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Sample records for clinical ffpe samples

  1. Optimized Clinical Use of RNALater and FFPE Samples for Quantitative Proteomics

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona;

    Introduction and Objectives The availability of patient samples is essential for clinical proteomic research. Biobanks worldwide store mainly samples stabilized in RNAlater as well as formalin-fixed and paraffin embedded (FFPE) biopsies. Biobank material is a potential source for clinical...... proteomics to provide retrospective information concerning biomarkers for diagnosis, prognosis and novel drug discovery. In this study, we assess as the first the influence of sample stabilization using RNAlater (Qiagen) on human derived samples for quantitative proteome analysis and pathway mapping, which...... we compare to FFPE and frozen samples being the control. Methods From the sigmoideum of two healthy participants’ twenty-four biopsies were extracted using endoscopy. The biopsies was stabilized either by being directly frozen, RNAlater, FFPE or incubated for 30 min at room temperature prior to FFPE...

  2. Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine

    Science.gov (United States)

    Allen, Eliezer M. Van; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L.; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C.; Kryukov, Gregory; Carter, Scott L.; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T.; Gentry, Jeff G.; Huang, Franklin W.; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S.; Gray, Stacy W.; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A.; Gabriel, Stacey; Getz, Gad; Garraway, Levi A.

    2013-01-01

    Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a “long tail” of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. In one patient, previously undetected findings guided clinical trial enrollment leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. PMID:24836576

  3. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

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    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  4. Utility of different massive parallel sequencing platforms for mutation profiling in clinical samples and identification of pitfalls using FFPE tissue.

    Science.gov (United States)

    Fassunke, Jana; Haller, Florian; Hebele, Simone; Moskalev, Evgeny A; Penzel, Roland; Pfarr, Nicole; Merkelbach-Bruse, Sabine; Endris, Volker

    2015-11-01

    In the growing field of personalised medicine, the analysis of numerous potential targets is becoming a challenge in terms of work load, tissue availability, as well as costs. The molecular analysis of non-small cell lung cancer (NSCLC) has shifted from the analysis of the epidermal growth factor receptor (EGFR) mutation status to the analysis of different gene regions, including resistance mutations or translocations. Massive parallel sequencing (MPS) allows rapid comprehensive mutation testing in routine molecular pathological diagnostics even on small formalin-fixed, paraffin‑embedded (FFPE) biopsies. In this study, we compared and evaluated currently used MPS platforms for their application in routine pathological diagnostics. We initiated a first round‑robin testing of 30 cases diagnosed with NSCLC and a known EGFR gene mutation status. In this study, three pathology institutes from Germany received FFPE tumour sections that had been individually processed. Fragment libraries were prepared by targeted multiplex PCR using institution‑specific gene panels. Sequencing was carried out using three MPS systems: MiSeq™, GS Junior and PGM Ion Torrent™. In two institutes, data analysis was performed with the platform-specific software and the Integrative Genomics Viewer. In one institute, data analysis was carried out using an in-house software system. Of 30 samples, 26 were analysed by all institutes. Concerning the EGFR mutation status, concordance was found in 26 out of 26 samples. The analysis of a few samples failed due to poor DNA quality in alternating institutes. We found 100% concordance when comparing the results of the EGFR mutation status. A total of 38 additional mutations were identified in the 26 samples. In two samples, minor variants were found which could not be confirmed by qPCR. Other characteristic variants were identified as fixation artefacts by reanalyzing the respective sample by Sanger sequencing. Overall, the results of this study

  5. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

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    Jessica K Miller

    Full Text Available Short tandem repeat (STR analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS. The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

  6. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-fixed paraffin-embedded (FFPE) Samples

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) samples provide a vast untapped resource for chemical safety and translational science. To date, genomic profiling of FFPE samples has been limited by poor RNA quality and inconsistent results with limited utility in dose-response assessmen...

  7. Multiplex bisulfite PCR resequencing of clinical FFPE DNA

    OpenAIRE

    Korbie, Darren; Lin, Erica; Wall, David; Nair, Shalima S; Stirzaker, Clare; Clark, Sue J; Trau, Matt

    2015-01-01

    Background The clinical utility of DNA methylation as a predictive or prognostic biomarker requires scalable resequencing protocols for bisulfite-converted DNA. Key features of any validation method should be adaptability for low- or high-throughput needs and high reproducibility, and should only require minimal amounts of precious clinical sample as input material. Critically, this method should also deliver robust results when working with bisulfite-converted DNA extracted from formalin-fix...

  8. Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues.

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    Xi Chen

    Full Text Available The prognosis of colorectal cancer (CRC stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.

  9. A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing.

    Science.gov (United States)

    Longuespée, Rémi; Alberts, Deborah; Pottier, Charles; Smargiasso, Nicolas; Mazzucchelli, Gabriel; Baiwir, Dominique; Kriegsmann, Mark; Herfs, Michael; Kriegsmann, Jörg; Delvenne, Philippe; De Pauw, Edwin

    2016-07-15

    Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no method has yet been proposed for the reproducible processing of small FFPE tissue samples to allow biomarker discovery. In this work, we tested several procedures to process laser microdissected tissue pieces bearing less than 3000 cells. Combined with appropriate settings for liquid chromatography mass spectrometry-mass spectrometry (LC-MS/MS) analysis, a citric acid antigen retrieval (CAAR)-based procedure was established, allowing to identify more than 1400 proteins from a single microdissected breast cancer tissue biopsy. This work demonstrates important considerations concerning the handling and processing of laser microdissected tissue samples of extremely limited size, in the process opening new perspectives in molecular pathology. A proof of the proposed method for biomarker discovery, with respect to these specific handling considerations, is illustrated using the differential proteomic analysis of invasive breast carcinoma of no special type and invasive lobular triple-negative breast cancer tissues. This work will be of utmost importance for early biomarker discovery or in support of matrix-assisted laser desorption/ionization (MALDI) imaging for microproteomics from small regions of interest. PMID:26690073

  10. Improved reproducibility in genome-wide DNA methylation analysis for PAXgene® fixed samples compared to restored FFPE DNA

    DEFF Research Database (Denmark)

    Andersen, Gitte Brinch; Hager, Henrik; Hansen, Lise Lotte;

    2014-01-01

    PAXgene Tissue System, developed for simultaneous preservation of morphology, proteins, and nucleic acids. In the current study, we compared the performance of DNA from either PAXgene or formalin-fixed tissues to snap-frozen material for genome-wide DNA methylation analysis using the Illumina 450K Bead......Chip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better......, precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap-freezing is the...

  11. Use of Sequenom Sample ID Plus® SNP Genotyping in Identification of FFPE Tumor Samples

    OpenAIRE

    Jessica K Miller; Nicholas Buchner; Lee Timms; Shirley Tam; Xuemei Luo; Brown, Andrew M. K.; Danielle Pasternack; Robert G Bristow; Michael Fraser; Boutros, Paul C; McPherson, John D.

    2014-01-01

    Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can re...

  12. Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.

    Directory of Open Access Journals (Sweden)

    Carina Heydt

    Full Text Available Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA. No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can

  13. The effects of age-in-block on RNA-seq analysis of archival formalin-fixed paraffin-embedded (FFPE) samples

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    Archival samples represent a vast resource for identification of chemical and pharmaceutical targets. Previous use of formalin-fixed paraffin-embedded (FFPE) samples has been limited due to changes in RNA introduced by fixation and embedding procedures. Recent advances in RNA-seq...

  14. Absolute quantitation of Met using mass spectrometry for clinical application: assay precision, stability, and correlation with MET gene amplification in FFPE tumor tissue.

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    Daniel V T Catenacci

    Full Text Available Overexpression of Met tyrosine kinase receptor is associated with poor prognosis. Overexpression, and particularly MET amplification, are predictive of response to Met-specific therapy in preclinical models. Immunohistochemistry (IHC of formalin-fixed paraffin-embedded (FFPE tissues is currently used to select for 'high Met' expressing tumors for Met inhibitor trials. IHC suffers from antibody non-specificity, lack of quantitative resolution, and, when quantifying multiple proteins, inefficient use of scarce tissue.After describing the development of the Liquid-Tissue-Selected Reaction Monitoring-mass spectrometry (LT-SRM-MS Met assay, we evaluated the expression level of Met in 130 FFPE gastroesophageal cancer (GEC tissues. We assessed the correlation of SRM Met expression to IHC and mean MET gene copy number (GCN/nucleus or MET/CEP7 ratio by fluorescence in situ hybridization (FISH.Proteomic mapping of recombinant Met identified 418TEFTTALQR426 as the optimal SRM peptide. Limits of detection (LOD and quantitation (LOQ for this peptide were 150 and 200 amol/µg tumor protein, respectively. The assay demonstrated excellent precision and temporal stability of measurements in serial sections analyzed one year apart. Expression levels of 130 GEC tissues ranged (<150 amol/µg to 4669.5 amol/µg. High correlation was observed between SRM Met expression and both MET GCN and MET/CEP7 ratio as determined by FISH (n = 30; R2 = 0.898. IHC did not correlate well with SRM (n = 44; R2 = 0.537 nor FISH GCN (n = 31; R2 = 0.509. A Met SRM level of ≥1500 amol/µg was 100% sensitive (95% CI 0.69-1 and 100% specific (95% CI 0.92-1 for MET amplification.The Met SRM assay measured the absolute Met levels in clinical tissues with high precision. Compared to IHC, SRM provided a quantitative and linear measurement of Met expression, reliably distinguishing between non-amplified and amplified MET tumors. These results demonstrate a novel

  15. Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues

    OpenAIRE

    Magdeldin, Sameh; Yamamoto, Tadashi

    2012-01-01

    Formalin-fixed paraffin-embedded (FFPE) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow-up.

  16. Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling

    OpenAIRE

    Foster, Joseph M.; Oumie, Assa; Togneri, Fiona S.; Vasques, Fabiana Ramos; Hau, Debra; Taylor, Morag; Tinkler-Hundal, Emma; Southward, Katie; Medlow, Paul; McGreeghan-Crosby, Keith; Halfpenny, Iris; McMullan, Dominic J.; Quirke, Phil; Keating, Katherine E; Griffiths, Mike

    2015-01-01

    Background Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations. Methods In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laborat...

  17. Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE Prostate Cancer Tissue

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    Saskia Biskup

    2012-07-01

    Full Text Available Next generation sequencing (NGS technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE tissue. This study’s aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The sequenced reads were mapped and compared. Our study was the first to show comparable exome sequencing results between FFPE and corresponding fresh-frozen cancer tissues using SOLiD sequencing. A prior study has been conducted comparing the validity of sequencing of FFPE vs. fresh frozen samples using other NGS platforms. Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing.

  18. Intraparenchymal mesenchymal chondrosarcoma of the frontal lobe--a case report and molecular detection of specific gene fusions from archival FFPE sample.

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    Sajjad, Emir Ahmed; Sikora, Katarzyna; Paciejewski, Tomasz; Garbicz, Filip; Paskal, Wiktor; Szacht, Milena; Grajkowska, Wieslawa; Włodarski, Pawel Krzysztof

    2015-01-01

    Mesenchymal chondrosarcoma is a rare tumor of cartilaginous origin characterized by its bimorphic pattern composed of highly undifferentiated small round cells separated by islands of well-differentiated hyaline cartilage. It exhibits higher malignancy and earlier occurrence in comparison to classic chondrosarcomas. Recently identified HEY1-NCOA2 and IRF2BP2-CDX1 gene fusions confirm their distinct molecular origin and pose a promising diagnostic marker. The majority of cases arise from craniofacial bones. In this study, we present a rare case of mesenchymal chondrosarcoma encompassed within the brain parenchyma of the frontal lobe without any dural or bone attachment. We demonstrate histopathological findings and confirm the HEY1-NCOA2 gene fusion in a formalin-fixed paraffin-embedded archival sample using simple reverse transcription polymerase chain reaction (RT-PCR) method. IRF2BP2-CDX1 gene fusion was absent in the analyzed sample. The clinical follow-up is also presented with a review of treatment modalities for this entity. PMID:25907264

  19. Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling.

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    Petersen, Annabeth Høgh; Aagaard, Mads Malik; Nielsen, Henriette Roed; Steffensen, Karina Dahl; Waldstrøm, Marianne; Bojesen, Anders

    2016-08-01

    Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1-14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0-43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0-38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible. PMID:26733283

  20. Two Methods for High-Throughput NGS Template Preparation for Small and Degraded Clinical Samples Without Automation

    OpenAIRE

    Kamberov, E.; Tesmer, T.; Mastronardi, M.; Langmore, John

    2012-01-01

    Clinical samples are difficult to prepare for NGS, because of the small amounts or degraded states of formalin-fixed tissue, plasma, urine, and single-cell DNA. Conventional whole genome amplification methods are too biased for NGS applications, and the existing NGS preparation kits require intermediate purifications and excessive time to prepare hundreds of samples in a day without expensive automation. We have tested two 96-well manual methods to make NGS templates from FFPE tissue, plasma,...

  1. Multiple immunofluorescence labelling of formalin-fixed paraffin-embedded (FFPE) tissue

    OpenAIRE

    Reis-Filho Jorge S; Savage Kay; Robertson David; Isacke Clare M

    2008-01-01

    Abstract Background Investigating the expression of candidate genes in tissue samples usually involves either immunohistochemical labelling of formalin-fixed paraffin-embedded (FFPE) sections or immunofluorescence labelling of cryosections. Although both of these methods provide essential data, both have important limitations as research tools. Consequently, there is a demand in the research community to be able to perform routine, high quality immunofluorescence labelling of FFPE tissues. Re...

  2. The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

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    Jing Cai

    Full Text Available Quantitative real-time PCR (qPCR is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD, an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA and nonparametric (Kruskal-Wallis tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.

  3. A microRNA isolation method from clinical samples

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    Zununi Vahed, Sepideh; Barzegari, Abolfazl; Rahbar Saadat, Yalda; Mohammadi, Somayeh; Samadi, Nasser

    2016-01-01

    Introduction: microRNAs (miRNAs) are considered to be novel molecular biomakers that could be exploited in the diagnosis and treatment of different diseases. The present study aimed to develop an efficient miRNA isolation method from different clinical specimens. Methods: Total RNAs were isolated by Trizol reagent followed by precipitation of the large RNAs with potassium acetate (KCH3COOH), polyethylene glycol (PEG) 4000 and 6000, and lithium chloride (LiCl). Then, small RNAs were enriched and recovered from the supernatants by applying a combination of LiCl and ethanol. The efficiency of the method was evaluated through the quality, quantity, and integrity of the recovered RNAs using the A260/280 absorbance ratio, reverse transcription PCR (RT-PCR), and quantitative real-time PCR (q-PCR). Results: Comparison of different RNA isolation methods based on the precipitation of DNA and large RNAs, high miRNA recovery and PCR efficiency revealed that applying potassium acetate with final precipitation of small RNAs using 2.5 M LiCl plus ethanol can provide high yield and quality small RNAs that can be exploited for clinical purposes. Conclusion: The current isolation method can be applied for most clinical samples including cells, formalin-fixed and paraffin-embedded (FFPE) tissues and even body fluids with a wide applicability in molecular biology investigations.

  4. Analytical Validation of AmpliChip p53 Research Test for Archival Human Ovarian FFPE Sections.

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    Matthew J Marton

    Full Text Available The p53 tumor suppressor gene (TP53 is reported to be mutated in nearly half of all tumors and plays a central role in genome integrity. Detection of mutations in p53 can be accomplished by many assays, including the AmpliChip p53 Research Test. The AmpliChip p53 Research Test has been successfully used to determine p53 status in hematologic malignancies and fresh frozen solid tissues but there are few reports of using the assay with formalin fixed, paraffin-embedded (FFPE tissue. The objective of this study was to describe analytical performance characterization of the AmpliChip p53 Research Test to detect p53 mutations in genomic DNA isolated from archival FFPE human ovarian tumor tissues. Method correlation with sequencing showed 96% mutation-wise agreement and 99% chip-wise agreement. We furthermore observed 100% agreement (113/113 of the most prevalent TP53 mutations. Workflow reproducibility was 96.8% across 8 samples, with 2 operators, 2 reagent lots and 2 instruments. Section-to-section reproducibility was 100% for each sample across a 60 μm region of the FFPE block from ovarian tumors. These data indicate that the AmpliChip p53 Research Test is an accurate and reproducible method for detecting mutations in TP53 from archival FFPE human ovarian specimens.

  5. Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue

    DEFF Research Database (Denmark)

    Petersen, Annabeth Høgh; Jørgensen, Mads Malik Aagaard; Nielsen, Henriette Roed;

    2016-01-01

    Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder...... mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild......1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE...

  6. Quantification of covalently closed circular DNA of hepatitis B virus in FFPE liver tissues of chronic hepatitis B patients

    OpenAIRE

    Jia-qi HAN; Yan-wei ZHONG; Xiao-qiang REN; Zheng-sheng ZOU; Liu, Shu-Hong; Xue-en LIU; Jing-min ZHAO; Dong-ping XU

    2011-01-01

    Objective To establish a method of detecting HBV covalently closed circular DNA(cccDNA) in micro-formalin fixed paraffin imbedding(FFPE) liver biopsy samples.Methods FFPE liver biopsies from 37 patients with chronic hepatitis B were studied.The intrahepatic HBV DNA was extracted and pre-treated with plasmid-safe ATP-dependent DNAse(PSAD),and then amplified by rolling circular amplification(RCA).The HBV cccDNA was quantitatively detected by Taqman real-time PCR with primers located on both sid...

  7. Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

    OpenAIRE

    Moran, Sebastián; Vizoso, Miguel; Martinez-Cardús, Anna; Gomez, Antonio; Matías-Guiu, Xavier; Chiavenna, Sebastián M; Fernandez, Andrés G; Esteller, Manel

    2014-01-01

    A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE results in comparison with matched FF samples, enabling us to use FFPE samples on the Infinium HumanMethyl...

  8. Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

    Science.gov (United States)

    Munchel, Sarah; Hoang, Yen; Zhao, Yue; Cottrell, Joseph; Klotzle, Brandy; Godwin, Andrew K; Koestler, Devin; Beyerlein, Peter; Fan, Jian-Bing; Bibikova, Marina; Chien, Jeremy

    2015-09-22

    Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C · G > T · A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes. PMID:26305677

  9. Sample Size Estimation in Clinical Trial

    OpenAIRE

    Tushar Vijay Sakpal

    2010-01-01

    Every clinical trial should be planned. This plan should include the objective of trial, primary and secondary end-point, method of collecting data, sample to be included, sample size with scientific justification, method of handling data, statistical methods and assumptions. This plan is termed as clinical trial protocol. One of the key aspects of this protocol is sample size estimation. The aim of this article is to discuss how important sample size estimation is for a clinical trial, and a...

  10. Profiling miRNAs in nasopharyngeal carcinoma FFPE tissue by microarray and Next Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Jin Peng

    2014-12-01

    Full Text Available Nasopharyngeal carcinoma (NPC is a non-lymphomatous, squamous-cell carcinoma that occurs in the epithelial lining of the nasopharynx. Nasopharyngeal carcinoma has a geographically well-defined distribution worldwide, with the highest prevalence in China, Southeast Asia, and Northern Africa. Symptoms of nascent NPC may be unapparent or trivial, with diagnosis based on the histopathology of biopsied tissue following endoscopy of the nasopharynx. The tumor node metastasis (TNM staging system is the benchmark for the prognosis of NPC and guides treatment strategy. However, there is a consensus that the TNM system is not sufficiently specific for the prognosis of NPC, as it does not reflect the biological heterogeneity of this tumor, making another biomarker for the detection of NPC a priority. We have previously reported on different approaches for microRNA (miRNA biomarker discovery for Formalin Fixed Paraffin Embedded (FFPE NPC tissue samples by both a targeted (microarray and an untargeted (small RNA-Seq discovery platform. Both miRNA discovery platforms produced similar results, narrowing the miRNA signature to 1–5% of the known mature human miRNAs, with untargeted (small RNA-Seq approach having the advantage of indicating “unknown” miRNAs associated with NPC. Both miRNA profiles strongly associated with NPC, providing two potential discovery platforms for biomarker signatures for NPC. Herein, we provide a detailed description of the methods that we used to interrogate FFPE samples to discover biomarkers for NPC.

  11. Quantification of covalently closed circular DNA of hepatitis B virus in FFPE liver tissues of chronic hepatitis B patients

    Directory of Open Access Journals (Sweden)

    Jia-qi HAN

    2011-05-01

    Full Text Available Objective To establish a method of detecting HBV covalently closed circular DNA(cccDNA in micro-formalin fixed paraffin imbedding(FFPE liver biopsy samples.Methods FFPE liver biopsies from 37 patients with chronic hepatitis B were studied.The intrahepatic HBV DNA was extracted and pre-treated with plasmid-safe ATP-dependent DNAse(PSAD,and then amplified by rolling circular amplification(RCA.The HBV cccDNA was quantitatively detected by Taqman real-time PCR with primers located on both sides of the gap of HBV DNA.The human β-actin gene served as the internal control.The sensitivity was tested by serially diluting the DNA templates with known concentrations.The repeatability and stability were evaluated with inter-assay and intra-assay.The level of intrahepatic HBV cccDNA,HBV total DNA,serum HBV DNA and ALT were also compared to find the relations between them.Results The quantitative detection method of cccDNA in micro-FFPE liver samples was successfully set up with considerable sensitivity,stability and specificity.The intrahepatic cccDNA level was significantly higher in the HBeAg-positive patients than in the HBeAg-negative patients(P < 0.05.The intrahepatic HBV cccDNA level was positively correlated with the serum and intra-hepatic HBV DNA level(r=0.539,P=0.001.Conclusion The assay established by present study is fit for the detection of HBV cccDNA in micro-FFPE liver biopsies.

  12. Three dimensional imaging of paraffin embedded human lung tissue samples by micro-computed tomography.

    Directory of Open Access Journals (Sweden)

    Anna E Scott

    Full Text Available Understanding the three-dimensional (3-D micro-architecture of lung tissue can provide insights into the pathology of lung disease. Micro computed tomography (µCT has previously been used to elucidate lung 3D histology and morphometry in fixed samples that have been stained with contrast agents or air inflated and dried. However, non-destructive microstructural 3D imaging of formalin-fixed paraffin embedded (FFPE tissues would facilitate retrospective analysis of extensive tissue archives of lung FFPE lung samples with linked clinical data.FFPE human lung tissue samples (n = 4 were scanned using a Nikon metrology µCT scanner. Semi-automatic techniques were used to segment the 3D structure of airways and blood vessels. Airspace size (mean linear intercept, Lm was measured on µCT images and on matched histological sections from the same FFPE samples imaged by light microscopy to validate µCT imaging.The µCT imaging protocol provided contrast between tissue and paraffin in FFPE samples (15 mm x 7 mm. Resolution (voxel size 6.7 µm in the reconstructed images was sufficient for semi-automatic image segmentation of airways and blood vessels as well as quantitative airspace analysis. The scans were also used to scout for regions of interest, enabling time-efficient preparation of conventional histological sections. The Lm measurements from µCT images were not significantly different to those from matched histological sections.We demonstrated how non-destructive imaging of routinely prepared FFPE samples by laboratory µCT can be used to visualize and assess the 3D morphology of the lung including by morphometric analysis.

  13. Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    Directory of Open Access Journals (Sweden)

    Done Susan J

    2011-06-01

    Full Text Available Abstract Background The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. Methods A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status. Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Results Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated

  14. Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    International Nuclear Information System (INIS)

    The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients. We

  15. Conducting Clinical Research Using Crowdsourced Convenience Samples.

    Science.gov (United States)

    Chandler, Jesse; Shapiro, Danielle

    2016-03-28

    Crowdsourcing has had a dramatic impact on the speed and scale at which scientific research can be conducted. Clinical scientists have particularly benefited from readily available research study participants and streamlined recruiting and payment systems afforded by Amazon Mechanical Turk (MTurk), a popular labor market for crowdsourcing workers. MTurk has been used in this capacity for more than five years. The popularity and novelty of the platform have spurred numerous methodological investigations, making it the most studied nonprobability sample available to researchers. This article summarizes what is known about MTurk sample composition and data quality with an emphasis on findings relevant to clinical psychological research. It then addresses methodological issues with using MTurk-many of which are common to other nonprobability samples but unfamiliar to clinical science researchers-and suggests concrete steps to avoid these issues or minimize their impact. PMID:26772208

  16. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.

    Directory of Open Access Journals (Sweden)

    Craig April

    Full Text Available BACKGROUND: We have developed a gene expression assay (Whole-Genome DASL, capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE specimens. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing the WG-DASL assay with an in vitro transcription-based labeling method yielded fold-change correlations of R(2 approximately 0.83, while fold-change comparisons with quantitative RT-PCR assays yielded R(2 approximately 0.86 and R(2 approximately 0.55 for intact and FFPE samples, respectively. Additionally, the WG-DASL assay yielded high self-correlations (R(2>0.98 with low intact RNA inputs ranging from 1 ng to 100 ng; reproducible expression profiles were also obtained with 250 pg total RNA (R(2 approximately 0.92, with approximately 71% of the probes detected in 100 ng total RNA also detected at the 250 pg level. When FFPE samples were assayed, 1 ng total RNA yielded self-correlations of R(2 approximately 0.80, while still maintaining a correlation of R(2 approximately 0.75 with standard FFPE inputs (200 ng. CONCLUSIONS/SIGNIFICANCE: Taken together, these results show that WG-DASL assay provides a reliable platform for genome-wide expression profiling in archived materials. It also possesses utility within clinical settings where only limited quantities of samples may be available (e.g. microdissected material or when minimally invasive procedures are performed (e

  17. Legionella detection from clinical and environmental samples

    Directory of Open Access Journals (Sweden)

    Maria Luisa Ricci

    2004-12-01

    Full Text Available

    Several methods are used for diagnosis of legionellosis: culture, urinary antigen detection, serologic tests, PCR etc., characterised by different level of specificity, sensitivity and rapidity. Microbiological diagnosis is an essential tool to for the prompt adoption of an adequate antimicrobial therapy and to understand the real diffusion of legionellosis.

    Likewise, the environmental samples analysis allows us to know the distribution of the Legionella in the environment and to detect the origin of the infection during an outbreak by comparing clinical and environmental strains.

  18. miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE hereditary breast tumors

    Directory of Open Access Journals (Sweden)

    Miljana Tanić

    2015-03-01

    Full Text Available Hereditary breast cancer constitutes only 5–10% of all breast cancer cases and is characterized by strong family history of breast and/or other associated cancer types. Only ~25% of hereditary breast cancer cases carry a mutation in BRCA1 or BRCA2 gene, while mutations in other rare high and moderate-risk genes and common low penetrance variants may account for additional 20% of the cases. Thus the majority of cases are still unaccounted for and designated as BRCAX tumors. MicroRNAs are small non-coding RNAs that play important roles as regulators of gene expression and are deregulated in cancer. To characterize hereditary breast tumors based on their miRNA expression profiles we performed global microarray miRNA expression profiling on a retrospective cohort of 80 FFPE breast tissues, including 66 hereditary breast tumors (13 BRCA1, 10 BRCA2 and 43 BRCAX, 10 sporadic breast carcinomas and 4 normal breast tissues, using Exiqon miRCURY LNA™ microRNA Array v.11.0. Here we describe in detail the miRNA microarray expression data and tumor samples used for the study of BRCAX tumor heterogeneity (Tanic et al., 2013 and biomarkers associated with positive BRCA1/2 mutation status (Tanic et al., 2014. Additionally, we provide the R code for data preprocessing and quality control.

  19. Sample size determination for clinical research

    OpenAIRE

    Wang, Duolao; Bakhai, Ameet; Del Buono, Angelo; Maffulli, Nicola

    2013-01-01

    Calculating the sample size is a most important determinant of statistical power of a study. A study with inadequate power, unless being conducted as a safety and feasibility study, is unethical. However, sample size calculation is not an exact science, and therefore it is important to make realistic and well researched assumptions before choosing an appropriate sample size accounting for dropouts and also including a plan for interim analyses during the study to amend the final sample size.

  20. Quality analysis and clinical application of RNA extracted from formalin-fixed paraffin-embedded samples%福尔马林固定石蜡包埋样本提取的RNA质量分析及其临床应用

    Institute of Scientific and Technical Information of China (English)

    薛洋; 曾富春; 舒骏; 丛伟

    2015-01-01

    Objective To evaluate the quality and clinical application of RNA extracted from formalin-fixed paraffin-embed-ded samples. Methods A total of 994 FFPE samples were collected and RNA was extracted. The quality of RNA was evaluated and the RNA was used for detection of the gene mutation status of EML4-ALK and ROS1 gene. Sanger sequencing was used for assessing the accuracy of gene mutation detection by using RNA samples. Results The A260/A280 and A260/A230 of RNA from 994 cas-es of FFPE samples were not less than 1.8, the average concentration of RNA was 204.23ng/μl and all of 992 RNA samples could be effectively amplified. The results of EML4-ALK and ROS1 gene fusion detection were consistent with that of Sanger sequenc-ing. Conclusions The RNA extracted from FFPE samples is of high quality and suitable for subsequent gene mutation detection by qRT-PCR, which can provide scientific and reliable evidence for selection of tumor targeting drugs.%目的:评估国内福尔马林固定石蜡包埋(formalin-fixed paraffin-embedded,FFPE)样本抽提的RNA质量及其临床应用。方法收集FFPE样本994例,采用RNA分离纯化试剂盒提取纯化RNA,检测提取RNA的质量,并检测RNA样本中的EML4-ALK和ROS1基因突变状态,同时采用Sanger测序法验证使用RNA样本进行基因突变检测的准确性。结果从994例FFPE样本中分离提取的RNA的A260/A280和A260/A230均能达到1.8以上,平均浓度为204.23ng/μl,992例样本均能进行有效扩增。 RNA样本的EML4-ALK和ROS1基因融合检测结果与Sanger测序结果一致。结论从FFPE样本中分离得到的RNA质量良好,适用于后续的基因突变检测,可为肿瘤靶向药物的选择提供科学、可靠的依据。

  1. Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples

    OpenAIRE

    Ensel Oh; Yoon-La Choi; Mi Jeong Kwon; Ryong Nam Kim; Yu Jin Kim; Ji-Young Song; Kyung Soo Jung; Young Kee Shin

    2015-01-01

    Formalin fixing with paraffin embedding (FFPE) has been a standard sample preparation method for decades, and archival FFPE samples are still very useful resources. Nonetheless, the use of FFPE samples in cancer genome analysis using next-generation sequencing, which is a powerful technique for the identification of genomic alterations at the nucleotide level, has been challenging due to poor DNA quality and artificial sequence alterations. In this study, we performed whole-exome sequencing o...

  2. Sample size determination in clinical trials with multiple endpoints

    CERN Document Server

    Sozu, Takashi; Hamasaki, Toshimitsu; Evans, Scott R

    2015-01-01

    This book integrates recent methodological developments for calculating the sample size and power in trials with more than one endpoint considered as multiple primary or co-primary, offering an important reference work for statisticians working in this area. The determination of sample size and the evaluation of power are fundamental and critical elements in the design of clinical trials. If the sample size is too small, important effects may go unnoticed; if the sample size is too large, it represents a waste of resources and unethically puts more participants at risk than necessary. Recently many clinical trials have been designed with more than one endpoint considered as multiple primary or co-primary, creating a need for new approaches to the design and analysis of these clinical trials. The book focuses on the evaluation of power and sample size determination when comparing the effects of two interventions in superiority clinical trials with multiple endpoints. Methods for sample size calculation in clin...

  3. Bacteriophages in clinical samples can interfere with microbiological diagnostic tools

    Science.gov (United States)

    Brown-Jaque, Maryury; Muniesa, Maite; Navarro, Ferran

    2016-01-01

    Bacteriophages are viruses that infect bacteria, and they are found everywhere their bacterial hosts are present, including the human body. To explore the presence of phages in clinical samples, we assessed 65 clinical samples (blood, ascitic fluid, urine, cerebrospinal fluid, and serum). Infectious tailed phages were detected in >45% of ascitic fluid and urine samples. Three examples of phage interference with bacterial isolation were observed. Phages prevented the confluent bacterial growth required for an antibiogram assay when the inoculum was taken from an agar plate containing lysis plaques, but not when taken from a single colony in a phage-free area. In addition, bacteria were isolated directly from ascitic fluid, but not after liquid enrichment culture of the same samples, since phage propagation lysed the bacteria. Lastly, Gram-negative bacilli observed in a urine sample did not grow on agar plates due to the high densities of infectious phages in the sample. PMID:27609086

  4. On an Approach to Bayesian Sample Sizing in Clinical Trials

    CERN Document Server

    Muirhead, Robb J

    2012-01-01

    This paper explores an approach to Bayesian sample size determination in clinical trials. The approach falls into the category of what is often called "proper Bayesian", in that it does not mix frequentist concepts with Bayesian ones. A criterion for a "successful trial" is defined in terms of a posterior probability, its probability is assessed using the marginal distribution of the data, and this probability forms the basis for choosing sample sizes. We illustrate with a standard problem in clinical trials, that of establishing superiority of a new drug over a control.

  5. Streptomycete community from the clinical samples, their properties and signification

    Czech Academy of Sciences Publication Activity Database

    Chroňáková, Alica; Scharfen, J.; Ježek, P.; Krištůfek, Václav

    Shanghai: Shanghai Jiao Tong University, 2009. s. 106. [International Symposium on the Biology of Actinomycetes /15./. 20.08.2009-25.08.2009, Shanghai] Institutional research plan: CEZ:AV0Z60660521 Keywords : streptomycete community * clinical samples Subject RIV: EH - Ecology, Behaviour

  6. Microfluidic hydrogel arrays for direct genotyping of clinical samples.

    Science.gov (United States)

    Jung, Yun Kyung; Kim, Jungkyu; Mathies, Richard A

    2016-05-15

    A microfluidic hydrogel DNA microarray is developed to overcome the limitations of conventional planar microarrays such as low sensitivity, long overnight hybridization time, lack of a melting verification of proper hybrid, and complicated sample preparation process for genotyping of clinical samples. Unlike our previous prototype hydrogel array which can analyze only single-stranded DNA (ssDNA) targets, the device is the first of its type to allow direct multiplexed single nucleotide polymorphism (SNP) detection of human clinical samples comprising double-stranded DNA (dsDNA). This advance is made possible by incorporating a streptavidin (SA) hydrogel capture/purification element in a double T-junction at the start of the linear hydrogel array structure and fabricating ten different probe DNAs-entrapped hydrogels in microfluidic channels. The purified or unpurified polymerase chain reaction (PCR) products labeled with a fluorophore and a biotin are electrophoresed through the SA hydrogel for binding and purification. After electrophoretic washing, the fluorophore-labeled DNA strand is then thermally released for hybridization capture by its complementary probe gel element. We demonstrate the precise and rapid discrimination of the genotypes of five different clinical targets by melting curve analysis based on temperature-gradient electrophoresis within 3h, which is at least 3-fold decrease in incubation time compared to conventional microarrays. In addition, a 1.7pg (0.024 femtomoles) limit of detection for clinical samples is achieved which is ~100-fold better sensitivity than planar microarrays. PMID:26735871

  7. Learning Adaptive Forecasting Models from Irregularly Sampled Multivariate Clinical Data

    Science.gov (United States)

    Liu, Zitao; Hauskrecht, Milos

    2016-01-01

    Building accurate predictive models of clinical multivariate time series is crucial for understanding of the patient condition, the dynamics of a disease, and clinical decision making. A challenging aspect of this process is that the model should be flexible and adaptive to reflect well patient-specific temporal behaviors and this also in the case when the available patient-specific data are sparse and short span. To address this problem we propose and develop an adaptive two-stage forecasting approach for modeling multivariate, irregularly sampled clinical time series of varying lengths. The proposed model (1) learns the population trend from a collection of time series for past patients; (2) captures individual-specific short-term multivariate variability; and (3) adapts by automatically adjusting its predictions based on new observations. The proposed forecasting model is evaluated on a real-world clinical time series dataset. The results demonstrate the benefits of our approach on the prediction tasks for multivariate, irregularly sampled clinical time series, and show that it can outperform both the population based and patient-specific time series prediction models in terms of prediction accuracy.

  8. Combining electrochemical sensors with miniaturized sample preparation for rapid detection in clinical samples.

    Science.gov (United States)

    Bunyakul, Natinan; Baeumner, Antje J

    2015-01-01

    Clinical analyses benefit world-wide from rapid and reliable diagnostics tests. New tests are sought with greatest demand not only for new analytes, but also to reduce costs, complexity and lengthy analysis times of current techniques. Among the myriad of possibilities available today to develop new test systems, amperometric biosensors are prominent players-best represented by the ubiquitous amperometric-based glucose sensors. Electrochemical approaches in general require little and often enough only simple hardware components, are rugged and yet provide low limits of detection. They thus offer many of the desirable attributes for point-of-care/point-of-need tests. This review focuses on investigating the important integration of sample preparation with (primarily electrochemical) biosensors. Sample clean up requirements, miniaturized sample preparation strategies, and their potential integration with sensors will be discussed, focusing on clinical sample analyses. PMID:25558994

  9. Cladosporium Species Recovered from Clinical Samples in the United States

    OpenAIRE

    Sandoval-Denis, Marcelo; Sutton, Deanna A.; Martin-Vicente, Adela; Cano-Lira, José F.; Wiederhold, Nathan; Guarro, Josep; Gené, Josepa

    2015-01-01

    Cladosporium species are ubiquitous, saprobic, dematiaceous fungi, only infrequently associated with human and animal opportunistic infections. We have studied a large set of Cladosporium isolates recovered from clinical samples in the United States to ascertain the predominant species there in light of recent taxonomic changes in this genus and to determine whether some could possibly be rare potential pathogens. A total of 92 isolates were identified using phenotypic and molecular methods, ...

  10. Vancomycin Resistance Pattern of Staphylococcus Aureus among Clinical Samples

    OpenAIRE

    S Saadat; K Solhjoo; A. Kazemi; Erfanian, S. (MSc); Ashrafian, F. (MSc)

    2014-01-01

    Background and Objective: Vancomycin is used for treatment of methicillin-resistant S. Aureus (MRSA) infections; therefore, resistance to this antibiotic is increasing. We aimed to determine the antibiotic resistance pattern and frequency of vancomycin resistant S. Areas (VRSA) strains isolated from clinical samples. Material and Methods: In this cross-sectional study, 100 S. Aureus isolates collected from hospitals in Shiraz during six months, 2012, were identified by biochemical, microbiolo...

  11. PCR Detection of Helicobacter pylori in Clinical Samples

    OpenAIRE

    Rimbara, Emiko; Sasatsu, Masanori; David Y Graham

    2013-01-01

    Helicobacter pylori is an important pathogen whose primary niche is the human stomach. H. pylori is etio-logically associated with gastric inflammation (gastritis), peptic ulcer disease, and gastric cancer. Both noninvasive (e.g., urea breath and stool antigen tests) and invasive (gastric biopsy for histology, culture, or PCR) tests are used for diagnosis. PCR detection of H. pylori has been reported using a variety of clinical samples including gastric biopsy, gastric juice, saliva, dental p...

  12. Antibiotic Susceptibilities of Acinetobacter Baumanii Strains Isolated from Clinical Samples

    OpenAIRE

    Harun Aðca

    2013-01-01

         Aim :  In this study it was aimed to investigate the antibiotic susceptibilities of Acinetobacter baumanii strains isolated from various clinical samples sent to Tavsanli State Hospital Microbiology Laboratory retrospectively. Material and Method: All of the cultures were examined for the agent and antibiotic susceptibilities. For the identification of bacteria, various chemical tests and BBL Crystal E/NF (Beckton Dickinson, ABD) system was used. Antibiotic susce...

  13. PCR detection of Helicobacter pylori in clinical samples.

    Science.gov (United States)

    Rimbara, Emiko; Sasatsu, Masanori; Graham, David Y

    2013-01-01

    Helicobacter pylori is an important pathogen whose primary niche is the human stomach. H. pylori is etiologically associated with gastric inflammation (gastritis), peptic ulcer disease, and gastric cancer. Both noninvasive (e.g., urea breath and stool antigen tests) and invasive (gastric biopsy for histology, culture, or PCR) tests are used for diagnosis. PCR detection of H. pylori has been reported using a variety of clinical samples including gastric biopsy, gastric juice, saliva, dental plaque, and stools as well as environmental samples. Whenever possibly, noninvasive tests are preferred over invasive tests. H. pylori are excreted in the stool. Culture from stool is variable whereas stool antigen testing is widely used. Stool consists of a complicated mixture of commensal bacteria and chemicals and often includes inhibitors of PCR. Nevertheless, simple extraction methods are available to efficiently extract DNA from human stools and nested-PCR targeting the 23S rRNA gene have proven to be highly sensitive for the detection of H. pylori. Detection of clarithromycin susceptibility/resistance is important clinically and the mutation of the 23S rRNA gene responsible for resistance can also be detected using stool. This described method can be modified for other clinical samples such as gastric juice or biopsy material. PMID:23104297

  14. Electron Transfer Dissociation Mass Spectrometry of Hemoglobin on Clinical Samples

    Science.gov (United States)

    Coelho Graça, Didia; Lescuyer, Pierre; Clerici, Lorella; Tsybin, Yury O.; Hartmer, Ralf; Meyer, Markus; Samii, Kaveh; Hochstrasser, Denis F.; Scherl, Alexander

    2012-10-01

    A mass spectrometry-based assay combining the specificity of selected reaction monitoring and the protein ion activation capabilities of electron transfer dissociation was developed and employed for the rapid identification of hemoglobin variants from whole blood without previous proteolytic cleavage. The analysis was performed in a robust ion trap mass spectrometer operating at nominal mass accuracy and resolution. Subtle differences in globin sequences, resulting with mass shifts of about one Da, can be unambiguously identified. These results suggest that mass spectrometry analysis of entire proteins using electron transfer dissociation can be employed on clinical samples in a workflow compatible with diagnostic applications.

  15. MicroRNA profiling of gastric cancer patients from formalin-fixed paraffin-embedded samples

    OpenAIRE

    OSAWA, SOSHI; Shimada, Yutaka; Sekine, Shinichi; Okumura, Tomoyuki; NAGATA, TAKUYA; Fukuoka, Junya; Tsukada, Kazuhiro

    2011-01-01

    MicroRNA (miRNA) is a small non-coding RNA that targets specific mRNA. Recent progress in the extraction of RNA from formalin-fixed paraffin-embedded (FFPE) tissues has facilitated miRNA profiling using samples stored in laboratories worldwide. In the present study, miRNA profiling of gastric cancer patients is determined using FFPE samples. First, criteria were established for determining evaluable RNA from the FFPE samples. miRNA profiling was then undertaken using miRNA oligo chips with 88...

  16. MicroRNA profile of paclitaxel-resistant serous ovarian carcinoma based on formalin-fixed paraffin-embedded samples

    International Nuclear Information System (INIS)

    To assess the feasibility of validating microRNA (miRNA) profile related to paclitaxel-sensitivity in formalin-fixed paraffin-embedded (FFPE) samples of serous ovarian carcinoma (OC) patients. Deregulated miRNAs identified by miRNA microarray were further detected in 45 FFPE OC samples using Realtime PCR. Correlations between paired FFPE and frozen tumor samples were analyzed. Survival times were compared between 6 high and low miRNAs groups. Western blot and luciferase reporter assay were used for validating the target of miRNA. Sixteen up-regulated miRNAs and twenty-three down-regulated miRNAs were revealed in pacilitaxel-resistant ST30 cells. The up-regulated miRNAs (miR-320a, 22 and 129-5p) and down-regulated miRNAs (miR-9, 155 and 640) were confirmed in paclitaxel-resistant FFPE tumor samples, compared with paclitaxel-sensitive samples. Higher miR-9 and miR-640 showed better survival time in OC patients. Expressions of miR-9, 155 and 22 in FFPE samples were closely mimicked by those in frozen tissues. RAB34 was validated as a direct target of miR-9. We validated miRNA profile in pacilitaxel-resistant OC using FFPE samples, which might enable treatment stratification and help us to predict outcomes in OC patients. FFPE samples are feasible materials for miRNA research

  17. Non-invasive prenatal chromosomal aneuploidy testing--clinical experience: 100,000 clinical samples.

    Directory of Open Access Journals (Sweden)

    Ron M McCullough

    Full Text Available OBJECTIVE: As the first laboratory to offer massively parallel sequencing-based noninvasive prenatal testing (NIPT for fetal aneuploidies, Sequenom Laboratories has been able to collect the largest clinical population experience data to date, including >100,000 clinical samples from all 50 U.S. states and 13 other countries. The objective of this study is to give a robust clinical picture of the current laboratory performance of the MaterniT21 PLUS LDT. STUDY DESIGN: The study includes plasma samples collected from patients with high-risk pregnancies in our CLIA-licensed, CAP-accredited laboratory between August 2012 to June 2013. Samples were assessed for trisomies 13, 18, 21 and for the presence of chromosome Y-specific DNA. Sample data and ad hoc outcome information provided by the clinician was compiled and reviewed to determine the characteristics of this patient population, as well as estimate the assay performance in a clinical setting. RESULTS: NIPT patients most commonly undergo testing at an average of 15 weeks, 3 days gestation; and average 35.1 years of age. The average turnaround time is 4.54 business days and an overall 1.3% not reportable rate. The positivity rate for Trisomy 21 was 1.51%, followed by 0.45% and 0.21% rate for Trisomies 18 and 13, respectively. NIPT positivity rates are similar to previous large clinical studies of aneuploidy in women of maternal age ≥ 35 undergoing amniocentesis. In this population 3519 patients had multifetal gestations (3.5% with 2.61% yielding a positive NIPT result. CONCLUSION: NIPT has been commercially offered for just over 2 years and the clinical use by patients and clinicians has increased significantly. The risks associated with invasive testing have been substantially reduced by providing another assessment of aneuploidy status in high-risk patients. The accuracy and NIPT assay positivity rate are as predicted by clinical validations and the test demonstrates improvement in the

  18. Antibiotic Susceptibilities of Acinetobacter Baumanii Strains Isolated from Clinical Samples

    Directory of Open Access Journals (Sweden)

    Harun Aðca

    2013-01-01

    Full Text Available      Aim :  In this study it was aimed to investigate the antibiotic susceptibilities of Acinetobacter baumanii strains isolated from various clinical samples sent to Tavsanli State Hospital Microbiology Laboratory retrospectively. Material and Method: All of the cultures were examined for the agent and antibiotic susceptibilities. For the identification of bacteria, various chemical tests and BBL Crystal E/NF (Beckton Dickinson, ABD system was used. Antibiotic susceptibilities were investigated according to CLSI criteria on Mueller Hinton agar by disc diffusion method. Results: There were 74 strains isolated and identified as Acinetobacter baumanii. Most of the strains were isolated from  tracheal aspirate specimens (46 % Most of the strains were isolated from nosocomial infections. Antibiotic resistance was high among strains. The most susceptible antibiotic was gentamicin (30%. Discussion: To prevent the development of resistance, antibiotics should be used carefully in appropriate doses and time, empirical  antibiotherapy should be determined for each centre according to resistance rates of the centre and should be regulated according to the antibiogram results. Increasing resistance rates in Acinetobacter strains leads to the usage of new alternative antibiotics.  

  19. Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Piccart Martine

    2009-09-01

    Full Text Available Abstract Background Proliferation and tumor differentiation captured by the genomic grade index (GGI are important prognostic indicators in breast cancer (BC especially for the estrogen receptor positive (ER+ disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI, which could be realized on formalin fixed paraffin embedded samples (FFPE, and to assess its prognostic performance and predictive value of clinical benefit in early and advanced ER+ BC patients treated with tamoxifen. Methods The accuracy and concordance of the PCR-GGI with the GGI was assessed using BC patients for which frozen and FFPE tissues as well as microarray data were available (n = 19. The evaluation of the prognostic value of the PCR-GGI was assessed on FFPE material using a consecutive series of 212 systemically treated early BC patients. The predictive performance for tamoxifen benefit was assessed using two ER+ BC populations treated either with adjuvant tamoxifen only (n = 77+139 or first-line tamoxifen for advanced disease (n = 270. Results The PCR-GGI is based on the expression of 8 genes (4 representative of the GGI and 4 reference genes. A significant correlation was observed between the microarray-derived GGI and the qRT-PCR assay using frozen (ρ = 0.95, p univar. = 1.89; [95CI:1.01-3.54], p = 0.05. The PCR-GGI further identified two subgroups of patients with statistically different time to distant metastasis free survival (DMFS across the two cohorts of ER+ BC patients treated with adjuvant tamoxifen. Additionally, the PCR-GGI was associated with response to tamoxifen in the advanced setting (HRunivar. = 1.98; [95CI:1.51-2.59], p = 6.9E-07. Conclusion PCR-GGI recapitulates in an accurate and reproducible manner the performances of the GGI using frozen and FFPE samples.

  20. KRAS Mutation Detection in Paired Frozen and Formalin-Fixed Paraffin-Embedded (FFPE) Colorectal Cancer Tissues

    OpenAIRE

    Solassol, Jérome; Ramos, Jeanne; Crapez, Evelyne; SAIFI, MAJDA; Mangé, Alain; Vianès, Evelyne; Lamy, Pierre-Jean; Costes, Valérie; Maudelonde, Thierry

    2011-01-01

    KRAS mutation has been unambiguously identified as a marker of resistance to cetuximab-based treatment in metastatic colorectal cancer (mCRC) patients. However, most studies of KRAS mutation analysis have been performed using homogenously archived CRC specimens, and studies that compare freshly frozen specimens and formalin-fixed paraffin-embedded (FFPE) specimens of CRC are lacking. The aim of the present study was to evaluate the impact of tissue preservation on the determination of KRAS mu...

  1. Clinical audit for occupational therapy intervention for children with autism spectrum disorder: sampling steps and sample size calculation

    OpenAIRE

    Weeks, Scott; Atlas, Alvin

    2015-01-01

    A priori sample size calculations are used to determine the adequate sample size to estimate the prevalence of the target population with good precision. However, published audits rarely report a priori calculations for their sample size. This article discusses a process in health services delivery mapping to generate a comprehensive sampling frame, which was used to calculate an a priori sample size for a targeted clinical record audit. We describe how we approached methodological and defini...

  2. A Method to Correlate mRNA Expression Datasets Obtained from Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Tissue Samples: A Matter of Thresholds.

    Directory of Open Access Journals (Sweden)

    Dana A M Mustafa

    Full Text Available Gene expression profiling of tumors is a successful tool for the discovery of new cancer biomarkers and potential targets for the development of new therapeutic strategies. Reliable profiling is preferably performed on fresh frozen (FF tissues in which the quality of nucleic acids is better preserved than in formalin-fixed paraffin-embedded (FFPE material. However, since snap-freezing of biopsy materials is often not part of daily routine in pathology laboratories, one may have to rely on archival FFPE material. Procedures to retrieve the RNAs from FFPE materials have been developed and therefore, datasets obtained from FFPE and FF materials need to be made compatible to ensure reliable comparisons are possible.To develop an efficient method to compare gene expression profiles obtained from FFPE and FF samples using the same platform.Twenty-six FFPE-FF sample pairs of the same tumors representing various cancer types, and two FFPE-FF sample pairs of breast cancer cell lines, were included. Total RNA was extracted and gene expression profiling was carried out using Illumina's Whole-Genome cDNA-mediated Annealing, Selection, extension and Ligation (WG-DASL V3 arrays, enabling the simultaneous detection of 24,526 mRNA transcripts. A sample exclusion criterion was created based on the expression of 11 stably expressed reference genes. Pearson correlation at the probe level was calculated for paired FFPE-FF, and three cut-off values were chosen. Spearman correlation coefficients between the matched FFPE and FF samples were calculated for three probe lists with varying levels of significance and compared to the correlation based on all measured probes. Unsupervised hierarchical cluster analysis was performed to verify performance of the included probe lists to compare matched FPPE-FF samples.Twenty-seven FFPE-FF pairs passed the sample exclusion criterion. From the profiles of 27 FFPE and FF matched samples, the best correlating probes were identified

  3. A sample size planning approach that considers both statistical significance and clinical significance

    OpenAIRE

    Jia, Bin; Lynn, Henry S

    2015-01-01

    Background The CONSORT statement requires clinical trials to report confidence intervals, which help to assess the precision and clinical importance of the treatment effect. Conventional sample size calculations for clinical trials, however, only consider issues of statistical significance (that is, significance level and power). Method A more consistent approach is proposed whereby sample size planning also incorporates information on clinical significance as indicated by the boundaries of t...

  4. Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples

    DEFF Research Database (Denmark)

    Løvendorf, Marianne B; Zibert, John R; Hagedorn, Peter H;

    2012-01-01

    MicroRNAs are non-coding RNA molecules modulating gene expression post-transcriptionally. Formalin-fixed, paraffin-embedding (FFPE) is a standard preservation method often used in clinical practices, but induces RNA degradation. Extracting high-quality RNA from human skin can be challenging as skin......-frozen (FS) and Tissue-Tek-embedding (OCT). We found a strong correlation of the microRNA expression levels between all preservation methods of matched psoriatic skin samples (r(s) ranging from 0.91 to 0.95 (P <0.001)). These observations were further confirmed with qRT-PCR. Our results demonstrate that...... contains high levels of RNases. As microRNAs are 19-23 nucleotides long and lack a poly-A tail, they may be less prone to RNA degradation than mRNAs. We investigated whether microRNAs in psoriatic (FFPE) samples reliably reflect microRNA expression in samples less prone to RNA degradation such as fresh...

  5. Analytical artefacts in the speciation of arsenic in clinical samples

    International Nuclear Information System (INIS)

    Urine and blood samples of cancer patients, treated with high doses of arsenic trioxide were analysed for arsenic species using HPLC-HGAFS and, in some cases, HPLC-ICPMS. Total arsenic was determined with either flow injection-HGAFS in urine or radiochemical neutron activation analysis in blood fractions (in serum/plasma, blood cells). The total arsenic concentrations (during prolonged, daily/weekly arsenic trioxide therapy) were in the μg mL-1 range for urine and in the ng g-1 range for blood fractions. The main arsenic species found in urine were As(III), MA and DMA and in blood As(V), MA and DMA. With proper sample preparation and storage of urine (no preservation agents/storage in liquid nitrogen) no analytical artefacts were observed and absence of significant amounts of alleged trivalent metabolites was proven. On the contrary, in blood samples a certain amount of arsenic can get lost in the speciation procedure what was especially noticeable for the blood cells although also plasma/serum gave rise to some disappearance of arsenic. The latter losses may be attributed to precipitation of As(III)-containing proteins/peptides during the methanol/water extraction procedure whereas the former losses were due to loss of specific As(III)-complexing proteins/peptides (e.g. cysteine, metallothionein, reduced GSH, ferritin) on the column (Hamilton PRP-X100) during the separation procedure. Contemporary analytical protocols are not able to completely avoid artefacts due to losses from the sampling to the detection stage so that it is recommended to be careful with the explanation of results, particularly regarding metabolic and pharmacokinetic interpretations, and always aim to compare the sum of species with the total arsenic concentration determined independently

  6. Analytical artefacts in the speciation of arsenic in clinical samples

    Energy Technology Data Exchange (ETDEWEB)

    Slejkovec, Zdenka [Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia)], E-mail: zdenka.slejkovec@ijs.si; Falnoga, Ingrid [Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia); Goessler, Walter [Institute of Chemistry - Analytical Chemistry, Karl-Franzens University Graz, Universitaetsplatz 1, Graz (Austria); Elteren, Johannes T. van [National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia); Raml, Reingard [Institute of Chemistry - Analytical Chemistry, Karl-Franzens University Graz, Universitaetsplatz 1, Graz (Austria); Podgornik, Helena; Cernelc, Peter [University Medical Centre Ljubljana, Zaloska 7, 1000 Ljubljana (Slovenia)

    2008-01-21

    Urine and blood samples of cancer patients, treated with high doses of arsenic trioxide were analysed for arsenic species using HPLC-HGAFS and, in some cases, HPLC-ICPMS. Total arsenic was determined with either flow injection-HGAFS in urine or radiochemical neutron activation analysis in blood fractions (in serum/plasma, blood cells). The total arsenic concentrations (during prolonged, daily/weekly arsenic trioxide therapy) were in the {mu}g mL{sup -1} range for urine and in the ng g{sup -1} range for blood fractions. The main arsenic species found in urine were As(III), MA and DMA and in blood As(V), MA and DMA. With proper sample preparation and storage of urine (no preservation agents/storage in liquid nitrogen) no analytical artefacts were observed and absence of significant amounts of alleged trivalent metabolites was proven. On the contrary, in blood samples a certain amount of arsenic can get lost in the speciation procedure what was especially noticeable for the blood cells although also plasma/serum gave rise to some disappearance of arsenic. The latter losses may be attributed to precipitation of As(III)-containing proteins/peptides during the methanol/water extraction procedure whereas the former losses were due to loss of specific As(III)-complexing proteins/peptides (e.g. cysteine, metallothionein, reduced GSH, ferritin) on the column (Hamilton PRP-X100) during the separation procedure. Contemporary analytical protocols are not able to completely avoid artefacts due to losses from the sampling to the detection stage so that it is recommended to be careful with the explanation of results, particularly regarding metabolic and pharmacokinetic interpretations, and always aim to compare the sum of species with the total arsenic concentration determined independently.

  7. Clinical audit for occupational therapy intervention for children with autism spectrum disorder: sampling steps and sample size calculation.

    Science.gov (United States)

    Weeks, Scott; Atlas, Alvin

    2015-01-01

    A priori sample size calculations are used to determine the adequate sample size to estimate the prevalence of the target population with good precision. However, published audits rarely report a priori calculations for their sample size. This article discusses a process in health services delivery mapping to generate a comprehensive sampling frame, which was used to calculate an a priori sample size for a targeted clinical record audit. We describe how we approached methodological and definitional issues in the following steps: (1) target population definition, (2) sampling frame construction, and (3) a priori sample size calculation. We recommend this process for clinicians, researchers, or policy makers when detailed information on a reference population is unavailable. PMID:26122044

  8. A Short Version of the Revised ‘Experience of Close Relationships Questionnaire’: Investigating Non-Clinical and Clinical Samples

    OpenAIRE

    Wongpakaran, Tinakon; Wongpakaran, Nahathai

    2012-01-01

    Aim: This study seeks to investigate the psychometric properties of the short version of the revised ‘Experience of Close Relationships’ questionnaire, comparing non-clinical and clinical samples. Methods: In total 702 subjects participated in this study, of whom 531 were non-clinical participants and 171 were psychiatric patients. They completed the short version of the revised ‘Experience of Close Relationships’ questionnaire (ECR-R-18), the Perceived Stress Scale-10(PSS-10), the Rosenberg ...

  9. DNA qualification workflow for next generation sequencing of histopathological samples.

    Directory of Open Access Journals (Sweden)

    Michele Simbolo

    Full Text Available Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF tissues, 6 formalin-fixed paraffin-embedded (FFPE tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard

  10. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil

    OpenAIRE

    Lin, Jianghai; Kennedy, Stephen H.; Svarovsky, Therese; Rogers, Jeffrey; Kemnitz, Joseph W.; Xu, Anlong; Zondervan, Krina T

    2009-01-01

    Extracting DNA from formalin-fixed and paraffin-embedded (FFPE) tissue remains a challenge, despite numerous attempts to develop a more effective method. Polymerase chain reaction (PCR) success rates with DNA extracted using current methods remain low. We extracted DNA from 140 long-term archived FFPE samples using a simple but effective deparaffinization method, removing the wax with mineral oil, and a commercially available DNA extraction kit. DNA quality was subsequently tested in a genoty...

  11. Prevalence of dermatophytes and other fungal agents isolated from clinical samples

    OpenAIRE

    Kannan P.; Janaki C; Selvi G

    2006-01-01

    The common cause of skin infections are dermatophytes and opportunistic fungi. Aim of this study was to isolate and identify the fungal agents from clinical samples from patients with different mycoses. Clinical samples from 165 patients were subjected to potassium hydroxide (KOH) examination and culture isolation; causative agents were identified macroscopically and microscopically. All the 165 specimens were KOH positive and 110/165 (66.7%) samples were culture positive. Of these, hi...

  12. The Reliability and Validity of the Clinical Perfectionism Questionnaire in Eating Disorder and Community Samples

    OpenAIRE

    Egan, Sarah J.; Shafran, Roz; Lee, Michelle; Fairburn, Christopher G.; Cooper, Zafra; Doll, Helen A.; Palmer, Robert L.; Watson, Hunna J.

    2015-01-01

    Background: Clinical perfectionism is a risk and maintaining factor for anxiety disorders, depression and eating disorders. Aims: The aim was to examine the psychometric properties of the 12-item Clinical Perfectionism Questionnaire (CPQ). Method: The research involved two samples. Study 1 comprised a nonclinical sample (n = 206) recruited via the internet. Study 2 comprised individuals in treatment for an eating disorder (n = 129) and a community sample (n = 80). Results: Study 1 factor anal...

  13. More than a (negative feeling: Validity of the perceived stress scale in Serbian clinical and non-clinical samples

    Directory of Open Access Journals (Sweden)

    Jovanović Veljko

    2015-01-01

    Full Text Available The goal of the present study was to test the validity of a Serbian version of the Perceived Stress Scale. The PSS was administered to 157 psychiatric outpatients, 165 adults from the non-clinical population, and 283 university students. The results of the confirmatory factor analysis supported a bifactor model of the PSS with one general factor and two specific factors reflecting perceived distress and perceived self-efficacy. Internal consistencies of the scale and its two subscales were adequate across clinical and non-clinical samples. Results supported the ability of the scale to discriminate between clinical and non-clinical samples. The PSS evidenced good convergent validity, showing moderate to high positive correlations with measures of unpleasant emotional states and moderate negative correlations with positive affect and life satisfaction. All but one correlation remained significant after controlling for the measures of emotional distress. The results of the present research support validity of the PSS and its use in both clinical and non-clinical samples. [Projekat Ministarstva nauke Republike Srbije, br. 179006

  14. Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens

    OpenAIRE

    Spencer, David H.; Sehn, Jennifer K.; Abel, Haley J.; Watson, Mark A.; Pfeifer, John D; Duncavage, Eric J.

    2013-01-01

    Next-generation sequencing (NGS) has emerged as a powerful technique for the detection of genetic variants in the clinical laboratory. NGS can be performed using DNA from FFPE tissue, but it is unknown whether such specimens are truly equivalent to unfixed tissue for NGS applications. To address this question, we performed hybridization-capture enrichment and multiplexed Illumina NGS for 27 cancer-related genes using DNA from 16 paired fresh-frozen and routine FFPE lung adenocarcinoma specime...

  15. Quality Control and Pre-Qualification of NGS Libraries Made from Clinical Samples

    OpenAIRE

    Langmore, John

    2013-01-01

    We have compared sequencing metrics from different types of clinical samples and different methods of making NGS libraries, for purposes of quality control of the samples and sample preps. We have performed the metrics using the HiSeq and MiSeq, however the same QC metrics could be measured on other platforms. By choosing metrics that can be measured from small amounts of data (e.g., 300,000 reads), we can measure the quality of the clinical samples and NGS libraries in a highly multiplexed f...

  16. Clinical, radiological and molecular diagnosis correlation in serum samples from patients with osteoarticular tuberculosis

    Directory of Open Access Journals (Sweden)

    Guadalupe García-Elorriaga

    2014-07-01

    Conclusions: Nested PCR in serum samples is a rapid, highly sensitive and specific modality for OTB detection. PCR should be performed in addition to clinical evaluation, imaging studies, acid-fast bacilli staining, culture and histopathology diagnosis, if possible.

  17. Nested-PCR for the detection of Mycoplasma hyopneumoniae in bronchial alveolar swabs, frozen tissues and formalin-fixed paraffin-embedded swine lung samples: comparative evaluation with immunohistochemical findings and histological features

    Directory of Open Access Journals (Sweden)

    Paula R. Almeida

    2012-08-01

    Full Text Available The diagnosis of Mycoplasma hyopneumoniae infection is often performed through histopathology, immunohistochemistry (IHC and polymerase chain reaction (PCR or a combination of these techniques. PCR can be performed on samples using several conservation methods, including swabs, frozen tissue or formalin-fixed and paraffin-embedded (FFPE tissue. However, the formalin fixation process often inhibits DNA amplification. To evaluate whether M. hyopneumoniae DNA could be recovered from FFPE tissues, 15 lungs with cranioventral consolidation lesions were collected in a slaughterhouse from swine bred in herds with respiratory disease. Bronchial swabs and fresh lung tissue were collected, and a fragment of the corresponding lung section was placed in neutral buffered formalin for 48 hours. A PCR assay was performed to compare FFPE tissue samples with samples that were only refrigerated (bronchial swabs or frozen (tissue pieces. M. hyopneumoniae was detected by PCR in all 15 samples of the swab and frozen tissue, while it was detected in only 11 of the 15 FFPE samples. Histological features of M. hyopneumoniae infection were presented in 11 cases and 7 of these samples stained positive in IHC. Concordance between the histological features and detection results was observed in 13 of the FFPE tissue samples. PCR was the most sensitive technique. Comparison of different sample conservation methods indicated that it is possible to detect M. hyopneumoniae from FFPE tissue. It is important to conduct further research using archived material because the efficiency of PCR could be compromised under these conditions.

  18. Psychotic experiences in a mental health clinic sample : implications for suicidality, multimorbidity and functioning

    NARCIS (Netherlands)

    Kelleher, I.; Devlin, N.; Wigman, J. T. W.; Kehoe, A.; Murtagh, A.; Fitzpatrick, C.; Cannon, M.

    2014-01-01

    Background Recent community-based research has suggested that psychotic experiences act as markers of severity of psychopathology. There has, however, been a lack of clinic-based research. We wished to investigate, in a clinical sample of adolescents referred to a state-funded mental health service,

  19. The Stice model of overeating: Tests in clinical and non-clinical samples

    NARCIS (Netherlands)

    Strien, T. van; Engels, R.C.M.E.; Leeuwe, J.F.J. van; Snoek, H.M.

    2005-01-01

    The present study tested the dual pathway model of Stice [Stice, E (1994). A review of the evidence for a sociocultural model of bulimia nervosa and an exploration of the mechanisms of action. Clinical Psychology Review, 14, 633-661 and Stice, E. (2001). A prospective test of the dual-pathway model

  20. Isolation and clinical sample typing of human leptospirosis cases in Argentina.

    Science.gov (United States)

    Chiani, Yosena; Jacob, Paulina; Varni, Vanina; Landolt, Noelia; Schmeling, María Fernanda; Pujato, Nazarena; Caimi, Karina; Vanasco, Bibiana

    2016-01-01

    Leptospira typing is carried out using isolated strains. Because of difficulties in obtaining them, direct identification of infective Leptospira in clinical samples is a high priority. Multilocus sequence typing (MLST) proved highly discriminatory for seven pathogenic species of Leptospira, allowing isolate characterization and robust assignment to species, in addition to phylogenetic evidence for the relatedness between species. In this study we characterized Leptospira strains circulating in Argentina, using typing methods applied to human clinical samples and isolates. Phylogenetic studies based on 16S ribosomal RNA gene sequences enabled typing of 8 isolates (6 Leptospira interrogans, one Leptospira wolffii and one Leptospira broomii) and 58 out of 85 (68.2%) clinical samples (55 L. interrogans, 2 Leptospira meyeri, and one Leptospira kirschneri). MLST results for the L. interrogans isolates indicated that five were probably Canicola serogroup (ST37) and one was probably Icterohaemorrhagiae serogroup (ST17). Eleven clinical samples (21.6%), provided MLST interpretable data: five were probably Pyrogenes serogroup (ST13), four Sejroe (ST20), one Autumnalis (ST22) and one Canicola (ST37). To the best of our knowledge this study is the first report of the use of an MLST typing scheme with seven loci to identify Leptospira directly from clinical samples in Argentina. The use of clinical samples presents the advantage of the possibility of knowing the infecting strain without resorting to isolates. This study also allowed, for the first time, the characterization of isolates of intermediate pathogenicity species (L. wolffii and L. broomii) from symptomatic patients. PMID:26658064

  1. The Dutch version of the Child Posttraumatic Cognitions Inventory: validation in a clinical sample and a school sample

    Directory of Open Access Journals (Sweden)

    Julia Diehle

    2015-02-01

    Full Text Available Background: With the inclusion of trauma-related cognitions in the DSM-5 criteria for posttraumatic stress disorder (PTSD, the assessment of these cognitions has become essential. Therefore, valid tools for the assessment of these cognitions are warranted. Objective: The current study aimed at validating the Dutch version of the Child Posttraumatic Cognitions Inventory (CPTCI. Method: We included children aged 8–19 years in our study and assessed the factor structure, reliability and validity of the CPTCI in a clinical sample (n=184 and a school sample (n=318. Results: Our results supported the two-factor structure of the CPTCI and showed good internal consistency for the total scale and the two subscales. We found significant positive correlations between the CPTCI and measures of PTSD, depression, and anxiety disorder. The CPTCI correlated negatively with a measure of quality of life. Furthermore, we found significantly higher scores in the clinical sample than in the school sample. For children who received treatment, we found that a decrease in CPTCI scores was accompanied by a decrease in posttraumatic stress symptoms and comorbid problems indicating that the CPTCI is able to detect treatment effects. Conclusion: Overall, our results suggest that the Dutch CPTCI is a reliable and valid instrument.

  2. Detection of classical swine fever virus (CSFV) in clinical samples by RT-PCR assay in clinical samples by RT-PCR assay using different pairs of primers

    International Nuclear Information System (INIS)

    The aim was to compare the efficiency of RT-PCT assays using four pairs of primers selected from different regions of the CSFV genome for the detection of CSFV in clinical samples of swine and wild boars. The four RT-PCR assays were able to detect CSFV in all 20 clinical samples which had been collected from dead swine and wild boars during the outbreaks of CSF in Slovakia in 1993 and 1994. The quality of the selected RT-PCR primers was determined as follows: gp55L/gp55U (E2), 324/326 (5'-NC), S1/S2 (NS5B) and gp54L/gp54U (NS2 genomic region). We conclude that gp55L/gp55U primers are the most suitable for direct detection of CSFV by RT-PCR in tissue homogenates of diseased animals

  3. The Validity of the Five-Factor Model Prototypes for Personality Disorders in Two Clinical Samples

    Science.gov (United States)

    Miller, Joshua D.; Reynolds, Sarah K.; Pilkonis, Paul A.

    2004-01-01

    The authors examined the validity of D. R. Lynam and T. A. Widiger's (2001) prototypes for personality disorders (PDs) derived from the facets of the 5-factor model (FFM) of personality in 2 clinical samples. In the 1st sample (N = 94), there was good agreement between the prototypes generated by experts and the profiles reported by patients.…

  4. Unreliability of Results of PCR Detection of Helicobacter pylori in Clinical or Environmental Samples ▿ †

    OpenAIRE

    Sugimoto, Mitsushige; Wu, Jeng-Yih; Abudayyeh, Suhaib; Hoffman, Jill; Brahem, Hajer; Al-Khatib, Khaldun; Yamaoka, Yoshio; David Y Graham

    2009-01-01

    The aim of this study was to compare published Helicobacter pylori primer pairs for their ability to reliably detect H. pylori in gastric biopsy specimens and salivary samples. Detection limits of the 26 PCR primer pairs previously described for detection of H. pylori DNA in clinical samples were determined. Sensitivity and specificity were determined using primers with detection limits of

  5. Sample size and power for comparing two or more treatment groups in clinical trials.

    OpenAIRE

    Day, S. J.; Graham, D F

    1989-01-01

    Methods for determining sample size and power when comparing two groups in clinical trials are widely available. Studies comparing three or more treatments are not uncommon but are more difficult to analyse. A linear nomogram was devised to help calculate the sample size required when comparing up to five parallel groups. It may also be used retrospectively to determine the power of a study of given sample size. In two worked examples the nomogram was efficient. Although the nomogram offers o...

  6. The Frequency of the Accidental Contamination with Laboratory Samples in Yazd Clinical Laboratories’ personnel in 2011

    Directory of Open Access Journals (Sweden)

    Jafari, AA. (PhD

    2014-05-01

    Full Text Available Background and Objective: laboratory personnel have always accidental exposure to clinical samples, which can cause the transmission of infection. This threat can be prevented and controlled by education for the use of safety instruments. The purpose was to determine the frequency of accidental exposure to laboratory samples among Yazd laboratory personnel in 2011. Material and Methods: This descriptive cross-sectional study was conducted on 100 of Yazd clinical laboratory personnel. The data was collected, using a valid and reliable questioner, via interview and analyzed by means of SPSS software. Results: Eighty-six percent of the subjects reported an experience of accidental exposure to clinical samples, such as blood, serum and urine. The causes were carelessness (41% and work overload (29%. Needle- stick was the most prevalent injury (52% particularly in sampler workers (51% and in their hands (69%. There wasn’t significant relationship between accidental exposure to laboratory samples and the variables such as private and governmental laboratories (p=0.517, kind of employment (p=0.411, record of services (p=0.439 and academic degree (p=0.454. The subjects aged 20-29 (p=0.034 and worked in sampling unit had the highest accidental exposure. Conclusion: based on the results, inexperience of the personnel especially in sampling room, overload at work and ignorance of applying safety instruments are known as the most important reasons for accidental exposure to clinical samples. Keywords: Contamination; accidental Exposure; Infectious agents; laboratory; personnel

  7. Patterns and predictors of health service utilization in adolescents with pain: comparison between a community and a clinical pain sample

    OpenAIRE

    Toliver-Sokol, Marisol; Murray, Caitlin B.; Wilson, Anna C.; Lewandowski, Amy; Palermo, Tonya M.

    2011-01-01

    There is limited research describing the patterns of healthcare utilization in adolescents with chronic pain. This study describes healthcare utilization in a clinical chronic pain sample, and compares the patterns of service use of this group to a community sample with intermittent pain complaints. We also investigated demographic and clinical factors that predicted healthcare visits and medication use in the clinical sample. Data on 117 adolescents (aged 12-18; n=59 clinical pain sample, n=...

  8. Symptoms of Children with Autism Spectrum Disorder,a clinical sample

    Directory of Open Access Journals (Sweden)

    Ali Alavi Shooshtari

    2009-12-01

    Full Text Available "n Objective: "n "nThe aim of this report was to study the gender role on autismsymptoms distribution and severity in a clinical sample from Iran. Then, the results were compared with the published study from the same community population sample, Iran. "nMethod: The subjects of this retrospective study were a convenient clinical sample of the referrals of children with pervasive developmental disorders. The diagnosis was made according to DSM-IV diagnostic criteria. "nResults: "nMost of the subjects were boys. Boys were referred for evaluation more frequently than girls. The sample included 61 children and adolescents aged 2.1 to 15 years; of whom, 49 had autism. The mean age of children with autism was 7.2(SD=3.2 years. The mean of age, the diagnosis and severity of the symptoms were not related to gender . "n "n "nConclusion: Usually, those with severe cases of autism refer to clinics for treatment. Therefore, the clinical sample of children with autism is just the tip of the iceberg and they may not be the actual representative of community sample of children with autism. Preventive programs should be more focused on the screening and referring of inflected girls for service utilization .

  9. Evaluation of a nonradiometric system (BACTEC 9000 MB) for detection of mycobacteria in human clinical samples.

    OpenAIRE

    ZANETTI, S.; Ardito, F; SECHI, L.; Sanguinetti, M.; Molicotti, P.; Delogu, G.; Pinna, M P; NACCI, A.; Fadda, G.

    1997-01-01

    This study was carried out to evaluate the rate of recovery and time required for detection of mycobacteria from pulmonary and extrapulmonary human clinical samples, by using a fluorescence-quenching-based oxygen sensor (BACTEC 9000 MB; Becton Dickinson Microbiology Systems, Sparks, Md.). The results were compared with those obtained by microscopy, conventional culture in Lowenstein-Jensen (LJ) medium, and a BACTEC radiometric system (BACTEC 460 TB; Becton Dickinson). Of the 779 clinical samp...

  10. Psychotic experiences in a mental health clinic sample: implications for suicidality, multimorbidity and functioning.

    OpenAIRE

    Kelleher, Ian; Devlin, Nina; Wigman, Johanna Tw; Kehoe, Anne; Murtagh, Aileen; Fitzpatrick, Carol; Cannon, Mary

    2014-01-01

    BACKGROUND: Recent community-based research has suggested that psychotic experiences act as markers of severity of psychopathology. There has, however, been a lack of clinic-based research. We wished to investigate, in a clinical sample of adolescents referred to a state-funded mental health service, the prevalence of (attenuated or frank) psychotic experiences and the relationship with (i) affective, anxiety and behavioural disorders, (ii) multimorbid psychopathology, (iii) global functionin...

  11. Ruminations on rumination: anger and sadness rumination in a normative and clinical sample

    OpenAIRE

    Peled, Maya

    2006-01-01

    Anger rumination and sadness rumination were examined concurrently in a normative sample of adults (Study 1) and a clinical adolescent sample (Study 2). The purpose of this research was to assess if rumination on anger and sadness have distinct emotional and behavioural associations, and whether it is warranted to conceptualize them as separate constructs. In both studies, factor analysis indicated that items from analogous anger rumination and sadness rumination measures loaded onto two fact...

  12. Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples.

    Science.gov (United States)

    Budding, Andries E; Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M J E; Savelkoul, Paul H M

    2016-04-01

    Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice. PMID:26763956

  13. Maternal Drug Abuse History, Maltreatment, and Functioning in a Clinical Sample of Urban Children

    Science.gov (United States)

    Onigu-Otite, Edore C.; Belcher, Harolyn M. E.

    2012-01-01

    Objective: This study examined the association between maternal drug abuse history, maltreatment exposure, and functioning, in a clinical sample of young children seeking therapy for maltreatment. Methods: Data were collected on 91 children, mean age 5.3 years (SD 1.0). The Preschool and Early Childhood Functional Assessment Scales (PECFAS) was…

  14. Likelihood of Condom Use When Sexually Transmitted Diseases Are Suspected: Results from a Clinic Sample

    Science.gov (United States)

    Crosby, Richard A.; Milhausen, Robin R.; Graham, Cynthia A.; Yarber, William L.; Sanders, Stephanie A.; Charnigo, Richard; Shrier, Lydia A.

    2014-01-01

    Objective: To determine the event-level associations between perceived risk of sexually transmitted disease (STD) acquisition/transmission and condom use during penile-vaginal intercourse (PVI) among STD clinic attendees. Method: A convenience sample (N = 622) completed daily electronic assessments. Two questions were proxies of perceived risk:…

  15. Protein Profile study of clinical samples using Laser Induced Fluorescence as the detection method

    DEFF Research Database (Denmark)

    Karemore, Gopal Raghunath; Raja, Sujatha N.; Rai, Lavanya;

    2009-01-01

      Protein profiles of tissue homogenates were recorded using HPLC separation and LIF detection method. The samples were collected from volunteers with clinically normal or cervical cancer conditions. It is shown that the protein profile can be classified as belonging to malignant or normal state ...

  16. Change in Academic Distress: Examining Differences between a Clinical and Nonclinical Sample of College Students

    Science.gov (United States)

    Lockard, Allison J.; Hayes, Jeffrey A.; McAleavey, Andrew A.; Locke, Benjamin D.

    2012-01-01

    The purpose of this study was to examine academic distress over the course of a semester for both a clinical and nonclinical sample of college students by administering the Counseling Center Assessment of Psychological Symptoms (CCAPS-62 and CCAPS-34) to students at a single university. Results revealed that students who were in counseling showed…

  17. Intrusions, avoidance and overgeneral memory in a non-clinical sample

    NARCIS (Netherlands)

    Hauer, Beatrijs J. A.; Wessel, I.; Merckelbach, H.

    2006-01-01

    Previous studies have shown a positive relationship between intrusions, effortful avoidance and overgeneral memory in people suffering from (mild) depression or PTSD. The purpose of the present study was to investigate these relationships in a non-clinical sample. As part of a mass testing session,

  18. A Mediation Model of Interparental Collaboration, Parenting Practices, and Child Externalizing Behavior in a Clinical Sample

    Science.gov (United States)

    Kjobli, John; Hagen, Kristine Amlund

    2009-01-01

    The present study examined maternal and paternal parenting practices as mediators of the link between interparental collaboration and children's externalizing behavior. Parent gender was tested as a moderator of the associations. A clinical sample consisting of 136 children with externalizing problems and their families participated in the study.…

  19. Radioimmunoassay in situ used to detect products of cloning mycoplasma pneumoniae DNA and clinical micro samples

    International Nuclear Information System (INIS)

    From the recombinants, which constructed in the laboratory, using plasmids as vector, one strain which express antigen of Mycoplasma pneumoniae by detecting in situ radioimmunoassay was obtained. The authors detected 7 children samples which were throat washing liquids of children suspected of atypical pneumoniae, 4 of them positive by using above method. This data indicated that it was suitable for clinical diagnosis directly

  20. Relations between Parenting Behavior and SES in a Clinical Sample: Validity of SES Measures

    Science.gov (United States)

    Callahan, Corissa L.; Eyberg, Sheila M.

    2010-01-01

    Two common methods of measuring socioeconomic status (SES) were examined in relation to observed parenting behaviors in a clinical sample of 89 mothers of 3- to 6-year-olds referred for treatment of oppositional defiant disorder. Families were 74% Caucasian, 9% African American, 5% Hispanic, 1% Asian, and 11% Biracial. Most children were male…

  1. Diagnostic of Epstein-Barr virus infection in clinical serum samples by SPR

    Czech Academy of Sciences Publication Activity Database

    Riedel, Tomáš; Rodriguez-Emmenegger, Cesar; de los Santos Pereira, Andres; Bedajankova, A.; Brynda, Eduard

    Athens : National Center for Scientific Research "Demokritos", 2014. SF-9. [Conference on Optical Chemical Sensors & Biosensors /12./ - EUROPT(R)ODE XII. 13.04.2014-16.04.2014, Athens] R&D Projects: GA MŠk EE2.3.30.0029 Institutional support: RVO:61389013 Keywords : SPR biosensor * EBV * clinical samples Subject RIV: CE - Biochemistry

  2. Clinical, radiological and molecular diagnosis correlation in serum samples from patients with osteoarticular tuberculosis

    Institute of Scientific and Technical Information of China (English)

    Guadalupe Garca-Elorriaga; Olga Martnez-Elizondo; Guillermo del Rey-Pineda; Csar Gonzlez-Bonilla

    2014-01-01

    Objective: To assess the role of polymerase chain reaction (PCR) in serum samples, in the diagnosis of osteoarticular tuberculosis (OTB) in a setting where only clinical and imaging diagnoses determine the treatment.Methods:A total of 44 consecutive serum specimens were collected from clinically suspected OTB patients, based on clinical and radiological [X-ray or magnetic resonance imaging/computed tomography] features. They were screened by in-house nested PCR. In addition, a few specimens were examined by Gram stain, acid-fast bacilli stain, histopathology and routine bacterial culture. A total of 39 specimens were collected from patients suffering from other bone diseases of nontuberculous origin and included as negative controls.Results:Of the 44 clinically suspected OTB patients, in-house nested PCR was positive in 40 (91%) cases; PCR was negative in 38 (97%) negative controls. Sensitivity and specificity of our in-house nested PCR was 90.9% and 97.4%, respectively. The PCR report was available within 48 h. It was possible to standardize serum PCR technique and in positive cases, a good correlation was observed in terms of an adequate treatment response.Conclusions:Nested PCR in serum samples is a rapid, highly sensitive and specific modality for OTB detection. PCR should be performed in addition to clinical evaluation, imaging studies, acid-fast bacilli staining, culture and histopathology diagnosis, if possible.

  3. Comparison of clinical samples for visceral Leishmaniasis diagnosis in asymptomatic dogs by PCR hybridization

    International Nuclear Information System (INIS)

    The canine visceral leishmaniasis (CVL) diagnosis still represents a challenge because of complexity of this disease. The aim of present study was to compare different clinical samples for diagnosis of CVL by Polymerase Chain Reaction (PCR) combined with hybridization of 32P labeled probes. Bone marrow (BM), skin biopsy (SB), peripheral blood (PB) and conjunctival swab (CS) were used in this work. With this purpose 40 asymptomatic dogs, all positive by parasitological test, were obtained. From each animal were collected SB with sterile punches from ear internal surface, 1.0 mL of PB, BM aspirates from sternum and CS from both lower eyelid. Each clinical sample was submitted to suitable DNA purification process and PCR-hybridization assays. The positive results obtained with PCR were 55%, 25%, 30% and 22.5% for CS, BM, SB and PB respectively while the PCR followed by hybridization showed a positivity of 87.5%, 50%, 45% and 27.5% respectively. The hybridization assay was able to increase the PCR positivity in all kinds of clinical samples. The best performance was obtained using CS samples. We concluded that the PCR associated with DNA radioactive probes was a very sensitive tool for diagnosis of CVL in asymptomatic dogs and the CS has an important potential for regular screening of dogs. (author)

  4. Comparison of clinical samples for visceral Leishmaniasis diagnosis in asymptomatic dogs by PCR hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Sidney A.; Ituassu, Leonardo T.; Melo, Maria N. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia], e-mail: saninoalmeida@gmail.com, e-mail: Itituassu@yahoo.com.br, e-mail: melo@icb.ufmg.br; Leite, Rodrigo S.; Andrade, Antero S.R. [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN-CNEN/MG), Belo Horizonte, MG (Brazil)], e-mail: rleite2005@gmail.com, e-mail: antero@cdtn.br

    2009-07-01

    The canine visceral leishmaniasis (CVL) diagnosis still represents a challenge because of complexity of this disease. The aim of present study was to compare different clinical samples for diagnosis of CVL by Polymerase Chain Reaction (PCR) combined with hybridization of {sup 32}P labeled probes. Bone marrow (BM), skin biopsy (SB), peripheral blood (PB) and conjunctival swab (CS) were used in this work. With this purpose 40 asymptomatic dogs, all positive by parasitological test, were obtained. From each animal were collected SB with sterile punches from ear internal surface, 1.0 mL of PB, BM aspirates from sternum and CS from both lower eyelid. Each clinical sample was submitted to suitable DNA purification process and PCR-hybridization assays. The positive results obtained with PCR were 55%, 25%, 30% and 22.5% for CS, BM, SB and PB respectively while the PCR followed by hybridization showed a positivity of 87.5%, 50%, 45% and 27.5% respectively. The hybridization assay was able to increase the PCR positivity in all kinds of clinical samples. The best performance was obtained using CS samples. We concluded that the PCR associated with DNA radioactive probes was a very sensitive tool for diagnosis of CVL in asymptomatic dogs and the CS has an important potential for regular screening of dogs. (author)

  5. Routine application of the polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples.

    Science.gov (United States)

    Noordhoek, G T; Kaan, J A; Mulder, S; Wilke, H; Kolk, A H

    1995-01-01

    AIM--To investigate the use of the polymerase chain reaction (PCR) in the routine laboratory for the detection of Mycobacterium tuberculosis in clinical samples. METHODS--Samples were divided and processed separately for the detection of M tuberculosis by microscopy, culture and PCR. After DNA extraction, PCR was performed with primers specific for the insertion element IS6110 and the product was analysed by agarose gel electrophoresis, Southern blotting or dot blotting and hybridisation with a digoxigenin labelled internal probe. Each sample was tested for inhibitors of Taq polymerase with the aid of an internal control. Multiple negative and positive controls were used to monitor each step of the procedure. RESULTS--The data from two laboratories, using the same operating procedures, were combined. Of 1957 specimens, 79 (4%) were culture and PCR positive, while 1839 (93.9%) were negative in both tests. Thirty specimens (1.5%) were PCR positive only and nine (0.5%) were culture positive but PCR negative. CONCLUSION--Using culture and clinical history as the gold standard, sensitivity and specificity for PCR were 92.1% and 99.8%, respectively. With elaborate precautions, PCR is a suitable and reliable method for the detection of M tuberculosis in clinical samples in a routine microbiology laboratory. Images PMID:7490312

  6. Profiling the clinical presentation of diagnostic characteristics of a sample of symptomatic TMD patients

    Directory of Open Access Journals (Sweden)

    e Silva Machado Luciana

    2012-08-01

    Full Text Available Abstract Background Temporomandibular disorder (TMD patients might present a number of concurrent clinical diagnoses that may be clustered according to their similarity. Profiling patients’ clinical presentations can be useful for better understanding the behavior of TMD and for providing appropriate treatment planning. The aim of this study was to simultaneously classify symptomatic patients diagnosed with a variety of subtypes of TMD into homogenous groups based on their clinical presentation and occurrence of comorbidities. Methods Clinical records of 357 consecutive TMD patients seeking treatment in a private specialized clinic were included in the study sample. Patients presenting multiple subtypes of TMD diagnosed simultaneously were categorized according to the AAOP criteria. Descriptive statistics and two-step cluster analysis were used to characterize the clinical presentation of these patients based on the primary and secondary clinical diagnoses. Results The most common diagnoses were localized masticatory muscle pain (n = 125 and disc displacement without reduction (n = 104. Comorbidity was identified in 288 patients. The automatic selection of an optimal number of clusters included 100% of cases, generating an initial 6-cluster solution and a final 4-cluster solution. The interpretation of within-group ranking of the importance of variables in the clustering solutions resulted in the following characterization of clusters: chronic facial pain (n = 36, acute muscle pain (n = 125, acute articular pain (n = 75 and chronic articular impairment (n = 121. Conclusion Subgroups of acute and chronic TMD patients seeking treatment can be identified using clustering methods to provide a better understanding of the clinical presentation of TMD when multiple diagnosis are present. Classifying patients into identifiable symptomatic profiles would help clinicians to estimate how common a disorder is within a population of

  7. Genetic Diversity of Mycobacterium avium Isolates Recovered from Clinical Samples and from the Environment: Molecular Characterization for Diagnostic Purposes▿

    OpenAIRE

    Álvarez, Julio; García, Ignacio Gómez; Aranaz, Alicia; Bezos, Javier; Romero, Beatriz; de Juan, Lucía; Mateos, Ana; Gómez-Mampaso, Enrique; Domínguez, Lucas

    2008-01-01

    Isolation of Mycobacterium avium complex (MAC) organisms from clinical samples may occur in patients without clinical disease, making the interpretation of results difficult. The clinical relevance of MAC isolates from different types of clinical samples (n = 47) from 39 patients in different sections of a hospital was assessed by comparison with environmental isolates (n = 17) from the hospital. Various methods for identification and typing (commercial probes, phenotypic characteristics, PCR...

  8. Intra-tumoral Heterogeneity of KRAS and BRAF Mutation Status in Patients with Advanced Colorectal Cancer (aCRC and Cost-Effectiveness of Multiple Sample Testing

    Directory of Open Access Journals (Sweden)

    Susan D. Richman

    2011-01-01

    Full Text Available KRAS mutation status is established as a predictive biomarker of benefit from anti-EGFr therapies. Mutations are normally assessed using DNA extracted from one formalin-fixed, paraffin-embedded (FFPE tumor block. We assessed heterogeneity of KRAS and BRAF mutation status intra-tumorally (multiple blocks from the same primary tumor. We also investigated the utility and efficiency of genotyping a ‘DNA cocktail’ prepared from multiple blocks. We studied 68 consenting patients in two randomized clinical trials. DNA was extracted, from ≥2 primary tumor FFPE blocks per patient. DNA was genotyped by pyrosequencing for KRAS codons 12, 13 and 61 and BRAF codon 600. In patients with heterogeneous mutation status, DNA cocktails were prepared and genotyped. Among 69 primary tumors in 68 patients, 7 (10.1% showed intratumoral heterogeneity; 5 (7.2% at KRAS codons 12, 13 and 2 (2.9% at BRAF codon 600. In patients displaying heterogeneity, the relevant KRAS or BRAF mutation was also identified in ‘DNA cocktail’ samples when including DNA from mutant and wild-type blocks. Heterogeneity is uncommon but not insignificant. Testing DNA from a single block will wrongly assign wild-type status to 10% patients. Testing more than one block, or preferably preparation of a ‘DNA cocktail’ from two or more tumor blocks, improves mutation detection at minimal extra cost.

  9. Microbiological Monitoring and Proteolytic Study of Clinical Samples From Burned and Burned Wounded Patients

    International Nuclear Information System (INIS)

    In this study, clinical samples were collected from 100 patients admitted to Burn and Plastic Surgery Department, Faculty of Medicine, Ain Shams University, Egypt, over a period of 12 months. The proteolytic activity of 110 clinical samples taken from surfaces swabs which taken from burned and burned wounded patients with different ages and gender was examined. Screening for the proteolytic activity produced by pathogenic bacteria isolated from burned and burned wounded patients was evaluated as gram positive Bacilli and gram negative bacilli showed high proteolytic activity (46.4%) while 17.9% showed no activity. The isolated bacteria proved to have proteolytic activity were classified into high, moderate and weak. The pathogenic bacteria isolated from burned and burned wounded patients and showing proteolytic activity were identified as Pseudomonas aeruginosa, Proteus mirabilis, Proteus vulgaris, Bacillus megaterium, Bacillus cereus, Staphylococcus aureus, Escherichia coli, Klebsiella ozaeanae, Klebsiella oxytoca, Klebsiella pneumoniae and Pseudomonas fluoresces.

  10. Diversity of Bipolaris species in clinical samples in the United States and their antifungal susceptibility profiles.

    Science.gov (United States)

    da Cunha, K C; Sutton, D A; Fothergill, A W; Cano, J; Gené, J; Madrid, H; De Hoog, S; Crous, P W; Guarro, J

    2012-12-01

    A set of 104 isolates from human clinical samples from the United States, morphologically compatible with Bipolaris, were morphologically and molecularly identified through the sequence analysis of the internal transcribed space (ITS) region of the nuclear ribosomal DNA (rDNA). The predominant species was Bipolaris spicifera (67.3%), followed by B. hawaiiensis (18.2%), B. cynodontis (8.6%), B. micropus (2.9%), B. australiensis (2%), and B. setariae (1%). Bipolaris cynodontis, B. micropus, and B. setariae represent new records from clinical samples. The most common anatomical sites where isolates were recovered were the nasal region (30.7%), skin (19.2%), lungs (14.4%), and eyes (12.5%). The antifungal susceptibilities of 5 species of Bipolaris to 9 drugs are provided. With the exception of fluconazole and flucytosine, the antifungals tested showed good activity. PMID:23052310

  11. Validation of the Novaco Anger Scale-Provocation Inventory (Danish) With Nonclinical, Clinical, and Offender Samples

    DEFF Research Database (Denmark)

    Moeller, Stine Bjerrum; Novaco, Raymond; Heinola-Nielsen, Vivian;

    2015-01-01

    Anger has high prevalence in clinical and forensic settings, and it is associated with aggressive behavior and ward atmosphere on psychiatric units. Dysregulated anger is a clinical problem in Danish mental health care systems, but no anger assessment instruments have been validated in Danish...... aggressive behavior in hospital. Regression analyses showed that higher scores on NAS increase the risk of having acted aggressively in the past and of acting aggressively in the future....... investigated with samples of 477 nonclinical, 250 clinical, 167 male prisoner, and 64 male forensic participants. Anger prevalence and its relationship with other anger measures, anxiety/depression, and aggression were examined. NAS-PI was found to have high reliability, concurrent validity, and discriminant...

  12. Psychometric Evaluation of the MMPI-2/MMPI-2-RF Restructured Clinical Scales in an Israeli Sample.

    Science.gov (United States)

    Shkalim, Eleanor

    2015-10-01

    The current study cross-culturally evaluated the psychometric properties of the Minnesota Multiphasic Personality Inventory-2 (MMPI-2)/MMPI-2-Restructured Form Restructured Clinical (RC) Scales in psychiatric settings in Israel with a sample of 100 men and 133 women. Participants were administered the MMPI-2 and were rated by their therapists on a 188-item Patient Description Form. Results indicated that in most instances the RC Scales demonstrated equivalent or better internal consistencies and improved intercorrelation patterns relative to their clinical counterparts. Furthermore, external analyses revealed comparable or improved convergent validity (with the exceptions of Antisocial Behavior [RC4] and Ideas of Persecution [RC6] among men), and mostly greater discriminant validity. Overall, the findings indicate that consistent with previous findings, the RC Scales generally exhibit comparable to improved psychometric properties over the Clinical Scales. Implications of the results, limitations, and recommendations for future research are discussed. PMID:25354670

  13. Validity Evidences for the Dimensional Clinical Personality Inventory in Outpatient Psychiatric Sample

    Directory of Open Access Journals (Sweden)

    Roberta Katz Abela

    2015-08-01

    Full Text Available The Dimensional Clinical Personality Inventory (IDCP was developed in Brazil for the assessment of pathological personality traits. This study aimed to seek validity evidence for the dimensions of IDCP based on external criteria, psychiatric diagnosis. We examined the profile in IDCP of 105 psychotherapy outpatients, previously diagnosed with personality disorders. The profiles were compared with the profile of the normative non-clinical sample and we conducted the repeated measures analysis to investigate whether the IDCP is able to discriminate consistent profiles for different diagnoses and compared the general population. The results suggest validity evidence based on external criteria for the IDCP dimensions and points to the clinical effectiveness of the instrument.

  14. Specific determination of clinical and toxicological important substances in biological samples by LC-MS

    International Nuclear Information System (INIS)

    This thesis of this dissertation is the specific determination of clinical and toxicological important substances in biological samples by LC-MS. Nicotine was determined in serum after application of nicotine plaster and nicotine nasal spray with HPLC-ESI-MS. Cotinine was determined direct in urine with HPLC-ESI-MS. Short time anesthetics were determined in blood and cytostatics were determined in liquor with HPLC-ESI-MS. (botek)

  15. Detection of Shiga toxins genes by Multiplex PCR in clinical samples

    OpenAIRE

    2013-01-01

    Background: Different methods have been used for detection of shiga toxins; such as,  cell culture, ELISA, and RFPLA. However, all of these methods suffer from high cost, time-consumption and relatively low sensitivity. In this study we used Multiplex PCR method for detection of genes encoding shiga toxins. Material and Methods: In this study, 63 clinical samples were obtained from positive cultures of Shigella and E. coli O157, from Bahman 1391 until Ordibehesht 1392 in Mazandaran provin...

  16. Assessing decentering: Validation, psychometric properties and clinical usefulness of the Experiences Questionnaire in a Spanish sample

    OpenAIRE

    Soler Ribaudi, Joaquim; Franquesa, Alba; Feliu-Soler, Albert; Cebolla i Martí, Ausiàs Josep; García Campayo, Javier; Tejedor, Rosa; Demarzo, Marcelo; Baños Rivera, Rosa María; Pascual, Juan Carlos; Portella, María J.

    2014-01-01

    Decentering is defined as the ability to observe one’s thoughts and feelings in a detached manner. The Experiences Questionnaire (EQ) is a self-report instrument that originally assessed decentering and rumination. The purpose of this study was to evaluate the psychometric properties of the Spanish version of EQ-Decentering and to explore its clinical usefulness. The 11-item EQ-Decentering subscale was translated into Spanish and psychometric properties were examined in a sample of 921 adult ...

  17. Vibrio parahaemolyticus Strains of Pandemic Serotypes Identified from Clinical and Environmental Samples from Jiangsu, China

    OpenAIRE

    Jingjiao eLi; Feng eXue; Zhenquan eYang; Xiaoping eZhang; Dexin eZeng; Guoxiang eChao; Yuan eJiang; Baoguang eLi

    2016-01-01

    Vibrio parahaemolyticus has emerged as a major foodborne pathogen in China, Japan, Thailand and other Asian countries. In this study, 72 strains of V. parahaemolyticus were isolated from clinical and environmental samples between 2006 and 2014 in Jiangsu, China. The serotypes and six virulence genes including thermostable direct hemolysin (TDR) and TDR-related hemolysin (TRH) genes were assessed among the isolates. Twenty five serotypes were identified and O3:K6 was one of the dominant seroty...

  18. A Simplified Method to Recover Urinary Vesicles for Clinical Applications, and Sample Banking

    OpenAIRE

    Musante, Luca; Tataruch, Dorota; Gu, Dongfeng; Benito-Martin, Alberto; Calzaferri, Giulio; Aherne, Sinead; Holthofer, Harry

    2014-01-01

    Urinary extracellular vesicles provide a novel source for valuable biomarkers for kidney and urogenital diseases: Current isolation protocols include laborious, sequential centrifugation steps which hampers their widespread research and clinical use. Furthermore, large individual urine sample volumes or sizable target cohorts are to be processed (e.g. for biobanking), the storage capacity is an additional problem. Thus, alternative methods are necessary to overcome such limitations. We have d...

  19. Diversity of Bipolaris species in clinical samples in the United States and their antifungal susceptibility profiles

    OpenAIRE

    Cunha, DA; Sutton, D.A.; Fothergill, A. W.; Cano, J.; Gene, J.; Madrid, H.; Hoog, de, G.S.; Crous, P.W.; Guarro, J

    2012-01-01

    A set of 104 isolates from human clinical samples from the United States, morphologically compatible with Bipolaris, were morphologically and molecularly identified through the sequence analysis of the internal transcribed space (ITS) region of the nuclear ribosomal DNA (rDNA). The predominant species was Bipolaris spicifera (67.3%), followed by B. hawaiiensis (18.2%), B. cynodontis (8.6%), B. micropus (2.9%), B. australiensis (2%), and B. setariae (1%). Bipolaris cynodontis, B. micropus, and...

  20. Clinical features and prognosis of a sample of patients with trisomy 13 (Patau syndrome) from Brazil.

    Science.gov (United States)

    Petry, Patrícia; Polli, Janaina B; Mattos, Vinícius F; Rosa, Rosana C M; Zen, Paulo R G; Graziadio, Carla; Paskulin, Giorgio A; Rosa, Rafael F M

    2013-06-01

    Trisomy 13 or Patau syndrome (PS) is a chromosomal disorder characterized by a well known presentation of multiple congenital anomalies. Our objective was to determine the clinical features and prognosis observed in a sample of patients with PS. The series was composed of patients with diagnosis of PS consecutively evaluated by a Clinical Genetics Service from a reference hospital of southern Brazil, in the period between 1975 and 2012. Statistical analysis was performed using PEPI program (version 4.0), with two-tailed Fisher's exact test for comparison of frequencies (P<0.05). The sample consisted of 30 patients, 60% male, median age at first evaluation of 9 days. Full trisomy of chromosome 13 was the main cytogenetic alteration (73%). The major clinical findings included: cryptorchidism (78%), abnormal auricles (77%), congenital heart defects (76%), polydactyly (63%), microphthalmia (60%) and micrognathia (50%). Four patients (13%) simultaneously had micro/anophthalmia, oral clefts and polydactyly. Some findings were only observed in our sample and included, among others, preauricular tags (10%), duplication of the hallux (3%) and spots following the lines of Blaschko (3%). Mosaicism (20% of cases) had a statistically significant association only with absence of cryptorchidism. The median of survival was 26 days. Patients with and without mosaicism had similar median of survival. Our findings, in agreement with the literature, show that the anomalies in patients with PS can be quite variable, sometimes even atypical. There is no pathognomonic finding, which may make the early identification of these patients challenging. PMID:23613355

  1. Significant Decline in Galactomannan Signal during Storage of Clinical Serum Samples

    Directory of Open Access Journals (Sweden)

    Samir G. Agrawal

    2013-06-01

    Full Text Available Galactomannan (GM is widely used for detection of invasive aspergillosis in high-risk haemato-oncology patients. Recent publications have reported a lack of repeatability of GM detection. The objective of this retrospective study was to assess the repeatability of GM levels during storage of clinical samples. In a GM screening strategy, positive sera were repeat tested as per manufacturer’s recommendations. Short-term (ST storage of samples was at +4 °C while long-term (LT storage was at −80 °C. Bronchoalveolar (BAL fluid was also repeating tested after ST storage and LT storage. Wilcoxon Signed Ranks Test was employed to assess the repeatability of GM levels. In a subset of 14 GM positive sera, repeat testing was performed on both the original serum and ethylenediaminetetraacetic acid (EDTA pre-treated sample. There was a significant reduction in GM signals on repeat testing following ST storage (median GM index: 0.65 vs. 0.19; p < 0.001 and LT storage (median GM index: 0.56 vs. 0.10; p < 0.001 of serum samples. Of samples that were initially GM positive, an average GM index reduction of 50% was seen, with approximately two-thirds becoming GM negative on repeat testing of the same sample. In contrast, GM signal loss was not seen on repeat testing of BAL fluid following ST or LT storage. When GM positive serum samples were repeat tested using EDTA pre-treated serum from the first step of the testing protocol, all samples remained GM positive. In contrast, when the same samples were repeat tested from the original collected serum, 9 samples (64% became GM negative. The significant reduction in GM signals during ST and LT storage of serum samples has implications for clinical management. Although the reasons for GM decline are unknown, they occur prior to the EDTA pre-treatment stage, indicating that the time from phlebotomy to testing should be minimized. BAL fluid GM index values remain stable.

  2. Clinical,radiological and molecular diagnosis correlation in serum samples from patients with osteoarticular tuberculosis

    Institute of Scientific and Technical Information of China (English)

    Guadalupe; Garcia-Elorriaga; Olga; Martinez-Elizondo; Guillermo; del; Rey-Pineda; Cesar; Gonzalez-Bonilla

    2014-01-01

    Objective:To assess the role of polymerase chain reaction(PCR)in serum sauples,in the diagnosis of osteoarticular tuberculosis(OTB)in a setting where only clinical and imaging diagnoses determine the treatment.Methods:A total of 44 consecutive serum specimens were collected from clinically suspected OTB patients,based on clinical and radiological[X-ray or magnetic resonance imagng/computecl tomography]features.They were scrcened by in-house nested PCR.In addition,a few specimens were examined by Gram stain,acid-fast bacilli stain,histand routine bacterial culture.A total of 39 specimens were collected from patients suffering from other bone diseases of nontuberculous origin and included as negative controls.Results:of the 44 clinically suspected OTB patients,in-house nested PCR was positive in 40(91%)cases;PCR was negative in 38(97%)negative controls.Sensitivity and specificity of our in—house nested PCR was 90.3%and 97.4%,respectively.The PCR report was available within 48 h.It was possible to standardize serum PCR technique and in positive cases,a good n was observed in terms of an adequate treatment response.Conclusions:Nested PCR in serum samples is a rapid,highly sensitive and specific modality for OTB detection,PCR should be performed in addition to clinical evaluation,imaging studies,acidfast bacilli staining,culture and histopathology diagnosis,if possible.

  3. [Sample size calculation in clinical post-marketing evaluation of traditional Chinese medicine].

    Science.gov (United States)

    Fu, Yingkun; Xie, Yanming

    2011-10-01

    In recent years, as the Chinese government and people pay more attention on the post-marketing research of Chinese Medicine, part of traditional Chinese medicine breed has or is about to begin after the listing of post-marketing evaluation study. In the post-marketing evaluation design, sample size calculation plays a decisive role. It not only ensures the accuracy and reliability of post-marketing evaluation. but also assures that the intended trials will have a desired power for correctly detecting a clinically meaningful difference of different medicine under study if such a difference truly exists. Up to now, there is no systemic method of sample size calculation in view of the traditional Chinese medicine. In this paper, according to the basic method of sample size calculation and the characteristic of the traditional Chinese medicine clinical evaluation, the sample size calculation methods of the Chinese medicine efficacy and safety are discussed respectively. We hope the paper would be beneficial to medical researchers, and pharmaceutical scientists who are engaged in the areas of Chinese medicine research. PMID:22292397

  4. Prevalence of Aspergillus species in clinical samples isolated in an Indian tertiary care hospital

    Directory of Open Access Journals (Sweden)

    Xess Immaculata

    2004-12-01

    Full Text Available CONTEXT (BACKGROUND: In recent times, it has become important to determine the prevalence of different Aspergillus species in clinical samples in view of difference in antifungal susceptibility noted in some species. AIMS: To determine the species prevalence of Aspergillus isolates in various clinical samples received in the Mycology Laboratory at our institute. METHOD: Over a period of 4-years, a total of 18,731 samples were processed, and species identification carried out by standard microbiological methods. RESULTS: Four hundred and fifty six samples (2.43% were culture positive for Aspergillus species. A.flavus (46.93% was the most common isolate, followed by A.fumigatus (37.72% and A.niger (15.35%. It was observed that A.fumigatus was the predominant species isolated from blood and respiratory specimens, A.flavus was predominantly isolated from nasal polyps whereas A.niger predominated in nail specimens. Culture positivity was highest in the age group 12-65 years and in males. Sixty-nine patients (15.13% were admitted to the intensive care unit. CONCLUSIONS: The study highlights the diverse manifestations caused by Aspergillus species in human beings and also throws light on the different species prevalent locally. The knowledge would prove useful in selecting empirical antifungal therapy and formulating prophylactic and pre-emptive strategies.

  5. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

    Directory of Open Access Journals (Sweden)

    Reis Patricia P

    2010-06-01

    Full Text Available Abstract Background MicroRNAs (miRs are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE tissue. Results Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p 35, we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p Conclusion Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.

  6. P25-S Gene Expression Profiling from Formalin-Fixed, Paraffin-Embedded Tissues Using the QuantiGene Branched DNA Assay

    OpenAIRE

    Davies, J.; Maqsodi, B.; Yang, W.; Ma, Y.; Luo, Y.; McMaster, G.

    2007-01-01

    Large numbers of formalin-fixed, paraffin-embedded (FFPE) human tissue specimens with known clinical outcome are archived worldwide, representing a vast resource for biomarker and gene-disease association studies. However, RNA quality in FFPE tissues is compromised by chemical modifications and extensive fragmentation caused by formalin fixation. As a result, quantifying RNA in FFPE samples can be problematic.

  7. How Suitable is Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight for Metabolite Imaging from Clinical Formalin-Fixed and Paraffin-Embedded Tissue Samples in Comparison to Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry?

    Science.gov (United States)

    Buck, Achim; Balluff, Benjamin; Voss, Andreas; Langer, Rupert; Zitzelsberger, Horst; Aichler, Michaela; Walch, Axel

    2016-05-17

    In research and clinical settings, formalin-fixed and paraffin-embedded (FFPE) tissue specimens are collected routinely and therefore this material constitutes a highly valuable source to gather insight in metabolic changes of diseases. Among mass spectrometry techniques to examine the molecular content of FFPE tissue, mass spectrometry imaging (MSI) is the most appropriate when morphological and histological features are to be related to metabolic information. Currently, high-resolution mass spectrometers are widely used for metabolomics studies. However, with regards to matrix-assisted laser desorption/ionization (MALDI) MSI, no study has so far addressed the necessity of instrumental mass resolving power in terms of clinical diagnosis and prognosis using archived FFPE tissue. For this matter we performed for the first time a comprehensive comparison between a high mass resolution Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer and a time-of-flight (TOF) instrument with lower mass resolving power. Spectra analysis revealed that about one-third of the detected peaks remained unresolved by MALDI-TOF, which led to a 3-5 times lower number of m/z features compared to FTICR measurements. Overlaid peak information and background noise in TOF images made a precise assignment of molecular attributes to morphological features more difficult and limited classification approaches. This clearly demonstrates the need for high-mass resolution capabilities for metabolite imaging. Nevertheless, MALDI-TOF allowed reproducing and verifying individual markers identified previously by MALDI-FTICR MSI. The systematic comparison gives rise to a synergistic combination of the different MSI platforms for high-throughput discovery and validation of biomarkers. PMID:27065343

  8. [Application of PASS in sample size estimation of non-inferiority, equivalence and superiority design in clinical trials].

    Science.gov (United States)

    Wang, Y Y; Sun, R H

    2016-05-10

    The sample size of non-inferiority, equivalence and superiority design in clinical trial was estimated by using PASS 11 software. The result was compared with that by using SAS to evaluate the practicability and accuracy of PASS 11 software for the purpose of providing reference for sample size estimation in clinical trial design. PMID:27188375

  9. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates.

    Science.gov (United States)

    Courbet, Alexis; Endy, Drew; Renard, Eric; Molina, Franck; Bonnet, Jérôme

    2015-05-27

    Whole-cell biosensors have several advantages for the detection of biological substances and have proven to be useful analytical tools. However, several hurdles have limited whole-cell biosensor application in the clinic, primarily their unreliable operation in complex media and low signal-to-noise ratio. We report that bacterial biosensors with genetically encoded digital amplifying genetic switches can detect clinically relevant biomarkers in human urine and serum. These bactosensors perform signal digitization and amplification, multiplexed signal processing with the use of Boolean logic gates, and data storage. In addition, we provide a framework with which to quantify whole-cell biosensor robustness in clinical samples together with a method for easily reprogramming the sensor module for distinct medical detection agendas. Last, we demonstrate that bactosensors can be used to detect pathological glycosuria in urine from diabetic patients. These next-generation whole-cell biosensors with improved computing and amplification capacity could meet clinical requirements and should enable new approaches for medical diagnosis. PMID:26019219

  10. Genotypic characterization, invasion index and antimicrobial resistance pattern in Listeria monocytogenes strains isolated from clinical samples

    Institute of Scientific and Technical Information of China (English)

    Behrooz Sadeghi Kalani; Abazar Pournajaf; Mansour Sedighi; Abbas Bahador; Gholamreza Irajian; Firuzeh Valian

    2015-01-01

    Objective: To evaluate antimicrobial resistance, invasion index and genetic profile in Listeriamonocytogenes isolated from clinical samples. Methods: At all, 170 clinical samples were collected from patients with spontaneous abortions hospitalized in Shariati hospital in Tehran during June 2010 to August 2013. Invasion index was determined using HeLa cells. The multiple-locus variable-number tandem-repeats analysis (MLVA) was used for evaluation of genetic relatedness. Results: Out of 14 L. monocytogenes isolates, 4 (28.57%), 2 (14.28%), 0 (0%), 5 (35.71%) and 3 (21.42%) were isolated from placental tissue, urine, blood, vaginal and rectal swabs, respectively. High resistance to penicillin and multidrug resistant were found amongst isolates. The invasion index was in the range of 0.001-0.007. Seven different types were obtained by MLVA assay and type 2 and 3 with 4 strains were the most frequent type. Strains isolated from the vagina and the placenta of the same type were also more resistant to penicillin. Conclusions: Since MLVA is a high-throughput screening method that is fairly inexpensive, easy to accomplish, rapid, and trustworthy, it is well suited to interlaboratory comparisons during epidemiological investigations. Also further studies of larger samples from a variety of sources such as food and animal specimens recommended comparing by MLVA method.

  11. Gender Differences in Borderline Personality Disorder: Results From a Multinational, Clinical Trial Sample.

    Science.gov (United States)

    Silberschmidt, Amy; Lee, Susanne; Zanarini, Mary; Schulz, S Charles

    2015-12-01

    This study aims to extend previous research by considering gender differences in borderline personality (BPD) using both dimensional self-reported and clinical measures of symptomatology. Drawing from a cross-cultural, clinical trial sample, the authors compared female and male BPD subjects (N = 770; 211 male) between the ages of 18 and 65 using diagnostic and self-report data. The authors found that women with BPD have greater hostility and relationship disruption than men. Gender differences in eating disorders, particularly bulimia, are more divergent than in the general population. Generally, gender differences in BPD in this sample are consistent with known general population differences. Women show greater overall symptomatology, including depressive, anxious, and somatic symptoms. Men have higher rates of antisocial personality disorder and a trend toward higher rates of narcissistic personality disorder. However, several gender differences consistently found in the general population are not present in this BPD sample. There are no differences in aggression, suicidality, substance abuse, panic disorder, or obsessive-compulsive disorder. Gender differences in major depression and posttraumatic stress disorder are attenuated. These findings support the conclusion that BPD may diminish normal gender differences. PMID:25562535

  12. Vibrio parahaemolyticus Strains of Pandemic Serotypes Identified from Clinical and Environmental Samples from Jiangsu, China

    Directory of Open Access Journals (Sweden)

    Jingjiao eLi

    2016-05-01

    Full Text Available Vibrio parahaemolyticus has emerged as a major foodborne pathogen in China, Japan, Thailand and other Asian countries. In this study, 72 strains of V. parahaemolyticus were isolated from clinical and environmental samples between 2006 and 2014 in Jiangsu, China. The serotypes and six virulence genes including thermostable direct hemolysin (TDR and TDR-related hemolysin (TRH genes were assessed among the isolates. Twenty five serotypes were identified and O3:K6 was one of the dominant serotypes. The genetic diversity was assessed by multilocus sequence typing (MLST analysis, and 48 sequence types (STs were found, suggesting this V. parahaemolyticus group is widely dispersed and undergoing rapid evolution. A total of 25 strains of pandemic serotypes such as O3:K6, O5:K17 and O1:KUT were identified. It is worth noting that the pandemic serotypes were not exclusively identified from clinical samples, rather, nine strains were also isolated from environmental samples; and some of these strains harbored several virulence genes, which may render those strains pathogenicity potential. Therefore, the emergence of these environmental pandemic V. parahaemolyticus strains may poses a new threat to the public health in China. Furthermore, six novel serotypes and 34 novel STs were identified among the 72 isolates, indicating that V. parahaemolyticus were widely distributed and fast evolving in the environment in Jiangsu, China. The findings of this study provide new insight into the phylogenic relationship between V. parahaemolyticus strains of pandemic serotypes from clinical and environmental sources and enhance the MLST database; and our proposed possible O- and K- antigen evolving paths of V. parahaemolyticus may help understand how the serotypes of this dispersed bacterial population evolve.

  13. Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures.

    Science.gov (United States)

    Foster, Matthew W; Gerhardt, Geoff; Robitaille, Lynda; Plante, Pier-Luc; Boivin, Guy; Corbeil, Jacques; Moseley, M Arthur

    2015-10-20

    The rapid, sensitive, and specific identification of infectious pathogens from clinical isolates is a critical need in the hospital setting. Mass spectrometry (MS) has been widely adopted for identification of bacterial pathogens, although polymerase chain reaction remains the mainstay for the identification of viral pathogens. Here, we explored the capability of MS for the detection of human metapneumovirus (HMPV), a common cause of respiratory tract infections in children. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) sequencing of a single HMPV reference strain (CAN97-83) was used to develop a multiple reaction monitoring (MRM) assay that employed stable isotope-labeled peptide internal standards for quantitation of HMPV. Using this assay, we confirmed the presence of HMPV in viral cultures from 10 infected patients and further assigned genetic lineage based on the presence/absence of variant peptides belonging to the viral matrix and nucleoproteins. Similar results were achieved for primary clinical samples (nasopharyngeal aspirates) from the same individuals. As validation, virus lineages, and variant coding sequences, were confirmed by next-generation sequencing of viral RNA obtained from the culture samples. Finally, separate dilution series of HMPV A and B lineages were used to further refine and assess the robustness of the assay and to determine limits of detection in nasopharyngeal aspirates. Our results demonstrate the applicability of MRM for identification of HMPV, and assignment of genetic lineage, from both viral cultures and clinical samples. More generally, this approach should prove tractable as an alternative to nucleic-acid based sequencing for the multiplexed identification of respiratory virus infections. PMID:26376123

  14. Rapid detection of Candida albicans by polymerase spiral reaction assay in clinical blood samples

    Directory of Open Access Journals (Sweden)

    Xiaoqun eJiang

    2016-06-01

    Full Text Available Candida albicans is the most common human yeast pathogen which causes mucosal infections and invasive fungal diseases. Early detection of this pathogen is needed to guide preventative and therapeutic treatment. The aim of this study was to establish a polymerase spiral reaction (PSR assay that rapidly and accurately detects C. albicans and to assess the clinical applicability of PSR-based diagnostic testing. Internal transcribed spacer 2 (ITS2, a region between 5.8S and 28S fungal ribosomal DNA, was used as the target sequence. Four primers were designed for amplification of ITS2 with the PSR method, which was evaluated using real time turbidity monitoring and visual detection using a pH indicator. Fourteen non- C. albicans yeast strains were negative for detection, which indicated the specificity of PSR assay was 100%. A 10-fold serial dilution of C. albicans genomic DNA was subjected to PSR and conventional PCR to compare their sensitivities. The detection limit of PSR was 6.9 pg/µl within 1 h, 10-fold higher than that of PCR (69.0 pg/µl. Blood samples (n=122 were collected from intensive care unit and hematological patients with proven or suspected C. albicans infection at two hospitals in Beijing, China. Both PSR assay and the culture method were used to analyze the samples. Of the 122 clinical samples, 34 were identified as positive by PSR. The result was consistent with those obtained by the culture method. In conclusion, a novel and effective C. albicans detection assay was developed that has a great potential for clinical screening and point-of-care testing.

  15. Self-esteem in a clinical sample of morbidly obese children and adolescents

    DEFF Research Database (Denmark)

    Nowicka, P; Höglund, P; Birgerstam, P;

    2009-01-01

    AIM: To study self-esteem in clinical sample of obese children and adolescents. METHODS: Obese children and adolescents aged 8-19 years (n = 107, mean age 13.2 years, mean BMI 32.5 [range 22.3-50.6], mean BMI z-score 3.22 [range 2.19-4.79]; 50 boys and 57 girls) were referred for treatment...... of primary obesity. Self-esteem was measured with a validated psychological test with five subscales: physical characteristics, talents and skills, psychological well-being, relations with the family and relations with others. A linear mixed effect model used the factors gender and adolescence group...

  16. Sexual revictimization in a clinical sample of women reporting childhood sexual abuse

    DEFF Research Database (Denmark)

    Lau, Marianne; Kristensen, Ellids

    2010-01-01

    BACKGROUND: Child and adolescent sexual abuse (CSA) increases the risk for adult sexual assault (ASA), and psychological vulnerability as well as aspects of CSA and upbringing might influence the risk. AIMS: The aims of this study were to investigate whether women who reported both CSA and ASA: 1......: The results showed an increased psychological vulnerability among women with ASA, but whether the results are cause or effect of sexual revictimization or can be generalized to other clinical samples are not clear. Interventions targeting the increased risk of ASA should be developed, implemented and tested...

  17. Statistical methods for detecting differentially abundant features in clinical metagenomic samples.

    Directory of Open Access Journals (Sweden)

    James Robert White

    2009-04-01

    Full Text Available Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them.We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software

  18. Unreliability of results of PCR detection of Helicobacter pylori in clinical or environmental samples.

    Science.gov (United States)

    Sugimoto, Mitsushige; Wu, Jeng-Yih; Abudayyeh, Suhaib; Hoffman, Jill; Brahem, Hajer; Al-Khatib, Khaldun; Yamaoka, Yoshio; Graham, David Y

    2009-03-01

    The aim of this study was to compare published Helicobacter pylori primer pairs for their ability to reliably detect H. pylori in gastric biopsy specimens and salivary samples. Detection limits of the 26 PCR primer pairs previously described for detection of H. pylori DNA in clinical samples were determined. Sensitivity and specificity were determined using primers with detection limits of pylori-positive and -negative (by concordance by culture and histology) coded gastric biopsy specimens. These results were then confirmed with gastric biopsy specimens and saliva from patients with confirmed H. pylori status. Five of the twenty-six previously reported primer pairs (HP64-f/HP64-r, HP1/HP2, EHC-U/EHC-L, VAG-F/VAG-R, and ICT37/ICT38) had detection limits of 90% with gastric biopsy specimens. No combinations of primer pairs improved the results. Using these five primer pairs, 54% of the positive saliva samples were determined to be false positive; both the HP64-f/HP64-r and the HP1/HP2 sets produced false positives with saliva. We conclude that clinicians should not rely on results using current PCR primers alone to decide the H. pylori status of an individual patient or as a basis for treatment decisions. The results of studies based on PCR identification of H. pylori in environmental samples should be viewed with caution. Possibly, specific primers sets can be identified based on the presence of multiple putative virulence factor genes. PMID:19129407

  19. Cognitive Predictors of Verbal Memory in a Mixed Clinical Pediatric Sample

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    Shelley C. Heaton

    2013-08-01

    Full Text Available Verbal memory problems, along with other cognitive difficulties, are common in children diagnosed with neurological and/or psychological disorders. Historically, these “memory problems” have been poorly characterized and often present with a heterogeneous pattern of performance across memory processes, even within a specific diagnostic group. The current study examined archival neuropsychological data from a large mixed clinical pediatric sample in order to understand whether functioning in other cognitive areas (i.e., verbal knowledge, attention, working memory, executive functioning may explain some of the performance variability seen across verbal memory tasks of the Children’s Memory Scale (CMS. Multivariate analyses revealed that among the cognitive functions examined, only verbal knowledge explained a significant amount of variance in overall verbal memory performance. Further univariate analyses examining the component processes of verbal memory indicated that verbal knowledge is specifically related to encoding, but not the retention or retrieval stages. Future research is needed to replicate these findings in other clinical samples, to examine whether verbal knowledge predicts performance on other verbal memory tasks and to explore whether these findings also hold true for visual memory tasks. Successful replication of the current study findings would indicate that interventions targeting verbal encoding deficits should include efforts to improve verbal knowledge.

  20. Childhood trauma associates with clinical features of schizophrenia in a sample of Chinese inpatients.

    Science.gov (United States)

    Li, Xian-Bin; Li, Qi-Yong; Liu, Jin-Tong; Zhang, Liang; Tang, Yi-Lang; Wang, Chuan-Yue

    2015-08-30

    This study examined the association between childhood trauma and clinical features, comorbid anxiety and post-traumatic stress disorder (PTSD) symptoms, and suicidal and aggressive behaviors in Chinese patients with schizophrenia. The Childhood Trauma Questionnaire - Short Form (CTQ-SF), the Impact of Events Scale - Revised (IES-R), and the State-Trait Anxiety Inventory (STAI) were administered to 182 Chinese inpatients with schizophrenia. The relationship between the severity and the number of traumic experiences and clinical features were analyzed. Physical neglect (PN) in childhood was reported in 71.7% of this sample, followed by emotional neglect (EN, 58.6%), sexual abuse (SA, 39.9%), emotional abuse (EA, 31.7%) and physical abuse (PA, 22.2%). Significant negative correlations existed between age of onset and the EA scores. Significant positive correlations were found between the subscores of IES-R, STAI and CTQ-SF. Patients with history of suicidal or aggressive behaviors had significantly higher trauma scores than patients without such behaviors. Exposure to childhood trauma is associated with early age of onset, more PTSD and anxiety symptoms, and history of suicidal and aggressive behaviors. A dose-effect may exist between severity, number of trauma experiences, and clinical features. PMID:26096662

  1. A review on the use of NEO-PI-R validity scales in normative, job selection, and clinical samples

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    Angel Blanch

    2009-06-01

    Full Text Available Background and Objectives: In this study we review the use of the Positive Presentation Management (PPM and Negative Presentation Management (NPM scales, two NEO-PI-R derived measures originally devised to control for biased and distorted responses. These scales have been used with normative, job selection and clinical samples, in cross-sectional and experimental studies. Methods: Web-based and manual searches in personality and psychological assessment journals were conducted, and information on the PPM and NPM scales was systematically recorded. Means, standard deviations and reliability coefficients were summarized and compared between three types of samples: normative, job selection and clinical. Results: Five studies were performed with normative samples (33%, 3 with employment samples (20% and 7 with clinical samples (47%. Cross-sectional designs were most common (60%, although there were also experimental studies (40%. Reported reliability coefficients were lower than usually accepted. There were differences in mean PPM and NPM scores in regard to the study sample background. Conclusions: There were some discrepancies when reporting PPM and NPM results across the reviewed studies. Normative and employment samples scored higher in PPM than clinical samples. Clinical samples scored higher in NPM than normative and employment samples The PPM and NPM scales could be useful in applied situations, although parallel sources of information should be taken into account to detect distorted responses to the questionnaire. However, the results on these scales should be systematically reported in future studies.

  2. Using Experience Sampling Methods/Ecological Momentary Assessment (ESM/EMA) in Clinical Assessment and Clinical Research: Introduction to the Special Section

    OpenAIRE

    Trull, Timothy J.; Ebner-Priemer, Ulrich W.

    2009-01-01

    This article introduces the special section on experience sampling methods and ecological momentary assessment in clinical assessment. We review the conceptual basis for experience sampling methods (ESM; Csikszentmihalyi & Larson, 1987) and ecological momentary assessment (EMA; Stone & Shiffman, 1994). Next, we highlight several advantageous features of ESM/EMA as applied to psychological assessment and clinical research. We provide a brief overview of the articles in this special section, ea...

  3. Prevalence of Extended –Spectrum-Beta-Lactamase-Producing Klebsiella Pneumonia Isolates from Clinical Samples

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    Alizade, H. (MSc

    2014-06-01

    Full Text Available Background and Objective: Klebsiella pneumonia (K.pneumonia is one of the common causes of nosocomial infections. The aim of this research was to determine the prevalence of beta-lactamase genes and phenotypic confirmation of extended–spectrum-beta-lactamase (ESBL producing K.pneumonia isolates from clinical samples. Material and Methods: In this study, 122 K.pneumonia were isolated from clinical specimens of Khoramabad city and were confirmed by standard bacteriological tests. The presence of ESBL enzymes was detected by combined disk diffusion method. PCR assay with specific primers was used to determine blaSHV, blaTEM, blaCTX-15 and blaCTX-M genes in the confirmed isolates. Results: of 122 K.pneumonia isolates, 78 (64.18% were positive for ESBL, using disk diffusion method. According to antibiogram results, 10.65% of isolates were resistant to cefotaxime, 3.27% to ceftazidime and 68.03% to both antibiotics. Ninety isolates (64.18% considered as ESBLs isolates, at the same time, with being resistant to cefotaxime and ceftazidime were also sensitive to cefotaxime-clavulanic acid and ceftazidime-clavulanic acid. In PCR assays, blaCTX-15, blaSHV, blaCTX-M and blaTEM genes were detected in 78.68%, 40.16%, 26.22% and 22.13% of isolates, respectively. Ten resistant patterns of genes were detected. Conclusion: The significance percentage of antibiotic resistant genes of K.pneumonia isolates from clinical samples in Khoramabad city had ESBLs genes; CTX-M category was the most prevalent encoding genes of these enzymes. Keywords: Klebsiella Pneumonia, Extended-Spectrum Beta-Lactamase, Antibiotic Resistance

  4. Evaluation of dengue NS1 antigen rapid tests and ELISA kits using clinical samples.

    Directory of Open Access Journals (Sweden)

    Subhamoy Pal

    Full Text Available Early diagnosis of dengue virus (DENV infection can improve clinical outcomes by ensuring close follow-up, initiating appropriate supportive therapies and raising awareness to the potential of hemorrhage or shock. Non-structural glycoprotein-1 (NS1 has proven to be a useful biomarker for early diagnosis of dengue. A number of rapid diagnostic tests (RDTs and enzyme-linked immunosorbent assays (ELISAs targeting NS1 antigen (Ag are now commercially available. Here we evaluated these tests using a well-characterized panel of clinical samples to determine their effectiveness for early diagnosis.Retrospective samples from South America were used to evaluate the following tests: (i "Dengue NS1 Ag STRIP" and (ii "Platelia Dengue NS1 Ag ELISA" (Bio-Rad, France, (iii "Dengue NS1 Detect Rapid Test (1st Generation" and (iv "DENV Detect NS1 ELISA" (InBios International, United States, (v "Panbio Dengue Early Rapid (1st generation" (vi "Panbio Dengue Early ELISA (2nd generation" and (vii "SD Bioline Dengue NS1 Ag Rapid Test" (Alere, United States. Overall, the sensitivity of the RDTs ranged from 71.9%-79.1% while the sensitivity of the ELISAs varied between 85.6-95.9%, using virus isolation as the reference method. Most tests had lower sensitivity for DENV-4 relative to the other three serotypes, were less sensitive in detecting secondary infections, and appeared to be most sensitive on Day 3-4 post symptom onset. The specificity of all evaluated tests ranged from 95%-100%.ELISAs had greater overall sensitivity than RDTs. In conjunction with other parameters, the performance data can help determine which dengue diagnostics should be used during the first few days of illness, when the patients are most likely to present to a clinic seeking care.

  5. The frequency of Listeria monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR

    OpenAIRE

    abazar pournajaf; lida lotfollahi; gholamreza irajian; abdollah ardebili; Behrooz Sadeghi kalani; mojtabata Taghizadeh armaki

    2013-01-01

    Background: Listeria monocytogenes is a facultative intracellular pathogen that causes listeriosis which has extensive clinical manifestations. Infections with L. monocytogenes are a serious threat to immunocompromised persons. The aim of this study was to determine the frequency of L. monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR. Materials and Methods: In this study, 617 specimens were analyzed. All specimens were cu...

  6. Evaluation of Inhibitor-Resistant Real-Time PCR Methods for Diagnostics in Clinical and Environmental Samples

    OpenAIRE

    Adrienne Trombley Hall; Ashley McKay Zovanyi; Deanna Rose Christensen; Jeffrey William Koehler; Timothy Devins Minogue

    2013-01-01

    Polymerase chain reaction (PCR) is commonly used for pathogen detection in clinical and environmental samples. These sample matrices often contain inhibitors of PCR, which is a primary reason for sample processing; however, the purification process is highly inefficient, becoming unacceptable at lower signature concentrations. One potential solution is direct PCR assessment without sample processing. Here, we evaluated nine inhibitor-resistant PCR reagents for direct detection of Francisella ...

  7. The phenomenology of the first panic attack in clinical and community-based samples.

    Science.gov (United States)

    Pané-Farré, Christiane A; Stender, Jan P; Fenske, Kristin; Deckert, Jürgen; Reif, Andreas; John, Ulrich; Schmidt, Carsten Oliver; Schulz, Andrea; Lang, Thomas; Alpers, Georg W; Kircher, Tilo; Vossbeck-Elsebusch, Anna N; Grabe, Hans J; Hamm, Alfons O

    2014-08-01

    The purpose of the study was to contrast first panic attacks (PAs) of patients with panic disorder (PD) with vs. without agoraphobia and to explore differences between first PAs leading to the development of PD and those that remain isolated. Data were drawn from a community survey (N=2259 including 88 isolated PAs and 75 PD cases). An additional sample of 234 PD patients was recruited in a clinical setting. A standardized interview assessed the symptoms of the first PA, context of its occurrence and subsequent coping attempts. Persons who developed PD reported more severe first PAs, more medical service utilization and exposure-limiting coping attempts than those with isolated PAs. The context of the first PA did not differ between PD and isolated PAs. PD with agoraphobia was specifically associated with greater symptom severity and occurrence of first attacks in public. Future research should validate these findings using a longitudinal approach. PMID:24973697

  8. Examination of Aerobic Bacteria from Milk Samples of Bitches with Clinical Mastitis

    Directory of Open Access Journals (Sweden)

    Tuğba Seval Fatma TOYDEMIR

    2015-07-01

    Full Text Available Canine mastitis occurs primarily during the postpartum period and may also occur during pseudopregnancy, as well as after early weaning of puppies. Clinical and bacteriological examinations of mammary secretion were performed in 17 bitches and results of the bacteriological examination of milk samples were evaluated. Staphylococcus intermedius (n=11 was the predominant isolate from the canine milk while the other microorganisms were Escherichia coli, Pseudomonas aeruginosa, S. aureus, Citrobacter freundii, S. epidermidis and S. hyicus. According to the antimicrobial susceptibility test results, isolates were found mostly to be sensitive to gentamycin, while cefixime was detected as the least effective antimicrobial agent. As we had limited number of dogs in our study, further studies on this subject will be helpful for the veterinarians working with pet animals. Because dogs and humans live very closely in urban life style zoonotic transmissibility of S. intermedius shall be of interest to examine further in the future.

  9. Preliminary Examination of the Interpersonal Psychological Theory of Suicide in an Adolescent Clinical Sample.

    Science.gov (United States)

    Horton, Sarah E; Hughes, Jennifer L; King, Jessica D; Kennard, Betsy D; Westers, Nicholas J; Mayes, Taryn L; Stewart, Sunita M

    2016-08-01

    This study offers a preliminary examination of the Interpersonal-Psychological Theory of Suicide (IPTS; Joiner 2005) in an adolescent clinical sample. The IPTS offers a nuanced framework that has many conceptual and practical merits. Although this theory has a growing base of evidence among adults, it has yet to be tested in adolescents using direct measures of its central constructs. Participants were 147 adolescents (76.2 % girls) on an inpatient psychiatric unit, who completed measures of key IPTS constructs of thwarted belongingness, perceived burdensomeness, acquired capability for suicide, as well as depression severity, hopelessness, and severity of suicidal symptoms. Our findings were largely consistent with hypotheses derived from the IPTS: perceived burdensomeness, and at a marginal level, thwarted belongingness, were independently associated with current suicidal ideation. The thwarted belongingness by perceived burdensomeness interaction marginally distinguished between adolescents with passive and active suicidal ideation. Acquired capability for suicide was associated with recent suicidal intent. Examination of all three IPTS constructs simultaneously revealed main effects of each construct (with a marginal effect of thwarted belongingness), and interaction effects for thwarted belongingness by perceived burdensomeness, and thwarted belongingness by perceived burdensomeness by acquired capability for suicide in association with suicidal symptom severity. Sex, age, depression severity, and hopelessness were controlled in all analyses. This study offers strong, albeit preliminary, support of the IPTS in a clinical adolescent sample. Assessment of IPTS constructs may be useful in determining persistent risk for suicide attempt. Prospective tests of the theory, and extensions to intervention and prevention should be considered in future IPTS research. PMID:26667025

  10. Psychotic experiences as indicators of suicidal ideation in a non-clinical college sample.

    Science.gov (United States)

    DeVylder, Jordan E; Thompson, Elizabeth; Reeves, Gloria; Schiffman, Jason

    2015-04-30

    Suicide is a leading cause of preventable death. Epidemiological studies have shown strong associations between sub-threshold psychotic experiences and risk for suicidal ideation and behavior. Screens designed to assess psychotic experiences may have clinical utility in improving suicide prevention efforts. In the current study, we hypothesized that the Prodromal Questionnaire-Brief (PQ-B) would reliably distinguish levels of suicidal ideation within a sample of college students (n=376). As predicted, PQ-B scores varied significantly across levels of suicidal ideation, both when treated as a raw count of sub-threshold psychotic experiences and when taking into account subjective distress associated with those symptoms. In addition, we explored the feasibility of developing a short screen based on the most discriminating items, finding that a six-item version of the PQ-B yielded higher accuracy for detecting elevated suicidal ideation over the full measure. The PQ-B has the potential for clinical utility in detecting groups that might be at increased risk for suicidal ideation. PMID:25746171

  11. A Multitrait-Multimethod Analysis of the Construct Validity of Child Anxiety Disorders in a Clinical Sample

    Science.gov (United States)

    Langer, David A.; Wood, Jeffrey J.; Bergman, R. Lindsey; Piacentini, John C.

    2010-01-01

    The present study examines the construct validity of separation anxiety disorder (SAD), social phobia (SoP), panic disorder (PD), and generalized anxiety disorder (GAD) in a clinical sample of children. Participants were 174 children, 6 to 17 years old (94 boys) who had undergone a diagnostic evaluation at a university hospital based clinic.…

  12. Examination of Racial Differences on the MMPI-2 Clinical and Restructured Clinical Scales in an Outpatient Sample

    Science.gov (United States)

    Castro, Yessenia; Gordon, Kathryn H.; Brown, Jessica S.; Anestis, Joye C.; Joiner, Thomas E., Jr.

    2008-01-01

    The current study examined the possibility of differential predictive accuracy of selected Minnesota Multiphasic Personality Inventory-Second Edition (MMPI-2) clinical and Restructured Clinical (RC) scales in a group of Black and White mental health center clients. Results indicate that Black clients scored higher than White clients on one…

  13. A simplified method to recover urinary vesicles for clinical applications, and sample banking.

    Science.gov (United States)

    Musante, Luca; Tataruch, Dorota; Gu, Dongfeng; Benito-Martin, Alberto; Calzaferri, Giulio; Aherne, Sinead; Holthofer, Harry

    2014-01-01

    Urinary extracellular vesicles provide a novel source for valuable biomarkers for kidney and urogenital diseases: Current isolation protocols include laborious, sequential centrifugation steps which hampers their widespread research and clinical use. Furthermore, large individual urine sample volumes or sizable target cohorts are to be processed (e.g. for biobanking), the storage capacity is an additional problem. Thus, alternative methods are necessary to overcome such limitations. We have developed a practical vesicle isolation technique to yield easily manageable sample volumes in an exceptionally cost efficient way to facilitate their full utilization in less privileged environments and maximize the benefit of biobanking. Urinary vesicles were isolated by hydrostatic dialysis with minimal interference of soluble proteins or vesicle loss. Large volumes of urine were concentrated up to 1/100 of original volume and the dialysis step allowed equalization of urine physico-chemical characteristics. Vesicle fractions were found suitable to any applications, including RNA analysis. In the yield, our hydrostatic filtration dialysis system outperforms the conventional ultracentrifugation-based methods and the labour intensive and potentially hazardous step of ultracentrifugations are eliminated. Likewise, the need for trained laboratory personnel and heavy initial investment is avoided. Thus, our method qualifies as a method for laboratories working with urinary vesicles and biobanking. PMID:25532487

  14. Rapid Isolation of Staphylococcus aureus Pathogens from Infected Clinical Samples Using Magnetic Beads Coated with Fc-Mannose Binding Lectin.

    Science.gov (United States)

    Bicart-See, A; Rottman, M; Cartwright, M; Seiler, B; Gamini, N; Rodas, M; Penary, M; Giordano, G; Oswald, E; Super, M; Ingber, D E

    2016-01-01

    Here we describe how Staphylococcus aureus bacteria can be rapidly isolated from clinical samples of articular fluid and synovial tissue using magnetic beads coated with the engineered chimeric human opsonin protein, Fc-mannose-binding lectin (FcMBL). The FcMBL-beads were used to capture and magnetically remove bacteria from purified cultures of 12 S. aureus strains, and from 8 articular fluid samples and 4 synovial tissue samples collected from patients with osteoarthritis or periprosthetic infections previously documented by positive S. aureus cultures. While the capture efficiency was high (85%) with purified S. aureus strains grown in vitro, direct FcMBL-bead capture from the clinical samples was initially disappointing (viscosity of these complex biological samples. Importantly, capture of pathogens using the FcMBL-beads was increased to 76% efficiency by pretreating clinical specimens with hypotonic washes, hyaluronidase and a protease cocktail. Using this approach, S. aureus bacteria could be isolated from infected osteoarthritic tissues within 2 hours after sample collection. This FcMBL-enabled magnetic method for rapid capture and concentration of pathogens from clinical samples could be integrated upstream of current processes used in clinical microbiology laboratories to identify pathogens and perform antibiotic sensitivity testing when bacterial culture is not possible or before colonies can be detected. PMID:27275840

  15. Rapid Isolation of Staphylococcus aureus Pathogens from Infected Clinical Samples Using Magnetic Beads Coated with Fc-Mannose Binding Lectin.

    Directory of Open Access Journals (Sweden)

    A Bicart-See

    Full Text Available Here we describe how Staphylococcus aureus bacteria can be rapidly isolated from clinical samples of articular fluid and synovial tissue using magnetic beads coated with the engineered chimeric human opsonin protein, Fc-mannose-binding lectin (FcMBL. The FcMBL-beads were used to capture and magnetically remove bacteria from purified cultures of 12 S. aureus strains, and from 8 articular fluid samples and 4 synovial tissue samples collected from patients with osteoarthritis or periprosthetic infections previously documented by positive S. aureus cultures. While the capture efficiency was high (85% with purified S. aureus strains grown in vitro, direct FcMBL-bead capture from the clinical samples was initially disappointing (< 5% efficiency. Further analysis revealed that inhibition of FcMBL binding was due to coating of the bacteria by immunoglobulins and immune cells that masked FcMBL binding sites, and to the high viscosity of these complex biological samples. Importantly, capture of pathogens using the FcMBL-beads was increased to 76% efficiency by pretreating clinical specimens with hypotonic washes, hyaluronidase and a protease cocktail. Using this approach, S. aureus bacteria could be isolated from infected osteoarthritic tissues within 2 hours after sample collection. This FcMBL-enabled magnetic method for rapid capture and concentration of pathogens from clinical samples could be integrated upstream of current processes used in clinical microbiology laboratories to identify pathogens and perform antibiotic sensitivity testing when bacterial culture is not possible or before colonies can be detected.

  16. Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

    Science.gov (United States)

    Rosseel, Toon; Haegeman, Andy; Fana, Mpolokang Elliot; Seoke, Latoa; Hyera, Joseph; Matlho, George; Vandenbussche, Frank; De Clercq, Kris

    2016-01-01

    The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals. PMID:27151795

  17. Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

    OpenAIRE

    Van Borm, Steven; Rosseel, Toon; Haegeman, Andy; Fana, Mpolokang Elliot; Seoke, Latoa; Hyera, Joseph; Matlho, George; Vandenbussche, Frank; De Clercq, Kris

    2016-01-01

    The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.

  18. Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010.

    Science.gov (United States)

    Van Borm, Steven; Rosseel, Toon; Haegeman, Andy; Fana, Mpolokang Elliot; Seoke, Latoa; Hyera, Joseph; Matlho, George; Vandenbussche, Frank; De Clercq, Kris

    2016-01-01

    The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals. PMID:27151795

  19. The Appraisal of Social Concerns Scale: Psychometric Validation with a Clinical Sample of Patients with Social Anxiety Disorder

    Science.gov (United States)

    Schultz, Luke T.; Heimberg, Richard G.; Rodebaugh, Thomas L.; Schneier, Franklin R.; Liebowitz, Michael R.; Telch, Michael J.

    2006-01-01

    The Appraisal of Social Concerns (ASC) Scale was created by Telch et al. (2004) to improve upon existing self-report measures of social anxiety-related cognition. In a largely nonclinical sample, the ASC was found to possess three factors and was psychometrically sound. In a smaller clinical sample, the ASC demonstrated sensitivity to the effects…

  20. Clinical evaluation of oral fluid samples for diagnosis of viral hepatitis.

    OpenAIRE

    Thieme, T.; Yoshihara, P; Piacentini, S; Beller, M.

    1992-01-01

    Oral fluid samples were compared with serum samples as a specimen source for hepatitis A, B, and C virus markers. Oral fluid was obtained with a treated absorbent pad and tested by using existing commercial enzyme immunoassays with only minor modifications. Compared with serum sampling the sensitivity and specificity of oral sampling were 100% (51 of 51 samples) and 98% (46 of 47 samples) for hepatitis A virus immunoglobulin M, 100% (29 of 29 samples) and 100% (29 of 29 samples) for hepatitis...

  1. Functionalized graphene oxide for clinical glucose biosensing in urine and serum samples

    Directory of Open Access Journals (Sweden)

    Veerapandian M

    2012-12-01

    Full Text Available Murugan Veerapandian,1 Yeong-Tai Seo,2 Hyunkyung Shin,3 Kyusik Yun,1 Min-Ho Lee41Department of Bionanotechnology, Gachon University, Gyeonggi-Do, 2School of Electrical Engineering and Computer Science, Seoul National University, Seoul, 3Department of Mathematics and Information, Gachon University, Gyeonggi-Do, 4Korea Electronics Technology Institute, Medical IT Technology, Gyeonggi-Do, Republic of KoreaAbstract: A novel clinical glucose biosensor fabricated using functionalized metalloid-polymer (silver-silica coated with polyethylene glycol hybrid nanoparticles on the surface of a graphene oxide nanosheet is reported. The cyclic voltammetric response of glucose oxidase modification on the surface of a functionalized graphene oxide electrode showed a surface-confined reaction and an effective redox potential near zero volts, with a wide linearity of 0.1–20 mM and a sensitivity of 7.66 µA mM-1 cm-2. The functionalized graphene oxide electrode showed a better electrocatalytic response toward oxidation of H2O2 and reduction of oxygen. The practical applicability of the functionalized graphene oxide electrode was demonstrated by measuring the peak current against multiple urine and serum samples from diabetic patients. This new hybrid nanoarchitecture combining a three-dimensional metalloid-polymer hybrid and two-dimensional graphene oxide provided a thin solid laminate on the electrode surface. The easy fabrication process and retention of bioactive immobilized enzymes on the functionalized graphene oxide electrode could potentially be extended to detection of other biomolecules, and have broad applications in electrochemical biosensing.Keywords: clinical diagnostics, glucose biosensor, metalloid-polymer nanoparticles, glucose oxidase, cyclic voltammetry

  2. Use of immunomagnetic reduction for C-reactive protein assay in clinical samples

    Directory of Open Access Journals (Sweden)

    Chang CH

    2012-08-01

    Full Text Available Chien-Hsi Chang,1 Zhi-Xian Lai,1 Hsiu-Li Lin,2 Che-Chuan Yang,3 Hsin-Hsien Chen,3,4 Shieh-Yueh Yang,5 Herng-Er Horng,3 Chin-Yih Hong,6 Hong-Chang Yang,4 Hsiu-Chen Lin1,71Department of Laboratory Medicine, Taipei Medical University Hospital, 2Department of Neurology, General Cathay Hospital, Sijhih Branch, 3Institute of Electro-optical Science and Technology, National Taiwan Normal University, 4Department of Physics, National Taiwan University, 5MagQu Co, Ltd, Sindian District, New Taipei City, 6Department of Mechanical Engineering, Nan-Kai University of Technology, Nan-tau County, 7Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, TaiwanBackground: Magnetic nanoparticles biofunctionalized with antibodies are able to recognize and bind to the corresponding antigens. In this work, anti-C-reactive protein (CRP antibody was covalently conjugated onto the surface of magnetic nanoparticles to label CRP specifically in serum.Methods: The level of serum CRP was detected by immunomagnetic reduction (IMR assay, which identifies the changes in the magnetic signal representing the level of interaction between antibody-conjugated magnetic nanoparticles and CRP proteins. To investigate the feasibility of IMR for clinical application, pure CRP solutions and 40 human serum samples were tested for IMR detection of CRP to characterize sensitivity, specificity, and interference.Results: In comparison with the immunoturbidimetry assay, the results of the IMR assay indicated higher sensitivity and had a high correlation with those of the current immunoturbidimetry assay.Conclusion: We have developed a novel and promising way to assay CRP in human serum using immunomagnetic reduction in clinical diagnosis.Keywords: magnetic nanoparticles, immunomagnetic reduction, C-reactive protein

  3. Levels and types of alcohol biomarkers in DUI and clinic samples for estimating workplace alcohol problems.

    Science.gov (United States)

    Marques, Paul R

    2012-02-01

    Widespread concern about illicit drugs as an aspect of workplace performance potentially diminishes attention on employee alcohol use. Alcohol is the dominant drug contributing to poor job performance; it also accounts for a third of the worldwide public health burden. Evidence from public roadways--a workplace for many--provides an example of work-related risk exposure and performance lapses. In most developed countries, alcohol is involved in 20-35% of fatal crashes; drugs other than alcohol are less prominently involved in fatalities. Alcohol biomarkers can improve detection by extending the timeframe for estimating problematic exposure levels and thereby provide better information for managers. But what levels and which markers are right for the workplace? In this paper, an established high-sensitivity proxy for alcohol-driving risk proclivity is used: an average eight months of failed blood alcohol concentration (BAC) breath tests from alcohol ignition interlock devices. Higher BAC test fail rates are known to presage higher rates of future impaired-driving convictions (driving under the influence; DUI). Drivers in alcohol interlock programmes log 5-7 daily BAC tests; in 12 months, this yields thousands of samples. Also, higher programme entry levels of alcohol biomarkers predict a higher likelihood of failed interlock BAC tests during subsequent months. This paper summarizes the potential of selected biomarkers for workplace screening. Markers include phosphatidylethanol (PEth), percent carbohydrate deficient transferrin (%CDT), gammaglutamyltransferase (GGT), gamma %CDT (γ%CDT), and ethylglucuronide (EtG) in hair. Clinical cut-off levels and median/mean levels of these markers in abstinent people, the general population, DUI drivers, and rehabilitation clinics are summarized for context. PMID:22311827

  4. Levels and Types of Alcohol Biomarkers in DUI and Clinic Samples for Estimating Workplace Alcohol Problemsa

    Science.gov (United States)

    Marques, Paul R

    2013-01-01

    Widespread concern about illicit drugs as an aspect of workplace performance potentially diminishes attention on employee alcohol use. Alcohol is the dominant drug contributing to poor job performance; it also accounts for a third of the worldwide public health burden. Evidence from public roadways – a workplace for many – provides an example for work-related risk exposure and performance lapses. In most developed countries, alcohol is involved in 20-35% of fatal crashes; drugs other than alcohol are less prominently involved in fatalities. Alcohol biomarkers can improve detection by extending the timeframe for estimating problematic exposure levels and thereby provide better information for managers. But what levels and which markers are right for the workplace? In this report, an established high-sensitivity proxy for alcohol-driving risk proclivity is used: an average 8 months of failed blood alcohol concentration (BAC) breath tests from alcohol ignition interlock devices. Higher BAC test fail rates are known to presage higher rates of future impaired-driving convictions (DUI). Drivers in alcohol interlock programs log 5-7 daily BAC tests; in 12 months, this yields thousands of samples. Also, higher program entry levels of alcohol biomarkers predict a higher likelihood of failed interlock BAC tests during subsequent months. This report summarizes selected biomarkers’ potential for workplace screening. Markers include phosphatidylethanol (PEth), percent carbohydrate deficient transferrin (%CDT), gammaglutamyltransferase (GGT), gamma %CDT (γ%CDT), and ethylglucuronide (EtG) in hair. Clinical cutoff levels and median/mean levels of these markers in abstinent people, the general population, DUI drivers, and rehabilitation clinics are summarized for context. PMID:22311827

  5. Philadelphia Brief Assessment of Cognition in healthy and clinical Brazilian sample

    Directory of Open Access Journals (Sweden)

    Danilo Assis Pereira

    2012-03-01

    Full Text Available The Philadelphia Brief Assessment of Cognition (PBAC is a neuropsychological screening instrument that assesses five cognitive domains: working memory, visuospatial functioning, language, episodic memory and comportment. The aim is to verify if PBAC can properly be used in the Brazilian sample. Participated in this study: (a 200 healthy volunteers - 100 young [21.6(2.5 years old] and 100 older adults [70.1(7.3 years old]; >12 years of education; (b 30 Alzheimer's patients (AD [73.7(5.7 years old], 4-11 years in education. The PBAC scores: (a 95.8(2.6, 90.0(4.4 and (b 65.0(10.8 were correlated with the Mini-Mental State Examination (MMSE for young 29.1(0.9, older adults 28.3(1.4 and AD 18.4(3.0 groups. A positive correlation between MMSE and PBAC (r=0.9, p<0.001 was found. Negative correlations were observed between PBAC domains [memory (-0.63, visuospatial abilities (-0.44 and working memory (-0.3 tasks]. MANOVA showed a better male performance in visuospatial functioning (F=8.5, p=0.004. The Brazilian version of PBAC proved to be a promising screening instrument for clinical purposes.

  6. Functionalized graphene oxide for clinical glucose biosensing in urine and serum samples.

    Science.gov (United States)

    Veerapandian, Murugan; Seo, Yeong-Tai; Shin, Hyunkyung; Yun, Kyusik; Lee, Min-Ho

    2012-01-01

    A novel clinical glucose biosensor fabricated using functionalized metalloid-polymer (silver-silica coated with polyethylene glycol) hybrid nanoparticles on the surface of a graphene oxide nanosheet is reported. The cyclic voltammetric response of glucose oxidase modification on the surface of a functionalized graphene oxide electrode showed a surface-confined reaction and an effective redox potential near zero volts, with a wide linearity of 0.1-20 mM and a sensitivity of 7.66 μA mM(-1) cm(-2). The functionalized graphene oxide electrode showed a better electrocatalytic response toward oxidation of H(2)O(2) and reduction of oxygen. The practical applicability of the functionalized graphene oxide electrode was demonstrated by measuring the peak current against multiple urine and serum samples from diabetic patients. This new hybrid nanoarchitecture combining a three-dimensional metalloid-polymer hybrid and two-dimensional graphene oxide provided a thin solid laminate on the electrode surface. The easy fabrication process and retention of bioactive immobilized enzymes on the functionalized graphene oxide electrode could potentially be extended to detection of other biomolecules, and have broad applications in electrochemical biosensing. PMID:23269871

  7. Turkish adaptation of the Fear of Spiders Questionnaire: Reliability and validity in non-clinical samples

    Directory of Open Access Journals (Sweden)

    Robert W. Booth

    2016-12-01

    Full Text Available The rapid, objective measurement of spider fear is important for clinicians, and for researchers studying fear. To facilitate this, we adapted the Fear of Spiders Questionnaire (FSQ into Turkish. The FSQ is quick to complete and easy to understand. Compared to the commonly used Spider Phobia Questionnaire, it has shown superior test-retest reliability and better discrimination of lower levels of spider fear, facilitating fear research in non-clinical samples. In two studies, with 137 and 105 undergraduates and unselected volunteers, our adapted FSQ showed excellent internal consistency (Cronbach’s α = .95 and .96 and test-retest reliability (r = .90, and good discriminant validity against the State–Trait Anxiety Inventory—Trait (r = .23 and Beck Anxiety Inventory—Trait (r = .07. Most importantly, our adapted FSQ significantly predicted 26 students’ self-reported discomfort upon approaching a caged tarantula; however, a measure of behavioural avoidance of the tarantula yielded little variability, so a more sensitive task will be required for future behavioural testing. Based on this initial testing, we recommend our adapted FSQ for research use. Further research is required to verify that our adapted FSQ discriminates individuals with and without phobia effectively. A Turkish-language report of the studies is included as supplementary material.

  8. Isolation, Detection, and Characterization of Enterotoxigenic Bacteroides fragilis in Clinical Samples

    Science.gov (United States)

    Fathi, Payam; Wu, Shaoguang

    2016-01-01

    Bacteroides fragilis is an extensively studied anaerobic bacterium comprising the normal flora of the human gut. B. fragilis is known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogen B. fragilis can cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form, B. fragilis is a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains of B. fragilis. This review outlines methods that are routinely employed in the isolation and detection of B. fragilis, with an emphasis on characterizing enterotoxigenic B. fragilis (ETBF) strains.

  9. Gender Differences in Risk Factors for Stice's Bulimia in a Non-Clinical Sample.

    Science.gov (United States)

    Ruisoto, Pablo; Cacho, Raúl; López-Goñi, José J; Real Deus, Eulogio; Vaca, Silvia; Mayoral, Paula

    2015-01-01

    Some females are at an increased risk of developing bulimia. However, etiological factors and their interplay remain controversial. The present study analyzed Sticefe Model for eating disorders in a non-clinical population by examining gender differences with respect to the following risk factors: body mass index (BMI), body dissatisfaction, perceived social pressure to be thin, body-thin internalization, and dieting behavior. A sample of 162 American college students (64 males and 91 females) was surveyed, and validated scales were used. The Sticey model was tested using Structural Equation Modeling. Our results supported Stice r Dual Pathway Model of bulimic pathology for females but not for males. Females reported significantly higher body dissatisfaction, perceived pressure to be thin and weight-loss oriented behaviors than males (p .05), a key predictor of body dissatisfaction (r = .33; p .05) although their BMI was significantly lower than males (d = 0,51). The results of this study fail to support the role of BMI as a predictor of dietary restraint in females, the main risk factor of eating disorders. Males may abstain from dietary restraint to gain muscular volume and in turn increase their BMI. Implications are discussed. PMID:26388326

  10. Structured Interview of Personality Organization (STIPO): preliminary psychometrics in a clinical sample.

    Science.gov (United States)

    Stern, Barry L; Caligor, Eve; Clarkin, John F; Critchfield, Kenneth L; Horz, Susanne; MacCornack, Verna; Lenzenweger, Mark F; Kernberg, Otto F

    2010-01-01

    In this article, we describe the development and preliminary psychometric properties of the Structured Interview of Personality Organization (STIPO), a semistructured interview designed for the dimensional assessment of identity, primitive defenses, and reality testing, the three primary content domains in the model of personality health and disorder elaborated by Kernberg (1984; Kernberg & Caligor, 2005). Results of this investigation, conducted in a clinical sample representing a broad range of personality pathology, indicate that identity and primitive defenses as operationalized in the STIPO are internally consistent and that interrater reliability for all 3 content domains is adequate. Validity findings suggest that the assessment of one's sense of self and significant others (Identity) is predictive of measures of positive and negative affect, whereas the maladaptive ways in which the subject uses his or her objects for purposes of regulating one's self experience (Primitive Defenses) is predictive of measures of aggression and personality disorder traits associated with cluster B personality disorders. We discuss implications of these findings in terms of the theory-driven and trait-based assessment of personality pathology. PMID:20013454

  11. Integrating clinical and biological information in a shanghai biobank: an introduction to the sample repository and information sharing platform project.

    Science.gov (United States)

    Cui, Wenbin; Zheng, Peiyong; Yang, Jiahong; Zhao, Rong; Gao, Jiechun; Yu, Guangjun

    2015-02-01

    Biobanks are important resources and central tools for translational medicine, which brings scientific research outcomes to clinical practice. The key purpose of biobanking in translational medicine and other medical research is to provide biological samples that are integrated with clinical information. In 2008, the Shanghai Municipal Government launched the "Shanghai Tissue Bank" in an effort to promote research in translational medicine. Now a sharing service platform has been constructed to integrate clinical practice and biological information that can be used in diverse medical and pharmaceutical research studies. The platform collects two kinds of data: sample data and clinical data. The sample data are obtained from the hospital biobank management system, and mainly include the donors' age, gender, marital status, sample source, sample type, collection time, deposit time, and storage method. The clinical data are collected from the "Hospital-Link" system (a medical information sharing system that connects 23 tertiary hospitals in Shanghai). The main contents include donors' corresponding medication information, test reports, inspection reports, and hospital information. As of the end of September 2014, the project has a collection of 16,020 donors and 148,282 samples, which were obtained from 12 medical institutions, and automatically acquired donors' corresponding clinical data from the "Hospital-Link" system for 6830 occurrences. This project will contribute to scientific research at medical institutions in Shanghai, and will also support the development of the biopharmaceutical industry. In this article, we will describe the significance, the construction phases, the application prospects, and benefits of the sample repository and information sharing service platform. PMID:25686046

  12. Association between CLN3 (Neuronal Ceroid Lipofuscinosis, CLN3 type gene expression and clinical characteristics of breast cancer patients

    Directory of Open Access Journals (Sweden)

    Rose-Mary eBoustany

    2015-10-01

    Full Text Available Breast cancer is the most common cancer in women worldwide. Elucidation of underlying biology and molecular pathways is necessary for improving therapeutic options and clinical outcomes. CLN3 protein (CLN3p, deficient in neurodegenerative CLN3 disease is anti-apoptotic, and defects in the CLN3 gene cause accelerated apoptosis of neurons in CLN3 disease and upregulation of ceramide. Dysregulated apoptotic pathways are often implicated in the development of the oncogenic phenotype. Predictably, CLN3 mRNA expression and CLN3 protein were upregulated in a number of human and murine breast cancer cell lines. Here, we determine CLN3 expression in non-tumor vs. tumor samples from fresh and formalin-fixed/paraffin-embedded (FFPE breast tissue and analyze the association between CLN3 overexpression and different clinicopathological characteristics of breast cancer patients. Additionally, gene expression of 28 enzymes involved in sphingolipid metabolism was determined. CLN3 mRNA is overexpressed in tumor vs. non-tumor breast tissue from FFPE and fresh samples, as well as in mouse MCF7 breast cancer compared to MCF10A normal cells. Of the clinicopathological characteristics of tumor grade, age, menopause status, estrogen receptor (ER, progesterone receptor (PR, and human epidermal growth factor receptor 2 (HER2, only absence of HER2 expression correlated with CLN3 overexpression. Sphingolipid genes for ceramide synthases 2 and 6 (CerS2; CerS6, delta(4-desaturase sphingolipid 2 (DEGS2 and acidic sphingomyelinase (SMPD1 displayed higher expression levels in breast cancer vs. control tissue, whereas, ceramide galactosyltransferase (UGT8 was underexpressed in breast cancer samples. CLN3 may be a novel molecular target for cancer drug discovery with the goal of modulation of ceramide pathways.

  13. The Structured Clinical Interview for DSM-IV Childhood Diagnoses (Kid-SCID): first psychometric evaluation in a Dutch sample of clinically referred youths

    NARCIS (Netherlands)

    J. Roelofs; P. Muris; C. Braet; A. Arntz; I. Beelen

    2014-01-01

    The Structured Clinical Interview for DSM-IV Childhood Disorders (Kid-SCID) is a semi-structured interview for the classification of psychiatric disorders in children and adolescents. This study presents a first evaluation of the psychometric properties of the Kid-SCID in a Dutch sample of children

  14. ISOLATION AND SPECIATION OF CANDIDA FROM CLINICAL SAMPLES IN A TERTIARY CARE HOSPITAL AT KURNOOL, ANDHRAPRADESH, INDIA

    OpenAIRE

    Dasari; Suguneswari; Mahendra; Sisira

    2014-01-01

    : Candida is one of the most frequently encountered opportunistic fungi that cause infection in humans. The pathogenesis of Candida is complex and probably varies with each infection. This study was conducted to understand the prevalence of Candida from various clinical specimens of patients and to show the emergence of Non albicans Candida in clinical samples. This study also focused on the antifungal susceptibility which guides the clinicians to treat the infection effective...

  15. Leptospira spp detection by Polymerase Chain Reaction (PCR) in clinical samples of captive black-capped Capuchin monkey (Cebus apella)

    OpenAIRE

    Scarcelli Eliana; Piatti Rosa Maria; Fedullo José Daniel Luzes; Simon Faiçal; Cardoso Maristela Vasconcellos; Castro Vanessa; Miyashiro Simone; Genovez Margareth Élide

    2003-01-01

    Leptospirosis is a widely distributed zoonosis that affects domestic and wild animals, and that has the man as the end point of its epidemiological chain. Leptospirosis diagnosis in primates is more difficult than in other animal species, as clinical signs and lesions are less evident and antibody response is detected only for short periods. The aim of this article was to describe the detection of Leptospira spp using polymerase chain reaction (PCR), in clinical samples from one captive black...

  16. A Multitrait–Multimethod Analysis of the Construct Validity of Child Anxiety Disorders in a Clinical Sample

    OpenAIRE

    Wood, Jeffrey J.; Bergman, R. Lindsey; Piacentini, John C.; Langer, David Adam

    2010-01-01

    The present study examines the construct validity of separation anxiety disorder (SAD), social phobia (SoP), panic disorder (PD), and generalized anxiety disorder (GAD) in a clinical sample of children. Participants were 174 children, 6 to 17 years old (94 boys) who had undergone a diagnostic evaluation at a university hospital based clinic. Parent and child ratings of symptom severity were assessed using the Multidimensional Anxiety Scale for Children (MASC). Diagnostician ratings were obtai...

  17. More than a (negative) feeling: Validity of the perceived stress scale in Serbian clinical and non-clinical samples

    OpenAIRE

    Jovanović Veljko; Gavrilov-Jerković Vesna

    2015-01-01

    The goal of the present study was to test the validity of a Serbian version of the Perceived Stress Scale. The PSS was administered to 157 psychiatric outpatients, 165 adults from the non-clinical population, and 283 university students. The results of the confirmatory factor analysis supported a bifactor model of the PSS with one general factor and two specific factors reflecting perceived distress and perceived self-efficacy. Internal consistencies of the...

  18. Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples.

    Science.gov (United States)

    Noberini, Roberta; Uggetti, Andrea; Pruneri, Giancarlo; Minucci, Saverio; Bonaldi, Tiziana

    2016-03-01

    Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue analysis of Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from formalin-fixed paraffin-embedded tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. As an initial application of the PAThology tissue analysis of Histones by Mass Spectrometry method, we analyzed breast cancer samples, revealing significant changes in histone H3 methylation patterns among Luminal A-like and Triple Negative disease subtypes. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with formalin-fixed paraffin-embedded archives. PMID:26463340

  19. [Identification of filamentous fungi isolated from clinical samples by two different methods and their susceptibility results].

    Science.gov (United States)

    Direkel, Sahin; Otağ, Feza; Aslan, Gönül; Ulger, Mahmut; Emekdaş, Gürol

    2012-01-01

    Molds are widely distributed in nature. Aspergillus spp. represent the most frequently observed causative agents, however less frequent pathogens Fusarium, Scedosporium and Zygomycetes have also been considered the most important causes of morbidity and mortality in profoundly immunosuppressed hosts. The aims of this study were to identify filamentous fungi isolated from clinical specimens by conventional and molecular methods, and to detect their antifungal susceptibilities. A total of 6742 clinical specimens obtained from hospitalized patients at critical units of Mersin University Medical Faculty Hospital and sent to our laboratory between April 2008-January 2010 were included in the study. The isolates were identified by classical mycological methods and polymerase chain reaction-based DNA sequencing. Susceptibilities to fluconazole and voriconazole were tested by disk diffusion method and to fluconazole, voriconazole, amfoterisin B, caspofungin and posaconazole by E-test. Filamentous fungi were isolated from 71 (1.05%) samples (13 sputum, 4 wound, 4 peritoneal fluid, 3 extrenal ear discharge, 3 abscess and one of each cerebrospinal fluid, blood, tissue biopsy, nasal swab and conjunctival swab) which belonged to 32 patients (13 female, 19 male; age range 7 months-77 years, mean age: 46.6 years). Of the patients 62.3% presented one or more risk factors such as chronic renal failure (n= 8), chronic obstructive lung disease (n= 6), malignancy (n= 6), diabetes mellitus (n= 5) and peripheral vascular disease (n= 5). Of the isolates six were identified as Aspergillus niger, six as Aspergillus flavus, five as Aspergillus fumigatus, four as Aspergillus terreus, five as Fusarium spp., two as Bipolaris spp., and one of each as Acremonium spp., Aurebasidium spp., Mucor spp., and Scedosporium spp. By conventional methods. Three isolates exhibited different identities by DNA sequencing. All Aspergillus isolates were correctly identified at species level by both methods

  20. Ultraminiaturized assay for rapid, low cost detection and quantification of clinical and biochemical samples.

    Science.gov (United States)

    Parween, Shahila; Nahar, Pradip

    2016-04-01

    Herein, we report a simple, sensitive, rapid and low-cost ultraminiaturized assay technique for quantitative detection of 1 μl of clinical or biochemical sample on a novel ultraminiaturized assay plate (UAP). UAP is prepared by making tiny cavities on a polypropylene sheet. As UAP cannot immobilize a biomolecule through absorption, we have activated the tiny cavities of UAP by 1-fluoro-2-nitro-4-azidobenzene in a photochemical reaction. Activated UAP (AUAP) can covalently immobilize any biomolecule having an active nucleophilic group such as amino group. Efficacy of AUAP is demonstrated by detecting human IgE, antibody of hepatitis C virus core antigen and oligonucleotides. Quantification is performed by capturing the image of the colored assay solution and digitally quantifying the image by color saturation without using costly NanoDrop spectrophotometer. Image - based detection of human IgE and an oligonucleotide shows an excellent correlation with absorbance - based assay (recorded in a NanoDrop spectrophotometer); it is validated by Pearson's product-moment correlation with correlation coefficient of r = 0.9545088 and r = 0.9947444 respectively. AUAP is further checked by detecting hepatitis C virus Ab where strong correlation of color saturation with absorbance with respect to concentration is observed. Ultraminiaturized assay successfully detects target oligonucleotides by perfectly hybridizing with their respective complementary oligonucleotide probes but not with a random oligonucleotide. Ultraminiaturized assay technique has substantially reduced the requirement of reagents by 100 times and assay timing by 50 times making it a potential alternative to conventional method. PMID:26973054

  1. Detection of Shiga toxins genes by Multiplex PCR in clinical samples

    Directory of Open Access Journals (Sweden)

    2013-09-01

    Full Text Available Background: Different methods have been used for detection of shiga toxins; such as,  cell culture, ELISA, and RFPLA. However, all of these methods suffer from high cost, time-consumption and relatively low sensitivity. In this study we used Multiplex PCR method for detection of genes encoding shiga toxins. Material and Methods: In this study, 63 clinical samples were obtained from positive cultures of Shigella and E. coli O157, from Bahman 1391 until Ordibehesht 1392 in Mazandaran province. Initial confirmation of shiga toxins producing bacteria was performed by biochemical and serological methods. After DNA extraction, detection of stx1 and stx2 genes was accomplished by multiplex PCR.  For confirmation of the PCR amplicon, DNA sequencing was used. Antibiotic sensitivity tests were performed by disk diffusion method. Results:  Among the positive strains, 13 strains contained stx2 genes, 4 strains contained Stx/Stx1 genes and 4 strains harbored both Stx/Stx1 and Stx2. The DNA extracted from other Gram-negative bacteria was not protected by the relevant parts of these toxins. Sequencing of the amplified fragments indicated the correct toxin sequences.  The sensitivity for identification of Stx/Stx1 gene was 1.56 pg/ µl and for Stx2 was 1.08 pg/µl. The toxin positive strains were all sensitive to Cefixime, Gentamicin, Amikacin, Ceftriaxone, and Nitrofurantoin. Conclusion: This method is fast and accurate for detection of bacteria producing shiga toxin and can be used to identify different types of shiga toxin.

  2. TruSeq Stranded mRNA and Total RNA Sample Preparation Kits

    Science.gov (United States)

    Total RNA-Seq enabled by ribosomal RNA (rRNA) reduction is compatible with formalin-fixed paraffin embedded (FFPE) samples, which contain potentially critical biological information. The family of TruSeq Stranded Total RNA sample preparation kits provides a unique combination of unmatched data quality for both mRNA and whole-transcriptome analyses, robust interrogation of both standard and low-quality samples and workflows compatible with a wide range of study designs.

  3. Clinical and molecular epidemiology of human bocavirus in respiratory and fecal samples from children in Hong Kong

    OpenAIRE

    Lau, SKP; Yip, CCY; Lau, YL; Woo, PCY; Yuen, KY; Que, TL; Lee, RA; AuYeung, RKH; Zhou, B.; So, LY; Chan, KH

    2007-01-01

    Background. Human bocavirus (HBoV) is a recently discovered parvovirus associated with respiratory tract infections in children. We conducted the first systematic prospective clinical and molecular study using nasopharyngeal aspirates (NPAs) and fecal samples. Methods. NPAs negative for influenza virus, parainfluenza virus, respiratory syncytial virus, adenovirus, and coronavirus and fecal samples from patients with acute gastroenteritis were included. On the basis of results from a pilot stu...

  4. Detection and genetic characterization of foot‐and‐mouth disease viruses in samples from clinically healthy animals in endemic settings

    DEFF Research Database (Denmark)

    Jamal, Syed Muhammad; Ferrari, G.; Hussain, M.;

    2012-01-01

    A total of 1501 oral swab samples from Pakistan, Afghanistan and Tajikistan were collected from clinically healthy animals between July 2008 and August 2009 and assayed for the presence of foot‐and‐mouth disease virus (FMDV) RNA. The oral swab samples from two (of four) live animal markets...... in Pakistan (n = 245), one (of three) live animal market in Afghanistan (n = 61) and both the live animal markets in Tajikistan (n = 120) all tested negative. However, 2 of 129 (∼2%) samples from Gondal and 11 of 123 (9%) from Chichawatni markets in Pakistan were positive for FMDV RNA. Similarly, 12 of 81 (15......%) samples from Kabul and 10 of 20 (50%) from Badakhshan in Afghanistan were found to be positive. Serotypes A and O of FMDV were identified within these samples. Oral swab samples were also collected from dairy colonies in Harbanspura, Lahore (n = 232) and Nagori, Karachi (n = 136), but all tested negative...

  5. Occurrence of ADHD in parents of ADHD children in a clinical sample

    Directory of Open Access Journals (Sweden)

    Starck M

    2016-03-01

    Full Text Available Martina Starck,1 Julia Grünwald,1 Angelika A Schlarb1,21Faculty of Science, Department of Psychology, University of Tuebingen, Tuebingen, 2Department of Psychology, Faculty for Psychology and Sport Science, University of Bielefeld, Bielefeld, GermanyBackground: Despite the fact that there is a large amount of research on childhood attention deficit hyperactivity disorder (ADHD treatment and an increasing amount of research on adult ADHD, little is known about the prevalence and influence of parental ADHD. Therefore, this study examined the frequency of parental ADHD in a clinical sample of German children suffering from ADHD. We also tried to find different levels of symptom severity for prognostic relevance. Furthermore, the association between subtypes of ADHD in children and their parents was investigated.Method: In this study, parents of 79 ADHD children were screened for ADHD according to the Diagnostic and Statistical Manual of Mental Disorders, 5th edition and International Classification of Diseases, 10th edition. The Wender Utah Rating Scale and the ADHS-Self-Report were given to 75 mothers and 49 fathers for retrospective and current symptoms. Frequency of ADHD symptoms and severity groups was calculated and relationship between parental and children’s ADHD was tested.Results: ADHD occurrence for mothers of children with ADHD was 41.3%, for fathers 51.0%. About 16.0% of the mothers had a mixed type, 9.3% had a hyperactive-impulsive subtype, and 16.0% had an inattentive subtype. Of the fathers, 18.4% had a mixed type, 10.2% had a hyperactive-impulsive subtype, and 22.4% had an inattentive subtype; 61% of the mothers and 46.9% of the fathers had low symptom severity. Medium symptom severity was reported by 37.7% mothers and 46.9% fathers, while 1.3% of the mothers and 6.2% of the fathers showed severe symptoms. No significant correlation between parental and child diagnoses was observed.Conclusion: As nearly half of the parents

  6. Occurrence of ADHD in parents of ADHD children in a clinical sample

    Science.gov (United States)

    Starck, Martina; Grünwald, Julia; Schlarb, Angelika A

    2016-01-01

    Background Despite the fact that there is a large amount of research on childhood attention deficit hyperactivity disorder (ADHD) treatment and an increasing amount of research on adult ADHD, little is known about the prevalence and influence of parental ADHD. Therefore, this study examined the frequency of parental ADHD in a clinical sample of German children suffering from ADHD. We also tried to find different levels of symptom severity for prognostic relevance. Furthermore, the association between subtypes of ADHD in children and their parents was investigated. Method In this study, parents of 79 ADHD children were screened for ADHD according to the Diagnostic and Statistical Manual of Mental Disorders, 5th edition and International Classification of Diseases, 10th edition. The Wender Utah Rating Scale and the ADHS-Self-Report were given to 75 mothers and 49 fathers for retrospective and current symptoms. Frequency of ADHD symptoms and severity groups was calculated and relationship between parental and children’s ADHD was tested. Results ADHD occurrence for mothers of children with ADHD was 41.3%, for fathers 51.0%. About 16.0% of the mothers had a mixed type, 9.3% had a hyperactive-impulsive subtype, and 16.0% had an inattentive subtype. Of the fathers, 18.4% had a mixed type, 10.2% had a hyperactive-impulsive subtype, and 22.4% had an inattentive subtype; 61% of the mothers and 46.9% of the fathers had low symptom severity. Medium symptom severity was reported by 37.7% mothers and 46.9% fathers, while 1.3% of the mothers and 6.2% of the fathers showed severe symptoms. No significant correlation between parental and child diagnoses was observed. Conclusion As nearly half of the parents suffered from ADHD, these results are a matter of concern in families with ADHD children. Besides parent–child interactions, parental ADHD symptoms might influence parental education style and also effects parent training as well as the child’s therapy outcome. In the

  7. Empirical Correlates of Low Scores on MMPI-2/MMPI-2-RF Restructured Clinical Scales in a Sample of University Students

    Science.gov (United States)

    Avdeyeva, Tatyana V.; Tellegen, Auke; Ben-Porath, Yossef S.

    2012-01-01

    In the present study, the authors explored the meaning of low scores on the MMPI-2/MMPI-2-RF Restructured Clinical (RC) scales. Using responses of a sample of university students (N = 811), the authors examined whether low (T less than 39), within-normal-limits (T = 39-64), and high (T greater than 65) score levels on the RC scales are…

  8. Bottom–up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance.

    Directory of Open Access Journals (Sweden)

    Peter Raus

    2015-12-01

    With 375 confidently identified proteins in the healthy adult tear, the obtained results are comprehensive and in large agreement with previously published observations on pooled samples of multiple patients. We conclude that, to a limited extent, bottom–up tear protein identifications from individual patients may have clinical relevance.

  9. Childhood Trauma in Substance Use Disorder and Depression: An Analysis by Gender among a Brazilian Clinical Sample

    Science.gov (United States)

    Tucci, Adriana M.; Kerr-Correa, Florence; Souza-Formigoni, Maria Lucia O.

    2010-01-01

    Objective: In this study, we compared the frequency and intensity of childhood traumas in alcohol- or other drug-dependent patients, in patients with depression, and in a control group without psychiatric diagnoses. Methods: The study had a retrospective design of a clinical sample of men and women from the groups listed above. They were evaluated…

  10. Inflammatory cytokine concentrations in uterine flush and serum samples from dairy cows with clinical or subclinical endometritis.

    Science.gov (United States)

    Kim, Ill-Hwa; Kang, Hyun-Gu; Jeong, Jae-Kwan; Hur, Tai-Young; Jung, Young-Hun

    2014-08-01

    The objective of this study was to compare the concentrations of inflammatory cytokines in uterine flush and serum from healthy postpartum dairy cows and cows with clinical or subclinical endometritis. Clinical endometritis was diagnosed by observation of vaginal discharges (>50% pus) and subclinical endometritis was diagnosed by evaluation of uterine cytology (neutrophils >18%) at 4 weeks postpartum. Uterine flush was obtained from 48 cows at 4, 6, and 8 weeks postpartum for evaluation of tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, IL-6, IL-8, and IL-10 concentrations. Serum samples were obtained from 34 cows just after calving and at 1, 2, 4, 6, and 8 weeks postpartum for evaluation of TNF-α, IL-1β, and IL-6 concentrations. Concentrations of TNF-α, IL-6, and IL-10 were greater (P cows with clinical endometritis than in cows with subclinical endometritis and healthy controls, whereas concentrations of IL-8 in both cows with clinical and subclinical endometritis were greater (P cows with clinical endometritis decreased (P cows with subclinical endometritis and controls did not change significantly with time; at 4 weeks postpartum, concentrations were greater (P cows with clinical endometritis. There were no significant effects of group, sampling time, or interaction on serum cytokine concentrations. In conclusion, cows with endometritis have greater inflammatory cytokine concentrations in uterine flush than healthy cows, but no differences were observed in serum. PMID:24933095

  11. "ISA-Lation" of Single-Stranded Positive-Sense RNA Viruses from Non-Infectious Clinical/Animal Samples.

    Directory of Open Access Journals (Sweden)

    Fabien Aubry

    Full Text Available Isolation of viral pathogens from clinical and/or animal samples has traditionally relied on either cell cultures or laboratory animal model systems. However, virus viability is notoriously susceptible to adverse conditions that may include inappropriate procedures for sample collection, storage temperature, support media and transportation. Using our recently described ISA method, we have developed a novel procedure to isolate infectious single-stranded positive-sense RNA viruses from clinical or animal samples. This approach, that we have now called "ISA-lation", exploits the capacity of viral cDNA subgenomic fragments to re-assemble and produce infectious viral RNA in susceptible cells. Here, it was successfully used to rescue enterovirus, Chikungunya and Tick-borne encephalitis viruses from a variety of inactivated animal and human samples. ISA-lation represents an effective option to rescue infectious virus from clinical and/or animal samples that may have deteriorated during the collection and storage period, but also potentially overcomes logistic and administrative difficulties generated when complying with current health and safety and biosecurity guidelines associated with shipment of infectious viral material.

  12. Scintigraphy and venous sampling in endocrine adrenal diseases. Clinical results in 85 patients

    International Nuclear Information System (INIS)

    The results obtained by adrenal scanning and venous sampling in 85 patients affected by various forms of adrenal pathology are reported and discussed. Pheochromocytoma rarely needs venous catheterization and blood sampling, since arteriography is almost always capable to visualize it. Scintigraphy alone is generally accurate enough to distinguish between bilateral hyperplasia and tumors in Cushing's and adrenogenital syndromes (100% of personal observations); only a tumoral situation benefits by venous catheterization. Blood samples and venography must be preceded by scintigraphy in Conn's syndrome

  13. WISC-III and CAS: Which Correlates Higher with Achievement for a Clinical Sample?

    Science.gov (United States)

    Naglieri, Jack A.; De Lauder, Brianna Y.; Goldstein, Sam; Schwebech, Adam

    2006-01-01

    The relationships between Wechsler Intelligence Scale for Children-Third Edition (WISC-III) and the Cognitive Assessment System (CAS) with the Woodcock-Johnson Tests of Achievement (WJ-III) were examined for a sample of 119 children (87 males and 32 females) ages 6 to 16. The sample was comprised of children who were referred to a specialty clinic…

  14. Evaluation of inhibitor-resistant real-time PCR methods for diagnostics in clinical and environmental samples.

    Science.gov (United States)

    Trombley Hall, Adrienne; McKay Zovanyi, Ashley; Christensen, Deanna Rose; Koehler, Jeffrey William; Devins Minogue, Timothy

    2013-01-01

    Polymerase chain reaction (PCR) is commonly used for pathogen detection in clinical and environmental samples. These sample matrices often contain inhibitors of PCR, which is a primary reason for sample processing; however, the purification process is highly inefficient, becoming unacceptable at lower signature concentrations. One potential solution is direct PCR assessment without sample processing. Here, we evaluated nine inhibitor-resistant PCR reagents for direct detection of Francisella tularensis in seven different clinical and environmental samples using an established real-time PCR assay to assess ability to overcome PCR inhibition. While several of these reagents were designed for standard PCR, the described inhibitor resistant properties (ex. Omni Klentaq can amplify target DNA samples of up to 20% whole blood or soil) led to our evaluation with real-time PCR. A preliminary limit of detection (LOD) was determined for each chemistry in whole blood and buffer, and LODs (20 replicates) were determined for the top five chemistries in each matrix (buffer, whole blood, sputum, stool, swab, soil, and sand). Not surprisingly, no single chemistry performed the best across all of the different matrices evaluated. For instance, Phusion Blood Direct PCR Kit, Phire Hot Start DNA polymerase, and Phire Hot Start DNA polymerase with STR Boost performed best for direct detection in whole blood while Phire Hot Start DNA polymerase with STR Boost were the only reagents to yield an LOD in the femtogram range for soil. Although not the best performer across all matrices, KAPA Blood PCR kit produced the most consistent results among the various conditions assessed. Overall, while these inhibitor resistant reagents show promise for direct amplification of complex samples by real-time PCR, the amount of template required for detection would not be in a clinically relevant range for most matrices. PMID:24040090

  15. Evaluation of inhibitor-resistant real-time PCR methods for diagnostics in clinical and environmental samples.

    Directory of Open Access Journals (Sweden)

    Adrienne Trombley Hall

    Full Text Available Polymerase chain reaction (PCR is commonly used for pathogen detection in clinical and environmental samples. These sample matrices often contain inhibitors of PCR, which is a primary reason for sample processing; however, the purification process is highly inefficient, becoming unacceptable at lower signature concentrations. One potential solution is direct PCR assessment without sample processing. Here, we evaluated nine inhibitor-resistant PCR reagents for direct detection of Francisella tularensis in seven different clinical and environmental samples using an established real-time PCR assay to assess ability to overcome PCR inhibition. While several of these reagents were designed for standard PCR, the described inhibitor resistant properties (ex. Omni Klentaq can amplify target DNA samples of up to 20% whole blood or soil led to our evaluation with real-time PCR. A preliminary limit of detection (LOD was determined for each chemistry in whole blood and buffer, and LODs (20 replicates were determined for the top five chemistries in each matrix (buffer, whole blood, sputum, stool, swab, soil, and sand. Not surprisingly, no single chemistry performed the best across all of the different matrices evaluated. For instance, Phusion Blood Direct PCR Kit, Phire Hot Start DNA polymerase, and Phire Hot Start DNA polymerase with STR Boost performed best for direct detection in whole blood while Phire Hot Start DNA polymerase with STR Boost were the only reagents to yield an LOD in the femtogram range for soil. Although not the best performer across all matrices, KAPA Blood PCR kit produced the most consistent results among the various conditions assessed. Overall, while these inhibitor resistant reagents show promise for direct amplification of complex samples by real-time PCR, the amount of template required for detection would not be in a clinically relevant range for most matrices.

  16. ISOLATION AND SPECIATION OF CANDIDA FROM CLINICAL SAMPLES IN A TERTIARY CARE HOSPITAL AT KURNOOL, ANDHRAPRADESH, INDIA

    Directory of Open Access Journals (Sweden)

    Dasari

    2014-12-01

    Full Text Available : Candida is one of the most frequently encountered opportunistic fungi that cause infection in humans. The pathogenesis of Candida is complex and probably varies with each infection. This study was conducted to understand the prevalence of Candida from various clinical specimens of patients and to show the emergence of Non albicans Candida in clinical samples. This study also focused on the antifungal susceptibility which guides the clinicians to treat the infection effectively. METHODS: Clinical samples were collected from outpatients and inpatients of Government General Hospital, Kurnool over a period of one year from March2008 to June2009. Isolation, culture, speciation of Candida was done by using standard methods. Antifungal susceptibility testing was done by disc diffusion technique against amphotericin B, nystatin, fluconazole and clotrimazole. RESULTS: Candida manifests in various sites depending on the predisposing factors and immune status of the person. In this study we found the association of Candida with various predisposing factors (Pregnancy, Oral contraceptive pills’s, Immune suppression, Diabetes. This study observed the dominance of non-albicans Candida (51% in the clinical samples over Candida albicans (49%. The maximum antifungal susceptibility was observed against amphotericin B in both the albicans and non-albicans Candia, but non-albicans Candida showed maximum resistance to azoles. CONCLUSION: Candida albicans was the most predominant species (49% isolated in various clinical samples. There was an increase in the prevalence of non albicans Candida in this study. Among the nonalbicans Candida (51% Candid tropicalis was the commonest species isolated. Candida albicans showed maximum susceptibility to amphotericin B and maximum resistance to azoles was seen in nonalbicans Candida.

  17. Detection of wild- and vaccine-type avian infectious laryngotracheitis virus in clinical samples and feather shafts of commercial chickens.

    Science.gov (United States)

    Davidson, Irit; Nagar, Sagit; Ribshtein, Israel; Shkoda, Irena; Perk, Shimon; Garcia, Maricarmen

    2009-12-01

    Infectious laryngotracheitis (ILT) is a respiratory disease of poultry caused by an alphaherpesvirus (ILTV). To evaluate differential detection of ILTVs belonging to the two types, wild-type or vaccine-type, both causing clinical signs, five PCRs were evaluated to detect wild-type and vaccine-type ILTV in clinical samples. By directly sampling the organs, we aimed to avoid changes in the virus genome and to facilitate a fast diagnosis. The samples were tracheal and spleen homogenates and feather shafts. The latter are easy to collect, nonlethal for the bird, and advantageous for monitoring purposes. We investigated the time interval for vaccine virus detection following commercial vaccination by the vent application, which is successfully practiced in Israel. The study indicated that ILTV amplification from feather shafts was possible in clinical cases for about a one-month period after vaccination. Vaccine strains were identified by nested PCR for the ILTV-gE gene and differed from wild-type ILTV strains by two criteria: (1) While avirulent vaccines could be detected for about a month after the vent application, wild-type virus could be detected, in conjunction with clinical signs, for an unlimited time period; and (2) The ILTV vaccine was present in the bird in minute quantities compared to the wild-type virus. We assessed the virus type that appeared in conjunction with the clinical signs and determined that the clinical signs appeared in conjunction with both molecular forms of ILTV. The vaccine virus-type and the wild-type ILTV differed by their distinct restriction pattern when using the HaeIII restriction enzyme digestion of the nested amplification product. PMID:20095166

  18. [Clinical characteristics and social determinants in a sample of non-homebound elderly].

    Science.gov (United States)

    Morsch, Patricia; Pereira, Gustavo Nunes; Navarro, Joel Hirtz do Nascimento; Trevisan, Margarete Diprat; Lopes, Diene Gomes Colvara; Bós, Ângelo José Gonçalves

    2015-05-01

    This study aimed to assess social and clinical factors associated with the fact that older adults (≥ 60 years) go out of their homes. The study interviewed 5,898 older adults identified through home visits, randomly selected in 59 cities in the State of Rio Grande do Sul, Brazil. Multivariate logistic regression was used to assess the association between the outcome and independent variables. Factors associated with going out were being men, younger and married, presence of arthrosis, ease in performing specific activities, and good self-rated health. Heart disease was a negative factor for going out. Given the importance of social activity for quality of life and the World Health Organization policy for active aging, it is extremely important to consider clinical conditions that allow the older adults to remain active in the community. Studies like this can help to adjust public policies for the elderly, especially acting on modifiable clinical and functional conditions. PMID:26083177

  19. Simulating an investigative study of clinical cancer samples: use of tissue slides and PCR-based promoter-hypermethylation analysis.

    Science.gov (United States)

    Chew, Yuan Yuan; Chin, Cheen Fei; Yeong, Foong May

    2015-01-01

    Topics on the molecular basis underlying cancer are quite popular among students. Also, excellent textbooks abound that provide interesting materials for discussion during lectures and tutorials about major events leading to cancer formation and progression. However, much less is available for students to conduct experiments for the analysis of cancer samples in undergraduate modules where there is a limited time-frame. Given the difficulty of working with cancer samples and the scarcity of good samples even in the clinical laboratories, it is impossible to run large-class practicals using patients' samples. Here, we describe the use of tissue slides in combination with polymerase-chain reaction (PCR) as a means of simulating an investigative approach to supplement students' learning of clinical research. By using tissue slides for histo-pathological examinations and specific budding yeast genomic DNA and primers adapted to demonstrate methylation-specific PCR, we designed an inquiry-based lab session to simulate the clinical investigation of a cohort of biopsies that students could analyze in a one-session practical. PMID:25395208

  20. Social and Emotional Outcomes of Child Sexual Abuse: A Clinical Sample in Turkey

    Science.gov (United States)

    Ozbaran, Burcu; Erermis, Serpil; Bukusoglu, Nagehan; Bildik, Tezan; Tamar, Muge; Ercan, Eyyup Sabri; Aydin, Cahide; Cetin, Saniye Korkmaz

    2009-01-01

    Childhood sexual abuse is a traumatic life event that may cause psychiatric disorders such as posttraumatic stress disorder and depression. During 2003-2004, 20 sexually abused children were referred to the Child and Adolescent Psychiatry Clinic of Ege University in Izmir, Turkey. Two years later, the psychological adjustment of these children (M…

  1. Clinical and Laboratory Data in a Sample of Greek Children with Autism Spectrum Disorders

    Science.gov (United States)

    Ververi, Athina; Vargiami, Efthymia; Papadopoulou, Vassiliki; Tryfonas, Dimitrios; Zafeiriou, Dimitrios I.

    2012-01-01

    The purpose of this study is to describe clinical and laboratory data, as well as comorbid disorders in Greek children with autism spectrum disorders (ASD). Data were retrospectively collected for 222 children aged 1.5-9 years. The mean age at diagnosis was 43.7 [plus or minus] 17.6 months. Significantly earlier diagnoses were noted in children…

  2. Evaluation of constitutive and inducible resistance to clindamycin in clinical samples of Staphylococcus aureus from a tertiary hospital

    Directory of Open Access Journals (Sweden)

    Angelita Bottega

    2014-10-01

    Full Text Available Introduction Infections caused by methicillin-resistant Staphylococcus aureus (MRSA have become common in hospitals and the community environment, and this wide resistance has limited patient treatment. Clindamycin (CL represents an important alternative therapy for infections caused by S. aureus. Antimicrobial susceptibility testing using standard methods may not detect inducible CL resistance. This study was performed to detect the phenotypes of resistance to macrolides-lincosamides-streptogramin B (MLSB antibiotics, including CL, in clinical samples of S. aureus from patients at a tertiary hospital in Santa Maria, State of Rio Grande do Sul, Brazil. Methods One hundred and forty clinical isolates were submitted to the disk diffusion induction test (D-test with an erythromycin (ER disk positioned at a distance of 20mm from a CL disk. The results were interpreted according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI. Results In this study, 29 (20.7% of the 140 S. aureus samples were resistant to methicillin (MRSA, and 111 (79.3% were susceptible to methicillin (MSSA. The constitutive resistance phenotype (cMLSB was observed in 20 (14.3% MRSA samples and in 5 (3.6% MSSA samples, whereas the inducible resistance phenotype (iMLSB was observed in 3 (2.1% MRSA samples and in 8 (5.8% MSSA samples. Conclusions The D-test is essential for detecting the iMLSB phenotype because the early identification of this phenotype allows clinicians to choose an appropriate treatment for patients. Furthermore, this test is simple, easy to perform and inexpensive.

  3. Targeted therapies in cancer - challenges and chances offered by newly developed techniques for protein analysis in clinical tissues

    Directory of Open Access Journals (Sweden)

    K Malinowsky, C Wolff, S Gündisch, D Berg, KF Becker

    2011-01-01

    Full Text Available In recent years, new anticancer therapies have accompanied the classical approaches of surgery and radio- and chemotherapy. These new forms of treatment aim to inhibit specific molecular targets namely altered or deregulated proteins, which offer the possibility of individualized therapies.The specificity and efficiency of these new approaches, however, bring about a number of challenges. First of all, it is essential to specifically identify and quantify protein targets in tumor tissues for the reasonable use of such targeted therapies. Additionally, it has become even more obvious in recent years that the presence of a target protein is not always sufficient to predict the outcome of targeted therapies. The deregulation of downstream signaling molecules might also play an important role in the success of such therapeutic approaches. For these reasons, the analysis of tumor-specific protein expression profiles prior to therapy has been suggested as the most effective way to predict possible therapeutic results. To further elucidate signaling networks underlying cancer development and to identify new targets, it is necessary to implement tools that allow the rapid, precise, inexpensive and simultaneous analysis of many network components while requiring only a small amount of clinical material.Reverse phase protein microarray (RPPA is a promising technology that meets these requirements while enabling the quantitative measurement of proteins. Together with recently developed protocols for the extraction of proteins from formalin-fixed, paraffin-embedded (FFPE tissues, RPPA may provide the means to quantify therapeutic targets and diagnostic markers in the near future and reliably screen for new protein targets.With the possibility to quantitatively analyze DNA, RNA and protein from a single FFPE tissue sample, the methods are available for integrated patient profiling at all levels of gene expression, thus allowing optimal patient stratification

  4. Detection of Clostridium tetani in human clinical samples using tetX specific primers targeting the neurotoxin.

    Science.gov (United States)

    Ganesh, Madhu; Sheikh, Nasira K; Shah, Pooja; Mehetre, Gajanan; Dharne, Mahesh S; Nagoba, Basavraj S

    2016-01-01

    Tetanus resulting from ear injury remains an important health problem, particularly in the developing world. We report the successful detection of Clostridium tetani using tetX specific primers targeting the Cl. tetani neurotoxin. The sample was obtained from an ear discharge of a case of otogenic tetanus in a 2-year-old male child. Based on the culture results of the ear discharge, Gram staining and virulence testing by genotyping, a diagnosis of tetanus was confirmed. This is the first report from India on the successful detection of Cl. tetani in a human clinical sample using tetX specific primers targeting the Cl. tetani neurotoxin. PMID:26220795

  5. A Short-Term, Prospective Test of the Interpersonal-Psychological Theory of Suicidal Ideation in an Adolescent Clinical Sample.

    Science.gov (United States)

    Miller, Adam Bryant; Esposito-Smythers, Christianne; Leichtweis, Richard N

    2016-06-01

    The present prospective study tested a portion of the interpersonal-psychological theory of suicide (IPTS) in an adolescent clinical sample. Participants were 143 adolescents consecutively admitted to a partial hospitalization program who completed assessments at intake and discharge from the program. Results partially supported the IPTS and suggest that (1) perceived burdensomeness may be an important socially based cognition for understanding concurrent risk for suicidal ideation (SI); (2) thwarted belongingness affects depression symptom severity over time, which indirectly predicts SI over a short follow-up time frame; and (3) the IPTS constructs may function differently in a high-risk clinical adolescent sample, compared to adults, although findings are preliminary. PMID:26456085

  6. Development of standardized methodology for identifying toxins in clinical samples and fish species associated with tetrodotoxin-borne poisoning incidents

    Directory of Open Access Journals (Sweden)

    Tai-Yuan Chen

    2016-01-01

    Full Text Available Tetrodotoxin (TTX is a naturally occurring toxin in food, especially in puffer fish. TTX poisoning is observed frequently in South East Asian regions. In TTX-derived food poisoning outbreaks, the amount of TTX recovered from suspicious fish samples or leftovers, and residual levels from biological fluids of victims are typically trace. However, liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry methods have been demonstrated to qualitatively and quantitatively determine TTX in clinical samples from victims. Identification and validation of the TTX-originating seafood species responsible for a food poisoning incident is needed. A polymerase chain reaction-based method on mitochondrial DNA analysis is useful for identification of fish species. This review aims to collect pertinent information available on TTX-borne food poisoning incidents with a special emphasis on the analytical methods employed for TTX detection in clinical laboratories as well as for the identification of TTX-bearing species.

  7. Matrix Metalloproteinase-9/Neutrophil Gelatinase-Associated Lipocalin Complex Activity in Human Glioma Samples Predicts Tumor Presence and Clinical Prognosis

    Directory of Open Access Journals (Sweden)

    Ming-Fa Liu

    2015-01-01

    Full Text Available Matrix metalloproteinase-9/neutrophil gelatinase-associated lipocalin (MMP-9/NGAL complex activity is elevated in brain tumors and may serve as a molecular marker for brain tumors. However, the relationship between MMP-9/NGAL activity in brain tumors and patient prognosis and treatment response remains unclear. Here, we compared the clinical characteristics of glioma patients with the MMP-9/NGAL activity measured in their respective tumor and urine samples. Using gelatin zymography assays, we found that MMP-9/NGAL activity was significantly increased in tumor tissues (TT and preoperative urine samples (Preop-1d urine. Activity was reduced by seven days after surgery (Postop-1w urine and elevated again in cases of tumor recurrence. The MMP-9/NGAL status correlated well with MRI-based tumor assessments. These findings suggest that MMP-9/NGAL activity could be a novel marker to detect gliomas and predict the clinical outcome of patients.

  8. Clinically significant fatigue: prevalence and associated factors in an international sample of adults with multiple sclerosis recruited via the internet.

    Directory of Open Access Journals (Sweden)

    Tracey J Weiland

    Full Text Available Fatigue contributes a significant burden of disease for people with multiple sclerosis (PwMS. Modifiable lifestyle factors have been recognized as having a role in a range of morbidity outcomes in PwMS. There is significant potential to prevent and treat fatigue in PwMS by addressing modifiable risk factors.To explore the associations between clinically significant fatigue and demographic factors, clinical factors (health-related quality of life, disability and relapse rate and modifiable lifestyle, disease-modifying drugs (DMD and supplement use in a large international sample of PwMS.PwMS were recruited to the study via Web 2.0 platforms and completed a comprehensive survey measuring demographic, lifestyle and clinical characteristics, including health-related quality of life, disability, and relapse rate.Of 2469 participants with confirmed MS, 2138 (86.6% completed a validated measure of clinically significant fatigue, the Fatigue Severity Scale. Participants were predominantly female from English speaking countries, with relatively high levels of education, and due to recruitment methods may have been highly pro-active about engaging in lifestyle management and self-help. Approximately two thirds of our sample (1402/2138; 65.6% (95% CI 63.7-67.7 screened positive for clinically significant fatigue. Bivariate associations were present between clinically significant fatigue and several demographic, clinical, lifestyle, and medication variables. After controlling for level of disability and a range of stable socio-demographic variables, we found increased odds of fatigue associated with obesity, DMD use, poor diet, and reduced odds of fatigue with exercise, fish consumption, moderate alcohol use, and supplementation with vitamin D and flaxseed oil.This study supports strong and significant associations between clinically significant fatigue and modifiable lifestyle factors. Longitudinal follow-up of this sample may help clarify the contribution

  9. Antimicrobial resistance trends among canine Escherichia coli isolates obtained from clinical samples in the northeastern USA, 2004–2011

    OpenAIRE

    Cummings, Kevin J.; Aprea, Victor A.; Altier, Craig

    2015-01-01

    Our objectives were to describe the antimicrobial susceptibility of Escherichia coli isolates from dogs in the northeastern USA and to identify temporal trends in resistance to selected antimicrobial agents. Data were collected retrospectively for all canine E. coli isolates from clinical samples submitted to Cornell University’s Animal Health Diagnostic Center between January 1, 2004 and December 31, 2011. Antimicrobial susceptibility testing was performed on 3519 canine E. coli isolates; fr...

  10. Examination of the Section III DSM-5 diagnostic system for personality disorders in an outpatient clinical sample

    OpenAIRE

    Few, Lauren R.; Miller, Joshua D.; Rothbaum, Alex; Meller, Suzanne; Maples, Jessica; Terry, Douglas P.; Collins, Brittany; MacKillop, James

    2013-01-01

    The DSM-5 includes a novel approach to the diagnosis of personality disorders (PDs) in Section III, in order to stimulate further research with the possibility that this proposal will be included more formally in future DSM iterations. The current study provides the first test of this proposal in a clinical sample by simultaneously examining its two primary components: a system for rating personality impairment and a newly developed dimensional model of pathological personality traits. Partic...

  11. Rapid Detection/pathotyping of Newcastle disease virus isolates in clinical samples using real time polymerase chain reaction assay

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Abdul Wajid, Muhammad Wasim, Tahir Yaqub, Shafqat F Rehmani, Tasra Bibi, Nadia Mukhtar, Javed Muhammad, Umar Bacha, Suliman Qadir Afridi, Muhammad Nauman Zahid, Zia u ddin, Muhammad Zubair Shabbir, Kamran Abbas & Muneer Ahmad ### Abstract In the present protocol we describe the real time reverse transcription polymerase chain reaction (rRT-PCR) assay for the rapid detection/pathotyping of Newcastle disease virus (NDV) isoaltes in clinical samples. Fusion gene and matrix ...

  12. Prevalence, clinical characteristics, and predictors of obesity hypoventilation syndrome in a large sample of Saudi patients with obstructive sleep apnea

    OpenAIRE

    Ahmed S BaHammam

    2015-01-01

    Objectives: To assess the prevalence, clinical characteristics, and predictors of obesity hypoventilation syndrome (OHS) in a large sample of Saudi patients with obstructive sleep apnea (OSA). Methods: This prospective observational study consisted of 1693 patients who were diagnosed to have sleep-disordered breathing using type I attended polysomnography (PSG) between January 2002 and December 2012 in the University Sleep Disorders Center (USDC) at King Saud University Hospital, Riyadh, King...

  13. Detection of Adenoviruses from clinical samples in bone marrow transplant patients by nested PCR (polymerase chain reaction)

    OpenAIRE

    Fatemeh Sabagh; Michael Roggendorf

    2012-01-01

    Adenoviruses are recognized as common human pathogens that are responsible for a wide variety of infectious syndromes. Bone marrow transplant patients are prone to life threatening opportunistic infections like adenoviruses. The nested polymerase chain reaction has provided an alternative, sensitive diagnostic method for detection of Adenoviruses. In this study we developed PCR from hexon genes as rapid diagnostic method of Advs infections on different clinical samples. Adenovirus infections ...

  14. Anxiety and depression in parents of a Brazilian non-clinical sample of attention-deficit/ hyperactivity disorder (ADHD) students

    OpenAIRE

    D. Segenreich; D. Fortes; G. Coutinho; G. Pastura; Mattos, P

    2009-01-01

    Higher prevalence rates of anxiety and depression have been reported in parents of children with attention-deficit/hyperactivity disorder (ADHD). The interaction between the burden of ADHD in offspring, a higher prevalence rate of this highly inherited disorder in parents, and comorbidities may explain this finding. Our objective was to investigate levels of ADHD, anxious and depressive symptomatology, and their relationship in parents of ADHD children from a non-clinical sample using a dimen...

  15. Neuropsychological Profiles Correlated with Clinical and Behavioral Impairments in a Sample of Brazilian Children with Attention-Deficit Hyperactivity Disorder

    OpenAIRE

    Rizzutti, Sueli; Schuch, Viviane; Augusto, Bruno Muszkat; Coimbra, Caio Colturato; Pereira, João Pedro Cabrera; Bueno, Orlando Francisco Amodeo

    2015-01-01

    Attention-deficit hyperactivity disorder (ADHD) is a complex neurodevelopmental disorder that implies several-step process, and there is no single test to diagnose both ADHD and associated comorbidities, such as oppositional-defiant disorder (ODD), anxiety disorder, depression, and certain types of learning disabilities. The purpose of the present study was to examine correlations between behavioral and clinical symptoms by administering an extensive neuropsychological battery to a sample of ...

  16. Psychopathic Personality and Emotional Processing in a Non-Clinical, Non-Criminal Sample: Evidence from the Emotional Interrupt Task

    OpenAIRE

    Ritchie, Stuart J.

    2009-01-01

    A sample of non-clinical, non-criminal individuals was investigated using a simple motor task which included emotionally- and neutrally-valenced distracters. In previous studies using this method, individuals with psychopathy had been found to have faster responses than controls to trials including emotional distracters (Mitchell et al., 2006). In addition, two personality inventories were completed by participants and compared: a specialist psychopathy inventory, and a measure of normal pers...

  17. Birth Order and Sibling Gender Ratio of a Clinical Sample of Children and Adolescents Diagnosed with Attention Deficit Hyperactivity Disorder

    OpenAIRE

    Ahmad Ghanizadeh; Marzie Abotorabi-Zarchi; Mohammad Reza Mohammadi; Ali Firoozabadi

    2012-01-01

    Objective: It is not clear whether sibling’s gender ratio is associated with attention deficit hyperactivity disorder (ADHD). This study examines whether inattentiveness severity and hyperactivity/impulsivity severity are associated with birth order of children with ADHD.Method: Participants are a clinical sample of 173 children and adolescents with ADHD and 43 ones without ADHD. Diagnoses were made using Diagnostic and Statistical Manual of Mental Disorders forth edition-Text Revision (DSM-I...

  18. Adult ADHD Symptoms and Five Factor Model Traits in a Clinical Sample: A Structural Equation Modeling Approach

    OpenAIRE

    Knouse, Laura E.; Traeger, Lara; O’Cleirigh, Conall; Safren, Steven A.

    2013-01-01

    Relationships among Attention-Deficit/Hyperactivity Disorder (ADHD) symptoms and adult personality traits have not been examined in larger clinically diagnosed samples. We collected multi-source ADHD symptom and self-report NEO Five-Factor Inventory (Costa & McCrae, 1992a) data from 117 adults with ADHD and tested symptom-trait associations using structural equation modeling. The final model fit the data. Inattention was positively associated with Neuroticism and negatively associated with Co...

  19. Cluster Analysis of the Yale Global Tic Severity Scale (YGTSS): Symptom Dimensions and Clinical Correlates in an Outpatient Youth Sample

    OpenAIRE

    Kircanski, Katharina; Woods, Douglas W.; Chang, Susanna W.; Ricketts, Emily J.; Piacentini, John C.

    2010-01-01

    Tic disorders are heterogeneous, with symptoms varying widely both within and across patients. Exploration of symptom clusters may aid in the identification of symptom dimensions of empirical and treatment import. This article presents the results of two studies investigating tic symptom clusters using a sample of 99 youth (M age = 10.7, 81% male, 77% Caucasian) diagnosed with a primary tic disorder (Tourette’s disorder or chronic tic disorder), across two university-based outpatient clinics ...

  20. Detection of Rare Drug Resistance Mutations by Digital PCR in a Human Influenza A Virus Model System and Clinical Samples.

    Science.gov (United States)

    Whale, Alexandra S; Bushell, Claire A; Grant, Paul R; Cowen, Simon; Gutierrez-Aguirre, Ion; O'Sullivan, Denise M; Žel, Jana; Milavec, Mojca; Foy, Carole A; Nastouli, Eleni; Garson, Jeremy A; Huggett, Jim F

    2016-02-01

    Digital PCR (dPCR) is being increasingly used for the quantification of sequence variations, including single nucleotide polymorphisms (SNPs), due to its high accuracy and precision in comparison with techniques such as quantitative PCR (qPCR) and melt curve analysis. To develop and evaluate dPCR for SNP detection using DNA, RNA, and clinical samples, an influenza virus model of resistance to oseltamivir (Tamiflu) was used. First, this study was able to recognize and reduce off-target amplification in dPCR quantification, thereby enabling technical sensitivities down to 0.1% SNP abundance at a range of template concentrations, a 50-fold improvement on the qPCR assay used routinely in the clinic. Second, a method was developed for determining the false-positive rate (background) signal. Finally, comparison of dPCR with qPCR results on clinical samples demonstrated the potential impact dPCR could have on clinical research and patient management by earlier (trace) detection of rare drug-resistant sequence variants. Ultimately this could reduce the quantity of ineffective drugs taken and facilitate early switching to alternative medication when available. In the short term such methods could advance our understanding of microbial dynamics and therapeutic responses in a range of infectious diseases such as HIV, viral hepatitis, and tuberculosis. Furthermore, the findings presented here are directly relevant to other diagnostic areas, such as the detection of rare SNPs in malignancy, monitoring of graft rejection, and fetal screening. PMID:26659206

  1. Conceptual Model of Clinical Governance Information System for Statistical Indicators by Using UML in Two Sample Hospitals

    Science.gov (United States)

    Jeddi, Fatemeh Rangraz; Farzandipoor, Mehrdad; Arabfard, Masoud; Hosseini, Azam Haj Mohammad

    2016-01-01

    Objective: The purpose of this study was investigating situation and presenting a conceptual model for clinical governance information system by using UML in two sample hospitals. Background: However, use of information is one of the fundamental components of clinical governance; but unfortunately, it does not pay much attention to information management. Material and Methods: A cross sectional study was conducted in October 2012- May 2013. Data were gathered through questionnaires and interviews in two sample hospitals. Face and content validity of the questionnaire has been confirmed by experts. Data were collected from a pilot hospital and reforms were carried out and Final questionnaire was prepared. Data were analyzed by descriptive statistics and SPSS 16 software. Results: With the scenario derived from questionnaires, UML diagrams are presented by using Rational Rose 7 software. The results showed that 32.14 percent Indicators of the hospitals were calculated. Database was not designed and 100 percent of the hospital’s clinical governance was required to create a database. Conclusion: Clinical governance unit of hospitals to perform its mission, do not have access to all the needed indicators. Defining of Processes and drawing of models and creating of database are essential for designing of information systems. PMID:27147804

  2. Survey and visual detection of Zaire ebolavirus in clinical samples targeting the nucleoprotein gene in Sierra Leone

    Directory of Open Access Journals (Sweden)

    Jing eYuan

    2015-12-01

    Full Text Available Ebola virus (EBOV can lead to severe hemorrhagic fever with a high risk of death in humans and other primates. To guide treatment and prevent spread of the viral infection, a rapid and sensitive detection method is required for clinical samples. Here, we described and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP method to detect Zaire ebolavirus using the nucleoprotein gene (NP as a target sequence. Two different techniques were used, a calcein/Mn2+ complex chromogenic method and real-time turbidity monitoring. The RT-LAMP assay detected the NP target sequence with a limit of 4.56 copies/μL within 45 min under 61°C, a similar even or increase in sensitivity than that of real-time reverse transcription-polymerase chain reaction (RT-PCR. Additionally, all pseudoviral particles or non- Zaire EBOV genomes were negative for LAMP detection, indicating that the assay was highly specific for EBOV. To appraise the availability of the RT-LAMP method for use in clinical diagnosis of EBOV, of 417 blood or swab samples collected from patients with clinically suspected infections in Sierra Leone, 307 were identified for RT-LAMP-based surveillance of EBOV. Therefore, the highly specific and sensitive RT-LAMP method allows the rapid detection of EBOV, and is a suitable tool for clinical screening, diagnosis, and primary quarantine purposes.

  3. Simultaneous Detection of Four Human Pathogenic Microsporidian Species from Clinical Samples by Oligonucleotide Microarray

    OpenAIRE

    Wang, Zheng; Orlandi, Palmer A.; David A Stenger

    2005-01-01

    Microsporidian species have been rapidly emerging as human enteric pathogens in immunocompromised and immunocompetent individuals in recent years. Routine diagnostic techniques for microsporidia in clinical laboratories are laborious and insensitive and tend to underestimate their presence. In most instances, they are unable to differentiate species of spores due to their small sizes and similar morphologies. In this study, we report the development of another protozoan oligonucleotide microa...

  4. Functionalized graphene oxide for clinical glucose biosensing in urine and serum samples

    OpenAIRE

    Veerapandian M; Seo YT; Shin H; Yun K; Lee MH

    2012-01-01

    Murugan Veerapandian,1 Yeong-Tai Seo,2 Hyunkyung Shin,3 Kyusik Yun,1 Min-Ho Lee41Department of Bionanotechnology, Gachon University, Gyeonggi-Do, 2School of Electrical Engineering and Computer Science, Seoul National University, Seoul, 3Department of Mathematics and Information, Gachon University, Gyeonggi-Do, 4Korea Electronics Technology Institute, Medical IT Technology, Gyeonggi-Do, Republic of KoreaAbstract: A novel clinical glucose biosensor fabricated using functionalized metalloid-poly...

  5. Reverse transcription multiplex PCR for differentiation between polio- and enteroviruses from clinical and environmental samples.

    OpenAIRE

    Egger, D.; Pasamontes, L; Ostermayer, M; Bienz, K

    1995-01-01

    For the rapid detection of polioviruses and their differentiation from nonpoliovirus enteroviruses, we developed a protocol in which clinical or environmental specimens are first inoculated onto cell cultures in tubes. After overnight incubation, the cultures are subjected to reverse transcription multiplex PCR with a primer pair which detects all enteroviruses (T. Hyypiä, P. Auvinen, and M. Maaronen, J. Gen. Virol. 70:3261-3268 1989) and two newly designed primer pairs specific for all 36 po...

  6. Evolution and Diversity of Listeria monocytogenes from Clinical and Food Samples in Shanghai, China.

    Science.gov (United States)

    Zhang, Jianmin; Cao, Guojie; Xu, Xuebin; Allard, Marc; Li, Peng; Brown, Eric; Yang, Xiaowei; Pan, Haijian; Meng, Jianghong

    2016-01-01

    Listeria monocytogenes is a significant foodborne pathogen causing severe systemic infections in humans with high mortality rates. The objectives of this work were to establish a phylogenetic framework of L. monocytogenes from China and to investigate sequence diversity among different serotypes. We selected 17 L. monocytogenes strains recovered from patients and foods in China representing serotypes 1/2a, 1/2b, and 1/2c. Draft genome sequences were determined using Illumina MiSeq technique and associated protocols. Open reading frames were assigned using prokaryotic genome annotation pipeline by NCBI. Twenty-four published genomes were included for comparative genomic and phylogenetic analysis. More than 154,000 single nucleotide polymorphisms (SNPs) were identified from multiple genome alignment and used to reconstruct maximum likelihood phylogenetic tree. The 41 genomes were differentiated into lineages I and II, which consisted of 4 and 11 subgroups, respectively. A clinical strain from China (SHL009) contained significant SNP differences compared to the rest genomes, whereas clinical strain SHL001 shared most recent common ancestor with strain SHL017 from food. Moreover, clinical strains SHL004 and SHL015 clustered together with two strains (08-5578 and 08-5923) recovered from an outbreak in Canada. Partial sequences of a plasmid found in the Canadian strain were also present in SHL004. We investigated the presence of various genes and gene clusters associated with virulence and subgroup-specific genes, including internalins, L. monocytogenes pathogenicity islands (LIPIs), L. monocytogenes genomic islands (LGIs), stress survival islet 1 (SSI-1), and clustered regularly interspaced short palindromic repeats (CRISPR)/cas system. A novel genomic island, denoted as LGI-2 was identified. Comparative sequence analysis revealed differences among the L. monocytogenes strains related to virulence, survival abilities, and attributes against foreign genetic elements. L

  7. Clinical Diagnosis by Whole-Genome Sequencing of a Prenatal Sample

    OpenAIRE

    Talkowski, Michael E.; Ordulu, Zehra; Pillalamarri, Vamsee; Benson, Carol B.; Blumenthal, Ian; Connolly, Susan; Hanscom, Carrie; Hussain, Naveed; Pereira, Shahrin; Picker, Jonathan; Rosenfeld, Jill A.; Shaffer, Lisa G.; Wilkins-Haug, Louise E.; Gusella, James F.; Morton, Cynthia C.

    2012-01-01

    Conventional cytogenetic testing offers low-resolution detection of balanced karyotypic abnormalities but cannot provide the precise, gene-level knowledge required to predict outcomes. The use of high-resolution whole-genome deep sequencing is currently impractical for the purpose of routine clinical care. We show here that whole-genome “jumping libraries” can offer an immediately applicable, nucleotide-level complement to conventional genetic diagnostics within a time frame that allows for c...

  8. Leptospira spp detection by Polymerase Chain Reaction (PCR in clinical samples of captive black-capped Capuchin monkey (Cebus apella

    Directory of Open Access Journals (Sweden)

    Scarcelli Eliana

    2003-01-01

    Full Text Available Leptospirosis is a widely distributed zoonosis that affects domestic and wild animals, and that has the man as the end point of its epidemiological chain. Leptospirosis diagnosis in primates is more difficult than in other animal species, as clinical signs and lesions are less evident and antibody response is detected only for short periods. The aim of this article was to describe the detection of Leptospira spp using polymerase chain reaction (PCR, in clinical samples from one captive black-capped Capuchin monkey (Cebus apella, which presented characteristics compatible with leptospirosis (jaundice and haemorrhagic kdney in the macroscopic post-mortem examination. A friable kidney fragment and urine sample were cultured and submitted to experimental inoculation in guinea pigs and PCR using genus specific primer pair targeting the 16S rRNA region from Leptospira interrogans serovar canicola. Isolation of the agent was negative both in culture and experimental inoculation. The PCR amplification of the clinical samples showed a 330 pb amplified fragment that corresponds to the Leptospira genus. Based on these results PCR was considered an important tool for leptospira detection in nonhumam primates, more sensitive and specific than other techniques, especially considering that the viability of the pathogen was not possible. These advantages enable the detection of the leptospiras in urine and kidney, even when autolysed, frozen or badly conserved, which prevented the isolation and experimental inoculation from positive results.

  9. MYCOLOGICAL PROFILE OF DERMATOPHYTES ISOLATED FROM CLINICAL SAMPLES IN KIMS HOSPITAL, BANGALORE

    Directory of Open Access Journals (Sweden)

    Anjana

    2015-01-01

    Full Text Available The dermatophytoses constitute a group of superficial fungal infections of keratinised tissue - epidermis, hair and nails, caused by a closely related group of filamentous fungi, the dermatophytes. OBJECTIVES: Isolation and speciation of dermatophytes by culture and to determine its prevalence. METHODOLOGY: The study was conducted from January 2012 - December 2013 at Kempegowda institute of medical sciences, Bangalore. All clinically suspected cases coming to the microbiology department where subjected to mycological work - up. Specimens like skin scraping, hair, and nail were collected and microscopically examined using 10%, 20% and 40% KOH respectively for fungal filaments. Culture was carried out using Sabouraud dextrose agar medium with and without cycloheximide. The growth in the culture tube was speciated based on the macroscopic and microscopic findings (with Lactophenol cotton blue staining. RESULTS: Total cases in the two year period were 609. The infection was found to be common in adults aged 20 - 30 years, the male to female ratio is 1.2:1. The KOH positives were 491(80%, and culture positives were 471(77%. Of the positive cultures Trichophyton rubrum (35% was the common isolate followed by Trichophyton mentagrophytes (17%, and Epidermophyton floccosum (6%. CONCLUSION : In the present study the most common clinical presentation is Tinea corporis followed by Tinea unguium and Tinea cruris and the common isolate was T.rubrum. The present study was undertaken to determine the clinical pattern of dermatophytosis and the common species that was prevalent here.

  10. Molecular method for the characterization of Coxiella burnetii from clinical and environmental samples: variability of genotypes in Spain

    Directory of Open Access Journals (Sweden)

    Jado Isabel

    2012-06-01

    Full Text Available Abstract Background Coxiella burnetii is a highly clonal microorganism which is difficult to culture, requiring BSL3 conditions for its propagation. This leads to a scarce availability of isolates worldwide. On the other hand, published methods of characterization have delineated up to 8 different genomic groups and 36 genotypes. However, all these methodologies, with the exception of one that exhibited limited discriminatory power (3 genotypes, rely on performing between 10 and 20 PCR amplifications or sequencing long fragments of DNA, which make their direct application to clinical samples impracticable and leads to a scarce accessibility of data on the circulation of C. burnetii genotypes. Results To assess the variability of this organism in Spain, we have developed a novel method that consists of a multiplex (8 targets PCR and hybridization with specific probes that reproduce the previous classification of this organism into 8 genomic groups, and up to 16 genotypes. It allows for a direct characterization from clinical and environmental samples in a single run, which will help in the study of the different genotypes circulating in wild and domestic cycles as well as from sporadic human cases and outbreaks. The method has been validated with reference isolates. A high variability of C. burnetii has been found in Spain among 90 samples tested, detecting 10 different genotypes, being those adaA negative associated with acute Q fever cases presenting as fever of intermediate duration with liver involvement and with chronic cases. Genotypes infecting humans are also found in sheep, goats, rats, wild boar and ticks, and the only genotype found in cattle has never been found among our clinical samples. Conclusions This newly developed methodology has permitted to demonstrate that C. burnetii is highly variable in Spain. With the data presented here, cattle seem not to participate in the transmission of C. burnetii to humans in the samples studied

  11. Indications, results, and clinical impact of endoscopic ultrasound (EUS)-guided sampling in gastroenterology

    DEFF Research Database (Denmark)

    Dumonceau, J-M; Polkowski, M; Larghi, A;

    2011-01-01

    This article is part of a combined publication that expresses the current view of the European Society of Gastrointestinal Endoscopy (ESGE) about endoscopic ultrasound (EUS)-guided sampling in gastroenterology, including EUS-guided fine needle aspiration (EUS-FNA) and EUS-guided trucut biopsy (EU...

  12. Usefulness of chorionic villus sampling for prenatal diagnosis of thalassaemia: a clinical study in eastern India

    Directory of Open Access Journals (Sweden)

    Sujoy Dasgupta

    2015-06-01

    Conclusions: Thalassaemia is a prevalent condition in Eastern India. Chorionic villus sampling is an effective and safe method for early diagnosis of fetal thalassaemia that helps to prevent birth of thalassaemic babies. [Int J Reprod Contracept Obstet Gynecol 2015; 4(3.000: 790-794

  13. Glycemic Control in a Clinic-Based Sample of Diabetics in M'Bour Senegal

    Science.gov (United States)

    BeLue, Rhonda; Ndiaye, Khadidiatou; NDao, Fatou; Ba, Fatou Niass Niang; Diaw, Mor

    2016-01-01

    Background: Sub-Saharan Africa (SSA) including Senegal is faced with a significant and increasing burden of type 2 diabetes. However, little information is available about diabetes management among Senegalese diabetics. Purpose: The current study aims to describe the level of glycemic control among a convenience sample of diabetics who receive…

  14. Clinical importance and representation of toxigenic and non-toxigenic Clostridium difficile cultivated from stool samples of hospitalized patients

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    Predrag Stojanovic

    2012-03-01

    Full Text Available The aim of this study was to fortify the clinical importance and representation of toxigenic and non-toxigenic Clostridium difficile isolated from stool samples of hospitalized patients. This survey included 80 hospitalized patients with diarrhea and positive findings of Clostridium difficile in stool samples, and 100 hospitalized patients with formed stool as a control group. Bacteriological examination of a stool samples was conducted using standard microbiological methods. Stool sample were inoculated directly on nutrient media for bacterial cultivation (blood agar using 5% sheep blood, Endo agar, selective Salmonella Shigella agar, Selenite-F broth, CIN agar and Skirrow's medium, and to selective cycloserine-cefoxitin-fructose agar (CCFA (Biomedics, Parg qe tehnicologico, Madrid, Spain for isolation of Clostridium difficile. Clostridium difficile toxin was detected by ELISA-ridascreen Clostridium difficile Toxin A/B (R-Biopharm AG, Germany and ColorPAC ToxinA test (Becton Dickinson, USA. Examination of stool specimens for the presence of parasites (causing diarrhea was done using standard methods (conventional microscopy, commercial concentration test Paraprep S Gold kit (Dia Mondial, France and RIDA®QUICK Cryptosporidium/Giardia Combi test (R-Biopharm AG, Germany. Examination of stool specimens for the presence of fungi (causing diarrhea was performed by standard methods. All stool samples positive for Clostridium difficile were tested for Rota, Noro, Astro and Adeno viruses by ELISA - ridascreen (R-Biopharm AG, Germany. In this research we isolated 99 Clostridium difficile strains from 116 stool samples of 80 hospitalized patients with diarrhea. The 53 (66.25% of patients with diarrhea were positive for toxins A and B, one (1.25% were positive for only toxin B. Non-toxigenic Clostridium difficile isolated from samples of 26 (32.5% patients. However, other pathogenic microorganisms of intestinal tract cultivated from samples of 16 patients

  15. Survey and rapid detection of Klebsiella pneumoniae in clinical samples targeting the rcsA gene in Beijing, China

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    Derong eDong

    2015-05-01

    Full Text Available Klebsiella pneumoniae is a wide-spread nosocomial pathogen. A rapid and sensitive molecular method for the detection of K. pneumoniae in clinical samples is needed to guide therapeutic treatment. In this study, we first described a loop-mediated isothermal amplification (LAMP method for the rapid detection of capsular polysaccharide synthesis regulating gene rcsA from K. pneumoniae in clinical samples by using two methods including real-time turbidity monitoring and fluorescence detection to assess the reaction. Then dissemination of K. pneumoniae strains was investigated from ICU patients in three top hospitals in Beijing, China. The results showed that the detection limit of the LAMP method was 0.115 pg/µl DNA within 60 min under isothermal conditions (61°C, a 100-fold increase in sensitivity compared with conventional PCR. All 30 non- K. pneumoniae strains tested were negative for LAMP detection, indicating the high specificity of the LAMP reaction. To evaluate the application of the LAMP assay to clinical diagnosis, of 110 clinical sputum samples collected from ICU patients with clinically suspected multi-resistant infections in China, a total of 32 K. pneumoniae isolates were identified for LAMP-based surveillance of rcsA. All isolates belonged to nine different K. pneumoniae multilocus sequence typing (MLST groups. Strikingly, of the 32 K. pneumoniae strains, 18 contained the Klebsiella pneumoniae Carbapenemase (KPC-encoding gene blaKPC-2 and had high resistance to β-lactam antibiotics. Moreover, K. pneumoniae WJ-64 was discovered to contain blaKPC-2 and blaNDM-1 genes simultaneously in the isolate. Our data showed the high prevalence of blaKPC-2 among K. pneumoniae and co-occurrence of many resistant genes in the clinical strains signal a rapid and continuing evolution of K. pneumoniae. In conclusion, we have developed a rapid and sensitive visual K. pneumoniae detection LAMP assay, which could be a useful tool for clinical screening

  16. Population Relationship of Vibrio parahaemolyticus Isolates Derived from Aquaculture Ponds, a Seafood Market, Restaurants, and Clinical Samples.

    Science.gov (United States)

    Gao, Lei; Deng, Yi Qin; Chen, Chang; Ke, Chang Wen; Li, Bo Sheng; Long, Yun Ying; Liu, Zhu Hong; Wei, Lu

    2016-06-01

    To study the relationship between environmental and clinical populations of Vibrio parahaemolyticus, we collected in total 86 isolates from Southern China during one and a half years. Sixty-eight isolates were recovered from aquaculture ponds, a seafood market, and restaurants, and 18 isolates were recovered from clinical samples. Virulence gene analysis revealed that 25 isolates (14 clinical and 11 environmental) tested positive for tdh, but only 4 carried trh. Interestingly, none of the tdh(+) environmental isolates was recovered from ponds. Both environmental and clinical tdh(+) isolates, except for one clinical isolate, harbor type III secretion system 2α (T3SS2α) and T3SS2β-related genes, including vopB2α, which was previously suggested to be absent from environmental strains. More than 70% of clinical isolates carried the pandemic marker of new toxRS (GS-PCR(+)), which was not present in the environmental isolates. Pulsed-field gel electrophoresis and multilocus sequence typing analysis showed a high degree of genetic diversity within the environmental isolates. In contrast, the clinical population formed a tight cluster that differed from the environmental isolates. These findings suggest that the pandemic strains of V. parahaemolyticus may not directly originate from marine animals. Rather the environments where they are maintained could serve as reservoirs for toxigenic, but not pandemic strains. These environments provide an ideal place for generation of new toxigenic strains through DNA exchange, which was revealed by extensive recombination events in recA sequences of the environmental isolates. PMID:27166752

  17. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.

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    Stephen J Salipante

    Full Text Available Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times and inexpensive for routine clinical use.

  18. Evaluation of two commercially available anti human immunodeficiency virus antibody Elisa Kits using clinical samples

    OpenAIRE

    Anuradha K; Ponamgi S; Lakshmi V

    2002-01-01

    Laboratory diagnosis is the mainstay in the diagnosis of HIV infection in an individual. The wide range of diagnostic kits available, for the detection of anti HIV antibodies, makes it mandatory that the kits are evaluated before they are made available in the market. We evaluated the performance of a Microlisa HIV kit (J.Mitra & Co.)† using a panel of HIV reactive and non reactive clinical specimens. The sensitivity and specificity of the kit were found to be 100% as com...

  19. The frequency of Listeria monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR

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    abazar pournajaf

    2013-09-01

    Full Text Available Background: Listeria monocytogenes is a facultative intracellular pathogen that causes listeriosis which has extensive clinical manifestations. Infections with L. monocytogenes are a serious threat to immunocompromised persons. The aim of this study was to determine the frequency of L. monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR. Materials and Methods: In this study, 617 specimens were analyzed. All specimens were cultured in the specific PALCAM agar. Colonies were initially identified by routine biochemical tests. Finally, PCR assays using primers specific for inlA gene were performed. Results: In all, 46 (8.2% L. monocytogenes isolates were recovered from 617 specimens. Fourteen (8.2% strains, including 4 (7.5%, 2 (5.7%, 5 (14.2% and 3 (8.5% isolates were obtained from placental tissue, urine, vaginal and rectal swabs, respectively. In addition, 9 (7.4% strains of L. monocytogenes which were isolated from 107 different dairy products originated from cheese 5 (7.1%, cream 2 (10% and kashk 2 (11.7%, respectively. Among 11 (5.2% strains isolated from 210 different meat products, 5 (5.5%, 4 (7.2% and 2 (3% strains belonged to sausage, meat and poultry extracts, respectively. Finally, 12 (9.2% Listeria strains were recovered from 130 animal specimens that included 6 (10%, 4 (8% and 2 (10% strains from goat, sheep and cattle, respectively. Furthermore, all Listeria isolates (100% were found to be carriers of  inlA gene in PCR assay. Conclusion: The present study showed that the clinical and non-clinical specimens were contaminated with L. monocytogenes. So, it seems necessary to use a simple and standard technique such as PCR for rapid detection of this organism from various sources.

  20. Slime production and antibiotic susceptibility in staphylococci isolated from clinical samples

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    Seza Arslan

    2007-02-01

    Full Text Available A total of 187 isolates from several clinical specimens were identified to species level as 129 Staphylococcus aureus strains and 58 coagulase-negative staphylococci (CNS strains by the API Staph System (Biomerieux. Slime production was detected both by the conventional Christensen's method as well as by the Congo red agar method. Seventy-two strains of staphylococci isolates (38.5% were found to be slime producers by Christensen's test tube method whereas 58 strains (31% were slime positive with Congo red agar method. There was no statistically significant difference between the two methods for the detection of slime production (P > 0.05. Susceptibility of isolates against antimicrobial agents was tested by the disk diffusion method. Staphylococcal species had resistance to one or more antibiotics. Among the various antimicrobial agents, oxacillin (71.1% and erythromycin (47.1% showed higher resistance than most of the agents used against all isolates. Oxacillin resistant S. aureus (ORSA and oxacillin resistant coagulase-negative staphylococci (ORCNS, 97 (75.2% and 36 (62.1% respectively were frequently observed in strains isolated from clinical materials. Among the ORSA strains, two strains were resistant to vancomycin. Moreover, 96 (74.4% of 129 S. aureus strains were positive for blactamase enzyme. However, 78 (81.25% of 96 b-lactamase positive S. aureus strains were b-lactamase positive ORSA isolates, but none of them had vancomycin resistance.

  1. Application of Atomic Dielectric Resonance Spectroscopy for the screening of blood samples from patients with clinical variant and sporadic CJD

    Directory of Open Access Journals (Sweden)

    Ironside James W

    2007-08-01

    Full Text Available Abstract Background Sub-clinical variant Creutzfeldt-Jakob disease (vCJD infection and reports of vCJD transmission through blood transfusion emphasise the need for blood screening assays to ensure the safety of blood and transplanted tissues. Most assays aim to detect abnormal prion protein (PrPSc, although achieving required sensitivity is a challenge. Methods We have used innovative Atomic Dielectric Resonance Spectroscopy (ADRS, which determines dielectric properties of materials which are established by reflectivity and penetration of radio/micro waves, to analyse blood samples from patients and controls to identify characteristic ADR signatures unique to blood from vCJD and to sCJD patients. Initial sets of blood samples from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors were screened as training samples to determine group-specific ADR characteristics, and provided a basis for classification of blinded sets of samples. Results Blood sample groups from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors screened by ADRS were classified with 100% specificity and sensitivity, discriminating these by a co-variance expert analysis system. Conclusion ADRS appears capable of recognising and discriminating serum samples from vCJD, sCJD, non-CJD neurological diseases, and normal healthy adults, and might be developed to provide a system for primary screening or confirmatory assay complementary to other screening systems.

  2. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.

    Science.gov (United States)

    Van Allen, Eliezer M; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C; Kryukov, Gregory; Carter, Scott L; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T; Gentry, Jeff G; Huang, Franklin W; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S; Gray, Stacy W; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A; Gabriel, Stacey; Getz, Gad; Garraway, Levi A

    2014-06-01

    Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. PMID:24836576

  3. Attachment, Obsessive Beliefs and Emotion Dysregulation in Obsessive Compulsive Disorder: A comparison with Normal and Clinical Sample

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    Sevginar Vatan

    2016-06-01

    Full Text Available Objective: The present study aimed at investigating the differences between nonclinical sample and clinical sample (OCD patients in attachment, obsessive beliefs and emotion regulation in Turkish sample. Methods: For these purposes 224 non clinical participants and 101 clinical OCD participants completed questionnaires related to research variables. Experience in Close Relationship Scale (Fraley, Waller & Brennan, 2000 to evaluate attachment, Obsessive Belief Questionnaire to evaluate obsessive beliefs and Difficulties of Emotion Regulation Scale (Gratz & Roemer, 2004 to evaluate emotion regulation abilities were used in this study. Results: A series of t-test for independent samples analyses were done. Findings of the analyses revealed that there was significant differences between two groups in anxiety level of attachment, but not in avoidance level. Also there were significant differences between two groups in all obsessive beliefs subscales such as responsibility and threat perception, perfectionism and need of certainty, the importance of thoughts and control. From emotional regulation perspective there were significant differences in non-acceptance of emotional response, difficulties in engaging goal-directed behavior, impulse control difficulties during emotional distress, limited access to emotional regulation strategies. However there was not significant differences between two groups in clarity about emotions and awareness of emotional arousal. Conclusion: To sum up according to results of this study attachment and obsessive beliefs follow the same pattern with the results in the literature. Moreover the difficulties of emotion regulation abilities thought to improve the knowledge about OCD. Because this part believed not to have enough findings in the OCD literature. The results were discussed in the light of the related literature and dependent recommendations to the area were given.

  4. Molecular identification of Coccidioides immitis in formalin-fixed, paraffin-embedded (FFPE) tissues from a Colombian patient.

    Science.gov (United States)

    Canteros, Cristina E; Vélez H, Alejandro; Toranzo, Adriana I; Suárez-Alvarez, Roberto; Tobón O, Ángela; Jimenez A, María del Pilar; Restrepo M, Ángela

    2015-06-01

    Coccidioides immitis and C. posadasii are the etiologic agents of coccidioidomycosis, an endemic fungal disease of the Americas. In Colombia, this mycosis is uncommon, and only five cases, two of them imported, have been documented.By means of DNA sequencing, C. immitis was identified in formalin-fixed, paraffin-embedded archival tissues samples from the 5th Colombian patient diagnosed in 1997. The patient was born in Pinto, Department of Magdalena, and had never visited other geographic regions, a reason to consider that the mycosis had been acquired locally.This species is primarily found in California although it has been occasionally reported in other geographic areas such as Mexico and Brazil. This is the first indigenous report of C. immitis-associated coccidioidomycosis in a Colombian patient. PMID:25908652

  5. Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples

    Science.gov (United States)

    Mougeot, Jean-Luc C.; Stevens, Craig B.; Cotton, Sean L.; Morton, Darla S.; Krishnan, Keerthana; Brennan, Michael T.; Lockhart, Peter B.; Paster, Bruce J.; Bahrani Mougeot, Farah K.

    2016-01-01

    Background Over 700 bacterial species reside in human oral cavity, many of which are associated with local or distant site infections. Extensive characterization of the oral microbiome depends on the technologies used to determine the presence and proportions of specific bacterial species in various oral sites. Objective The objective of this study was to compare the microbial composition of dental plaque at baseline using Human Oral Microbe Identification Microarray (HOMIM) and Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technologies, which are based on 16S rRNA. Methods Dental plaque samples were collected from 96 patients at baseline prior to a dental procedure involving manipulation of gingival tissues. The samples were surveyed for 293 and 597 oral bacterial species via HOMIM and HOMINGS, respectively, based on 16S rRNA gene sequences. We determined the concordance between the two technologies for common species. Genus level analysis was performed using HOMINGS-specific genus identification capabilities. Results HOMINGS detected twice the number of species in the same dental plaque samples compared to HOMIM. For the species detected by both HOMIM and HOMINGS, there was no difference in relative proportions of overall bacterial composition at the species, genus or phylum levels. Additionally, there was no difference in relative proportion for total species per patient between the two technologies. Conclusion HOMINGS significantly expanded oral bacterial species identification compared to HOMIM. The genus and species probes, combined in HOMINGS, provided a more comprehensive representation of oral bacterial community, critical for future characterization of oral microbes in distant site infections. PMID:27065347

  6. Indications, results, and clinical impact of endoscopic ultrasound (EUS)-guided sampling in gastroenterology

    DEFF Research Database (Denmark)

    Dumonceau, J-M; Polkowski, M; Larghi, A;

    2011-01-01

    -TCB), of submucosal tumors, diffuse esophageal/gastric wall thickening, pancreatic solid masses and cystic-appearing lesions, mediastinal lesions unrelated to lung or esophageal cancer, cancer of the esophagus, stomach, and rectum, lymph nodes of unknown origin, adrenal gland masses, and focal liver...... circumstances that warrant its use. A two-page executive summary of evidence statements and recommendations is provided. A separate Technical Guideline describes the general technique of EUS-guided sampling, particular techniques to maximize the diagnostic yield depending on the nature of the target lesion, and...

  7. A comparison of new and revised Rorschach measures of schizophrenic functioning in a Serbian clinical sample.

    Science.gov (United States)

    Dzamonja-Ignjatovic, Tamara; Smith, Bruce L; Djuric Jocic, Dragana; Milanovic, Marko

    2013-01-01

    We empirically evaluated indexes derived from the Rorschach Comprehensive System (CS) and the Rorschach Performance Assessment System (R-PAS) that are used for the assessment of psychotic functioning in schizophrenia. We compared the Perceptual Thinking Index (PTI) and the Ego Impairment Index (EII-2) with their revised versions: Thought and Perception Composite (TP-Comp) and EII-3. We evaluated their predictive validity for differentiating schizophrenic from nonschizophrenic patients in a Serbian sample. The sample consisted of 211 (109 men and 102 women, 18-50 years old) inpatients in Serbia who were divided into 2 groups: schizophrenic (100) and nonschizophrenic (111). Test administration, coding, and form quality classification followed CS guidelines. Logistic regression analysis indicated that the new indexes TP-Comp and EII-3 have slightly better predictive power than their counterparts, PTI and EII-2, in identification of schizophrenia, and that TP-Comp performed better than other indexes, although all 4 indexes were successful in differentiating these groups. The results supported the use of TP-Comp in diagnosis of schizophrenia and generally provided evidence for the utility of the Rorschach in evaluating psychosis and for its use in a cross-national context. PMID:23844937

  8. Clinical syndromes, personality and recovery from stress: A study in occupational samples

    Directory of Open Access Journals (Sweden)

    José Miguel Rodríguez Molina

    2012-12-01

    Full Text Available Introduction. Stress manifests itself with different intensity and effects on different people. In many cases it leads to serious health problems or may worsen the prognosis of certain diseases. Stress has been linked to many conditions such as cancer, cardiovascular diseases and infectious diseases. The workplace can be a source of chronic stress. Many variables have been described that allegedly modulate stress response. Aim. To rank the relationship between some of these variables. A model is presented in this study whereby psychopathological personality traits should be related to one of those modulating variables and thus, with the subject's ability to recover from stress. Design. A cross-sectional descriptive design was used. Participants. The sample consisted of 108 volunteers: 15 drivers of Madrid city buses, 44 Iberia flight attendants and 49 waiters in bars in the Community of Madrid. Only 4 bus drivers refused to participate. All flight attendants and waiters consented to be included in the study. Intervention. Tests RESTQ-WORK of Kallus and Jiménez and MCMI of Millon were applied to a sample of 108 workers (bus drivers, bar tender and flight attendants. Outcomes. The hypothesis was verified through Hierarchical Multiple Regression Analysis for each dependant variable.

  9. Correlation Between Clinical Dosimetry and Physical Controls Based on Personal Sampling

    International Nuclear Information System (INIS)

    During a period of eighteen months, various persons exposed to atmospheric contamination in a radioisotope production plant were monitored by two different methods: one was based on personal samples taken over a limited period and used to establish the exposures undergone, qualitatively and quantitatively, from filter examination; the other method involved systematic examination using whole- body spectrometry. Iodine-131 is the radioisotope to which the persons in question were most frequently exposed. Taking account of the effective decay arising between the moment of inhalation and the moment of making the spectrometric measurements, the authors established a ratio K between the inhaled activity, estimated from samples and corrected for decay, and the activity measured directly on the individual. For 34 results obtained on six different individuals, who performed the same tasks in rotation, it seems that these K ratios have a log-normal distribution characterized by a geometric mean Kg = 1.3 and a standard geometric deviation og = 2.2. If the activity retained by the body is 75% of the inhaled activity, it seems likely that the results of the two control methods are, on average, identical. Results have also been obtained with other radioisotopes, especially caesium-137. It is shown how the two methods can be used simultaneously to resolve practical difficulties. (author)

  10. Bipolar disorder in late life: clinical characteristics in a sample of older adults admitted for manic episode

    Directory of Open Access Journals (Sweden)

    Musetti Laura

    2008-07-01

    Full Text Available Abstract Background Although manic episodes in older adults are not rare, little published data exist on late-life manic episodes. Resistance to treatment and concomitant neurological lesions are frequent correlates of elderly mania. The aim of this study was to investigate the prevalence of hospitalizations due to mania in patients older than 64 years through a period of 5 years in an Italian public psychiatric ward. Moreover, we aimed at describing clinical presentation of elderly manic episodes. Methods A retrospective chart review was conducted in order to describe clinical presentation of 20 elderly patients hospitalized for manic episode; moreover, we compared age at onset, the presence of family history for mood disorders, psychosis and irritability between the elderly group and a matched group of 20 younger manic inpatients. Results Seven percent of the whole inpatient elderly people suffered from mania. Half of those patients had a mood disorder age at onset after 50 years and 5 patients were at their first manic episode. Geriatric- and adulthood mania showed similar clinical presentation but younger people had more frequently a mood disorders family history. Conclusion Half of our older manic inpatients consisted of "classic" bipolar patients with an extension of clinical manifestations into later life; the other half of our sample was heterogeneous, even though it was not possible to identify clearly which patients may have had vascular lesions related to the onset of mania.

  11. Enhanced expression of polysialic acid correlates with malignant phenotype in breast cancer cell lines and clinical tissue samples.

    Science.gov (United States)

    Wang, Xin; Li, Xiang; Zeng, Ying-Nan; He, Fa; Yang, Xiao-Min; Guan, Feng

    2016-01-01

    Polysialic acid (PSA) is highly expressed during embryonic development, but barely expressed during postnatal development, and may be 're-expressed' in cancer tissues. In this study, motility and migration assays were performed to compare the changes in cell behavior between non-malignant and maligant cells. Next, the expression levels of PSA were evaluated in 4 human and mouse normal breast or breast cancer (BC) cell lines using 1,2-diamino-4,5-methylenedioxybenzene-labeling HPLC technology, as well as in human clinical BC tissue samples. PSA expression was significantly higher in malignant cells (where it appeared to facilitate cell migration and motility) than in non-malignant cells. Enhanced PSA expression levels were also observed during epithelial-mesenchymal transition (EMT), a leading cause of cancer cell metastasis, which was induced in the NMuMG and MCF10A cells by treatment with transforming growth factor-β1 (TGF-β1). An increased PSA expression also correlated with the disease stage in the patients with BC (PPST) and polysialyltransferase ST8SiaII (STX), which are responsible for PSA synthesis, were differently expressed in the tested BC samples. However, PST, but not STX, was re-expressed in 14 out of 20 clinical BC samples. The findings of the present study indicate that the pathophysiology of BC involves the aberrant regulation of PSA expression and PST gene expression. PMID:26530860

  12. A STUDY OF METALLO-BETA-LACTATAMASE PRODUCING PSEUDOMONAS AERUGINOSA IN CLINICAL SAMPLES OF S.S.G. HOSPITAL

    Directory of Open Access Journals (Sweden)

    Mehul S Chaudhari Tanuja B Javadekar Govind Ninama Neelam Pandya Jivraj Damor

    2011-04-01

    Full Text Available Introduction: Pseudomonas spp. is common pathogen causing nosocomial infection. Acquired drug resistance is frequent in nosocomial isolates of Pseudomonas spp. Acquired metallo-β-lactamases (MBL in pseudomonas spp. have recently emerged as one of the most worrisome resistance mechanism because of their capacity to hydrolyze all beta-lactam antibiotics including penicillins, cephalosporins and carbapenems, with the exception of aztreonam. Aim: To detect metallo-β-lactamase producing isolates of Pseudomonas aerugenosa from various clinical samples from patients admitted in our hospital. Material and methods : In this studyt we studied the prevalence, following standard methods of isolation and identification techniques of these bacteria from clinical materials Source : Samples of patients from different wards of S.S.G.Hosital are proceeded in Microbiology department , Medical College and S.S.G.Hospital Baroda. Results: Of total study of 150 isolates of Pseudomonas aeruginosa, 8 isolates are resistance to Imipenem . Of 8 samples , all are producing Metallo-Beta-Lactamase enzyme. Conclusion :Infection cause by MBL (metallo-β-lactamase positive isolates of Pseudomonas aerugenosa is important to identify because it poses not only therapeutic problem, but also a serious concern for infection control management. [National J of Med Res 2011; 1(2.000: 60-63

  13. Sample Size in Clinical Cardioprotection Trials Using Myocardial Salvage Index, Infarct Size, or Biochemical Markers as Endpoint

    DEFF Research Database (Denmark)

    Engblom, Henrik; Heiberg, Einar; Erlinge, David; Jensen, Svend Eggert; Nordrehaug, Jan Erik; Dubois-Randé, Jean-Luc; Halvorsen, Sigrun; Hoffmann, Pavel; Koul, Sasha; Carlsson, Marcus; Atar, Dan; Arheden, Håkan

    2016-01-01

    biochemical markers in clinical cardioprotection trials and how scan day affect sample size. METHODS AND RESULTS: Controls (n=90) from the recent CHILL-MI and MITOCARE trials were included. MI size, MaR, and MSI were assessed from CMR. High-sensitivity troponin T (hsTnT) and creatine kinase isoenzyme MB (CKMB......) levels were assessed in CHILL-MI patients (n=50). Utilizing distribution of these variables, 100 000 clinical trials were simulated for calculation of sample size required to reach sufficient power. For a treatment effect of 25% decrease in outcome variables, 50 patients were required in each arm using...... MSI compared to 93, 98, 120, 141, and 143 for MI size alone, hsTnT (area under the curve [AUC] and peak), and CKMB (AUC and peak) in order to reach a power of 90%. If average CMR scan day between treatment and control arms differed by 1 day, sample size needs to be increased by 54% (77 vs 50) to avoid...

  14. A psychometric evaluation of the Personality Assessment Inventory - short form clinical scales in an inpatient psychiatric sample.

    Science.gov (United States)

    Sinclair, Samuel J; Siefert, Caleb J; Shorey, Hal S; Antonius, Daniel; Shiva, Andrew; Kehl-Fie, Kendra; Blais, Mark A

    2009-12-30

    Few studies have assessed the psychometric properties of the Personality Assessment Inventory short-form (PAI-SF) clinical scales, and none have conducted these evaluations using participants from psychiatric inpatient units. The present study evaluated item-level tests of scaling assumptions of the PAI-SF using a large (N=503) clinical sample of participants who completed the PAI during their admission to a psychiatric inpatient unit. Internal consistency reliability was high across scales, and tests of item-scale convergence and discrimination generally confirmed hypothesized item groupings. Scale-level correlations supported unique variance being measured by each scale. Finally, agreement between the PAI short- and full-form scales was found to be high. The results are discussed with regards to scale interpretation. PMID:19879654

  15. Mapping the MMPI-2/MMPI-2-RF Restructured Clinical Scales Onto Mood Markers in an Israeli Sample.

    Science.gov (United States)

    Shkalim, Eleanor; Ben-Porath, Yossef S; Almagor, Moshe

    2016-01-01

    This study cross-culturally evaluated the Minnesota Multiphasic Personality Inventory-2/MMPI-2 Restructured Form (MMPI-2/MMPI-2-RF) emotion-focused Restructured Clinical (RC) Scales to examine whether their patterns of associations with positive affect (PA) and negative affect (NA) are as expected based on Tellegen, Watson, and Clark's ( 1999a , 1999b ) mood model. The sample was composed of 100 men and 133 women from psychiatric settings in Israel who completed the MMPI-2 and the Mood Check List (MCL; Zevon & Tellegen, 1982 ). Results indicated that RCd was substantially correlated with both PA and NA in opposite directions, and that RC2 and RC7 were more highly correlated with PA and NA, respectively. Further, when compared with their Clinical Scale counterparts, RC2 and RC7 exhibited comparable convergent validities and improved discriminant properties. Findings provide support for Tellegen et al.'s ( 2003 ) goal to link the RC scales to contemporary conceptualizations of mood. PMID:26960114

  16. Pancratistatin induces apoptosis in clinical leukemia samples with minimal effect on non-cancerous peripheral blood mononuclear cells

    Directory of Open Access Journals (Sweden)

    McNulty James

    2010-03-01

    Full Text Available Abstract Background Pancratistatin, a natural compound extracted from Hymenocallis littoralis, can selectively induce apoptosis in several cancer cell lines. In this ex vivo study, we evaluated the effect of pancratistatin on peripheral blood mononuclear cells obtained from 15 leukemia patients prior to clinical intervention of newly diagnosed patients, as well as others of different ages in relapse and at various disease progression states. Results Mononuclear cells from healthy volunteers and leukemia patients were exposed to 1 μM pancratistatin for up to 48 h. Irrespective of leukemia type, pancratistatin induced apoptosis in the leukemic samples, with minimal effects on non-cancerous peripheral blood mononuclear control cells. Conclusion Our results show that pancratistatin is an effective and selective anti-cancer agent with potential for advancement to clinical trials.

  17. German Screen for Child Anxiety Related Emotional Disorders (SCARED: Reliability, Validity, and Cross-Informant Agreement in a Clinical Sample

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    Wiegand-Grefe Silke

    2010-06-01

    Full Text Available Abstract Background The psychometric properties and cross-informant agreement of a German translation of the Screen for Child Anxiety Related Emotional Disorders (SCARED were assessed in a clinical sample Methods 102 children and adolescents in outpatient psychotherapy and their parents filled out the SCARED and Youth Self Report/Child Behaviour Checklist (YSR/CBCL. Results The German SCARED showed good internal consistency for both parent and self-report version, and proved to be convergently and discriminantly valid when compared with YSR/CBCL scales. Cross-informant agreement was moderate with children reporting both a larger number as well as higher severity of anxiety symptoms than their parents. Conclusion In conclusion, the German SCARED is a valid and reliable anxiety scale and may be used in a clinical setting

  18. The relationship between emotional intelligence and depression in a clinical sample

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    Luke A. Downey

    2008-06-01

    Full Text Available Background and Objectives: Although depression is a commonly occurring mental illness, research concerning strategies for early detection and prophylaxis has not until now focused on the possible utility of measures of Emotional Intelligence (EI as a potential predictive factor. The current study aimed to investigate the relationship between EI and a clinical diagnosis of depression in a cohort of adults. Methods: Sixty-two patients (59.70% female with a DSM-IV-TR diagnosis of a major affective disorder and 39 aged matched controls (56.40% female completed self-report instruments assessing EI and depression in a cross-sectional study. Results: Significant associations were observed between severity of depression and the EI dimensions of Emotional Management (r = -0.56 and Emotional Control (r = -0.62. The results show a reduced social involvement, an increased prior institutionalization and an increased incidence of "Schizophrenic Psychosis" and "Abnormal Personalities" in the sub-group of repeated admissions. Conclusions: Measures of EI may have predictive value in terms of early identification of those at risk for developing depression. The current study points to the potential value of conducting further studies of a prospective nature.

  19. Brain structural correlates of schizotypy and psychosis proneness in a non-clinical healthy volunteer sample.

    Science.gov (United States)

    Nenadic, Igor; Lorenz, Carsten; Langbein, Kerstin; Dietzek, Maren; Smesny, Stefan; Schönfeld, Nils; Fañanás, Lourdes; Sauer, Heinrich; Gaser, Christian

    2015-10-01

    Schizotypal traits are phenotypic risk factors for schizophrenia, associated with biological changes across a putative schizophrenia spectrum. In this study, we tested the hypothesis that brain structural changes in key brain areas relevant to this spectrum (esp. medial and lateral prefrontal cortex) would vary across different degrees of schizotypal trait expression and/or phenotypic markers of psychosis proneness in healthy non-clinical volunteers. We analysed high-resolution 3Tesla magnetic resonance images (MRI) of 59 healthy volunteers using voxel-based morphometry (VBM), correlating grey matter values to the positive and negative symptom factors of the schizotypal personality questionnaire (SPQ, German version) and a measure of psychosis proneness (community assessment of psychic experiences, CAPE). We found positive correlations between positive SPQ dimension and bilateral inferior and right superior frontal cortices, and positive CAPE dimension and left inferior frontal cortex, as well as CAPE negative dimension and right supplementary motor area (SMA) and left inferior parietal cortex. However, only the positive correlation of the right precuneus with negative schizotypy scores was significant after FWE correction for multiple comparisons. Our findings confirm an effect of schizotypal traits and psychosis proneness on brain structure in healthy subjects, providing further support to a biological continuum model. PMID:26164819

  20. Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples

    DEFF Research Database (Denmark)

    Hansen, Kasper Lage; Szallasi, Zoltan Imre; Eklund, Aron Charles; Gyorffy, B; Molnar, B

    2009-01-01

    Several preprocessing algorithms for Affymetrix gene expression microarrays have been developed, and their performance on spike-in data sets has been evaluated previously. However, a comprehensive comparison of preprocessing algorithms on samples taken under research conditions has not been...... performed. METHODOLOGY/PRINCIPAL FINDINGS: We used TaqMan RT-PCR arrays as a reference to evaluate the accuracy of expression values from Affymetrix microarrays in two experimental data sets: one comprising 84 genes in 36 colon biopsies, and the other comprising 75 genes in 29 cancer cell lines. We...... evaluated consistency using the Pearson correlation between measurements obtained on the two platforms. Also, we introduce the log-ratio discrepancy as a more relevant measure of discordance between gene expression platforms. Of nine preprocessing algorithms tested, PLIER+16 produced expression values that...

  1. [The Dresden Body Image Inventory (DKB-35): validity in a clinical sample].

    Science.gov (United States)

    Pöhlmann, Karin; Roth, Marcus; Brähler, Elmar; Joraschky, Peter

    2014-03-01

    The Dresden Body Image Questionnaire (DKB-35) measures 5 dimensions of body image: vitality, self-acceptance, self-aggrandisement, physical closeness, and sexual fulfilment. This article presents data on the reliability and validity of the DKB-35. The sample consisted of 560 pa-tients with psychosomatic disorders. To analyse the factor structure, a confirmatory factor analysis was conducted. To examine the convergent validity, correlations between the DKB-35 scales and the Frankfurt Body Concept Scales (FKKS, [1]), the Narcissism Personality Inventory (NPI, [2]) and the self-esteem subscale of the Frankfurt Self-Concept Scales (FSKN, [3]) were computed. The 5 scales of the DKB-35 showed excellent reliability. Between the 5 DKB-35 scales and the corresponding scales of the FKKS, the NPI, and the FSKN, moderate correlations were found. The results confirm the reliability and validity of the DKB-35. Possible fields of applications and further developments are discussed. PMID:23966276

  2. Neuropsychological Profiles Correlated with Clinical and Behavioral Impairments in a Sample of Brazilian Children with Attention-Deficit Hyperactivity Disorder

    Science.gov (United States)

    Rizzutti, Sueli; Schuch, Viviane; Augusto, Bruno Muszkat; Coimbra, Caio Colturato; Pereira, João Pedro Cabrera; Bueno, Orlando Francisco Amodeo

    2015-01-01

    Attention-deficit hyperactivity disorder (ADHD) is a complex neurodevelopmental disorder that implies several-step process, and there is no single test to diagnose both ADHD and associated comorbidities, such as oppositional-defiant disorder (ODD), anxiety disorder, depression, and certain types of learning disabilities. The purpose of the present study was to examine correlations between behavioral and clinical symptoms by administering an extensive neuropsychological battery to a sample of children and adolescents from a developing country. The sample was divided into three groups: non-ADHD, ADHD-non-comorbid, and ADHD + comorbidity. A full neuropsychological battery and clinical assessment found that 105 children met DSM-5 criteria, of whom 46.6% had the predominantly inattentive presentation, 37.3% had combined presentation, and 16% were predominantly hyperactive/impulsive presentation. The internal correlation between neuropsychological tests did not reach statistical significance in the comparison between ADHD and non-ADHD cases (p disorder showed close correlations between clinical CBCL profiles and externalized symptoms. Our findings suggest that ADHD + comorbidity and ADHD non-comorbid cases may be differentiated by a number of neuropsychological measures, such as processing speed, inhibitory control, and working memory, that may reflect different levels of involvement of the hot and cool executive domains, which are more impaired in cases of severe symptomatic-externalized behavior and emotional regulation problems. Therefore, profiles based on clinical and behavioral findings can help clinicians select better strategies for detecting neuropsychological impairment in Brazilian children with ADHD. PMID:26635638

  3. A factor analytic investigation of the Tripartite model of affect in a clinical sample of young Australians

    Directory of Open Access Journals (Sweden)

    Cosgrave Elizabeth M

    2008-09-01

    Full Text Available Abstract Background The Mood and Anxiety Symptom Questionnaire (MASQ was designed to specifically measure the Tripartite model of affect and is proposed to offer a delineation between the core components of anxiety and depression. Factor analytic data from adult clinical samples has shown mixed results; however no studies employing confirmatory factor analysis (CFA have supported the predicted structure of distinct Depression, Anxiety and General Distress factors. The Tripartite model has not been validated in a clinical sample of older adolescents and young adults. The aim of the present study was to examine the validity of the Tripartite model using scale-level data from the MASQ and correlational and confirmatory factor analysis techniques. Methods 137 young people (M = 17.78, SD = 2.63 referred to a specialist mental health service for adolescents and young adults completed the MASQ and diagnostic interview. Results All MASQ scales were highly inter-correlated, with the lowest correlation between the depression- and anxiety-specific scales (r = .59. This pattern of correlations was observed for all participants rating for an Axis-I disorder but not for participants without a current disorder (r = .18. Confirmatory factor analyses were conducted to evaluate the model fit of a number of solutions. The predicted Tripartite structure was not supported. A 2-factor model demonstrated superior model fit and parsimony compared to 1- or 3-factor models. These broad factors represented Depression and Anxiety and were highly correlated (r = .88. Conclusion The present data lend support to the notion that the Tripartite model does not adequately explain the relationship between anxiety and depression in all clinical populations. Indeed, in the present study this model was found to be inappropriate for a help-seeking community sample of older adolescents and young adults.

  4. Relationship between acne vulgaris and attention-deficit/hyperactivity disorder symptoms in a clinical sample of women.

    Science.gov (United States)

    Bilgic, Ayhan; Bilgic, Özlem; Çolak, Rukiye Sivri; Altınyazar, Hilmi Cevdet

    2016-04-01

    Acne vulgaris has recently been reported to be associated with elevated rates of attention deficit/hyperactivity disorder in epidemiological studies. This report examines childhood and current attention-deficit/hyperactivity disorder symptoms in a clinical sample of female adults. Ninety-one women with acne vulgaris and 53 controls were included in this study. The aforementioned symptoms were measured in participants. No significant differences were found between patients and controls in any of the measurements. Contrary to the findings of epidemiological studies, this study did not uncover a link between acne vulgaris and attention-deficit/hyperactivity disorder. PMID:27192533

  5. A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies

    DEFF Research Database (Denmark)

    Grønbæk, Kirsten; Müller-Tidow, Carsten; Perini, Giovanni; Lehmann, Sören; Bach Treppendahl, Marianne; Mills, Ken; Plass, Christoph; Schlegelberger, Brigitte

    2012-01-01

    provide the pros and cons of the currently most feasible methods used for characterizing the methylome in clinical samples, and give a brief introduction to novel approaches to sequencing that may revolutionize our abilities to characterize the genomes and epigenomes in acute myeloid leukemia and......, prognostication and to monitor minimal residual disease. In addition, we now have the capability to pharmaceutically target epigenetic modifications, and there is an urgent need for early validation of the efficacy of the drugs. Also, an improved understanding of the functionality of epigenetic modifications may...

  6. Performance of the Liaison XL Murex HIV Ab/Ag Test on Clinical Samples Representing Current Epidemic HIV Variants

    OpenAIRE

    Lemee, Véronique; Leoz, Marie; Etienne, Manuel; De Oliveira, Fabienne; Plantier, Jean-Christophe

    2014-01-01

    Screening for HIV infection has improved since the first immunoassays. Today, diagnosis of HIV infection can be performed with fourth-generation tests that track both the patient's antibodies and HIV antigen. The objective of this study was to evaluate the clinical sensitivity and specificity of the new DiaSorin Liaison XL Murex HIV Ab/Ag assay compared to another fourth-generation assay, the Abbott Architect HIV Ag/Ab Combo kit. This work was performed on a large panel of 900 samples, includ...

  7. tetA and tetB Genes in Klebsiella Pneumoniae Isolated From Clinical Samples

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    Bokaeian

    2014-05-01

    Full Text Available Background The emergence of antibiotic resistance among clinical and nonclinical bacteria is a global public health problem. Klebsiella Pneumoniae is one of the most pathogens that contains a variety of gens and shows resistance to many antibiotics. Perpetual monitoring of the resistant bacteria is an important in order to limit the development of resistance among these pathogens. Objectives The current study aimed to monitor the prevalence of tetA and tetB resistance genes in Klebsiella Pneumoniae species isolated from the patients with urinary tract infection who hospitalized in Mir Hospital of Zabol, Iran from 2011 to 2012. Materials and Methods In the present cross-sectional study, a total of 30 strains of K. pneumoniae were isolated from urine cultures of hospitalized patients in Mir Hospital (Zabol, south-east of Iran who had urinary tract infections from 2011 to 2012. Antibiotic susceptibility of isolates was evaluated for four antibiotics including ceftazidime, cefixime, tetracycline and erythromycin using standard Kirby-Bauer disk diffusion method. The K. pneumoniae genome was extracted by simple boiling method, and polymerase chain reaction (PCR method also was used to detect tetA and tetB genes by specific pair of primers. Results The K. pneumonia isolates were resistant to erythromycin (70%, cefixime (53.3%, tetracycline (50% and ceftazidime (36.6%. The amplification of tetA and tetB genes of K. pneumonia revealed that all of the isolates harbored these genes. Conclusions Resistance to tetracycline and other antibiotics, and the presence of various resistance genes in K. pneumonia strains are alarming signs in Zabol area. The current study strongly recommends limiting the consumption of antibiotics including tetracycline. Further studies should be conducted in order to find out the extent of the problem in other areas.

  8. Implementation of formalin-fixed, paraffin-embedded cell line pellets as high-quality process controls in quality assessment programs for KRAS mutation analysis

    DEFF Research Database (Denmark)

    Dijkstra, Jeroen R; Opdam, Frank J M; Boonyaratanakornkit, Jerry;

    2013-01-01

    control sample. We assessed a novel synthetic control for formalin-fixed, paraffin-embedded (FFPE) tumor samples in a blind study conducted within nine laboratories across Europe. We show that FFPE material can, at least in part, mimic clinical samples and we demonstrate this control to be a valuable tool...

  9. The resilience scale for adults in italy: A validation study comparing clinical substance abusers with a nonclinical sample.

    Science.gov (United States)

    Bonfiglio, Natale Salvatore; Renati, Roberta; Hjemdal, Odin; Friborg, Oddgeir

    2016-06-01

    This article reports a validation study of the Italian version of the Resilience Scale for Adults (RSA), a measure designed to assess individual, family, and social resilience protective resources. The RSA was administered to a clinical (i.e., substance use disorders, or SUD; N = 437) and a nonclinical sample (N = 337). A confirmatory factor analyses supported the original 6-factor structure of the RSA in both samples. The RSA correlated positively with functional coping strategies and negatively with perceived stress and dysfunctional coping strategies. Moreover, the RSA subscales discriminated between SUD and non-SUD individuals. Factorial invariance testing also confirmed comparable psychometric properties across gender. The results confirm good psychometric properties of the Italian RSA and provide support for the construct validity of the scale. The RSA may be suited for use in studies examining natural course and intervention trials. (PsycINFO Database Record PMID:27031088

  10. Associations of Age, Gender, and Subtypes With ADHD Symptoms and Related Comorbidity in a Danish Sample of Clinically Referred Adults

    DEFF Research Database (Denmark)

    Soendergaard, Helle Moeller; Thomsen, Per Hove; Pedersen, Erik;

    2015-01-01

    Objective: The aim was to examine associations of age and gender with ADHD subtypes and subsequently to examine associations of age, gender, and subtypes with comorbid psychiatric disorders. Method: Odds ratios were calculated and logistic regression performed using information from a clinical...... sample of 155 ADHD adults referred to a Danish specialized ADHD unit from 2010 to 2011. Results: A majority of men (65%) was found in the sample. Most patients were subtyped ADHD combined (78%), followed by ADHD inattentive (18%), and ADHD hyperactive-impulsive (4%). No significant differences were found...... in gender and age across subtypes. Current comorbid disorders were found in 57% of the ADHD patients. Significantly more comorbidity was found in the ADHD combined type and in patients ≥25 years. Significantly more men had substance use disorders and significantly more women had personality disorders...

  11. DETECTION & PREVALENCE OF EXTENDED SPECTRUM ΒETA - LACTAMASES AMONG ENTEROBACTERIACEAE SPECIES FROM VARIOUS CLINICAL SAMPLES AT KIMS, AMALAPURAM.

    Directory of Open Access Journals (Sweden)

    Padmaja

    2012-10-01

    Full Text Available ABSTRACT: The present study was conducted in the Department of Microbiology, KIMS, Amalapuram, East Godavari from January 2012 to July 2012. Out of 100 different clinical samples, 50 were culture positive. Of the 100 samples collected, more were from post operative wound sepsis - 44 (44%, followed by cellulites - 20 (20%, Ulcers - 17 (17%, Injuries 15 (15%. Least number of cases are from burns - 4 (4% . Among 50 culture positive cases, 38 (76% isolates belonged to Enterobacteriaceae famil y, followed by Pseudomonas aeruginosa - 8 (16%, followed by Staphylococcus aureus - 4 (8%. Among 38 of Enterobacteriaceae family isolates, 15 were ESBL producers. Among ESBL positiv e strains, more drug resistance was seen to Ceftazidime and Ampicillin (93.33%, followed by Ceftriaxone (86.66%, Aztreonam & Cefotaxime (80%.

  12. A confirmatory factor analysis of the cognitive capacity screening examination in a clinical sample.

    Science.gov (United States)

    Anderson, D A; Burton, D B; Parker, J D; Godding, P R

    2001-01-01

    Structured mental status examinations offer several advantages over unstructured mental status examinations; however, few have been subjected to advanced psychometric analysis. Confirmatory factor analysis empirically tests the predictive validity of individual test indices within an a priori methodological framework. With such analysis, one can test hypotheses about the structure of latent variability within a given data set. The purpose of this study was to perform a confirmatory factor analysis of the Cognitive Capacity Screening Examination, the most comprehensive of the brief structured mental status examinations. A confirmatory factor analysis of the Cognitive Capacity Screening Examination (CCSE) was performed by applying LISREL 7 to a sample of 924 male veterans, 409 patients from a chemical dependence treatment program, and 515 individuals from a psychology consultation service. Constructs were derived from previous exploratory analysis of the scale. The results of the confirmatory factor analysis and three indices of model fit support an 11 factor model more complex than that originally formulated for the CCSE. However, three of these factors (digit span with interference, complex mental mathematics, and verbal memory) were more sensitive to impairment than other factors, accounting for over 90% of the CCSE total score variance. Although the CCSE is a more complex test than originally envisioned by its designers, it may not be necessary to give all items on the test. Either a subset of the CCSE items (the CCSE-A) or a relatively brief, informal mental status exam may be adequate for many patients. PMID:11912677

  13. Using co-occurrence to evaluate belief coherence in a large non clinical sample.

    Directory of Open Access Journals (Sweden)

    Rachel Pechey

    Full Text Available Much of the recent neuropsychological literature on false beliefs (delusions has tended to focus on individual or single beliefs, with few studies actually investigating the relationship or co-occurrence between different types of co-existing beliefs. Quine and Ullian proposed the hypothesis that our beliefs form an interconnected web in which the beliefs that make up that system must somehow "cohere" with one another and avoid cognitive dissonance. As such beliefs are unlikely to be encapsulated (i.e., exist in isolation from other beliefs. The aim of this preliminary study was to empirically evaluate the probability of belief co-occurrence as one indicator of coherence in a large sample of subjects involving three different thematic sets of beliefs (delusion-like, paranormal & religious, and societal/cultural. Results showed that the degree of belief co-endorsement between beliefs within thematic groupings was greater than random occurrence, lending support to Quine and Ullian's coherentist account. Some associations, however, were relatively weak, providing for well-established examples of cognitive dissonance.

  14. Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Sterile or Nonsterile Clinical Samples by a New Molecular Assay

    Science.gov (United States)

    Francois, Patrice; Pittet, Didier; Bento, Manuela; Pepey, Béatrice; Vaudaux, Pierre; Lew, Daniel; Schrenzel, Jacques

    2003-01-01

    A rapid procedure was developed for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) directly from sterile sites or mixed flora samples (e.g., nose or inguinal swabs). After a rapid conditioning of samples, the method consists of two main steps: (i) immunomagnetic enrichment in S. aureus and (ii) amplification-detection profile on DNA extracts using multiplex quantitative PCR (5′-exonuclease qPCR, TaqMan). The triplex qPCR assay measures simultaneously the following targets: (i) mecA gene, conferring methicillin resistance, common to both S. aureus and Staphylococcus epidermidis; (ii) femA gene from S. aureus; and (iii) femA gene from S. epidermidis. This quantitative approach allows discrimination of the origin of the measured mecA signal. qPCR data were calibrated using two reference strains (MRSA and methicillin-resistant S. epidermidis) processed in parallel to clinical samples. This 96-well format assay allowed analysis of 30 swab samples per run and detection of the presence of MRSA with exquisite sensitivity compared to optimal culture-based techniques. The complete protocol may provide results in less than 6 h (while standard procedure needs 2 to 3 days), thus allowing prompt and cost-effective implementation of contact precautions. PMID:12517857

  15. Sub-2 μm chromatography and fast flow injection analysis for high-throughput analysis of clinical samples

    International Nuclear Information System (INIS)

    Complete text of publication follows. In HPLC the size of commercially available particles has been recently extended to 1.8 and 1.5 μm leading to an immense improvement of both chromatographic and economic efficiency due to the higher chromatographic resolution and the possibility of shorter cycle times. The present work aimed at the development and assessment of a high-throughput HPLC method for accurate quantification of oxaliplatin in clinical samples. A sub-2 μm stationary phase has been evaluated for complementary speciation of oxaliplatin via HPLC-ICP-MS and HPLC-ESI-TOFMS. We have selected ICP-QMS and ESI-TOFMS as chromatographic detectors, since both mass spectrometers are providing satisfactory time constants and sampling rates for a combination with ultra-fast HPLC. The two instruments were compared evaluating their detection capabilities and influence on the chromatographic performance. The second part of the presentation deals with the implementation of fast flow injection set-up for rapid analysis of clinically relevant elements with ICP-SFMS. First results will be presented.

  16. Alexithymia and its relationships with body checking and body image in a non-clinical female sample.

    Science.gov (United States)

    De Berardis, Domenico; Carano, Alessandro; Gambi, Francesco; Campanella, Daniela; Giannetti, Paola; Ceci, Anna; Mancini, Enrico; La Rovere, Raffaella; Cicconetti, Alessandra; Penna, Laura; Di Matteo, Danilo; Scorrano, Barbara; Cotellessa, Carla; Salerno, Rosa Maria; Serroni, Nicola; Ferro, Filippo Maria

    2007-08-01

    The aim of the present study was to evaluate in a non-clinical sample of undergraduate women, the relationships between alexithymia, body checking and body image, identifying predictive factors associated with the possible risk of developing an Eating Disorder (ED). The Toronto Alexithymia Scale (TAS-20), Body Checking Questionnaire (BCQ), Eating Attitudes Test (EAT-26), Body Shape Questionnaire (BSQ), Interaction Anxiousness Scale (IAS), Rosenberg Self-Esteem Scale (RSES) and the Beck Depression Inventory (BDI) were completed by 254 undergraduate females. We found that alexithymics had more consistent body checking behaviors and higher body dissatisfaction than nonalexithymics. In addition, alexithymics also reported a higher potential risk for ED (higher scores on EAT-26) when compared to nonalexithymics. Difficulty in identifying and describing feelings subscales of TAS-20, Overall appearance and Specific Body Parts subscales of BCQ as well as lower self-esteem was associated with higher ED risk in a linear regression analysis. Thus, a combination of alexithymia, low self-esteem, body checking behaviors and body dissatisfaction may be a risk factor for symptoms of ED at least in a non-clinical sample of university women. PMID:17606227

  17. A pressure cooking-based DNA extraction from archival formalin fixed, paraffin embedded tissue

    OpenAIRE

    Chung, Joon-Yong; Yi, Joo Mi; Xie, Ran; Brown, Victoria; Lee, Olivia; Ahuja, Nita; Braunschweig, Till; Hewitt, Stephen M.

    2012-01-01

    As emerging novel DNA-based methodologies are adopted, nucleic acid-based assays depend critically on the quality and quantity of extracted DNA. Formalin fixed, paraffin embedded (FFPE) tissue samples provide an invaluable resource for subsequent molecular studies of clinical phenotypes, but high quality DNA extraction from archival FFPE tissue specimen remains complex and time consuming. To address this challenge, we have developed a reliable rapid DNA extraction method for FFPE tissue speci...

  18. Morphological and clinical characteristics of the torus palatinus and torus mandibularis in a sample of young and adults' Romanian people.

    Science.gov (United States)

    Scrieciu, Monica; MercuŢ, Veronica; MercuŢ, Răzvan; Bîrjovanu, Carrol; Stan, Mihaela Cristina; Marinescu, Iulia Roxana; Niculescu, Mihaela; Iorgulescu, Daniel; Bătăiosu, Marilena

    2016-01-01

    The oral exostoses are protuberance located on the alveolar surfaces of the jawbones with nodular, flat or pedunculated shape. The purpose of this study was to highlight the variability of the morphological and clinical characteristics of torus palatinus (TP) and torus mandibularis (TM) in a sample of young and adults' Romanian people. The study was conducted on 74 participants examined in Dental Prosthetics Clinic of the Faculty of Dentistry, University of Medicine and Pharmacy of Craiova, Romania, during October-December 2014. The morphological characteristics of the tori were non-metrical evaluated by the standard procedures of the clinical examination. Descriptive statistics only including means, averages and percentage incidence have been used to describe the results. Of the 74 study participants, 31 (41.89%) were males and 43 (55.40%) were females. Six had only TP, seven had only TM and three participants had both TP and TM. The most of the palatal tori had spindle shaped, located in all area of the hard palate The round mandibular tori with big size were located in the area of both premolars, and those with elongate shape were located in the canine-premolars area. The palatal tori were more frequently in women and the frequency of mandibular tori was equally in men and women. Most of the palatal tori had spindle shape and most of the mandibular tori were solitary bilateral. PMID:27151699

  19. Embedded Measures of Performance Validity in the Rey Complex Figure Test in a Clinical Sample of Veterans.

    Science.gov (United States)

    Sugarman, Michael A; Holcomb, Erin M; Axelrod, Bradley N; Meyers, John E; Liethen, Philip C

    2016-01-01

    The purpose of this study was to determine how well scores from the Rey Complex Figure Test (RCFT) could serve as embedded measures of performance validity in a large, heterogeneous clinical sample at an urban-based Veterans' Affairs hospital. Participants were divided into credible performance (n = 244) and noncredible performance (n = 87) groups based on common performance validity tests during their respective clinical evaluations. We evaluated how well preselected RCFT scores could discriminate between the 2 groups using cut scores from single indexes as well as multivariate logistic regression prediction models. Additionally, we evaluated how well memory error patterns (MEPs) could discriminate between the 2 groups. Optimal discrimination occurred when indexes from the Copy and Recognition trials were simultaneous predictors in logistic regression models, with 91% specificity and at least 53% sensitivity. Logistic regression yielded superior discrimination compared with individual indexes and compared with the use of MEPs. Specific scores on the RCFT, including the Copy and Recognition trials, can serve as adequate indexes of performance validity, when using both cut scores and logistic regression prediction models. We provide logistic regression equations that can be applied in similar clinical settings to assist in determining performance validity. PMID:26384155

  20. Comparison of Enterococcus faecium and Enterococcus faecalis Strains isolated from water and clinical samples: antimicrobial susceptibility and genetic relationships.

    Directory of Open Access Journals (Sweden)

    Gonzalo Castillo-Rojas

    Full Text Available Enterococci are part of the normal intestinal flora in a large number of mammals, and these microbes are currently used as indicators of fecal contamination in water and food for human consumption. These organisms are considered one of the primary causes of nosocomial and environmental infections due to their ability to survive in the environment and to their intrinsic resistance to antimicrobials. The aims of this study were to determine the biochemical patterns and antimicrobial susceptibilities of Enterococcus faecalis and E. faecium isolates from clinical samples and from water (groundwater, water from the Xochimilco wetland, and treated water from the Mexico City Metropolitan Area and to determine the genetic relationships among these isolates. A total of 121 enterococcus strains were studied; 31 and 90 strains were isolated from clinical samples and water (groundwater, water from the Xochimilco wetland, and water for agricultural irrigation, respectively. Identification to the species level was performed using a multiplex PCR assay, and antimicrobial profiles were obtained using a commercial kit. Twenty-eight strains were analyzed by pulsed-field gel electrophoresis (PFGE. E. faecium strains isolated from water showed an atypical biochemical pattern. The clinical isolates showed higher resistance to antibiotics than those from water. Both the enterococci isolated from humans, and those isolated from water showed high genetic diversity according to the PFGE analysis, although some strains seemed to be closely related. In conclusion, enterococci isolated from humans and water are genetically different. However, water represents a potential route of transmission to the community and a source of antimicrobial resistance genes that may be readily transmitted to other, different bacterial species.

  1. Identification by FFPE RNA-Seq of a new recurrent inversion leading to RBM10-TFE3 fusion in renal cell carcinoma with subtle TFE3 break-apart FISH pattern.

    Science.gov (United States)

    Just, Pierre-Alexandre; Letourneur, Franck; Pouliquen, Christelle; Dome, Florence; Audebourg, Anne; Biquet, Philippe; Vidaud, Michel; Terris, Benoit; Sibony, Mathilde; Pasmant, Eric

    2016-06-01

    Gene fusions involving TFE3 defines the "Xp11.2 translocations" subclass of renal cell carcinomas (RCCs) belonging to the MiT family translocation RCC. Four recurrent TFE3 fusion partners were identified to date: PRCC, ASPSCR1, SFPQ, and NONO. Break-apart TFE3 fluorescence in situ hybridization (FISH) on formalin-fixed and paraffin-embedded (FFPE) tissue sections is currently the gold standard for identification of TFE3 rearrangements. Herein, we report a case of RCC with a morphological appearance of Xp11.2 translocation, and positive TFE3 immunostaining. By FISH, the spots constituting the split signal were barely spaced, suggestive of a chromosome X inversion rather than a translocation. We performed RNA-seq from FFPE material to test this hypothesis. RNA-seq suggested a fusion of RBM10 gene exon 17 (Xp11.23) with TFE3 gene exon 5 (Xp11.2). RBM10-TFE3 fusion transcript was confirmed using specific RT-PCR. Our work showed that RNA-Seq is a robust technique to detect fusion transcripts from FFPE material. A RBM10-TFE3 fusion was previously described in single case of Xp11.2 RCC. Although rare, RBM10-TFE3 fusion variant (from chromosome X paracentric inversion), therefore, appears to be a recurrent molecular event in Xp11.2 RCCs. RBM10-TFE3 fusion should be added in the list of screened fusion transcripts in targeted molecular diagnostic multiplex RT-PCR. © 2016 Wiley Periodicals, Inc. PMID:26998913

  2. Isolation, Identification, and In Vitro Antifungal Susceptibility Testing of Dermatophytes from Clinical Samples at Sohag University Hospital in Egypt

    Science.gov (United States)

    Shalaby, Mona Fattouh Mohamed; El-din, Asmaa Nasr; El-Hamd, Mohammed Abu

    2016-01-01

    Aim The objective of this study was to isolate, identify, and explore the in-vitro antifungal susceptibility pattern of dermatophytes isolated from clinically suspected cases of dermatophytosis (tinea infections) attending the Dermatology Outpatient Clinic. Methods This study was conducted at Sohag University Hospital from December 2014 to December 2015. Clinical samples (e.g., skin scrapings and hair stumps) were collected under aseptic precautions. The identification of dermatophytes was performed through microscopic examination using 10% potassium hydroxide (KOH) with 40% dimethyl sulphoxide (DMSO) mounts and culture on Sabouraud dextrose agar (SDA) and on Dermasel agar base media, both supplemented with chloramphenicol and cycloheximide. All dermatophytes isolates were subjected to antifungal susceptibility testing using the agar-based disk diffusion (ABDD) method against Clotrimazole, Miconazole, Fluconazole, and Griseofulvin. Data were analyzed via SPSS 16, using Chi square and a screening test (cross-tabulation method). Results A total of 110 patients of dermatophytosis were studied. The patients were clinically diagnosed and mycologically confirmed as having tinea capitis (49), tinea corporis (30), tinea pedis (16), tinea cruris (9), or tinea barbae (6). The dermatophytes isolates belonged to 4 species: Microsporum canis 58 (52.7%), Microsporum gypseum 23 (20.9%), Trichophyton mentagrophytes 18 (16.4%), and Microsporum audouinii 11 (10%). The most effective antifungal drugs tested were Clotrimazole, followed by Miconazole (95.5% and 84.5% of isolates were susceptible, respectively). Conclusion Every patient with a tinea infection should be properly studied for a mycological examination and should be treated accordingly. Dermasel agar is more useful as an identification medium in the isolation of dermatophytes. The ABDD method appears to be a simple, cost-effective, and promising method for the evaluation of antifungal susceptibility of dermatophytes. PMID

  3. Measurement of DSM-5 section II personality disorder constructs using the MMPI-2-RF in clinical and forensic samples.

    Science.gov (United States)

    Anderson, Jaime L; Sellbom, Martin; Pymont, Carly; Smid, Wineke; De Saeger, Hilde; Kamphuis, Jan H

    2015-09-01

    In the current study, we evaluated the associations between the Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF; Ben-Porath & Tellegen, 2008) scale scores and the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5; American Psychiatric Association, 2013) Section II personality disorder (PD) criterion counts in inpatient and forensic psychiatric samples from The Netherlands using structured clinical interviews to operationalize PDs. The inpatient psychiatric sample included 190 male and female patients and the forensic sample included 162 male psychiatric patients. We conducted correlation and count regression analyses to evaluate the utility of relevant MMPI-2-RF scales in predicting PD criterion count scores. Generally, results from these analyses emerged as conceptually expected and provided evidence that MMPI-2-RF scales can be useful in assessing PDs. At the zero-order level, most hypothesized associations between Section II disorders and MMPI-2-RF scales were supported. Similarly, in the regression analyses, a unique set of predictors emerged for each PD that was generally in line with conceptual expectations. Additionally, the results provided general evidence that PDs can be captured by dimensional psychopathology constructs, which has implications for both DSM-5 Section III specifically and the personality psychopathology literature more broadly. PMID:25799092

  4. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma

    OpenAIRE

    Van Allen, Eliezer M.; Wagle, Nikhil; Sucker, Antje; Treacy, Daniel; Johannessen, Cory; Goetz, Eva M.; Place, Chelsea S.; Taylor-Weiner, Amaro; Whittaker, Steven; Kryukov, Gregory; Hodis, Eran; Rosenberg, Mara; McKenna, Aaron; Cibulskis, Kristian; Farlow, Deborah

    2013-01-01

    Most patients with BRAFV600 metastatic melanoma develop resistance to selective RAF kinase inhibitors. The spectrum of clinical genetic resistance mechanisms to RAF inhibitors and options for salvage therapy are incompletely understood. We performed whole exome sequencing on formalin-fixed, paraffin embedded (FFPE) tumors from 45 patients with BRAFV600 metastatic melanoma who received vemurafenib or dabrafenib monotherapy. Genetic alterations in known or putative RAF inhibitor resistance gene...

  5. WITHDRAWN: Clinical fitting of CAD/CAM zirconia single crowns generated from digital intraoral impressions based on active wavefront sampling.

    Science.gov (United States)

    Scotti, Roberto; Cardelli, Paolo; Baldissara, Paolo; Monaco, Carlo

    2011-10-17

    OBJECTIVES: The aim of this clinical trial was to test the accuracy of single all-ceramic zirconia crowns resulting from digital intraoral impressions with active wavefront sampling technology by measuring the marginal and internal fits of the crowns. MATERIALS AND METHODS: Thirty-seven teeth (24 anterior and 13 posterior) in fifteen patients were restored with single zirconia-ceramic crowns (Lava/Lava Ceram; 3M ESPE) generated from a digital intraoral scanner (Lava Chairside Oral Scanner; 3M ESPE). Before definitive insertion, silicone replicas were produced for all 37 crowns. The sample was cut in four sections; each section was evaluated in four points: marginal gap, mid-axial wall, axio-occlusal edge and centro-occlusal. A total of 592 measurements (148 for each evaluation point) was examined using stereomicroscopy with a magnification of 50×. The Mann-Whitney U test was used to evaluate whether there were differences between anterior and posterior values (alpha=0.05). RESULTS: The mean values for each point were: 48.65μm (SD 29.45μm) for the marginal gap, 112.25μm (SD 55.54μm) at the mid-axial wall, 137.81μm (SD 71.31μm) at the axio-occlusal edge of the abutments, and 157.25μm (SD 75.51μm) at the centro-occlusal location. No statistical differences were found between the anterior and posterior group for each point (p-values: P1=0.39; P2=0.38; P3=0.07; P4=0.30). CONCLUSIONS: The marginal and internal fitting values obtained were within literature agreed as clinically acceptable for both anterior and posterior teeth. CLINICAL RELEVANCE: Single crown restorations obtained using digital intraoral impressions based on active wavefront sampling technology presented enough accuracy to be used as an alternative to the conventional impression techniques. PMID:22027653

  6. A Novel Quantitative Sampling Technique for Detection and Monitoring of Clostridium difficile Contamination in the Clinical Environment.

    Science.gov (United States)

    Ali, Shanom; Muzslay, Monika; Wilson, Peter

    2015-08-01

    The horizontal transmission of Clostridium difficile in the hospital environment is difficult to establish. Current methods to detect C. difficile spores on surfaces are not quantitative, lack sensitivity, and are protracted. We propose a novel rapid method to detect and quantify C. difficile contamination on surfaces. Sponge swabbing was compared to contact plate sampling to assess the in vitro recovery of C. difficile ribotype 027 contamination (∼10(0), 10(1), or 10(2) CFU of spores) from test surfaces (a bed rail, a stainless steel sheet, or a polypropylene work surface). Sponge swab contents were concentrated by vacuum filtration, and the filter membrane was plated onto selective agar. The efficacy of each technique for the recovery of C. difficile from sites in the clinical environment that are touched at a high frequency was evaluated. Contact plates recovered 19 to 32% of the total contamination on test surfaces, whereas sponge swabs recovered 76 to 94% of the total contamination, and contact plates failed to detect C. difficile contamination below a detection limit of 10 CFU/25 cm(2) (0.4 CFU/cm(2)). In use, contact plates failed to detect C. difficile contamination (0/96 contact plates; 4 case wards), while sponge swabs recovered C. difficile from 29% (87/301) of the surfaces tested in the clinical environment. Approximately 74% (36/49) of the area in the vicinity of the patient was contaminated (∼1.34 ± 6.88 CFU/cm(2) C. difficile spores). Reservoirs of C. difficile extended to beyond the areas near the patient: a dirty utility room sink (2.26 ± 5.90 CFU/cm(2)), toilet floor (1.87 ± 2.40 CFU/cm(2)), and chair arm (1.33 ± 4.69 CFU/cm(2)). C. difficile was present on floors in ∼90% of case wards. This study highlights that sampling with a contact plate may fail to detect C. difficile contamination and result in false-negative reporting. Our sponge sampling technique permitted the rapid and quantitative measurement of C. difficile contamination on

  7. Genotyping of human parvovirus B19 in clinical samples from Brazil and Paraguay using heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing

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    Marcos César Lima de Mendonça

    2011-06-01

    Full Text Available Heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing were utilised to genotype human parvovirus B19 samples from Brazil and Paraguay. Ninety-seven serum samples were collected from individuals presenting with abortion or erythema infectiosum, arthropathies, severe anaemia and transient aplastic crisis; two additional skin samples were collected by biopsy. After the procedure, all clinical samples were classified as genotype 1.

  8. A clinical trial alert tool to recruit large patient samples and assess selection bias in general practice research

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    Scheidt-Nave Christa

    2011-02-01

    Full Text Available Abstract Background Many research projects in general practice face problems when recruiting patients, often resulting in low recruitment rates and an unknown selection bias, thus limiting their value for health services research. The objective of the study is to evaluate the recruitment performance of the practice staff in 25 participating general practices when using a clinical trial alert (CTA tool. Methods The CTA tool was developed for an osteoporosis survey of patients at risk for osteoporosis and fractures. The tool used data from electronic patient records (EPRs to automatically identify the population at risk (net sample, to apply eligibility criteria, to contact eligible patients, to enrol and survey at least 200 patients per practice. The effects of the CTA intervention were evaluated on the basis of recruitment efficiency and selection bias. Results The CTA tool identified a net sample of 16,067 patients (range 162 to 1,316 per practice, of which the practice staff reviewed 5,161 (32% cases for eligibility. They excluded 3,248 patients and contacted 1,913 patients. Of these, 1,526 patients (range 4 to 202 per practice were successfully enrolled and surveyed. This made up 9% of the net sample and 80% of the patients contacted. Men and older patients were underrepresented in the study population. Conclusion Although the recruitment target was unreachable for most practices, the practice staff in the participating practices used the CTA tool successfully to identify, document and survey a large patient sample. The tool also helped the research team to precisely determine a slight selection bias.

  9. Clinical and neuropsychological assessment of attention and ADHD comorbidity in a sample of children and adolescents with idiopathic epilepsy

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    Celia Regina Carvalho Machado da Costa

    2015-02-01

    Full Text Available Children with epilepsy present significant problems concerning attention and comorbidity with attention deficit hyperactivity disorder (ADHD. Objective To determine the prevalence of attention complaints, ADHD diagnosis and attention profile in a sample of children and adolescents with idiopathic epilepsy. Method 36 children and adolescents with idiopathic epilepsy and 37 genre and age matched healthy controls underwent several procedures to diagnose their neuropsychological profile and comorbidity with ADHD. Results The prevalence of ADHD was higher in patients with epilepsy [χ2= 4.1, p = 0.043, 6 (16.7% vs 1 (2.7%], with worse results in attention related WISC items and factors in patients with epilepsy comparing to the controls, but not between patients with and without ADHD. Clinical characteristics did not influence those results. Conclusion This study found a greater prevalence of problems wih attention in pediatric patients with idiopathic epilepsy, but not a distinct profile between those with or without ADHD.

  10. Validation of the Marijuana Effect Expectancies Questionnaire (MEEQ in a Non-Clinical French-Speaking Adolescent Sample

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    Emilie Schmits

    2016-02-01

    Full Text Available Teenagers commonly use cannabis. Expectancies related to the effects of cannabis play an important role in its consumption and are frequently measured with the Marijuana Effect Expectancies Questionnaire (MEEQ. This study aims to assess the psychometric properties (factor structure, internal consistency reliability, criterion validity of the French MEEQ. A sample of 1,343 non-clinical teenagers (14–18 years were recruited to answer a self-report questionnaire; 877 of them responded twice (one-year interval. A four-factor structure was obtained: Cognitive Impairment and Negative, Relaxation and Social Facilitation, Perceptual Enhancement and Craving and Negative Behavioral Effect Expectancies. It is concluded that the French MEEQ constitutes an appropriate tool to measure cannabis effect expectancies among adolescents.

  11. Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples

    OpenAIRE

    Bovee Judith VMG; Hogendoorn Pancras CW; Meijer Danielle; Verbeke Sofie LJ; de Jong Danielle; Szuhai Károly

    2011-01-01

    Abstract Background Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research. Findings The goal of our study w...

  12. Evaluation of the hyplex® TBC PCR test for detection of Mycobacterium tuberculosis complex in clinical samples

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    Hoffmann Harald

    2010-03-01

    Full Text Available Abstract Background Tuberculosis (TB is one of the major public health concerns worldwide. The detection of the pathogen Mycobacterium tuberculosis complex (MTBC as early as possible has a great impact on the effective control of the spread of the disease. In our study, we evaluated the hyplex® TBC PCR test (BAG Health Care GmbH, a novel assay using a nucleic acid amplification technique (NAAT with reverse hybridisation and ELISA read out for the rapid detection of M. tuberculosis directly in clinical samples. Results A total of 581 respiratory and non-respiratory specimens from our pneumological hospital and the National TB Institute of Uzbekistan were used for the evaluation of the PCR assay. Of these, 292 were classified as TB samples and 289 as non-TB samples based on the results of the TB cultures as reference method. The PCR results were initially used to optimise the cut-off value of the hyplex® TBC test system by means of a ROC analysis. The overall sensitivity of the assay was determined to be 83.1%. In smear-positive TB samples, the sensitivity of the hyplex® TBC PCR test was estimated to 93.4% versus 45.1% in smear-negative samples. The specificity of the test was 99.25%. Of the two specimens (0.75% with false-positive PCR results, one yielded a culture positive for non-tuberculous mycobacteria. Based on the assumption of a prevalence of 8% TB positives among the samples in our diagnostic TB laboratory, the positive and negative predictive values were estimated to 90.4% and 98.5%, respectively. Conclusions The hyplex® TBC PCR test is an accurate NAAT assay for a rapid and reliable detection of M. tuberculosis in various respiratory and non-respiratory specimens. Compared to many other conventional NAAT assays, the hyplex® TBC PCR test is in a low price segment which makes it an attractive option for developing and emerging countries with high TB burdens.

  13. Acceptability, effectiveness, and cost-effectiveness of internet-based exposure treatment for irritable bowel syndrome in a clinical sample: a randomized controlled trial

    OpenAIRE

    Andréewitch Sergej; Lindfors Perjohan; Hedman Erik; Andersson Erik; Andersson Gerhard; Ljótsson Brjánn; Rück Christian; Lindefors Nils

    2011-01-01

    Background: Internet-based cognitive behavior therapy (ICBT) has shown promising effects in the treatment of irritable bowel syndrome (IBS). However, to date no study has used a design where participants have been sampled solely from a clinical population. We aimed to investigate the acceptability, effectiveness, and cost-effectiveness of ICBT for IBS using a consecutively recruited sample from a gastroenterological clinic. less thanbrgreater than less thanbrgreater thanMethods: Sixty-one pat...

  14. Clinical expression of bipolar disorder type I as a function of age and polarity at onset: convergent findings in samples from France and the United States.

    OpenAIRE

    Etain, Bruno; Lajnef, Mohamed; Bellivier, Frank; Mathieu, Flavie; Raust, Aurélie; Cochet, Barbara; Gard, Sébastien; M'Bailara, Katia; Kahn, Jean-Pierre; Elgrabli, Orly; Cohen, Renaud,; Jamain, Stéphane; Vieta, Eduard; Leboyer, Marion; Henry, Chantal

    2012-01-01

    BACKGROUND: The clinical presentation, course, and comorbidities of bipolar disorder type I are highly heterogeneous, and this variability remains poorly predictable. Certain onset characteristics (eg, age and polarity at onset) may delineate subgroups differing in clinical expression and outcome. METHOD: We retrospectively investigated the association between both age and polarity at onset and the clinical characteristics of bipolar I disorder (DSM-IV) in 2 independent adult samples: 480 Fre...

  15. The Construct Validity of the Dutch Personality Inventory for DSM-5 Personality Disorders (PID-5) in a Clinical Sample.

    Science.gov (United States)

    Bastiaens, Tim; Claes, Laurence; Smits, Dirk; De Clercq, Barbara; De Fruyt, Filip; Rossi, Gina; Vanwalleghem, Dominique; Vermote, Rudi; Lowyck, Benedicte; Claes, Stephan; De Hert, Marc

    2016-02-01

    The factor structure and the convergent validity of the Personality Inventory for DSM-5 (PID-5), a self-report questionnaire designed to measure personality pathology as advocated in the fifth edition, Section III of Diagnostic and Statistical Manual of Mental Disorders (DSM-5), are already demonstrated in general population samples, but need replication in clinical samples. In 240 Flemish inpatients, we examined the factor structure of the PID-5 by means of exploratory structural equation modeling. Additionally, we investigated differences in PID-5 higher order domain scores according to gender, age and educational level, and explored convergent and discriminant validity by relating the PID-5 with the Dimensional Assessment of Personality Pathology-Basic Questionnaire and by comparing PID-5 scores of inpatients with and without a DSM-IV categorical personality disorder diagnosis. Our results confirmed the original five-factor structure of the PID-5. The reliability and the convergent and discriminant validity of the PID-5 proved to be adequate. Implications for future research are discussed. PMID:25736039

  16. A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

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    Granier Claude

    2008-10-01

    Full Text Available Abstract Background In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user. Results We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.. We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects. Conclusion Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.

  17. A fully integrated paperfluidic molecular diagnostic chip for the extraction, amplification, and detection of nucleic acids from clinical samples.

    Science.gov (United States)

    Rodriguez, Natalia M; Wong, Winnie S; Liu, Lena; Dewar, Rajan; Klapperich, Catherine M

    2016-02-21

    Paper diagnostics have successfully been employed to detect the presence of antigens or small molecules in clinical samples through immunoassays; however, the detection of many disease targets relies on the much higher sensitivity and specificity achieved via nucleic acid amplification tests (NAAT). The steps involved in NAAT have recently begun to be explored in paper matrices, and our group, among others, has reported on paper-based extraction, amplification, and detection of DNA and RNA targets. Here, we integrate these paper-based NAAT steps into a single paperfluidic chip in a modular, foldable system that allows for fully integrated fluidic handling from sample to result. We showcase the functionality of the chip by combining nucleic acid isolation, isothermal amplification, and lateral flow detection of human papillomavirus (HPV) 16 DNA directly from crude cervical specimens in less than 1 hour for rapid, early detection of cervical cancer. The chip is made entirely of paper and adhesive sheets, making it low-cost, portable, and disposable, and offering the potential for a point-of-care molecular diagnostic platform even in remote and resource-limited settings. PMID:26785636

  18. Anxiety and depression in parents of a Brazilian non-clinical sample of attention-deficit/ hyperactivity disorder (ADHD students

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    D. Segenreich

    2009-05-01

    Full Text Available Higher prevalence rates of anxiety and depression have been reported in parents of children with attention-deficit/hyperactivity disorder (ADHD. The interaction between the burden of ADHD in offspring, a higher prevalence rate of this highly inherited disorder in parents, and comorbidities may explain this finding. Our objective was to investigate levels of ADHD, anxious and depressive symptomatology, and their relationship in parents of ADHD children from a non-clinical sample using a dimensional approach. The sample included 396 students enrolled in all eight grades of a public school who were screened for ADHD using the SNAP IV rating scale. Positive cases were confirmed through a semi-structured interview. Parents of all 26 ADHD students and 31 paired controls were enrolled. A sample of 36 parents of ADHD children (21 mothers, 15 fathers and 30 parents of control children (18 mothers, 12 fathers completed the Adult Self Report Scale, State-Trait Anxiety Inventory, and Beck Depression Inventory in order to investigate anxious and depressive symptomatology. Probands' mothers presented a higher level of ADHD symptomatology (with only inattention being a significant cluster. Again, mothers of ADHD children presented higher depressive and anxiety levels; however, these did not correlate with their own ADHD symptomatology. Only trait-anxiety levels were higher in ADHD mothers. Our findings suggest that: 1 anxious and depressive symptoms might be more prevalent in mothers of ADHD students; 2 anxious and depressive symptomatology might be independent of impairment associated with ADHD symptoms; 3 anxious and depressive symptoms are independent of the presence of ADHD.

  19. Intestinal parasites and genotyping of Giardia duodenalis in children: first report of genotype B in isolates from human clinical samples in Mexico

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    Julio César Torres-Romero

    2014-06-01

    Full Text Available Giardia duodenalis is one of the most prevalent enteroparasites in children. This parasite produces several clinical manifestations. The aim of this study was to determine the prevalence of genotypes of G. duodenalis causing infection in a region of southeastern Mexico. G. duodenalis cysts were isolated (33/429 from stool samples of children and molecular genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP analysis, targeting the triosephosphate isomerase ( tpi and glutamate dehydrogenase ( gdh genes. The tpi gene was amplified in all of the cyst samples, either for assemblage A (27 samples or assemblage B (6 samples. RFLP analysis classified the 27 tpi -A amplicons in assemblage A, subgenotype I. Samples classified as assemblage B were further analysed using PCR-RFLP of the gdh gene and identified as assemblage B, subgenotype III. To our knowledge, this is the first report of assemblage B of G. duodenalis in human clinical samples from Mexico.

  20. Diffuse myocardial fibrosis evaluation using cardiac magnetic resonance T1 mapping: sample size considerations for clinical trials

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    Liu Songtao

    2012-12-01

    Full Text Available Abstract Background Cardiac magnetic resonance (CMR T1 mapping has been used to characterize myocardial diffuse fibrosis. The aim of this study is to determine the reproducibility and sample size of CMR fibrosis measurements that would be applicable in clinical trials. Methods A modified Look-Locker with inversion recovery (MOLLI sequence was used to determine myocardial T1 values pre-, and 12 and 25min post-administration of a gadolinium-based contrast agent at 3 Tesla. For 24 healthy subjects (8 men; 29 ± 6 years, two separate scans were obtained a with a bolus of 0.15mmol/kg of gadopentate dimeglumine and b 0.1mmol/kg of gadobenate dimeglumine, respectively, with averaged of 51 ± 34 days between two scans. Separately, 25 heart failure subjects (12 men; 63 ± 14 years, were evaluated after a bolus of 0.15mmol/kg of gadopentate dimeglumine. Myocardial partition coefficient (λ was calculated according to (ΔR1myocardium/ΔR1blood, and ECV was derived from λ by adjusting (1-hematocrit. Results Mean ECV and λ were both significantly higher in HF subjects than healthy (ECV: 0.287 ± 0.034 vs. 0.267 ± 0.028, p=0.002; λ: 0.481 ± 0.052 vs. 442 ± 0.037, p Conclusion ECV and λ quantification have a low variability across scans, and could be a viable tool for evaluating clinical trial outcome.

  1. Stability of Self-Reported Arousal to Sexual Fantasies Involving Children in a Clinical Sample of Pedophiles and Hebephiles.

    Science.gov (United States)

    Grundmann, Dorit; Krupp, Jurian; Scherner, Gerold; Amelung, Till; Beier, Klaus M

    2016-07-01

    In forensic research, there is a controversial discussion concerning the changeability or stability of pedophilia. Seto (2012) conceptualized pedophilia as a sexual age orientation characterized by an early onset, correlations with sexual and romantic behavior, and stability over time. However, empirical data are sparse and are mostly based on samples of detected offenders. The present study examined self-reported arousal to sexual fantasies involving children in a clinical sample of pedo-/hebephiles. In Study 1, retrospective self-reports on the age of onset and duration of sexual interest in minors were examined. In Study 2, the stability and variability of self-reported arousal to sexual fantasies involving children were evaluated prospectively. Non-prosecuted self-identifying pedo-/hebephilic men seeking professional help were recruited within the Berlin Prevention Project Dunkelfeld. Between 2005 and 2013, 494 participants completed the intake assessment. Self-reported data were collected via questionnaire focusing on sexual arousal to fantasies during masturbation involving prepubescent and/or early pubescent minors. Subsequent assessments of sexual arousal were obtained for 121 of the participants. The average time between the first and last assessment was approximately 29 months. Spearman's correlation coefficients examined the between-group rank-order and Wilcoxon signed-rank tests examined the within-individual mean-level stability. The majority of subjects reported an early onset of their pedo-/hebephilic sexual arousal. The rank-order stability was medium to high. Over the investigated period, the majority of subjects showed no or only minimal decrease or increase of self-reported sexual arousal. These results suggested that sexual arousal to fantasies involving prepubescent and/or early pubescent children is stable. Furthermore, the results support the conceptualization of pedo-/hebephilia as a sexual age orientation in men. PMID:27113471

  2. Birth Order and Sibling Gender Ratio of a Clinical Sample of Children and Adolescents Diagnosed with Attention Deficit Hyperactivity Disorder

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    Ahmad Ghanizadeh

    2012-09-01

    Full Text Available Objective: It is not clear whether sibling’s gender ratio is associated with attention deficit hyperactivity disorder (ADHD. This study examines whether inattentiveness severity and hyperactivity/impulsivity severity are associated with birth order of children with ADHD.Method: Participants are a clinical sample of 173 children and adolescents with ADHD and 43 ones without ADHD. Diagnoses were made using Diagnostic and Statistical Manual of Mental Disorders forth edition-Text Revision (DSM-IV-TR, diagnostic criteria according to face-to-face interview with the children and their parents. ADHD DSM-IV checklist was used to measure inattentiveness and hyperactivity/impulsivity scores.Results: The association of birth order and diagnosis of ADHD was not statistically significant after adjusting for covariate factors. The gender ratio of siblings is not associated with ADHD.Conclusion: Birth order and siblings gender ratio are independent of ADHD diagnosis. The results of this study support the fact that genetic factors rather than environmental factor of birth order is associated with ADHD. Moreover, contrary to autism, the current results do not suggest the androgen theory for ADHD.

  3. Incidence of Cyp51 A key mutations in Aspergillus fumigatus-a study on primary clinical samples of immunocompromised patients in the period of 1995-2013.

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    Birgit Spiess

    Full Text Available As the incidence of azole resistance in Aspergillus fumigatus is rising and the diagnosis of invasive aspergillosis (IA in immunocompromised patients is rarely based on positive culture yield, we screened our Aspergillus DNA sample collection for the occurrence of azole resistance mediating cyp51 A key mutations. Using two established, a modified and a novel polymerase chain reaction (PCR assays followed by DNA sequence analysis to detect the most frequent mutations in the A. fumigatus cyp51 A gene conferring azole resistance (TR34 (tandem repeat, L98H and M220 alterations. We analyzed two itraconazole and voriconazole and two multi-azole resistant clinical isolates and screened 181 DNA aliquots derived from clinical samples (blood, bronchoalveolar lavage (BAL, biopsies, cerebrospinal fluid (CSF of 155 immunocompromised patients of our Aspergillus DNA sample collection, previously tested positive for Aspergillus DNA and collected between 1995 and 2013. Using a novel PCR assay for the detection of the cyp51 A 46 bp tandem repeat (TR46 directly from clinical samples, we found the alteration in a TR46/Y121F/T289A positive clinical isolate. Fifty stored DNA aliquots from clinical samples were TR46 negative. DNA sequence analysis revealed a single L98H mutation in 2010, two times the L98H alteration combined with TR34 in 2011 and 2012 and a so far unknown N90K mutation in 1998. In addition, four clinical isolates were tested positive for the TR34/L98H combination in the year 2012. We consider our assay of epidemiological relevance to detect A. fumigatus azole resistance in culture-negative clinical samples of immunocompromised patients; a prospective study is ongoing.

  4. ITS1 PCR-RFLP Diagnosis and Characterization of Leishmania in Clinical Samples and Strains from Cases of Human Cutaneous Leishmaniasis in States of the Mexican Southeast

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    Amalia Monroy-Ostria

    2014-01-01

    Full Text Available American cutaneous leishmaniasis includes a spectrum of clinical forms localized cutaneous, diffuse cutaneous, and mucocutaneous leishmaniasis which can be caused by different strains of Leishmania belonging to the L. mexicana or L. braziliensis complexes which may coexist in the same endemic area. We evaluated the PCR-RFLP assay of the ITS1 genes for direct identification of Leishmania species in 163 clinical samples and 21 Mexican isolates of Leishmania. In relation to the Mexican isolates of Leishmania 52% displayed a pattern similar to the L. (L. mexicana, 5% showed a mixed pattern compatible with L. (L. mexicana and L. (V. braziliensis, eight with L. (L. amazonensis and L. (L. mexicana, and one to L. (V. braziliensis. Most of the clinical samples, 109/116 (94%, gave a pattern similar to that of the L. mexicana, two clinical samples gave similar patterns to that of Leishmania braziliensis, and 5 samples gave patterns that suggest a coinfection of L. (L. mexicana and L. (V. braziliensis or L. (L. mexicana and L. (L. amazonensis. The ITS1 PCR-RFLP assay is a multipurpose tool for diagnosis of Leishmania from clinical samples and enables determination of the infecting species of New World Leishmania in the field in relatively short time and low cost.

  5. Effect of sample pooling and transport conditions on the clinical sensitivity of a real-time polymerase chain reaction assay for Campylobacter fetus subsp. venerealis in preputial samples from bulls.

    Science.gov (United States)

    García-Guerra, Alvaro; Waldner, Cheryl L; Pellegrino, Andrea; Macdonald, Nicole; Chaban, Bonnie; Hill, Janet E; Hendrick, Steven H

    2016-01-01

    The diagnosis of bovine genital campylobacteriosis (BGC) presents significant challenges, as traditional methods lack sensitivity when prolonged transport of samples is required. Assays of preputial samples by means of real-time polymerase chain reaction (PCR) provide good sensitivity and high throughput capabilities. However, there is limited information on the acceptable duration of transport and temperature during transport of samples. In addition, the use of pooled samples has proven to be a valuable strategy for the diagnosis of other venereal diseases in cattle. The objectives of the present study were to determine the effect of sample pooling and of transport time and temperature on the clinical sensitivity of a real-time quantitative PCR (qPCR) assay for Campylobacter fetus subsp. venerealis in preputial samples from beef bulls. Eight infected bulls and 176 virgin yearling bulls were used as the source of samples. The qPCR sensitivity was comparable for unpooled samples and pools of 5 samples, whereas sensitivity was decreased for pools of 10 samples. Sensitivity for the various pool sizes improved with repeated sampling. For shorter-term transport (2 and 48 h), sensitivity was greatest when the samples were stored at 4°C and 30°C, whereas for longer-term transport (96 h) sensitivity was greatest when the samples were stored at -20°C. The creation of pools of 5 samples is therefore a good option to decrease costs when screening bulls for BGC with the qPCR assay of direct preputial samples. Ideally the samples should be stored at 4°C and arrive at the laboratory within 48 h of collection, but when that is not possible freezing at -20°C could minimize the loss of sensitivity. PMID:26733730

  6. Copy number variants in a sample of patients with psychotic disorders: is standard screening relevant for actual clinical practice?

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    Van de Kerkhof NW

    2012-07-01

    Full Text Available Noortje WA Van de Kerkhof,1 Ilse Feenstra,2 Jos IM Egger,1,3,4 Nicole de Leeuw,2 Rolph Pfundt,2 Gerald Stöber,5 Frank MMA van der Heijden,1 Willem MA Verhoeven1,61Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, The Netherlands; 2Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands; 3Donders Institute for Brain, Cognition and Behaviour, 4Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands; 5University of Würzburg, Department of Psychiatry, Psychosomatics and Psychotherapy, Würzburg, Germany; 6Erasmus University Medical Centre, Department of Psychiatry, Rotterdam, The NetherlandsAbstract: With the introduction of new genetic techniques such as genome-wide array comparative genomic hybridization, studies on the putative genetic etiology of schizophrenia have focused on the detection of copy number variants (CNVs, ie, microdeletions and/or microduplications, that are estimated to be present in up to 3% of patients with schizophrenia. In this study, out of a sample of 100 patients with psychotic disorders, 80 were investigated by array for the presence of CNVs. The assessment of the severity of psychiatric symptoms was performed using standardized instruments and ICD-10 was applied for diagnostic classification. In three patients, a submicroscopic CNV was demonstrated, one with a loss in 1q21.1 and two with a gain in 1p13.3 and 7q11.2, respectively. The association between these or other CNVs and schizophrenia or schizophrenia-like psychoses and their clinical implications still remain equivocal. While the CNV affected genes may enhance the vulnerability for psychiatric disorders via effects on neuronal architecture, these insights have not resulted in major changes in clinical practice as yet. Therefore, genome-wide array analysis should presently be restricted to those patients in whom psychotic symptoms are paired with other

  7. Lower urinary tract symptoms associated with neurological conditions: Observations on a clinical sample of outpatients neurorehabilitation service

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    Fabrizio Torelli

    2015-07-01

    Full Text Available Objectives: The overall aims of this study were to investigate the lower urinary tract symptoms (LUTS associated with neurological conditions and their prevalence and impact on a clinical sample of outpatients of a neurorehabilitation service. Materials and methods: We reviewed the files of 132 patients treated in our neurorehabilitation service from December 2012 to December 2013. Patients were divided into several subgroups based on the neurological diagnosis: Multiple Sclerosis (MS, other demyelinating diseases, Peripheral Neuropathy, neurovascular disorders (ND, neoplastic disease, traumatic brain injury (TBI, Parkinson and Parkinsonism, spinal cord injuries (SCI. Urinary status was based on medical evaluations of history of LUTS, type, degree, onset and duration of symptoms. We tried to analyze prevalence, kind of disorder, timing of presentation (if before or after the neurological onset and eventual persistence of urological disorders (in the main group and in all subgroups. Results: At the time of admission to our rehabilitation service, LUTS were observed in 14 out of 132 cases (11%. A high proportion of these outpatients (64.2% presented bothersome urinary symptoms such as incontinence, frequency and urgency (storage LUTS. The most frequent symptom was urinary urge incontinence (42.8%. This symptom was found to be prevalent in the multiple sclerosis and neurovascular disorders. In 93% the urinary symptoms arose as a result of neurologic conditions and 78.5% did not present a complete recovery of urological symptoms in spite of improved selfreported functional activity limitations. None of these patients performed urological rehabilitation. Conclusions: Neurological disorders are a significant issue in rehabilitation services and it can lead to lower tract dysfunction, which causes LUTS. Storage symptoms are more common, especially urge incontinence. Current literature reports that a further optimization of the rehabilitation potential

  8. Using Rasch Measurement to Create a Quality of Sleep Scale for a Non-Clinical Sample Based on the Pittsburgh Sleep Quality Index (PSQI

    Directory of Open Access Journals (Sweden)

    Panayiotis Panayides

    2013-02-01

    Full Text Available Originally, the aim of the present study was to investigate the psychometric properties and the appropriateness of the Greek version of the PSQI for a non-clinical sample. However, the scale was deemed not to be appropriate and results suggested some major modifications (study 1. The modified scale was administered to a second sample of Cypriots and was shown to be unidimensional and to have a high degree of reliability (study 2. The items define a theoretical linear quality of sleep continuum of increasing difficulty and cover a wide range of that continuum. Furthermore, a 3-point (instead of the original 4-point Likert scale was shown to be optimal and the scale was found to be appropriate for a non-clinical sample. The resulting scale is suitable for research purposes in studies regarding quality of sleep in academia, medicine and marketing. It could be used either for individuals or for large scale samples.

  9. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Directory of Open Access Journals (Sweden)

    Heike Horn

    Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  10. [Sample Quality Control through the Depository and Distribution of Cancer-Related Human Materials: Experience of Kanagawa Cancer Research & Information Association (KCRIA)].

    Science.gov (United States)

    Miyagi, Yohei

    2015-01-01

    Kanagawa Prefecture and its department of hospital business established the Kanagawa Cancer Research and Information Association (KCRIA) in 2006, and the Kanagawa Cancer Center (KCC) and related institutes have started to collect and distribute patient-derived cancer-related biomaterials to researchers. The tumor tissue center of KCC is collecting frozen tumor tissues, formalin-fixed and paraffin-embedded (FFPE) tumor tissues, serum of patients before treatment, and genomic DNA of peripheral white blood cells. Corresponding normal tissues are also collected if possible. Clinical information on patients is annotated in each sample as accurately as possible under linkable anonymization to follow the prognosis. We are evaluating the quality of tumor samples with two indices: the RNA Integrity Number (RIN) of extracted total RNAs from randomly chosen frozen tissues examined with the 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA), and the histopathological examination of parts of all frozen tissues prepared in the Optimal Cutting Temperature (OTC) compound and evaluation of the contents of tumor cells. Management of the sample quality is an important issue for any biomaterial repository. The quality of samples is influenced by the procedures of sample collection and storage, and also by the storage duration. The quality could be periodically examined by monitoring analyte stability and integrity, such as RIN of frozen cancer tissues. However, the best way to collect and store RNA might not always be the same for different analytes. Therefore, sample quality control at biomaterial repositories that are preparing samples for future studies on undefined analytes is a very difficult problem. At least the standard sample operation procedure (SOP) should be available for users. PMID:26524887

  11. MMPI-2 Characteristics of the Old Order Amish: A Comparison of Clinical, Nonclinical, and United States Normative Samples

    Science.gov (United States)

    Knabb, Joshua J.; Vogt, Ronald G.; Newgren, Kevin P.

    2011-01-01

    In the current study, we investigated Minnesota Multiphasic Personality Inventory-2 (MMPI-2) characteristics in an Old Order Amish nonclinical sample (N = 84), comparing these data with both the United States normative sample (N = 2,600) and a sample of Old Order Amish outpatients (N = 136). Consistent with our hypothesis, the Old Order Amish…

  12. Mothers' and Fathers' Ratings of Family Relationship Quality: Associations with Preadolescent and Adolescent Anxiety and Depressive Symptoms in a Clinical Sample

    Science.gov (United States)

    Queen, Alexander H.; Stewart, Lindsay M.; Ehrenreich-May, Jill; Pincus, Donna B.

    2013-01-01

    This study examined the independent associations among three family relationship quality factors--cohesion, expressiveness, and conflict--with youth self-reported depressive and anxiety symptoms in a clinical sample of anxious and depressed youth. Ratings of family relationship quality were obtained through both mother and father report. The…

  13. 改良醋酸铵盐析法提取福尔马林固定石蜡包埋组织DNA%The improved ammonium acetate method in the application of DNA extraction from formalin-fixed and paraffin-embedded ( FFPE ) tissues

    Institute of Scientific and Technical Information of China (English)

    周勤虎; 丁梅; 王保捷; 庞灏; 徐振亮; 张晨; 冯春梅; 王巍巍

    2012-01-01

    目的 采用改良醋酸铵盐析法提取福尔马林固定石蜡包埋组织DNA,并评价其应用价值.方法 取死后24h内人体肾组织用10%中性福尔马林溶液固定7d,石蜡包埋.采用酚/氯仿法、Chelex- 100法及改良醋酸铵盐析法提取DNA.经用紫外分光光度计法、AGE及PCR-PAGE检测比较不同方法提取DNA的质量.结果 改良醋酸铵盐析法、酚/氯仿法、Chelex-100法OD260/OD280比值分别为1.962±0.195、2.110±0.470、1.018±0.124,两两比较均有显著性差异(P<0.05);3种方法提取DNA含量(μg)分别为0.515±0.447、0.328±0.345、5.346±1.994; AGE电泳图谱可印证上述结果;PCR-PAGE检测显示改良醋酸铵盐析法提取DNA的谱带清晰度好于其它两种方法.结论 改良醋酸铵盐析法更适合微量福尔马林固定石蜡包埋组织样本DNA的提取.%Objective The modified ammonium acetate method was used to extract DNA from the formalin-fixed and paraffin-embedded ( FFPE) tissues and its application was evaluated. Methods The human kidney tissues were obtained by autopsy within 24 hours post-death and then were embedded in paraffin after fixing with 10% neutral formalin solution for 7 days. The DNA from FFPE tissues were extracted by the methods of modified ammonium acetate, phenol/chloroform, and Chelex-100. The quality and the quantity of the DNA extracted by three different methods were evaluated by UV spectrophotometer, AGE and PCR-PAGE. Results The ratio of OD260/OD280 in modified ammonium acetate method was 1. 962 ±0. 195. There was a significant difference (p <0. 05), in comparison with the ratio in phenol/chloroform (2. 110 ±0. 470) and Chelex-100 (1. 018 ±0. 124). The yields (μg) of DNA extracted by three different methods were 0. 515 ± 0. 447, 0. 328 ± 0. 345 and 5. 346 ± 1.994, separately. Furthermore, the above results were confirmed by AGE and the PCR-PAGE. DNA extracted by the modified ammonium acetate method showed more clear bands than that by

  14. [Evaluation of the diagnostic performance of Xpert MTB/RIF test for the detection of Mycobacterium tuberculosis and rifampin resistance in clinical samples].

    Science.gov (United States)

    Gürsoy, Nafia Canan; Yakupoğulları, Yusuf; Tekerekoğlu, Mehmet Sait; Otlu, Barış

    2016-04-01

    Rapid and accurate detection of active tuberculosis (TB) cases is one of the most important goal of tuberculosis control programme. For this purpose, new methods are being developed to isolate, serotype and determine the drug resistance of the agent. Xpert MTB/RIF test (CepheidGeneXpert® System, USA) that has been recently developed, is a real-time polymerase chain reaction-based method which detects Mycobacterium tuberculosis complex and resistance of the strain to rifampicin (RIF) from the clinical sample directly within a couple of hours. However, there are not sufficient data about the performance of that test for extrapulmonary samples and pulmonary samples other than sputum. The aims of this study were to investigate the sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF test in detection of M. tuberculosis and the performance in the determination of rifampicin resistance of the isolates from pulmonary and extrapulmonary clinical samples. A total of 2160 clinical samples, in which 1141 (52.8%) were pulmonary and 1019 (47.2%) were extrapulmonary samples, sent to our laboratory between July 2013 to December 2014, were included in the study. Sixty seven of the evaluated samples (3.1%) were positive with microscopy (acid-fast stain; AFS), 116 samples (5.1%) were positive with culture and 98 samples (4.5%) were positive with Xpert MTB/RIF test. When the culture was considered as the reference method, the sensitivity and specificity of Xpert MTB/RIF test were determined as 73.3% and 99.3%, respectively for all samples; 77.5% and 99.5%, respectively for pulmonary samples and 63.9% and 99.2%, respectively for extrapulmonary samples. Among AFS positive samples, the sensitivity was 100% and specificity was 66.7%; whereas among AFS negative samples those values were 40.4% and 99.4%, respectively. Among all the samples involved in the study, RIF resistance was determined only in three samples with Xpert MTB/ RIF test and that was also

  15. PCR assay based on DNA coding for 16S rRNA for detection and identification of mycobacteria in clinical samples.

    Science.gov (United States)

    Kox, L F; van Leeuwen, J; Knijper, S; Jansen, H M; Kolk, A H

    1995-01-01

    A PCR and a reverse cross blot hybridization assay were developed for the detection and identification of mycobacteria in clinical samples. The PCR amplifies a part of the DNA coding for 16S rRNA with a set of primers that is specific for the genus Mycobacterium and that flanks species-specific sequences within the genes coding for 16S rRNA. The PCR product is analyzed in a reverse cross blot hybridization assay with probes specific for M. tuberculosis complex (pTub1), M. avium (pAvi3), M. intracellulare (pInt5 and pInt7), M. kansasii complex-M. scrofulaceum complex (pKan1), M. xenopi (pXen1), M. fortuitum (pFor1), M. smegmatis (pSme1), and Mycobacterium spp. (pMyc5a). The PCR assay can detect 10 fg of DNA, the equivalent of two mycobacteria. The specificities of the probes were tested with 108 mycobacterial strains (33 species) and 31 nonmycobacterial strains (of 17 genera). The probes pAvi3, pInt5, pInt7, pKan1, pXen1, and pMyc5a were specific. With probes pTub1, pFor1, and pSme1, slight cross hybridization occurred. However, the mycobacterial strains from which the cross-hybridizing PCR products were derived belonged to nonpathogenic or nonopportunistic species which do not occur in clinical samples. The test was used on 31 different clinical specimens obtained from patients suspected of having mycobacterial disease, including a patient with a double mycobacterial infection. The samples included sputum, bronchoalveolar lavage, tissue biopsy samples, cerebrospinal fluid, pus, peritoneal fluid, pleural fluid, and blood. The results of the PCR assay agreed with those of conventional identification methods or with clinical data, showing that the test can be used for the direct and rapid detection and identification of mycobacteria in clinical samples. PMID:8586707

  16. Clinical procedure for colon carcinoma tissue sampling directly affects the cancer marker-capacity of VEGF family members

    International Nuclear Information System (INIS)

    mRNA levels of members of the Vascular Endothelial Growth Factor family (VEGF-A, -B, -C, -D, Placental Growth Factor/PlGF) have been investigated as tissue-based markers of colon cancer. These studies, which used specimens obtained by surgical resection or colonoscopic biopsy, yielded contradictory results. We studied the effect of the sampling method on the marker accuracy of VEGF family members. Comparative RT-qPCR analysis was performed on healthy colon and colon carcinoma samples obtained by biopsy (n = 38) or resection (n = 39) to measure mRNA expression levels of individual VEGF family members. mRNA levels of genes encoding the eicosanoid enzymes cyclooxygenase 2 (COX2) and 5-lipoxygenase (5-LOX) and of genes encoding the hypoxia markers glucose transporter 1 (GLUT-1) and carbonic anhydrase IX (CAIX) were included as markers for cellular stress and hypoxia. Expression levels of COX2, 5-LOX, GLUT-1 and CAIX revealed the occurrence in healthy colon resection samples of hypoxic cellular stress and a concurrent increment of basal expression levels of VEGF family members. This increment abolished differential expression of VEGF-B and VEGF-C in matched carcinoma resection samples and created a surgery-induced underexpression of VEGF-D. VEGF-A and PlGF showed strong overexpression in carcinoma samples regardless of the sampling method. Sampling-induced hypoxia in resection samples but not in biopsy samples affects the marker-reliability of VEGF family members. Therefore, biopsy samples provide a more accurate report on VEGF family mRNA levels. Furthermore, this limited expression analysis proposes VEGF-A and PlGF as reliable, sampling procedure insensitive mRNA-markers for molecular diagnosis of colon cancer

  17. Effects of state and trait anxiety on selective attention to threatening stimuli in a non-clinical sample of school children

    Directory of Open Access Journals (Sweden)

    Jeniffer Ortega Marín

    2015-01-01

    Full Text Available Attentional biases, consisting of a preferential processing of threatening stimuli, have been found in anxious adults as predicted by several cognitive models. However, studies with non-clinical samples of children have provided mixed results. therefore, the aim of this research was to determine the effects of state and trait anxiety on the selective attention towards threatening stimuli in a non-clinical sample of school children (age: 8 to 13, n = 110 using the dot-probe task. This study did not reveal an effect of trait anxiety on selective attention towards threatening stimuli. However, a significant difference was found between participants with low state anxiety and high state anxiety. Nevertheless, the effect size was small. Specifically, participants with low state anxiety showed a bias towards threatening stimuli. Overall, the findings of this research with a non-clinical sample of school children suggest that attentional biases towards threatening information, which has been repeatedly found in anxious adults, are not necessarily inherent to non-clinical anxiety in children and on the other hand, the relationship between attentional biases and anxiety in this population might be moderated by other cognitive processes.

  18. The influence of variations in eating disorder-related symptoms on processing of emotional faces in a non-clinical female sample: An eye-tracking study.

    Science.gov (United States)

    Sharpe, Emma; Wallis, Deborah J; Ridout, Nathan

    2016-06-30

    This study aimed to: (i) determine if the attention bias towards angry faces reported in eating disorders generalises to a non-clinical sample varying in eating disorder-related symptoms; (ii) examine if the bias occurs during initial orientation or later strategic processing; and (iii) confirm previous findings of impaired facial emotion recognition in non-clinical disordered eating. Fifty-two females viewed a series of face-pairs (happy or angry paired with neutral) whilst their attentional deployment was continuously monitored using an eye-tracker. They subsequently identified the emotion portrayed in a separate series of faces. The highest (n=18) and lowest scorers (n=17) on the Eating Disorders Inventory (EDI) were compared on the attention and facial emotion recognition tasks. Those with relatively high scores exhibited impaired facial emotion recognition, confirming previous findings in similar non-clinical samples. They also displayed biased attention away from emotional faces during later strategic processing, which is consistent with previously observed impairments in clinical samples. These differences were related to drive-for-thinness. Although we found no evidence of a bias towards angry faces, it is plausible that the observed impairments in emotion recognition and avoidance of emotional faces could disrupt social functioning and act as a risk factor for the development of eating disorders. PMID:27138825

  19. A study of trait anhedonia in non-clinical Chinese samples: evidence from the Chapman Scales for Physical and Social Anhedonia.

    Directory of Open Access Journals (Sweden)

    Raymond C K Chan

    Full Text Available BACKGROUND: Recent studies suggest that anhedonia, an inability to experience pleasure, can be measured as an enduring trait in non-clinical samples. In order to examine trait anhedonia in a non-clinical sample, we examined the properties of a range of widely used questionnaires capturing anhedonia. METHODS: 887 young adults were recruited from colleges. All of them were administered a set of checklists, including Chapman Scale for Social Anhedonia (CRSAS and the Chapman Scale for Physical Anhedonia Scale (CPAS, The Temporal Experience of Pleasure Scale(TEPS, and The Schizotypal Personality Questionnaire (SPQ. RESULTS: Males showed significantly higher level of physical (F = 5.09, p<0.001 and social (F = 4.38, p<0.005 anhedonia than females. As expected, individuals with schizotypal personality features also demonstrated significantly higher scores of physical (t = 3.81, p<0.001 and social (t = 7.33, p<0.001 trait anhedonia than individuals without SPD features, but no difference on self-report anticipatory and consummatory pleasure experience. CONCLUSIONS: Concerning the comparison on each item of physical and social anhedonia, the results indicated that individuals with SPD feature exhibited higher than individuals without SPD features on more items of social anhedonia than physical anhedonia scale. These preliminary findings suggested that trait anhedonia can be identified a non-clinical sample. Exploring the demographic and clinical correlates of trait anhedonia in the general population may provide clues to the pathogenesis of psychotic disorder.

  20. A prospective survey of Aspergillus spp. in respiratory tract samples: prevalence, clinical impact and antifungal susceptibility

    DEFF Research Database (Denmark)

    Mortensen, K L; Johansen, H K; Fuursted, Kurt;

    2011-01-01

    A three-month laboratory-based prospective survey was conducted at four major university hospitals covering one-third of the Danish population in order to determine the prevalence, significance, and susceptibility pattern of aspergilli in airway samples. Samples received in January-March 2007 for...

  1. Evaluation of Factors Affecting Continuous Performance Test Identical Pairs Version Score of Schizophrenic Patients in a Japanese Clinical Sample

    Directory of Open Access Journals (Sweden)

    Takayoshi Koide

    2012-01-01

    Full Text Available Aim. Cognitive impairment in schizophrenia strongly relates to social outcome and is a good candidate for endophenotypes. When we accurately measure drug efficacy or effects of genes or variants relevant to schizophrenia on cognitive impairment, clinical factors that can affect scores on cognitive tests, such as age and severity of symptoms, should be considered. To elucidate the effect of clinical factors, we conducted multiple regression analysis using scores of the Continuous Performance Test Identical Pairs Version (CPT-IP, which is often used to measure attention/vigilance in schizophrenia. Methods. We conducted the CPT-IP (4-4 digit and examined clinical information (sex, age, education years, onset age, duration of illness, chlorpromazine-equivalent dose, and Positive and Negative Symptom Scale (PANSS scores in 126 schizophrenia patients in Japanese population. Multiple regression analysis was used to evaluate the effect of clinical factors. Results. Age, chlorpromazine-equivalent dose, and PANSS-negative symptom score were associated with mean d′ score in patients. These three clinical factors explained about 28% of the variance in mean d′ score. Conclusions. As conclusion, CPT-IP score in schizophrenia patients is influenced by age, chlorpromazine-equivalent dose and PANSS negative symptom score.

  2. Clinical and neuropsychological assessment of executive function in a sample of children and adolescents with idiopathic epilepsy

    Directory of Open Access Journals (Sweden)

    Andrea Bandeira de Lima

    2014-12-01

    Full Text Available Objective To compare the executive functions of children and adolescents with idiopathic epilepsy with a control group and to correlate with clinical data, intelligence and academic performance. Method Cross-sectional, descriptive and analytical study. Thirty-one cases and thirty-five controls were evaluated by the WCST (Wisconsin Card Sorting Test.The results were compared with clinical data (seizure type and frequency, disease duration and number of antiepileptic drugs used, IQ (WISC-III and academic performance (APT. Results Patients with epilepsy had poorer executive function scores. There was no positive linear correlation between test scores and epilepsy variables. There was a positive association between academic performance and some executive function results. Conclusion Children with well controlled idiopathic epilepsy may show deficits in executive functions in spite of clinical variables. Those deficits may influence academic performance.

  3. Indicators of Anxiety and Depression in Women with the Fragile X Premutation: Assessment of a Clinical Sample

    Science.gov (United States)

    Lachiewicz, A.; Dawson, D.; Spiridigliozzi, G.; Cuccaro, M.; Lachiewicz, M.; McConkie-Rosell, A.

    2010-01-01

    Background: Current research suggests that depression and anxiety may be common problems in women with the fragile X (FMR1) premutation. Methods: To learn more about this in a clinical setting, we asked 33 women with the FMR1 premutation and 20 women without the FMR1 premutation to complete the Brief Carroll Depression Scale (Brief CDS) and the…

  4. Gesture Production in School vs. Clinical Samples of Children with Developmental Coordination Disorder (DCD) and Typically Developing Children

    Science.gov (United States)

    Sinani, Charikleia; Sugden, David A.; Hill, Elisabeth L.

    2011-01-01

    Dyspraxia, a difficulty in executing an operationalised act, has been associated with Developmental Coordination Disorder (DCD). However, issues relating to the area such as comparisons across modalities, comparisons of school vs. clinical populations, and developmental delay vs. pathology have not been addressed in the same, comprehensive study.…

  5. Posttraumatic stress disorder with and without alcohol use disorders: Diagnostic and clinical correlates in a psychiatric sample

    OpenAIRE

    Ray, Lara A.; Capone, Christy; Sheets, Erin; Young, Diane; Chelminski, Iwona; Zimmerman, Mark

    2009-01-01

    This study compared outpatients (n = 196) with PTSD versus PTSD + alcohol use disorders (AUD) on clinical measures. PTSD + AUD patients were more likely to meet criteria for Borderline and Antisocial Personality Disorders. Emotion dysregulation may help account for the relationship between PTSD and AUD.

  6. Associations between delusion proneness and personality structure in non-clinical participants : Comparison between young and elderly samples

    NARCIS (Netherlands)

    Laroi, Frank; Van der Linden, Martial; DeFruyt, Filip; van Os, Jim; Aleman, Andre

    2006-01-01

    Background: Few studies have explored the prevalence of delusions in the non-clinical, elderly population. In addition, the association between personality structure and delusions remains poorly investigated. The aims of the present study were, first, to explore the relation between age and the prev

  7. Associations between delusion proneness and personality structure in non-clinical participants: Comparison between young and elderly samples

    NARCIS (Netherlands)

    Laroi, F.; Van der Linden, M.; DeFruyt, F.; Van Os, J.; Aleman, A.

    2006-01-01

    Background: Few studies have explored the prevalence of delusions in the non-clinical, elderly population. In addition, the association between personality structure and delusions remains poorly investigated. The aims of the present study were, first, to explore the relation between age and the prev

  8. Different EV enrichment methods suitable for clinical settings yield different subpopulations of urinary extracellular vesicles from human samples

    OpenAIRE

    Royo, Felix; Zuñiga-Garcia, Patricia; Sanchez-Mosquera, Pilar; Egia, Ainara; Perez, Amparo; Loizaga, Ana; Arceo, Raquel; Lacasa, Isabel; Rabade, Ainara; Arrieta, Edurne; Bilbao, Roberto; Unda, Miguel; Carracedo, Arkaitz; Falcon-Perez, Juan M.

    2016-01-01

    Urine sample analysis is irreplaceable as a non-invasive method for disease diagnosis and follow-up. However, in urine samples, non-degraded protein and RNA may be only found in urinary extracellular vesicles (uEVs). In recent years, various methods of uEV enrichment using low volumes of urine and unsophisticated equipment have been developed, with variable success. We compared the results of the differential ultracentrifugation procedure with 4 of these methods. The methods tested were a lec...

  9. Epidemiology and clinical outcome of virus-positive respiratory samples in ventilated patients: a prospective cohort study.

    OpenAIRE

    Daubin, Cédric; Parienti, Jean-Jacques; Vincent, Sophie; Vabret, Astrid; du Cheyron, Damien; Ramakers, Michel; Freymuth, François; Charbonneau, Pierre

    2006-01-01

    INTRODUCTION: Respiratory viruses are a major cause of respiratory tract infections. The prevalence of a virus-positive respiratory sample and its significance in patients requiring mechanical ventilation remain unknown. METHODS: We conducted a cohort study in all consecutive adults ventilated for more than 48 hours admitted to a 22-bed medical intensive care unit during a 12-month period. Respiratory samples at the time of intubation were assessed by culture, by indirect immunofluorescence a...

  10. Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Sterile or Nonsterile Clinical Samples by a New Molecular Assay

    OpenAIRE

    Francois, Patrice; Pittet, Didier; Bento, Manuela; Pepey, Béatrice; Vaudaux, Pierre; Lew, Daniel; Schrenzel, Jacques

    2003-01-01

    A rapid procedure was developed for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) directly from sterile sites or mixed flora samples (e.g., nose or inguinal swabs). After a rapid conditioning of samples, the method consists of two main steps: (i) immunomagnetic enrichment in S. aureus and (ii) amplification-detection profile on DNA extracts using multiplex quantitative PCR (5′-exonuclease qPCR, TaqMan). The triplex qPCR assay measures simultaneously the fo...

  11. Assessing Eating Disorder Risk: The Pivotal Role of Achievement Anxiety, Depression and Female Gender in Non-Clinical Samples

    OpenAIRE

    Christos C. Frangos; Fragkos, Konstantinos C.

    2013-01-01

    The objective of the present study was to assess factors predicting eating disorder risk in a sample of undergraduate students. A structured questionnaire was employed on a random sample (n = 1865) consisting of the following sections: demographics, SCOFF (Sick, Control, One stone, Fat, Food) questionnaire for screening eating disorders and the Achievement Anxiety Test and the Depression, Anxiety and Stress Scale. The students at risk for eating disorders (SCOFF score ≥2) were 39.7%. Eating d...

  12. Sample Preparation and Extraction in Small Sample Volumes Suitable for Pediatric Clinical Studies: Challenges, Advances, and Experiences of a Bioanalytical HPLC-MS/MS Method Validation Using Enalapril and Enalaprilat

    Directory of Open Access Journals (Sweden)

    Bjoern B. Burckhardt

    2015-01-01

    Full Text Available In USA and Europe, medicines agencies force the development of child-appropriate medications and intend to increase the availability of information on the pediatric use. This asks for bioanalytical methods which are able to deal with small sample volumes as the trial-related blood lost is very restricted in children. Broadly used HPLC-MS/MS, being able to cope with small volumes, is susceptible to matrix effects. The latter restrains the precise drug quantification through, for example, causing signal suppression. Sophisticated sample preparation and purification utilizing solid-phase extraction was applied to reduce and control matrix effects. A scale-up from vacuum manifold to positive pressure manifold was conducted to meet the demands of high-throughput within a clinical setting. Faced challenges, advances, and experiences in solid-phase extraction are exemplarily presented on the basis of the bioanalytical method development and validation of low-volume samples (50 μL serum. Enalapril, enalaprilat, and benazepril served as sample drugs. The applied sample preparation and extraction successfully reduced the absolute and relative matrix effect to comply with international guidelines. Recoveries ranged from 77 to 104% for enalapril and from 93 to 118% for enalaprilat. The bioanalytical method comprising sample extraction by solid-phase extraction was fully validated according to FDA and EMA bioanalytical guidelines and was used in a Phase I study in 24 volunteers.

  13. Direct 16S rRNA Gene Sequencing from Clinical Specimens, with Special Focus on Polybacterial Samples and Interpretation of Mixed DNA Chromatograms ▿

    OpenAIRE

    Kommedal, Øyvind; Kvello, Kristine; Skjåstad, Rune; Langeland, Nina; Wiker, Harald G.

    2009-01-01

    RipSeq (iSentio, Bergen, Norway) is a web-based application for the analysis of mixed DNA chromatograms. It opens the possibility to analyze chromatograms obtained by direct 16S rRNA gene sequencing from polybacterial human clinical samples. In this study, we used direct 16S rRNA gene sequencing to investigate 264 samples from a wide range of suspected human bacterial infections. The sequence-based identification was compared with the results from routine culture-based identification. A total...

  14. Acceptability, effectiveness, and cost-effectiveness of internet-based exposure treatment for irritable bowel syndrome in a clinical sample: a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Andréewitch Sergej

    2011-10-01

    Full Text Available Abstract Background Internet-based cognitive behavior therapy (ICBT has shown promising effects in the treatment of irritable bowel syndrome (IBS. However, to date no study has used a design where participants have been sampled solely from a clinical population. We aimed to investigate the acceptability, effectiveness, and cost-effectiveness of ICBT for IBS using a consecutively recruited sample from a gastroenterological clinic. Methods Sixty-one patients were randomized to 10 weeks of ICBT (n = 30 or a waiting list control (n = 31. The ICBT was guided by an online therapist and emphasized acceptance of symptoms through exposure and mindfulness training. Severity of IBS symptoms was measured with the Gastrointestinal symptom rating scale - IBS version (GSRS-IBS. Patients in both groups were assessed at pre- and post-treatment while only the ICBT group was assessed 12 months after treatment completion. Health economic data were also gathered at all assessment points and analyzed using bootstrap sampling. Results Fifty of 61 patients (82% completed the post-treatment assessment and 20 of 30 patients (67% in the ICBT group were assessed at 12-month follow-up. The ICBT group demonstrated significantly (p d = 0.77 (95% CI: 0.19-1.34. Similar effects were noted on measures of quality of life and IBS-related fear and avoidance behaviors. Improvements in the ICBT group were maintained at 12-month follow-up. The ICBT condition was found to be more cost-effective than the waiting list, with an 87% chance of leading to reduced societal costs combined with clinical effectiveness. The cost-effectiveness was sustained over the 12-month period. Conclusions ICBT proved to be a cost-effective treatment when delivered to a sample recruited from a gastroenterological clinic. However, many of the included patients dropped out of the study and the overall treatment effects were smaller than previous studies with referred and self-referred samples. ICBT may

  15. Comparative analysis of genetic diversity and incidence of virulence factors and antibiotic resistance among enterococcal populations from raw fruit and vegetable foods, water and soil, and clinical samples.

    Science.gov (United States)

    Abriouel, Hikmate; Omar, Nabil Ben; Molinos, Antonio Cobo; López, Rosario Lucas; Grande, Maria José; Martínez-Viedma, Pilar; Ortega, Elena; Cañamero, Magdalena Martínez; Galvez, Antonio

    2008-03-31

    A comparative study was carried out among enterococci isolated from fruits and vegetable foods, water and soil, and clinical samples. Results indicate strong differences in the numbers of enterococcal species found in different environments as well as their abundance. While Enterococcus faecalis was clearly the predominant species in clinical samples, Enterococcus faecium predominated in vegetables, and it slightly outnumbered E. faecalis in water samples. Other species (Enterococcus hirae, Enterococcus mundtii, Enterococcus durans, Enterococcus gallinarum and Enterococcus casseliflavus) were found more frequently in vegetables, water, and specially in soil. Isolates from vegetable foods showed a lower incidence of antibiotic resistance compared to clinical isolates for most antimicrobials tested, especially erythromycin, tetracycline, chloramphenicol, ciprofloxacin, levofloxacin, gentamicin and streptomycin for E. faecalis, and quinupristin/dalfopristin, ampicillin, penicillin, ciprofloxacin, levofloxacin, rifampicin, choramphenicol, gentamicin and nitrofurantoin for E. faecium. E. faecium isolates from vegetable foods and water showed an average lower number of antibiotic resistance traits (2.95 and 3.09 traits for vegetable and water isolates, respectively) compared to clinical samples (7.5 traits). Multi-resistant strains were also frequent among clinical E. faecalis isolates (5.46 traits on average). None of E. faecalis or E. faecium isolates from vegetable foods, water and soil showed beta-haemolytic activity, while 25.64% of clinical E. faecalis did. A 51.28% of E. faecalis clinical isolates tested positive for the cylA, cylB, cylM set of genes, while some or all of these genes were missing in the rest of isolates. In clinical E. faecalis and E. faecium isolates, the genetic determinants for the enterococcal surface protein gene (esp), the collagen adhesin gene (ace) and the sex pheromone gene ccf (as well as cob in E. faecalis) showed a clearly higher

  16. Intestinal parasites and genotyping of Giardia duodenalis in children: first report of genotype B in isolates from human clinical samples in Mexico

    OpenAIRE

    Julio César Torres-Romero; Antonio de Jesus Euan-Canto; Namibya Benito-González; Nayely Padilla-Montaño; Claribel Huchin-Chan; Julio Lara-Riegos; Roberto Cedillo-Rivera

    2014-01-01

    Giardia duodenalis is one of the most prevalent enteroparasites in children. This parasite produces several clinical manifestations. The aim of this study was to determine the prevalence of genotypes of G. duodenalis causing infection in a region of southeastern Mexico. G. duodenalis cysts were isolated (33/429) from stool samples of children and molecular genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, targeting the trioseph...

  17. A randomised clinical trial on cardiotocography plus fetal blood sampling versus cardiotocography plus ST-analysis of the fetal electrocardiogram (STAN®) for intrapartum monitoring

    OpenAIRE

    Rijnders Robbert JP; Porath Martina M; Oei S Guid; Nijhuis Jan G; Mol Ben WJ; van Lith Jan MM; van Geijn Herman P; Drogtrop Addy P; Bijvoet Saskia M; van Beek Erik; Moons Karel GM; Westerhuis Michelle EMH; Schuitemaker Nico WE; van der Tweel Ingeborg; Visser Gerard HA

    2007-01-01

    Abstract Background Cardiotocography (CTG) is worldwide the method for fetal surveillance during labour. However, CTG alone shows many false positive test results and without fetal blood sampling (FBS), it results in an increase in operative deliveries without improvement of fetal outcome. FBS requires additional expertise, is invasive and has often to be repeated during labour. Two clinical trials have shown that a combination of CTG and ST-analysis of the fetal electrocardiogram (ECG) reduc...

  18. Gender ratio in a clinical population sample, age of diagnosis and duration of assessment in children and adults with autism spectrum disorder.

    OpenAIRE

    Rutherford, Marion; McKenzie, Karen; Johnson, Tess; Catchpole, Ciara; O'Hare, Anne; McClure, Iain; Forsyth, Kirsty; McCartney, Deborah; Murray, Aja Louise

    2016-01-01

    This article reports on gender ratio, age of diagnosis and the duration of assessment procedures in autism spectrum disorder diagnosis in a national study which included all types of clinical services for children and adults. Findings are reported from a retrospective case note analysis undertaken with a representative sample of 150 Scottish children and adults recently diagnosed with autism spectrum disorder. The study reports key findings that the gender ratio in this consecutively referred...

  19. Quality Control Trial for Human Immunodeficiency Virus Type 1 Drug Resistance Testing Using Clinical Samples Reveals Problems with Detecting Minority Species and Interpretation of Test Results

    OpenAIRE

    Korn, Klaus; Reil, Heide; Walter, Hauke; Schmidt, Barbara

    2003-01-01

    Between January and March 2000, a quality control panel for human immunodeficiency virus (HIV) drug resistance testing was analyzed by 20 laboratories in five countries. The panel consisted of three clinical samples with different drug resistance genotypes and phenotypes and one HIV-negative plasma. Participants were asked to report the methods used for amplification and sequencing, a list of drug resistance-associated mutations that were detected in the protease and reverse transcriptase of ...

  20. Antibiotic Resistance and the Frequency of Extended-Spectrum B-Lactamase in Acinetobacter baumannii Isolated from Clinical Samples through Phenotypic Methods

    OpenAIRE

    Somayeh Vafaei; Reza Mirnejad; Nour Amirmozafari; Abbasali Imani Fooladi; Faramarz Masjedian

    2013-01-01

    AbstractBackground and objectives: Nowadays Acinetobacter baumannii is as one of the problematic opportunistic pathogens, especially in intensive care because of the incidence of drug-resistant strains in the world. The purpose of current study was to define the antibiotic susceptibility patterns and detect the prevalence of producing strains of extended-spectrum β-lactamase (ESBL) in A. baumannii isolates which had been isolated from clinical samples with combined disk test.Materials and met...

  1. Development of Novel PCR Assays To Detect Azole Resistance-Mediating Mutations of the Aspergillus fumigatus cyp51A Gene in Primary Clinical Samples from Neutropenic Patients

    OpenAIRE

    Spiess, Birgit; Seifarth, Wolfgang; Merker, Natalia; Howard, Susan J.; Reinwald, Mark; Dietz, Anne; Hofmann, Wolf-Karsten; Buchheidt, Dieter

    2012-01-01

    The increasing incidence of azole resistance in Aspergillus fumigatus causing invasive aspergillosis (IA) in immunocompromised/hematological patients emphasizes the need to improve the detection of resistance-mediating cyp51A gene mutations from primary clinical samples, particularly as the diagnosis of invasive aspergillosis is rarely based on a positive culture yield in this group of patients. We generated primers from the unique sequence of the Aspergillus fumigatus cyp51A gene to establis...

  2. Identification of a Novel Proteoform of Prostate Specific Antigen (SNP-L132I) in Clinical Samples by Multiple Reaction Monitoring.

    OpenAIRE

    Végvári, Ákos; Sjödin, Karin; Rezeli, Melinda; Malm, Johan; Lilja, Hans; Laurell, Thomas; Marko-Varga, György

    2013-01-01

    Prostate specific antigen (PSA) is a well-established tumor marker that is frequently employed as model biomarker in the development and evaluation of emerging quantitative proteomics techniques, partially as a result of wide access to commercialized immunoassays serving as “gold standards.” We designed a multiple reaction monitoring (MRM) assay to detect PSA proteoforms in clinical samples (n = 72), utilizing the specificity and sensitivity of the method. We report, for the first time, a PSA...

  3. Identification of Anxiety Sensitivity Classes and Clinical Cut-Scores in a Sample of Adult Smokers: Results from a Factor Mixture Model

    OpenAIRE

    Allan, Nicholas P.; Raines, Amanda M.; Capron, Daniel W.; Norr, Aaron M.; Zvolensky, Michael J.; Schmidt, Norman B.

    2014-01-01

    Anxiety sensitivity (AS), a multidimensional construct, has been implicated in the development and maintenance of anxiety and related disorders. Recent evidence suggests that AS is a dimensional-categorical construct within individuals. Factor mixture modeling was conducted in a sample of 579 adult smokers (M age = 36.87 years, SD = 13.47) to examine the underlying structure. Participants completed the Anxiety Sensitivity Index-3 and were also given a Structured Clinical Interview for DSM-IV-...

  4. Distribution of contagious and environmental mastitis agents isolated from milk samples collected from clinically health buffalo cows between brazilian dry and rainy seasons of the year

    OpenAIRE

    Maia, R.P.; D.J. Sturion; D.L. Ravena; E.B.S. Ferreira; H. Tonhati; H Langoni; T.A.B. Santos; A. Nader Filho; G. Mendoza-Sánchez; R. Bonini Pardo

    2010-01-01

    The present study was performed to evaluate the microbiological characteristics of clinically health quarters submitted to milking and also to observe the distribution of contagious and environmental agents between brazilian dry and rainy seasons of the year. During nine months 734 quarters from 37 buffalo cows were submitted monthly to udder inspection, palpation and strip cup test before milking. 734 asseptic milk samples were inoculated in 10% ovine blood agar and in MacConkey agar media, ...

  5. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations

    OpenAIRE

    Stürenburg, E

    2009-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) isolates is a serious public health problem whose ever-increasing rate is commensurate with the pressure it is exerting on the healthcare system. At present, more than 20% of clinical S. aureus isolates in German hospitals are methicillin resistant. Strategies from low-prevalence countries show that this development is not necessarily inevitable. In the Scandinavian countries and the Netherlands, thanks to a rigorous prevention programme, M...

  6. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations

    OpenAIRE

    Stürenburg, Enno

    2009-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) isolates is a serious public health problem whose ever-increasing rate is commensurate with the pressure it is exerting on the healthcare system. At present, more than 20% of clinical S. aureus isolates in German hospitals are methicillin resistant. Strategies from low-prevalence countries show that this development is not necessarily inevitable. In the Scandinavian countries and the Netherlands, thanks to a rigorous prevention programme, MRS...

  7. Measuring volitional competences: psychometric properties of a short form of the Volitional Components Questionnaire (VCQ) in a clinical sample

    OpenAIRE

    Forstmeier, Simon; Rüddel, H

    2008-01-01

    Volitional competences (skills of will), including self-regulation skills such as self-motivation and emotion regulation and self-control skills such as impulse control, are particularly necessary for patients with psychiatric and psychosomatic disorders. The Volitional Components Questionnaire (VCQ) is an instrument designed to measure volitional competences. However, its length of 190 items prevents its routine application in clinical settings. This study evaluates a new 36-item short form ...

  8. Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods.

    OpenAIRE

    Shawar, R M; el-Zaatari, F A; Nataraj, A; Clarridge, J E

    1993-01-01

    Detection of Mycobacterium tuberculosis in clinical specimens by the polymerase chain reaction (PCR) was compared with detection by culture. A 317-bp segment within the M. tuberculosis-specific insertion sequence IS6110 was amplified. The detection limit of the PCR assay for cultured mycobacteria was 50 cells per reaction by ethidium bromide-stained agarose gel electrophoresis and 5 cells per reaction by hybridization with an oligonucleotide probe conjugated with either digoxigenin or alkalin...

  9. Pancratistatin induces apoptosis in clinical leukemia samples with minimal effect on non-cancerous peripheral blood mononuclear cells

    OpenAIRE

    McNulty James; Hamm Caroline; Griffin Carly; Pandey Siyaram

    2010-01-01

    Abstract Background Pancratistatin, a natural compound extracted from Hymenocallis littoralis, can selectively induce apoptosis in several cancer cell lines. In this ex vivo study, we evaluated the effect of pancratistatin on peripheral blood mononuclear cells obtained from 15 leukemia patients prior to clinical intervention of newly diagnosed patients, as well as others of different ages in relapse and at various disease progression states. Results Mononuclear cells from healthy volunteers a...

  10. A clinical trial alert tool to recruit large patient samples and assess selection bias in general practice research

    OpenAIRE

    Scheidt-Nave Christa; Schäfer Tobias; Wedeken Sven; Thüring Sabine; Heinemann Stephanie; Ketterer Mirko; Himmel Wolfgang

    2011-01-01

    Abstract Background Many research projects in general practice face problems when recruiting patients, often resulting in low recruitment rates and an unknown selection bias, thus limiting their value for health services research. The objective of the study is to evaluate the recruitment performance of the practice staff in 25 participating general practices when using a clinical trial alert (CTA) tool. Methods The CTA tool was developed for an osteoporosis survey of patients at risk for oste...

  11. Sense of Purpose in Life and Escape from Self as the Predictors of Quality of Life in Clinical Samples

    OpenAIRE

    Błażek, Magdalena; Kaźmierczak, Maria; Besta, Tomasz

    2014-01-01

    Depression is a leading mental disorder from which suffer Europeans and especially women. In clinical groups with elevated risk of suicidal tendencies, both the negative factors and psychological variables that can protect a person should be analyzed. The aims of the current study were analysis of purpose in life function in perceived quality of life—self-efficacy and life satisfaction among people suffering from depression in comparison with control group and analysis of escape from self (Ef...

  12. Frequency and Antibiotic Resistance Pattern in Staphylococcus aureus Strains Isolated from Clinical Samples of Tehran’s Araad Hospital in 2007-2011

    Directory of Open Access Journals (Sweden)

    Hamed Molaabaszadeh

    2014-01-01

    Full Text Available ABSTRACT Background and objective: Todays, the resistance to antibiotics among of pathogen bacteria is one of the main concerns of doctors all around the world, with consideration to different reports about Staphylococcus aureus bacteria’s sensitivity, this study was done to examine the pattern of sensitivity and antibiotic resistance of Staphylococcus aureus strains collected from clinical samples of patients hospitalized in Tehran’s Araad hospital. Materials and methods: In this descriptive examination, after extracting Staphylococcus aureus derivations from clinical samples (urine, catheter, phlegm, wound, bronchial and blood, their sensitivity was measured using standard Kirby-Bauer test, in contract with following antibiotics Amikacin, Ciprofloxacin, Vancomycin, Imipenem, Sulfametoxazole Trimetoprime, Tetracycline, Oxacillin, Ceftriaxone and Penicillin. Results: In this study 260 samples of Staphylococcus aureus isolated from clinical specimens in three years. The most sensivity was to Vancomycin and the most resistance was to Penicillin and Oxacillin. Conclusion: The results of this study are indicating that Staphylococcus aureus strains resistance has increased against Penicillin and Oxacillin; presumably it is due to excessive consumption of these antibiotics. It is obvious that, with regard to increasing consumption of antibiotics and consequently, augmentation of antibacterial resistance, control of this resistance factor is necessary and inevitable, so it is recommended to avoid unnecessary usage of antibiotics.

  13. Schizotypal personality questionnaire - brief revised (updated): An update of norms, factor structure, and item content in a large non-clinical young adult sample.

    Science.gov (United States)

    Davidson, Charlie A; Hoffman, Lesa; Spaulding, William D

    2016-04-30

    This study updates and provides evidence for the dimensionality, reliability, and validity of a standard instrument for detection and measurement of schizotypy in non-clinical young adults. Schizotypy represents a set of traits on which both nonclinical and schizophrenia-spectrum populations vary meaningfully. These traits are linked to biological, cognitive, and social dimensions of serious mental illness (SMI), to clinical and subclinical variation in personal and social functioning, and to risk for SMI. Reliable and valid identification of schizotypal traits has important implications for clinical practice and research. Four consecutive independent samples of undergraduates were administered the SPQ-BR (N=2552). Confirmatory factor analyses suggested a minor item wording change improved reliability, and this Updated questionnaire was implemented for three-quarters of the sample (SPQ-BRU). A, single-order, nine-factor structure had acceptable psychometric properties. The best fitting second-order structure included four higher-order factors that distinguished Social Anxiety and Interpersonal factors. This differentiation was supported by differential relationships with treatment history. The Disorganized factor had the greatest unique relationship with personal and family treatment history. With few exceptions, factor loadings showed stability across samples. Overall, the higher-order and lower-order factors of schizotypy demonstrated reliability and convergent and discriminant validity; detailed psychometric data are presented in a supplement. PMID:27086255

  14. Informatics in radiology: improving clinical work flow through an AIM database: a sample web-based lesion tracking application.

    Science.gov (United States)

    Abajian, Aaron C; Levy, Mia; Rubin, Daniel L

    2012-01-01

    Quantitative assessments on images are crucial to clinical decision making, especially in cancer patients, in whom measurements of lesions are tracked over time. However, the potential value of quantitative approaches to imaging is impeded by the difficulty and time-intensive nature of compiling this information from prior studies and reporting corresponding information on current studies. The authors believe that the quantitative imaging work flow can be automated by making temporal data computationally accessible. In this article, they demonstrate the utility of the Annotation and Image Markup standard in a World Wide Web-based application that was developed to automatically summarize prior and current quantitative imaging measurements. The system calculates the Response Evaluation Criteria in Solid Tumors metric, along with several alternative indicators of cancer treatment response, by using the data stored in the annotation files. The application also allows the user to overlay the recorded metrics on the original images for visual inspection. Clinical evaluation of the system demonstrates its potential utility in accelerating the standard radiology work flow and in providing a means to evaluate alternative response metrics that are difficult to compute by hand. The system, which illustrates the utility of capturing quantitative information in a standard format and linking it to the image from which it was derived, could enhance quantitative imaging in clinical practice without adversely affecting the current work flow. PMID:22745220

  15. How Many Samples and How Many Culture Media To Diagnose a Prosthetic Joint Infection: a Clinical and Microbiological Prospective Multicenter Study.

    Science.gov (United States)

    Bémer, Pascale; Léger, Julie; Tandé, Didier; Plouzeau, Chloé; Valentin, Anne Sophie; Jolivet-Gougeon, Anne; Lemarié, Carole; Kempf, Marie; Héry-Arnaud, Geneviève; Bret, Laurent; Juvin, Marie Emmanuelle; Giraudeau, Bruno; Corvec, Stéphane; Burucoa, Christophe

    2016-02-01

    Although numerous perioperative samples and culture media are required to diagnose prosthetic joint infection (PJI), their exact number and types have not yet been definitely determined with a high level of proof. We conducted a prospective multicenter study to determine the minimal number of samples and culture media required for accurate diagnosis of PJI. Over a 2-year period, consecutive patients with clinical signs suggesting PJI were included, with five perioperative samples per patient. The bacteriological and PJI diagnosis criteria were assessed using a random selection of two, three, or four samples and compared with those obtained using the recommended five samples (references guidelines). The results obtained with two or three culture media were then compared with those obtained with five culture media for both criteria. The times-to-positivity of the different culture media were calculated. PJI was confirmed in 215/264 suspected cases, with a bacteriological criterion in 192 (89%). The PJI was monomicrobial (85%) or polymicrobial (15%). Percentages of agreement of 98.1% and 99.7%, respectively, for the bacteriological criterion and confirmed PJI diagnosis were obtained when four perioperative samples were considered. The highest percentages of agreement were obtained with the association of three culture media, a blood culture bottle, a chocolate agar plate, and Schaedler broth, incubated for 5, 7, and 14 days, respectively. This new procedure leads to significant cost saving. Our prospective multicenter study showed that four samples seeded on three culture media are sufficient for diagnosing PJI. PMID:26637380

  16. Cluster Analysis of the Yale Global Tic Severity Scale (YGTSS): Symptom Dimensions and Clinical Correlates in an Outpatient Youth Sample

    Science.gov (United States)

    Kircanski, Katharina; Woods, Douglas W.; Chang, Susanna W.; Ricketts, Emily J.; Piacentini, John C.

    2010-01-01

    Tic disorders are heterogeneous, with symptoms varying widely both within and across patients. Exploration of symptom clusters may aid in the identification of symptom dimensions of empirical and treatment import. This article presents the results of two studies investigating tic symptom clusters using a sample of 99 youth (M age = 10.7, 81% male,…

  17. Evaluating 3D printing to solve the sample-to-device interface for LRS and POC diagnostics: example of an interlock meter-mix device for metering and lysing clinical urine samples.

    Science.gov (United States)

    Jue, Erik; Schoepp, Nathan G; Witters, Daan; Ismagilov, Rustem F

    2016-05-21

    This paper evaluates the potential of 3D printing, a semi-automated additive prototyping technology, as a means to design and prototype a sample-to-device interface, amenable to diagnostics in limited-resource settings, where speed, accuracy and user-friendly design are critical components. As a test case, we built and validated an interlock meter-mix device for accurately metering and lysing human urine samples for use in downstream nucleic acid amplification. Two plungers and a multivalve generated and controlled fluid flow through the device and demonstrate the utility of 3D printing to create leak-free seals. Device operation consists of three simple steps that must be performed sequentially, eliminating manual pipetting and vortexing to provide rapid (5 to 10 s) and accurate metering and mixing. Bretherton's prediction was applied, using the bond number to guide a design that prevents potentially biohazardous samples from leaking from the device. We employed multi-material 3D printing technology, which allows composites with rigid and elastomeric properties to be printed as a single part. To validate the meter-mix device with a clinically relevant sample, we used urine spiked with inactivated Chlamydia trachomatis and Neisseria gonorrhoeae. A downstream nucleic acid amplification by quantitative PCR (qPCR) confirmed there was no statistically significant difference between samples metered and mixed using the standard protocol and those prepared with the meter-mix device, showing the 3D-printed device could accurately meter, mix and dispense a human urine sample without loss of nucleic acids. Although there are some limitations to 3D printing capabilities (e.g. dimension limitations related to support material used in the printing process), the advantages of customizability, modularity and rapid prototyping illustrate the utility of 3D printing for developing sample-to-device interfaces for diagnostics. PMID:27122199

  18. Diagnosis of rubella infection by detecting specific immunoglobulin M antibodies in saliva samples: a clinic-based study in Niterói, RJ, Brazil

    Directory of Open Access Journals (Sweden)

    Oliveira Solange Artimos de

    2000-01-01

    Full Text Available This study was designed to investigate whether saliva could be a feasible alternative to serum for the diagnosis of recent rubella infection in a clinic setting. Forty-five paired blood and saliva samples collected 1 to 29 days after onset of illness were tested for specific immunoglobulin (Ig M by antibody-capture radioimmunoassay (MACRIA. Rubella IgM was detected in all serum samples and in 38 (84.4% saliva specimens. Forty-six serum and saliva samples from other patients with rash diseases were tested by MACRIA for control purposes and two saliva specimens were reactive. The saliva test had specificity of 96%. These results indicate that salivary IgM detection may be a convenient non-invasive alternative to serum for investigation of recent rubella cases, especially for disease surveillance and control programmes.

  19. The relationship between different types of dissociation and psychosis-like experiences in a non-clinical sample.

    Science.gov (United States)

    Humpston, Clara S; Walsh, Eamonn; Oakley, David A; Mehta, Mitul A; Bell, Vaughan; Deeley, Quinton

    2016-04-01

    This study investigated whether detachment-type dissociation, compartmentalisation-type dissociation or absorption was most strongly associated with psychosis-like experiences in the general population. Healthy participants (N=215) were tested with the Dissociative Experiences Scale (DES, for detachment-related dissociative experiences); the Harvard Group Scale of Hypnotic Susceptibility (HGSHS: A, for dissociative compartmentalisation); the Tellegen Absorption Scale (TAS, for non-clinical 'functional' dissociative experience); and two measures of psychotic-like experiences, the 21-item Peters et al. Delusions Inventory (PDI-21) and the Cardiff Anomalous Perceptions Scale (CAPS). In multiple regression analyses, DES and TAS but not HGSHS: A scores were found to be significantly associated with PDI-21 and CAPS overall scores. A post hoc hierarchical cluster analysis checking for cluster overlap between DES and CAPS items, and the TAS and CAPS items showed no overlap between items on the DES and CAPS and minimal overlap between TAS and CAPS items, suggesting the scales measure statistically distinct phenomena. These results show that detachment-type dissociation and absorption, but not compartmentalisation-type dissociation are significantly associated with psychosis-like experiences in a non-clinical population. PMID:26896781

  20. "Not Just Right Experiences" are specific to obsessive-compulsive disorder: further evidence from Italian clinical samples.

    Science.gov (United States)

    Sica, Claudio; Bottesi, Gioia; Orsucci, Antonella; Pieraccioli, Caterina; Sighinolfi, Cecilia; Ghisi, Marta

    2015-04-01

    Not Just Right Experiences (NJREs) are considered to be a perceptually tinged phenomenon mainly related to obsessive-compulsive disorder (OCD). The evidence of an association between NJREs and OCD or OC symptoms have been accumulating in the last few years, whereas there is a paucity of studies about the role of this construct in other clinical conditions considered part of the "OCD spectrum". In the current study, the NJRE-Q-R Severity scale (a well-validated measure of NJREs) was administered to 41 patients with OCD, 53 with hair-pulling disorder (HPD), 38 with gambling disorder (GD) and 43 with eating disorders (ED) along with measures of OC symptoms and general distress. In each group, NJREs were consistently associated with OC symptoms; moreover, the pattern of associations appeared coherent with the main clinical features of each disorder. The OCD group reported higher levels of NJREs severity than GD and ED, whereas there were no differences between the OCD and HPD groups. However, HPD patients did not have higher scores of NJREs severity than GD and ED counterparts. NJREs appear to be specific to OCD, but further study is needed to establish the role of this construct in OCD-related disorders. PMID:25743760

  1. FACE Analysis as a Fast and Reliable Methodology to Monitor the Sulfation and Total Amount of Chondroitin Sulfate in Biological Samples of Clinical Importance

    Directory of Open Access Journals (Sweden)

    Evgenia Karousou

    2014-06-01

    Full Text Available Glycosaminoglycans (GAGs due to their hydrophilic character and high anionic charge densities play important roles in various (pathophysiological processes. The identification and quantification of GAGs in biological samples and tissues could be useful prognostic and diagnostic tools in pathological conditions. Despite the noteworthy progress in the development of sensitive and accurate methodologies for the determination of GAGs, there is a significant lack in methodologies regarding sample preparation and reliable fast analysis methods enabling the simultaneous analysis of several biological samples. In this report, developed protocols for the isolation of GAGs in biological samples were applied to analyze various sulfated chondroitin sulfate- and hyaluronan-derived disaccharides using fluorophore-assisted carbohydrate electrophoresis (FACE. Applications to biologic samples of clinical importance include blood serum, lens capsule tissue and urine. The sample preparation protocol followed by FACE analysis allows quantification with an optimal linearity over the concentration range 1.0–220.0 µg/mL, affording a limit of quantitation of 50 ng of disaccharides. Validation of FACE results was performed by capillary electrophoresis and high performance liquid chromatography techniques.

  2. The contribution of social rank and attachment theory to depression in a non clinical sample of adolescents

    OpenAIRE

    Puissant, Sylvia Pinna; Gauthier, Jean-Marie; Van Oirbeek, R. KUL

    2011-01-01

    This study explores the relative contribution of the overall quality of attachment to the mother, to the father and to peers (Inventory of Parent and Peer Attachment scales), the style of attachment towards peers (Attachment Questionnaire for Children scale), the social rank variables (submissive behavior and social comparison), and sex and age variables in predicting the depression score (Center of Epidemiological Studies Depression Scale) on a non-psychiatric sample of 13-18 year old adoles...

  3. Evaluate the frequency distribution of nonadhesive virulence factors in carbapenemase-producing Acinetobacter baumannii isolated from clinical samples in Kermanshah

    OpenAIRE

    Mohajeri, Parviz; Sharbati, Saba; Farahani, Abbas; Rezaei, Zhaleh

    2016-01-01

    Background: Acinetobacter baumannii which is a Gram-negative bacterium can cause several different infections. The appearance of carbapenemase-producing A. baumannii in recent years has made the treatment process more difficult. The identification of virulence factors (VFs), such as nonadhesives in A. baumannii, helps to fight against related infections. Materials and Methods: A total of 104 samples from teaching hospitals in Kermanshah, Iran, were collected during a 24 months period (2011-20...

  4. Molecular characterization of Leptospira sp by multilocus variable number tandem repeat analysis (MLVA) from clinical samples: a case report

    OpenAIRE

    Hélène Pailhoriès; Rodolphe Buzelé; Mathieu Picardeau; Sylvie Robert; Emmanuelle Mercier; Laurent Mereghetti; Philippe Lanotte

    2015-01-01

    Leptospirosis is a zoonotic infection for which diagnosis is difficult. It has appeared as a global emerging infectious disease over recent years. Genotype determination often requires a Leptospira strain obtained by culture, which is a long and fastidious technique. A method based on multilocus variable number tandem repeat analysis (MLVA) to determine the genotype of Leptospira interrogans, performed directly on blood or urine samples, is proposed. This method was applied to a fatal case of...

  5. A Novel Quantitative Sampling Technique for Detection and Monitoring of Clostridium difficile Contamination in the Clinical Environment

    OpenAIRE

    Ali, Shanom; Muzslay, Monika; Wilson, Peter

    2015-01-01

    The horizontal transmission of Clostridium difficile in the hospital environment is difficult to establish. Current methods to detect C. difficile spores on surfaces are not quantitative, lack sensitivity, and are protracted. We propose a novel rapid method to detect and quantify C. difficile contamination on surfaces. Sponge swabbing was compared to contact plate sampling to assess the in vitro recovery of C. difficile ribotype 027 contamination (∼100, 101, or 102 CFU of spores) from test su...

  6. Gender differences on the Five to Fifteen questionnaire in a non-referred sample with inattention and hyperactivity-impulsivity and a clinic-referred sample with hyperkinetic disorder

    DEFF Research Database (Denmark)

    Lambek, Rikke; Trillingsgaard, Anegen; Kadesjö, Björn;

    2010-01-01

    The aim of the present study was to examine gender differences in children with inattention, hyperactivity, and impulsivity on the Five to Fifteen (FTF) parent questionnaire. First, non-referred girls (n = 43) and boys (n = 51) with problems of attention and hyperactivity-impulsivity and then...... questionnaire. Secondly, it was examined whether the application of gender mixed norms versus gender specific norms would result in varying proportions of clinic-referred children with HKD being identified as impaired on the subdomains of the FTF questionnaire. Based on results it was concluded that the use of...... a gender mixed normative sample may lead to overestimation of impairment in boys with HKD, but the type of sample applied to define impairment on the FTF should depend on the purpose for applying the questionnaire....

  7. Electrochemical genosensor array for the simultaneous detection of multiple high-risk human papillomavirus sequences in clinical samples

    Energy Technology Data Exchange (ETDEWEB)

    Civit, Laia [Nanobiotechnology and Bioanalysis Group, Departament d' Enginyeria Quimica, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Fragoso, Alex, E-mail: alex.fragoso@urv.cat [Nanobiotechnology and Bioanalysis Group, Departament d' Enginyeria Quimica, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Hoelters, Sebastian; Duerst, Matthias [Department for Gynecology, Jena University Hospital, Friedrich-Schiller-University Jena, D-07743 Jena (Germany); O' Sullivan, Ciara K., E-mail: ciara.osullivan@urv.cat [Nanobiotechnology and Bioanalysis Group, Departament d' Enginyeria Quimica, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Institucio Catalana de Recerca i Estudis Avancats, Passeig Lluis Companys 23, 08010 Barcelona (Spain)

    2012-02-17

    Highlights: Black-Right-Pointing-Pointer High-risk human papillomavirus is detected in virtually all-invasive cervical cancers. Black-Right-Pointing-Pointer Electrochemical genosensor for simultaneous detection of multiple high-risk HPV applied to cervical scrape samples. Black-Right-Pointing-Pointer Excellent correlation with HPV genotyping carried out within a hospital laboratory. - Abstract: An electrochemical genosensor array for the simultaneous detection of three high-risk human papillomavirus (HPV) DNA sequences, HPV16, 18 and 45, exhibiting high sensitivity and selectivity is presented. The electrodes of a 4 Multiplication-Sign 4 array were modified via co-immobilization of a 1:100 (mol/mol) mixture of a thiolated probe and an oligoethyleneglycol-terminated bipodal thiol. Detection of synthetic and PCR products was carried out in a sandwich type format, with the target hybridized between a surface immobilized probe and a horseradish peroxidase-labelled secondary reporter probe. The detection limits obtained in the detection of each individual target were in the pM range, allowing the application of this sensor for the detection of samples obtained from PCR amplification of cervical scrape samples. The results obtained exhibited an excellent correlation with the HPV genotyping carried out within a hospital laboratory. Multiplexing and cross-reactivity studies demonstrated high selectivity over potential interfering sequences, facilitating application of the developed platform for the high-throughput screening of multiple high-risk DNA sequences.

  8. Evaluation of kDNA PCR hybridization and ITS1 nPCR methods in different clinical samples for visceral leishmaniasis diagnosis in dogs with and without clinical signs

    International Nuclear Information System (INIS)

    Visceral leishmaniasis (VL) in Brazil is caused by Leishmania infantum and dogs are considered the main domestic reservoirs of this parasite. The VL control program in Brazil emphasizes the use of serological surveys, followed by elimination of seropositive dogs. However, serologic tests have limitations in terms of sensitivity and specificity. Molecular methods such as PCR (Polymerase Chain Reaction) associated with hybridization using 32P radiolabeled DNA probes (kDNA PCR hybridization) are useful tools in this scenario, since they are more specific and sensitive than conventional methods. A variety of samples can be employed with PCR; however non-invasive procedures are the most adequate. One of main obstacles for implementation of PCR in the canine visceral leishmaniasis (CVL) diagnosis is the lack of standardization. Few studies up to the moment compared the effectiveness of the different PCR methods and clinical samples available. The objective of this study was to compare the kDNA PCR hybridization and the Internal Transcribed Spacer 1 nested PCR (ITS1 nPCR) methods and four types of clinical samples for the diagnosis of CVL in dogs with and without clinical signs of the disease. The methods were compared using samples of conjunctival swab (SC), bone marrow (BM), skin (S) and peripheral blood (PB). A group of 60 mongrel dogs, all positive in serological and parasitological tests, were equally divided in two groups: S (with clinical signs) and A (without clinical signs). The frequencies of positive results for the kDNA PCR hybridization in the S group were: CS 97% (29/30), BM 83 % (25/30), S 63% (19/30) and PB 4 7% (14/30). By the same method the following results were obtained in the A group: CS 70% (21/30), BM 63% (19/30), S 57% (17/30) and PB 17% (5/30). The ITS1 nPCR allowed the following positivities for the S group: CS 83% (25/30), BM 97% (29/30), S 83% (25/30) and PB 70% (21/30). For the A group the following results were obtained: CS and BM 83% (25

  9. Evaluation of kDNA PCR hybridization and ITS1 nPCR methods in different clinical samples for visceral leishmaniasis diagnosis in dogs with and without clinical signs

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Aline Leandra C.; Carregal, Virginia M.; Leite, Rodrigo S.; Ferreira, Sidney A.; Andrade, Antero Silva R., E-mail: alineleandra@hotmail.com, E-mail: streptos@hotmail.com, E-mail: rleite2005@gmail.com, E-mail: vidasnino@yahoo.com.br, E-mail: antero@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil). Lab. de Radiobiologia; Melo, Maria N., E-mail: melo@icb.ufmg.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia

    2013-07-01

    Visceral leishmaniasis (VL) in Brazil is caused by Leishmania infantum and dogs are considered the main domestic reservoirs of this parasite. The VL control program in Brazil emphasizes the use of serological surveys, followed by elimination of seropositive dogs. However, serologic tests have limitations in terms of sensitivity and specificity. Molecular methods such as PCR (Polymerase Chain Reaction) associated with hybridization using {sup 32}P radiolabeled DNA probes (kDNA PCR hybridization) are useful tools in this scenario, since they are more specific and sensitive than conventional methods. A variety of samples can be employed with PCR; however non-invasive procedures are the most adequate. One of main obstacles for implementation of PCR in the canine visceral leishmaniasis (CVL) diagnosis is the lack of standardization. Few studies up to the moment compared the effectiveness of the different PCR methods and clinical samples available. The objective of this study was to compare the kDNA PCR hybridization and the Internal Transcribed Spacer 1 nested PCR (ITS1 nPCR) methods and four types of clinical samples for the diagnosis of CVL in dogs with and without clinical signs of the disease. The methods were compared using samples of conjunctival swab (SC), bone marrow (BM), skin (S) and peripheral blood (PB). A group of 60 mongrel dogs, all positive in serological and parasitological tests, were equally divided in two groups: S (with clinical signs) and A (without clinical signs). The frequencies of positive results for the kDNA PCR hybridization in the S group were: CS 97% (29/30), BM 83 % (25/30), S 63% (19/30) and PB 4 7% (14/30). By the same method the following results were obtained in the A group: CS 70% (21/30), BM 63% (19/30), S 57% (17/30) and PB 17% (5/30). The ITS1 nPCR allowed the following positivities for the S group: CS 83% (25/30), BM 97% (29/30), S 83% (25/30) and PB 70% (21/30). For the A group the following results were obtained: CS and BM 83

  10. Changes in disengagement coping mediate changes in affect following mindfulness-based cognitive therapy in a non-clinical sample.

    Science.gov (United States)

    Cousin, Gaëtan; Crane, Catherine

    2016-08-01

    Past research has shown that mindfulness-based interventions increase positive affect in non-clinical populations. However, the mechanisms underlying this increase are poorly understood. On the basis of previous empirical and theoretical accounts, we hypothesized that a decreased use of disengagement coping strategies in daily life would explain the benefits of a mindfulness-based intervention in terms of increased positive affect. We analysed the data of 75 healthy adult participants (58 women; 17 men) of different ages (M = 49 years old; SD = 13; age range 19-81) who had been randomly allocated to 8-week Mindfulness-Based Cognitive Therapy (MBCT) or to a waitlist control group. The results confirmed our hypothesis: Participants in the MBCT group showed significant improvements in positive affect compared to the control group, with decreased use of disengagement coping styles mediating these improvements. The implications of this study are discussed. PMID:26385256

  11. Molecular detection and characterization of infectious laryngotracheitis virus (Gallid herpesvirus-1) from clinical samples of commercial poultry flocks in India.

    Science.gov (United States)

    Gowthaman, Vasudevan; Singh, Sambhu Dayal; Dhama, Kuldeep; Barathidasan, Rajamani; Mathapati, Basavaraj S; Srinivasan, Palani; Saravanan, Sellappan; Ramakrishnan, Muthannan Andavar

    2014-01-01

    Although the existence of infectious laryngotracheitis virus (ILTV) in India was first reported in 1964, no reports are available regarding its molecular detection and characterization. The present study was aimed to detect and characterize ILTV from recent respiratory disease complex (RDC) outbreaks of commercial poultry flocks in different parts of the country by using envelope glycoprotein G gene (US4 gene) based PCR and sequencing. A total of thirty two flocks with a history of RDC were investigated. Overall, all the strains/breeds of birds and all ages of birds are equally susceptible and depending on the severity, the clinical signs and gross lesions were varied. Out of 32 flocks investigated 10 were found positive for ILTV infection by PCR. The phylogenetic analyses of eight representative sequences in the present study deciphered that Indian ILT viruses are closely related to chicken embryo origin vaccine strains of Italy, USA, China and Brazil. PMID:25674602

  12. Blood-Injection-Injury Phobia and Dog Phobia in Youth: Psychological Characteristics and Associated Features in a Clinical Sample.

    Science.gov (United States)

    Oar, Ella L; Farrell, Lara J; Waters, Allison M; Ollendick, Thomas H

    2016-05-01

    Blood-Injection-Injury (BII) phobia is a particularly debilitating condition that has been largely ignored in the child literature. The present study examined the clinical phenomenology of BII phobia in 27 youths, relative to 25 youths with dog phobia-one of the most common and well-studied phobia subtypes in youth. Children were compared on measures of phobia severity, functional impairment, comorbidity, threat appraisals (danger expectancies and coping), focus of fear, and physiological responding, as well as vulnerability factors including disgust sensitivity and family history. Children and adolescents with BII phobia had greater diagnostic severity. In addition, they were more likely to have a comorbid diagnosis of a physical health condition, to report more exaggerated danger expectancies, and to report fears that focused more on physical symptoms (e.g., faintness and nausea) in comparison to youth with dog phobia. The present study advances knowledge relating to this poorly understood condition in youth. PMID:27157026

  13. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations

    Directory of Open Access Journals (Sweden)

    Stürenburg, Enno

    2009-07-01

    Full Text Available Methicillin-resistant Staphylococcus aureus (MRSA isolates is a serious public health problem whose ever-increasing rate is commensurate with the pressure it is exerting on the healthcare system. At present, more than 20% of clinical S. aureus isolates in German hospitals are methicillin resistant. Strategies from low-prevalence countries show that this development is not necessarily inevitable. In the Scandinavian countries and the Netherlands, thanks to a rigorous prevention programme, MRSA prevalence has been kept at an acceptably low level (<1–3%. Central to these ‘search and destroy’ control strategies is an admission screening using several MRSA swabs taken from mucocutaneous colonisation sites of high-risk patients (‘MRSA surveillance’. It has also been reported that the speed with which MRSA carriage is detected has an important role to play, as it is a key component of any effective strategy to prevent the pathogen from spreading. Since MRSA culturing involves a 2–3 day delay before the final results are available, rapid detection techniques (commonly referred to as ‘MRSA rapid tests’ using PCR methods and, most recently, rapid culturing methods have been developed. The implementation of rapid tests reduces the time of detection of MRSA carriers from 48–72 to 2–5 h. Clinical evaluation data have shown that MRSA can thus be detected with very high sensitivity. Specificity however is sometimes impaired due to false-positive PCR signals occurring in mixed flora specimens. In order to rule out any false-positive PCR results, a culture screen must always be carried out simultaneously.The data provide preliminary evidence that a PCR assay can reduce nosocomial MRSA transmission in high-risk patients or high-risk areas, whereas an approach that screens all patients admitted to the hospital is probably not effective. Information concerning the cost-effectiveness of rapid MRSA tests is still sparse and thus the issue remains

  14. Confirmatory factor analysis of the Wechsler Intelligence Scale for Children--Third Edition in an Australian clinical sample.

    Science.gov (United States)

    Cockshott, Felicity C; Marsh, Nigel V; Hine, Donald W

    2006-09-01

    A confirmatory factor analysis was conducted on the Wechsler Intelligence Scale for Children-Third Edition (WISC-III; D. Wechsler, 1991) with a sample of 579 Australian children referred for assessment because of academic difficulties in the classroom. The children were administered the WISC-III as part of the initial eligibility determination process for funding of special education services. The children were aged between 6 years and 16 years 7 months. One-, two-, three-, and four-factor models were tested. The four-factor model proposed in the WISC-III manual fit the data significantly better than all other models tested. PMID:16953739

  15. Evaluation of Sensitivity of Multiplex PCR for Detection of Mycobacterium tuberculosis and Pneumocystis jirovecii in Clinical Samples

    OpenAIRE

    Boondireke, Sirirat; Mungthin, Mathirut; Tan-ariya, Peerapan; Boonyongsunchai, Petchara; Naaglor, Tawee; Wattanathum, Anan; Treewatchareekorn, Sompong; Leelayoova, Saovanee

    2010-01-01

    A multiplex PCR assay for the simultaneous detection of Mycobacterium tuberculosis and Pneumocystis jirovecii was developed using IS6110-based detection for M. tuberculosis and mitochondrial large-subunit (mtLSU) rRNA gene detection for P. jirovecii. Ninety-five pulmonary blinded samples were examined using the developed multiplex PCR assay, and the results were compared with those obtained by the single nested PCRs targeting IS6110 for M. tuberculosis and mtLSU rRNA for P. jirovecii. Of the ...

  16. Detection of Spliced mRNA from Human Bocavirus 1 in Clinical Samples from Children with Respiratory Tract Infections

    OpenAIRE

    Christensen, Andreas; Døllner, Henrik; Skanke, Lars Høsøien; Krokstad, Sidsel; Moe, Nina; Nordbø, Svein Arne

    2013-01-01

    Human bocavirus 1 (HBoV1) is a parvovirus associated with respiratory tract infections (RTIs) in children, but a causal relation has not yet been confirmed. To develop a qualitative reverse transcription PCR to detect spliced mRNA from HBoV1 and to determine whether HBoV1 mRNA correlated better with RTIs than did HBoV1 DNA, we used samples from HBoV1 DNA–positive children, with and without RTIs, to evaluate the test. A real-time reverse transcription PCR, targeting 2 alternatively spliced mRN...

  17. Molecular characterization of Leptospira sp by multilocus variable number tandem repeat analysis (MLVA from clinical samples: a case report

    Directory of Open Access Journals (Sweden)

    Hélène Pailhoriès

    2015-08-01

    Full Text Available Leptospirosis is a zoonotic infection for which diagnosis is difficult. It has appeared as a global emerging infectious disease over recent years. Genotype determination often requires a Leptospira strain obtained by culture, which is a long and fastidious technique. A method based on multilocus variable number tandem repeat analysis (MLVA to determine the genotype of Leptospira interrogans, performed directly on blood or urine samples, is proposed. This method was applied to a fatal case of leptospirosis for which the geographical origin of infection was unknown. This technique will allow a genotype to be obtained for L. interrogans, even when cultures remain negative.

  18. Prevalence of virulence factors and antibiotic resistance in vancomycin-resistant Enterococcus faecium isolated from sewage and clinical samples in Iran

    Directory of Open Access Journals (Sweden)

    Jahangiri S

    2010-01-01

    Full Text Available Purpose: The purpose of the present study was to perform a molecular epidemiological survey by investigating the antibiotic resistance and the presence of known virulence factors in Enterococcus faecium isolates in Iran. The data collected from this study would allow us to control the spread and develop strategies for treatment of the enterococcal infections. Materials and Methods: In this study, 156 vancomycin-sensitive E. faecium (VSEF; 58 and vancomycin-resistant E. faecium (VREF; 98 samples were isolated from clinical specimen and sewage treatment plants (STPs. These isolates were screened for the presence of genes encoding for aggregation substance (asa1, cytolysin (cyl, enterococcal surface protein (esp, gelatinase (gelE and hyaluronidase (hyl by polymerase chain reaction (PCR. Results: Although significantly different, the results showed the presence of hyl and esp genes in both clinical (41 and 75%, respectively and sewage (3.2 and 41%, respectively isolates. Sensitivity of all isolates to seven antibiotics was examined. The results of the clinical isolates showed that the majority of esp positive isolates were also resistant to vancomycin, ciprofloxacin and erythromycin. Furthermore, cyl, gelE and asa1 were not found in either clinical or STP isolates. Finally, we determined the distinct types of isolates using Pulse Field Gel Electrophoresis (PFGE, which confirmed that most of the isolates were clonally unrelated. Conclusion: Our results demonstrated that higher number of the clinical E. faecium isolates carried virulence genes than the isolates from STP. Finally, the lack of the genes in clinical and STP isolates confirmed that these genes do not transfer horizontally.

  19. Differential Diagnosis of Entamoeba spp. in Clinical Stool Samples Using SYBR Green Real-Time Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Thiago dos Santos Gomes

    2014-01-01

    Full Text Available Amoebiasis, a disease caused by Entamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of the E. histolytica/E. dispar complex. Furthermore, morphologically similar species such as Entamoeba hartmanni contribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system for E. histolytica and E. dispar and a single real-time PCR for E. hartmanni. The multiplex protocol detected up to 0.0143 pg of E. histolytica DNA and 0.5156 pg of E. dispar DNA, and the average melting temperature (Tm was 73°C and 70°C, respectively. For E. hartmanni, the Tm was 73°C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested, E. dispar DNA was detected in 37; none exhibited E. histolytica DNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however, E. hartmanni DNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries.

  20. Differential diagnosis of Entamoeba spp. in clinical stool samples using SYBR green real-time polymerase chain reaction.

    Science.gov (United States)

    Gomes, Thiago Dos Santos; Garcia, Mariana Coimbra; de Souza Cunha, Flavia; Werneck de Macedo, Heloisa; Peralta, José Mauro; Peralta, Regina Helena Saramago

    2014-01-01

    Amoebiasis, a disease caused by Entamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of the E. histolytica/E. dispar complex. Furthermore, morphologically similar species such as Entamoeba hartmanni contribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system for E. histolytica and E. dispar and a single real-time PCR for E. hartmanni. The multiplex protocol detected up to 0.0143 pg of E. histolytica DNA and 0.5156 pg of E. dispar DNA, and the average melting temperature (T(m)) was 73 °C and 70 °C, respectively. For E. hartmanni, the T(m) was 73 °C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested, E. dispar DNA was detected in 37; none exhibited E. histolytica DNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however, E. hartmanni DNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries. PMID:24693242

  1. Assessing Eating Disorder Risk: The Pivotal Role of Achievement Anxiety, Depression and Female Gender in Non-Clinical Samples

    Directory of Open Access Journals (Sweden)

    Christos C. Frangos

    2013-03-01

    Full Text Available The objective of the present study was to assess factors predicting eating disorder risk in a sample of undergraduate students. A structured questionnaire was employed on a random sample (n = 1865 consisting of the following sections: demographics, SCOFF (Sick, Control, One stone, Fat, Food questionnaire for screening eating disorders and the Achievement Anxiety Test and the Depression, Anxiety and Stress Scale. The students at risk for eating disorders (SCOFF score ≥2 were 39.7%. Eating disorder risk was more frequent in females, students with divorced parents, students who lived alone, students who were seeking a romantic relationship or were married, students who were at a post-secondary vocational institute/college (private-public educational level and who were more likely to have marks under merit level. Also, the mean scores for the psychological factors of depression, stress and anxiety were higher in students with eating disorder risk. A logistic regression model was produced depicting that depression, stress, female gender, being married and searching for a romantic relationship were risk factors of having an eating disorder risk. The suggested psychological model examined with structural equation modelling signified the role of academic anxiety as an immediate precursor of general anxiety. Hence, college populations in Greece need organized infrastructures of nutrition health services and campaigns to assist in reducing the risk of eating disorders.

  2. Gene expression data from acetaminophen-induced toxicity in human hepatic in vitro systems and clinical liver samples

    Directory of Open Access Journals (Sweden)

    Robim M. Rodrigues

    2016-06-01

    Full Text Available This data set is composed of transcriptomics analyses of (i liver samples from patients suffering from acetaminophen-induced acute liver failure (ALF and (ii hepatic cell systems exposed to acetaminophen and their respective controls. The in vitro systems include widely employed cell lines i.e. HepaRG and HepG2 cells as well as a novel stem cell-derived model i.e. human skin-precursors-derived hepatocyte-like cells (hSKP-HPC. Data from primary human hepatocytes was also added to the data set “Open TG-GATEs: a large-scale toxicogenomics database” (Igarashi et al., 2015 [1]. Changes in gene expression due to acetaminophen intoxication as well as comparative information between human in vivo and in vitro samples are provided. The microarray data have been deposited in NCBI׳s Gene Expression Omnibus and are accessible through GEO Series accession number GEO: GSE74000. The provided data is used to evaluate the predictive capacity of each hepatic in vitro system and can be directly compared with large-scale publically available toxicogenomics databases. Further interpretation and discussion of these data feature in the corresponding research article “Toxicogenomics-based prediction of acetaminophen-induced liver injury using human hepatic cell systems” (Rodrigues et al., 2016 [2].

  3. Antibiotic Resistance and the Frequency of Extended-Spectrum B-Lactamase in Acinetobacter baumannii Isolated from Clinical Samples through Phenotypic Methods

    Directory of Open Access Journals (Sweden)

    Somayeh Vafaei

    2013-07-01

    Full Text Available AbstractBackground and objectives: Nowadays Acinetobacter baumannii is as one of the problematic opportunistic pathogens, especially in intensive care because of the incidence of drug-resistant strains in the world. The purpose of current study was to define the antibiotic susceptibility patterns and detect the prevalence of producing strains of extended-spectrum β-lactamase (ESBL in A. baumannii isolates which had been isolated from clinical samples with combined disk test.Materials and methods: This study was conducted in 3 major hospitals in Tehran on 500 clinical samples during 6 months. After identification of isolates in species level using cultural and biochemical methods, in order to determine sensitivity of 100 isolates of A. baumannii to 11 antibiotics, the susceptibility tests were carried out according to CLSI guidelines using disk diffusion method. Also MIC (Minimum inhibitory concentrations was determined for cefepime and ceftazidime, and finally to identify of producing strains of ESBL was applied phenotypic method of combined disk. Results: In this survey, 100 A. baumannii strains, 30 A. lwoffii strains and other Acinetobacter species were isolated from patients. The majority of isolates were from blood specimens. Isolates of A.baumannii revealed the highest resistance to cefepime, ceftriaxone, amikacin, imipenem, piperacillin - tazobactam, meropenem, gentamicin, tobramycina and tetracycline, respectively. Ampicillin - sulbactam and polymyxin B considered as effective drugs in this study. Multi-drug resistance in these strains was 70%. The Total isolates studied the Minimum inhibitory concentrations of ceftazidime in 84% samples was MIC ≥ 128 μg/ml and Minimum inhibitory concentrations of cefepime in 91% samples was MIC≥ 128 μg/ml. According to the results of combined disk test, 20% of total samples were demonstrated to be ESBL positive.Conclusion: Regarding to produce of ESBL in this bacterium and possibility of

  4. Detection of Bartonella henselae DNA in clinical samples including peripheral blood of immune competent and immune compromised patients by three nested amplifications

    Directory of Open Access Journals (Sweden)

    Karina Hatamoto Kawasato

    2013-02-01

    Full Text Available Bacteria of the genus Bartonella are emerging pathogens detected in lymph node biopsies and aspirates probably caused by increased concentration of bacteria. Twenty-three samples of 18 patients with clinical, laboratory and/or epidemiological data suggesting bartonellosis were subjected to three nested amplifications targeting a fragment of the 60-kDa heat shock protein (HSP, the internal transcribed spacer 16S-23S rRNA (ITS and the cell division (FtsZ of Bartonella henselae, in order to improve detection in clinical samples. In the first amplification 01, 04 and 05 samples, were positive by HSP (4.3%, FtsZ (17.4% and ITS (21.7%, respectively. After the second round six positive samples were identified by nested-HSP (26%, eight by nested-ITS (34.8% and 18 by nested-FtsZ (78.2%, corresponding to 10 peripheral blood samples, five lymph node biopsies, two skin biopsies and one lymph node aspirate. The nested-FtsZ was more sensitive than nested-HSP and nested-ITS (p < 0.0001, enabling the detection of Bartonella henselae DNA in 15 of 18 patients (83.3%. In this study, three nested-PCR that should be specific for Bartonella henselae amplification were developed, but only the nested-FtsZ did not amplify DNA from Bartonella quintana. We conclude that nested amplifications increased detection of B. henselae DNA, and that the nested-FtsZ was the most sensitive and the only specific to B. henselae in different biological samples. As all samples detected by nested-HSP and nested-ITS, were also by nested-FtsZ, we infer that in our series infections were caused by Bartonella henselae. The high number of positive blood samples draws attention to the use of this biological material in the investigation of bartonellosis, regardless of the immune status of patients. This fact is important in the case of critically ill patients and young children to avoid more invasive procedures such as lymph nodes biopsies and aspirates.

  5. Detection of E. coli O157:H7 and Shigella dysenteriae toxins in clinical samples by PCR-ELISA

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    Jafar Amani

    2015-06-01

    Full Text Available Shiga toxin producing bacteria are potential causes of serious human disease such as hemorrhagic colitis, severe inflammations of ileocolonic regions of gastrointestinal tract, thrombocytopenia, septicemia, malignant disorders in urinary ducts, hemolytic uremic syndrome (HUS Shiga toxin 1 (stx1, shiga toxin 2 (stx2, or a combination of both are responsible for most clinical symptoms of these diseases. A lot of methods have been developed so far to detect shiga toxins such as cell culture, ELISA, and RFPLA, but due to high costs and labor time in addition to low sensitivity, they have not received much attention. In this study, PCR-ELISA method was used to detect genes encoding shiga toxins 1 and 2 (stx1 and stx2. To detect stx1 and stx2 genes, two primer pairs were designed for Multiplex-PCR then PCR-ELISA. PCR products (490 and 275, respectively were subsequently verified by sequencing. Sensitivity and specificity of PCR-ELISA method were determined by using genome serial dilution and Enterobacteriastrains. PCR-ELISA method used in this study proved to be a rapid and precise approach to detect different types of shiga toxins and can be used to detect bacterial genes encoding shiga toxins.

  6. An evaluation of service utilization among male to female transgender youth: qualitative study of a clinic-based sample.

    Science.gov (United States)

    Corliss, Heather L; Belzer, Marvin; Forbes, Catherine; Wilson, Erin C

    2007-01-01

    This qualitative study examined experiences with health and social service institutions and experiences related to education, employment, and other social networks among 18 ethnically diverse, male to female (MTF) transgender youth aged 16 to 24 years. Participants were recruited from a youth health clinic where they were receiving services for their transgender/transsexual identity. In-depth, semi-structured interviews explored youths' patterns of service utilization, reasons for seeking care, beliefs about the usefulness of services received, experiences with service providers, barriers to care, and suggestions for improving services tailored to them. Similar to other studies with this population, participants described a multitude of health and social risk experiences as well as complex needs related to healthcare, education, employment, housing, personal relationships, and safety. Results suggest a mixed pattern of both positive and negative experiences within the medical, social and mental health services arenas. To improve support for transgender youth and assist in their positive development, it is essential to improve and expand the availability of culturally competent and effective services for this population. PMID:19835041

  7. Application of a pathogen microarray for the analysis of viruses and bacteria in clinical diagnostic samples from pigs.

    Science.gov (United States)

    Jaing, Crystal J; Thissen, James B; Gardner, Shea N; McLoughlin, Kevin S; Hullinger, Pam J; Monday, Nicholas A; Niederwerder, Megan C; Rowland, Raymond R R

    2015-05-01

    Many of the disease syndromes challenging the commercial swine industry involve the analysis of complex problems caused by polymicrobial, emerging or reemerging, and transboundary pathogens. This study investigated the utility of the Lawrence Livermore Microbial Detection Array (Lawrence Livermore National Laboratory, Livermore, California), designed to detect 8,101 species of microbes, in the evaluation of known and unknown microbes in serum, oral fluid, and tonsil from pigs experimentally coinfected with Porcine reproductive and respiratory syndrome virus (PRRSV) and Porcine circovirus-2 (PCV-2). The array easily identified PRRSV and PCV-2, but at decreased sensitivities compared to standard polymerase chain reaction detection methods. The oral fluid sample was the most informative, possessing additional signatures for several swine-associated bacteria, including Streptococcus sp., Clostridium sp., and Staphylococcus sp. PMID:25855363

  8. Characterization of dengue virus infections in a sample of patients suggests unique clinical, immunological, and virological profiles that impact on the diagnosis of dengue and dengue hemorrhagic fever.

    Science.gov (United States)

    Senaratne, Thamarasi; Wimalaratne, Harith; Alahakoon, D G S; Gunawardane, Nirmali; Carr, Jillian; Noordeen, Faseeha

    2016-10-01

    Dengue virus (DENV) infections are increasing with respect to incidence and severity in the Central Province of Sri Lanka. The objective of this study was to define the clinical, immunological, and virological profiles of patients admitted to the General Hospital, Kandy with clinically apparent dengue. Demographic, clinical, hematological parameters, liver enzymes (ALT and AST), and blood samples were collected from 292 patients with fever dengue fever/dengue hemorrhagic fever (DF/DHF). Samples were analyzed for, anti-DENV IgM, IgG, and DENV nucleic acid. Myalgia was the commonest complaint by 65% of the patients. Packed cell volume was >45% in 27% of the patients while 42.12% had reduced platelets and 62.67% had reduced white blood cell counts. In contrast to other studies, positive tourniquet test (PTT) and petechiae were not major indicators of DENV infection or severity of the disease. Clinical profiles were significantly different between DF and DHF/DSS and showed many similarities to that reported elsewhere. Altogether, 43 patients (14.73%) were viremic as detected by RT-PCR; 181 patients (62%) were positive for anti-DENV IgM, and 245 (84%) patients were positive for anti-DENV IgG. In combination, anti-DENV IgM and RT-PCR assays detected 224 (77.5%) of DENV infected cases, thus improving the DENV diagnosis rate. Hence, the diagnostic utility of PTT, anti-DENV IgM/IgG serology, or RT-PCR used alone in the early phase of illness is low in Sri Lanka but the diagnostic value can be improved by a combination of serology and RT-PCR. J. Med. Virol. 88:1703-1710, 2016. © 2016 Wiley Periodicals, Inc. PMID:26990973

  9. Analytical investigations of toxic p-phenylenediamine (PPD levels in clinical urine samples with special focus on MALDI-MS/MS.

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    Gero P Hooff

    Full Text Available Para-phenylenediamine (PPD is a common chromophoric ingredient in oxidative hair-dyes. In some African countries like Sudan, Egypt and Morocco but also in India this chemical is used alone or in combination with colouring extracts like Henna for dyeing of the hair or the skin. Excessive dermal exposure to PPD mainly leads to the N-mono- and N,N'-diacetylated products (MAPPD, DAPPD by N-acetyltransferase 1 and 2 (NAT1 and 2 catalyzed reactions. Metabolites and PPD are mainly excreted via renal clearance. Despite a low risk of intoxication when used in due form, there are numerous cases of acute intoxication in those countries every year. At the ENT Hospital - Khartoum (Sudan alone more than 300 cases are reported every year (~10% fatal, mostly caused by either an accidental or intended (suicidal high systemic exposure to pure PPD. Intoxication leads to a severe clinical syndrome including laryngeal edema, rhabdomyolysis and subsequent renal failure, neurotoxicity and acute toxic hepatitis. To date, there is no defined clinical treatment or antidote available and treatment is largely supportive. Herein, we show the development of a quick on-site identification assay to facilitate differential diagnosis in the clinic and, more importantly, the implementation of an advanced analytical platform for future in-depth investigations of PPD intoxication and metabolism is described. The current work shows a sensitive (~25 µM wet chemistry assay, a validated MALDI-MS/MS and HPLC-UV assay for the determination of PPD and its metabolites in human urine. We show the feasibility of the methods for measuring PPD over a range of 50-1000 µM. The validation criteria included linearity, lower limit of quantification (LLOQ, accuracy and precision, recovery and stability. Finally, PPD concentrations were determined in clinical urine samples of cases of acute intoxication and the applied technique was expanded to identify MAPPD and DAPPD in the identical samples.

  10. Two to five repeated measurements per patient reduced the required sample size considerably in a randomized clinical trial for patients with inflammatory rheumatic diseases

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    Smedslund Geir

    2013-02-01

    Full Text Available Abstract Background Patient reported outcomes are accepted as important outcome measures in rheumatology. The fluctuating symptoms in patients with rheumatic diseases have serious implications for sample size in clinical trials. We estimated the effects of measuring the outcome 1-5 times on the sample size required in a two-armed trial. Findings In a randomized controlled trial that evaluated the effects of a mindfulness-based group intervention for patients with inflammatory arthritis (n=71, the outcome variables Numerical Rating Scales (NRS (pain, fatigue, disease activity, self-care ability, and emotional wellbeing and General Health Questionnaire (GHQ-20 were measured five times before and after the intervention. For each variable we calculated the necessary sample sizes for obtaining 80% power (α=.05 for one up to five measurements. Two, three, and four measures reduced the required sample sizes by 15%, 21%, and 24%, respectively. With three (and five measures, the required sample size per group was reduced from 56 to 39 (32 for the GHQ-20, from 71 to 60 (55 for pain, 96 to 71 (73 for fatigue, 57 to 51 (48 for disease activity, 59 to 44 (45 for self-care, and 47 to 37 (33 for emotional wellbeing. Conclusions Measuring the outcomes five times rather than once reduced the necessary sample size by an average of 27%. When planning a study, researchers should carefully compare the advantages and disadvantages of increasing sample size versus employing three to five repeated measurements in order to obtain the required statistical power.

  11. The Social Appearance Anxiety Scale in Italian adolescent populations: Construct validation and group discrimination in community and clinical eating disorders samples

    OpenAIRE

    Dakanalis, Antonios; Carrà, Giuseppe; Calogero, Rachel M.; Zanetti, M. Assunta; Volpato, Chiara; Riva, Giuseppe; Clerici, Massimo; Cipresso, Pietro

    2015-01-01

    Anxiety in situations where one’s overall appearance (including body shape) may be negatively evaluated is hypothesized to play a central role in Eating Disorders (EDs) and in their co-occurrence with Social Anxiety Disorder (SAD). Three studies were conducted among community (N = 1995) and clinical (N = 703) ED samples of 11- to 18-year-old Italian girls and boys to (a) evaluate the psychometric qualities and measurement equivalence/invariance (ME/I) of the Social Appearance Anxiety (SAA) Sc...

  12. Molecular characterization of vancomycin-resistant Enterococcus faecium strains isolated from carriage and clinical samples in a tertiary hospital, Turkey.

    Science.gov (United States)

    Gozalan, Aysegul; Coskun-Ari, Fatma Filiz; Ozdem, Birsen; Unaldi, Ozlem; Celikbilek, Nevreste; Kirca, Fisun; Aydogan, Sibel; Muderris, Tuba; Guven, Tumer; Acikgoz, Ziya Cibali; Durmaz, Riza

    2015-07-01

    This study aimed to determine the presence of vancomycin resistance (vanA and vanB) and virulence genes (esp, asa1, gelE, ace, hyl, cylA, cpd and ebpA) in vancomycin-resistant Enterococcus faecium (VREfm) strains and to analyse the clonal relationships among the strains. E. faecium strains were identified from rectal and clinical specimens by biochemical tests and the API-20 Strep kit. Susceptibility testing was performed using disc-diffusion and broth-dilution methods. PFGE was used for molecular typing of the VREfm strains. The vancomycin resistance and virulence genes were amplified by two-step multiplex PCR. All 55 VREfm isolates were resistant to penicillin G, ampicillin and high-level gentamicin but were susceptible to quinupristin/dalfopristin and linezolid. Multiplex PCR analysis indicated that all isolates harboured vanA and that 41 (75 %) were positive for virulence genes. The esp gene was the most common virulence factor and was detected in nine (41 %) invasive and 32 (96.7 %) non-invasive isolates. Multiple virulence genes were observed only in two non-invasive isolates; one harboured esp and ebpA and the other harboured esp, ebpA, asa1, gelE and cpd. PFGE typing yielded 16 different types, seven of which were clusters with two to 14 strains each. The clustering rates of the rectal swab, blood and urine isolates were 72.7 %, 61.5 % and 87.5 %, respectively. The genetic similarity observed among the VREfm isolates indicated cross-transmission in the hospital. Further studies on the virulence factors present in the strains might provide insight into the acquisition of these traits and their contribution to increased prevalence of VREfm. PMID:25976005

  13. The clinical value of HPV genotyping in triage of women with high-risk-HPV-positive self-samples.

    Science.gov (United States)

    Ebisch, Renée M F; de Kuyper-de Ridder, Gabriëlle M; Bosgraaf, Remko P; Massuger, Leon F A G; IntHout, Joanna; Verhoef, Viola M J; Heideman, Daniëlle A M; Snijders, Peter J F; Meijer, Chris J L M; van Kemenade, Folkert J; Bulten, Johan; Siebers, Albert G; Bekkers, Ruud L M; Melchers, Willem J G

    2016-08-01

    Cytology alone, or combined with HPV16/18 genotyping, might be an acceptable method for triage in hrHPV-cervical cancer screening. Previously studied HPV-genotype based triage algorithms are based on cytology performed without knowledge of hrHPV status. The aim of this study was to explore the value of hrHPV genotyping combined with cytology as triage tool for hrHPV-positive women. 520 hrHPV-positive women were included from a randomised controlled self-sampling trial on screening non-attendees (PROHTECT-3B). Eighteen baseline triage strategies were evaluated for cytology and hrHPV genotyping (Roche Cobas 4800) on physician-sampled triage material. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), referral rate, and number of referrals needed to diagnose (NRND) were calculated for CIN2+ and CIN3+. A triage strategy was considered acceptable if the NPV for CIN3+ was ≥98%, combined with maintenance or improvement of sensitivity and an increase in specificity in reference to the comparator, being cytology with a threshold of atypical cells of undetermined significance (ASC-US). Three triage strategies met the criteria: HPV16+ and/or ≥LSIL; HPV16+ and/or ≥HSIL; (HPV16+ and/or HPV18+) and/or ≥HSIL. Combining HPV16+ and/or ≥HSIL yielded the highest specificity (74.9%, 95% CI 70.5-78.9), with a sensitivity (94.4%, 95% CI 89.0-97.7) similar to the comparator (93.5%, 95% CI 87.7-97.1), and a decrease in referral rate from 52.2% to 39.5%. In case of prior knowledge of hrHPV presence, triage by cytology testing can be improved by adjusting its threshold, and combining it with HPV16/18 genotyping. These strategies improve the referral rate and specificity for detecting CIN3+ lesions, while maintaining adequate sensitivity. PMID:26991464

  14. The self-report Version of the LSAS-CA: Psychometric Properties of the French Version in a non-clinical adolescent sample

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    Emilie Schmits

    2014-02-01

    Full Text Available The Liebowitz Social Anxiety Scale (LSAS is one of the most popular measures of social anxiety in adults. The LSAS has been adapted for clinical assessment of children and adolescents (LSAS-CA. The psychometric properties of the self-report version of the LSAS-CA (LSAS-CA-SR have been investigated in a Spanish population. However, no study to date has adapted and validated this scale in French. The purpose of this study was to develop a French version of the LSAS-CA-SR and to assess its score reliability and structural validity in a French-speaking community sample. The sample was made up of 1,343 teenagers from secondary schools, aged between 14 and 18 years. Confirmatory factor analyses established the structural validity of the French version of the LSAS-CA-SR and good psychometric properties, including reliable internal consistency, were observed.

  15. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study.

    Science.gov (United States)

    Colman, Rebecca E; Anderson, Julia; Lemmer, Darrin; Lehmkuhl, Erik; Georghiou, Sophia B; Heaton, Hannah; Wiggins, Kristin; Gillece, John D; Schupp, James M; Catanzaro, Donald G; Crudu, Valeriu; Cohen, Ted; Rodwell, Timothy C; Engelthaler, David M

    2016-08-01

    Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool. PMID:27225403

  16. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study

    Science.gov (United States)

    Anderson, Julia; Lemmer, Darrin; Lehmkuhl, Erik; Georghiou, Sophia B.; Heaton, Hannah; Wiggins, Kristin; Gillece, John D.; Schupp, James M.; Catanzaro, Donald G.; Crudu, Valeriu; Cohen, Ted; Rodwell, Timothy C.; Engelthaler, David M.

    2016-01-01

    Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool. PMID:27225403

  17. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification

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    Smolich Beverly D

    2003-02-01

    Full Text Available Abstract Background Microarray-based gene expression profiling is a powerful approach for the identification of molecular biomarkers of disease, particularly in human cancers. Utility of this approach to measure responses to therapy is less well established, in part due to challenges in obtaining serial biopsies. Identification of suitable surrogate tissues will help minimize limitations imposed by those challenges. This study describes an approach used to identify gene expression changes that might serve as surrogate biomarkers of drug activity. Methods Expression profiling using microarrays was applied to peripheral blood mononuclear cell (PBMC samples obtained from patients with advanced colorectal cancer participating in a Phase III clinical trial. The PBMC samples were harvested pre-treatment and at the end of the first 6-week cycle from patients receiving standard of care chemotherapy or standard of care plus SU5416, a vascular endothelial growth factor (VEGF receptor tyrosine kinase (RTK inhibitor. Results from matched pairs of PBMC samples from 23 patients were queried for expression changes that consistently correlated with SU5416 administration. Results Thirteen transcripts met this selection criterion; six were further tested by quantitative RT-PCR analysis of 62 additional samples from this trial and a second SU5416 Phase III trial of similar design. This method confirmed four of these transcripts (CD24, lactoferrin, lipocalin 2, and MMP-9 as potential biomarkers of drug treatment. Discriminant analysis showed that expression profiles of these 4 transcripts could be used to classify patients by treatment arm in a predictive fashion. Conclusions These results establish a foundation for the further exploration of peripheral blood cells as a surrogate system for biomarker analyses in clinical oncology studies.

  18. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification

    International Nuclear Information System (INIS)

    Microarray-based gene expression profiling is a powerful approach for the identification of molecular biomarkers of disease, particularly in human cancers. Utility of this approach to measure responses to therapy is less well established, in part due to challenges in obtaining serial biopsies. Identification of suitable surrogate tissues will help minimize limitations imposed by those challenges. This study describes an approach used to identify gene expression changes that might serve as surrogate biomarkers of drug activity. Expression profiling using microarrays was applied to peripheral blood mononuclear cell (PBMC) samples obtained from patients with advanced colorectal cancer participating in a Phase III clinical trial. The PBMC samples were harvested pre-treatment and at the end of the first 6-week cycle from patients receiving standard of care chemotherapy or standard of care plus SU5416, a vascular endothelial growth factor (VEGF) receptor tyrosine kinase (RTK) inhibitor. Results from matched pairs of PBMC samples from 23 patients were queried for expression changes that consistently correlated with SU5416 administration. Thirteen transcripts met this selection criterion; six were further tested by quantitative RT-PCR analysis of 62 additional samples from this trial and a second SU5416 Phase III trial of similar design. This method confirmed four of these transcripts (CD24, lactoferrin, lipocalin 2, and MMP-9) as potential biomarkers of drug treatment. Discriminant analysis showed that expression profiles of these 4 transcripts could be used to classify patients by treatment arm in a predictive fashion. These results establish a foundation for the further exploration of peripheral blood cells as a surrogate system for biomarker analyses in clinical oncology studies

  19. High-throughput sequencing of frozen and paraffin-embedded tumor and normal tissue

    OpenAIRE

    Kerick, M; Timmermann, B; Schweiger, M.

    2010-01-01

    Until now high-throughput sequencing of tumor samples relied on DNA isolated from fresh frozen tissues, the preparation of which, however, is relatively laborious. The use of preserved material, i.e. from tissue banks, could help to avoid this limitation and would enable the reanalysis of diverse clinical trials. So far we have shown that formalin-fixed paraffin-embedded (FFPE) tissue samples can be used for genomic re-sequencing processes. FFPE samples are amply available from surgical tumor...

  20. Clinical Validation and Implications of Dried Blood Spot Sampling of Carbamazepine, Valproic Acid and Phenytoin in Patients with Epilepsy

    Science.gov (United States)

    Kong, Sing Teang; Lim, Shih-Hui; Lee, Wee Beng; Kumar, Pasikanthi Kishore; Wang, Hwee Yi Stella; Ng, Yan Lam Shannon; Wong, Pei Shieen; Ho, Paul C.

    2014-01-01

    To facilitate therapeutic monitoring of antiepileptic drugs (AEDs) by healthcare professionals for patients with epilepsy (PWE), we applied a GC-MS assay to measure three AEDs: carbamazepine (CBZ), phenytoin (PHT) and valproic acid (VPA) levels concurrently in one dried blood spot (DBS), and validated the DBS-measured levels to their plasma levels. 169 PWE on either mono- or polytherapy of CBZ, PHT or/and VPA were included. One DBS, containing ∼15 µL of blood, was acquired for the simultaneous measurement of the drug levels using GC-MS. Simple Deming regressions were performed to correlate the DBS levels with the plasma levels determined by the conventional immunoturbimetric assay in clinical practice. Statistical analyses of the results were done using MedCalc Version 12.6.1.0 and SPSS 21. DBS concentrations (Cdbs) were well-correlated to the plasma concentrations (Cplasma): r = 0.8381, 0.9305 and 0.8531 for CBZ, PHT and VPA respectively, The conversion formulas from Cdbs to plasma concentrations were [0.89×CdbsCBZ+1.00]µg/mL, [1.11×CdbsPHT−1.00]µg/mL and [0.92×CdbsVPA+12.48]µg/mL respectively. Inclusion of the red blood cells (RBC)/plasma partition ratio (K) and the individual hematocrit levels in the estimation of the theoretical Cplasma from Cdbs of PHT and VPA further improved the identity between the observed and the estimated theoretical Cplasma. Bland-Altman plots indicated that the theoretical and observed Cplasma of PHT and VPA agreed well, and >93.0% of concentrations was within 95% CI (±2SD); and similar agreement (1∶1) was also found between the observed Cdbs and Cplasma of CBZ. As the Cplasma of CBZ, PHT and VPA can be accurately estimated from their Cdbs, DBS can therefore be used for drug monitoring in PWE on any of these AEDs. PMID:25255292

  1. Molecular identification and antifungal susceptibility profiles of Candida parapsilosis complex species isolated from culture collection of clinical samples

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    Fábio Silvestre Ataides

    2015-08-01

    Full Text Available AbstractINTRODUCTION:Candida parapsilosis is a common yeast species found in cases of onychomycosis and candidemia associated with infected intravascular devices. In this study, we differentiated Candida parapsilosis sensu stricto, Candida orthopsilosis , and Candida metapsilosis from a culture collection containing blood and subungual scraping samples. Furthermore, we assessed the in vitro antifungal susceptibility of these species to fluconazole, itraconazole, voriconazole, posaconazole, amphotericin B, and caspofungin.METHODS:Differentiation of C. parapsilosis complex species was performed by amplification of the secondary alcohol dehydrogenase (SADH gene and digestion by the restriction enzyme Ban I. All isolates were evaluated for the determination of minimal inhibitory concentrations using Etest, a method for antifungal susceptibility testing.RESULTS:Among the 87 isolates, 78 (89.7% were identified as C. parapsilosis sensu stricto , five (5.7% were identified as C. orthopsilosis , and four (4.6% were identified as C. metapsilosis . Analysis of antifungal susceptibility showed that C. parapsilosis sensu strictoisolates were less susceptible to amphotericin B and itraconazole. One C. parapsilosis sensu stricto isolate was resistant to amphotericin B and itraconazole. Moreover, 10.2% of C. parapsilosis sensu stricto isolates were resistant to caspofungin. Two C. parapsilosis sensu strictoisolates and one C. metapsilosis isolate were susceptible to fluconazole in a dose-dependent manner.CONCLUSIONS:We reported the first molecular identification of C. parapsilosiscomplex species in State of Goiás, Brazil. Additionally, we showed that although the three species exhibited differences in antifungal susceptibility profiles, the primary susceptibility of this species was to caspofungin.

  2. Application of fluorescence based molecular assays for improved detection and typing of Brucella strains in clinical samples

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    Kiril Krstevski

    2015-10-01

    Full Text Available Bacteria from the genus Brucella are causative agents of brucellosis – a zoonotic disease which affects many wild and domestic animal species and humans. Taking into account the significant socio-economic and public health impact of brucellosis, its control is of great importance for endemic areas. The chosen control strategy could be successful only if adapted to the current epidemiological situation. This implies that a choice of appropriate diagnostic procedures for detection and typing of Brucella spp. strains are of essential importance. Significant advancement of molecular techniques and their advantages compared to classical methods, give strong arguments in promotion of these techniques as a powerful tool for comprehensive diagnostics of brucellosis. Considering this, the major tasks of the study were to select and implement molecular tests for detection and genotyping Brucella spp. and evaluate their performances using DNA from cultivated brucellae (islolates and limited number of tissue samples from seropositive animals. The obtained results confirmed that implemented real time PCR for Brucella spp. detection, as well as MLVA-16 used for genotyping, have excellent analytical sensitivity (4.2 fg of Brucella DNA were successfully detected and genotyped. Furthermore, compared to bacteriological cultivation of Brucella spp., real time PCR and MLVA-16 protocols showed superior diagnostic sensitivity and detected Brucella DNA in tissues from which Brucella could not be cultivated. Based on the summarized study results, we propose a diagnostic algorithm for detection and genotyping of Brucella spp. bacteria. Routine use of proposed diagnostic algorithm will improve the effectiveness of infection confirmation and help for accurate evaluation of epidemiological situation.

  3. Assessing a dysphoric arousal model of acute stress disorder symptoms in a clinical sample of rape and bank robbery victims

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    Maj Hansen

    2012-06-01

    Full Text Available Background: Since the introduction of Acute Stress Disorder (ASD into the 4th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV research has focused on the ability of ASD to predict PTSD rather than focusing on addressing ASD's underlying latent structure. The few existing confirmatory factor analytic (CFA studies of ASD have failed to reach a clear consensus regarding ASD's underlying dimensionality. Although, the discrepancy in the results may be due to varying ASD prevalence rates, it remains possible that the model capturing the latent structure of ASD has not yet been put forward. One such model may be a replication of a new five-factor model of PTSD, which separates the arousal symptom cluster into Dysphoric and Anxious Arousal. Given the pending DSM-5, uncovering ASD's latent structure is more pertinent than ever. Objective:Using CFA, four different models of the latent structure of ASD were specified and tested: the proposed DSM-5 model, the DSM-IV model, a three factor model, and a five factor model separating the arousal symptom cluster. Method:The analyses were based on a combined sample of rape and bank robbery victims, who all met the diagnostic criteria for ASD (N = 404 using the Acute Stress Disorder Scale. Results:The results showed that the five factor model provided the best fit to the data. Conclusions:The results of the present study suggest that the dimensionality of ASD may be best characterized as a five factor structure which separates dysphoric and anxious arousal items into two separate factors, akin to recent research on PTSD's latent structure. Thus, the current study adds to the debate about how ASD should be conceptualized in the pending DSM-5.

  4. SELDI-TOF-MS determination of hepcidin in clinical samples using stable isotope labelled hepcidin as an internal standard

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    Johnson Philip J

    2008-10-01

    Full Text Available Abstract Background Hepcidin is a 25-residue peptide hormone crucial to iron homeostasis. It is essential to measure the concentration of hepcidin in cells, tissues and body fluids to understand its mechanisms and roles in physiology and pathophysiology. With a mass of 2791 Da hepcidin is readily detectable by mass spectrometry and LC-ESI, MALDI and SELDI have been used to estimate systemic hepcidin concentrations by analysing serum or urine. However, peak heights in mass spectra may not always reflect concentrations in samples due to competition during binding steps and variations in ionisation efficiency. Thus the purpose of this study was to develop a robust assay for measuring hepcidin using a stable isotope labelled hepcidin spiking approach in conjunction with SELDI-TOF-MS. Results We synthesised and re-folded hepcidin labelled with 13C/15N phenylalanine at position 9 to generate an internal standard for mass spectrometry experiments. This labelled hepcidin is 10 Daltons heavier than the endogenous peptides and does not overlap with the isotopic envelope of the endogenous hepcidin or other common peaks in human serum or urine mass spectra and can be distinguished in low resolution mass spectrometers. We report the validation of adding labelled hepcidin into serum followed by SELDI analysis to generate an improved assay for hepcidin. Conclusion We demonstrate that without utilising a spiking approach the hepcidin peak height in SELDI spectra gives a good indication of hepcidin concentration. However, a stable isotope labelled hepcidin spiking approach provides a more robust assay, measures the absolute concentration of hepcidin and should facilitate inter-laboratory hepcidin comparisons.

  5. First report of mecC MRSA in human samples from Austria: molecular characteristics and clinical data

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    H. Kerschner

    2015-01-01

    Full Text Available Reports of mecC methicillin-resistant Staphylococcus aureus (MRSA strains have been published from several European countries. We describe the first six mecC MRSA isolates of human origin from Austria and report the application of a rapid PCR test. Candidate isolates (n = 295 received between 2009 and 2013 were investigated phenotypically by cefoxitin screening and streaking on ChromID MRSA plates. The presence of mecC was confirmed in six isolates from blood cultures, wound swabs and screening samples of four female and two male patients (age range 7–89 years by an in-house PCR method and the new Genspeed MRSA test (Greiner Bio-One, Kremsmünster, Austria. The mecC MRSA were further characterized by whole genome sequencing, multilocus sequence and spa typing. Antimicrobial susceptibility testing was performed by Eucast disk-diffusion method and Vitek 2. The six mecC MRSA isolates were from two clonal lineages (CC130, including a new single-locus variant, and CC599 and four different spa types (t843, t1535, t3256, t5930. Analysis for virulence factor genes yielded lukED, eta, etd2 and edin-B (CC130 isolates and tst, lukED, eta and sel (ST599 isolates. The Genspeed MRSA test identified mecC in all isolates whereas Vitek 2 failed to detect methicillin resistance in one isolate. The strains were susceptible to a wide range of non-β-lactam antibiotics. All patients were successfully treated or decolonized. mecC MRSA are present in Austria as colonizers but may also cause infections. Thus, laboratories must choose appropriate test methods such as cefoxitin screening and confirmation using molecular assays specifically targeting mecC.

  6. Optimization and Isolation of Dermatophytes from Clinical Samples and In Vitro Antifungal Susceptibility Testing By Disc Diffusion Method

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    Amodkumar Yadav

    2013-06-01

    Full Text Available India is a large subcontinent with remarkably varied topography, situated within the tropical and subtropical belts of the world. In the study patients with Tinea infections were examined clinically by dermatologist. Isolation, confirmatory test were done as per the standard procedure, and Antifungal Susceptibility test was done by Disc diffusion method.Other conditions such as seborrheic dermatitis, psoriasis, alopecia areata, folliculitis and pseudopelade may mimic ringworm of head and other tinea must be identified. A total of sixty six patients of dermatophytosis were studied. Males were predominantly affected 51 (77% cases as compared to females15 (23% cases. Male to female ratio was 3.4:1. Most common age group affected was 21-30 years with 20 cases (23%. Least common age group affected was 61-70 years with 3 cases (4%.Tinea corporis was more common in the age group 21-30 years with 13 cases (37.14% and in males with 29 cases (82.85% than females with 6 cases (17.15%.Tinea unguium was more common in the age group of 31-40 years with 6 cases (37.5% and in males with 10 cases (62.5% than females with 6 cases (37.5%.Tinea cruris was more common in the age group 51-60 years with 2 cases (40% and was more common in males with 5 cases (100%.In tinea pedis, one case was seen in the age group of 11-20 years and the other in the age group of 41-50 and 51-60 years, and was more common in males with 3 cases (100%.Tinea barbae was more common in the age group 21-30 years with 2 cases (66.66% .Tinea capitis was more common in the age group of 31-40 years with 2 cases (66.66% and was more common in females with 3 cases (100%. Tinea manuum was more common in the age group of 31-40 years and in males with 1 case (100%. In males, commonest infection was T. corporis while in female commonest infection was T.corporis.rate of direct microscopy and culture (78.79%. About 89.47% of the dermatophytes grew faster in DTM with compare to SDA, so the growth rate of

  7. High diversity of human polyomaviruses in environmental and clinical samples in Argentina: Detection of JC, BK, Merkel-cell, Malawi, and human 6 and 7 polyomaviruses.

    Science.gov (United States)

    Torres, Carolina; Barrios, Melina Elizabeth; Cammarata, Robertina Viviana; Cisterna, Daniel Marcelo; Estrada, Tatiana; Martini Novas, Sergio; Cahn, Pedro; Blanco Fernández, María Dolores; Mbayed, Viviana Andrea

    2016-01-15

    New human polyomaviruses have been recently described. The aim of this work was to detect and characterize human polyomaviruses circulating in Argentina by recovering viruses from environmental and sewage samples and evaluating their potential role as viral indicators of human waste contamination. Analysis was performed in a wider context including viruses from clinical samples from an immunocompromised population. River water and sewage samples were analyzed as a strategy to study the molecular epidemiology of viruses excreted by millions of people. Samples belonged to the Matanza-Riachuelo River (2005-2006: n=25 and 2012: n=20) and sewage from Buenos Aires city and suburbs (2011 and 2013: n=24). Viral detection was performed by PCR and the amplified viral genomes were characterized by phylogenetic analysis. Polyomaviruses were detected in 95.8% of sewage samples, identifying BKPyV (87.5%), JCPyV (83.3%), MCPyV (8.3%) and HPyV6 (8.3%). Besides, one sample collected in 2009 resulted positive for HPyV7. In 2005-2006, polyomaviruses were detected in 84.0% of river water samples, with the highest detection for MCPyV (52.0%), followed by BKPyV (44.0%), JCPyV (20.0%) and MWPyV (4.0%). In 2012, polyomaviruses were detected in 85.0% of river samples, finding JCPyV (85.0%), BKPyV (75.0%), MCPyV (25.0%) and HPyV6 (25.0%). Also, polyomaviruses, including JCPyV, BKPyV and MCPyV, were detected in 63.2% of urine samples from patients infected with HIV (n=19). Characterization indicated the coexistence of different genotypes and variants for each virus, particularly in sewage. MCPyV sequences (the only sequences from Argentina) formed a monophyletic group with the single sequence available for South America (French Guiana). The high level of detection and viral diversity found by environmental surveillance, which involved the characterization of viruses not previously described in South America, reinforces the usefulness of this approach to monitor viral contamination and

  8. Isolation and speciation of Enterococci from various clinical samples and their antimicrobial susceptibility pattern with special reference to high level Aminoglycoside resistance

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    :Saroj Golia, Nirmala AR, Asha S Kamath B

    2014-07-01

    Full Text Available Background and Objectives: Enterococci are important nosocomial agents and strains resistant to penicillin and other antibiotics occur frequently. Enterococci are intrinsically resistant to cephalosporins and offer low level resistance to aminoglycosides. In penicillin sensitive strains, synergism occurs with combination treatment with penicillin and aminoglycoside. Serious infections caused by them are treated with penicillin and aminoglycoside combination. But the synergistic effect is lost, when the strain develops high level aminoglycoside resistance. The choice of drug for infections due to such strains is vancomycin. The present study was carried out to isolate and speciate Enterococci from various clinical samples, to know the susceptibility pattern of the isolates, to determine the High Level Aminoglycoside Resistance (HLAR among Enterococcal isolates. Methods: A total of One hundred Enterococcal species isolated from various clinical samples were identified by various biochemical reactions. Antimicrobial susceptibility testing and HLAR were determined by Kirby- Bauer disc diffusion method. Results: Out of 100 Enterococcal isolates, 59 were E. faecalis, 38 were E. faecium, 3 were other Enterococcal species. Among these 53 isolates showed High Level Aminoglycoside Resistance. Conclusion: Present study shows the presence of drug resistance to most of commonly used antibiotics and HLAR is also more in E.faecium compared to E.fecalis.

  9. The expression of small regulatory RNAs in clinical samples reflects the different life styles of Staphylococcus aureus in colonization vs. infection.

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    Juan Song

    Full Text Available Small RNAs (sRNAs are involved in the post-transcriptional regulation of metabolic pathways and in responses to stress and virulence. We analyzed the expression levels of five sRNAs of Staphylococcus aureus during human colonization or infection. Total RNA was isolated from nasal carriers, abscesses and cystic fibrosis patients (20 subjects per condition. The expression levels of the sRNAs were measured in the clinical samples and compared with those of the corresponding strains grown in vitro. Five sRNAs were encoded and expressed in all clinical strains in vitro. In vivo, the global expression of the five sRNAs was extremely variable in the abscessed patients, more homogeneous in the cystic fibrosis patients, and highly uniform in the nasal carrier samples. The expression levels of the sRNAs in vivo resembled those obtained at exponential phase or late exponential phase of growth in vitro, for three and one sRNA respectively; while for one sRNA, the expression was always higher in vivo as compared to in vitro growth. The in vitro conditions do not uniformly mimic the in vivo conditions for sRNA expression. Nasal colonization is associated with a unique expression pattern of sRNA that might reflect the commensalism of S. aureus in this niche.

  10. Convergent and divergent validity of K-SADS-PL anxiety and attention deficit hyperactivity disorder diagnoses in a clinical sample of school-aged children.

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    Villabø, Marianne A; Oerbeck, Beate; Skirbekk, Benedicte; Hansen, Berit Hjelde; Kristensen, Hanne

    2016-07-01

    Background The Schedule for Affective Disorders and Schizophrenia for School Age Children, Present and Lifetime Version (K-SADS-PL) is a commonly used diagnostic interview both in research and clinical settings, yet published data on the psychometric properties of the interview generated diagnoses are scarce. Aims To examine the convergent and divergent validity of the Norwegian version of the K-SADS-PL current diagnoses of anxiety disorders and attention deficit hyperactivity disorder (ADHD). Method Participants were 105 children aged 7-13 years referred for treatment at child mental health clinics and 36 controls. Diagnostic status was determined based on K-SADS-PL interviews with the mothers. Child and mother reported child symptoms of anxiety on the Multidimensional Anxiety Scale for Children and teachers reported anxiety symptoms on the Teacher Report Form. Mother and teacher reported on symptoms of ADHD on the Disruptive Behavior Rating Scale. Results Rating scale data from multiple informants in a clinical sample and healthy controls supported the convergent and divergent validity of K-SADS-PL anxiety diagnoses combined, and, specifically, the diagnoses of separation anxiety disorder, social phobia, and specific phobia. Support was also observed for convergent and divergent validity of ADHD diagnoses, including the predominately inattentive subtype. Conclusion The K-SADS-PL generates valid diagnoses of anxiety disorders and ADHD. PMID:26836986

  11. Age and gender effect on alexithymia in large, Japanese community and clinical samples: a cross-validation study of the Toronto Alexithymia Scale (TAS-20

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    Kubo Chiharu

    2007-03-01

    Full Text Available Abstract Background The construct validity of alexithymia and its assessment using the 20-item Toronto Alexithymia Scale (TAS-20 in Japan is unknown. Low reliability has been found for the third factor of the TAS-20 in some cultures, and the factor structure for psychosomatic disorder patients has not been adequately investigated. Although alexithymia most likely has certain developmental aspects, this has infrequently been investigated. Methods The newly-developed Japanese TAS-20 was administered to a normative sample (n = 2,718; 14–84 y.o., along with the NEO Five-Factor Inventory (NEO-FFI for cross validation. Psychosomatic patients (n = 1,924, 12–87 y.o. were tested to evaluate the factor structure in a clinical sample. College students (n = 196 were used for a test-retest study. Internal reliability and consistency were assessed, and the factorial structure was evaluated using confirmatory and exploratory factor analyses for both the normative and the clinical samples. The correlations between the TAS-20 and the NEO-FFI factor scores were evaluated. Age-related and gender differences in the TAS-20 were explored using analysis of variance in the normative sample. Results The original three-factor model of the TAS-20 was confirmed to be valid for these Japanese samples, although a 4-factor solution that included negatively keyed items (NKI as an additional factor was more effective. Significant correlations of the TAS-20 with the NEO-FFI were found, as has been previously reported. Factor analyses of the normative and patient samples showed similar patterns. The TAS-20 total, difficulty in identifying feelings (DIF, and difficulty in describing feelings (DDF scores were high for teenagers, decreased with age, and from 30s did not change significantly. In contrast, externally oriented thinking (EOT scores showed an almost linear positive correlation with age. DIF scores were higher for females, while EOT scores were higher for males

  12. Infection frequency of Epstein-Barr virus in subgingival samples from patients with different periodontal status and its correlation with clinical parameters

    Institute of Scientific and Technical Information of China (English)

    WU Yan-min; YAN Jie; CHEN Li-li; SUN Wei-lian; GU Zhi-yuan

    2006-01-01

    Objective: To detect the infection frequencies of different genotypes of Epstein-Barr virus (EBV) in subgingival samples from chronic periodontitis (CP) patients, and to discuss the correlation between infection with EBV and clinical parameters. Methods: Nested-PCR assay was used to detect EBV-1 and EBV-2 in subgingival samples from 65 CP patients, 65ivitis patients and 24 periodontally healthy individuals. The amplicons were further identified by restriction fragment length polymorphism analysis (RFLP) with endonucleases Afa I and Stu I. Clinical parameters mainly included bleeding on probing riodontally healthy individuals, the infection frequencies were 47.7% , 24.6% and 16.7% for EBV-1, and 15.4% , 7.7% and 0% for EBV-2,ectively. In 2 out of the 65 CP patients co-infection of EBV-1 and EBV-2 was found. The positive rate of EBV-1 in chronic periodontitis patients was higher than that in gingivitis patients (P=0.01) and periodontally healthy individuals (P=-0.01). But no .05) or in EBV-2frequency among the three groups (P>0.05). In CP patients, higher mean BOP value was found in EBV-1 or EBV-2 positive egative ones (P<0.01), but with no statistical difference in the mean PD or AL value between EBV positive and negative patients (P>0.05). After initial periodontal treatment, 12 out of the 21 EBV-1 positive CP patients did not s a sensitive, specific and stable method to detect EBV-1 and EBV-2 in subgingival samples. Subgingival infection with EBV-1 is closely associated with chronic correlated with BOP.

  13. Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

    Science.gov (United States)

    Cura, Carolina I.; Duffy, Tomas; Lucero, Raúl H.; Bisio, Margarita; Péneau, Julie; Jimenez-Coello, Matilde; Calabuig, Eva; Gimenez, María J.; Valencia Ayala, Edward; Kjos, Sonia A.; Santalla, José; Mahaney, Susan M.; Cayo, Nelly M.; Nagel, Claudia; Barcán, Laura; Málaga Machaca, Edith S.; Acosta Viana, Karla Y.; Brutus, Laurent; Ocampo, Susana B.; Aznar, Christine; Cuba Cuba, Cesar A.; Gürtler, Ricardo E.; Ramsey, Janine M.; Ribeiro, Isabela; VandeBerg, John L.; Yadon, Zaida E.; Osuna, Antonio; Schijman, Alejandro G.

    2015-01-01

    Background Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). Methods/Principal Findings The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. Conclusions/Significance Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production. PMID:25993316

  14. The Trauma of Commercial Sexual Exploitation of Youth: A Comparison of CSE Victims to Sexual Abuse Victims in a Clinical Sample.

    Science.gov (United States)

    Cole, Jennifer; Sprang, Ginny; Lee, Robert; Cohen, Judith

    2016-01-01

    This study examined the demographic features, trauma profiles, clinical severity indicators, problem behaviors, and service utilization characteristics of youth victims of commercial sexual exploitation (CSE) compared with a matched sample of sexually abused/assaulted youth who were not exploited in commercial sex. Secondary data analysis and propensity score matching were used to select a sample of 215 help-seeking youth who were exploited in prostitution (n = 43) or who were sexually abused/assaulted but not exploited in prostitution (n = 172) from the National Child Traumatic Stress Network Core Data Set (NCTSN CDS). Propensity Score Matching was used to select a comparison sample based on age, race, ethnicity, and primary residence. Statistically significant differences were noted between the groups on standardized (e.g., UCLA Posttraumatic Stress Disorder Reaction Index [PTSD-RI], Child Behavior Checklist [CBCL]) and other measures of emotional and behavioral problems (e.g., avoidance and hyperarousal symptoms, dissociation, truancy, running away, conduct disorder, sexualized behaviors, and substance abuse). This study provides useful insight into the symptom and service utilization profiles of youth exploited in commercial sex as compared with youth with other types of sexually exploitive experiences. Targeted screening and event-sensitive measures are recommended to more accurately identify youth exploited in commercial sex. More research is needed to determine if and what modifications to trauma therapies may be required to address the more severe symptomatology and behavior problems associated with youth exploited in commercial sex. PMID:25381275

  15. Development of a set of multiplex standard polymerase chain reaction assays for the identification of infectious agents from aborted bovine clinical samples.

    Science.gov (United States)

    Tramuta, Clara; Lacerenza, Daniela; Zoppi, Simona; Goria, Mariella; Dondo, Alessandro; Ferroglio, Ezio; Nebbia, Patrizia; Rosati, Sergio

    2011-07-01

    The current study describes the development of a set of 5 multiplex polymerase chain reaction (mPCR) assays for the simultaneous detection of abortive infection agents in bovine fetal tissues, including Brucella spp., Leptospira spp., and Campylobacter fetus (mPCR1); Hammondia heydorni, Neospora caninum, and Toxoplasma gondii (mPCR2); Coxiella burnetii and Chlamydophila psittaci (mPCR3); Mycoplasma bovis, Mycoplasma bovigenitalium, and Ureaplasma diversum (mPCR4); and Bovine viral diarrhea virus (BVDV) and Bovine herpesvirus-1 (BoHV-1; mPCR5). The protocol was tested on different tissue samples collected from 50 aborted bovine fetuses, and it showed that out of the 50 fetuses, 7 (14%, mPCR2) were PCR-positive for N. caninum, 4 (8%, mPCR5) were PCR-positive for BVDV, and 2 (4%, mPCR4) were PCR-positive for U. diversum. The results obtained by using each multiplex PCR were 100% concordant with those obtained by using the respective PCR assays targeting single genes on the same specimens. Moreover, all multiplex PCR assays on clinical samples were compared with reference methods, obtaining a perfect accordance in all samples and confirming the validity of the set of multiplex PCR assays. The proposed set of multiplex PCR assays is, therefore, suitable for the simultaneous detection of the main infectious agents responsible for bovine abortion. PMID:21908306

  16. Cross-cultural confirmation of bi-factor models of a symptom distress measure: Symptom Checklist-90-Revised in clinical samples.

    Science.gov (United States)

    Urbán, Róbert; Arrindell, Willem A; Demetrovics, Zsolt; Unoka, Zsolt; Timman, Reinier

    2016-05-30

    Four decades have elapsed since the introduction for clinical and research purposes of the Symptom Checklist-90(-R). Yet, its underlying dimensional structure has not been clearly delineated. A shift has been observed in the methods utilized-from predominantly exploratory factor analytic in nature in the first two decades or so to different confirmatory methods in recent years. A need remains to search for a structure that remains invariant across samples and nations. In that context, the present study attempted to replicate and extend recent findings yielded in a Hungarian general population sample (N=2,874) with two psychiatric patient samples from Hungary (N=972) and The Netherlands (N=1,902). In doing so, four models were contrasted: the one-factor model, Derogatis' nine factor model, a second-ordered factor model, and a bi-factor model. The bi-factor model was shown to yield the closest fit to the data in both countries. Further studies are needed to determine the stable number and kind of subscale scores that reflect the specific (primary) symptoms best, that is, those subscales with minimal shared variance with the overall general psychological distress dimension. PMID:27039011

  17. COMPARATIVE EFFECTIVENESS OF DISINFECTANTS WITH PHE NOL ON MULTIDRUG RESISTANT BACTERIA AND FUNGI ISOLATED FRO M THE CLINICAL SAMPLE – AN IN VITRO PRELIMINARY STUDY

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    Mannur

    2013-05-01

    Full Text Available ABSTRACT: BACKGROUND: The emergence of multidrug resistant (MDR microor ganism infections has generated considerable attention in the recent past . The primary goal of infection control procedures is to prevent cross contamination betwee n patients as well as between patients and health care providers. This can be achieved by the safe disposal of body fluids and cultures having such microorganisms from the hospital ward and labo ratory. This study aimed at comparing the efficacy of comme rcially available disinfectants on microorganisms isolated from clinical samples. MATERIAL AND METHOD: Four commonly used disinfectants namely Savlon, 70% Ethanol, Dettol an d Lysol were tested for their Antibacterial and Anti fungal effects against multidrug resistant bac teria and fungi isolated from clinical samples from inpatients admitted to Sri Siddhartha Medical Colle ge Hospital, Tumkur. Multi- drug resistant (MDR microorganisms E. coli, S. aureus, K. pneumoniae, P . aeruginosa, C. albicans, A. niger and A flavus isolated from clinical samples were used for testin g the effectiveness of disinfectants. Agar Well- diffusion method using Mueller Hinton Agar and Modi fied Muller Hinton agar was used to assess the effectiveness of disinfectants. Phenol was consider ed to be the standard disinfectant to which other disinfectants were compared. The zone of inhibitio n (ZOI for each isolate was measured. These were compared to the ZOI of Phenol (40mm. The resu lts were statistically analyzed by descriptive statistical methods. RESULTS: The ZOI against S. aureus and E. coli of Savlon was 33mm & 34mm and for Dettol 38mm & 37mm, respectively. But for K . pneumoniae the ZOI was 29mm & 30mm and for P. aeruginosa was 24mm and 30mm for Savlon and Dettol, respectively. The ZOI for 70% ethanol ranged from 32mm to 34 mm on all the isolates. The ZOI for Lysol ranged from 22mm to 24mm on isolates. CONCLUSION: The disinfectants -- Savlon and Dettol can be used as

  18. The influence of psychoeducation on regulating biological rhythm in a sample of patients with bipolar II disorder: a randomized clinical trial

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    Faria AD

    2014-06-01

    Full Text Available Augusto Duarte Faria,1 Luciano Dias de Mattos Souza,2 Taiane de Azevedo Cardoso,2 Karen Amaral Tavares Pinheiro,2 Ricardo Tavares Pinheiro,2 Ricardo Azevedo da Silva,2 Karen Jansen21Department of Clinical and Health Psychology, Universidade Federal do Rio Grande – FURG, Rio Grande, RS, Brazil; 2Health and Behavior Postgraduate Program, Universidade Católica de Pelotas – UCPEL, Pelotas, RS, BrazilIntroduction: Changes in biological rhythm are among the various characteristics of bipolar disorder, and have long been associated with the functional impairment of the disease. There are only a few viable options of psychosocial interventions that deal with this specific topic; one of them is psychoeducation, a model that, although it has been used by practitioners for some time, only recently have studies shown its efficacy in clinical practice.Aim: To assess if patients undergoing psychosocial intervention in addition to a pharmacological treatment have better regulation of their biological rhythm than those only using medication.Method: This study is a randomized clinical trial that compares a standard medication intervention to an intervention combined with drugs and psychoeducation. The evaluation of the biological rhythm was made using the Biological Rhythm Interview of Assessment in Neuropsychiatry, an 18-item scale divided in four areas (sleep, activity, social rhythm, and eating pattern. The combined intervention consisted of medication and a short-term psychoeducation model summarized in a protocol of six individual sessions of 1 hour each.Results: The sample consisted of 61 patients with bipolar II disorder, but during the study, there were 14 losses to follow-up. Therefore, the final sample consisted of 45 individuals (26 for standard intervention and 19 for combined. The results showed that, in this sample and time period evaluated, the combined treatment of medication and psychoeducation had no statistically significant impact on the

  19. Evidence for different mechanisms of ‘unhooking’ for melphalan and cisplatin-induced DNA interstrand cross-links in vitro and in clinical acquired resistant tumour samples

    International Nuclear Information System (INIS)

    DNA interstrand cross-links (ICLs) are critical lesions produced by several cancer chemotherapy agents including platinum drugs and nitrogen mustards. We have previously shown in haematological (multiple myeloma) and solid tumours (ovarian cancer) that clinical sensitivity to such agents can result from a defect in DNA ICL processing leading to their persistence. Conversely, enhanced repair can result in clinical acquired resistance following chemotherapy. The repair of ICLs is complex but it is assumed that the ‘unhooking’ step is common to all ICLs. Using a modification of the single cell gel electrophoresis (Comet) assay we measured the formation and unhooking of melphalan and cisplatin-induced ICLs in cell lines and clinical samples. DNA damage response in the form of γ-H2AX foci formation and the formation of RAD51 foci as a marker of homologous recombination were also determined. Real-time PCR of 84 genes involved in DNA damage signalling pathways was also examined pre- and post-treatment. Plasma cells from multiple myeloma patients known to be clinically resistant to melphalan showed significant unhooking of melphalan-induced ICLs at 48 hours, but did not unhook cisplatin-induced ICLs. In ovarian cancer cells obtained from patients following platinum-based chemotherapy, unhooking of cisplatin-induced ICLs was observed at 48 hours, but no unhooking of melphalan-induced ICLs. In vitro, A549 cells were proficient at unhooking both melphalan and cisplatin-induced ICLs. γ-H2AX foci formation closely followed the formation of ICLs for both drugs, and rapidly declined following the peak of formation. RPMI8226 cells unhooked melphalan, but not cisplatin-induced ICLs. In these cells, although cross-links form with cisplatin, the γ-H2AX response is weak. In A549 cells, addition of 3nM gemcitabine resulted in complete inhibition of cisplatin-induced ICL unhooking but no effect on repair of melphalan ICLs. The RAD51 foci response was both drug and cell line

  20. A Multiplex real-time PCR for detection of Mycoplasma gallisepticum and Mycoplasma synoviae in clinical samples from Brazilian commercial poultry flocks

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    Aline Padilha Fraga

    2013-01-01

    Full Text Available Mycoplasma gallisepticum (MS and Mycoplasma synoviae (MS are important avian pathogens and cause economic losses to the poultry industry. Molecular biology techniques are currently used for a rapid detection of these pathogens and the adoption of control measures of the diseases. The aim of this study was to develop and validate a technique for simultaneous detection of MG and MS by multiplex real time polymerase chain reaction (PCR. The complete assay (Multiplex MGMS was designed with primers and probes specific for each pathogen and developed to be carried out in a single tube reaction. Vaccines, MG and MS isolates and DNA from other Mycoplasma species were used for the development and validation of the method. Further, 78 pooled clinical samples from different poultry flocks in Brazil were obtained and used to determine the sensitivity and specificity of the technique in comparison to 2 real time PCR assays specific for MG (MG PCR and MS (MS PCR. The results demonstrated an agreement of 100% (23 positive and 44 negative samples between Multiplex MGMS and MG PCR in the analysis of 67 samples from MG positive and negative poultry flocks, and an agreement of 96.9% between Multiplex MGMS and MS PCR in the analysis of 64 samples from MS positive and negative poultry flocks. Considering the single amplification tests as the gold standard, the Multiplex MGMS showed 100% of specificity and sensitivity in the MG analysis and 94.7% sensitivity and 100% specificity in the MS analysis. This new assay could be used for rapid analysis of MG and MS in the poultry industry laboratories.

  1. Diagnosis of canine visceral leishmaniasis with radiolabelled probes: comparison of the kDNA PCR-hybridization with three molecular methods in different clinical samples

    International Nuclear Information System (INIS)

    Leishmania (Leishmania) chagasi is responsible for visceral leishmaniasis (VL) in Brazil and the dog is the main domestic reservoir. Disease control is based on the elimination of infected animals and the use of a sensitive and specific diagnostic test is necessary. The Brazilian VL control program emphasizes serologic surveys, mainly using the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescence antibody test (IFAT), followed by the elimination of the seropositive dogs. However, these techniques present limitations in terms of sensitivity and specificity. The Polymerase Chain Reaction (PCR) associated to hybridization with DNA probes labeled with 32P has been recognized as a valuable tool for Leishmania identification. In this study, the sensitivity of kDNA PCR hybridization method was compared with three other molecular methods: Internal Transcribed Spacer 1 Nested PCR (ITS-1nPCR), Leishmania nested PCR (LnPCR) and Seminested kDNA PCR (kDNA snPCR). The comparison was performed in different clinical specimens: conjunctival swab, skin, blood and bone marrow. A group of thirty symptomatic dogs, positive in the parasitological and serological tests, was used. When. The techniques targeting kDNA mini-circles (kDNA snPCR and KDNA PCR-hybridization) showed the worst result for blood samples. The KDNA-PCR hybridization showed the best sensitivity for conjunctival swab. By comparing the samples on the basis of positivity obtained by the sum of all methods, the blood showed the worst outcome (71/120).The bone marrow showed the highest positivity (106/120), followed by conjunctival swab (100/120) and skin (89/120). Since the bone marrow samples are unsuitable for routine epidemiological surveys, the conjunctival swab was recommended because it allows high sensitivity, especially when associated with kDNA PCR hybridization method, and is a noninvasive sampling method. (author)

  2. Diagnosis of canine visceral leishmaniasis with radiolabelled probes: comparison of the kDNA PCR-hybridization with three molecular methods in different clinical samples

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Aline Leandra C.; Ferreira, Sidney A.; Carregal, Virginia M.; Andrade, Antero Silva R., E-mail: antero@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil). Lab. de Radiobiologia; Melo, Maria N., E-mail: melo@icb.ufmg.br [Departamento de Parasitologia. Instituto de Ciencias Biologicas. Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil)

    2011-07-01

    Leishmania (Leishmania) chagasi is responsible for visceral leishmaniasis (VL) in Brazil and the dog is the main domestic reservoir. Disease control is based on the elimination of infected animals and the use of a sensitive and specific diagnostic test is necessary. The Brazilian VL control program emphasizes serologic surveys, mainly using the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescence antibody test (IFAT), followed by the elimination of the seropositive dogs. However, these techniques present limitations in terms of sensitivity and specificity. The Polymerase Chain Reaction (PCR) associated to hybridization with DNA probes labeled with {sup 32}P has been recognized as a valuable tool for Leishmania identification. In this study, the sensitivity of kDNA PCR hybridization method was compared with three other molecular methods: Internal Transcribed Spacer 1 Nested PCR (ITS-1nPCR), Leishmania nested PCR (LnPCR) and Seminested kDNA PCR (kDNA snPCR). The comparison was performed in different clinical specimens: conjunctival swab, skin, blood and bone marrow. A group of thirty symptomatic dogs, positive in the parasitological and serological tests, was used. When. The techniques targeting kDNA mini-circles (kDNA snPCR and KDNA PCR-hybridization) showed the worst result for blood samples. The KDNA-PCR hybridization showed the best sensitivity for conjunctival swab. By comparing the samples on the basis of positivity obtained by the sum of all methods, the blood showed the worst outcome (71/120).The bone marrow showed the highest positivity (106/120), followed by conjunctival swab (100/120) and skin (89/120). Since the bone marrow samples are unsuitable for routine epidemiological surveys, the conjunctival swab was recommended because it allows high sensitivity, especially when associated with kDNA PCR hybridization method, and is a noninvasive sampling method. (author)

  3. Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas

    Directory of Open Access Journals (Sweden)

    Wu Thomas D

    2009-05-01

    Full Text Available Abstract Background Gene expression profiling of formalin-fixed, paraffin-embedded (FFPE samples represents a valuable approach for advancing oncology diagnostics and enhancing retrospective clinical studies; however, at present, this methodology still requires optimization and thus has not been extensively used. Here, we utilized thorough quality control methods to assess RNA extracted from FFPE samples and then compared it to RNA extracted from matched fresh-frozen (FF counterparts. We preformed genome-wide expression profiling of FF and FFPE ovarian serous adenocarcinoma sample pairs and compared their gene signatures to normal ovary samples. Methods RNA from FFPE samples was extracted using two different methods, Ambion and Agencourt, and its quality was determined by profiling starting total RNA on Bioanalyzer and by amplifying increasing size fragments of beta actin (ACTB and claudin 3 (CLDN3 by reverse-transcriptase polymerase chain reaction. Five matched FF and FFPE ovarian serous adenocarcinoma samples, as well as a set of normal ovary samples, were profiled using whole genome Agilent microarrays. Reproducibility of the FF and FFPE replicates was measured using Pearson correlation, whereas comparison between the FF and FFPE samples was done using a Z-score analysis. Results Data analysis showed high reproducibility of expression within each FF and FFPE method, whereas matched FF and FFPE pairs demonstrated lower similarity, emphasizing an inherent difference between the two sample types. Z-score analysis of matched FF and FFPE samples revealed good concordance of top 100 differentially expressed genes with the highest correlation of 0.84. Genes characteristic of ovarian serous adenocarcinoma, including a well known marker CLDN3, as well as potentially some novel markers, were identified by comparing gene expression profiles of ovarian adenocarcinoma to those of normal ovary. Conclusion Conclusively, we showed that systematic assessment

  4. High stability of microRNAs in tissue samples of compromised quality.

    Science.gov (United States)

    Peiró-Chova, Lorena; Peña-Chilet, María; López-Guerrero, José Antonio; García-Giménez, José Luis; Alonso-Yuste, Elisa; Burgues, Octavio; Lluch, Ana; Ferrer-Lozano, Jaime; Ribas, Gloria

    2013-12-01

    Degradation of tissue samples limits performing RNA-based molecular studies, but little is known about the potential usefulness of samples of compromised quality for studies focused on miRNAs. In this work we analyze a series of cryopreserved tissue samples (n = 14), frozen samples that underwent a severe thawing process (n = 10), and their paired formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 24) from patients with breast cancer obtained during primary surgical resection and collected in 2011. Quality and integrity analyses of the total and small fraction of RNA were carried out. Recovery of specific RNA molecules (miRNAs hsa-miR-21, hsa-miR-125b, and hsa-miR-191; snoRNA RNU6B; and mRNAs GAPDH and HPRT1) was also analyzed by quantitative RT-PCR. Our results suggest that visualisation of the small RNA electrophoretic profiles obtained using the Agilent 2100 bioanalyzer makes it possible to differentiate between the three groups of samples (optimally frozen, thawed, and FFPE). We demonstrate that specific miRNA molecules can be similarly recovered from different tissue sample sources, which supports their high degree of stability. We conclude that miRNAs are robustly detected irrespective of the quality of the tissue sample. In this regard, a word of caution should be raised before degraded samples are discarded: although prior quality assessment of the biological material to be analyzed is recommended, our work demonstrates that degraded tissue samples are also suitable for miRNA studies. PMID:24197449

  5. Gender ratio in a clinical population sample, age of diagnosis and duration of assessment in children and adults with autism spectrum disorder.

    Science.gov (United States)

    Rutherford, Marion; McKenzie, Karen; Johnson, Tess; Catchpole, Ciara; O'Hare, Anne; McClure, Iain; Forsyth, Kirsty; McCartney, Deborah; Murray, Aja

    2016-07-01

    This article reports on gender ratio, age of diagnosis and the duration of assessment procedures in autism spectrum disorder diagnosis in a national study which included all types of clinical services for children and adults. Findings are reported from a retrospective case note analysis undertaken with a representative sample of 150 Scottish children and adults recently diagnosed with autism spectrum disorder. The study reports key findings that the gender ratio in this consecutively referred cohort is lower than anticipated in some age groups and reduces with increasing age. The gender ratio in children, together with the significant difference in the mean age of referral and diagnosis for girls compared to boys, adds evidence of delayed recognition of autism spectrum disorder in younger girls. There was no significant difference in duration of assessment for males and females suggesting that delays in diagnosis of females occur prior to referral for assessment. Implications for practice and research are considered. PMID:26825959

  6. Adult attention deficit hyperactivity disorder symptoms and five-factor model traits in a clinical sample: a structural equation modeling approach.

    Science.gov (United States)

    Knouse, Laura E; Traeger, Lara; O'Cleirigh, Conall; Safren, Steven A

    2013-10-01

    Relationships among attention deficit hyperactivity disorder (ADHD) symptoms and adult personality traits have not been examined in larger clinically diagnosed samples. We collected multisource ADHD symptom and self-report NEO Five-Factor Inventory (Costa and McCrae [Odessa, FL: Psychological Assessment Resources, Inc, 1992) data from 117 adults with ADHD and tested symptom-trait associations using structural equation modeling. The final model fit the data. Inattention was positively associated with neuroticism and negatively associated with conscientiousness. On the basis of ADHD expression in adulthood, hyperactivity and impulsivity were estimated as separate constructs and showed differential relationships to extraversion and agreeableness. A significant positive relationship between hyperactivity and conscientiousness arose in the context of other pathways. ADHD symptoms are reliably associated with personality traits, suggesting a complex interplay across development that warrants prospective study into adulthood. PMID:24080671

  7. Human papillomavirus 16 E2 interacts with neuregulin receptor degradation protein 1 affecting ErbB-3 expression in vitro and in clinical samples of cervical lesions.

    Science.gov (United States)

    Paolini, Francesca; Curzio, Gianfranca; Melucci, Elisa; Terrenato, Irene; Antoniani, Barbara; Carosi, Mariantonia; Mottolese, Marcella; Vici, Patrizia; Mariani, Luciano; Venuti, Aldo

    2016-05-01

    The ErbB tyrosine kinase receptors play a key role in regulating many cellular functions and human papillomaviruses (HPVs) may interact with transductional pathway of different growth factor receptors. Here, these interactions were analysed in W12 cell line carrying HPV 16 genome and in clinical samples. W12 cells, in which HPV16 becomes integrated during passages, were utilised to detect viral and ErbB family expression at early (W12E) and late passages (W12G). Interestingly, a strong reduction of ErbB-3 expression was observed in W12G. Loss of the E2 and E5 viral genes occurs in W12G and this may affect ErbB-3 receptor expression. E2 and E5 rescue experiments demonstrated that only E2 gene was able to restore ErbB-3 expression. E2 is a transcriptional factor but the expression levels of ErbB3 were unaffected and ErbB-3 promoter did not show any consensus sequence for E2, thus E2 may interact in another way with ErbB3. Indeed, HPV 16 E2 can modulate ErbB-3 by interacting with the ubiquitin ligase neuregulin receptor degradation protein 1 (Nrdp-1) that is involved in the regulation of this receptor, via ubiquitination and degradation. E2 co-immunoprecipitated in a complex with Nrdp-1 leading to hypothesise an involvement of this interaction in ErbB-3 regulation. In addition, 90% of the clinical samples with integrated virus and E2 loss showed no or low ErbB-3 positivity, confirming in vitro results. In conclusion, the new discovered interaction of HPV-16 E2 with Nrdp-1 may affect ErbB-3 expression. PMID:26963794

  8. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array

    Directory of Open Access Journals (Sweden)

    Godínez Jose M

    2011-11-01

    Full Text Available Abstract Background Certain Human Papillomaviruses (HPVs are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA technologies. Results The concordances and kappa statistics (k for each technique compared with HC2 were 98.69% (k = 0.94 for LQ, 98.03% (k = 0.91 for RH and 91.80% (k = 0.82 for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90, HPV18 (k.r.= 0.74-0.80 and HPV45 (k.r.= 0.82-0.90. Conclusions The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  9. Distribution of Candida Species in different clinical samples and their virulence: Biofilm formation, proteinase and phospholipase production: A study on hospitalized patients in Southern India

    Directory of Open Access Journals (Sweden)

    Vinitha Mohandas

    2011-01-01

    Full Text Available Introduction: Candida species are normal inhabitants of the skin and mucosa. The importance of epidemiological monitoring of yeasts involved in pathogenic processes is unquestionable due to the increase of these infections over the last decade; Materials and Methods: The clinical samples from the respiratory tract (sputum, bronchial wash, tracheal secretions, saliva, blood, urine, middle ear discharge, vitreous fluid, corneal ulcer, and plastic devices (endotracheal tube, catheter tip, suction tip were collected and cultured. The species of Candida isolated were identified. Results: A total of 111 isolates of Candida species were recovered from 250 diverse clinical sources. C. albicans (39.64% was the most isolated species, although the Candida non albicans species with 60.36% showed the major prevalence. In blood cultures, C. krusei (38.23% and C. albicans (20.58% were isolated frequently. C. albicans (63.27% was the predominant species in mucosal surface. Urinary tract infections caused by yeasts were more frequent in hospitalized patients, C. krusei (50.0% being commonly isolated, followed by C. albicans (25.0%. Discussion: Several virulence factors like, biofilm, proteinase, phospholipase, etc. contribute to the pathogenecity. Early detection of virulence factors by Candida is useful in clinical decision making. We therefore have aimed at demonstrating the formation of biofilm using the method proposed by Branchini et al, (1994. The proteinase produced by Candida was estimated as per the method of Staib et al, (1965. Phospholipase assay was carried out as per the method of Samaranayake et al, (2005. Conclusions : The data suggests that the capacity of Candida species to produce biofilm may be a reflection of the pathogenic potential of the isolates. C. krusei and C. tropicalis showed strong slime production. The non-Candida albicans produced more proteinase than C. albicans. C. albicans produced higher levels of phospholipase than non

  10. Prevalence of the different Axis I clinical subtypes in a sample of patients with orofacial pain and temporomandibular disorders in the Andalusian Healthcare Service

    Science.gov (United States)

    Blanco-Aguilera, Antonio; Blanco-Aguilera, Elena; Serrano-del-Rosal, Rafael; Biedma-Velázquez, Lourdes; Rodríguez-Torronteras, Alejandro; Segura-Saint-Gerons, Rafael

    2016-01-01

    Background The main objective of this paper is to analyze the prevalence of each of the different clinical subtypes of temporomandibular disorders (TMD) in a sample of patients with this pathology. In addition, a second objective was to analyze their distribution according to gender. Material and Methods To this end, the results of 1603 patients who went to the Unit of Temporomandibular Disorders in the Córdoba Healthcare District because they suffered from this pathology were analyzed. In order to diagnose them, the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) were applied, analyzing the different Axis I subtypes (myopathy, discopathy and arthropathy) and obtaining the combined Axis I for each patient and the relation of all these variables according to gender. The null-hypothesis test confirmed the lack of connection between the gender variable and the different subtypes in the clinical analysis, and between the former and the combined Axis I of the RDC/TMD. Results The prevalence was high for the muscle disorders subtype in general, showing an 88.7% prevalence, while the presence of discopathies or arthropathies was much lower. Among discopathies, the most frequent ones were disc displacements with reduction, with 39.7% and 42.8% for the left and right temporomandibular joints (TMJ), respectively, while the prevalence of arthropathies was 26.3% for the right TMJ and 32.9% for the left TMJ. The bivariate analysis on the connection with gender reveals a p≥ 0.05 value for the muscle and arthralgia subtypes. Conclusions The patients seen at the TMD Unit where mostly middle-aged women whose main clinical axis subtype was the muscle disorder subtype. For their part, both discopathies and arthropathies, although present, are much less prevalent. Key words:RDCTMD, axis I, orofacial pain, temporomandibular disorders, gender. PMID:26615508

  11. Occurrence of Ambler Class B Metallo-β-Lactamase Gene in Imipenem-Resistant Pseudomonas Aeruginosa Strains Isolated from Clinical Samples

    Directory of Open Access Journals (Sweden)

    Zeynab Golshani

    2014-02-01

    Full Text Available Background: 5TMetallo-β-lactamase (MBLs can hydrolyze a broad spectrum of beta-lactams, including penicillins, cephalosporins, and carbapenems. Genes encoding these enzymes are located on the plasmid that can easily be transferred to other bacteria. The aim of this study was to isolate and identify the Pseudomonas aeruginosa strains encoding VIM1 gene, in clinical samples, using the PCR technique. Materials and Methods: During a 4 month period, 100 strains of Pseudomonas aeruginosa from clinical specimens were collected. Standard tests were performed to identify strains of Pseudomonas aeruginosa. Resistance to antibiotics was examined and then the PCR was used to detect VIM1gene. Results:In this study, the highest rates of resistance to antibiotics, amikacin and cefotaxime was observed (65% and 62%, the lowest resistance to antibiotics piperacillin (48% and imipenem and cefepime with 55% resistance was reported. DDST method was performed for 37 strains for the MBl detection. Among the 37 isolate, 30 strains were MBL-producing with imipenem-EDTA method. Twelve strains (18% were carriers of VIM1 gene using the PCR method. Conclusion: In the present study, the prevalence of strains producing MBL genes in strains of hospitals is a growing trend; correct prescription of medications can prevent the spread of resistant pathogens. It is suggested that molecular methods for rapid detection of resistance genes can be used to prevent the spread of this genes.

  12. Clinical profiles as a function of level and type of impulsivity in a sample group of at-risk and pathological gamblers seeking treatment.

    Science.gov (United States)

    Grall-Bronnec, Marie; Wainstein, Laura; Feuillet, Fanny; Bouju, Gaëlle; Rocher, Bruno; Vénisse, Jean-Luc; Sébille-Rivain, Véronique

    2012-06-01

    Level and type of impulsivity are essential variables to be taken into consideration during the initial evaluation of a pathological gambler. The aim of this study was to measure the score for 4 impulsivity-related traits (Urgency, (lack of) Premeditation, (lack of) Perseverance and Sensation seeking) in a sample group of at-risk and pathological gamblers, and to highlight any links with certain elements of clinical data. The UPPS Impulsive Behaviour Scale was administered to 84 problem gamblers seeking treatment. The severity of gambling disorders was evaluated using the diagnostic criteria of the DSM-IV. Psychiatric and addictive comorbidities were also explored. The results indicated that the score for the Urgency facet had a positive correlation with the severity of gambling disorders. It appeared that participants displayed different clinical profiles according to the level and type of impulsivity. Several of the UPPS scales were identified as risk factors for mood disorders, risk of suicide, alcohol use disorders, and Attention Deficit/Hyperactivity Disorder (ADHD). The results confirm both the complexity of the multi-dimensional concept of impulsivity and the reason why the UPPS is of interest for a more in-depth study of the subject. PMID:21698341

  13. Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue

    OpenAIRE

    Giobbie-Hurder Anita; Thürlimann Beat; Oberli Andrea; Baltzer Anna; Wirapati Pratyaksha; Delorenzi Mauro; Popovici Vlad; Antonov Janine; Viale Giuseppe; Altermatt Hans; Aebi Stefan; Jaggi Rolf

    2010-01-01

    Abstract Background The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months. Methods RNA from fresh frozen (FF) and FFPE tumor samples of 82 patients were used for quality control, and independent FFPE tissues of 342 postmenopausal participants of BIG 1-98 with ER-positive cancer were analyzed by measuring prospect...

  14. Investigating the Prevalence of Pervasive Developmental Disorders According to Sex in a Sample of Iranian Children Referred to Medical-Rehabilitation Centers and Psychiatrics Clinics

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    K. Khushabi

    2006-04-01

    Full Text Available Introduction & Objective: According to significance of pervasive developmental disorders (PDD in children and the increasing rate of its prevalence in referred patients to clinic in recent years and due to absence of any report about the rate of PPD in our country, this study was carried out. The aim of this study was to determine the prevalence of PPD in a sample of Iranian children who referred to medical and rehabilitation centers.Materials & Methods: 248 children who referred to three medical-rehabilitation centers were participated in the research. Accessible sampling with diagnosis of PDD based on DSM-IV criteria was chosen. The obtained data were analyzed using descriptive statistics methods such as percent and frequency distribution. Results: Autistics disorder was most prevalent among pervasive developmental disorders. In this research Autistic disorder (proportion 4/1 to 1, Asperger disorder (proportion 3 to 1 and childhood disintegrative disease were more prevalent in boys than girls. Ret disorders was observed only in girls and pervasive developmental disease (NOS was seen in both sexes. Conclusion: The results showed that pervasive developmental disorders are 4 times more prevalent in boys than girls and the findings of this research were consistent with those of previous studies.

  15. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples.

    Science.gov (United States)

    Meyler, Kenneth L; Meehan, Mary; Bennett, Desiree; Cunney, Robert; Cafferkey, Mary

    2012-12-01

    Since the introduction of the Haemophilus influenzae serotype b vaccine, invasive H. influenzae disease has become dominated by nontypeable (NT) strains. Several widely used molecular diagnostic methods have been shown to lack sensitivity or specificity in the detection of some of these strains. Novel real-time assays targeting the fucK, licA, and ompP2 genes were developed and evaluated. The fucK assay detected all strains of H. influenzae tested (n = 116) and had an analytical sensitivity of 10 genome copies/polymerase chain reaction (PCR). This assay detected both serotype b and NT H. influenzae in 12 previously positive specimens (culture and/or bexA PCR) and also detected H. influenzae in a further 5 of 883 culture-negative blood and cerebrospinal fluid (CSF) samples. The fucK assay has excellent potential as a diagnostic test for detection of typeable and nontypeable strains of invasive H. influenzae in clinical samples of blood and CSF. PMID:23017260

  16. Distribution of contagious and environmental mastitis agents isolated from milk samples collected from clinically health buffalo cows between brazilian dry and rainy seasons of the year

    Directory of Open Access Journals (Sweden)

    R.P. Maia

    2010-02-01

    Full Text Available The present study was performed to evaluate the microbiological characteristics of clinically health quarters submitted to milking and also to observe the distribution of contagious and environmental agents between brazilian dry and rainy seasons of the year. During nine months 734 quarters from 37 buffalo cows were submitted monthly to udder inspection, palpation and strip cup test before milking. 734 asseptic milk samples were inoculated in 10% ovine blood agar and in MacConkey agar media, then incubated for 72 hours at 37oC. Among the 580 isolated microrganisms, 182 (31,38% were recovered from samples collected during the rainy season and 398 (68,62% from the dry season. In the rainy period the most prevalent agents were: bacteria from the genus Corynebacterium sp (53,30%, Staphylococcus sp (19,78% and Rhodococcus equi (13,74%. In the dry period, the commonest ones were: Corynebacterium sp (44,97%, Staphylococcus sp (18,84% and Micrococcus sp (9,55%. The results demonstrated that the methods used to select health quarters in brazilian dairy buffalo farms allow the transmission of contagious bacteria during both seasons of the year, maintaining Ital.J.Anim.Sci. vol. 6, (Suppl. 2, 896-899, 2007 897 VIII World Buffalo Congress agents known to cause mainly subclinical inflammatory reactions that compromise cronically the physiology and production of the mammary gland.

  17. The Social Appearance Anxiety Scale in Italian Adolescent Populations: Construct Validation and Group Discrimination in Community and Clinical Eating Disorders Samples.

    Science.gov (United States)

    Dakanalis, Antonios; Carrà, Giuseppe; Calogero, Rachel; Zanetti, M Assunta; Volpato, Chiara; Riva, Giuseppe; Clerici, Massimo; Cipresso, Pietro

    2016-02-01

    Anxiety in situations where one's overall appearance (including body shape) may be negatively evaluated is hypothesized to play a central role in Eating Disorders (EDs) and in their co-occurrence with Social Anxiety Disorder (SAD). Three studies were conducted among community (N = 1995) and clinical (N = 703) ED samples of 11- to 18-year-old Italian girls and boys to (a) evaluate the psychometric qualities and measurement equivalence/invariance (ME/I) of the Social Appearance Anxiety (SAA) Scale (SAAS) and (b) determine to what extent SAA or other situational domains of social anxiety related to EDs distinguish adolescents with an ED only from those with SAD. Results upheld the one-factor structure and ME/I of the SAAS across samples, gender, age categories, and diagnostic status (i.e., ED participants with and without comorbid SAD). The SAAS demonstrated high internal consistency and 3-week test-retest reliability. The strength of the inter-relationships between SAAS and measures of body image, teasing about appearance, ED symptoms, depression, social anxiety, avoidance, and distress, as well as the ability of SAAS to discriminate community adolescents with high and low levels of ED symptoms and community participants from ED participants provided construct validity evidence. Only SAA strongly differentiated adolescents with any ED from those with comorbid SAD (23.2 %). Latent mean comparisons across all study groups were performed and discussed. PMID:25976291

  18. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples.

    LENUS (Irish Health Repository)

    Meyler, Kenneth L

    2012-12-01

    Since the introduction of the Haemophilus influenzae serotype b vaccine, invasive H. influenzae disease has become dominated by nontypeable (NT) strains. Several widely used molecular diagnostic methods have been shown to lack sensitivity or specificity in the detection of some of these strains. Novel real-time assays targeting the fucK, licA, and ompP2 genes were developed and evaluated. The fucK assay detected all strains of H. influenzae tested (n = 116) and had an analytical sensitivity of 10 genome copies\\/polymerase chain reaction (PCR). This assay detected both serotype b and NT H. influenzae in 12 previously positive specimens (culture and\\/or bexA PCR) and also detected H. influenzae in a further 5 of 883 culture-negative blood and cerebrospinal fluid (CSF) samples. The fucK assay has excellent potential as a diagnostic test for detection of typeable and nontypeable strains of invasive H. influenzae in clinical samples of blood and CSF.

  19. Stromal expression of heat-shock protein 27 is associated with worse clinical outcome in patients with colorectal cancer lung metastases.

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    Thomas Schweiger

    Full Text Available Pulmonary metastases are common in patients with primary colorectal cancer (CRC. Heat-shock protein 27 (Hsp27 is upregulated in activated fibroblasts during wound healing and systemically elevated in various diseases. Cancer-associated fibroblasts (CAFs are also thought to play a role as prognostic and predictive markers in various malignancies including CRC. Surprisingly, the expression of Hsp27 has never been assessed in CAFs. Therefore we aimed to investigate the expression level of Hsp27 in CAFs and its clinical implications in patients with CRC lung metastases.FFPE tissue samples from 51 pulmonary metastases (PMs and 33 paired primary tumors were evaluated for alpha-SMA, CD31, Hsp27 and vimentin expression by immunohistochemistry and correlated with clinicopathological variables. 25 liver metastases served as control group. Moreover, serum samples (n=10 before and after pulmonary metastasectomy were assessed for circulating phospho-Hsp27 and total Hsp27 by ELISA.Stromal expression of Hsp27 was observed in all PM and showed strong correlation with alpha-SMA (P<0.001 and vimentin (P<0.001. Strong stromal Hsp27 was associated with higher microvessel density in primary CRC and PM. Moreover, high stromal Hsp27 and αSMA expression were associated with decreased recurrence-free survival after pulmonary metastasectomy (P=0.018 and P=0.008, respectively and overall survival (P=0.031 and P=0.017, respectively. Serum levels of phospho- and total Hsp27 dropped after metastasectomy to levels comparable to healthy controls.Herein we describe for the first time that Hsp27 is highly expressed in tumor stroma of CRC. Stromal α-SMA and Hsp27 expressions correlate with the clinical outcome after pulmonary metastasectomy. Moreover, serum Hsp27 might pose a future marker for metastatic disease in CRC.

  20. Use of Raman Spectroscopy in Characterizing Formalin-Fixed, Paraffin-Embedded Breast Tumor Samples (abstract)

    Science.gov (United States)

    Downey, Frances; Cade, Nicholas; Cook, Richard; Springall, Robert; Gillet, Cheryl; Richards, David; Festy, Frederic

    2009-04-01

    Formalin-fixed, paraffin-embedded (FFPE) sections of breast tissue are used by pathologists to correctly type and grade the primary tumor and to assess the extent of a patient's disease. The cut sections represent a reproducible likeness of the morphology of the tissue when viewed through a microscope, although the fixation technique creates some artifacts. What is not known is how the sections differ chemically from how the tumor would look or behave within the breast. Raman spectroscopy is, like many other optical techniques, fast, noninvasive, and generally inexpensive. The advantage Raman has over other techniques is its powerful ability to identify specific chemicals, molecules, and bonds within a sample. Using Raman spectroscopy the chemicals present in both fresh tissue and FFPE sections can be identified and compared, allowing any differences between them to be identified. This information may be useful to the pathologist as an aid to further treatment regimes or novel molecular techniques, and as an aid to patient management. If these sections are found to be chemically similar to fresh tissue, they could be used to further characterize breast tumors, particularly rare tumors, using Raman spectroscopy.

  1. Study of the Prevalence of Causative Bacterial&Protozoal Agents of in Stool Samples of 470 Gastroenteritis Patients Referring to the Nikoopour Clinic in Yazd,Iran

    Directory of Open Access Journals (Sweden)

    MR Sharifi

    2004-04-01

    Full Text Available Interoduction: Gasteroenteritis is one of the problems worth consideration all over the world. It is one of the important causes of mortality, especially in children < 5 years of age, in developing countries including Iran. The aim of this descriptive study was to determine the demographic conditions influencing the presence of causative bacteria and protozoa, followed by antibiograms of isolated bacteria from stool samples of patients with gasteroenteritis referring to Nikoopour Clinic in the city of Yazd, Iran from 1998 – 2001. Materials and method: A total of 470 samples were microbiologically examined by direct method, culture and then antibiogramed. In order to isolate the possible bacteria, differential and selected media were used. Also, wet – mount technique was applied for detection of protozoa. Results: Results revealed that 272 samples (57.9% were infected by pathogenic bacteria or protozoa. 138 (50.8% pathogenic specimens were from male patients and the remaining 134(49.3% were from female patients. Isolated species were: Enteropathogenic E.coli 117(43%, Shigella 51(18.8%, Salmonella.interetidis 25(9.2%, C.jejuni 16(5.9%, Giardia lambdia 51(18.8% and Amoebae spp 12(4.4%. The most commonly detected shigella species was dysenteriae, (74.5% while boydii with 2% was the least common type observed in the specimens. Except shigella, all the other bacteria were more common in males than female, but insignificant statistically. In order to determine the sensitivity and/or resistance of pathogenic bacteria, antibiogram test was performed using selected antibiotic disks such as Ampicillin, Nalidixic Acid, Ciprofloxacin, Gentamycin and Sulfamethaxazole. Conclusion: Results revealed that some patients were probably infected by pathogenic factors other than bacteria or protozoa. Since all viruses and parasites are almost resistant to antibiotics and on the other hand, administration of antibiotics may lead to resistance of bacterial agents

  2. Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis

    OpenAIRE

    Kommedal, Øyvind; Lekang, Katrine; Langeland, Nina; Wiker, Harald G.

    2011-01-01

    The standard use of a single universal broad-range PCR in direct 16S rDNA sequencing from polybacterial samples leaves the minor constituents at risk of remaining undetected because all bacterial DNA will be competing for the same reagents. In this article we introduce a set of three broad-range group-specific 16S rDNA PCRs that together cover the clinically relevant bacteria and apply them in the investigation of 25 polybacterial clinical samples. Mixed DNA chromatograms from samples contain...

  3. Clinical application of stool sample collectors%大便标本采样装置在临床应用中的效果观察

    Institute of Scientific and Technical Information of China (English)

    于丽华; 贾荣娟

    2016-01-01

    目的 观察大便标本采样装置在临床应用中的效果.方法 选择2014年5至7月某三甲医院肠道门诊收治的65例患者为对照组,2014年8至10月该医院肠道门诊收治的67例患者设为观察组.对照组采用常规方法留取大便,大便排入便池后,用采样勺留取送检;观察组应用大便标本采样装置留取大便,用采样勺留取送检.观察两组患者大便标本及时送检率和满意度.结果 观察组标本及时送检率为92.5%,明显高于对照组(75.4%);患者满意率为98.5%,明显高于对照组(89.2%),组间比较差异均有统计学意义(x2 =7.255 8,P=0.0071;x2=4.9870,P=0.025 5).结论 大便标本采样装置具有操作简便、省时省力,能明显提高肠道门诊患者大便标本及时送检率和满意度,值得推广应用.%Objective To evaluate the effect of stool specimen sampling device in clinical application.Methods 65 patients with diarrhea treated at a hospital from May to July,2014 were selected as a control group and were conventionally collected stool specimens:when stool was defecated into toilet bowl,specimens were sampled with spoon for inspection.67 patients with diarrhea treated at the hospital from August to October,2014 were selected as an observation group.The stool specimens were collected with stool specimen sampling device and saved with sampling spoon for inspection in the observation group.The sample-submitted-in-time rate and patients' satisfaction degree were compared between these two groups.Results The sample-submitted-in-time rate and patients' satisfaction degree were 92.5% and 98.5% in the observation group and were 75.4% and 89.2% in the control group,with statistical differences (x 2 =7.255 8,P =0.007 1;x 2=4.987 0,P=0.025 5).Conclusions Stool specimen sampling device is simple,convenient,time-saving,and work-saving and can increase samplesubmitted-in-time rate and patients' satisfaction degree,so it is worth being generalized.

  4. Developmental trajectories of clinically significant attention-deficit/hyperactivity disorder (ADHD) symptoms from grade 3 through 12 in a high-risk sample: Predictors and outcomes.

    Science.gov (United States)

    Sasser, Tyler R; Kalvin, Carla B; Bierman, Karen L

    2016-02-01

    Developmental trajectories of clinically significant attention-deficit/hyperactivity (ADHD) symptoms were explored in a sample of 413 children identified as high risk because of elevated kindergarten conduct problems. Symptoms of inattention and hyperactivity-impulsivity were modeled simultaneously in a longitudinal latent class analyses, using parent reports collected in Grades 3, 6, 9, and 12. Three developmental trajectories emerged: (1) low levels of inattention and hyperactivity (low), (2) initially high but then declining symptoms (declining), and (3) continuously high symptoms that featured hyperactivity in childhood and early adolescence and inattention in adolescence (high). Multinomial logistic regressions examined child characteristics and family risk factors as predictors of ADHD trajectories. Relative to the low class, children in the high and declining classes displayed similar elevations of inattention and hyperactivity in early childhood. The high class was distinguished from the declining class by higher rates of aggression and hyperactivity at school and emotion dysregulation at home. In contrast, the declining class displayed more social isolation at home and school, relative to the low class. Families of children in both high and declining trajectory classes experienced elevated life stressors, and parents of children in the high class were also more inconsistent in their discipline practices relative to the low class. By late adolescence, children in the high class were significantly more antisocial than those in the low class, with higher rates of arrests, school dropout, and unemployment, whereas children in the declining class did not differ from those in the low trajectory class. The developmental and clinical implications of these findings are discussed. PMID:26854506

  5. Conventional and molecular cytogenetics of human non-medullary thyroid carcinoma: characterization of eight cell line models and review of the literature on clinical samples

    Directory of Open Access Journals (Sweden)

    Rocha Ana

    2008-12-01

    Full Text Available Abstract Background Cell lines are often poorly characterized from a genetic point of view, reducing their usefulness as tumor models. Our purpose was to assess the genetic background of eight commonly used human thyroid carcinoma models and to compare the findings with those reported for primary tumors of the gland. Methods We used chromosome banding analysis and comparative genomic hybridization to profile eight non-medullary thyroid carcinoma cell lines of papillary (TPC-1, FB2, K1 and B-CPAP, follicular (XTC-1 or anaplastic origin (8505C, C643 and HTH74. To assess the representativeness of the findings, we additionally performed a thorough review of cytogenetic (n = 125 and DNA copy number information (n = 270 available in the literature on clinical samples of thyroid carcinoma. Results The detailed characterization of chromosomal markers specific for each cell line revealed two cases of mistaken identities: FB2 was shown to derive from TPC-1 cells, whereas K1 cells have their origin in cell line GLAG-66. All cellular models displayed genomic aberrations of varying complexity, and recurrent gains at 5p, 5q, 8q, and 20q (6/7 cell lines and losses at 8p, 13q, 18q, and Xp (4/7 cell lines were seen. Importantly, the genomic profiles were compatible with those of the respective primary tumors, as seen in the meta-analysis of the existing literature data. Conclusion We provide the genomic background of seven independent thyroid carcinoma models representative of the clinical tumors of the corresponding histotypes, and highlight regions of recurrent aberrations that may guide future studies aimed at identifying target genes. Our findings further support the importance of routinely performing cytogenetic studies on cell lines, to detect cross-contamination mishaps such as those identified here.

  6. Selection of the treatment effect for sample size determination in a superiority clinical trial using a hybrid classical and Bayesian procedure.

    Science.gov (United States)

    Ciarleglio, Maria M; Arendt, Christopher D; Makuch, Robert W; Peduzzi, Peter N

    2015-03-01

    Specification of the treatment effect that a clinical trial is designed to detect (θA) plays a critical role in sample size and power calculations. However, no formal method exists for using prior information to guide the choice of θA. This paper presents a hybrid classical and Bayesian procedure for choosing an estimate of the treatment effect to be detected in a clinical trial that formally integrates prior information into this aspect of trial design. The value of θA is found that equates the pre-specified frequentist power and the conditional expected power of the trial. The conditional expected power averages the traditional frequentist power curve using the conditional prior distribution of the true unknown treatment effect θ as the averaging weight. The Bayesian prior distribution summarizes current knowledge of both the magnitude of the treatment effect and the strength of the prior information through the assumed spread of the distribution. By using a hybrid classical and Bayesian approach, we are able to formally integrate prior information on the uncertainty and variability of the treatment effect into the design of the study, mitigating the risk that the power calculation will be overly optimistic while maintaining a frequentist framework for the final analysis. The value of θA found using this method may be written as a function of the prior mean μ0 and standard deviation τ0, with a unique relationship for a given ratio of μ0/τ0. Results are presented for Normal, Uniform, and Gamma priors for θ. PMID:25583273

  7. Resting and reactive frontal brain electrical activity (EEG among a non-clinical sample of socially anxious adults: Does concurrent depressive mood matter?

    Directory of Open Access Journals (Sweden)

    Elliott A Beaton

    2008-03-01

    Full Text Available Elliott A Beaton1, Louis A Schmidt2, Andrea R Ashbaugh2,5, Diane L Santesso2, Martin M Antony1,3,4, Randi E McCabe1,31Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada; 2Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ontario, Canada; 3Anxiety Treatment and Research Centre, St. Joseph’s Healthcare, Hamilton, Ontario, Canada; 4Department of Psychology, Ryerson University, Toronto, Ontario, Canada; 5Concordia University, Montreal, Quebec, CanadaAbstract: A number of studies have noted that the pattern of resting frontal brain electrical activity (EEG is related to individual differences in affective style in healthy infants, children, and adults and some clinical populations when symptoms are reduced or in remission. We measured self-reported trait shyness and sociability, concurrent depressive mood, and frontal brain electrical activity (EEG at rest and in anticipation of a speech task in a non-clinical sample of healthy young adults selected for high and low social anxiety. Although the patterns of resting and reactive frontal EEG asymmetry did not distinguish among individual differences in social anxiety, the pattern of resting frontal EEG asymmetry was related to trait shyness after controlling for concurrent depressive mood. Individuals who reported a higher degree of shyness were likely to exhibit greater relative right frontal EEG activity at rest. However, trait shyness was not related to frontal EEG asymmetry measured during the speech-preparation task, even after controlling for concurrent depressive mood. These findings replicate and extend prior work on resting frontal EEG asymmetry and individual differences in affective style in adults. Findings also highlight the importance of considering concurrent emotional states of participants when examining psychophysiological correlates of personality.Keywords: social anxiety, shyness, sociability

  8. Conventional and molecular cytogenetics of human non-medullary thyroid carcinoma: characterization of eight cell line models and review of the literature on clinical samples

    International Nuclear Information System (INIS)

    Cell lines are often poorly characterized from a genetic point of view, reducing their usefulness as tumor models. Our purpose was to assess the genetic background of eight commonly used human thyroid carcinoma models and to compare the findings with those reported for primary tumors of the gland. We used chromosome banding analysis and comparative genomic hybridization to profile eight non-medullary thyroid carcinoma cell lines of papillary (TPC-1, FB2, K1 and B-CPAP), follicular (XTC-1) or anaplastic origin (8505C, C643 and HTH74). To assess the representativeness of the findings, we additionally performed a thorough review of cytogenetic (n = 125) and DNA copy number information (n = 270) available in the literature on clinical samples of thyroid carcinoma. The detailed characterization of chromosomal markers specific for each cell line revealed two cases of mistaken identities: FB2 was shown to derive from TPC-1 cells, whereas K1 cells have their origin in cell line GLAG-66. All cellular models displayed genomic aberrations of varying complexity, and recurrent gains at 5p, 5q, 8q, and 20q (6/7 cell lines) and losses at 8p, 13q, 18q, and Xp (4/7 cell lines) were seen. Importantly, the genomic profiles were compatible with those of the respective primary tumors, as seen in the meta-analysis of the existing literature data. We provide the genomic background of seven independent thyroid carcinoma models representative of the clinical tumors of the corresponding histotypes, and highlight regions of recurrent aberrations that may guide future studies aimed at identifying target genes. Our findings further support the importance of routinely performing cytogenetic studies on cell lines, to detect cross-contamination mishaps such as those identified here

  9. KRAS mutation analysis in ovarian samples using a high sensitivity biochip assay

    Directory of Open Access Journals (Sweden)

    Reinthaller Alexander

    2009-04-01

    Full Text Available Abstract Background Mutations in the KRAS gene are one of the most frequent genetic abnormalities in ovarian carcinoma. They are of renewed interest as new epidermal growth factor receptor (EGFR-targeted therapies are being investigated for use in ovarian carcinoma. As KRAS mutations are associated with poor response and resistance to EGFR-targeting drugs, this study was conducted to obtain more information on the spectrum of KRAS mutations in ovarian carcinoma. Methods The presence of KRAS mutations in codon 12 and 13 was analyzed in frozen and formalin-fixed paraffin-embedded (FFPE tissue with a low density biochip platform. 381 malignant (29 borderline malignancy, 270 primary carcinomas, and 82 recurrent carcinomas and 22 benign tissue samples from a total of 394 patients were examined. KRAS mutational status of each sample was correlated with dignity, FIGO stage, grade, histology, and survival. Results KRAS mutations were found in 60 (15% samples with 58 samples deriving from malignant tissue and 2 samples deriving from benign tissue. In 55 (92% samples codon 12 was found to be mutated. Frozen and FFPE samples concurred with respect to KRAS mutation status. Conclusion KRAS mutation is a common event in ovarian cancer primarily in carcinomas of lower grade, lower FIGO stage, and mucinous histotype. The KRAS mutational status is no prognostic factor for patients treated with standard therapy. However, in line with experience from colorectal cancer and non-small-cell-lung cancer (NSCLC, it may be important for prediction of response to EGFR-targeted therapies.

  10. A Comparison of Clinical and Non-Clinical Samples Using the Concepts of: Individual Personality, Family Structure, Family of Origin Perception, Sexuality, and Adjustment/Adaptability To Determine Family Risk for Father Daughter Incest.

    Science.gov (United States)

    Utesch, William E.

    Father-daughter incest is more traumatic than any other type of child-sexual molestation. This study examines some of the factors which may lead to father-daughter incest. The author divided 40 Caucasian couples into three groups: (1) clinical incest group; (2) clinical non-incest group (to control for clinical status); and (3) non-clinical group.…

  11. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma

    Science.gov (United States)

    Van Allen, Eliezer M.; Wagle, Nikhil; Sucker, Antje; Treacy, Daniel; Johannessen, Cory; Goetz, Eva M.; Place, Chelsea S.; Taylor-Weiner, Amaro; Whittaker, Steven; Kryukov, Gregory; Hodis, Eran; Rosenberg, Mara; McKenna, Aaron; Cibulskis, Kristian; Farlow, Deborah; Zimmer, Lisa; Hillen, Uwe; Gutzmer, Ralf; Goldinger, Simone M.; Ugurel, Selma; Gogas, Helen J.; Egberts, Friederike; Berking, Carola; Trefzer, Uwe; Loquai, Carmen; Weide, Benjamin; Hassel, Jessica C.; Gabriel, Stacey B.; Carter, Scott L.; Getz, Gad; Garraway, Levi A.; Schadendorf, Dirk

    2013-01-01

    Most patients with BRAFV600 metastatic melanoma develop resistance to selective RAF kinase inhibitors. The spectrum of clinical genetic resistance mechanisms to RAF inhibitors and options for salvage therapy are incompletely understood. We performed whole exome sequencing on formalin-fixed, paraffin embedded (FFPE) tumors from 45 patients with BRAFV600 metastatic melanoma who received vemurafenib or dabrafenib monotherapy. Genetic alterations in known or putative RAF inhibitor resistance genes were observed in 23 of 45 patients (51%). Besides previously characterized alterations, we discovered a “long tail” of new MAPK pathway alterations (MAP2K2, MITF) that confer RAF inhibitor resistance. In three cases, multiple resistance gene alterations were observed within the same tumor biopsy. Overall, RAF inhibitor therapy leads to diverse clinical genetic resistance mechanisms, mostly involving MAPK pathway reactivation. Novel therapeutic combinations may be needed to achieve durable clinical control of BRAFV600 melanoma. Integrating clinical genomics with preclinical screens may model subsequent resistance studies. PMID:24265153

  12. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling

    DEFF Research Database (Denmark)

    Glud, M.; Klausen, M.; Gniadecki, R.;

    2009-01-01

    surgical specimens are formalin fixed and paraffin embedded (FFPE). To explore whether FFPE material would be suitable for miRNA profiling in melanocytic lesions, we compared miRNA expression patterns in FFPE versus fresh frozen samples, obtained from 15 human melanocytic nevi. Out of microarray data, we...... therefore serve as biomarkers that may be useful in a clinical environment for diagnosis of various diseases. Most miRNA profiling studies have used fresh tissue samples. However, in some types of cancer, including malignant melanoma, fresh material is difficult to obtain from primary tumors, and most...... identified 84 miRNAs that were expressed in both types of samples and represented an miRNA profile of melanocytic nevi. Our results showed a high correlation in miRNA expression (Spearman r-value of 0.80) between paired FFPE and fresh frozen material. The data were further validated by quantitative RT...

  13. Sugar, stress, and the Supplemental Nutrition Assistance Program: early childhood obesity risks among a clinic-based sample of low-income Hispanics.

    Science.gov (United States)

    Watt, Toni Terling; Appel, Louis; Roberts, Kelley; Flores, Bianca; Morris, Sarajane

    2013-06-01

    The nationwide epidemic of pediatric obesity is more prevalent among Hispanic children than white children. Recent literature suggests that obesity has early origins, leading scholars to call for interventions in pregnancy and infancy. However, there is little theoretical or empirical research to guide the development of early prevention programs for Hispanics. The present study seeks to identify risk factors for early childhood obesity among a low-income, predominately Hispanic sample. Data were gathered to inform the design of a primary care childhood obesity prevention program targeting pregnancy through age 12 months. Baseline data were gathered on 153 women attending the clinic for prenatal care or for their child's 2, 6 or 12 month well-check. All women completed surveys on diet, exercise, social support, food security, stress, infant feeding practices, health, and demographics. For women with children (n = 66), survey data were matched with medical records data on infant weight. Results reveal that 55 % of women in the sample had an infant profiling in the 85th percentile or higher, confirming the need for an early childhood obesity intervention. While mothers exhibited several potential risk factors for childhood obesity (e.g. fast food consumption), only maternal consumption of sweets and sugar-sweetened beverages, stress, and SNAP (food stamp receipt) were associated with infant overweight. Findings further reveal that stress and SNAP relate to child overweight, in part, through mothers' sugar-sweetened beverage consumption. Results suggest that obesity prevention efforts must address specific individual choices as well as the external environment that shapes these consumption patterns. PMID:23197136

  14. High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue.

    Science.gov (United States)

    Ly, Alice; Buck, Achim; Balluff, Benjamin; Sun, Na; Gorzolka, Karin; Feuchtinger, Annette; Janssen, Klaus-Peter; Kuppen, Peter J K; van de Velde, Cornelis J H; Weirich, Gregor; Erlmeier, Franziska; Langer, Rupert; Aubele, Michaela; Zitzelsberger, Horst; McDonnell, Liam; Aichler, Michaela; Walch, Axel

    2016-08-01

    Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in metabolite content or chemical state due to tissue processing. We present a protocol for the in situ analysis of metabolite content from FFPE samples using a high-mass-resolution matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR-MSI) platform. The method involves FFPE tissue sections that undergo deparaffinization and matrix coating by 9-aminoacridine before MALDI-MSI. Using this platform, we previously detected ∼1,500 m/z species in the mass range m/z 50-1,000 in FFPE samples; the overlap compared with fresh frozen samples is 72% of m/z species, indicating that metabolites are largely conserved in FFPE tissue samples. This protocol can be reproducibly performed on FFPE tissues, including small samples such as tissue microarrays and biopsies. The procedure can be completed in a day, depending on the size of the sample measured and raster size used. Advantages of this approach include easy sample handling, reproducibility, high throughput and the ability to demonstrate molecular spatial distributions in situ. The data acquired with this protocol can be used in research and clinical practice. PMID:27414759

  15. Social anxiety symptoms and suicidal ideation in a clinical sample of early adolescents: examining loneliness and social support as longitudinal mediators.

    Science.gov (United States)

    Gallagher, Michelle; Prinstein, Mitchell J; Simon, Valerie; Spirito, Anthony

    2014-08-01

    Recent research has shown that social anxiety may be related to increased risk for suicidal ideation in teens, although this research largely has been cross-sectional and has not examined potential mediators of this relationship. A clinical sample of 144 early adolescents (72 % female; 12-15 years old) was assessed during psychiatric inpatient hospitalization and followed up at 9 and 18 months post-baseline. Symptoms of social anxiety, depression, suicidal ideation, loneliness, and perceived social support were assessed via structured interviews and self-report instruments. Structural equation modeling revealed a significant direct relationship between social anxiety symptoms at baseline and suicidal ideation at 18 months post-baseline, even after controlling for baseline depressive symptoms and ideation. A second multiple mediation model revealed that baseline social anxiety had a significant indirect effect on suicidal ideation at 18 months post-baseline through loneliness at 9 months post-baseline. Social anxiety did not have a significant indirect effect on suicidal ideation through perceived social support from either parents or close friends. Findings suggest that loneliness may be particularly implicated in the relationship between social anxiety and suicidality in teens. Clinicians should assess and address feelings of loneliness when treating socially anxious adolescents. PMID:24390470

  16. Can the Theory of Planned Behavior predict dietary intention and future dieting in an ethnically diverse sample of overweight and obese veterans attending medical clinics?

    Science.gov (United States)

    Lash, Denise N; Smith, Jane Ellen; Rinehart, Jenny K

    2016-04-01

    Obesity has become a world-wide epidemic; in the United States (U.S.) approximately two-thirds of adults are classified as overweight or obese. Military veterans' numbers are even higher, with 77% of retired or discharged U.S. veterans falling in these weight categories. One of the most common methods of changing one's weight is through dieting, yet little is known regarding the factors that facilitate successful dieting behavior. The current investigation tested the Theory of Planned Behavior's (TPB) ability to predict dietary intention and future dieting in a sample of 84 overweight and obese patients attending medical clinics at a Veterans Affairs Hospital in the southwestern part of the U.S. Participants primarily were male (92%) and ethnic/racial minorities (58%). Perceived need and anticipated regret were added to the standard TPB model. While the TPB predicted dietary intention, it did not significantly account for improved dietary behaviors. Anticipated regret significantly enhanced the basic TPB's ability to predict intention to diet, while perceived need did not. These findings highlight the difficulty in predicting sustained change in a complex behavior such as dieting to lose weight. The need for more work with older, overweight/obese medical patients attending veterans' facilities is stressed, as is the need for such work with male patients and ethnic minorities in particular. PMID:26792774

  17. Using tablet computers compared to interactive voice response to improve subject recruitment in osteoporosis pragmatic clinical trials: feasibility, satisfaction, and sample size

    Directory of Open Access Journals (Sweden)

    Mudano AS

    2013-06-01

    Full Text Available Amy S Mudano,1,2,3 Lisa C Gary,1,2,3 Ana L Oliveira,1,2,3 Mary Melton,1,2,3 Nicole C Wright,1,2,3 Jeffrey R Curtis,1,2,3 Elizabeth Delzell,1,2,3 T Michael Harrington,1,2,3 Meredith L Kilgore,1,2,3 Cora Elizabeth Lewis,1,2,3 Jasvinder A Singh,1,2,3,4 Amy H Warriner,1,2,3 Wilson D Pace,5 Kenneth G Saag1,2,31Center for Education and Research on Therapeutics (CERTs, 2Center for Outcomes Effectiveness Research and Education (COERE, and 3Center for Clinical and Translational Sciences (CCTS, (University of Alabama at Birmingham, Birmingham, AL, USA; 4Veterans Affairs Medical Center, Birmingham, AL, USA; 5Distributed Ambulatory Research in Therapeutics Network (DARTNet, American Academy of Family Physicians (AAFP, University of Colorado, Denver, CO, USAIntroduction: Pragmatic clinical trials (PCTs provide large sample sizes and enhanced generalizability to assess therapeutic effectiveness, but efficient patient enrollment procedures are a challenge, especially for community physicians. Advances in technology may improve methods of patient recruitment and screening in PCTs. Our study looked at a tablet computer versus an integrated voice response system (IVRS for patient recruitment and screening for an osteoporosis PCT in community physician offices.Materials and methods: We recruited women ≥ 65 years of age from community physician offices to answer screening questions for a hypothetical osteoporosis active comparator PCT using a tablet computer or IVRS. We assessed the feasibility of these technologies for patient recruitment as well as for patient, physician, and office staff satisfaction with the process. We also evaluated the implications of these novel recruitment processes in determining the number of primary care practices and screened patients needed to conduct the proposed trial.Results: A total of 160 women (80% of those approached agreed to complete the osteoporosis screening questions in ten family physicians’ offices. Women using the

  18. Anxiety disorders in an attention-deficit/hyperactivity disorder clinical sample Transtorno de ansiedade em amostra de pacientes com déficit de atenção e hiperatividade

    OpenAIRE

    Isabella de Souza; Maria Antônia Pinheiro; Paulo Mattos

    2005-01-01

    OBJECTIVE: To evaluate the prevalence of anxiety disorders in a clinical referred sample of children and adolescents with attention deficit/hyperactivity disorder (ADHD). METHOD: 78 children and adolescents with ADHD according to DSM-IV criteria were investigated with a semi-structured interview (P-CHIPS), complemented by clinical interviews with the children or adolescents and their parents. Their IQ was calculated with neuropsychological testing. RESULTS: A high prevalence of anxiety disord...

  19. Who are the children and adolescent patients of a national referral service of eating disorders in Brazil?: a cross-sectional study of a clinical sample

    Directory of Open Access Journals (Sweden)

    Vanessa Dentzien Pinzon

    2013-01-01

    Full Text Available Objectives: To investigate the sociodemographic and clinical profile of patients receiving treatment at a specialized service for children and adolescents with eating disorders (ED in São Paulo, Brazil, and to compare data with the relevant literature. Methods: This cross-sectional study assessed male and female patients with ED up to 18 years of age. All data were collected upon admission. Results: A total of 100 subjects were assessed. Mean age was 15.41±0.18 years, and mean age at ED onset was 13.5±0.19 years. Mean disease duration was 21.06 ±1.67 months. Of the total sample, 82% of the patients were female, 84% were Caucasian, 64% came from A and B economic tiers. Moreover, in 60% ED started at 14 years of age or less, and 74% had psychiatric comorbidities. Anorexia nervosa was the most prevalent diagnosis (43%. Hospitalized patients had lower body mass index, longer ED duration, and more severe scores on the Children's Global Assessment Scale than outpatients (p < 0.05. Conclusions: Our young Brazilian patients with ED present epidemiological and symptomatic characteristics very similar to those found in the scientific literature, including a high prevalence of psychiatric comorbidities. The higher frequency of full syndrome ED, the predominance of cases with an early onset, the delay in beginning specialized treatment, and the more severe state of inpatients provide grounds for concern because these factors differ from what has been reported in reference studies and indicate greater ED severity.

  20. Ultrasensitive electrochemical immunosensor based on dual signal amplification process for p16(INK4a) cervical cancer detection in clinical samples.

    Science.gov (United States)

    Duangkaew, Pattasuda; Tapaneeyakorn, Satita; Apiwat, Chayachon; Dharakul, Tararaj; Laiwejpithaya, Somsak; Kanatharana, Proespichaya; Laocharoensuk, Rawiwan

    2015-12-15

    The p16(INK4a) (p16) is a cyclin-dependent kinase inhibitor, which has been evaluated in several studies as a diagnostic marker of cervical cancer. Immunostaining using p16 specific antibody has confirmed an over-expression of p16 protein in cervical cancer cells and its association with disease progression. This article reports an ultrasensitive electrochemical immunosensor for specific detection of p16 and demonstrates its performance for detection of solubilized p16 protein in cell lysates obtained from patients. Sandwich-based immunoreaction couple with double signal amplification strategy based on catalytic enlargement of particle tag was used for high sensitivity and specificity. The conditions were optimized to create an immunoassay protocol. Disposable screen-printed electrode modified with capture antibodies (Ab1) was selected for further implementation towards point-of-care diagnostics. Small gold nanoparticles (15 nm diameter) conjugated with detection antibodies (Ab2) were found to better serve as a detection label due to limited interference with antigen-antibody interaction. Double signal enhancement was performed by sequential depositions of gold and silver layers. This gave the sensitivity of 1.78 μA mL(ng GST-p16)(-1) cm(-2) and detection limit of 1.3 ng mL(-1) for GST-p16 protein which is equivalent to 0.49 ng mL(-1) for p16 protein and 28 cells for HeLa cervical cancer cells. In addition to purified protein, the proposed immunosensor effectively detected elevated p16 level in cervical swab samples obtained from 10 patients with positive result from standard Pap smear test, indicating that an electrochemical immunosensors hold an excellent promise for detection of cervical cancer in clinical setting. PMID:26201985

  1. Assessing next-generation sequencing and 4 bioinformatics tools for detection of Enterovirus D68 and other respiratory viruses in clinical samples.

    Science.gov (United States)

    Huang, Weihua; Wang, Guiqing; Lin, Henry; Zhuge, Jian; Nolan, Sheila M; Vail, Eric; Dimitrova, Nevenka; Fallon, John T

    2016-05-01

    We used 4 different bioinformatics algorithms to evaluate the application of a metagenomic shot-gun sequencing method in detection of Enterovirus D68 and other respiratory viruses in clinical specimens. Our data supported that next-generation sequencing, combined with improved bioinformatics tools, is practically feasible and useful for clinical diagnosis of viral infections. PMID:26971640

  2. A randomised clinical trial on cardiotocography plus fetal blood sampling versus cardiotocography plus ST-analysis of the fetal electrocardiogram (STAN® for intrapartum monitoring

    Directory of Open Access Journals (Sweden)

    Rijnders Robbert JP

    2007-07-01

    Full Text Available Abstract Background Cardiotocography (CTG is worldwide the method for fetal surveillance during labour. However, CTG alone shows many false positive test results and without fetal blood sampling (FBS, it results in an increase in operative deliveries without improvement of fetal outcome. FBS requires additional expertise, is invasive and has often to be repeated during labour. Two clinical trials have shown that a combination of CTG and ST-analysis of the fetal electrocardiogram (ECG reduces the rates of metabolic acidosis and instrumental delivery. However, in both trials FBS was still performed in the ST-analysis arm, and it is therefore still unknown if the observed results were indeed due to the ST-analysis or to the use of FBS in combination with ST-analysis. Methods/Design We aim to evaluate the effectiveness of non-invasive monitoring (CTG + ST-analysis as compared to normal care (CTG + FBS, in a multicentre randomised clinical trial setting. Secondary aims are: 1 to judge whether ST-analysis of fetal electrocardiogram can significantly decrease frequency of performance of FBS or even replace it; 2 perform a cost analysis to establish the economic impact of the two treatment options. Women in labour with a gestational age ≥ 36 weeks and an indication for CTG-monitoring can be included in the trial. Eligible women will be randomised for fetal surveillance with CTG and, if necessary, FBS or CTG combined with ST-analysis of the fetal ECG. The primary outcome of the study is the incidence of serious metabolic acidosis (defined as pH ecf > 12 mmol/L in the umbilical cord artery. Secondary outcome measures are: instrumental delivery, neonatal outcome (Apgar score, admission to a neonatal ward, incidence of performance of FBS in both arms and cost-effectiveness of both monitoring strategies across hospitals. The analysis will follow the intention to treat principle. The incidence of metabolic acidosis will be compared across both groups

  3. Diagnostic potential of IS6110, 38kDa, 65kDa and 85B sequence-based polymerase chain reaction in the diagnosis of Mycobacterium tuberculosis in clinical samples

    Directory of Open Access Journals (Sweden)

    Negi S

    2007-01-01

    Full Text Available Purpose: The correlation between the presence of specific gene sequence of M. tuberculosis and specific diagnosis of clinical tuberculosis is not known. This study compared the results of polymerase chain reaction (PCR amplification of M . tuberculosis specific DNA sequences (IS6110, 65kDa, 38kDa and mRNA coding for 85 B protein from different clinical samples of pulmonary and extrapulmonary tuberculosis. Methods: One hundred and seventy-two clinical samples from suspected tuberculosis patients were tested for smear examination, culture (LJ and rapid BACTEC 460 TB system and PCR. PCR was performed with specific primers for the targets: IS6110, 65kDa, 38kDa and 85B. Results: Each PCR test was found to have a much higher positivity than conventional test and BACTEC culture ( P < 0.05. Smear positive samples (56 and the samples (36 showing positive results by conventional methods (smear and LJ medium culture and BACTEC were found to be positive by all PCR protocols. No significant difference was found between the four PCR protocols ( P >0.05. The primer specific for amplifying the 123bp IS6110 fragment gave the highest positivity (83%, followed by 65kDa, 38kDa and 85B RT-PCR in descending order. Conclusions: These data suggest that the presence of IS6110 correlates more closely with the diagnosis of clinical tuberculosis than that of 65kDa, 38kDa and 85B proteins.

  4. Screening for proteinuria in a rheumatology clinic: comparison of dipstick testing, 24 hour urine quantitative protein, and protein/creatinine ratio in random urine samples.

    OpenAIRE

    Ralston, S. H.; Caine, N; Richards, I; O'REILLY, D; Sturrock, R D; Capell, H A

    1988-01-01

    Measurements of protein/creatinine ratio in 'spot' urine samples were compared with measurements of 24 hour quantitative proteinuria and side room 'dipstick' testing in 104 samples from 90 patients presenting consecutively to a rheumatology unit. Linear regression analysis showed a highly significant correlation between the random urinary protein/creatinine ratio and total protein excretion in 24 hour urine samples (r = 0.92, p less than 0.001, y = 6.55x + 0.04). Although an approximation of ...

  5. Prevalence of HIV, STIs, and risk behaviors in a cross-sectional community- and clinic-based sample of men who have sex with men (MSM in Lima, Peru.

    Directory of Open Access Journals (Sweden)

    Amaya G Perez-Brumer

    Full Text Available Further research is necessary to understand the factors contributing to the high prevalence of HIV/STIs among men who have sex with men (MSM in Peru. We compared HIV/STI prevalence and risk factors between two non-probability samples of MSM, one passively enrolled from an STI clinic and the other actively enrolled from community venues surrounding the clinic in Lima, Peru.A total of 560 self-identified MSM were enrolled between May-December, 2007. 438 subjects enrolled from a municipal STI clinic and 122 subjects enrolled during community outreach visits. All participants underwent screening for HIV, syphilis, HSV-2, gonorrhoea, and chlamydia and completed a survey assessing their history of HIV/STIs, prior HIV testing, and sexual behavior.HIV prevalence was significantly higher among MSM enrolled from the clinic, with previously undiagnosed HIV identified in 9.1% compared with 2.6% of community participants. 15.4 % of all MSM screened were infected with ≥ 1 curable STI, 7.4% with early syphilis (RPR ≥ 1:16 and 5.5% with urethral gonorrhoea and/or chlamydia. No significant differences between populations were reported in prevalence of STIs, number of male sex partners, history of unprotected anal intercourse, or alcohol and/or drug use prior to sex. Exchange of sex for money or goods was reported by 33.5% of MSM enrolled from the clinic and 21.2% of MSM from the community (p = 0.01.Our data demonstrate that the prevalence of HIV and STIs, including syphilis, gonorrhoea, and chlamydia are extremely high among MSM enrolled from both clinic and community venues in urban Peru. New strategies are needed to address differences in HIV/STI epidemiology between clinic- and community-enrolled samples of MSM.

  6. The Relationship between Childhood Sexual Abuse, Complex Post-Traumatic Stress Disorder and Alexithymia in Two Outpatient Samples: Examination of Women Treated in Community and Institutional Clinics

    Science.gov (United States)

    McLean, Linda M.; Toner, Brenda; Jackson, Jennifer; Desrocher, Mary; Stuckless, Noreen

    2006-01-01

    Relationships between trauma variables, complex post-traumatic stress disorder (complex PTSD), affect dysregulation, dissociation, somatization, and alexithymia were studied in 70 women with early-onset sexual abuse treated in community-based private (n = 25) or clinic outpatient settings (n = 45). Measures were the Toronto Alexithymia Scale-20…

  7. Detection of Cryptic Genospecies Misidentified as Haemophilus influenzae in Routine Clinical Samples by Assessment of Marker Genes fucK, hap, and sodC▿

    OpenAIRE

    Nørskov-Lauritsen, Niels

    2009-01-01

    Clinical isolates of Haemophilus influenzae were assessed for the presence of fucK, hap, and sodC by hybridization with gene-specific probes, and isolates diverging from the expected H. influenzae genotype were characterized by phenotype and 16S rRNA gene sequencing. Two of 480 isolates were finally classified as variant strains (“nonhemolytic Haemophilus haemolyticus”).

  8. Detection of cryptic genospecies misidentified as Haemophilus influenzae in routine clinical samples by assessment of marker genes fucK, hap, and sodC.

    Science.gov (United States)

    Nørskov-Lauritsen, Niels

    2009-08-01

    Clinical isolates of Haemophilus influenzae were assessed for the presence of fucK, hap, and sodC by hybridization with gene-specific probes, and isolates diverging from the expected H. influenzae genotype were characterized by phenotype and 16S rRNA gene sequencing. Two of 480 isolates were finally classified as variant strains ("nonhemolytic Haemophilus haemolyticus"). PMID:19535530

  9. A Randomized Clinical Trial of Cogmed Working Memory Training in School-Age Children with ADHD: A Replication in a Diverse Sample Using a Control Condition

    Science.gov (United States)

    Chacko, A.; Bedard, A. C.; Marks, D. J.; Feirsen, N.; Uderman, J. Z.; Chimiklis, A.; Rajwan, E.; Cornwell, M.; Anderson, L.; Zwilling, A.; Ramon, M.

    2014-01-01

    Background: Cogmed Working Memory Training (CWMT) has received considerable attention as a promising intervention for the treatment of Attention-Deficit/Hyperactivity Disorder (ADHD) in children. At the same time, methodological weaknesses in previous clinical trials call into question reported efficacy of CWMT. In particular, lack of equivalence…

  10. Follow-up factor structure of schizotypy and its clinical associations in a help-seeking sample meeting ultra-high risk for psychosis criteria at baseline

    NARCIS (Netherlands)

    Lin, Ashleigh; Wigman, Johanna T. W.; Nelson, Barnaby; Wood, Stephen J.; Vollebergh, Wilma A. M.; van Os, Jim; Yung, Alison R.

    2013-01-01

    Background: Schizotypy is a multidimensional construct indexing psychometric risk for schizophrenia. This study investigated the factor structure and clinical associations of the Oxford-Liverpool Inventory of Feelings and Experiences (O-LIFE) short scales, assessed at follow-up in an originally help

  11. A Comparative Study of Clinical Utility of Spot Urine Samples with 24-h Urine Albumin Excretion for Screening of Microalbuminuria in Type 2 Diabetic Patients

    OpenAIRE

    Chavan, Vilas U.; Durgawale, Pushpa P.; Sayyed, Anjum K.; Sontakke, Ajit V.; Attar, Nazir R.; Patel, Swati B.; Patil, Sangita R.; Nilakhe, Shreyasprasad D.

    2011-01-01

    Twenty-four hour urinary albumin excretion (UAE) is considered as gold standard method for albuminuria measurement, but collection of 24-h urine is inconvenient. The aim of present study was to evaluate whether albumin: creatinine ratio (ACR) and urinary albumin concentration (UAC) in different spot urine samples correlate or not with 24-h UAE for screening of microalbuminuria in type 2 diabetic patients. We collected first morning void (FMV), random urine sample (RUS) and 24-h urine, separat...

  12. Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Nevin Belder

    2016-03-01

    Full Text Available Formalin-fixed paraffin-embedded (FFPE tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013 [1]; Scicchitano et al., Scicchitano et al. (2006 [2]; Frank et al., Frank et al. (2007 [3]; Fedorowicz et al., Fedorowicz et al. (2009 [4]. However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples.

  13. Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.

    Science.gov (United States)

    Belder, Nevin; Coşkun, Öznur; Erdoğan, Beyza Doğanay; Savaş, Berna; Ensari, Arzu; Özdağ, Hilal

    2016-03-01

    Formalin-fixed paraffin-embedded (FFPE) tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013) [1]; Scicchitano et al., Scicchitano et al. (2006) [2]; Frank et al., Frank et al. (2007) [3]; Fedorowicz et al., Fedorowicz et al. (2009) [4]). However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO) database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples. PMID:26981433

  14. Health-related quality of life in overweight German children and adolescents: do treatment-seeking youth have lower quality of life levels? Comparison of a clinical sample with the general population using a multilevel model approach

    OpenAIRE

    Finne, Emily; Reinehr, Thomas; Schaefer, Anke; Winkel, Katrin; Kolip, Petra

    2013-01-01

    BACKGROUND: Health-related quality of life (HRQoL) is reduced in obese children and adolescents, especially in clinical samples. However, little is known regarding the HRQoL of moderately overweight youth. Moreover, several studies have indicated perceived overweight as a critical factor associated with lower HRQoL. Our main objective was to compare HRQoL between treatment-seeking overweight youth and the general adolescent population, whilst separating the effects of treatment-seeking sta...

  15. Differences in Early Maladaptive Schemas between a Sample of Young Adult Female Substance Abusers and a Non-clinical Comparison Group

    OpenAIRE

    Shorey, Ryan C.; Stuart, Gregory L.; Anderson, Scott

    2012-01-01

    Early maladaptive schemas, defined as cognitive and behavioural patterns of viewing oneself and the world that cause considerable distress, are increasingly being recognized as an important underlying correlate of mental health problems. Recent research has begun to examine early maladaptive schemas among individuals seeking treatment for substance abuse. Unfortunately, there is limited research on whether substance abusers score higher on early maladaptive schemas than non-clinical controls....

  16. Prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know?

    OpenAIRE

    Minodier, Laetitia; Charrel, Remi N.; Ceccaldi, Pierre-Emmanuel; van der Werf, Sylvie; Blanchon, Thierry; Hanslik, Thomas; Falchi, Alessandra

    2015-01-01

    This review provides for the first time an assessment of the current understanding about the occurrence and the clinical significance of gastrointestinal (GI) symptoms in influenza patients, and their correlation with the presence of human influenza viruses in stools of patients with confirmed influenza virus infection. Studies exploring how human influenza viruses spread to the patient’s GI tract after a primary respiratory infection have been summarized. We conducted a systematic search of ...

  17. Lipoprotein cholesterol and triglyceride concentrations associated with dog body condition score; effect of recommended fasting duration on sample concentrations in Japanese private clinics

    OpenAIRE

    USUI, Shiho; YASUDA, Hidemi; KOKETSU, Yuzo

    2015-01-01

    The objectives of this study were to survey clinics’ guidance about recommended fasting duration (FD) prior to lipoprotein analysis, and to characterize lipoprotein cholesterol and triglyceride concentrations in obese and overweight dogs categorized on the basis of the 5-point body condition score (BCS) scale. A dataset was created from lipoprotein analysis medical records of 1,538 dogs from 75 breeds in 354 clinics from 2012 to 2013. A phone survey was conducted to obtain the clinics’ FD. Tw...

  18. Behavioural predictors of subsequent hepatitis C diagnosis in a UK clinic sample of HIV positive men who have sex with men

    OpenAIRE

    Turner, J. M.; Rider, A. T.; Imrie, J.; Copas, A J; Edwards, S G; Dodds, J. P.; Stephenson, J M; SHARP Study Grp

    2006-01-01

    Objective: To explore the associations between self reported high risk sexual behaviours and subsequent diagnosis with hepatitis C virus (HCV) infection.Methods: The Sex, Health and Anti-Retrovirals Project (SHARP) was a cross sectional study of sexual behaviour in HIV positive, men who have sex with men (MSM) attending a London outpatient clinic. From July 1999 to August 2000 participants completed a computer assisted self interview questionnaire (CASI) on recent sexual behaviour, recreation...

  19. Validation of the partner version of the multidimensional vaginal penetration disorder questionnaire: A tool for clinical assessment of lifelong vaginismus in a sample of Iranian population

    OpenAIRE

    Molaeinezhad, Mitra; Khoei, Effat Merghati; Salehi, Mehrdad; Yousfy, Alireza; Roudsari, Robab Latifnejad

    2014-01-01

    Background: The role of spousal response in woman's experience of pain during the vaginal penetration attempts believed to be an important factor; however, studies are rather limited in this area. The aim of this study was to develop and investigate the psychometric indexes of the partner version of a multidimensional vaginal penetration disorder questionnaire (PV-MVPDQ); hence, the clinical assessment of spousal psychosexual reactions to vaginismus by specialists will be easier. Materials an...

  20. Daytime of Sampling, Tooth-Brushing and Ascorbic Acid Influence Salivary Thiobarbituric Acid Reacting Substances – A Potential Clinical Marker of Gingival Status

    OpenAIRE

    Július Hodosy; Peter Celec

    2005-01-01

    Background. Salivary thiobarbituric acid reacting substances (TBARS) have been previously shown to correlate with the impairment of gingival tissue. Although the details on the origin and the composition of this heterogeneous group of compounds in saliva are unknown, the potential clinical usefulness makes necessary the studies of factors influencing the salivary TBARS levels. Aim. To observe the effects of daily dynamics, tooth-brushing and ascorbic acid administration on salivary TBARS leve...

  1. Long-term storage of clinical samples in CyMol® medium for PNA- FISH® and culturing from the eSwab™ system

    DEFF Research Database (Denmark)

    Larsen, Lone Heimann; Xu, Yijuan; Pedersen, Malene Schibler;

    Objectives: A steadily growing diversity of bacteria is reported in foreign body infections, and culture-independent methods have been shown to supplement established culture methods. Therefore, sampling and preservation of specimens have become an important issue. We report here experience from a...... analytical methods. Methods: Sampling for both culture-dependent and -independent analyses were done over a period of two years. Specimens were transferred directly to the lab, and cultures of tissue biopsies, joint fluid, sonication fluid from the prosthesis components, and eSwab™ (Copan, Italy) were...... performed within 24 h after sampling. The corresponding specimens for culture-independent methods were stored at -80°C until analyzed in batchs. Specimens for fluorescence in situ hybridization (FISH) analysis were stored for app. one year at -80°C in CyMol® (Copan, Italy), an alcohol based media, before...

  2. The Relationship between Self-Efficacy for Behaviors that Promote Healthy Weight and Clinical Indicators of Adiposity in a Sample of Early Adolescents

    Science.gov (United States)

    Steele, Michael M.; Daratha, Kenn B.; Bindler, Ruth C.; Power, Thomas G.

    2011-01-01

    Objective: Examine the relationship between self-efficacy and various measures of adiposity in a sample of teens. Methods: A total of 132 teens were selected from schools participating in an existing research study titled Teen Eating and Activity Mentoring in Schools (TEAMS). Teens completed demographic questionnaires and healthy eating-specific…

  3. Evaluation of a single-tube fluorogenic RT-PCR assay for detection of bovine respiratory syncytial virus in clinical samples

    DEFF Research Database (Denmark)

    Hakhverdyan, Mikhayil; Hägglund, Sara; Larsen, Lars Erik;

    2005-01-01

    Bovine respiratory syncytial virus (BRSV) causes severe disease in naive cattle of all ages and is a common pathogen in the respiratory disease complex of calves. Simplified methods for rapid BRSV diagnosis would encourage sampling during outbreaks and would consequently lead to an extended...

  4. Validity of the MMPI-2-RF (Restructured Form) L-r and K-r Scales in Detecting Underreporting in Clinical and Nonclinical Samples

    Science.gov (United States)

    Sellbom, Martin; Bagby, R. Michael

    2008-01-01

    In the current investigation, the authors examined the validity of the L-r and K-r scales on the recently developed Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; Y. S. Ben-Porath & A. Tellegen, in press) in measuring underreported response bias. Three archival samples previously collected for examining MMPI-2 validity…

  5. Detection of Giardia lamblia, Cryptosporidium spp. and Entamoeba histolytica in clinical stool samples by using multiplex real-time PCR after automated DNA isolation

    NARCIS (Netherlands)

    Van Lint, P; Rossen, J W; Vermeiren, S; Ver Elst, K; Weekx, S; Van Schaeren, J; Jeurissen, A

    2013-01-01

    Diagnosis of intestinal parasites in stool samples is generally still carried out by microscopy; however, this technique is known to suffer from a low sensitivity and is unable to discriminate between certain protozoa. In order to overcome these limitations, a real-time multiplex PCR was evaluated a

  6. Reliability at the Lower Limits of HIV-1 RNA Quantification in Clinical Samples: A Comparison of RT-PCR versus bDNA Assays

    OpenAIRE

    Lubelchek, Ronald J.; Max, Blake; Sandusky, Caroline J.; Hota, Bala; Barker, David E.

    2009-01-01

    Introduction To explore whether an assay change was responsible for an increasing proportion of patients with undetectable HIV viral loads at our urban HIV clinic, we selected highly stable patients, examining their viral loads before and after changing assays. We compared the proportion with detectable viremia during RT-PCR vs. bDNA periods. Methodology/Principal Findings We selected patients with ≥1 viral loads assessed during both RT-PCR and bDNA periods. We included patients with stable C...

  7. The experience of premature birth for fathers: the application of the Clinical Interview for Parents of High-Risk Infants (CLIP) to an Italian sample

    Science.gov (United States)

    Candelori, Carla; Trumello, Carmen; Babore, Alessandra; Keren, Miri; Romanelli, Roberta

    2015-01-01

    Aim: The study explored fathers’ experience of premature birth during the hospitalization of their infants, analyzing levels of depressive and anxiety symptoms as compared with mothers. Moreover the Italian version of the Clinical Interview for Parents of High-Risk Infant (CLIP) was tested through confirmatory factor analysis. Methods: Couples of parents (N = 64) of preterm infants (gestational age < 37 weeks) were administered a socio-demographic questionnaire, the Edinburgh Postnatal Depression Scale, the State-Trait Anxiety Inventory and the CLIP after the admission to the Neonatal Intensive Care Unit (NICU). Results: Significant levels of anxiety and depressive symptoms and high percentages of subjects above the corresponding risk thresholds were found among fathers and mothers with higher scores among the latters. Confirmatory factor analysis of the CLIP showed an adequate structure, with better fit for mothers than for fathers. Conclusion: Results highlighted the importance for nurses and clinicians working in the NICU to consider not only the maternal difficulties but also the paternal ones, even if these are often more hidden and silent. In addition the CLIP may be considered an useful interview for research and clinical purposes to be used with parents of high-risk infants. PMID:26483712

  8. The role of co-parenting alliance as a mediator between trait anxiety, family system maladjustment, and parenting stress in a sample of non-clinical Italian parents

    OpenAIRE

    Delvecchio, Elisa; Sciandra, Andrea; Finos, Livio; Mazzeschi, Claudia; Riso, Daniela Di

    2015-01-01

    This study investigated the role of co-parenting alliance in mediating the influence of parents’ trait anxiety on family system maladjustment and parenting stress. A sample of 1606 Italian parents (803 mothers and 803 fathers) of children aged one to 13 years completed measures of trait anxiety (State Trait Anxiety Inventory—Y), co-parenting alliance (Parenting Alliance Measure), family system maladjustment (Family Assessment Measure—III), and parenting stress (Parenting Stress Inventory—Shor...

  9. The role of co-parenting alliance as a mediator between trait anxiety, family system maladjustment, and parenting stress in a sample of non-clinical Italian parents.

    OpenAIRE

    Elisa eDelvecchio; Andrea eSciandra; Livio eFinos; Claudia eMazzeschi; Daniela eDi Riso

    2015-01-01

    This study investigated the role of co-parenting alliance in mediating the influence of parents’ trait anxiety on family system maladjustment and parenting stress. A sample of 1606 Italian parents (803 mothers and 803 fathers) of children aged one to thirteen years completed measures of trait anxiety (State Trait Anxiety Inventory - Y), co-parenting alliance (Parenting Alliance Measure), family system maladjustment (Family Assessment Measure - III), and parenting stress (Parenting Stress Inve...

  10. 16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles

    OpenAIRE

    Hang, Jun; Desai, Valmik; Zavaljevski, Nela; Yang, Yu; Lin, Xiaoxu; Satya, Ravi Vijaya; Martinez, Luis J.; Blaylock, Jason M.; Jarman, Richard G.; Thomas, Stephen J.; Kuschner, Robert A.

    2014-01-01

    Background Sample storage conditions, extraction methods, PCR primers, and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing. Most published studies were limited to the comparison of only one or two types of these factors. Systematic multi-factor explorations are needed to evaluate the conditions that may impact validity of a microbiome analysis. This study was aimed to improve methodological options to facilitate the best technical app...

  11. Evaluation of Simplexa Flu A/B & RSV for direct detection of influenza viruses (A and B) and respiratory syncytial virus in patient clinical samples.

    Science.gov (United States)

    Hindiyeh, Musa; Kolet, Liat; Meningher, Tal; Weil, Merav; Mendelson, Ella; Mandelboim, Michal

    2013-07-01

    We evaluated the performance of the Simplexa Flu A/B & RSV kit on 170 prospective respiratory samples using a modified protocol, supplied by the manufacturer, that eliminates the RNA extraction step. Overall, compared against our laboratory-developed assay, the assay's sensitivity, specificity, and positive and negative predictive values were 95.1%, 99.6%, 98.7%, and 98.6%, respectively. PMID:23658256

  12. Evaluation of Simplexa Flu A/B & RSV for Direct Detection of Influenza Viruses (A and B) and Respiratory Syncytial Virus in Patient Clinical Samples

    Science.gov (United States)

    Kolet, Liat; Meningher, Tal; Weil, Merav; Mendelson, Ella; Mandelboim, Michal

    2013-01-01

    We evaluated the performance of the Simplexa Flu A/B & RSV kit on 170 prospective respiratory samples using a modified protocol, supplied by the manufacturer, that eliminates the RNA extraction step. Overall, compared against our laboratory-developed assay, the assay's sensitivity, specificity, and positive and negative predictive values were 95.1%, 99.6%, 98.7%, and 98.6%, respectively. PMID:23658256

  13. Using Language Sample Analysis in Clinical Practice: Measures of Grammatical Accuracy for Identifying Language Impairment in Preschool and School-Aged Children.

    Science.gov (United States)

    Eisenberg, Sarita; Guo, Ling-Yu

    2016-05-01

    This article reviews the existing literature on the diagnostic accuracy of two grammatical accuracy measures for differentiating children with and without language impairment (LI) at preschool and early school age based on language samples. The first measure, the finite verb morphology composite (FVMC), is a narrow grammatical measure that computes children's overall accuracy of four verb tense morphemes. The second measure, percent grammatical utterances (PGU), is a broader grammatical measure that computes children's accuracy in producing grammatical utterances. The extant studies show that FVMC demonstrates acceptable (i.e., 80 to 89% accurate) to good (i.e., 90% accurate or higher) diagnostic accuracy for children between 4;0 (years;months) and 6;11 in conversational or narrative samples. In contrast, PGU yields acceptable to good diagnostic accuracy for children between 3;0 and 8;11 regardless of sample types. Given the diagnostic accuracy shown in the literature, we suggest that FVMC and PGU can be used as one piece of evidence for identifying children with LI in assessment when appropriate. However, FVMC or PGU should not be used as therapy goals directly. Instead, when children are low in FVMC or PGU, we suggest that follow-up analyses should be conducted to determine the verb tense morphemes or grammatical structures that children have difficulty with. PMID:27111270

  14. Identification of clinically antibiotic resistant genes Aac(3-IIa and Aac(6’-Ib in wastewater samples by multiplex PCR

    Directory of Open Access Journals (Sweden)

    Naser Samadi

    2015-06-01

    Full Text Available Background: Aminoglycoside antibiotics are widely used in medical centers, particularly to treat infections. The resistance developed against these agents is a huge concern in health care. A number of researchers have reported that hospital and municipal wastewaters are among the most important dissemination sources of these agent into the environment. Some, however, do not agree with this opinion. In the present study, the prevalence of aminoglycoside resistance genes was investigated in raw and effluent wastewater from hospital and municipal wastewater treatment plants. Methods: To conduct this descriptive-analytical study, 30 samples were taken according to sampling principles and cold cycle and transferred to the molecular laboratory. DNA was extracted by the freeze-thaw method using a kit (Promega. The genes aac(3-IIa and aac(6’-Ib which code aminoglycoside resistance were examined in this study. Results: The results indicated that the studied genes are present in 35% of urban and hospital wastewaters, and their frequency percentage is higher in hospital wastewater (52% than urban wastewater (48%. The studied genes were identified in 61% of raw hospital wastewater samples; however, they were not detected in the output wastewater from the studied treatment plants. Conclusion: Although, the studied genes were not detected in the final effluent, there is a high potential for their release into the environment. The current study demonstrated that the coding genes of aminoglycoside antibiotic resistance are present in raw urban and hospital wastewaters. In the case of improper exploitation of wastewater treatment plants, the output water can contaminate other environmental sections, such as soil and water resources, and result in the emission of these contaminants.

  15. Molecular characterization of Chikungunya virus isolates from clinical samples and adult Aedes albopictus mosquitoes emerged from larvae from Kerala, South India

    Directory of Open Access Journals (Sweden)

    Niyas Kudukkil P

    2010-08-01

    Full Text Available Abstract Chikungunya virus (CHIKV, an arthritogenic alphavirus, is transmitted to humans by infected Aedes (Ae. aegypti and Ae.albopictus mosquitoes. In the study, reverse-transcription PCR (RT PCR and virus isolation detected CHIKV in patient samples and also in adult Ae.albopictus mosquitoes that was derived from larvae collected during a chikungunya (CHIK outbreak in Kerala in 2009. The CHIKV strains involved in the outbreak were the East, Central and South African (ECSA genotype that had the E1 A226V mutation. The viral strains from the mosquitoes and CHIK patients from the same area showed a close relationship based on phylogenetic analysis. Genetic characterization by partial sequencing of non-structural protein 2 (nsP2; 378 bp, envelope E1 (505 bp and E2 (428 bp identified one critical mutation in the E2 protein coding region of these CHIKV strains. This novel, non-conservative mutation, L210Q, consistently present in both human and mosquito-derived samples studied, was within the region of the E2 protein (amino acids E2 200-220 that determines mosquito cell infectivity in many alpha viruses. Our results show the involvement of Ae. albopictus in this outbreak in Kerala and appearance of CHIKV with novel genetic changes. Detection of virus in adult mosquitoes, emerged in the laboratory from larvae, also points to the possibility of transovarial transmission (TOT of mutant CHIKV strains in mosquitoes.

  16. Molecular characterization of Chikungunya virus isolates from clinical samples and adult Aedes albopictus mosquitoes emerged from larvae from Kerala, South India.

    Science.gov (United States)

    Niyas, Kudukkil P; Abraham, Rachy; Unnikrishnan, Ramakrishnan Nair; Mathew, Thomas; Nair, Sajith; Manakkadan, Anoop; Issac, Aneesh; Sreekumar, Easwaran

    2010-01-01

    Chikungunya virus (CHIKV), an arthritogenic alphavirus, is transmitted to humans by infected Aedes (Ae.) aegypti and Ae.albopictus mosquitoes. In the study, reverse-transcription PCR (RT PCR) and virus isolation detected CHIKV in patient samples and also in adult Ae.albopictus mosquitoes that was derived from larvae collected during a chikungunya (CHIK) outbreak in Kerala in 2009. The CHIKV strains involved in the outbreak were the East, Central and South African (ECSA) genotype that had the E1 A226V mutation. The viral strains from the mosquitoes and CHIK patients from the same area showed a close relationship based on phylogenetic analysis. Genetic characterization by partial sequencing of non-structural protein 2 (nsP2; 378 bp), envelope E1 (505 bp) and E2 (428 bp) identified one critical mutation in the E2 protein coding region of these CHIKV strains. This novel, non-conservative mutation, L210Q, consistently present in both human and mosquito-derived samples studied, was within the region of the E2 protein (amino acids E2 200-220) that determines mosquito cell infectivity in many alpha viruses. Our results show the involvement of Ae. albopictus in this outbreak in Kerala and appearance of CHIKV with novel genetic changes. Detection of virus in adult mosquitoes, emerged in the laboratory from larvae, also points to the possibility of transovarial transmission (TOT) of mutant CHIKV strains in mosquitoes. PMID:20704755

  17. Dental Erosion in Patients with Gastroesophageal Reflux Disease (GERD in a Sample of Patients Referred to the Motahari Clinic, Shiraz, Iran

    Directory of Open Access Journals (Sweden)

    Alavi G.

    2014-03-01

    Full Text Available Statement of Problem: Systematic reviews of the literature show that the dental erosion is associated with the gastroesophageal reflux disease (GERD.The prevalence of the problem may not be exclusively similar in different countries. Purpose: The purpose of this study was to investigate the association of gastro-oesophageal reflux disease (GERD with dental erosion in a sample of Iranian popula-tion regarding the standing difference in the Iranian oral hygiene and diet. Materials and Method: 140 patients with the average age of 30 to 50 years old com-prised the study group. The participants were already eligible for the endoscopy examination, diagnosed by their gastroenterologist. All patients completed a detailed questionnaire regarding the medical and dental situations. After completing the questionnaire and before endoscopy, dental examination was performed by two blinded dentists.The endoscopy was then performed by a gastroenterologist and the patients were divided into three groups of healthy, suspected to GERD, and positive GERD. Data were collected and analysed by Chi- Square test. The cross tabulation test was performed to compare the qualitative variants and discover the correlations. The statistical significance was adopted as p < 0.05. Results: The prevalence of dental erosion in GERD patients (22.6% was found to be higher than the suspected (5.3% and the healthy (7% individuals. Conclusion: This study declared the GERD patients are at higher risk of developing dental erosion compared to the healthy individuals in a sample of Iranian population.

  18. Sampling methods

    OpenAIRE

    Kılıç, Selim

    2013-01-01

    Most of the studies related to health are conducted with samples. Selection of sampling may be performed with random or nonrandom sampling methods. Sampling methods may vary with respect to some characteristics of study population, researchers’ aims and facilities. It is necessary to select samples by random sampling methods in order to provide the representativeness of the study population. The advantages and disadvantages of different sampling methods are presented in this manuscript which ...

  19. Use of real-time PCR on faecal samples for detection of sub-clinical Salmonella infection in cattle did not improve the detection sensitivity compared to conventional bacteriology.

    Science.gov (United States)

    Jensen, A N; Nielsen, L R; Baggesen, D L

    2013-05-01

    There is a need for more sensitive detection methods to improve effectiveness of control programmes of Salmonella enterica subsp. enterica serotypes (Salmonella) in cattle. We assessed the performance of a rapid, molecular-based, real-time PCR (rt-PCR) method against the conventional bacteriological culture-reference method (BCRM) on cattle faecal samples for detection of sub-clinical Salmonella infections in cattle. Thirty faecal samples were artificially contaminated with either 10 or 50 CFU of one of five strains of S. Dublin (SD) and S. Typhimurium (ST). The overall detection sensitivity of both rt-PCR and BCRM was 100% for ST and 78% for SD. Furthermore, 163 faecal samples from cattle herds with suspected Salmonella infection were tested to compare the relative performance of rt-PCR to BCRM on samples from naturally infected herds. The relative sensitivity of rt-PCR was 20% (3/15 BCRM positive samples) while the relative specificity and accuracy was 99% and 92%, respectively. Both methods had limitations for detecting low levels of SD (Salmonella-infectious cattle. PMID:23391438

  20. Boat sampling

    International Nuclear Information System (INIS)

    This presentation describes essential boat sampling activities: on site boat sampling process optimization and qualification; boat sampling of base material (beltline region); boat sampling of weld material (weld No. 4); problems accompanied with weld crown varieties, RPV shell inner radius tolerance, local corrosion pitting and water clarity. The equipment used for boat sampling is described too. 7 pictures