in worsening of the patient’s disease and a poor visual outcome. Laboratory analysis of vitreous fluid via diagnostic pars plana vitrectomy is an important technique in the diagnostic armamentarium, but the most important aspects of sample collection include rapid processing, close coordination with an ophthalmic pathology laboratory, and directed testing on this limited collected sample. Culture and staining has utility in bacterial, fungal, and nocardial infection. Polymerase chain reaction (PCR) analysis has shown promising results for bacterial endophthalmitis and infection with mycobacterium tuberculosis whereas PCR testing for viral retinitides and ocular toxoplasmosis has a more established role. Antibody testing is appropriate for toxoplasmosis and toxocariasis, and may be complementary to PCR for viral retinitis. Masquerade syndromes represent neoplastic conditions that clinically appear as infectious or inflammatory conditions and should be considered as part of the differential diagnosis. Diagnostic vitrectomy and chorioretinal biopsy are thus critical tools for the management of patients in whom an infectious etiology of uveitis is suspected. PMID:24613892

  12. Diagnostics in Japan's microgravity experiments

    NASA Technical Reports Server (NTRS)

    Kadota, Toshikazu

    1995-01-01

    The achievement of the combustion research under microgravity depends substantially on the availability of diagnostic systems. The non-intrusive diagnostic systems are potentially applicable for providing the accurate, realistic and detailed information on momentum, mass and energy transport, complex gas phase chemistry, and phase change in the combustion field under microgravity. The non-intrusive nature of optical instruments is essential to the measurement of combustion process under microgravity which is very nervous to any perturbation. However, the implementation of the non-intrusive combustion diagnostic systems under microgravity is accompanied by several constraints. Usually, a very limited space is only available for constructing a highly sophisticated system which is so sensitive that it is easily affected by the magnitude of the gravitational force, vibration and heterogeneous field of temperature and density of the environments. The system should be properly adjusted prior to the experiment. Generally, it is quite difficult to tune the instruments during measurements. The programmed sequence of operation should also be provided. Extensive effort has been toward the development of non-intrusive diagnostic systems available for the combustion experiments under microgravity. This paper aims to describe the current art and the future strategy on the non-intrusive diagnostic systems potentially applicable to the combustion experiments under microgravity in Japan.

  13. Viral diagnostics: will new technology save the day

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Technology for infectious agent detection continues to evolve, particularly molecular methods which first emerged in the mid-1970’s. The goals of new technology in diagnostics are to achieve the highest sensitivity and specificity possible to accurately identify the infection status of an individua...

  14. Factors influencing hospital employee motivation: a diagnostic instrument.

    PubMed

    Alpander, G G

    1985-01-01

    This article presents a diagnostic instrument which identifies the most salient elements of employee motivation in hospitals. Application of this instrument in medium-sized U.S. hospitals indicates that recognition is the primary motivating factor. The results are greatly different in other countries.

  15. Pea Disease Diagnostic Series- Rhizoctonia seed, seedling and root rot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pea disease diagnostic cards that growers can carry with them into the field that are water resistant and durable which can be used to identify the signs and symptoms of major pea pathogens were developed. Color photographs of major fungal, bacterial, and viral pathogens on peas and a brief descript...

  16. Diagnostic Delay and Antibiotic Overuse in Acute Pulmonary Blastomycosis.

    PubMed

    Alpern, Jonathan D; Bahr, Nathan C; Vazquez-Benitez, Gabriela; Boulware, David R; Sellman, Jonathan S; Sarosi, George A

    2016-04-01

    The diagnosis of blastomycosis is often delayed. We identified 28 cases of pulmonary blastomycosis in a retrospective chart review. Most patients received multiple antibiotic courses before being diagnosed, and the sputum KOH smear was rarely used. Diagnostic delay can be decreased with higher suspicion for pulmonary blastomycosis and early use of the sputum KOH smear. PMID:27419155

  17. Diagnostic Assessment of Writing: A Comparison of Two Rating Scales

    ERIC Educational Resources Information Center

    Knoch, Ute

    2009-01-01

    Alderson (2005) suggests that diagnostic tests should identify strengths and weaknesses in learners' use of language and focus on specific elements rather than global abilities. However, rating scales used in performance assessment have been repeatedly criticized for being imprecise and therefore often resulting in holistic marking by raters…

  18. Enhancing ADHD and LD Diagnostic Accuracy Using Career Instruments

    ERIC Educational Resources Information Center

    Dipeolu, Abiola; Hargrave, Stephanie; Storlie, Cassandra A.

    2015-01-01

    Individuals diagnosed with mental health disorders may have work-related difficulties that impact functioning in all life domains. With limited research on the integration of career and mental health counseling, authors used a discriminant function analysis to assess the predictability of accurately identifying diagnostic categories among 258…

  19. Clearinghouse: Diagnostic Categories and Obstetric Complication Histories in Disturbed Children

    ERIC Educational Resources Information Center

    McNeil, Thomas F.; Wiegerink, Ronald

    1971-01-01

    No significant differences in the obstetric complication measures were found among the various diagnostic groupings of 61 psychologically or behaviorally disturbed children, nor between any complication measures and any of the three disturbed behavior patterns identified (psychotic withdrawal, acting-out aggression, organic signs). (KW)

  20. Diagnostic Delay and Antibiotic Overuse in Acute Pulmonary Blastomycosis.

    PubMed

    Alpern, Jonathan D; Bahr, Nathan C; Vazquez-Benitez, Gabriela; Boulware, David R; Sellman, Jonathan S; Sarosi, George A

    2016-04-01

    The diagnosis of blastomycosis is often delayed. We identified 28 cases of pulmonary blastomycosis in a retrospective chart review. Most patients received multiple antibiotic courses before being diagnosed, and the sputum KOH smear was rarely used. Diagnostic delay can be decreased with higher suspicion for pulmonary blastomycosis and early use of the sputum KOH smear.

  1. A Tool for Helping Veterinary Students Learn Diagnostic Problem Solving.

    ERIC Educational Resources Information Center

    Danielson, Jared A.; Bender, Holly S.; Mills, Eric M.; Vermeer, Pamela J.; Lockee, Barbara B.

    2003-01-01

    Describes the result of implementing the Problem List Generator, a computer-based tool designed to help clinical pathology veterinary students learn diagnostic problem solving. Findings suggest that student problem solving ability improved, because students identified all relevant data before providing a solution. (MES)

  2. Exploring Undergraduates' Understanding of Photosynthesis Using Diagnostic Question Clusters

    ERIC Educational Resources Information Center

    Parker, Joyce M.; Anderson, Charles W.; Heidemann, Merle; Merrill, John; Merritt, Brett; Richmond, Gail; Urban-Lurain, Mark

    2012-01-01

    We present a diagnostic question cluster (DQC) that assesses undergraduates' thinking about photosynthesis. This assessment tool is not designed to identify individual misconceptions. Rather, it is focused on students' abilities to apply basic concepts about photosynthesis by reasoning with a coordinated set of practices based on a few scientific…

  3. Diagnostic Delay and Antibiotic Overuse in Acute Pulmonary Blastomycosis

    PubMed Central

    Alpern, Jonathan D.; Bahr, Nathan C.; Vazquez-Benitez, Gabriela; Boulware, David R.; Sellman, Jonathan S.; Sarosi, George A.

    2016-01-01

    The diagnosis of blastomycosis is often delayed. We identified 28 cases of pulmonary blastomycosis in a retrospective chart review. Most patients received multiple antibiotic courses before being diagnosed, and the sputum KOH smear was rarely used. Diagnostic delay can be decreased with higher suspicion for pulmonary blastomycosis and early use of the sputum KOH smear. PMID:27419155

  4. Factors influencing hospital employee motivation: a diagnostic instrument.

    PubMed

    Alpander, G G

    1985-01-01

    This article presents a diagnostic instrument which identifies the most salient elements of employee motivation in hospitals. Application of this instrument in medium-sized U.S. hospitals indicates that recognition is the primary motivating factor. The results are greatly different in other countries. PMID:10270713

  5. Diagnostics for the ATA beam propagation experiments

    SciTech Connect

    Fessenden, T.J.; Atchison, W.L.; Barletta, W.A.

    1981-11-01

    This report contains a discussion of the diagnostics required for the beam propagation experiment to be done with the ATA accelerator. Included are a list of the diagnostics needed; a description of the ATA experimental environment; the status of beam diagnostics available at Livermore including recent developments, and a prioritized list of accelerator and propagation diagnostics under consideration or in various stages of development.

  6. Diagnostics for neutral-beam-heated tokamaks

    SciTech Connect

    Goldston, R.J.

    1982-12-01

    Diagnostic techniques for neutral-beam-heated tokamak plasmas fall into three categories: (1) magnetic diagnostics for measurements of gross stored energy, (2) profile diagnostics for measurements of stored thermal and beam energy, impurity content and plasma rotation, and (3) fast time resolution diagnostics to study MHD fluctuations and micro-turbulence.

  7. Appropriateness of diagnostics tests.

    PubMed

    Cappelletti, P

    2016-05-01

    The evolution of the concept of 'appropriateness', in the three past decades, from 'no harm' and 'no waste' to 'medical decision-making' and 'determining outcomes' highlights two main points: its foundation is evidence-based medicine, and it is a quality of every phase of the total testing process, not only for the selection of tests. Nevertheless, appropriateness in Laboratory Hematology, as well as in Laboratory Medicine, is an elusive concept: 'Appropriateness' interplays with 'patient's safety', 'healthcare costs', 'clinical decision-making', and 'effectiveness', and the criteria for appropriateness, mainly adherence to clinical guidelines, are often not evidence-based and not always consensus-based. Moreover, practising appropriateness is a complex issue because of the ambiguity of the criteria and targets, the never-ending work of implementing guidelines and their audit, and the uniqueness of the clinical situation of the individual patient. Authors agree on some practical rules: establishing a multidisciplinary and multiprofessional team, choosing carefully clinical targets, finding or building evidences, sharing guidelines with clinicians, choosing adequate tools for changing, working hard on implementation, identifying the 'right' laboratory methods and processes, checking progress indefinitely, providing information, interpretations, and consultations, and promoting feedback and audits. The success depends on the 'right' combination of educational, operative, and reinforcing interventions. Competences in organization, in implementation science, and in interpersonal relationship management are essential as well as knowledge and experience in Hematology, not only in Laboratory Hematology. PMID:27161094

  8. On identified predictive control

    NASA Technical Reports Server (NTRS)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  9. Identifying conical singularities

    SciTech Connect

    Oliveira-Neto, G. |

    1996-09-01

    A method based upon the concept of holonomy of a metric space{endash}time ({ital M},{ital g}), in order to identify the presence of conical singularities in {ital M} is proposed. The validity and usefulness of this so-called holonomy method is proven by applying it to a set of four-dimensional space{endash}times and one three-dimensional space{endash}time. The holonomy method predictions are confirmed by the comparison with the predictions obtained after coordinate transformations which take the metrics {ital g}, to a new basis where the global properties of conical singularities are explicitly seen. {copyright} {ital 1996 American Institute of Physics.}

  10. [Diagnostic protocol and special tests].

    PubMed

    Bellia, M; Pennarola, R

    2008-01-01

    Diagnostic protocol and special tests to ionizing radiations have a preventive function in the medical surveillance of the exposed worker. This protocol must be provided with laboratory and special test assessing fitness for working at the risk of ionizing radiations. The health of workers must be compatible with working conditions and radiation risk. This healthiness of workers is evalued in the time to give an assessment fitness for working at ionizing radiations. For this purpose the basic diagnostic protocol must guarantee minimum information about state of organs and apparatus in addition to the normality of the metabolisms. The diagnostic protocol of the exposed worker to ionizing radiations must be adapted to the specific clinical situation so as to finally make a costs-benefits balance sheet. PMID:19288808

  11. Molecular diagnostics of neurodegenerative disorders

    PubMed Central

    Agrawal, Megha; Biswas, Abhijit

    2015-01-01

    Molecular diagnostics provide a powerful method to detect and diagnose various neurological diseases such as Alzheimer's and Parkinson's disease. The confirmation of such diagnosis allows early detection and subsequent medical counseling that help specific patients to undergo clinically important drug trials. This provides a medical pathway to have better insight of neurogenesis and eventual cure of the neurodegenerative diseases. In this short review, we present recent advances in molecular diagnostics especially biomarkers and imaging spectroscopy for neurological diseases. We describe advances made in Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD), and finally present a perspective on the future directions to provide a framework for further developments and refinements of molecular diagnostics to combat neurodegenerative disorders. PMID:26442283

  12. Enhanced NIF neutron activation diagnostics

    SciTech Connect

    Yeamans, C. B.; Bleuel, D. L.; Bernstein, L. A.

    2012-10-15

    The NIF neutron activation diagnostic suite relies on removable activation samples, leading to operational inefficiencies and a fundamental lower limit on the half-life of the activated product that can be observed. A neutron diagnostic system measuring activation of permanently installed samples could remove these limitations and significantly enhance overall neutron diagnostic capabilities. The physics and engineering aspects of two proposed systems are considered: one measuring the {sup 89}Zr/{sup 89m}Zr isomer ratio in the existing Zr activation medium and the other using potassium zirconate as the activation medium. Both proposed systems could improve the signal-to-noise ratio of the current system by at least a factor of 5 and would allow independent measurement of fusion core velocity and fuel areal density.

  13. Optical beam diagnostics on PEP

    SciTech Connect

    Sabersky, A.P.

    1981-02-01

    In designing the PEP optical diagnostics we have been able to build on the experience gained with SPEAR. Most of the problems at SPEAR could be traced to the optical diagnostic system being inside the tunnel. A machine shutdown is required for any maintenance or modification. This implies that in order to make such an instrument successful, a large engineering effort must be mounted to ensure 100% operation at startup. The functions that do not work at startup may never be made to work; this has happened at several machines. Experimental setups are likewise risky and time consuming. A point which has been borne out in both SPEAR and PEP is that the mechanical part of the instrument, the special vacuum chamber, the optical mounts, the alignment and adjustments, require approximately 60% of the effort and cost of the optical diagnostics. It is far better to economize on detectors and electronics than on mechanical and optical essentials.

  14. Enhanced NIF neutron activation diagnostics.

    PubMed

    Yeamans, C B; Bleuel, D L; Bernstein, L A

    2012-10-01

    The NIF neutron activation diagnostic suite relies on removable activation samples, leading to operational inefficiencies and a fundamental lower limit on the half-life of the activated product that can be observed. A neutron diagnostic system measuring activation of permanently installed samples could remove these limitations and significantly enhance overall neutron diagnostic capabilities. The physics and engineering aspects of two proposed systems are considered: one measuring the (89)Zr/(89 m)Zr isomer ratio in the existing Zr activation medium and the other using potassium zirconate as the activation medium. Both proposed systems could improve the signal-to-noise ratio of the current system by at least a factor of 5 and would allow independent measurement of fusion core velocity and fuel areal density.

  15. Dual processing and diagnostic errors.

    PubMed

    Norman, Geoff

    2009-09-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. "Dual Process" theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be made with either a fast, unconscious, contextual process called System 1 or a slow, analytical, conscious, and conceptual process, called System 2. Exemplar theories of categorization propose that many category decisions in everyday life are made by unconscious matching to a particular example in memory, and these remain available and retrievable individually. I then review studies of clinical reasoning based on these theories, and show that the two processes are equally effective; System 1, despite its reliance in idiosyncratic, individual experience, is no more prone to cognitive bias or diagnostic error than System 2. Further, I review evidence that instructions directed at encouraging the clinician to explicitly use both strategies can lead to consistent reduction in error rates.

  16. Using and interpreting diagnostic tests.

    PubMed

    McKenna, Shawn L B; Dohoo, Ian R

    2006-03-01

    Diagnostic tests are invaluable to the practice of veterinary medicine. Using them correctly and interpreting the results appropriately depend on having a good understanding of the basic principles outlined in this article. Topics covered include sensitivity and specificity, agreement among tests, using multiple tests, and other issues related to the use and interpretation of diagnostic tests. The most important principle is recognition that the interpretation of test results varies across populations and requires an estimate of the prevalence of the infection (or disease) in the population being studied.

  17. Diagnostic imaging in bovine orthopedics.

    PubMed

    Kofler, Johann; Geissbühler, Urs; Steiner, Adrian

    2014-03-01

    Although a radiographic unit is not standard equipment for bovine practitioners in hospital or field situations, ultrasound machines with 7.5-MHz linear transducers have been used in bovine reproduction for many years, and are eminently suitable for evaluation of orthopedic disorders. The goal of this article is to encourage veterinarians to use radiology and ultrasonography for the evaluation of bovine orthopedic disorders. These diagnostic imaging techniques improve the likelihood of a definitive diagnosis in every bovine patient but especially in highly valuable cattle, whose owners demand increasingly more diagnostic and surgical interventions that require high-level specialized techniques.

  18. Diagnostic imaging in internal medicine

    SciTech Connect

    Eisenberg, R.L.

    1985-01-01

    This book examines medical diagnostic techniques. Topics considered include biological considerations in the approach to clinical medicines; infectious diseases; disorders of the heart; disorders of the vascular system; disorders of the respiratory system; diseases of the kidneys and urinary tract; disorders of the alimentary tract; disorders of the hepatobiliary system and pancreas; disorders of the hematopoietic system; disorders of bone and bone mineralization; disorders of the joints, connective tissues, and striated muscles; disorders of the nervous system; miscellaneous disorders; and procedures in diagnostic imaging.

  19. First Wall and Operational Diagnostics

    SciTech Connect

    Lasnier, C; Allen, S; Boedo, J; Groth, M; Brooks, N; McLean, A; LaBombard, B; Sharpe, J; Skinner, C; Whyte, D; Rudakov, D; West, W; Wong, C

    2006-06-19

    In this chapter we review numerous diagnostics capable of measurements at or near the first wall, many of which contribute information useful for safe operation of a tokamak. There are sections discussing infrared cameras, visible and VUV cameras, pressure gauges and RGAs, Langmuir probes, thermocouples, and erosion and deposition measurements by insertable probes and quartz microbalance. Also discussed are dust measurements by electrostatic detectors, laser scattering, visible and IR cameras, and manual collection of samples after machine opening. In each case the diagnostic is discussed with a view toward application to a burning plasma machine such as ITER.

  20. Non- contacting capacitive diagnostic device

    DOEpatents

    Ellison, Timothy

    2005-07-12

    A non-contacting capacitive diagnostic device includes a pulsed light source for producing an electric field in a semiconductor or photovoltaic device or material to be evaluated and a circuit responsive to the electric field. The circuit is not in physical contact with the device or material being evaluated and produces an electrical signal characteristic of the electric field produced in the device or material. The diagnostic device permits quality control and evaluation of semiconductor or photovoltaic device properties in continuous manufacturing processes.

  1. Recoverable Plasma Diagnostics Package (RPDP)

    NASA Technical Reports Server (NTRS)

    Roberts, B.

    1986-01-01

    The recoverable plasma diagnostics package (RPDP) is an ejectable and recoverable satellite with flight and ground support systems so that it can be utilized in three modes: attached to an remote manipulator system; tethered; or as a subsatellite. The satellite is well instrumented with particle and field diagnostic as well as optical sensors to: investigate the dynamics of the natural environment or ejected perturbations from particle beams; measure the characteristics and propagation of electrostatic and electromagnetic waves; study wave particle interactions; and study natural properties of the magnetosphere, ionosphere, and upper atmosphere.

  2. Recoverable Plasma Diagnostics Package (RPDP)

    NASA Technical Reports Server (NTRS)

    Roberts, W. T.

    1985-01-01

    The recoverable plasma diagnostics package (RPDP) is an ejectable and recoverable satellite with flight and ground support systems so that it can be utilized in three modes: attached to an remote manipulator system; tethered; or as a subsatellite. The satellite is well instrumented with particle and field diagnostic as well as optical sensors to: investigate the dynamics of the natural environment or ejected perturbations from particle beams; measure the characteristics and propagation of electrostatic and electromagnetic waves; study wave particle interactions; and study natural properties of the magnetosphere, ionosphere, and upper atmosphere.

  3. New Diagnostics for Childhood Tuberculosis.

    PubMed

    Chiang, Silvia S; Swanson, Douglas S; Starke, Jeffrey R

    2015-09-01

    The challenge of diagnosing childhood tuberculosis (TB) results from its paucibacillary nature and the difficulties of sputum collection in children. Mycobacterial culture, the diagnostic gold standard, provides microbiological confirmation in only 30% to 40% of childhood pulmonary TB cases and takes up to 6 weeks to result. Conventional drug susceptibility testing requires an additional 2 to 4 weeks after culture confirmation. In response to the low sensitivity and long wait time of the traditional diagnostic approach, many new assays have been developed. These new tools have shortened time to result; however, none of them offer greater sensitivity than culture.

  4. [The diagnostic possibilities of saliva].

    PubMed

    Kochurova, E V; Kozlov, S V

    2014-01-01

    Saliva is a clinically informative biological fluid which contains multitude of bio-markers. This characteristic makes it possible to carry out numerous analyzes for developing mode to test patient in situ, express-tests included. The diagnostic by saliva is a new area of more simple application both markers and analyzers that can be useful in diagnostic of diseases of oral cavity, oncological diseases included. The using of saliva expands perspectives for making clinical diagnosis and establishment of dynamics and monitoring of disease.

  5. List identifies threatened ecosystems

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  6. Identifying potential academic leaders

    PubMed Central

    White, David; Krueger, Paul; Meaney, Christopher; Antao, Viola; Kim, Florence; Kwong, Jeffrey C.

    2016-01-01

    Objective To identify variables associated with willingness to undertake leadership roles among academic family medicine faculty. Design Web-based survey. Bivariate and multivariable analyses (logistic regression) were used to identify variables associated with willingness to undertake leadership roles. Setting Department of Family and Community Medicine at the University of Toronto in Ontario. Participants A total of 687 faculty members. Main outcome measures Variables related to respondents’ willingness to take on various academic leadership roles. Results Of all 1029 faculty members invited to participate in the survey, 687 (66.8%) members responded. Of the respondents, 596 (86.8%) indicated their level of willingness to take on various academic leadership roles. Multivariable analysis revealed that the predictors associated with willingness to take on leadership roles were as follows: pursuit of professional development opportunities (odds ratio [OR] 3.79, 95% CI 2.29 to 6.27); currently holding at least 1 leadership role (OR 5.37, 95% CI 3.38 to 8.53); a history of leadership training (OR 1.86, 95% CI 1.25 to 2.78); the perception that mentorship is important for one’s current role (OR 2.25, 95% CI 1.40 to 3.60); and younger age (OR 0.97, 95% CI 0.95 to 0.99). Conclusion Willingness to undertake new or additional leadership roles was associated with 2 variables related to leadership experiences, 2 variables related to perceptions of mentorship and professional development, and 1 demographic variable (younger age). Interventions that support opportunities in these areas might expand the pool and strengthen the academic leadership potential of faculty members. PMID:27331226

  7. Role of advanced diagnostics for eosinophilic esophagitis.

    PubMed

    Hirano, Ikuo

    2014-01-01

    In eosinophilic esophagitis (EoE), diagnostic tests aid in the identification of pathophysiologic consequences and accurate detection of the disease. The EoE Endoscopic Reference Score (EREFS) classifies and grades the severity of the five major endoscopically identified esophageal features of EoE (edema, rings, exudates, furrows and strictures). The EREFS may be useful in the evaluation of disease severity and as an objective outcome of response to therapy. pH monitoring identifies the presence of abnormal degrees of acid exposure in the esophagus that characterizes gastroesophageal reflux disease. The presence of acid reflux, however, does not indicate that the reflux is responsible for esophageal eosinophilia. Esophageal manometry has not demonstrated a characteristic abnormality with sufficient sensitivity to make the test of diagnostic value in clinical practice. On the other hand, manometric characteristics of esophageal pressurization and longitudinal muscle dysfunction may help identify important pathophysiologic consequences of EoE. Esophageal impedance testing has demonstrated increased baseline mucosal impedance that correlates with increased epithelial permeability in EoE. Reduced mucosal integrity may provide intraluminal allergens access to antigen-presenting cells, serving as an early event in the pathogenesis of EoE. The functional luminal impedance probe (FLIP) provides quantitative assessment of esophageal mural compliance, a physiologic correlate of remodeling in EoE. Studies using FLIP have associated reductions in esophageal distensibility in EoE with the important outcome of food impaction risk. Finally, confocal endomicroscopy, multiphoton fluorescence microscopy and novel eosinophil-enhancing contrast agents are emerging methods that may allow for in vivo visualization of esophageal eosinophilic inflammation, thereby improving the detection and understanding of this emerging disease. PMID:24603385

  8. Advanced Diagnostics for High Pressure Spray Combustion.

    SciTech Connect

    Skeen, Scott A.; Manin, Julien Luc; Pickett, Lyle M.

    2014-06-01

    The development of accurate predictive engine simulations requires experimental data to both inform and validate the models, but very limited information is presently available about the chemical structure of high pressure spray flames under engine- relevant conditions. Probing such flames for chemical information using non- intrusive optical methods or intrusive sampling techniques, however, is challenging because of the physical and optical harshness of the environment. This work details two new diagnostics that have been developed and deployed to obtain quantitative species concentrations and soot volume fractions from a high-pressure combusting spray. A high-speed, high-pressure sampling system was developed to extract gaseous species (including soot precursor species) from within the flame for offline analysis by time-of-flight mass spectrometry. A high-speed multi-wavelength optical extinction diagnostic was also developed to quantify transient and quasi-steady soot processes. High-pressure sampling and offline characterization of gas-phase species formed following the pre-burn event was accomplished as well as characterization of gas-phase species present in the lift-off region of a high-pressure n-dodecane spray flame. For the initial samples discussed in this work several species were identified, including polycyclic aromatic hydrocarbons (PAH); however, quantitative mole fractions were not determined. Nevertheless, the diagnostic developed here does have this capability. Quantitative, time-resolved measurements of soot extinction were also accomplished and the novel use of multiple incident wavelengths proved valuable toward characterizing changes in soot optical properties within different regions of the spray flame.

  9. SDQ: discriminative validity and diagnostic potential

    PubMed Central

    Silva, Thaysa B. F.; Osório, Flávia L.; Loureiro, Sonia R.

    2015-01-01

    The Strengths and Difficulties Questionnaire (SDQ) was designed to screen for behavioral problems in youths based on cutoff points that favor the instrument's diagnostic sensitivity. The present study aimed to analyze the discriminative validity of the SDQ to identify behavioral difficulties and prosocial resources in school-age children compared with the diagnostic data collected by the corresponding sections of the Development and Well-being Assessment (DAWBA). In addition, new cutoff points that value specificity were defined for the SDQ scales, exploring its diagnostic potential. This study was conducted in Brazil and assessed a community convenience sample that consisted of 120 children aged 6–12 years who were not under psychological/psychiatric treatment. The mothers of the participants also completed a sociodemographic questionnaire. Descriptive statistics were used to clinically characterize the sample. A ROC curve was used to assess the discriminant validity of the SDQ, and new cutoff points were established to maximize the instrument's specificity. The new cutoff points enabled a significant increase in specificity without a significant loss of sensitivity, which favors approaches based on measures of screening and diagnosis yet does not damage the instrument's screening capacity. The following increases were observed: 100% for the depressive disorder scale (cutoff point = 7), 95.1% for the generalized anxiety disorder scale (cutoff point = 7), 46.6% for the conduct disorder scale (cutoff point = 6), 19.2% for the hyperactive disorder scale (cutoff point = 8), and 27.6% for the antisocial personality disorder scale (cutoff point = 6). A cutoff point of 8 was applied to the prosocial behavior scale, which exhibited a 62.1% increase in specificity. The use of more specific cutoff points generated more accurate results and favored SDQ's use, particularly in contexts of care that require more precise and faster procedures for identification of problems

  10. Managing waiting times in diagnostic medical imaging

    PubMed Central

    Nuti, Sabina; Vainieri, Milena

    2012-01-01

    Objective This paper aims to analyse the variation in the delivery of diagnostic imaging services in order to suggest possible solutions for the reduction of waiting times, increase the quality of services and reduce financial costs. Design This study provides a logic model to manage waiting times in a regional context. Waiting times measured per day were compared on the basis of the variability in the use rates of CT and MRI examinations in Tuscany for the population, as well as on the basis of the capacity offered with respect to the number of radiologists available. The analysis was performed at the local health authority level to support the decision-making process of local managers. Setting Diagnostic imaging services, in particular the CT and MRI examinations. The study involved all the 12 local health authorities that provide services for 3.7 million inhabitants of the Italian Tuscany Region. Primary and secondary outcome measures Participants: the study uses regional administrative data on outpatients and survey data on inpatient diagnostic examinations in order to measure productivity. Primary and secondary outcome measures The study uses the volumes per 1000 inhabitants, the days of waiting times and the number of examinations per radiologist. Variability was measured using the traditional SD measures. Results A significant variation in areas considered homogeneous in terms of age, gender or mortality may indicate that the use of radiological services is not optimal and underuse or overuse occurs and that there is room for improvement in the service organisation. Conclusions Considering that there is a high level of variability among district use rates and waiting times, this study provides managers with a specific tool to find the cause of the problem, identify a possible solution, assess the financial impact and initiate the eventual reduction of waste. PMID:23242480

  11. New Developments in Smart Bandage Technologies for Wound Diagnostics.

    PubMed

    McLister, Anna; McHugh, Jolene; Cundell, Jill; Davis, James

    2016-07-01

    The pH of wound fluid has long been recognized as an important diagnostic for assessing wound condition, but as yet there are few technological options available to the clinician. The availability of sensors that can measure wound pH, either in the clinic or at home could significantly improve clinical outcome - particularly in the early identification of complications such as infection. New material designs and electrochemical research strategies that are being targeted at wound diagnostics are identified and a critical overview of emerging research that could be pivotal in setting the direction for future devices is provided.

  12. Porphyria or Catatonia: Diagnostic Dilemma on the Medical Wards.

    PubMed

    Kurkjian, Natalie; Tucker, Phebe

    2016-01-01

    A 24-year-old Caucasian female, DD, was admitted to the medical service at an academic hospital with symptoms of weakness in bilateral lower extremities, falls, headaches, and altered mental status. Psychiatry was consulted to evaluate for psychiatric causes of her symptoms. This case presented a diagnostic challenge as the patient's identified symptoms changed almost daily, depending on what practitioner or medical service she encountered. In this study, we discuss the differential diagnoses, tests and treatments the patient received, with a review of literature helping differentiate between diagnostic parameters.

  13. Diagnostic Teaching, Writing and Mathematics.

    ERIC Educational Resources Information Center

    Fennel, Francis

    1991-01-01

    Provides ethnographic information about preservice teachers and their formative relationships to diagnostic teaching and letter writing within the school mathematics curriculum. Also, indicates that elementary school students benefit from letter writing as it relates to mathematics attitudes and achievement levels. (nine references) (JJK)

  14. Selected microgravity combustion diagnostic techniques

    NASA Technical Reports Server (NTRS)

    Griffin, Devon W.; Greenberg, Paul S.

    1993-01-01

    During FY 1989-1992, several diagnostic techniques for studying microgravity combustion have moved from the laboratory to use in reduced-gravity facilities. This paper discusses current instrumentation for rainbow schlieren deflectometry and thermophoretic sampling of soot from gas jet diffusion flames.

  15. Immunosensors in Clinical Laboratory Diagnostics.

    PubMed

    Justino, Celine I L; Duarte, Armando C; Rocha-Santos, Teresa A P

    2016-01-01

    The application of simple, cost-effective, rapid, and accurate diagnostic technologies for detection and identification of cardiac and cancer biomarkers has been a central point in the clinical area. Biosensors have been recognized as efficient alternatives for the diagnostics of various diseases due to their specificity and potential for application on real samples. The role of nanotechnology in the construction of immunological biosensors, that is, immunosensors, has contributed to the improvement of sensitivity, since they are based in the affinity between antibody and antigen. Other analytes than biomarkers such as hormones, pathogenic bacteria, and virus have also been detected by immunosensors for clinical point-of-care applications. In this chapter, we first introduced the various types of immunosensors and discussed their applications in clinical diagnostics over the recent 6 years, mainly as point-of-care technologies for the determination of cardiac and cancer biomarkers, hormones, pathogenic bacteria, and virus. The future perspectives of these devices in the field of clinical diagnostics are also evaluated. PMID:26975970

  16. Diagnostic techniques for thermal plasmas

    SciTech Connect

    Fincke, J.R.; Snyder, S.C.; Swank, W.D.; Haggard, D.C.; Reynolds, L.D.

    1994-12-31

    The plasma diagnostic techniques discussed are Rayleigh and coherent Thomson scattering, Coherent-Anti-Stokes-Raman Spectroscopy (CARS) and enthalpy probes. The quantities measured are heavy species and electron temperature, ionized fraction, plasma composition, and velocity. Examples of results from both subsonic and supersonic jets are presented and limitations discussed.

  17. Advanced diagnostics for reacting flows

    NASA Astrophysics Data System (ADS)

    Hanson, R. K.; Baganoff, D.; Bowman, C. T.; Byer, R. L.; Cantwell, B. J.

    1983-11-01

    Progress is reported for the third year of an interdisciplinary program to innovate modern diagnostic techniques for application to reacting flows. Project areas are: (1) fiber optic absorption/fluorescence probes for species measurements employing tunable ultraviolet, visable and infrared laser sources; (2) wavelength modulation spectroscopy, using rapid-scanning ultraviolet, visible and infrared laser sources, for measurements of species, temperature and absorption lineshapes, (3) quantitative flow visualization, including temporally and spatially resolved species measurements in a plane, using laser-induced fluorescence; (4) multiple-point velocity visualization; (5) plasma diagnostics, utilizing planar laser-induced fluorescence and wavelength modulation techniques; (6) diagnostic techniques for thermionic converter plasmas; (7) application of advanced diagnostic techniques for studies of turbulent reacting flows; (8) development of measurement techniques and a novel facility for investigations of droplet evaporation in turbulent flows; (9) holographic display techniques for 3-D visualization of flowfield data; (10) coherent anti-Stokes Raman spectroscopy (CARS) for temperature and velocity measurements in a supersonic jet; and (11) computed absorption tomography system for species measurements in a plane.

  18. Cognitive Diagnostic Modeling Using R

    ERIC Educational Resources Information Center

    Ravand, Hamdollah

    2015-01-01

    Cognitive diagnostic models (CDM) have been around for more than a decade but their application is far from widespread for mainly two reasons: (1) CDMs are novel, as compared to traditional IRT models. Consequently, many researchers lack familiarity with them and their properties, and (2) Software programs doing CDMs have been expensive and not…

  19. Advanced diagnostic methods in avionics

    NASA Astrophysics Data System (ADS)

    Popyack, Leonard Joseph, Jr.

    Advanced diagnostic systems facilitate further enhancement of reliability and safety of modern aircraft. Unlike classical reliability analyses, addressing specific classes of systems or devices, this research is aimed at the development of methods for assessment of the individual reliability characteristics of particular system components subjected to their unique histories of operational conditions and exposure to adverse environmental factors. Individual reliability characteristics are crucial for the implementation of the most efficient maintenance practice of flight-critical system components, known as "condition-based maintenance." The dissertation presents hardware and software aspects of a computer-based system, Time-Stress Monitoring Device, developed to record, store, and analyze raw data characterizing operational and environmental conditions and performance of electro-mechanical flight control system components and aircraft electronics (avionics). Availability of this data facilitates formulation and solution of such diagnostic problems as estimation of the probability of failure and life expectancy of particular components, failure detection, identification, and prediction. Statistical aspects of system diagnostics are considered. Particular diagnostic procedures utilizing cluster analysis, Bayes' technique, and regression analysis are formulated. Laboratory and simulation experiment that verify the obtained results are provided.

  20. Drive Diagnostic Filter Wheel Control

    SciTech Connect

    Uhlich, D.

    2007-07-17

    DrD Filter Wheel Control is National Instrument's Labview software that drives a Drive Diagnostic filter wheel. The software can drive the filter wheel between each end limit, detect the positive and negative limit and each home position and post the stepper motot values to an Excel spreadsheet. The software can also be used to cycle the assembly between the end limits.

  1. Maximum entropy beam diagnostic tomography

    SciTech Connect

    Mottershead, C.T.

    1985-01-01

    This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore. 11 refs., 4 figs.

  2. A Forward Search Procedure for Identifying Influential Observations in the Estimation of a Covariance Matrix

    ERIC Educational Resources Information Center

    Poon, Wai-Yin; Wong, Yuen-Kwan

    2004-01-01

    This study uses a Cook's distance type diagnostic statistic to identify unusual observations in a data set that unduly influence the estimation of a covariance matrix. Similar to many other deletion-type diagnostic statistics, this proposed measure is susceptible to masking or swamping effect in the presence of several unusual observations. In…

  3. R&D ERL: Diagnostics

    SciTech Connect

    Gassner, D.

    2010-01-01

    The Energy Recovery Linac (ERL) prototype project is currently under development at the Brookhaven National Laboratory. The ERL is expected to demonstrate energy recovery of high intensity beams with a current of up to a few hundred milliamps, while preserving the emittance of bunches with a charge of a few nanocoulombs produced by a high current SRF gun. To successfully accomplish this task the machine will include beam diagnostics that will be used for accurate characterization of the three dimensional beam phase space at the injection and recirculation energies, transverse and longitudinal beam matching, orbit alignment, beam current measurement, and machine protection. This report outlines requirements on the ERL diagnostics and describes its setup and modes of operation. The BNL Prototype ERL is an R&D effort aimed at reducing risks and costs associated with the proposed RHIC II electron cooler and eRHIC collider. The ERL will serve as a test bed for developing and testing instrumentation and studying physics and technological issues relevant to very high current ERL's. The prototype ERL, mated to a high current SRF gun, is expected to demonstrate production and energy recovery of high intensity, low emittance beams with a current of up to a few hundred milliamps. To successfully accomplish this task the ERL will include beam diagnostics required to characterize and tune beam parameters, as well as for machine protection. A preliminary diagnostics plan was presented in earlier publications. In this report, we describe the diagnostics presently planned to provide the data needed to meet these goals.

  4. Laser diagnostics of materials and chemistry

    SciTech Connect

    Hartford, A. Jr.

    1984-01-01

    Several examples are given of the ability of laser-based diagnostic techniques to make noninvasive measurements in hostile environments. Using coherent anti-Stokes Raman scattering both majority and minority species concentrations, as well as temperature, have been measured in the hot, high-pressure, particle-laden stream of a coal gasifier. In addition, numerous toxic and corrosive elements in the gasifier stream have been identified, but not yet quantified. In addition to providing the capability for making analytical determinations, laser techniques have been extensively employed to measure the rates of elementary chemical reactions. Recently, the temperature regime over which such meaurements are possible has been expanded. Although much of the laser diagnostic activity to date has involved investigations of the gas phase, significant information concerning heterogeneous phenomena can still be inferred. For instance, gas-solid reactions can manifest themselves as changes in vapor phase composition. Furthermore, in the future we expect expanded studies involving reactions of refractory metals (both atoms and clusters) and additional investigations of processes occurring at interfaces and on surfaces.

  5. Functional reasoning in diagnostic problem solving

    NASA Technical Reports Server (NTRS)

    Sticklen, Jon; Bond, W. E.; Stclair, D. C.

    1988-01-01

    This work is one facet of an integrated approach to diagnostic problem solving for aircraft and space systems currently under development. The authors are applying a method of modeling and reasoning about deep knowledge based on a functional viewpoint. The approach recognizes a level of device understanding which is intermediate between a compiled level of typical Expert Systems, and a deep level at which large-scale device behavior is derived from known properties of device structure and component behavior. At this intermediate functional level, a device is modeled in three steps. First, a component decomposition of the device is defined. Second, the functionality of each device/subdevice is abstractly identified. Third, the state sequences which implement each function are specified. Given a functional representation and a set of initial conditions, the functional reasoner acts as a consequence finder. The output of the consequence finder can be utilized in diagnostic problem solving. The paper also discussed ways in which this functional approach may find application in the aerospace field.

  6. Diagnostic findings in 132 great horned owls

    USGS Publications Warehouse

    Franson, J.C.; Little, S.E.

    1996-01-01

    We reviewed diagnostic findings for 132 great horned owl (Bubo virginianus) carcasses that were submitted to the National Wildlife Health Center from 1975-93. The carcasses were collected in 24 states but most came from Colorado (N = 21), Missouri (N = 12), Oregon (N = 12), Wyoming (N = 11), Illinois (N = 10), and Wisconsin (N = 9). Forty-two birds were emaciated but presumptive causes of emaciation, including old injuries, chronic lesions in various organs, and exposure to dieldrin, were found in only 16. A greater proportion of juveniles (56%) than adults (29%) were emaciated. Twelve owls were shot and 35 died from other traumatic injuries. Poisonings were diagnosed in 11 birds, including five associated with hydrogen sulfide exposure in oil fields and six cases of agricultural pesticide poisonings. Electrocution killed nine birds and infectious diseases were found in six. Miscellaneous conditions, including egg impaction, drowning, and visceral gout were diagnosed in three of the birds and the cause of death was undetermined in 14 owls. While this review identifies major diagnostic findings in great horned owls, sample bias prevents definitive conclusions regarding actual proportional causes of mortality.

  7. [Diagnostic tools for canine parvovirus infection].

    PubMed

    Proksch, A L; Hartmann, K

    2015-01-01

    Canine parvovirus (CPV) infection is one of the most important and common infectious diseases in dogs, in particular affecting young puppies when maternal antibodies have waned and vaccine-induced antibodies have not yet developed. The mortality rate remains high. Therefore, a rapid and safe diagnostic tool is essential to diagnose the disease to 1) provide intensive care treatment and 2) to identify virus-shedding animals and thus prevent virus spread. Whilst the detection of antibodies against CPV is considered unsuitable to diagnose the disease, there are several different methods to directly detect complete virus, virus antigen or DNA. Additionally, to test in commercial laboratories, rapid in-house tests based on ELISA are available worldwide. The specificity of the ELISA rapid in-house tests is reported to be excellent. However, results on sensitivity vary and high numbers of false-negative results are commonly reported, which potentially leads to misdiagnosis. Polymerase chain reaction (PCR) is a very sensitive and specific diagnostic tool. It also provides the opportunity to differentiate vaccine strains from natural infection when sequencing is performed after PCR.

  8. Diagnostics techniques in nonmuscle invasive bladder cancer

    PubMed Central

    Soubra, Ayman; Risk, Michael C.

    2015-01-01

    Introduction: Nonmuscle invasive bladder cancer (NMIBC) is the most common presentation of bladder cancer and is often treatable with endoscopic resection and intravesical therapies. Cystoscopy and urine cytology are the gold standard in diagnosis and surveillance but are limited by their sensitivity in some situations. We seek to provide an overview of recent additions to the diagnostic armamentarium for urologists treating this disease. Methods: Articles were identified through a literature review of articles obtained through PubMed searches including the terms “bladder cancer” and various diagnostic techniques described in the article. Results: A variety of urinary biomarkers are available to assist the diagnosis and management of patients with NMIBC. Many have improved sensitivity over urine cytology, but less specificity. There are certain situations in which this has proved valuable, but as yet these are not part of the standard guidelines for NMIBC. Fluorescence cystoscopy has level 1 evidence demonstrating increased rates of tumor detection and prolonged recurrence-free survival when utilized for transurethral resection. Other technologies seeking to enhance cystoscopy, such as narrow band imaging, confocal laser endomicroscopy, and optical coherence tomography are still under evaluation. Conclusions: A variety of urine biomarker and adjunctive endoscopic technologies have been developed to assist the management of NMIBC. While some, such as fluorescence cystoscopy, have demonstrated a definite benefit in this disease, others are still finding their place in the diagnosis and treatment of this disease. Future studies should shed light on how these can be incorporated to improve outcomes in NMIBC. PMID:26604438

  9. Dynamic diagnostic and decision procedures under uncertainty

    SciTech Connect

    Baranov, V.V.

    1995-01-01

    In this paper, we consider uncertainty that arises when the true state x {element_of} E is not accessible to direct observation and remains unknown. Instead, we observe some features {theta} {element_of} {Theta} that carry a certain information about the true state. This information is described by the conditional distribution P({Theta}{vert_bar}E), which we call the linkage distribution. Regarding this distribution we assume that it exists but is unknown. This leads to uncertainty with respect to states from E and the linkage distribution P({Theta}{vert_bar}E), which we denote by NEP. The substantive problem can be stated as follows: from observations of the features {theta}{element_of}{Theta} made at each time instant n = 1,2,...,recognize the state x {element_of} E, identify the linkage distribution P, and use the results of recognition and identification to choose a decision y {element_of} Y so that the decision process is optimal in some sense. State recognition is the subject of diagnostics. The uncertainty NEP thus generates a problem of diagnostics and dynamic decision making.

  10. Diagnostic imaging techniques in thyroid cancer

    SciTech Connect

    Friedman, M.; Toriumi, D.M.; Mafee, M.F.

    1988-02-01

    With the refinement of fine-needle aspiration, the specific applications of thyroid imaging techniques need to be reevaluated for efficiency and cost containment. No thyroid imaging test should be routinely obtained. Radionuclide scanning is most beneficial in evaluating the functional status of thyroid nodules when fine-needle aspiration is inadequate, the findings are benign, or when there is no discrete nodule that is palpated in an enlarged gland. When fine-needle aspiration is unavailable or unreliable, radionuclide scanning becomes a first-line diagnostic tool. Ultrasonography should be used primarily for identifying a solid component of a cystic nodule, determining the size of nodules on thyroxine suppression that are not easily palpable, or for performing guided fine-needle aspiration. Computerized tomography and magnetic resonance imaging both have a definite role in the evaluation of thyroid tumors. Magnetic resonance imaging is superior to computerized tomography for the evaluation of metastatic, retrotracheal, or mediastinal involvement of large thyroid tumors or goiters. Careful selection of the diagnostic techniques will ensure more accurate diagnosis and reduce unnecessary patient costs in the treatment of thyroid cancer.

  11. Reducing Diagnostic Errors through Effective Communication: Harnessing the Power of Information Technology

    PubMed Central

    Naik, Aanand Dinkar; Rao, Raghuram; Petersen, Laura Ann

    2008-01-01

    Diagnostic errors are poorly understood despite being a frequent cause of medical errors. Recent efforts have aimed to advance the "basic science" of diagnostic error prevention by tracing errors to their most basic origins. Although a refined theory of diagnostic error prevention will take years to formulate, we focus on communication breakdown, a major contributor to diagnostic errors and an increasingly recognized preventable factor in medical mishaps. We describe a comprehensive framework that integrates the potential sources of communication breakdowns within the diagnostic process and identifies vulnerable steps in the diagnostic process where various types of communication breakdowns can precipitate error. We then discuss potential information technology-based interventions that may have efficacy in preventing one or more forms of these breakdowns. These possible intervention strategies include using new technologies to enhance communication between health providers and health systems, improve patient involvement, and facilitate management of information in the medical record. PMID:18373151

  12. [Cross-Mapping: diagnostic labels formulated according to the ICNP® versus diagnosis of NANDA International].

    PubMed

    Tannure, Meire Chucre; Salgado, Patrícia de Oliveira; Chianca, Tânia Couto Machado

    2014-01-01

    This descriptive study aimed at elaborating nursing diagnostic labels according to ICNP®; conducting a cross-mapping between the diagnostic formulations and the diagnostic labels of NANDA-I; identifying the diagnostic labels thus obtained that were also listed in the NANDA-I; and mapping them according to Basic Human Needs. The workshop technique was applied to 32 intensive care nurses, the cross-mapping and validation based on agreement with experts. The workshop produced 1665 diagnostic labels which were further refined into 120 labels. They were then submitted to a cross-mapping process with both NANDA-I diagnostic labels and the Basic Human Needs. The mapping results underwent content validation by two expert nurses leading to concordance rates of 92% and 100%. It was found that 63 labels were listed in NANDA-I and 47 were not.

  13. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder.

    PubMed

    Ziats, Mark N; Rennert, Owen M

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome. PMID:27200076

  14. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder

    PubMed Central

    Ziats, Mark N.; Rennert, Owen M.

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome. PMID:27200076

  15. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder.

    PubMed

    Ziats, Mark N; Rennert, Owen M

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome.

  16. The Clinical and Health Economic Value of Clinical Laboratory Diagnostics

    PubMed Central

    Mitchell, Cheryl; Anderson, Andy; Farkas, Norbert; Batrla, Richard

    2015-01-01

    The ultimate goal of diagnostic testing is to guide disease management in order to improve patient outcomes and patient well-being. Patient populations are rarely homogenous and accurate diagnostic tests can dissect the patient population and identify those patients with similar symptoms but very different underlying pathophysiology that will respond differently to different treatments. This stratification of patients can direct patients to appropriate treatment and is likely to result in clinical benefits for patients and economic benefits for the healthcare system. In this article we look at the clinical and economic benefits afforded by clinical laboratory diagnostics in three disease areas that represent substantial clinical and healthcare burdens to society; heart failure, Alzheimer’s disease and asthma.

  17. The Clinical and Health Economic Value of Clinical Laboratory Diagnostics

    PubMed Central

    Mitchell, Cheryl; Anderson, Andy; Farkas, Norbert; Batrla, Richard

    2015-01-01

    The ultimate goal of diagnostic testing is to guide disease management in order to improve patient outcomes and patient well-being. Patient populations are rarely homogenous and accurate diagnostic tests can dissect the patient population and identify those patients with similar symptoms but very different underlying pathophysiology that will respond differently to different treatments. This stratification of patients can direct patients to appropriate treatment and is likely to result in clinical benefits for patients and economic benefits for the healthcare system. In this article we look at the clinical and economic benefits afforded by clinical laboratory diagnostics in three disease areas that represent substantial clinical and healthcare burdens to society; heart failure, Alzheimer’s disease and asthma. PMID:27683481

  18. Pigmented purpuric dermatosis or mycosis fungoides: A diagnostic dilemma.

    PubMed

    Riyaz, Najeeba; Sasidharanpillai, Sarita; Abdul Latheef, Ettappurath N; Davul, Hena; Ashraf, Febin

    2016-01-01

    Pigmented purpuric dermatoses (PPD), a group of vascular disorders with variable clinical picture is reported in all races and age groups with a male predilection. There are reports of mycosis fungoides manifesting as pigmented purpura as well as progression of PPD to cutaneous T-cell lymphoma. The diagnostic dilemma is compounded by PPD manifesting histological similarity to mycosis fungoides. Currently, it is believed that PPD with monoclonal T-cell population is more likely to progress to malignancy. We report a 31-year-old male patient who presented with the lichenoid clinical variant of PPD lesions that mimicked mycosis fungoides on histopathology. Gene rearrangement studies identified a polyclonal T-cell population. The patient responded to photochemotherapy, which is beneficial in both PPD and mycosis fungoides. Our case signifies the limitations of current diagnostic modalities in accurately distinguishing PPD from cutaneous lymphoma. Data on disease progression in similar cases may enable us to formulate better diagnostic definitions.

  19. Pigmented purpuric dermatosis or mycosis fungoides: A diagnostic dilemma

    PubMed Central

    Riyaz, Najeeba; Sasidharanpillai, Sarita; Abdul Latheef, Ettappurath N.; Davul, Hena; Ashraf, Febin

    2016-01-01

    Pigmented purpuric dermatoses (PPD), a group of vascular disorders with variable clinical picture is reported in all races and age groups with a male predilection. There are reports of mycosis fungoides manifesting as pigmented purpura as well as progression of PPD to cutaneous T-cell lymphoma. The diagnostic dilemma is compounded by PPD manifesting histological similarity to mycosis fungoides. Currently, it is believed that PPD with monoclonal T-cell population is more likely to progress to malignancy. We report a 31-year-old male patient who presented with the lichenoid clinical variant of PPD lesions that mimicked mycosis fungoides on histopathology. Gene rearrangement studies identified a polyclonal T-cell population. The patient responded to photochemotherapy, which is beneficial in both PPD and mycosis fungoides. Our case signifies the limitations of current diagnostic modalities in accurately distinguishing PPD from cutaneous lymphoma. Data on disease progression in similar cases may enable us to formulate better diagnostic definitions. PMID:27294054

  20. Identifying Adolescent Sleep Problems

    PubMed Central

    Short, Michelle A.; Gradisar, Michael; Gill, Jason; Camfferman, Danny

    2013-01-01

    Objectives To examine the efficacy of self-report and parental report of adolescent sleep problems and compare these findings to the incidence of adolescents who fulfill clinical criteria for a sleep problem. Sleep and daytime functioning factors that predict adolescents’ self-identification of a sleep problem will also be examined. Method 308 adolescents (aged 13–17 years) from eight socioeconomically diverse South Australian high schools participated in this study. Participants completed a survey battery during class time, followed by a 7-day Sleep Diary and the Flinders Fatigue Scale completed on the final day of the study. Parents completed a Sleep, Medical, Education and Family History Survey. Results The percentage of adolescents fulfilling one or more of the criteria for a sleep problem was inordinately high at 66%. Adolescent self-reporting a sleep problem was significantly lower than the adolescents who had one or more of the clinical criteria for a sleep problem (23.1% vs. 66.6%; χ2 = 17.46, p<.001). Parental report of their adolescent having a sleep problem was significantly lower than adolescent self-report (14.3% vs. 21.1%, p<.001). Adolescents who reported unrefreshing sleep were 4.81 times more likely to report a sleep problem. For every hour that bedtime was delayed, the odds of self-reporting a sleep problem increased by 1.91 times, while each additional 10 minutes taken to fall asleep increased the odds 1.40 times. Conclusion While many adolescents were found to have sleep patterns indicative of a sleep problem, only a third of this number self-identify having a sleep problem, while only a sixth of this number are indicated by parental report. This study highlights important features to target in future sleep education and intervention strategies for both adolescents and parents. PMID:24086501

  1. Irritable bowel syndrome: diagnostic approaches in clinical practice

    PubMed Central

    Burbige, Eugene J

    2010-01-01

    Background: Irritable bowel syndrome (IBS), a functional gastrointestinal disorder long considered a diagnosis of exclusion, has chronic symptoms that vary over time and overlap with those of non-IBS disorders. Traditional symptom-based criteria effectively identify IBS patients but are not easily applied in clinical practice, leaving >40% of patients to experience symptoms up to 5 years before diagnosis. Objective: To review the diagnostic evaluation of patients with suspected IBS, strengths and weaknesses of current methodologies, and newer diagnostic tools that can augment current symptom-based criteria. Methods: The peer-reviewed literature (PubMed) was searched for primary reports and reviews using the limiters of date (1999–2009) and English language and the search terms irritable bowel syndrome, diagnosis, gastrointestinal disease, symptom-based criteria, outcome, serology, and fecal markers. Abstracts from Digestive Disease Week 2008–2009 and reference lists of identified articles were reviewed. Results: A disconnect is apparent between practice guidelines and clinical practice. The American Gastroenterological Association and American College of Gastroenterology recommend diagnosing IBS in patients without alarm features of organic disease using symptom-based criteria (eg, Rome). However, physicians report confidence in a symptom-based diagnosis without further testing only up to 42% of the time; many order laboratory tests and perform sigmoidoscopies or colonoscopies despite good evidence showing no utility for this work-up in uncomplicated cases. In the absence of diagnostic criteria easily usable in a busy practice, newer diagnostic methods, such as stool-form examination, fecal inflammatory markers, and serum biomarkers, have been proposed as adjunctive tools to aid in an IBS diagnosis by increasing physicians’ confidence and changing the diagnostic paradigm to one of inclusion rather than exclusion. Conclusion: New adjunctive testing for IBS can

  2. 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.

  3. Tinea cutis glabrae: causes of diagnostic challenge

    PubMed Central

    Łuczkowska, Magdalena; Żaba, Ryszard; Adamski, Zygmunt

    2014-01-01

    Dermatophytoses belong to the most common disease entities encountered in everyday dermatological practice. Despite the fact that their clinical presentation, course and treatment response remain rather typical, they often present a considerable diagnostic and therapeutic challenge. We present a case of a 54-year-old male who presented to the outpatient clinic of the Department of Dermatology in December 2012 with the diagnosis of erythema gyratum repens for further diagnosis and treatment of skin lesions gradually intensifying in the previous 2 years. The skin changes presented as spreading annular erythematous lesions, with papules and plaques located peripherally, and accompanying pruritus. Due to the clinical presentation and anamnesis, working conditions (poultry farm), and lack of response to previous treatment, mycological culture was performed. Epithelial scrapings of the trunk and the groins proved to be positive. After 3 weeks, Trichophyton mentagrophytes var mentagrophytes was identified by epithelial cell culture. PMID:25610361

  4. Current early diagnostic biomarkers of prostate cancer

    PubMed Central

    Qu, Min; Ren, Shan-Cheng; Sun, Ying-Hao

    2014-01-01

    Prostate cancer (PCa) has become to have the highest incidence and the second mortality rate in western countries, affecting men's health to a large extent. Although prostate-specific antigen (PSA) was discovered to help diagnose the cancer in an early stage for decades, its specificity is relative low, resulting in unnecessary biopsy for healthy people and over-treatment for patients. Thus, it is imperative to identify more and more effective biomarkers for early diagnosis of PCa in order to distinguish patients from healthy populations, which helps guide an early treatment to lower disease-related mortality by noninvasive or minimal invasive approaches. This review generally describes the current early diagnostic biomarkers of PCa in addition to PSA and summarizes the advantages and disadvantages of these biomarkers. PMID:24830695

  5. Diagnostic procedures for submucosal tumors in the gastrointestinal tract

    PubMed Central

    Ponsaing, Laura Graves; Kiss, Katalin; Loft, Annika; Jensen, Lise Ingemann; Hansen, Mark Berner

    2007-01-01

    This review is part one of three, which will present an update on diagnostic procedures for gastrointestinal (GI) submucosal tumors (SMTs). Part two identifies the classification and part three the therapeutic methods regarding GI SMTs. Submucosal tumors are typically asymptomatic and therefore encountered incidentally. Advances in diagnostic tools for gastrointestinal submucosal tumors have emerged over the past decade. The aim of this paper is to provide the readers with guidelines for the use of diagnostic procedures, when a submucosal tumor is suspected. Literature searches were performed to find information on diagnostics for gastrointestinal submucosal tumors. Based on the searches, the optimal diagnostic procedures and specific features of the submucosal tumors could be outlined. Standard endoscppy, capsule endoscopy and push-and-pull enteroscopy (PPE) together with barium contrast X-ray do not alone provide sufficient information, when examining submucosal tumors. Endoscopic ultrasound (EUS), computed tomography (CT), magnetic resonance imaging (MRI) and fluorodeoxyglucose-labeled positron emission tomography (FDG-PET) are recommended as supplementary tools. PMID:17659668

  6. Diagnostic marker signature for esophageal cancer from transcriptome analysis.

    PubMed

    Warnecke-Eberz, Ute; Metzger, Ralf; Hölscher, Arnulf H; Drebber, Uta; Bollschweiler, Elfriede

    2016-05-01

    Esophageal cancer is often diagnosed at an advanced stage. Diagnostic markers are needed for achieving a cure in esophageal cancer detecting and treating tumor cells earlier. In patients with locally advanced squamous cell carcinoma of the esophagus (ESCC), we profiled the gene expression of ESCC compared to corresponding normal biopsies for diagnostic markers by genome microarrays. Profiling of gene expression identified 4844 genes differentially expressed, 2122 upregulated and 2722 downregulated in ESCC. Twenty-three overexpressed candidates with best scores from significance analysis have been selected for further analysis by TaqMan low-density array-technique using a validation cohort of 40 patients. The verification rate was 100 % for ESCC. Twenty-two markers were additionally overexpressed in adenocarcinoma of the esophagus (EAC). The markers significantly overexpressed already in earlier tumor stages (pT1-2) of both histological subtypes (n = 19) have been clustered in a "diagnostic signature": PLA2G7, PRAME, MMP1, MMP3, MMP12, LIlRB2, TREM2, CHST2, IGFBP2, IGFBP7, KCNJ8, EMILIN2, CTHRC1, EMR2, WDR72, LPCAT1, COL4A2, CCL4, and SNX10. The marker signature will be translated to clinical practice to prove its diagnostic impact. This diagnostic signature may contribute to the earlier detection of tumor cells, with the aim to complement clinical techniques resulting in the development of better detection of concepts of esophageal cancer for earlier therapy and more favorite prognosis. PMID:26631031

  7. Diagnostic Utility of Galectin-3 in Thyroid Cancer

    PubMed Central

    Chiu, Connie G.; Strugnell, Scott S.; Griffith, Obi L.; Jones, Steven J.M.; Gown, Allen M.; Walker, Blair; Nabi, Ivan R.; Wiseman, Sam M.

    2010-01-01

    Galectin-3 (Gal-3), which has received significant recent attention for its utility as a diagnostic marker for thyroid cancer, represents the most well-studied molecular candidate for thyroid cancer diagnosis. Gal-3 is a protein that binds to β-galactosidase residues on cell surface glycoproteins and has also been identified in the cytoplasmic and nuclear compartment. This marker has been implicated in regulation of normal cellular proliferation and apoptosis, as well as malignant transformation and the metastasis of cancer cells. We here present a mechanistic review of Gal-3 and its role in cancer development and progression. Gal-3 expression studies in thyroid tissue and cytologic tumor specimens and their methodological considerations are also discussed in this article. Despite great variance in their methodology, the majority of immunohistochemical studies found that Gal-3 was differentially expressed in thyroid carcinoma compared with benign and normal thyroid specimens, suggesting that Gal-3 is a good diagnostic marker for thyroid cancer. Recent studies have also demonstrated improved methodological reliability. On the other hand, Gal-3 genomic expression studies have shown inconsistent results for diagnostic utility and are not recommended. Overall, the development of Gal-3 as a diagnostic marker for thyroid cancer represents a promising avenue for future study, and its clinical application could significantly reduce the number of diagnostic thyroid operations performed for cases of indeterminant fine needle aspiration biopsy cytology, and thus positively impact the current management of thyroid nodular disease. PMID:20363921

  8. Diagnostic stages of the parasites of the Florida manatee, Trichechus manatus latirostris.

    PubMed

    Bando, Monica; Larkin, Iskande V; Wright, Scott D; Greiner, Ellis C

    2014-02-01

    Limited information is available on diagnostic stages of parasites in Florida manatees (Trichechus manatus latirostris). We examined 67 fecal samples from captive and wild manatees to define the diagnostic stages of the parasite fauna known to occur in Florida manatees. Parasite eggs were freshly extracted ex utero from identified mature helminths and subsequently characterized, illustrated, and matched to those isolated from fecal samples. In addition, coccidian oocysts in the fecal samples were identified. These diagnostic stages included eggs from 5 species of trematodes (Chiorchis fabaceus, Chiorchis groschafti, Pulmonicola cochleotrema, Moniligerum blairi, and Nudacotyle undicola), 1 nematode (Heterocheilus tunicatus), and oocysts of 2 coccidians (Eimeria manatus and Eimeria nodulosa).

  9. Diagnostic stages of the parasites of the Florida manatee, Trichechus manatus latirostris.

    PubMed

    Bando, Monica; Larkin, Iskande V; Wright, Scott D; Greiner, Ellis C

    2014-02-01

    Limited information is available on diagnostic stages of parasites in Florida manatees (Trichechus manatus latirostris). We examined 67 fecal samples from captive and wild manatees to define the diagnostic stages of the parasite fauna known to occur in Florida manatees. Parasite eggs were freshly extracted ex utero from identified mature helminths and subsequently characterized, illustrated, and matched to those isolated from fecal samples. In addition, coccidian oocysts in the fecal samples were identified. These diagnostic stages included eggs from 5 species of trematodes (Chiorchis fabaceus, Chiorchis groschafti, Pulmonicola cochleotrema, Moniligerum blairi, and Nudacotyle undicola), 1 nematode (Heterocheilus tunicatus), and oocysts of 2 coccidians (Eimeria manatus and Eimeria nodulosa). PMID:24116863

  10. Myasthenia Gravis: Tests and Diagnostic Methods

    MedlinePlus

    ... Affiliations Foundation Focus Newsletter E-Update Test & Diagnostic methods In addition to a complete medical and neurological ... How can I help? About MGFA Test & Diagnostic methods Treatment for MG FAQ's Upcoming Events Spring 2016 ...

  11. Progeria Research Foundation Diagnostic Testing Program

    MedlinePlus

    ... PRF By The Numbers Medical Database Cell & Tissue Bank Diagnostic Testing Research Funding Opportunities Scientific Meetings Scientific ... New in Progeria Research Medical Database Cell & Tissue Bank Diagnostic Testing Research Funding Opportunities Scientific Meetings Scientific ...

  12. Cochrane diagnostic test accuracy reviews.

    PubMed

    Leeflang, Mariska M G; Deeks, Jonathan J; Takwoingi, Yemisi; Macaskill, Petra

    2013-10-07

    In 1996, shortly after the founding of The Cochrane Collaboration, leading figures in test evaluation research established a Methods Group to focus on the relatively new and rapidly evolving methods for the systematic review of studies of diagnostic tests. Seven years later, the Collaboration decided it was time to develop a publication format and methodology for Diagnostic Test Accuracy (DTA) reviews, as well as the software needed to implement these reviews in The Cochrane Library. A meeting hosted by the German Cochrane Centre in 2004 brought together key methodologists in the area, many of whom became closely involved in the subsequent development of the methodological framework for DTA reviews. DTA reviews first appeared in The Cochrane Library in 2008 and are now an integral part of the work of the Collaboration.

  13. Huntington Disease: Molecular Diagnostics Approach.

    PubMed

    Bastepe, Murat; Xin, Winnie

    2015-10-06

    Huntington disease (HD) is caused by expansion of a CAG trinucleotide repeat in the first exon of the Huntingtin (HTT) gene. Molecular testing of Huntington disease for diagnostic confirmation and disease prediction requires detection of the CAG repeat expansion. There are three main types of HD genetic testing: (1) diagnostic testing to confirm or rule out disease, (2) presymptomatic testing to determine whether an at-risk individual inherited the expanded allele, and (3) prenatal testing to determine whether the fetus has inherited the expanded allele. This unit includes protocols that describe the complementary use of polymerase chain reactions (PCR) and Southern blot hybridization to accurately measure the CAG trinucleotide repeat size and interpret the test results. In addition, an indirect linkage analysis that does not reveal the unwanted parental HD status in a prenatal testing will also be discussed.

  14. Novette diagnostic support. Final report

    SciTech Connect

    Cirigliano, R.; Franco, E.; Koppel, L.; Rodrigues, B.; Smith, J.

    1985-02-01

    The primary research areas were the following: (1) contribute x-ray diagnostic, experimental, and data reduction and analysis support for the Novette DANTE x-ray spectrometer experiments. This effort was expanded to improve the overall quality of the Novette database; (2) experimental and calculational characterization of the x-ray imaging properties of an ellipsoidal x-ray collection optic serving as a sensitivity enhancing component of the Transmission Grating Streak Spectrometer; (3) performance simulation of the x-ray dispersion properties of candidate x-ray laser cavity, normal incidence end-mirror optics; (4) contribute x-ray diagnostic, experimental, and data reduction and analysis support for the Novette Henway crystal spectrometer and the MCPIGS microchannel plate intensified grazing incident spectrometer experiments; and (5) perform a technical performance vs cost evaluation of commercially available hardware required to perform the NOVA neutron time-of-flight experiments.

  15. [Diagnostic workup of fragrance allergy].

    PubMed

    Geier, J; Uter, W

    2015-09-01

    The diagnostic workup of contact allergy to fragrances must not be limited to patch testing with the two well-established fragrance mixes. False-positive reactions to these mixes occur in up to 50 % of the patch tested patients. For the diagnostic work-up of positive reactions, and in cases of suspected fragrance allergy, patch testing with the single mix components and additional fragrances is mandatory. Frequently sensitizing fragrance materials are the 14 components of the two fragrance mixes and tree moss (Evernia furfuracea), ylang ylang oil (I + II; Cananga odorata), lemongrass oil (Cymbopogon schoenanthus), sandalwood oil (Santalum album), jasmine absolute (Jasminum spp.), and, less frequently, clove oil (Eugenia caryophyllus), cedarwood oil (Cedrus atlantica/deodara, Juniperus virginiana), Neroli oil (Citrus aurantium amara flower oil), salicylaldehyde, narcissus absolute (Narcissus spp.), and patchouli oil (Pogostemon cablin). PMID:26253114

  16. Molecular Diagnostic Tests for Microsporidia

    PubMed Central

    Ghosh, Kaya; Weiss, Louis M.

    2009-01-01

    The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans. PMID:19657457

  17. Saliva as a diagnostic fluid.

    PubMed

    Samaranayake, Lakshman

    2007-10-01

    The use of saliva as a diagnostic fluid for various human ailments is gaining popularity as it offers distinct advantages over serum. These include the non-invasive nature of saliva collection compared with phlebotomy, simplicity of collection even for individuals with a modest training and the cost-effective applicability for screening large populations. Whole saliva is most frequently used for diagnosis of systemic diseases since it is readily collected and contains serum constituents while gland-specific saliva is useful for investigating pathology of major salivary glands. Broadly, saliva analysis is currently used for the diagnosis of infectious and malignant diseases, hereditary disorders, autoimmune diseases, and endocrine disorders, as well as for the assessment of therapeutic drug levels, particularly in monitoring drug abuse. This review addresses the current status of salivary diagnostics and their future potential.

  18. [Diagnostic workup of fragrance allergy].

    PubMed

    Geier, J; Uter, W

    2015-09-01

    The diagnostic workup of contact allergy to fragrances must not be limited to patch testing with the two well-established fragrance mixes. False-positive reactions to these mixes occur in up to 50 % of the patch tested patients. For the diagnostic work-up of positive reactions, and in cases of suspected fragrance allergy, patch testing with the single mix components and additional fragrances is mandatory. Frequently sensitizing fragrance materials are the 14 components of the two fragrance mixes and tree moss (Evernia furfuracea), ylang ylang oil (I + II; Cananga odorata), lemongrass oil (Cymbopogon schoenanthus), sandalwood oil (Santalum album), jasmine absolute (Jasminum spp.), and, less frequently, clove oil (Eugenia caryophyllus), cedarwood oil (Cedrus atlantica/deodara, Juniperus virginiana), Neroli oil (Citrus aurantium amara flower oil), salicylaldehyde, narcissus absolute (Narcissus spp.), and patchouli oil (Pogostemon cablin).

  19. Diagnostic Procedures in Parasitic Diseases

    PubMed Central

    Seah, S. K. K.

    1976-01-01

    This article offers some guidelines for investigating patients with suspected tropical and parasitic diseases. The common symptoms of tropical diseases as seen in Canadians returning from the tropics are discussed and diagnostic approaches suggested. Simple office laboratory procedures for the diagnosis of the common intestinal and blood parasites are outlined. The value and pitfalls of serological tests in parasitic diseases are discussed. ImagesFigure 1Figure 2 PMID:21308049

  20. Diagnostic accuracy of the Composite International Diagnostic Interview (CIDI 3.0) PTSD module among female Vietnam-era veterans.

    PubMed

    Kimerling, Rachel; Serpi, Tracey; Weathers, Frank; Kilbourne, Amy M; Kang, Han; Collins, Joseph F; Cypel, Yasmin; Frayne, Susan M; Furey, Joan; Huang, Grant D; Reinhard, Matthew J; Spiro, Avron; Magruder, Kathryn

    2014-04-01

    The World Health Organization (WHO) Composite International Diagnostic Interview (CIDI) posttraumatic stress disorder (PTSD) module is widely used in epidemiological studies of PTSD, yet relatively few data attest to the instrument's diagnostic utility. The current study evaluated the diagnostic utility of the CIDI 3.0 PTSD module with U. S. women Vietnam-era veterans. The CIDI and the Clinician-Administered PTSD Scale (CAPS) were independently administered to a stratified sample of 160 women, oversampled for current PTSD. Both lifetime PTSD and recent (past year) PTSD were assessed within a 3-week interval. Forty-five percent of the sample met criteria for a CAPS diagnosis of lifetime PTSD, and 21.9% of the sample met criteria for a CAPS diagnosis of past-year PTSD. Using CAPS as the diagnostic criterion, the CIDI correctly classified 78.8% of cases for lifetime PTSD (κ = .56) and 82.0% of past year PTSD cases (κ = .51). Estimates of diagnostic performance for the CIDI were sensitivity of .61 and specificity of .91 for lifetime PTSD and sensitivity of .71 and specificity of .85 for past-year PTSD. Results suggest that the CIDI has good utility for identifying PTSD, though it is a somewhat conservative indicator of lifetime PTSD as compared to the CAPS. PMID:24740869

  1. Diagnostics for PLX-alpha

    NASA Astrophysics Data System (ADS)

    Gilmore, Mark; Hsu, Scott

    2015-11-01

    The goal of the Plasma Liner eXperiment PLX-alpha at Los Alamos National Laboratory is to establish the viability of creating a spherically imploding plasma liner for MIF and HED applications, using a spherical array of supersonic plasma jets launched by innovative contoured-gap coaxial plasma guns. PLX- α experiments will focus in particular on establishing the ram pressure and uniformity scalings of partial and fully spherical plasma liners. In order to characterize these parameters experimentally, a suite of diagnostics is planned, including multi-camera fast imaging, a 16-channel visible interferometer (upgraded from 8 channels) with reconfigurable, fiber-coupled front end, and visible and VUV high-resolution and survey spectroscopy. Tomographic reconstruction and data fusion techniques will be used in conjunction with interferometry, imaging, and synthetic diagnostics from modeling to characterize liner uniformity in 3D. Diagnostic and data analysis design, implementation, and status will be presented. Supported by the Advanced Research Projects Agency - Energy - U.S. Department of Energy.

  2. Malaria diagnostics in clinical trials.

    PubMed

    Murphy, Sean C; Shott, Joseph P; Parikh, Sunil; Etter, Paige; Prescott, William R; Stewart, V Ann

    2013-11-01

    Malaria diagnostics are widely used in epidemiologic studies to investigate natural history of disease and in drug and vaccine clinical trials to exclude participants or evaluate efficacy. The Malaria Laboratory Network (MLN), managed by the Office of HIV/AIDS Network Coordination, is an international working group with mutual interests in malaria disease and diagnosis and in human immunodeficiency virus/acquired immunodeficiency syndrome clinical trials. The MLN considered and studied the wide array of available malaria diagnostic tests for their suitability for screening trial participants and/or obtaining study endpoints for malaria clinical trials, including studies of HIV/malaria co-infection and other malaria natural history studies. The MLN provides recommendations on microscopy, rapid diagnostic tests, serologic tests, and molecular assays to guide selection of the most appropriate test(s) for specific research objectives. In addition, this report provides recommendations regarding quality management to ensure reproducibility across sites in clinical trials. Performance evaluation, quality control, and external quality assessment are critical processes that must be implemented in all clinical trials using malaria tests.

  3. Fluorescence diagnostics in oncological gynecology

    NASA Astrophysics Data System (ADS)

    Belyaeva, Ludmila A.; Adamyan, Leila V.; Kozachenko, Vladimir P.; Stratonnikov, Alexander A.; Stranadko, Eugene F.; Loschenov, Victor B.

    2003-10-01

    The method of fluorescent diagnostics (FD) of tumors is a promising tool that may allow to increase sensitivity of tumor detection especially at initial stages. One of the most promising photosensitizers today is 5-aminolevulinic acid (5-ALA) that, actually, is not photosensitizer itself but precursor of protoporphyrin IX (PpIX). This paper deals with cancer diagnostics in gynecology by means of ALA-induced Pp IX laser-fluorescence spectroscopy. The tissue fluorescence spectra in vivo were studied in patients with various pathologies of ovaries, uterine and vulva after 5-aminolevulinic acid administration. It was shown that different pathologies varies in accumulation of Pp IX. Coefficient of fluorescence kf for normal tissue is not high, but exceptions are endometrium and mucous membrane of uterine tubes. Benign tumors of uterus and ovary have low values of kf, but polyps of endometrium exhibit high kf. Optical express-biopsy is important for diagnosis of ovarian cancer and micrometastatic spread. Coefficients of diagnostic contrast were determined for cancer of endometrium, cervical cancer, vulvar cancer.

  4. Diagnostics for Fast Ignition Science

    SciTech Connect

    MacPhee, A; Akli, K; Beg, F; Chen, C; Chen, H; Clarke, R; Hey, D; Freeman, R; Kemp, A; Key, M; King, J; LePape, S; Link, A; Ma, T; Nakamura, N; Offermann, D; Ovchinnikov, V; Patel, P; Phillips, T; Stephens, R; Town, R; Wei, M; VanWoerkom, L; Mackinnon, A

    2008-05-06

    The concept for Electron Fast Ignition Inertial Confinement Fusion demands sufficient laser energy be transferred from the ignitor pulse to the assembled fuel core via {approx}MeV electrons. We have assembled a suite of diagnostics to characterize such transfer. Recent experiments have simultaneously fielded absolutely calibrated extreme ultraviolet multilayer imagers at 68 and 256eV; spherically bent crystal imagers at 4 and 8keV; multi-keV crystal spectrometers; MeV x-ray bremmstrahlung and electron and proton spectrometers (along the same line of sight); nuclear activation samples and a picosecond optical probe based interferometer. These diagnostics allow careful measurement of energy transport and deposition during and following laser-plasma interactions at extremely high intensities in both planar and conical targets. Augmented with accurate on-shot laser focal spot and pre-pulse characterization, these measurements are yielding new insight into energy coupling and are providing critical data for validating numerical PIC and hybrid PIC simulation codes in an area that is crucial for many applications, particularly fast ignition. Novel aspects of these diagnostics and how they are combined to extract quantitative data on ultra high intensity laser plasma interactions are discussed, together with implications for full-scale fast ignition experiments.

  5. DNA Microarray-Based Diagnostics.

    PubMed

    Marzancola, Mahsa Gharibi; Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

    The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.

  6. Properties of plasma radiation diagnostics

    SciTech Connect

    Idzorek, G.C.; Oona, H.

    1996-06-01

    A number of diagnostics utilizing the radiation emitted from high-temperature plasmas have been developed at Los Alamos. Photoemissive x-ray diodes with photon energy bandpass filters provide time resolved rough spectral data from bout 6 eV to > 10 keV photon energy. Filtered silicon photodiodes can be used down to 1 eV and offer the advantages of nominally flat response and ability to operate in poor vacuum conditions. Both types of diodes will provide a rough time resolved spectrum and both are relatively inexpensive, reliable, and passive (i.e. no synchronization problems). For higher energy resolution bent crystal spectrographs are used in the x-ray region. With the addition of streak cameras or gated microchannel plates these systems provide data with high energy and high time resolution. To measure the total energy output a thin foil bolometer is used that measures the change in foil resistance as it is heated by the plasma radiation. Information on the physical location of the plasma is provided by a suite of visible framing cameras and x-ray pinhole cameras. By combining these diagnostics into a complementary set good diagnostic information can be guaranteed on any plasma experiment.

  7. Temporomandibular joint diagnostics using CBCT.

    PubMed

    Larheim, T A; Abrahamsson, A-K; Kristensen, M; Arvidsson, L Z

    2015-01-01

    The present review will give an update on temporomandibular joint (TMJ) imaging using CBCT. It will focus on diagnostic accuracy and the value of CBCT compared with other imaging modalities for the evaluation of TMJs in different categories of patients; osteoarthritis (OA), juvenile OA, rheumatoid arthritis and related joint diseases, juvenile idiopathic arthritis and other intra-articular conditions. Finally, sections on other aspects of CBCT research related to the TMJ, clinical decision-making and concluding remarks are added. CBCT has emerged as a cost- and dose-effective imaging modality for the diagnostic assessment of a variety of TMJ conditions. The imaging modality has been found to be superior to conventional radiographical examinations as well as MRI in assessment of the TMJ. However, it should be emphasized that the diagnostic information obtained is limited to the morphology of the osseous joint components, cortical bone integrity and subcortical bone destruction/production. For evaluation of soft-tissue abnormalities, MRI is mandatory. There is an obvious need for research on the impact of CBCT examinations on patient outcome.

  8. High Energy Laser Diagnostic Sensors

    SciTech Connect

    Luke, James R.; Goddard, Douglas N.; Thomas, David; Lewis, Jay

    2010-10-08

    Recent advancements in high energy laser (HEL) sources have outpaced diagnostic tools capable of accurately quantifying system performance. Diagnostic tools are needed that allow system developers to measure the parameters that define HEL effectiveness. The two critical parameters for quantifying HEL effectiveness are the irradiance on target and resultant rise in target temperature. Off-board sensing has its limitations, including unpredictable changes in the reflectivity of the target, smoke and outgassing, and atmospheric distortion. On-board sensors overcome the limitations of off-board techniques but must survive high irradiance levels and extreme temperatures.We have developed sensors for on-target diagnostics of high energy laser beams and for the measurement of the thermal response of the target. The conformal sensors consist of an array of quantum dot photodetectors and resistive temperature detectors. The sensor arrays are lithographically fabricated on flexible substrates and can be attached to a variety of laser targets. We have developed a nanoparticle adhesive process that provides good thermal contact with the target and that ensures the sensor remains attached to the target for as long as the target survives. We have calibrated the temperature and irradiance sensors and demonstrated them in a HEL environment.

  9. Temporomandibular joint diagnostics using CBCT

    PubMed Central

    Abrahamsson, A-K; Kristensen, M; Arvidsson, L Z

    2015-01-01

    The present review will give an update on temporomandibular joint (TMJ) imaging using CBCT. It will focus on diagnostic accuracy and the value of CBCT compared with other imaging modalities for the evaluation of TMJs in different categories of patients; osteoarthritis (OA), juvenile OA, rheumatoid arthritis and related joint diseases, juvenile idiopathic arthritis and other intra-articular conditions. Finally, sections on other aspects of CBCT research related to the TMJ, clinical decision-making and concluding remarks are added. CBCT has emerged as a cost- and dose-effective imaging modality for the diagnostic assessment of a variety of TMJ conditions. The imaging modality has been found to be superior to conventional radiographical examinations as well as MRI in assessment of the TMJ. However, it should be emphasized that the diagnostic information obtained is limited to the morphology of the osseous joint components, cortical bone integrity and subcortical bone destruction/production. For evaluation of soft-tissue abnormalities, MRI is mandatory. There is an obvious need for research on the impact of CBCT examinations on patient outcome. PMID:25369205

  10. Diagnostic Challenges of Cryptococcus neoformans in an Immunocompetent Individual Masquerading as Chronic Hydrocephalus.

    PubMed

    Mahajan, Kedar R; Roberts, Amity L; Curtis, Mark T; Fortuna, Danielle; Dharia, Robin; Sheehan, Lori

    2016-01-01

    Cryptococcus neoformans can cause disseminated meningoencephalitis and evade immunosurveillance with expression of a major virulence factor, the polysaccharide capsule. Direct diagnostic assays often rely on the presence of the cryptococcal glucuronoxylomannan capsular antigen (CrAg) or visualization of the capsule. Strain specific phenotypic traits and environmental conditions influence differences in expression that can thereby compromise detection and timely diagnosis. Immunocompetent hosts may manifest clinical signs and symptoms indolently, often expanding the differential and delaying appropriate treatment and diagnosis. We describe a 63-year-old man who presented with a progressive four-year history of ambulatory dysfunction, headache, and communicating hydrocephalus. Serial lumbar punctures (LPs) revealed elevated protein (153-300 mg/dL), hypoglycorrhachia (19-47 mg/dL), lymphocytic pleocytosis (89-95% lymphocyte, WBC 67-303 mg/dL, and RBC 34-108 mg/dL), and normal opening pressure (13-16 cm H2O). Two different cerebrospinal fluid (CSF) CrAg assays were negative. A large volume CSF fungal culture grew unencapsulated C. neoformans. He was initiated on induction therapy with amphotericin B plus flucytosine and consolidation/maintenance therapy with flucytosine, but he died following discharge due to complications. Elevated levels of CSF Th1 cytokines and decreased IL6 may have affected the virulence and detection of the pathogen. PMID:27525140

  11. Diagnostic Challenges of Cryptococcus neoformans in an Immunocompetent Individual Masquerading as Chronic Hydrocephalus

    PubMed Central

    Fortuna, Danielle; Dharia, Robin

    2016-01-01

    Cryptococcus neoformans can cause disseminated meningoencephalitis and evade immunosurveillance with expression of a major virulence factor, the polysaccharide capsule. Direct diagnostic assays often rely on the presence of the cryptococcal glucuronoxylomannan capsular antigen (CrAg) or visualization of the capsule. Strain specific phenotypic traits and environmental conditions influence differences in expression that can thereby compromise detection and timely diagnosis. Immunocompetent hosts may manifest clinical signs and symptoms indolently, often expanding the differential and delaying appropriate treatment and diagnosis. We describe a 63-year-old man who presented with a progressive four-year history of ambulatory dysfunction, headache, and communicating hydrocephalus. Serial lumbar punctures (LPs) revealed elevated protein (153–300 mg/dL), hypoglycorrhachia (19–47 mg/dL), lymphocytic pleocytosis (89–95% lymphocyte, WBC 67–303 mg/dL, and RBC 34–108 mg/dL), and normal opening pressure (13–16 cm H2O). Two different cerebrospinal fluid (CSF) CrAg assays were negative. A large volume CSF fungal culture grew unencapsulated C. neoformans. He was initiated on induction therapy with amphotericin B plus flucytosine and consolidation/maintenance therapy with flucytosine, but he died following discharge due to complications. Elevated levels of CSF Th1 cytokines and decreased IL6 may have affected the virulence and detection of the pathogen. PMID:27525140

  12. Identifying Inefficient Single-Family Homes With Utility Bill Analysis: Preprint

    SciTech Connect

    Casey, S.; Krarti, M.; Bianchi, M.; Roberts, D.

    2010-08-01

    Differentiating between energy-efficient and inefficient single-family homes on a community scale helps identify and prioritize candidates for energy-efficiency upgrades. Prescreening diagnostic procedures can further retrofit efforts by providing efficiency information before a site-visit is conducted. We applied the prescreening diagnostic to a simulated community of homes in Boulder, Colorado and analyzed energy consumption data to identify energy-inefficient homes.

  13. DDS: The Dental Diagnostic Simulation System.

    ERIC Educational Resources Information Center

    Tira, Daniel E.

    The Dental Diagnostic Simulation (DDS) System provides an alternative to simulation systems which represent diagnostic case studies of relatively limited scope. It may be used to generate simulated case studies in all of the dental specialty areas with case materials progressing through the gamut of the diagnostic process. The generation of a…

  14. 21 CFR 868.1840 - Diagnostic spirometer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Diagnostic spirometer. 868.1840 Section 868.1840 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES ANESTHESIOLOGY DEVICES Diagnostic Devices § 868.1840 Diagnostic spirometer....

  15. 21 CFR 868.1840 - Diagnostic spirometer.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Diagnostic spirometer. 868.1840 Section 868.1840 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES ANESTHESIOLOGY DEVICES Diagnostic Devices § 868.1840 Diagnostic spirometer....

  16. 21 CFR 868.1840 - Diagnostic spirometer.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Diagnostic spirometer. 868.1840 Section 868.1840 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES ANESTHESIOLOGY DEVICES Diagnostic Devices § 868.1840 Diagnostic spirometer....

  17. 21 CFR 868.1840 - Diagnostic spirometer.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Diagnostic spirometer. 868.1840 Section 868.1840 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES ANESTHESIOLOGY DEVICES Diagnostic Devices § 868.1840 Diagnostic spirometer....

  18. 21 CFR 868.1840 - Diagnostic spirometer.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Diagnostic spirometer. 868.1840 Section 868.1840 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES ANESTHESIOLOGY DEVICES Diagnostic Devices § 868.1840 Diagnostic spirometer....

  19. MFTF-B plasma-diagnostic system

    SciTech Connect

    Throop, A.L.; Goerz, D.A.; Thomas, S.R.

    1981-10-21

    This paper describes the current design status of the plasma diagnostic system for MFTF-B. In this paper we describe the system requirement changes which have occurred as a result of the funded rescoping of the original MFTF facility into MFTF-B. We outline the diagnostic instruments which are currently planned, and present an overview of the diagnostic system.

  20. Enhancing Force Concept Inventory Diagnostics to Identify Dominant Misconceptions in First-Year Engineering Physics

    ERIC Educational Resources Information Center

    Martin-Blas, Teresa; Seidel, Luis; Serrano-Fernandez, Ana

    2010-01-01

    This work presents the results of a study whose aim is to detect systematic errors about the concept of force among freshmen students. The researchers analysed the results of the Force Concept Inventory test, which was administered to two different groups of students. The results show that, although there were significant performance variations…

  1. Enhancing Force Concept Inventory diagnostics to identify dominant misconceptions in first-year engineering physics

    NASA Astrophysics Data System (ADS)

    Martín-Blas, Teresa; Seidel, Luis; Serrano-Fernández, Ana

    2010-12-01

    This work presents the results of a study whose aim is to detect systematic errors about the concept of force among freshmen students. The researchers analysed the results of the Force Concept Inventory test, which was administered to two different groups of students. The results show that, although there were significant performance variations between the two groups, they, nonetheless, shared common incorrect answers that were consistently triggered by the same misconceptions. The analysis proposed in this paper could also be applied in other universities to reveal the students' a priori mindset in Newtonian mechanics and serve as a guideline for developing effective computer simulations or other tools.

  2. Use of Malaria Rapid Diagnostic Test to Identify Plasmodium knowlesi Infection

    PubMed Central

    Piper, Robert C.; Makler, Michael T.

    2008-01-01

    Reports of human infection with Plasmodium knowlesi, a monkey malaria, suggest that it and other nonhuman malaria species may be an emerging health problem. We report the use of a rapid test to supplement microscopic analysis in distinguishing the 5 malaria species that infect humans. PMID:18976561

  3. Inferences of clinical diagnostic reasoning and diagnostic error.

    PubMed

    Lawson, Anton E; Daniel, Erno S

    2011-06-01

    This paper discusses clinical diagnostic reasoning in terms of a pattern of If/then/Therefore reasoning driven by data gathering and the inference of abduction, as defined in the present paper, and the inferences of retroduction, deduction, and induction as defined by philosopher Charles Sanders Peirce. The complex inferential reasoning driving clinical diagnosis often takes place subconsciously and so rapidly that its nature remains largely hidden from the diagnostician. Nevertheless, we propose that raising such reasoning to the conscious level reveals not its basic pattern and basic inferences, it also reveals where errors can and do occur and how such errors might be reduced or even eliminated.

  4. Inferences of clinical diagnostic reasoning and diagnostic error.

    PubMed

    Lawson, Anton E; Daniel, Erno S

    2011-06-01

    This paper discusses clinical diagnostic reasoning in terms of a pattern of If/then/Therefore reasoning driven by data gathering and the inference of abduction, as defined in the present paper, and the inferences of retroduction, deduction, and induction as defined by philosopher Charles Sanders Peirce. The complex inferential reasoning driving clinical diagnosis often takes place subconsciously and so rapidly that its nature remains largely hidden from the diagnostician. Nevertheless, we propose that raising such reasoning to the conscious level reveals not its basic pattern and basic inferences, it also reveals where errors can and do occur and how such errors might be reduced or even eliminated. PMID:20093196

  5. Advancing the development of diagnostic tests and biomarkers for tuberculosis.

    PubMed

    Yasinskaya, Y; Plikaytis, B; Sizemore, C; Sacks, L

    2011-07-01

    High costs and limited returns on investment have hampered progress in developing new diagnostic tests and treatments for tuberculosis (TB). We need new biomarkers to develop assays that can rapidly, efficiently and reliably detect Mycobacterium tuberculosis infection and disease, identify drug resistance and expedite drug and vaccine development. This can only be accomplished through cross-disciplinary collaborations to facilitate access to human specimens. The Food and Drug Administration, Centers for Disease Control and Prevention, National Institutes of Health, the industry and academia experts came together in a June 2010 workshop to examine the field of TB diagnostic test development and biomarker discovery, identify areas of most urgent need and formulate strategies to address those needs.

  6. Utility of Component-Resolved Diagnostics in Food Allergy.

    PubMed

    Tuano, Karen S; Davis, Carla M

    2015-06-01

    Allergen component-resolved diagnostic testing (CRD) is a new methodology in clinical food allergy diagnosis, improving the ability to identify specific clinical phenotypes. Instead of relying on the crude allergen extracts used in standard allergy diagnostics, CRD utilizes purified or recombinant allergens for identification of specific molecules causing sensitization or allergy. This method is able to determine risk of the severity of allergic reactions in specific cases, like soy, peanut, and hazelnut allergy. The severity of allergic reaction can be predicted in peanut allergy with Ara h 2, and clinically relevant disease in pollen-allergic patients can be identified. However, age and geographic differences affect CRD results and it should always be utilized in the context of a clinical history. In the future, clinical phenotypes may be differentiated with larger prospective studies utilizing food challenges.

  7. Polymerase chain reaction: A molecular diagnostic tool in periodontology.

    PubMed

    Maheaswari, Rajendran; Kshirsagar, Jaishree Tukaram; Lavanya, Nallasivam

    2016-01-01

    This review discusses the principles of polymerase chain reaction (PCR) and its application as a diagnostic tool in periodontology. The relevant MEDLINE and PubMed indexed journals were searched manually and electronically by typing PCR, applications of PCR, PCR in periodontics, polymorphism studies in periodontitis, and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review. PCR has now become a standard diagnostic and research tool in periodontology. Various studies reveal that its sensitivity and specificity allow it as a rapid, efficient method of detecting, identifying, and quantifying organism. Different immune and inflammatory markers can be identified at the mRNA expression level, and also the determination of genetic polymorphisms, thus providing the deeper insight into the mechanisms underlying the periodontal disease.

  8. Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

    PubMed Central

    Rai, Aswathy N.; Epperson, William B.; Nanduri, Bindu

    2015-01-01

    Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are avail-able, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches. PMID:26526746

  9. Polymerase chain reaction: A molecular diagnostic tool in periodontology

    PubMed Central

    Maheaswari, Rajendran; Kshirsagar, Jaishree Tukaram; Lavanya, Nallasivam

    2016-01-01

    This review discusses the principles of polymerase chain reaction (PCR) and its application as a diagnostic tool in periodontology. The relevant MEDLINE and PubMed indexed journals were searched manually and electronically by typing PCR, applications of PCR, PCR in periodontics, polymorphism studies in periodontitis, and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review. PCR has now become a standard diagnostic and research tool in periodontology. Various studies reveal that its sensitivity and specificity allow it as a rapid, efficient method of detecting, identifying, and quantifying organism. Different immune and inflammatory markers can be identified at the mRNA expression level, and also the determination of genetic polymorphisms, thus providing the deeper insight into the mechanisms underlying the periodontal disease. PMID:27143822

  10. Groin pain in athletes: a novel diagnostic approach

    PubMed Central

    Shetty, Vijay D.; Shetty, Nikhil S.; Shetty, Amith P.

    2015-01-01

    Groin pain in a performing athlete can be very challenging to diagnose and treat. The differential diagnosis includes intra-articular causes, extra-articular causes and non-musculoskeletal causes. A detailed clinical and radiological assessment of groin pain in this group is critical and can identify the underlying pathology. Diagnostic hip block is a valuable tool to differentiate intra-articular causes from extra-articular causes. Hip arthroscopy can help in identifying some of the elusive intra-articular conditions, which were once undiagnosed and therefore, left untreated, resulting in premature ending of competitive careers. This article attempts to explore current thinking on evaluation of groin pain, particularly in young individuals, and to establish a simple protocol for a clinical and diagnostic approach to this difficult problem. PMID:27163072

  11. Measures of Diagnostic Accuracy: Basic Definitions

    PubMed Central

    Šimundić, Ana-Maria

    2009-01-01

    Diagnostic accuracy relates to the ability of a test to discriminate between the target condition and health. This discriminative potential can be quantified by the measures of diagnostic accuracy such as sensitivity and specificity, predictive values, likelihood ratios, the area under the ROC curve, Youden's index and diagnostic odds ratio. Different measures of diagnostic accuracy relate to the different aspects of diagnostic procedure: while some measures are used to assess the discriminative property of the test, others are used to assess its predictive ability. Measures of diagnostic accuracy are not fixed indicators of a test performance, some are very sensitive to the disease prevalence, while others to the spectrum and definition of the disease. Furthermore, measures of diagnostic accuracy are extremely sensitive to the design of the study. Studies not meeting strict methodological standards usually over- or under-estimate the indicators of test performance as well as they limit the applicability of the results of the study. STARD initiative was a very important step toward the improvement the quality of reporting of studies of diagnostic accuracy. STARD statement should be included into the Instructions to authors by scientific journals and authors should be encouraged to use the checklist whenever reporting their studies on diagnostic accuracy. Such efforts could make a substantial difference in the quality of reporting of studies of diagnostic accuracy and serve to provide the best possible evidence to the best for the patient care. This brief review outlines some basic definitions and characteristics of the measures of diagnostic accuracy.

  12. [Incontinence - Etiology, diagnostics and Therapy].

    PubMed

    Frieling, Thomas

    2016-08-01

    Fecal incontinence is defined by the unintentional loss of solid or liquid stool, and anal incontinence includes leakage of gas and / or fecal incontinence. Anal-fecal incontinence is not a diagnosis but a symptom. Many patients hide the problem from their families, friends, and even their doctors. Epidemiologic studies indicate a prevalence between 7-15 %, up to 30 % in hospitals and up to 70 % in longterm care settings. Anal-fecal incontinence causes a significant socio-economic burden. There is no widely accepted approach for classifying anal-fecal incontinence available. Anal-fecal continence is maintained by anatomical factors, rectoanal sensation, and rectal compliance. The diagnostic approach comprises muscle and nerve injuries by iatrogenic, obstetric or surgical trauma, descending pelvic floor or associated diseases. A basic diagnostic workup is sufficient to characterize the different manifestations of fecal incontinence in most of the cases. This includes patient history with a daily stool protocol and digital rectal investigation. Additional investigations may include anorectal manometry, anal sphincter EMG, conduction velocity of the pudendal nerve, needle EMG, barostat investigation, defecography and the dynamic MRI. Therapeutic interventions are focused on the individual symptoms and should be provided in close cooperation with gastroenterologists, surgeons, gynecologists, urologists, physiotherapeutics and psychologists (nutritional-training, food fibre content, pharmacological treatment of diarrhea/constipation, toilet training, pelvic floor gymnastic, anal sphincter training, biofeedback). Surgical therapy includes the STARR operation for rectoanal prolapse and sacral nerve stimulation for chronic constipation and anal-fecal incontinence. Surgery should not be applied unless the diagnostic work-up is complete and all conservative treatment options failed. PMID:27557074

  13. The diagnostic dilemma of barodontalgia. Report of two cases.

    PubMed

    Senia, E S; Cunningham, K W; Marx, R E

    1985-08-01

    Although rare, barodontalgia can be a problem for those who fly. Two cases are presented, one which occurred during simulated high-altitude flight in the altitude chamber and the other during actual flight. The case that occurred during actual flight was resolved by treatment of the most suspect tooth after diagnostic tests failed to identify the problem. The other case was eventually treated successfully when symptoms became localized. The difficulties encountered in making a diagnosis are described.

  14. [Forensic-medical diagnostics of doping cases in sports].

    PubMed

    Khodasevich, L S; Kuzin, S G; Khodasevich, A L

    2013-01-01

    The present review of the literature is focused on the problem of forensic-medical diagnostics of doping cases in sports, with special reference to the main classes of pharmaceutical products forbidden for use by the International Olympic Committee. The main causes of death among the athletes as a result of using doping substances are considered. Much attention is given to adverse reactions induced by long-time intake of anabolic steroids many of which can be identified at autopsy.

  15. Theoretical studies in molecular fragmentation: Processes, energetics and diagnostics

    NASA Astrophysics Data System (ADS)

    Kirby, K. P.

    1983-09-01

    This research is directed toward providing diagnostic tools with which to identify and quantify the presence of fragment species and their energy states resulting from molecular destruction processes. Ab initio methods were used to calculate potential energy curves and transition moments for excited Sigma + and 1 Pi states of CO. Vibration rotation transition probabilities for vibrationally hot CN have been obtained. Work is commencing on the excited electronic states of NH.

  16. Measure Guideline. Air Conditioner Diagnostics, Maintenance, and Replacement

    SciTech Connect

    Springer, David; Dakin, Bill

    2013-03-01

    This guideline responds to the need for an efficient means of identifying, diagnosing, and repairing faults in air conditioning systems in existing homes that are undergoing energy upgrades. Inadequate airflow due to constricted ducts or undersized filters, improper refrigerant charge, and other system defects can be corrected at a fraction of the cost of equipment replacement and can yield significant savings. The guideline presents a two-step approach to diagnostics and repair.

  17. Measure Guideline: Air Conditioner Diagnostics, Maintenance, and Replacement

    SciTech Connect

    Springer, D.; Dakin, B.

    2013-03-01

    This guideline responds to the need for an efficient means of identifying, diagnosing, and repairing faults in air conditioning systems in existing homes that are undergoing energy upgrades. Inadequate airflow due to constricted ducts or undersized filters, improper refrigerant charge, and other system defects can be corrected at a fraction of the cost of equipment replacement and can yield significant savings. The guideline presents a two-step approach to diagnostics and repair.

  18. [Pedophilia. Prevalence, etiology, and diagnostics].

    PubMed

    Mokros, A; Osterheider, M; Nitschke, J

    2012-03-01

    Pedophilia is a disorder of sexual preference that increases the risk for committing sexual offenses against children. Consequently, pedophilia is not only relevant in psychiatric therapy and prognostics, but also greatly influences the public attitude towards criminality. Public opinion seems to equate pedophilia with child sexual abuse and vice versa which leads to stigmatization of patients and may impede treatment. The present paper provides information on recent studies on the potential origins of the disorder and introduces new diagnostic methods. Moreover, the article presents estimates on the prevalence of pedophilic sexual interest.

  19. Optoelectronic tweezers for medical diagnostics

    NASA Astrophysics Data System (ADS)

    Kremer, Clemens; Neale, Steven; Menachery, Anoop; Barrett, Mike; Cooper, Jonathan M.

    2012-01-01

    Optoelectronic tweezers (OET) allows the spatial patterning of electric fields through selected illumination of a photoconductive surface. This enables the manipulation of micro particles and cells by creating non-uniform electrical fields that then produce dielectrophoretic (DEP) forces. The DEP responses of cells differ and can produce negative or positive (repelled or attracted to areas of high electric field) forces. Therefore OET can be used to manipulate individual cells and separate different cell types from each other. Thus OET has many applications for medical diagnostics, demonstrated here with work towards diagnosing Human African Trypanosomiasis, also known as sleeping sickness.

  20. Spectrum analysis in beam diagnostics

    SciTech Connect

    Zhang, S.Y.; Weng, W.T.

    1993-04-23

    In this article, we discuss fundamentals of the spectrum analysis in beam diagnostics, where several important particle motions in a circular accelerator are considered. The properties of the Fourier transform are presented. Then the coasting and the bunched beam motion in both longitudinal and transverse are studied. The discussions are separated for the signal particle, multiple particle, and the Schottky noise cases. To demonstrate the interesting properties of the beam motion spectrum, time domain functions are generated, and then the associated spectra are calculated and plotted. In order to show the whole picture in a single plot, some data have been scaled, therefore they may not be realistic in an accelerator.