Prevalence of Estimated GFR Reporting Among US Clinical Laboratories

PubMed Central

Accetta, Nancy A.; Gladstone, Elisa H.; DiSogra, Charles; Wright, Elizabeth C.; Briggs, Michael; Narva, Andrew S.

2008-01-01

Background Routine laboratory reporting of estimated glomerular filtration rate (eGFR) may help clinicians detect kidney disease. The current national prevalence of eGFR reporting among clinical laboratories is unknown, thus the extent of the situation of laboratories not routinely reporting eGFR with serum creatinine (SCr) results is not quantified. Design Observational analysis. Setting National Kidney Disease Education Program survey of clinical laboratory conducted in 2006-7 by mail, Web, and telephone follow up. Participants A national random sample, 6,350 clinical laboratories, drawn from the Federal Clinical Laboratory Improvement Amendments database and stratified by six major laboratory types/groupings. Predictors Laboratory reports SCr results. Outcomes Reporting eGFR values along with SCr results. Measurements Percent of laboratories reporting eGFR along with reporting SCr, reporting protocol, eGFR formula used, and style of reporting cutoff values. Results Among laboratories reporting SCr, 38.4% report eGFR (physician offices, 25.8%; hospitals, 43.6%; independents, 38.9%; community clinics, 47.2%; health fair/insurance/public health, 45.5%; others, 43.2%). Physician office laboratories have a reporting prevalence lower than other laboratory types (p < 0.001). Among laboratories reporting eGFR, 66.7% do so routinely with all adult SCr determinations; 71.6% use the 4-variable Modification of Diet in Renal Disease Study equation; and 45.3% use the “>60 mL/min/1.73 m2” reporting convention. Independent laboratories are least likely to routinely report eGFR, (50.6%, p < .05) and most likely to report only when specifically requested (45.4%, p < 0.05). High-volume laboratories across all strata are more likely to report eGFR (p < 0.001). Limitations Self-reporting by laboratories, Federal database did not have names of laboratory directors/managers (intended respondents), assumed accuracy of Federal database for sample purposes. Conclusions Routine eGFR reporting with SCr is not yet universal and laboratories vary in their reporting practices. PMID:18676076

Validation of the Italian version of the Clinical Outcomes in Routine Evaluation Outcome Measure (CORE-OM).

PubMed

Palmieri, Gaspare; Evans, Chris; Hansen, Vidje; Brancaleoni, Greta; Ferrari, Silvia; Porcelli, Piero; Reitano, Francesco; Rigatelli, Marco

2009-01-01

The Clinical Outcomes in Routine Evaluation--Outcome Measure (CORE-OM) was translated into Italian and tested in non-clinical (n = 263) and clinical (n = 647) samples. The translation showed good acceptability, internal consistency and convergent validity in both samples. There were large and statistically significant differences between clinical and non-clinical datasets on all scores. The reliable change criteria were similar to those for the UK referential data. Some of the clinically significant change criteria, particularly for the men, were moderately different from the UK cutting points. The Italian version of the CORE-OM showed respectable psychometric parameters. However, it seemed plausible that non-clinical and clinical distributions of self-report scores on psychopathology and functioning measures may differ by language and culture. *A good quality Italian translation of the CORE-OM, and hence the GP-CORE, CORE-10 and CORE-5 measures also, is now available for use by practitioners and anyone surveying or exploring general psychological state. The measures can be obtained from CORE-IMS or yourself and practitioners are encouraged to share anonymised data so that good clinical and non-clinical referential databases can be established for Italy.

Bacterial contamination and stethoscope disinfection practices: a cross-sectional survey of healthcare workers in Karachi, Pakistan.

PubMed

Rao, Danish Ahmed; Aman, Aiysha; Muhammad Mubeen, Syed; Shah, Ahmed

2017-07-01

Stethoscopes routinely used for clinical examination of patients may potentially transfer micro-organisms and cause iatrogenic infections. This study was undertaken to detect the presence of microorganisms on stethoscopes used clinically in hospitals of Karachi, Pakistan and to ascertain the infection control practices of healthcare workers (HCWs). In a cross-sectional study, 118 samples were collected from public and private institutions. Samples were tested for the presence and sensitivity of pathogenic microorganisms. Microorganisms were found on diaphragms of 33/64 (51.6%) and 19/57 (33.3%) stethoscopes in public and private sector hospitals, respectively. Methycillin resistance was identified in all staphylococcally contaminated samples. Only 33 (18%) respondents reported cleaning their stethoscopes regularly. We highlight the need for more and better on-the-job routines for decontaminating stethoscopes among HCWs in Karachi.

Lipemia interferences in routine clinical biochemical tests.

PubMed

Calmarza, Pilar; Cordero, José

2011-01-01

Lipemic specimens are a common and frequent, but yet unresolved problem in clinical chemistry, and may produce significant interferences in the analytical results of different biochemical parameters. The aim of this study was to examine the effect of lipid removal using ultracentrifugation of lipemic samples, on some routine biochemistry parameters. Among all the samples obtained daily in our laboratory, the ones which were visibly muddy were selected and underwent to a process of ultracentrifugation, being determined a variety of biochemical tests before and after ultracentrifugation. A total of 110 samples were studied. We found significant differences in all the parameters studied except for total bilirubin, glucose, gamma-glutamyl transferase (GGT) and aspartate aminotransferase (AST). The greatest differences in the parameters analyzed were found in the concentration of alanine aminotransferase (ALT) (7.36%) and the smallest ones in the concentration of glucose (0.014%). Clinically significant interferences were found for phosphorus, creatinine, total protein and calcium. Lipemia causes clinically significant interferences for phosphorus, creatinine, total protein and calcium measurement and those interferences could be effectively removed by ultracentrifugation.

RNA-Stabilized Whole Blood Samples but Not Peripheral Blood Mononuclear Cells Can Be Stored for Prolonged Time Periods Prior to Transcriptome Analysis

PubMed Central

Debey-Pascher, Svenja; Hofmann, Andrea; Kreusch, Fatima; Schuler, Gerold; Schuler-Thurner, Beatrice; Schultze, Joachim L.; Staratschek-Jox, Andrea

2011-01-01

Microarray-based transcriptome analysis of peripheral blood as surrogate tissue has become an important approach in clinical implementations. However, application of gene expression profiling in routine clinical settings requires careful consideration of the influence of sample handling and RNA isolation methods on gene expression profile outcome. We evaluated the effect of different sample preservation strategies (eg, cryopreservation of peripheral blood mononuclear cells or freezing of PAXgene-stabilized whole blood samples) on gene expression profiles. Expression profiles obtained from cryopreserved peripheral blood mononuclear cells differed substantially from those of their nonfrozen counterpart samples. Furthermore, expression profiles in cryopreserved peripheral blood mononuclear cell samples were found to undergo significant alterations with increasing storage period, whereas long-term freezing of PAXgene RNA stabilized whole blood samples did not significantly affect stability of gene expression profiles. This report describes important technical aspects contributing toward the establishment of robust and reliable guidance for gene expression studies using peripheral blood and provides a promising strategy for reliable implementation in routine handling for diagnostic purposes. PMID:21704280

The factor structure and psychometric properties of the Clinical Outcomes in Routine Evaluation – Outcome Measure (CORE-OM) in Norwegian clinical and non-clinical samples

PubMed Central

2013-01-01

Background The Clinical Outcomes in Routine Evaluation - Outcome Measure (CORE-OM) is a 34-item instrument developed to monitor clinically significant change in out-patients. The CORE-OM covers four domains: well-being, problems/symptoms, functioning and risk, and sums up in two total scores: the mean of All items, and the mean of All non-risk items. The aim of this study was to examine the psychometric properties of the Norwegian translation of the CORE-OM. Methods A clinical sample of 527 out-patients from North Norwegian specialist psychiatric services, and a non-clinical sample of 464 persons were obtained. The non-clinical sample was a convenience sample consisting of friends and family of health personnel, and of students of medicine and clinical psychology. Students also reported psychological stress. Exploratory factor analysis (EFA) was employed in half the clinical sample. Confirmatory (CFA) factor analyses modelling the theoretical sub-domains were performed in the remaining half of the clinical sample. Internal consistency, means, and gender and age differences were studied by comparing the clinical and non-clinical samples. Stability, effect of language (Norwegian versus English), and of psychological stress was studied in the sub-sample of students. Finally, cut-off scores were calculated, and distributions of scores were compared between clinical and non-clinical samples, and between students reporting stress or no stress. Results The results indicate that the CORE-OM both measures general (g) psychological distress and sub-domains, of which risk of harm separates most clearly from the g factor. Internal consistency, stability and cut-off scores compared well with the original English version. No, or only negligible, language effects were found. Gender differences were only found for the well-being domain in the non-clinical sample and for the risk domain in the clinical sample. Current patient status explained differences between clinical and non-clinical samples, also when gender and age were controlled for. Students reporting psychological distress during last week scored significantly higher than students reporting no stress. These results further validate the recommended cut-off point of 1 between clinical and non-clinical populations. Conclusions The CORE-OM in Norwegian has psychometric properties at the same level as the English original, and could be recommended for general clinical use. A cut-off point of 1 is recommended for both genders. PMID:23521746

Development and Validation of the Pediatric Diabetes Routines Questionnaire for Adolescents.

PubMed

Pierce, Jessica S; Jordan, Sara S; Arnau, Randolph C

2018-04-06

This study describes the development and psychometric evaluation of an adolescent self-report version of the Pediatric Diabetes Routines Questionnaire (PDRQ:A), a measure of diabetes-specific routines for youth with type 1 diabetes, and further validation of the parent-version (PDRQ:P) in an adolescent sample. Participants included 120 parent-adolescent dyads (ages 12-17) and an additional 24 parents who completed measures of diabetes-specific adolescent routines, general adolescent routines, diabetes self-care, and family support of youth diabetes care. The PDRQ:P/A demonstrated good internal consistency, test-retest reliability, and parent-child agreement, and adequate validity coefficients. Confirmatory factor analysis supported a one-factor model. Promising results were obtained. The PDRQ:P/A is a clinically feasible parent- and self-report measure that can provide valuable information regarding how frequently adolescents engage in their diabetes management tasks in a consistent manner. Addition of an adolescent report format will enhance the utility of the measure for clinical and research use.

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples.

PubMed

Lewandowska, Dagmara W; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kufner, Verena; Schmutz, Stefan; Böni, Jürg; Metzner, Karin J; Trkola, Alexandra; Huber, Michael

2017-08-08

Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.

Pitfalls in lung cancer molecular pathology: how to limit them in routine practice?

PubMed

Ilie, M; Hofman, P

2012-01-01

New treatment options in advanced non-small cell lung carcinoma (NSCLC) targeting activating epidermal growth factor receptor (EGFR) gene mutations and other genetic alterations demonstrated the clinical significance of the molecular features of specific subsets of tumors. Therefore, the development of personalized medicine has stimulated the routine integration into pathology departments of somatic mutation testing. However, clinical mutation testing must be optimized and standardized with regard to histological profile, type of samples, pre-analytical steps, methodology and result reporting. Routine molecular testing in NSCLC is currently moving beyond EGFR mutational analysis. Recent progress of targeted therapies will require molecular testing for a wide panel of mutations for a personalized molecular diagnosis. As a consequence, efficient testing of multiple molecular abnormalities is an urgent requirement in thoracic oncology. Moreover, increasingly limited tumor sample becomes a major challenge for molecular pathology. Continuous efforts should be made for safe, effective and specific molecular analyses. This must be based on close collaboration between the departments involved in the management of lung cancer. In this review we explored the practical issues and pitfalls surrounding the routine implementation of molecular testing in NSCLC in a pathology laboratory.

Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients.

PubMed

Heeke, Simon; Hofman, Véronique; Long-Mira, Elodie; Lespinet, Virginie; Lalvée, Salomé; Bordone, Olivier; Ribeyre, Camille; Tanga, Virginie; Benzaquen, Jonathan; Leroy, Sylvie; Cohen, Charlotte; Mouroux, Jérôme; Marquette, Charles Hugo; Ilié, Marius; Hofman, Paul

2018-03-21

Background : With the integration of various targeted therapies into the clinical management of patients with advanced lung adenocarcinoma, next-generation sequencing (NGS) has become the technology of choice and has led to an increase in simultaneously interrogated genes. However, the broader adoption of NGS for routine clinical practice is still hampered by sophisticated workflows, complex bioinformatics analysis and medical interpretation. Therefore, the performance of the novel QIAGEN GeneReader NGS system was compared to an in-house ISO-15189 certified Ion PGM NGS platform. Methods : Clinical samples from 90 patients (60 Retrospectively and 30 Prospectively) with lung adenocarcinoma were sequenced with both systems. Mutations were analyzed and EGFR , KRAS , BRAF , NRAS , ALK , PIK3CA and ERBB2 genes were compared and sampling time and suitability for clinical testing were assessed. Results : Both sequencing systems showed perfect concordance for the overlapping genes. Correlation of allele frequency was r ² = 0.93 for the retrospective patients and r ² = 0.81 for the prospective patients. Hands-on time and total run time were shorter using the PGM system, while the GeneReader platform provided good traceability and up-to-date interpretation of the results. Conclusion : We demonstrated the suitability of the GeneReader NGS system in routine practice in a clinical pathology laboratory setting.

Rapid targeted somatic mutation analysis of solid tumors in routine clinical diagnostics.

PubMed

Magliacane, Gilda; Grassini, Greta; Bartocci, Paola; Francaviglia, Ilaria; Dal Cin, Elena; Barbieri, Gianluca; Arrigoni, Gianluigi; Pecciarini, Lorenza; Doglioni, Claudio; Cangi, Maria Giulia

2015-10-13

Tumor genotyping is an essential step in routine clinical practice and pathology laboratories face a major challenge in being able to provide rapid, sensitive and updated molecular tests. We developed a novel mass spectrometry multiplexed genotyping platform named PentaPanel to concurrently assess single nucleotide polymorphisms in 56 hotspots of the 5 most clinically relevant cancer genes, KRAS, NRAS, BRAF, EGFR and PIK3CA for a total of 221 detectable mutations. To both evaluate and validate the PentaPanel performance, we investigated 1025 tumor specimens of 6 different cancer types (carcinomas of colon, lung, breast, pancreas, and biliary tract, and melanomas), systematically addressing sensitivity, specificity, and reproducibility of our platform. Sanger sequencing was also performed for all the study samples. Our data showed that PentaPanel is a high throughput and robust tool, allowing genotyping for targeted therapy selection of 10 patients in the same run, with a practical turnaround time of 2 working days. Importantly, it was successfully used to interrogate different DNAs isolated from routinely processed specimens (formalin-fixed paraffin embedded, frozen, and cytological samples), covering all the requirements of clinical tests. In conclusion, the PentaPanel platform can provide an immediate, accurate and cost effective multiplex approach for clinically relevant gene mutation analysis in many solid tumors and its utility across many diseases can be particularly relevant in multiple clinical trials, including the new basket trial approach, aiming to identify appropriate targeted drug combination strategies.

Laboratory and clinical evaluation of on-site urine drug testing.

PubMed

Beck, Olof; Carlsson, Sten; Tusic, Marinela; Olsson, Robert; Franzen, Lisa; Hulten, Peter

2014-11-01

Products for on-site urine drug testing offer the possibility to perform screening for drugs of abuse directly at the point-of-care. This is a well-established routine in emergency and dependency clinics but further evaluation of performance is needed due to inherent limitations with the available products. Urine drug testing by an on-site product was compared with routine laboratory methods. First, on-site testing was performed at the laboratory in addition to the routine method. Second, the on-site testing was performed at a dependency clinic and urine samples were subsequently sent to the laboratory for additional analytical investigation. The on-site testing products did not perform with assigned cut-off levels. The subjective reading between the presence of a spot (i.e. negative test result) being present or no spot (positive result) was difficult in 3.2% of the cases, and occurred for all parameters. The tests performed more accurately in drug negative samples (specificity 96%) but less accurately for detecting positives (sensitivity 79%). Of all incorrect results by the on-site test the proportion of false negatives was 42%. The overall agreement between on-site and laboratory testing was 95% in the laboratory study and 98% in the clinical study. Although a high degree of agreement was observed between on-site and routine laboratory urine drug testing, the performance of on-site testing was not acceptable due to significant number of false negative results. The limited sensitivity of on-site testing compared to laboratory testing reduces the applicability of these tests.

[Blood sampling using "dried blood spot": a clinical biology revolution underway?].

PubMed

Hirtz, Christophe; Lehmann, Sylvain

2015-01-01

Blood testing using the dried blood spot (DBS) is used since the 1960s in clinical analysis, mainly within the framework of the neonatal screening (Guthrie test). Since then numerous analytes such as nucleic acids, small molecules or lipids, were successfully measured on the DBS. While this pre-analytical method represents an interesting alternative to classic blood sampling, its use in routine is still limited. We review here the different clinical applications of the blood sampling on DBS and estimate its future place, supported by the new methods of analysis as the LC-MS mass spectrometry.

Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics.

PubMed

Boers, Stefan A; Hiltemann, Saskia D; Stubbs, Andrew P; Jansen, Ruud; Hays, John P

2018-06-01

Microbiota profiling has the potential to greatly impact on routine clinical diagnostics by detecting DNA derived from live, fastidious, and dead bacterial cells present within clinical samples. Such results could potentially be used to benefit patients by influencing antibiotic prescribing practices or to generate new classical-based diagnostic methods, e.g., culture or PCR. However, technical flaws in 16S rRNA gene next-generation sequencing (NGS) protocols, together with the requirement for access to bioinformatics, currently hinder the introduction of microbiota analysis into clinical diagnostics. Here, we report on the development and evaluation of an "end-to-end" microbiota profiling platform (MYcrobiota), which combines our previously validated micelle PCR/NGS (micPCR/NGS) methodology with an easy-to-use, dedicated bioinformatics pipeline. The newly designed bioinformatics pipeline processes micPCR/NGS data automatically and summarizes the results in interactive, but simple web reports. In order to explore the utility of MYcrobiota in clinical diagnostics, 47 clinical samples (40 "damaged skin" samples and 7 synovial fluids) were investigated using routine bacterial culture as comparator. MYcrobiota confirmed the presence of bacterial DNA in 37/37 culture-positive samples and detected bacterial taxa in 2/10 culture-negative samples. Moreover, 36/38 potentially relevant aerobic bacterial taxa and 3/3 mixtures of anaerobic bacteria were identified using culture and MYcrobiota, with the sensitivity and specificity being 95%. Interestingly, the majority of the 448 bacterial taxa identified using MYcrobiota were not identified using culture, which could potentially have an impact on clinical decision-making. Taken together, the development of MYcrobiota is a promising step towards the introduction of microbiota analysis into clinical diagnostic laboratories.

First external quality assurance program of the Italian HLA-B*57:01 Network assessing the performance of clinical virology laboratories in HLA-B*57:01 testing.

PubMed

Meini, Genny; Dello Russo, Cinzia; Allice, Tiziano; Barresi, Renata; D'Arrigo, Roberta; Falasca, Francesca; Lipsi, Maria Rosaria; Paolucci, Stefania; Zanussi, Stefania; Antonetti, Raffaele; Baldanti, Fausto; Basaglia, Giancarlo; Bruzzone, Bianca; Polilli, Ennio; Ghisetti, Valeria; Pucillo, Leopoldo Paolo; Turriziani, Ombretta; Pirazzoli, Antonella; Navarra, Pierluigi; Zazzi, Maurizio

2016-05-01

Since the HLA-B*57:01 allele is strongly associated with abacavir hypersensitivity reaction, testing for the presence of HLA-B*57:01 is mandatory before administration of abacavir. While HLA-B*57:01 testing is usually provided by pharmacogenetics, genetics or blood transfusion services, clinical virology laboratories can be an optimal opportunity for HLA-B*57:01 testing since they receive blood samples for routine HIV monitoring and have the expertise for convenient and less expensive PCR-based point mutation assays. The Italian HLA-B*57:01 Network gathers accredited clinical virology laboratories offering HLA-B*57:01 testing in Italy with the aim to share protocols, test new methods, develop and maintain external quality assurance (EQA) programs. A panel of 9HLA-B*57:01-positive and 16HLA-B*57:01-negative frozen blood samples were blindly distributed to 10 units including 9 clinical virology laboratories and one reference pharmacology laboratory. Each laboratory was free to use its own routine method for DNA extraction and HLA-B*57:01 testing. DNA was extracted by automated workstations in 6 units and by manual spin columns in 4. Eight units used the Duplicα Real Time HLA-B*57:01 kit by Euroclone and two units used two different PCR homemade protocols. All the 10 units correctly identified all the 25 samples. The first HLA-B*57:01 EQA program run in Italy showed that clinical virology units are equipped and proficient for providing HLA-B*57:01 testing by inexpensive assays easy to integrate into their routine. Copyright © 2016 Elsevier B.V. All rights reserved.

Can Unmanned Aerial Systems (Drones) Be Used for the Routine Transport of Chemistry, Hematology, and Coagulation Laboratory Specimens?

PubMed

Amukele, Timothy K; Sokoll, Lori J; Pepper, Daniel; Howard, Dana P; Street, Jeff

2015-01-01

Unmanned Aerial Systems (UAS or drones) could potentially be used for the routine transport of small goods such as diagnostic clinical laboratory specimens. To the best of our knowledge, there is no published study of the impact of UAS transportation on laboratory tests. Three paired samples were obtained from each one of 56 adult volunteers in a single phlebotomy event (336 samples total): two tubes each for chemistry, hematology, and coagulation testing respectively. 168 samples were driven to the flight field and held stationary. The other 168 samples were flown in the UAS for a range of times, from 6 to 38 minutes. After the flight, 33 of the most common chemistry, hematology, and coagulation tests were performed. Statistical methods as well as performance criteria from four distinct clinical, academic, and regulatory bodies were used to evaluate the results. Results from flown and stationary sample pairs were similar for all 33 analytes. Bias and intercepts were <10% and <13% respectively for all analytes. Bland-Altman comparisons showed a mean difference of 3.2% for Glucose and <1% for other analytes. Only bicarbonate did not meet the strictest (Royal College of Pathologists of Australasia Quality Assurance Program) performance criteria. This was due to poor precision rather than bias. There were no systematic differences between laboratory-derived (analytic) CV's and the CV's of our flown versus terrestrial sample pairs however CV's from the sample pairs tended to be slightly higher than analytic CV's. The overall concordance, based on clinical stratification (normal versus abnormal), was 97%. Length of flight had no impact on the results. Transportation of laboratory specimens via small UASs does not affect the accuracy of routine chemistry, hematology, and coagulation tests results from selfsame samples. However it results in slightly poorer precision for some analytes.

Standardization and performance evaluation of "modified" and "ultrasensitive" versions of the Abbott RealTime HIV-1 assay, adapted to quantify minimal residual viremia.

PubMed

Amendola, Alessandra; Bloisi, Maria; Marsella, Patrizia; Sabatini, Rosella; Bibbò, Angela; Angeletti, Claudio; Capobianchi, Maria Rosaria

2011-09-01

Numerous studies investigating clinical significance of HIV-1 minimal residual viremia (MRV) suggest potential utility of assays more sensitive than those routinely used to monitor viral suppression. However currently available methods, based on different technologies, show great variation in detection limit and input plasma volume, and generally suffer from lack of standardization. In order to establish new tools suitable for routine quantification of minimal residual viremia in patients under virological suppression, some modifications were introduced into standard procedure of the Abbott RealTime HIV-1 assay leading to a "modified" and an "ultrasensitive" protocols. The following modifications were introduced: calibration curve extended towards low HIV-1 RNA concentration; 4 fold increased sample volume by concentrating starting material; reduced volume of internal control; adoption of "open-mode" software for quantification. Analytical performances were evaluated using the HIV-1 RNA Working Reagent 1 for NAT assays (NIBSC). Both tests were applied to clinical samples from virologically suppressed patients. The "modified" and the "ultrasensitive" configurations of the assay reached a limit of detection of 18.8 (95% CI: 11.1-51.0 cp/mL) and 4.8 cp/mL (95% CI: 2.6-9.1 cp/mL), respectively, with high precision and accuracy. In clinical samples from virologically suppressed patients, "modified" and "ultrasensitive" protocols allowed to detect and quantify HIV RNA in 12.7% and 46.6%, respectively, of samples resulted "not-detectable", and in 70.0% and 69.5%, respectively, of samples "detected <40 cp/mL" in the standard assay. The "modified" and "ultrasensitive" assays are precise and accurate, and easily adoptable in routine diagnostic laboratories for measuring MRV. Copyright © 2011 Elsevier B.V. All rights reserved.

Routine conventional karyotyping of lymphoma staging bone marrow samples does not contribute clinically relevant information.

PubMed

Nardi, Valentina; Pulluqi, Olja; Abramson, Jeremy S; Dal Cin, Paola; Hasserjian, Robert P

2015-06-01

Bone marrow (BM) evaluation is an important part of lymphoma staging, which guides patient management. Although positive staging marrow is defined as morphologically identifiable disease, such samples often also include flow cytometric analysis and conventional karyotyping. Cytogenetic analysis is a labor-intensive and costly procedure and its utility in this setting is uncertain. We retrospectively reviewed pathological reports of 526 staging marrow specimens in which conventional karyotyping had been performed. All samples originated from a single institution from patients with previously untreated Hodgkin and non-Hodgkin lymphomas presenting in an extramedullary site. Cytogenetic analysis revealed clonal abnormalities in only eight marrow samples (1.5%), all of which were positive for lymphoma by morphologic evaluation. Flow cytometry showed a small clonal lymphoid population in three of the 443 morphologically negative marrow samples (0.7%). Conventional karyotyping is rarely positive in lymphoma staging marrow samples and, in our cohort, the BM karyotype did not contribute clinically relevant information in the vast majority of cases. Our findings suggest that karyotyping should not be performed routinely on BM samples taken to stage previously diagnosed extramedullary lymphomas unless there is pathological evidence of BM involvement by lymphoma. © 2015 Wiley Periodicals, Inc.

Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients.

PubMed

König, Katharina; Peifer, Martin; Fassunke, Jana; Ihle, Michaela A; Künstlinger, Helen; Heydt, Carina; Stamm, Katrin; Ueckeroth, Frank; Vollbrecht, Claudia; Bos, Marc; Gardizi, Masyar; Scheffler, Matthias; Nogova, Lucia; Leenders, Frauke; Albus, Kerstin; Meder, Lydia; Becker, Kerstin; Florin, Alexandra; Rommerscheidt-Fuss, Ursula; Altmüller, Janine; Kloth, Michael; Nürnberg, Peter; Henkel, Thomas; Bikár, Sven-Ernö; Sos, Martin L; Geese, William J; Strauss, Lewis; Ko, Yon-Dschun; Gerigk, Ulrich; Odenthal, Margarete; Zander, Thomas; Wolf, Jürgen; Merkelbach-Bruse, Sabine; Buettner, Reinhard; Heukamp, Lukas C

2015-07-01

The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer performing molecular analyses of more than 3500 patients annually. Because sequential analysis of the relevant driver mutations on fixated samples is challenging in terms of workload, tissue availability, and cost, we established multiplex parallel sequencing in routine diagnostics. The aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy sequencing of single polymerase chain reaction amplicons. In this study, we demonstrate the feasibility of a 102 amplicon multiplex polymerase chain reaction followed by sequencing on an Illumina sequencer on formalin-fixed paraffin-embedded tissue in routine diagnostics. Analysis of a validation cohort of 180 samples showed this approach to require significantly less input material and to be more reliable, robust, and cost-effective than conventional dideoxy sequencing. Subsequently, 2657 lung cancer patients were analyzed. We observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, we identified driver mutations at the expected prevalence. Furthermore we found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas. Overall, our data demonstrate the utility of systematic sequencing analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.

Can routine surveillance samples from tracheal aspirate predict bacterial flora in cases of ventilator-associated pneumonia?

PubMed

Lampati, L; Maggioni, E; Langer, M; Malacarne, P; Mozzo, R; Pesenti, A; Fumagalli, R

2009-10-01

The aim of this study was to investigate the hypothesis that periodical sampling of the tracheo-bronchial tree in the absence of clinical suspicion of pneumonia is useful to identify bacteria responsible for subsequent late ventilator associated pneumonia (VAP). This was a retrospective observational human study carried out in two medical-surgical intensive care units of two different hospitals. From January 1999 to December 2000, 559 patients, who received invasive respiratory support for more than 48 hours, were screened. Tracheal aspiration (TA) was performed once or twice weekly in all mechanically ventilated patients. The microbiological findings from TA surveillance cultures done in the eight days before suspicion of VAP were compared to those isolated from the positive diagnostic samples done for late onset VAP (after more than four days of mechanical ventilation). The sensitivity, specificity, and positive/negative predictive values of the ability of the surveillance sample to anticipate the VAP pathogen were calculated. Among the microorganisms isolated from TA, 68% were retrieved from diagnostic samples. All VAP pathogens previously isolated were from 43% of the TA samples. If TA was collected 2-4 days before the clinical diagnosis of VAP, pathogens were detected in 58% of samples. In contrast, only 27% were collected more than four days earlier (P<0.05). The positive predictive values for Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus from routine TA samples were 92% and 90%, respectively. The negative predictive values for Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus from routine TA samples were 75% and 89%, respectively. TA cultures in ventilated patients may help to predict pathogens. Early detection may lead to earlier treatment in long term ventilated patients when VAP is suspected.

Management of asthma in Australian general practice: care is still not in line with clinical practice guidelines.

PubMed

Barton, Christopher; Proudfoot, Judith; Amoroso, Cheryl; Ramsay, Emmae; Holton, Christine; Bubner, Tanya; Harris, Mark; Beilby, Justin

2009-06-01

We investigated the quality of primary care asthma management in a sample of Australian general practices. 247 general practitioners (GPs) from 97 practices completed a structured interview about management of asthma, diabetes and hypertension/heart disease. A further structured interview with the senior practice principal and practice manager was used to collect information about practice capacity for chronic disease management. Just under half of GPs (47%) had access to an asthma register and the majority (76%) had access to spirometry in their practice. In terms of routine management of asthma, 12% of GPs reported using spirometry routinely, 13% routinely reviewed written asthma action plans, 27% routinely provided education about trigger factors, 30% routinely reviewed inhaler technique, 24% routinely assessed asthma severity, and 29% routinely assessed physical activity. Practice characteristics such as practice size (p=1.0) and locality (rural/metropolitan) (p=0.7) did not predict quality of asthma management nor did indicators of practice capacity including Business maturity, IT/IM maturity, Multidisciplinary teamwork, and Clinical linkages. Gaps remain in the provision of evidence-based care for patients with asthma in general practice. Markers of practice capacity measured here were not associated with guideline-based respiratory care within practices.

Impact of deploying multiple point-of-care tests with a 'sample first' approach on a sexual health clinical care pathway. A service evaluation.

PubMed

Harding-Esch, Emma M; Nori, Achyuta V; Hegazi, Aseel; Pond, Marcus J; Okolo, Olanike; Nardone, Anthony; Lowndes, Catherine M; Hay, Phillip; Sadiq, S Tariq

2017-09-01

To assess clinical service value of STI point-of-care test (POCT) use in a 'sample first' clinical pathway (patients providing samples on arrival at clinic, before clinician consultation). Specific outcomes were: patient acceptability; whether a rapid nucleic acid amplification test (NAAT) for Chlamydia trachomatis/Neisseria gonorrhoeae (CT/NG) could be used as a POCT in practice; feasibility of non-NAAT POCT implementation for Trichomonas vaginalis (TV) and bacterial vaginosis (BV); impact on patient diagnosis and treatment. Service evaluation in a south London sexual health clinic. Symptomatic female and male patients and sexual contacts of CT/NG-positive individuals provided samples for diagnostic testing on clinic arrival, prior to clinical consultation. Tests included routine culture and microscopy; CT/NG (GeneXpert) NAAT; non-NAAT POCTs for TV and BV. All 70 (35 males, 35 females) patients approached participated. The 'sample first' pathway was acceptable, with >90% reporting they were happy to give samples on arrival and receive results in the same visit. Non-NAAT POCT results were available for all patients prior to leaving clinic; rapid CT/NG results were available for only 21.4% (15/70; 5 males, 10 females) of patients prior to leaving clinic. Known negative CT/NG results led to two females avoiding presumptive treatment, and one male receiving treatment directed at possible Mycoplasma genitalium infection causing non-gonococcal urethritis. Non-NAAT POCTs detected more positives than routine microscopy (TV 3 vs 2; BV 24 vs 7), resulting in more patients receiving treatment. A 'sample first' clinical pathway to enable multiple POCT use was acceptable to patients and feasible in a busy sexual health clinic, but rapid CT/NG processing time was too long to enable POCT use. There is need for further development to improve test processing times to enable POC use of rapid NAATs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Effectiveness of outpatient cognitive-behavioral therapy for adolescents under routine care conditions on behavioral and emotional problems rated by parents and patients: an observational study.

PubMed

Walter, Daniel; Dachs, Lydia; Faber, Martin; Goletz, Hildegard; Goertz-Dorten, Anja; Hautmann, Christopher; Kinnen, Claudia; Rademacher, Christiane; Schuermann, Stephanie; Metternich-Kaizman, Tanja Wolff; Doepfner, Manfred

2018-01-01

Few studies have examined the effectiveness of outpatient cognitive-behavioral therapy (CBT) delivered in routine care settings for children and adolescents with mental disorders. This observational study examined changes in behavioral and emotional problems of adolescents with mental disorders during routine outpatient CBT delivered at a university outpatient clinic and compared them with a historical control group of youths who received academic tutoring of comparable length and intensity. Assessments were made at the start and end of treatment (pre- and post-assessment) using parent ratings of the German versions of the Child Behavior Checklist (CBCL) and self-ratings of the Youth Self-Report (YSR) scale. For the main analysis, 677 adolescents aged 11‒21 years had complete data. Changes from pre- to post-assessment showed significant reductions in mental health problems on both parent- and self-ratings. Pre- to post-effect sizes (Cohen's d) were small-to-medium for the total sample (d = 0.23 to d = 0.62) and medium-to-large for those adolescents rated in the clinical range on each (sub)scale at the start of treatment (d = 0.65 to d = 1.48). We obtained medium net effect sizes (d = 0.69) for the CBCL and YSR total scores when patients in the clinical range were compared to historical controls. However, a substantial part of the sample remained in the clinical range at treatment end. The results suggest that CBT is effective for adolescents with mental disorders when administered under routine care conditions but must be interpreted conservatively due to the lack of a direct control condition.

Clinical applications of gas chromatograph/mass spectrometer/computer systems.

PubMed

Horning, M G; Nowlin, J; Butler, C M; Lertratanangkoon, K; Sommer, K; Hill, R M

1975-08-01

Gas chromatograph/mass spectrometer/computer systems can be used to quantify a wide variety of compounds of clinical interest. A quadrupole instrument operated in the chemical ionization (Cl) mode was used in these studies. Because of the sensitivity and specificity of selective ion detection, it is possible to make measurements routinely in the nanogram to picogram range, with 0.1-1.0 ml samples of plasma and 1-5 ml samples or urine. Internal standards, preferably stable-isotope-labeled compounds, were added to the biological samples before isolation was begun. We describe clinical applications of these procedures to problems in toxicology, pharmacokinetics, and perinatal pharmacology.

Taking a new biomarker into routine use – A perspective from the routine clinical biochemistry laboratory

PubMed Central

Sturgeon, Catharine; Hill, Robert; Hortin, Glen L; Thompson, Douglas

2010-01-01

There is increasing pressure to provide cost-effective healthcare based on “best practice.” Consequently, new biomarkers are only likely to be introduced into routine clinical biochemistry departments if they are supported by a strong evidence base and if the results will improve patient management and outcome. This requires convincing evidence of the benefits of introducing the new test, ideally reflected in fewer hospital admissions, fewer additional investigations and/or fewer clinic visits. Carefully designed audit and cost-benefit studies in relevant patient groups must demonstrate that introducing the biomarker delivers an improved and more effective clinical pathway. From the laboratory perspective, pre-analytical requirements must be thoroughly investigated at an early stage. Good stability of the biomarker in relevant physiological matrices is essential to avoid the need for special processing. Absence of specific timing requirements for sampling and knowledge of the effect of medications that might be used to treat the patients in whom the biomarker will be measured is also highly desirable. Analytically, automation is essential in modern high-throughput clinical laboratories. Assays must therefore be robust, fulfilling standard requirements for linearity on dilution, precision and reproducibility, both within- and between-run. Provision of measurements by a limited number of specialized reference laboratories may be most appropriate, especially when a new biomarker is first introduced into routine practice. PMID:21137030

Analytical evaluation of the automated galectin-3 assay on the Abbott ARCHITECT immunoassay instruments.

PubMed

Gaze, David C; Prante, Christian; Dreier, Jens; Knabbe, Cornelius; Collet, Corinne; Launay, Jean-Marie; Franekova, Janka; Jabor, Antonin; Lennartz, Lieselotte; Shih, Jessie; del Rey, Jose Manuel; Zaninotto, Martina; Plebani, Mario; Collinson, Paul O

2014-06-01

Galectin-3 is secreted from macrophages and binds and activates fibroblasts forming collagen. Tissue fibrosis is central to the progression of chronic heart failure (CHF). We performed a European multicentered evaluation of the analytical performance of the two-step routine and Short Turn-Around-Time (STAT) galectin-3 immunoassay on the ARCHITECT i1000SR, i2000SR, and i4000SR (Abbott Laboratories). We evaluated the assay precision and dilution linearity for both routine and STAT assays and compared serum and plasma, and fresh vs. frozen samples. The reference interval and biological variability were also assessed. Measurable samples were compared between ARCHITECT instruments and between the routine and STAT assays and also to a galectin-3 ELISA (BG Medicine). The total assay coefficient of variation (CV%) was 2.3%-6.2% and 1.7%-7.4% for the routine and STAT assays, respectively. Both assays demonstrated linearity up to 120 ng/mL. Galectin-3 concentrations were higher in plasma samples than in serum samples and correlated well between fresh and frozen samples (R=0.997), between the routine and STAT assays, between the ARCHITECT i1000 and i2000 instruments and with the galectin-3 ELISA. The reference interval on 627 apparently healthy individuals (53% male) yielded upper 95th and 97.5th percentiles of 25.2 and 28.4 ng/mL, respectively. Values were significantly lower in subjects younger than 50 years. The galectin-3 routine and STAT assays on the Abbott ARCHITECT instruments demonstrated good analytical performance. Further clinical studies are required to demonstrate the diagnostic and prognostic potential of this novel marker in patients with CHF.

MALDI-TOF-mass spectrometry applications in clinical microbiology.

PubMed

Seng, Piseth; Rolain, Jean-Marc; Fournier, Pierre Edouard; La Scola, Bernard; Drancourt, Michel; Raoult, Didier

2010-11-01

MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost-effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

Mould routine identification in the clinical laboratory by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Cassagne, Carole; Ranque, Stéphane; Normand, Anne-Cécile; Fourquet, Patrick; Thiebault, Sandrine; Planard, Chantal; Hendrickx, Marijke; Piarroux, Renaud

2011-01-01

MALDI-TOF MS recently emerged as a valuable identification tool for bacteria and yeasts and revolutionized the daily clinical laboratory routine. But it has not been established for routine mould identification. This study aimed to validate a standardized procedure for MALDI-TOF MS-based mould identification in clinical laboratory. First, pre-extraction and extraction procedures were optimized. With this standardized procedure, a 143 mould strains reference spectra library was built. Then, the mould isolates cultured from sequential clinical samples were prospectively subjected to this MALDI-TOF MS based-identification assay. MALDI-TOF MS-based identification was considered correct if it was concordant with the phenotypic identification; otherwise, the gold standard was DNA sequence comparison-based identification. The optimized procedure comprised a culture on sabouraud-gentamicin-chloramphenicol agar followed by a chemical extraction of the fungal colonies with formic acid and acetonitril. The identification was done using a reference database built with references from at least four culture replicates. For five months, 197 clinical isolates were analyzed; 20 were excluded because they were not identified at the species level. MALDI-TOF MS-based approach correctly identified 87% (154/177) of the isolates analyzed in a routine clinical laboratory activity. It failed in 12% (21/177), whose species were not represented in the reference library. MALDI-TOF MS-based identification was correct in 154 out of the remaining 156 isolates. One Beauveria bassiana was not identified and one Rhizopus oryzae was misidentified as Mucor circinelloides. This work's seminal finding is that a standardized procedure can also be used for MALDI-TOF MS-based identification of a wide array of clinically relevant mould species. It thus makes it possible to identify moulds in the routine clinical laboratory setting and opens new avenues for the development of an integrated MALDI-TOF MS-based solution for the identification of any clinically relevant microorganism.

Hepatitis B Virus Genotyping: Is the Time Ripe for Routine Clinical Use?

PubMed Central

Madan, Kaushal; Tyagi, Pankaj

2012-01-01

Hepatitis B is one of the major causes of end-stage liver disease and liver cancer worldwide. A number of host and viral factors influence the disease course and outcomes. One such viral factor is hepatitis B virus (HBV) genotypes. There are eight major HBV genotypes described from various geographic regions of the world. Although direct sequencing appears to be the gold standard for HBV genotyping, it is expensive and laborintensive and therefore cannot be applied for routine clinical use. The newer molecular methods including serotyping have made genotyping easier and simple to apply to large number of samples rapidly. The data collected mainly over the last decade have suggested that HBV genotypes may have a bearing over the natural course of the disease and its response to therapy. This review summarizes the available literature and highlights how genotyping could be incorporated into routine clinical practice in order to improve delivery of care to HBV-infected individuals. PMID:25755425

Sweat: a sample with limited present applications and promising future in metabolomics.

PubMed

Mena-Bravo, A; Luque de Castro, M D

2014-03-01

Sweat is a biofluid with present scant use as clinical sample. This review tries to demonstrate the advantages of sweat over other biofluids such as blood or urine for routine clinical analyses and the potential when related to metabolomics. With this aim, critical discussion of sweat samplers and equipment for analysis of target compounds in this sample is made. Well established routine analyses in sweat as is that to diagnose cystic fibrosis, and the advantages and disadvantages of sweat versus urine or blood for doping control have also been discussed. Methods for analytes such as essential metals and xenometals, ethanol and electrolytes in sweat in fact constitute target metabolomics approaches or belong to any metabolomics subdiscipline such as metallomics, ionomics or xenometabolomics. The higher development of biomarkers based on genomics or proteomics as omics older than metabolomics is discussed and also the potential role of metabolomics in systems biology taking into account its emergent implementation. Normalization of the volume of sampled sweat constitutes a present unsolved shortcoming that deserves investigation. Foreseeable trends in this area are outlined. Copyright © 2013 Elsevier B.V. All rights reserved.

An Optimized Set of Fluorescence In Situ Hybridization Probes for Detection of Pancreatobiliary Tract Cancer in Cytology Brush Samples.

PubMed

Barr Fritcher, Emily G; Voss, Jesse S; Brankley, Shannon M; Campion, Michael B; Jenkins, Sarah M; Keeney, Matthew E; Henry, Michael R; Kerr, Sarah M; Chaiteerakij, Roongruedee; Pestova, Ekaterina V; Clayton, Amy C; Zhang, Jun; Roberts, Lewis R; Gores, Gregory J; Halling, Kevin C; Kipp, Benjamin R

2015-12-01

Pancreatobiliary cancer is detected by fluorescence in situ hybridization (FISH) of pancreatobiliary brush samples with UroVysion probes, originally designed to detect bladder cancer. We designed a set of new probes to detect pancreatobiliary cancer and compared its performance with that of UroVysion and routine cytology analysis. We tested a set of FISH probes on tumor tissues (cholangiocarcinoma or pancreatic carcinoma) and non-tumor tissues from 29 patients. We identified 4 probes that had high specificity for tumor vs non-tumor tissues; we called this set of probes pancreatobiliary FISH. We performed a retrospective analysis of brush samples from 272 patients who underwent endoscopic retrograde cholangiopancreatography for evaluation of malignancy at the Mayo Clinic; results were available from routine cytology and FISH with UroVysion probes. Archived residual specimens were retrieved and used to evaluate the pancreatobiliary FISH probes. Cutoff values for FISH with the pancreatobiliary probes were determined using 89 samples and validated in the remaining 183 samples. Clinical and pathologic evidence of malignancy in the pancreatobiliary tract within 2 years of brush sample collection was used as the standard; samples from patients without malignancies were used as negative controls. The validation cohort included 85 patients with malignancies (46.4%) and 114 patients with primary sclerosing cholangitis (62.3%). Samples containing cells above the cutoff for polysomy (copy number gain of ≥2 probes) were classified as positive in FISH with the UroVysion and pancreatobiliary probes. Multivariable logistic regression was used to estimate associations between clinical and pathology findings and results from FISH. The combination of FISH probes 1q21, 7p12, 8q24, and 9p21 identified cancer cells with 93% sensitivity and 100% specificity in pancreatobiliary tissue samples and were therefore included in the pancreatobiliary probe set. In the validation cohort of brush samples, pancreatobiliary FISH identified samples from patients with malignancy with a significantly higher level of sensitivity (64.7%) than the UroVysion probes (45.9%) (P < .001) or routine cytology analysis (18.8%) (P < .001), but similar specificity (92.9%, 90.8%, and 100.0% respectively). Factors significantly associated with detection of carcinoma, in adjusted analyses, included detection of polysomy by pancreatobiliary FISH (P < .001), a mass by cross-sectional imaging (P < .001), cancer cells by routine cytology (overall P = .003), as well as absence of primary sclerosing cholangitis (P = .011). We identified a set of FISH probes that detects cancer cells in pancreatobiliary brush samples from patients with and without primary sclerosing cholangitis with higher levels of sensitivity than UroVysion probes. Cytologic brushing test results and clinical features were independently associated with detection of cancer and might be used to identify patients with pancreatobiliary cancers. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing.

PubMed

Leo, Stefano; Gaïa, Nadia; Ruppé, Etienne; Emonet, Stephane; Girard, Myriam; Lazarevic, Vladimir; Schrenzel, Jacques

2017-09-20

The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Microbial community composition was determined by k-mer analysis or by mapping to taxonomic markers. Results were compared to those obtained by conventional clinical culture and molecular methods. Compared to mechanical cell disruption, a sequential lysis protocol resulted in a significantly increased proportion of bacterial DNA over human DNA and higher sequence coverage of Mycobacterium abscessus , Corynebacterium jeikeium and Rothia dentocariosa , the bacteria reported by clinical microbiology tests. In addition, we identified anaerobic bacteria not searched for by the clinical laboratory. Our results further support the implementation of WMGS in clinical routine diagnosis for bacterial identification.

Occurrence of occult CSF leaks during standard FESS procedures.

PubMed

Bucher, S; Kugler, A; Probst, E; Epprecht, L; Stadler, R S; Holzmann, D; Soyka, M B

2018-03-18

To determine the incidence of occult cerebrospinal fluid leaks (CSF) after functional endoscopic sinus surgery (FESS) and to evaluate the diagnostic performance of beta2-transferrin in blood-contaminated conditions. Prospective cohort study. An analysis of 57 intraoperative samples using hydrogel 6 beta2-transferrin assay after FESS was undertaken. In case of CSF positive samples and continuing rhinorrhea, reanalysis after more than 1 year was conducted. In-vivo analysis of a primary spontaneous CSF leak sample took place to verify difficulties in detecting beta2-transferrin in blood-contaminated settings. Own titrations were performed to evaluate detection limits of CSF by beta2-transferrin and beta-trace protein assays in these settings. An incidence of 13% for occult CSF leaks after FESS was found. In blood-contaminated conditions, routine beta2-transferrin assays showed low sensitivity. In over 1 year follow-up, all samples were negative for CSF and none of them developed clinical relevant CSF leaks or meningitis. Occult and clinically irrelevant CSF leaks do occur in a significant proportion of patients during and shortly after FESS. Intra- and postoperatively, routine beta2-transferrin assays show low sensitivity. They should not be used in these settings. The clinical course of patients with occult CSF leaks indicated possibility of an uneventful follow-up.

Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer

PubMed Central

Solassol, Jérôme; Vendrell, Julie; Märkl, Bruno; Haas, Christian; Bellosillo, Beatriz; Montagut, Clara; Smith, Matthew; O’Sullivan, Brendan; D’Haene, Nicky; Le Mercier, Marie; Grauslund, Morten; Melchior, Linea Cecilie; Burt, Emma; Cotter, Finbarr; Stieber, Daniel; Schmitt, Fernando de Lander; Motta, Valentina; Lauricella, Calogero; Colling, Richard; Soilleux, Elizabeth; Fassan, Matteo; Mescoli, Claudia; Collin, Christine; Pagès, Jean-Christophe; Sillekens, Peter

2016-01-01

Since the advent of monoclonal antibodies against epidermal growth factor receptor (EGFR) in colorectal cancer therapy, the determination of RAS mutational status is needed for therapeutic decision-making. Most prevalent in colorectal cancer are KRAS exon 2 mutations (40% prevalence); lower prevalence is observed for KRAS exon 3 and 4 mutations (6%) and NRAS exon 2, 3, and 4 mutations (5%). The Idylla™ KRAS Mutation Test on the molecular diagnostics Idylla™ platform is a simple (<2 minutes hands-on time), highly reliable, and rapid (approximately 2 hours turnaround time) in vitro diagnostic sample-to-result solution. This test enables qualitative detection of 21 mutations in codons 12, 13, 59, 61, 117, and 146 of the KRAS oncogene being clinically relevant according to the latest clinical guidelines. Here, the performance of the Idylla™ KRAS Mutation Assay, for Research Use Only, was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE samples tested, the overall concordance between the Idylla™ KRAS Mutation Assay and the confirmed reference routine test results was found to be 98.9%. The Idylla™ KRAS Mutation Assay enabled detection of 5 additional KRAS-mutated samples not detected previously with reference methods. As conclusion the Idylla™ KRAS Mutation Test can be applied as routine tool in any clinical setting, without needing molecular infrastructure or expertise, to guide the personalized treatment of colorectal cancer patients. PMID:27685259

Advanced Techniques in Pulmonary Function Test Analysis Interpretation and Diagnosis

PubMed Central

Gildea, T.J.; Bell, C. William

1980-01-01

The Pulmonary Functions Analysis and Diagnostic System is an advanced clinical processing system developed for use at the Pulmonary Division, Department of Medicine at the University of Nebraska Medical Center. The system generates comparative results and diagnostic impressions for a variety of routine and specialized pulmonary functions test data. Routine evaluation deals with static lung volumes, breathing mechanics, diffusing capacity, and blood gases while specialized tests include lung compliance studies, small airways dysfunction studies and dead space to tidal volume ratios. Output includes tabular results of normal vs. observed values, clinical impressions and commentary and, where indicated, a diagnostic impression. A number of pulmonary physiological and state variables are entered or sampled (A to D) with periodic status reports generated for the test supervisor. Among the various physiological variables sampled are respiratory frequency, minute ventilation, oxygen consumption, carbon dioxide production, and arterial oxygen saturation.

Detection of Cytomegalovirus (CMV) DNA in EDTA Whole-Blood Samples: Evaluation of the Quantitative artus CMV LightCycler PCR Kit in Conjunction with Automated Sample Preparation▿

PubMed Central

Michelin, Birgit D. A.; Hadžisejdić, Ita; Bozic, Michael; Grahovac, Maja; Hess, Markus; Grahovac, Blaženka; Marth, Egon; Kessler, Harald H.

2008-01-01

Whole blood has been found to be a reliable matrix for the detection and quantitation of cytomegalovirus (CMV) DNA. In this study, the performance of the artus CMV LightCycler (LC) PCR kit in conjunction with automated sample preparation on a BioRobot EZ1 workstation was evaluated. The accuracy, linearity, analytical sensitivity, and inter- and intra-assay variations were determined. A total of 102 clinical EDTA whole-blood samples were investigated, and results were compared with those obtained with the in vitro diagnostics (IVD)/Conformité Européene (CE)-labeled CMV HHV6,7,8 R-gene quantification kit. When the accuracy of the new kit was tested, seven of eight results were found to be within ±0.5 log10 unit of the expected panel results. Determination of linearity resulted in a quasilinear curve over more than 5 log units. The lower limit of detection of the assay was determined to be 139 copies/ml in EDTA whole blood. The interassay variation ranged from 15 to 58%, and the intra-assay variation ranged from 7 to 35%. When clinical samples were tested and the results were compared with those of the routinely used IVD/CE-labeled assay, 53 samples tested positive and 13 samples tested negative by both of the assays. One sample was found to be positive with the artus CMV LC PCR kit only, and 35 samples tested positive with the routinely used assay only. The majority of discrepant results were found with low-titer samples. In conclusion, use of the artus CMV LC PCR kit in conjunction with automated sample preparation on the BioRobot EZ1 workstation may be suitable for the detection and quantitation of CMV DNA in EDTA whole blood in the routine low-throughput laboratory; however, low-positive results may be missed by this assay. PMID:18272703

Detection of cytomegalovirus (CMV) DNA in EDTA whole-blood samples: evaluation of the quantitative artus CMV LightCycler PCR kit in conjunction with automated sample preparation.

PubMed

Michelin, Birgit D A; Hadzisejdic, Ita; Bozic, Michael; Grahovac, Maja; Hess, Markus; Grahovac, Blazenka; Marth, Egon; Kessler, Harald H

2008-04-01

Whole blood has been found to be a reliable matrix for the detection and quantitation of cytomegalovirus (CMV) DNA. In this study, the performance of the artus CMV LightCycler (LC) PCR kit in conjunction with automated sample preparation on a BioRobot EZ1 workstation was evaluated. The accuracy, linearity, analytical sensitivity, and inter- and intra-assay variations were determined. A total of 102 clinical EDTA whole-blood samples were investigated, and results were compared with those obtained with the in vitro diagnostics (IVD)/Conformité Européene (CE)-labeled CMV HHV6,7,8 R-gene quantification kit. When the accuracy of the new kit was tested, seven of eight results were found to be within +/-0.5 log(10) unit of the expected panel results. Determination of linearity resulted in a quasilinear curve over more than 5 log units. The lower limit of detection of the assay was determined to be 139 copies/ml in EDTA whole blood. The interassay variation ranged from 15 to 58%, and the intra-assay variation ranged from 7 to 35%. When clinical samples were tested and the results were compared with those of the routinely used IVD/CE-labeled assay, 53 samples tested positive and 13 samples tested negative by both of the assays. One sample was found to be positive with the artus CMV LC PCR kit only, and 35 samples tested positive with the routinely used assay only. The majority of discrepant results were found with low-titer samples. In conclusion, use of the artus CMV LC PCR kit in conjunction with automated sample preparation on the BioRobot EZ1 workstation may be suitable for the detection and quantitation of CMV DNA in EDTA whole blood in the routine low-throughput laboratory; however, low-positive results may be missed by this assay.

TU-AB-BRC-11: Moving a GPU-OpenCL-Based Monte Carlo (MC) Dose Engine Towards Routine Clinical Use: Automatic Beam Commissioning and Efficient Source Sampling

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

Tian, Z; Folkerts, M; Jiang, S

Purpose: We have previously developed a GPU-OpenCL-based MC dose engine named goMC with built-in analytical linac beam model. To move goMC towards routine clinical use, we have developed an automatic beam-commissioning method, and an efficient source sampling strategy to facilitate dose calculations for real treatment plans. Methods: Our commissioning method is to automatically adjust the relative weights among the sub-sources, through an optimization process minimizing the discrepancies between calculated dose and measurements. Six models built for Varian Truebeam linac photon beams (6MV, 10MV, 15MV, 18MV, 6MVFFF, 10MVFFF) were commissioned using measurement data acquired at our institution. To facilitate dose calculationsmore » for real treatment plans, we employed inverse sampling method to efficiently incorporate MLC leaf-sequencing into source sampling. Specifically, instead of sampling source particles control-point by control-point and rejecting the particles blocked by MLC, we assigned a control-point index to each sampled source particle, according to MLC leaf-open duration of each control-point at the pixel where the particle intersects the iso-center plane. Results: Our auto-commissioning method decreased distance-to-agreement (DTA) of depth dose at build-up regions by 36.2% averagely, making it within 1mm. Lateral profiles were better matched for all beams, with biggest improvement found at 15MV for which root-mean-square difference was reduced from 1.44% to 0.50%. Maximum differences of output factors were reduced to less than 0.7% for all beams, with largest decrease being from1.70% to 0.37% found at 10FFF. Our new sampling strategy was tested on a Head&Neck VMAT patient case. Achieving clinically acceptable accuracy, the new strategy could reduce the required history number by a factor of ∼2.8 given a statistical uncertainty level and hence achieve a similar speed-up factor. Conclusion: Our studies have demonstrated the feasibility and effectiveness of our auto-commissioning approach and new efficient source sampling strategy, implying the potential of our GPU-based MC dose engine goMC for routine clinical use.« less

Patient-based health status assessments in an outpatient psychiatry setting.

PubMed

Adler, D A; Bungay, K M; Cynn, D J; Kosinski, M

2000-03-01

The reliability, validity, and feasibility of the routine use of a generic health status instrument, the Short-Form-36 Health Survey (SF-36), were examined in a psychiatric outpatient clinic of a general hospital. The sample comprised 411 patients referred to an outpatient psychiatry department between April 1994 and March 1995. They filled out the SF-36 along with their admission forms. Scores and reports were generated, and the results were returned to the charts and used at weekly clinical conference discussions. Feasibility was evaluated using subjective and objective data on administration of the instrument, its psychometric properties, and costs. Results from the outpatient psychiatry patients were compared with those from patients scheduled for elective surgery and a healthy normative sample. Routine administration of the SF-36 was successfully achieved with minimal resistance from staff and patients. The SF-36 provided reliable and valid data. As predicted, patients with emotional disorders scored lower, indicating more impairment, on scales measuring mental health than did the elective surgery patients and the normative sample. However, the psychiatric patients' scores on the physical health scale were lower than clinicians expected. Compared with the elective surgery patients, the psychiatric patients were less impaired on only the physical functioning and bodily pain scales; no difference was found between the two groups in role functioning due to physical problems. Routine use of the SF-36 in a general hospital psychiatric outpatient clinic was feasible, and the results were reliable, valid, and helpful to clinicians. Psychiatric patients' significantly lower scores in physical health and social and role functioning provided additional information about their difficulties.

Development and Validation of a Laboratory-Developed Multiplex Real-Time PCR Assay on the BD Max System for Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA in Various Clinical Specimens.

PubMed

Pillet, Sylvie; Verhoeven, Paul O; Epercieux, Amélie; Bourlet, Thomas; Pozzetto, Bruno

2015-06-01

A multiplex real-time PCR (quantitative PCR [qPCR]) assay detecting herpes simplex virus (HSV) and varicella-zoster virus (VZV) DNA together with an internal control was developed on the BD Max platform combining automated DNA extraction and an open amplification procedure. Its performance was compared to those of PCR assays routinely used in the laboratory, namely, a laboratory-developed test for HSV DNA on the LightCycler instrument and a test using a commercial master mix for VZV DNA on the ABI7500fast system. Using a pool of negative cerebrospinal fluid (CSF) samples spiked with either calibrated controls for HSV-1 and VZV or dilutions of a clinical strain that was previously quantified for HSV-2, the empirical limit of detection of the BD Max assay was 195.65, 91.80, and 414.07 copies/ml for HSV-1, HSV-2, and VZV, respectively. All the samples from HSV and VZV DNA quality control panels (Quality Control for Molecular Diagnostics [QCMD], 2013, Glasgow, United Kingdom) were correctly identified by the BD Max assay. From 180 clinical specimens of various origins, 2 CSF samples were found invalid by the BD Max assay due to the absence of detection of the internal control; a concordance of 100% was observed between the BD Max assay and the corresponding routine tests. The BD Max assay detected the PCR signal 3 to 4 cycles earlier than did the routine methods. With results available within 2 h on a wide range of specimens, this sensitive and fully automated PCR assay exhibited the qualities required for detecting simultaneously HSV and VZV DNA on a routine basis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Differences in clinical characteristics between patients assessed for NHS specialist psychotherapy and primary care counselling.

PubMed

Chiesa, Marco; Fonagy, Peter; Bateman, Anthony W

2007-12-01

Although several studies have described patient populations in primary care counselling settings and NHS (National Health Service) specialist psychotherapy settings, there is a paucity of studies specifically comparing differences in clinical characteristics between the two groups of patients. The aim of this study is to ascertain if specialist psychotherapy referrals represent a more challenging client group than primary care counselling patients. We compare the socio-demographic features and severity of presentation in the symptomatic, interpersonal problems and global adjustment dimensions of a sample of patients (N=384) assessed by a primary care counselling service located in North London and a sample of patients (N=853) assessed in eight NHS psychotherapy centres located within urban settings in England. Both the groups completed the Brief Symptom Inventory, the Inventory of Interpersonal Problems and Clinical Outcomes in Routine Evaluation Outcome Measure. Patients referred for specialist psychotherapy services were more dysfunctional than those referred for primary care counselling. The linear function constructed to discriminate the groups showed that a combination of more psychotic symptoms, social inhibitions and higher risk of self-harm effectively identified those referred to psychotherapy services, while patients exhibiting greater levels of somatic and anxiety symptoms and non-assertiveness were more likely to be seen in primary care settings. However, similarities between the two samples were also marked, as shown by the overlap in the distribution of clinical outcomes in routine evaluation clinical scores in the two samples. The findings are discussed in terms of their implications for policy and service delivery of these two types of psychological therapy services.

Culture-independent Analysis of Pediatric Broncho-alveolar Lavage (BAL) Specimens.

PubMed

Zachariah, Philip; Ryan, Chanelle; Nadimpalli, Sruti; Coscia, Gina; Kolb, Michelle; Smith, Hannah; Foca, Marc; Saiman, Lisa; Planet, Paul J

2018-06-07

The clinical utility of culture-independent testing of pediatric bronchoalveolar lavage (BAL) specimens is unknown. Additionally, the variability of the pediatric pulmonary microbiome with patient characteristics is not well understood. Study subjects were ≤22 years old and underwent BAL from May 2013 - July 2015 as part of clinical care. DNA extracted from BAL specimens was used for 16S rRNA gene-based (16S-based) microbiome analysis, and results compared to routine cultures from the same samples. Indices of microbial diversity and relative taxon abundances were compared based on subject characteristics. From 81 participants (51% male, median age 9 years), 89 samples were collected and the 16S rRNA genes of 77 (86.5%) samples were successfully analyzed. Subjects included 23 cystic fibrosis (CF), 19 immunocompromised (IC), and 28 non-immunocompromised (nIC) patients. Of 68 organisms identified in culture, 16S-based analyses were concordant with culture results in 66 (97.1%), and also identified potentially clinically significant taxa missed by cultures (e.g. Staphylococcus, Legionella, Pseudomonas). Significant differences in abundance were noted mostly for non-cultured taxa with diagnosis and antibiotic use (Veillonella, Corynebacterium, Haemophilus). The microbiota of CF samples was less diverse and a "core" group of fifteen taxa shared across samples was identified. 16S-based culture independent analysis was concordant with routine cultures and showed potential to detect non-cultured pathogens. While 16S- based testing identified relative changes in organism abundance associated with clinical characteristics, distinct microbiome profiles associated with disease states were not identified.

Performance Evaluation of the Elecsys Syphilis Assay for the Detection of Total Antibodies to Treponema pallidum

PubMed Central

Enders, Martin; Hunjet, Andrea; Gleich, Michael; Imdahl, Roland; Mühlbacher, Annelies; Schennach, Harald; Chaiwong, Kriangsak; Sakuldamrongpanich, Tasanee; Turhan, Ajda; Sertöz, Rüchan; Wolf, Eva; Mayer, Wolfgang; Tao, Chuanmin; Wang, Lan Lan; Semprini, Simona

2014-01-01

Syphilis is a health problem of increasing incidence in recent years that may have severe complications if not diagnosed and treated at an early stage. There are many diagnostic tests available for syphilis, but there is no gold standard, and diagnosis therefore usually relies upon a combination of tests. In this multicenter study, we evaluated the treponemal Elecsys syphilis assay for use in the diagnosis of syphilis in routine samples, i.e., when syphilis is suspected or during antenatal or blood donation screening. The sensitivity and specificity of the Elecsys syphilis assay were compared head to head with those of other treponemal assays used in routine clinical practice and were assessed in potentially cross-reactive samples from patients with Epstein-Barr virus, HIV, and Lyme disease. In a total of 8,063 syphilis-negative samples collected from routine diagnostic requests and blood donations, the Elecsys syphilis assay had a specificity of 99.88%. In 928 samples previously identified as syphilis positive, the sensitivity was 99.57 to 100% (the result is presented as a range depending on whether four initially indeterminate samples are included in the assessment). The specificity of the Elecsys syphilis assay in patients with other infections was 100%; no false-positive samples were identified. PMID:25355799

Post-analytical stability of 23 common chemistry and immunochemistry analytes in incurred samples.

PubMed

Nielsen, Betina Klint; Frederiksen, Tina; Friis-Hansen, Lennart; Larsen, Pia Bükmann

2017-12-01

Storage of blood samples after centrifugation, decapping and initial sampling allows ordering of additional blood tests. The pre-analytic stability of biochemistry and immunochemistry analytes has been studied in detail, but little is known about the post-analytical stability in incurred samples. We examined the stability of 23 routine analytes on the Dimension Vista® (Siemens Healthineers, Denmark): 42-60 routine samples in lithium-heparin gel tubes (Vacutainer, BD, USA) were centrifuged at 3000×g for 10min. Immediately after centrifugation, initial concentration of analytes were measured in duplicate (t=0). The tubes were stored decapped at room temperature and re-analyzed after 2, 4, 6, 8 and 10h in singletons. The concentration from reanalysis were normalized to initial concentration (t=0). Internal acceptance criteria for bias and total error were used to determine stability of each analyte. Additionally, evaporation from the decapped blood collection tubes and the residual platelet count in the plasma after centrifugation were quantified. We report a post-analytical stability of most routine analytes of ≥8h and do therefore - with few exceptions - suggest a standard 8hour-time limit for reordering and reanalysis of analytes in incurred samples. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

External evaluation of the Dimension Vista 1500® intelligent lab system.

PubMed

Bruneel, Arnaud; Dehoux, Monique; Barnier, Anne; Boutten, Anne

2012-09-01

Dimension Vista® analyzer combines four technologies (photometry, nephelometry, V-LYTE® integrated multisensor potentiometry, and LOCI® chemiluminescence) into one high-throughput system. We assessed analytical performance of assays routinely performed in our emergency laboratory according to the VALTEC protocol, and practicability. Precision was good for most parameters. Analytical domain was large and suitable for undiluted analysis in most clinical settings encountered in our hospital. Data were comparable and correlated to our routine analyzers (Roche Modular DP®, Abbott AXSYM®, Siemens Dimension® RxL, and BN ProSpec®). Performance of nephelometric and LOCI modules was excellent. Functional sensitivity of high-sensitivity C-reactive protein and cardiac troponin I were 0.165 mg/l and 0.03 ng/ml, respectively (coefficient of variation; CV < 10%). The influence of interfering substances (i.e., hemoglobin, bilirubin, or lipids) was moderate, and Dimension Vista® specifically alerted for interference according to HIL (hemolysis, icterus, lipemia) indices. Good instrument performance and full functionality (no reagent or sample carryover in the conditions evaluated, effective sample-volume detection, and clot detection) were confirmed. Simulated routine testing demonstrated excellent practicability, throughput, ease of use of software and security. Performance and practicability of Dimension Vista® are highly suitable for both routine and emergency use. Since no volume detection and thus no warning is available on limited sample racks, pediatric samples require special caution to the Siemens protocol to be analyzed in secured conditions. Our experience in routine practice is also discussed, i.e., the impact of daily workload, "manual" steps resulting from dilutions and pediatric samples, maintenances, flex hydration on instrument's performance on throughput and turnaround time. © 2012 Wiley Periodicals, Inc.

Neural cell adhesion molecule-180 expression as a prognostic criterion in colorectal carcinoma: Feasible or not?

PubMed Central

Tascilar, Oge; Cakmak, Güldeniz Karadeniz; Tekin, Ishak Ozel; Emre, Ali Ugur; Ucan, Bulent Hamdi; Irkorucu, Oktay; Karakaya, Kemal; Gül, Mesut; Engin, Hüseyin Bülent; Comert, Mustafa

2007-01-01

AIM: To evaluate the frequency of neural cell adhesion molecule (NCAM)-180 expression in fresh tumor tissue samples and to discuss the prognostic value of NCAM-180 in routine clinical practice. METHODS: Twenty-six patients (16 men, 10 women) with colorectal cancer were included in the study. Fresh tumor tissue samples and macroscopically healthy proximal margins of each specimen were subjected to flow-cytometric analysis for NCAM-180 expression. RESULTS: Flow-cytometric analysis determined NCAM-180 expression in whole tissue samples of macroscopically healthy colorectal tissues. However, NCAM-180 expression was positive in only one case (3.84%) with well-differentiated Stage II disease who experienced no active disease at 30 mon follow-up. CONCLUSION: As a consequence of the limited number of cases in our series, it might not be possible to make a generalisation, nevertheless the routine use of NCAM-180 expression as a prognostic marker for colorectal carcinoma seems to be unfeasible and not cost-effective in clinical practice due to its very low incidence. PMID:17907291

Gene expression profiling in multiple myeloma--reporting of entities, risk, and targets in clinical routine.

PubMed

Meissner, Tobias; Seckinger, Anja; Rème, Thierry; Hielscher, Thomas; Möhler, Thomas; Neben, Kai; Goldschmidt, Hartmut; Klein, Bernard; Hose, Dirk

2011-12-01

Multiple myeloma is an incurable malignant plasma cell disease characterized by survival ranging from several months to more than 15 years. Assessment of risk and underlying molecular heterogeneity can be excellently done by gene expression profiling (GEP), but its way into clinical routine is hampered by the lack of an appropriate reporting tool and the integration with other prognostic factors into a single "meta" risk stratification. The GEP-report (GEP-R) was built as an open-source software developed in R for gene expression reporting in clinical practice using Affymetrix microarrays. GEP-R processes new samples by applying a documentation-by-value strategy to the raw data to be able to assign thresholds and grouping algorithms defined on a reference cohort of 262 patients with multiple myeloma. Furthermore, we integrated expression-based and conventional prognostic factors within one risk stratification (HM-metascore). The GEP-R comprises (i) quality control, (ii) sample identity control, (iii) biologic classification, (iv) risk stratification, and (v) assessment of target genes. The resulting HM-metascore is defined as the sum over the weighted factors gene expression-based risk-assessment (UAMS-, IFM-score), proliferation, International Staging System (ISS) stage, t(4;14), and expression of prognostic target genes (AURKA, IGF1R) for which clinical grade inhibitors exist. The HM-score delineates three significantly different groups of 13.1%, 72.1%, and 14.7% of patients with a 6-year survival rate of 89.3%, 60.6%, and 18.6%, respectively. GEP reporting allows prospective assessment of risk and target gene expression and integration of current prognostic factors in clinical routine, being customizable about novel parameters or other cancer entities. ©2011 AACR.

Preanalytical quality in clinical chemistry laboratory.

PubMed

Ahmad, M Imteyaz; Ramesh, K L; Kumar, Ravi

2014-01-01

Haemolysis is usually caused by inadequate specimen collection or preanalytical handling and is suggested to be a suitable indicator of preanalytical quality. We investigated the prevalence of detectable haemolysis in all routine venous blood samples in OPDs and IPDs to identify differences in preanalytical quality. Haemolysis index (HI) values were obtained from a Vitros 5,1 in the routine clinical chemistry laboratory for samples collected in the outpatient department (OPD) collection centres, a hospital, and inpatient departments (IPD). Haemolysis was defined as a HI > or = 15 (detection limit). Samples from the OPD with the highest prevalence of haemolysis were 6.1 times (95% confidence interval (CI) 4.0 - 9.2) more often haemolysed compared to the center with the lowest prevalence. Of the samples collected in primary health care, 10.4% were haemolysed compared to 31.1% in the IPDs (p = 0.001). A notable difference in haemolysed samples was found between the IPDs section staffed by emergency medicine physicians and the section staffed by primary health care physicians (34.8% vs. 11.3%, p = 0.001). The significant variation in haemolysis indices among the investigated units is likely to reflect varying preanalytical conditions. The HI is a valuable tool for estimation and follow-up of preanalytical quality in the health care laboratory.

Evaluating predictive modeling’s potential to improve teleretinal screening participation in urban safety net clinics

PubMed Central

Ogunyemi, Omolola; Teklehaimanot, Senait; Patty, Lauren; Moran, Erin; George, Sheba

2013-01-01

Introduction Screening guidelines for diabetic patients recommend yearly eye examinations to detect diabetic retinopathy and other forms of diabetic eye disease. However, annual screening rates for retinopathy in US urban safety net settings remain low. Methods Using data gathered from a study of teleretinal screening in six urban safety net clinics, we assessed whether predictive modeling could be of value in identifying patients at risk of developing retinopathy. We developed and examined the accuracy of two predictive modeling approaches for diabetic retinopathy in a sample of 513 diabetic individuals, using routinely available clinical variables from retrospective medical record reviews. Bayesian networks and radial basis function (neural) networks were learned using ten-fold cross-validation. Results The predictive models were modestly predictive with the best model having an AUC of 0.71. Discussion Using routinely available clinical variables to predict patients at risk of developing retinopathy and to target them for annual eye screenings may be of some usefulness to safety net clinics. PMID:23920536

Evaluating predictive modeling's potential to improve teleretinal screening participation in urban safety net clinics.

PubMed

Ogunyemi, Omolola; Teklehaimanot, Senait; Patty, Lauren; Moran, Erin; George, Sheba

2013-01-01

Screening guidelines for diabetic patients recommend yearly eye examinations to detect diabetic retinopathy and other forms of diabetic eye disease. However, annual screening rates for retinopathy in US urban safety net settings remain low. Using data gathered from a study of teleretinal screening in six urban safety net clinics, we assessed whether predictive modeling could be of value in identifying patients at risk of developing retinopathy. We developed and examined the accuracy of two predictive modeling approaches for diabetic retinopathy in a sample of 513 diabetic individuals, using routinely available clinical variables from retrospective medical record reviews. Bayesian networks and radial basis function (neural) networks were learned using ten-fold cross-validation. The predictive models were modestly predictive with the best model having an AUC of 0.71. Using routinely available clinical variables to predict patients at risk of developing retinopathy and to target them for annual eye screenings may be of some usefulness to safety net clinics.

Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline.

PubMed

Wyllie, David H; Sanderson, Nicholas; Myers, Richard; Peto, Tim; Robinson, Esther; Crook, Derrick W; Smith, E Grace; Walker, A Sarah

2018-06-06

Contact tracing requires reliable identification of closely related bacterial isolates. When we noticed the reporting of artefactual variation between M. tuberculosis isolates during routine next generation sequencing of Mycobacterium spp, we investigated its basis in 2,018 consecutive M. tuberculosis isolates. In the routine process used, clinical samples were decontaminated and inoculated into broth cultures; from positive broth cultures DNA was extracted, sequenced, reads mapped, and consensus sequences determined. We investigated the process of consensus sequence determination, which selects the most common nucleotide at each position. Having determined the high-quality read depth and depth of minor variants across 8,006 M. tuberculosis genomic regions, we quantified the relationship between the minor variant depth and the amount of non-Mycobacterial bacterial DNA, which originates from commensal microbes killed during sample decontamination. In the presence of non-Mycobacterial bacterial DNA, we found significant increases in minor variant frequencies of more than 1.5 fold in 242 regions covering 5.1% of the M. tuberculosis genome. Included within these were four high variation regions strongly influenced by the amount of non-Mycobacterial bacterial DNA. Excluding these four regions from pairwise distance comparisons reduced biologically implausible variation from 5.2% to 0% in an independent validation set derived from 226 individuals. Thus, we have demonstrated an approach identifying critical genomic regions contributing to clinically relevant artefactual variation in bacterial similarity searches. The approach described monitors the outputs of the complex multi-step laboratory and bioinformatics process, allows periodic process adjustments, and will have application to quality control of routine bacterial genomics. Copyright © 2018 Wyllie et al.

Public attitudes to the storage of blood left over from routine general practice tests and its use in research.

PubMed

Treweek, Shaun; Doney, Alex; Leiman, David

2009-01-01

There is increasing international interest in DNA biobanks but relatively little evidence concerning appropriate recruitment methods for these repositories of genetic information linked to patient-specific phenotypic data. To this end, our study aimed to investigate the attitudes of members of the public recruited through general practices to the donation and storage of blood left over from routine clinical tests in general practice. A questionnaire was mailed to 2600 individuals randomly selected from two general practice patient lists in Dundee, Scotland. Using a 7-point Likert scale, respondents rated their attitudes toward DNA biobanks in general, and procurement of blood samples specifically. Overall, 841 (34%) of 2471 delivered questionnaires were returned. Compared with patients on the practice lists, respondents were older and more likely to be women. A majority of respondents (61%) were unequivocally positive about storing blood left over from routine tests. Despite general support for this collection method, when asked about open-ended consent, respondents expressed concern about future uses. Respondents' increasing age and level of deprivation had significant adverse effects on attitudes towards making leftover routine biological samples available for research (P = 0.013 and P = 0.034, respectively). The study had three main limitations: there was a low response rate (34%) such that respondents were not entirely respresentative of the survey population; some respondents had difficulty with the questionnaire; and the study was somewhat underpowered for some comparisons. Despite its limitations, this first survey of a general practice population suggests that the majority would be willing to consider giving open-ended consent for the use of blood left over from routine clinical tests in general practice to be stored and used later for medical research.

A simple method for plasma total vitamin C analysis suitable for routine clinical laboratory use.

PubMed

Robitaille, Line; Hoffer, L John

2016-04-21

In-hospital hypovitaminosis C is highly prevalent but almost completely unrecognized. Medical awareness of this potentially important disorder is hindered by the inability of most hospital laboratories to determine plasma vitamin C concentrations. The availability of a simple, reliable method for analyzing plasma vitamin C could increase opportunities for routine plasma vitamin C analysis in clinical medicine. Plasma vitamin C can be analyzed by high performance liquid chromatography (HPLC) with electrochemical (EC) or ultraviolet (UV) light detection. We modified existing UV-HPLC methods for plasma total vitamin C analysis (the sum of ascorbic and dehydroascorbic acid) to develop a simple, constant-low-pH sample reduction procedure followed by isocratic reverse-phase HPLC separation using a purely aqueous low-pH non-buffered mobile phase. Although EC-HPLC is widely recommended over UV-HPLC for plasma total vitamin C analysis, the two methods have never been directly compared. We formally compared the simplified UV-HPLC method with EC-HPLC in 80 consecutive clinical samples. The simplified UV-HPLC method was less expensive, easier to set up, required fewer reagents and no pH adjustments, and demonstrated greater sample stability than many existing methods for plasma vitamin C analysis. When compared with the gold-standard EC-HPLC method in 80 consecutive clinical samples exhibiting a wide range of plasma vitamin C concentrations, it performed equivalently. The easy set up, simplicity and sensitivity of the plasma vitamin C analysis method described here could make it practical in a normally equipped hospital laboratory. Unlike any prior UV-HPLC method for plasma total vitamin C analysis, it was rigorously compared with the gold-standard EC-HPLC method and performed equivalently. Adoption of this method could increase the availability of plasma vitamin C analysis in clinical medicine.

Prevalence of etravirine-associated mutations in clinical samples with resistance to nevirapine and efavirenz.

PubMed

Llibre, J M; Santos, J R; Puig, T; Moltó, J; Ruiz, L; Paredes, R; Clotet, B

2008-11-01

To evaluate the expected activity of etravirine in clinical samples, according to mutational patterns associated with decreased virological response (VR). We identified 1586 routine clinical samples with resistance-associated mutations (RAMs) to nevirapine and efavirenz (K103N 60%, Y181C 37%, G190A 27%, V108I 13%). Concerning in vitro identified etravirine mutations, samples with F227C, Y181I, M230L or L100I plus K103N plus Y181C were considered highly resistant. Samples with two RAMs plus Y181C or V179D or K101E or Y188L were considered intermediate. The prevalence of 13 RAMs recently associated with decreased VR to etravirine in the DUET clinical trials was also investigated. Most samples (69%) harboured more than one IAS-USA RAM to first-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs): 42% harboured two RAMs, 21% three RAMs and 6% four or more RAMs. The prevalence of 13 specific etravirine RAMs was V179F 0.12%, G190S 3.9%, Y181V 0.1%, V106I 2.6%, V179D 1.6%, K101P 2.0%, K101E 10.1%, Y181C 36.9%, A98G 5.9%, V90I 6.9%, Y181I 3.6%, G190A 27% and L100I 9.1%. The five RAMs with the most impact on VR (V179F/D, G190S, Y181V and V106I) occurred less often. Overall, 8.2% of the samples had three or more etravirine RAMs and only 1.1% had four or more. In addition, patterns of RAMs previously associated with intermediate etravirine resistance were present in 26.2% of the samples, whereas 4.85% displayed patterns of high-degree resistance. For RAMs associated with decreased VR, etravirine resistance in routine clinical samples was lower than previously reported. High-degree resistance was uncommon, even in patients with resistance to first-generation NNRTIs, whereas low-to-intermediate etravirine resistance was more common.

Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital, Switzerland.

PubMed

Cordey, Samuel; Vu, Diem-Lan; Zanella, Marie-Celine; Turin, Lara; Mamin, Aline; Kaiser, Laurent

2017-09-20

Classical human astroviruses (HAstV) are the third most common cause of non-bacterial acute gastroenteritis. Due to the lack of routine molecular assays, novel HAstV are underdiagnosed and the magnitude of their contribution to clinical disease remains unknown. To better understand their prevalence and the susceptible patient profile, we conducted a comprehensive screening of novel and classical HAstV in stool and cerebrospinal fluid (CSF) samples collected for clinical care in a tertiary care hospital using a specially designed rRT-PCR panel for the detection of novel (MLB1-3 and VA1-4) and classical HAstV. Of the 654 stool samples, 20 were positive for HAstV, and the novel (n=10; 3 MLB1, 4 MLB2; 3 VA2) and classical (n=10) serotypes were equally prevalent. None of the 105 CSF samples were positive. Investigating the patient profile, we found a higher prevalence (P=0.0002) of both novel and classical HAstV in pediatric stool samples (3.4% and 3%, respectively) compared with adult stool samples (0.5% and 0.7%, respectively). Furthermore, all novel and classical HAstV-positive pediatric subjects were ≤four years old, demonstrating similar susceptible populations. Forty-five percent of positive patients were immunocompromised (novel: 40%, classical: 50%). A comparison of novel and classical HAstV-positive cases showed a lower viral load for novel HAstV (P=0.0007) with significantly more upper respiratory symptoms (70% of subjects; P=0.02); this observation may suggest a unique pathogenic pathway. This study confirms the clinical and epidemiological relevance of novel HAstV and identifies a target population in which routine screening may yield clinically valuable information.

Rectal swab sampling followed by an enrichment culture-based real-time PCR assay to detect Salmonella enterocolitis in children.

PubMed

Lin, L-H; Tsai, C-Y; Hung, M-H; Fang, Y-T; Ling, Q-D

2011-09-01

Although routine bacterial culture is the traditional reference standard method for the detection of Salmonella infection in children with diarrhoea, it is a time-consuming procedure that usually only gives results after 3-4 days. Some molecular detection methods can improve the turn-around time to within 24 h, but these methods are not applied directly from stool or rectal swab specimens as routine diagnostic methods for the detection of gastrointestinal pathogens. In this study, we tested the feasibility of a bacterial enrichment culture-based real-time PCR assay method for detecting and screening for diarrhoea in children caused by Salmonella. Our results showed that the minimum real-time PCR assay time required to detect enriched bacterial culture from a swab was 3 h. In all children with suspected Salmonella diarrhoea, the enrichment culture-based real-time PCR achieved 85.4% sensitivity and 98.1% specificity, as compared with the 53.7% sensitivity and 100% specificity of detection with the routine bacterial culture method. We suggest that rectal swab sampling followed by enrichment culture-based real-time PCR is suitable as a rapid method for detecting and screening for Salmonella in paediatric patients. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory.

PubMed

Kimbacher, Christine; Paar, Christian; Freystetter, Andrea; Berg, Joerg

2018-05-01

Genotyping for clinically important single nucleotide polymorphisms (SNPs) is performed by many clinical routine laboratories. To support testing, quality controls and reference materials are needed. Those may be derived from residual patient samples, left over samples of external quality assurance schemes, plasmid DNA or DNA from cell lines. DNAs from cell lines are commutable and available in large amounts. DNA from 38 cell lines were examined for suitability as controls in 11 SNP assays that are frequently used in a clinical routine laboratory: FV (1691G>A), FII (20210G>A), PAI-1 4G/5G polymorphism, MTHFR (677C>T, 1298A>C), HFE (H63D, S65C, C282Y), APOE (E2, E3, E4), LPH (-13910C>T), UGT1A1 (*28, *36, *37), TPMT (*2, *3A, *3B, *3C), VKORC1 (-1639G>A, 1173C>T), CYP2C9 (*2, *3, *5). Genotyping was performed by real-time PCR with melting curve analysis and confirmed by bi-directional sequencing. We find an almost complete spectrum of genotypic constellations within these 38 cell lines. About 12 cell lines appear sufficient as genotypic controls for the 11 SNP assays by covering almost all of the genotypes. However, hetero- and homozygous genotypes for FII and the alleles TPMT*2, UGT1A1*37 and CYP2C9*5 were not detected in any of the cell lines. DNA from most of the examined cell lines appear suitable as quality controls for these SNP assays in the laboratory routine, as to the implementation of those assays or to prepare samples for quality assurance schemes. Our study may serve as a pilot to further characterize these cell lines to arrive at the status of reference materials.

Generalizability of Clinical Trial Results for Adolescent Major Depressive Disorder.

PubMed

Blanco, Carlos; Hoertel, Nicolas; Franco, Silvia; Olfson, Mark; He, Jian-Ping; López, Saioa; González-Pinto, Ana; Limosin, Frédéric; Merikangas, Kathleen R

2017-12-01

Although there have been a number of clinical trials evaluating treatments for adolescents with major depressive disorder (MDD), the generalizability of those trials to samples of depressed adolescents who present for routine clinical care is unknown. Examining the generalizability of clinical trials of pharmacological and psychotherapy interventions for adolescent depression can help administrators and frontline practitioners determine the relevance of these studies for their patients and may also guide eligibility criteria for future clinical trials in this clinical population. Data on nationally representative adolescents were derived from the National Comorbidity Survey: Adolescent Supplement. To assess the generalizability of adolescent clinical trials for MDD, we applied a standard set of eligibility criteria representative of clinical trials to all adolescents in the National Comorbidity Survey: Adolescent Supplement with a Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition diagnosis of MDD ( N = 592). From the overall MDD sample, 61.9% would have been excluded from a typical pharmacological trial, whereas 42.2% would have been excluded from a psychotherapy trial. Among those who sought treatment ( n = 412), the corresponding exclusion rates were 72.7% for a pharmacological trial and 52.2% for a psychotherapy trial. The criterion leading to the largest number of exclusions was "significant risk of suicide" in both pharmacological and psychotherapy trials. Pharmacological and, to a lesser extent, psychotherapy clinical trials likely exclude most adolescents with MDD. Careful consideration should be given to balancing eligibility criteria and internal validity with applicability in routine clinical care while ensuring patient safety. Copyright © 2017 by the American Academy of Pediatrics.

Detection of cryptic genospecies misidentified as Haemophilus influenzae in routine clinical samples by assessment of marker genes fucK, hap, and sodC.

PubMed

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").

Variations in the detection of ZAP-70 in chronic lymphocytic leukemia: Comparison with IgV(H) mutation analysis.

PubMed

Sheikholeslami, M R; Jilani, I; Keating, M; Uyeji, J; Chen, K; Kantarjian, H; O'Brien, S; Giles, F; Albitar, M

2006-07-15

Lack of immunoglobulin heavy chain genes (IgV(H)) mutation in patients with chronic lymphocytic leukemia (CLL) is associated with rapid disease progression and shorter survival. The zeta-chain (T-cell receptor) associated protein kinase 70 kDa (ZAP-70) has been reported to be a surrogate marker for IgV(H) mutation status, and its expression in leukemic cells correlates with unmutated IgV(H). However, ZAP-70 detection by flow cytometry varies significantly dependant on the antibodies used, the method of performing the assay, and the condition of the cells in the specimen. The clinical value of ZAP-70 testing when samples are shipped under poorly controlled conditions is not known. Furthermore, testing in a research environment may differ from testing in a routine clinical laboratory. We validated an assay for ZAP-70 by comparing results with clinical outcome and the mutation status of the IgV(H). Using stored samples, we show significant correlation between ZAP-70 expression and clinical outcome as well as IgV(H) mutation at a cut-off point of 15%. While positive samples (>15% positivity) remain positive when kept in the laboratory environment for 48 h after initial testing, results obtained from samples from CLL patients tested after shipping at room temperature for routine testing showed no correlation with IgV(H) mutation status when 15% cut-off was used. In these samples, cut-point of 10% correlated with the IgV(H) mutation (P = 0.0001). This data suggests that although ZAP-70 positivity correlates with IgV(H) mutation status and survival, variations in sample handling and preparation may influence results. We show that IgV(H) mutation results, unlike ZAP-70 remain correlated with CD38 expression and beta-2 microglobulin in shipped samples, and ZAP-70 testing should not be used as the sole criterion for stratifying patients for therapy. (c) 2006 International Society for Analytical Cytology.

Evaluative Assay of Nuclear and Mitochondrial Genes to Diagnose Leishmania Species in Clinical Specimens.

PubMed

Esmaeili Rastaghi, Ahmad Reza; Spotin, Adel; Khataminezhad, Mohammad Reza; Jafarpour, Mostafa; Alaeenovin, Elnaz; Najafzadeh, Narmin; Samei, Neda; Taleshi, Neda; Mohammadi, Somayeh; Parvizi, Parviz

2017-10-01

Leishmaniasis as an emerging and reemerging disease is increasing worldwide with high prevalence and new incidence in recent years. For epidemiological investigation and accurate identification of Leishmania species, three nuclear and mitochondrial genes (ITS-rDNA, Hsp70, and Cyt b ) were employed and analyzed from clinical samples in three important Zoonotic Cutaneous Leishmaniasis (ZCL) foci of Iran. In this cross-sectional/descriptive study conducted in 2014-15, serous smears of lesions were directly prepared from suspected patients of ZCL in Turkmen in northeast, Abarkouh in center and Shush district in southwest of Iran. They were directly prepared from suspected patients and DNA was extracted. Two nuclear genes of ITS-rDNA, Hsp70 and one mitochondrial gene of Cyt b within Leishmania parasites were amplified. RFLP was performed on PCR-positive samples. PCR products were sequenced, aligned and edited with sequencher 4.1.4 and phylogenic analyses performed using MEGA 5.05 software. Overall, 203 out of 360 clinical samples from suspected patients were Leishmania positive using routine laboratory methods and 231 samples were positive by molecular techniques. L. major L. tropica , and L. turanica were firmly identified by employing different molecular genes and phylogenic analyses. By combining different molecular genes, Leishmania parasites were identified accurately. The sensitivity and specificity three genes were evaluated and had more advantages to compare routine laboratory methods. ITS-rDNA gene is more appropriate for firm identification of Leishmania species.

Infection Control Measures in Private Dental Clinics in Lebanon.

PubMed

Dagher, Jihad; Sfeir, Charles; Abdallah, Ahmad; Majzoub, Zeina

2017-01-01

Evaluate infection control knowledge, attitude, and practice in Lebanese private dental clinics. A survey including 46 questions related to routine safety procedures was sent to 1150 Lebanese dentists between July 1st and 2nd, 2015. The study sample was selected from the database of registered dentists based on a proportional random sampling ensuring equitable representation of the 5 geographic regions of Lebanon. A subset of 29 questions was used to generate an overall score of compliance (excellent, good, fair, and poor). Comparisons according to gender, type, region, and years of practice were performed. 417 dentists returned the completed questionnaires. 96% expressed concern about infection transmission, 90.6% were vaccinated against Hepatitis B, and 61.8% asked routinely about patients medical history. Only 43% used protective eyewear. Although most dentists (65%) used autoclaves, dry heat was still used. Significant correlations were found between gender and use of personal protective equipment. Less compliance was shown by clinicians with fewer years of experience. In the overall compliance questionnaire, the mean percentage of correct answers was roughly 54% with <5% of the practitioners scoring "excellent." Conclusions . The study found inadequacy of compliance in private Lebanese dental clinics necessitating improved educational training and sustained monitoring by regulatory bodies.

A novel enterovirus and parechovirus multiplex one-step real-time PCR-validation and clinical experience.

PubMed

Nielsen, Alex Christian Yde; Böttiger, Blenda; Midgley, Sofie Elisabeth; Nielsen, Lars Peter

2013-11-01

As the number of new enteroviruses and human parechoviruses seems ever growing, the necessity for updated diagnostics is relevant. We have updated an enterovirus assay and combined it with a previously published assay for human parechovirus resulting in a multiplex one-step RT-PCR assay. The multiplex assay was validated by analysing the sensitivity and specificity of the assay compared to the respective monoplex assays, and a good concordance was found. Furthermore, the enterovirus assay was able to detect 42 reference strains from all 4 species, and an additional 9 genotypes during panel testing and routine usage. During 15 months of routine use, from October 2008 to December 2009, we received and analysed 2187 samples (stool samples, cerebrospinal fluids, blood samples, respiratory samples and autopsy samples) were tested, from 1546 patients and detected enteroviruses and parechoviruses in 171 (8%) and 66 (3%) of the samples, respectively. 180 of the positive samples could be genotyped by PCR and sequencing and the most common genotypes found were human parechovirus type 3, echovirus 9, enterovirus 71, Coxsackievirus A16, and echovirus 25. During 2009 in Denmark, both enterovirus and human parechovirus type 3 had a similar seasonal pattern with a peak during the summer and autumn. Human parechovirus type 3 was almost invariably found in children less than 4 months of age. In conclusion, a multiplex assay was developed allowing simultaneous detection of 2 viruses, which can cause similar clinical symptoms. Copyright © 2013 Elsevier B.V. All rights reserved.

Safety of ranibizumab in routine clinical practice: 1-year retrospective pooled analysis of four European neovascular AMD registries within the LUMINOUS programme.

PubMed

Holz, Frank G; Bandello, Francesco; Gillies, Mark; Mitchell, Paul; Osborne, Aaron; Sheidow, Tom; Souied, Eric; Figueroa, Marta S

2013-09-01

Evaluation of 1-year safety profile of intravitreal ranibizumab 0.5 mg in neovascular age-related macular degeneration (NV-AMD) within routine clinical practice. The LUMINOUS programme comprises a prospective observational study assessing ranibizumab 'real-world' safety and clinical effectiveness across licensed indications worldwide and an annual retrospective pooled safety analysis from completed NV-AMD ranibizumab registries. 1-year data from four European registries are available. This retrospective pooled safety analysis assessed 1-year incidence rates for safety events of particular interest (key ocular or systemic events possibly related to the injection procedure or vascular endothelial growth factor inhibition) together with treatment exposure. Patients were treated according to local protocols within the ranibizumab licence. Data of 4444 patients from registries in Germany (n=3470), the Netherlands (n=243), Belgium (n=260) and Sweden (n=471) were retrospectively pooled. Between 70.4% and 84.4% of enrolled patients completed 1 year of follow-up. Most frequent overall ocular events of particular interest were retinal pigment epithelial tears (27 patients; <1%) and intraocular pressure-related events (12 patients; <0.3%). Most frequent non-ocular event of particular interest was stroke (19 patients; 0.4%); annual incidence of stroke was low across all registries (0.0-0.5%). Ranibizumab demonstrated favourable 1-year safety profile for NV-AMD in this routine clinical practice sample, consistent with previous reported trial data. Additional data from a larger patient population are needed to better describe the long-term safety profile of ranibizumab in routine clinical practice and further evaluate risk for infrequent but serious events in 'real-life' settings. The 5-year LUMINOUS prospective observational study will address this need.

Safety of ranibizumab in routine clinical practice: 1-year retrospective pooled analysis of four European neovascular AMD registries within the LUMINOUS programme

PubMed Central

Holz, Frank G; Bandello, Francesco; Gillies, Mark; Mitchell, Paul; Osborne, Aaron; Sheidow, Tom; Souied, Eric; Figueroa, Marta S

2013-01-01

Purpose Evaluation of 1-year safety profile of intravitreal ranibizumab 0.5 mg in neovascular age-related macular degeneration (NV-AMD) within routine clinical practice. Methods The LUMINOUS programme comprises a prospective observational study assessing ranibizumab ‘real-world’ safety and clinical effectiveness across licensed indications worldwide and an annual retrospective pooled safety analysis from completed NV-AMD ranibizumab registries. 1-year data from four European registries are available. This retrospective pooled safety analysis assessed 1-year incidence rates for safety events of particular interest (key ocular or systemic events possibly related to the injection procedure or vascular endothelial growth factor inhibition) together with treatment exposure. Patients were treated according to local protocols within the ranibizumab licence. Results Data of 4444 patients from registries in Germany (n=3470), the Netherlands (n=243), Belgium (n=260) and Sweden (n=471) were retrospectively pooled. Between 70.4% and 84.4% of enrolled patients completed 1 year of follow-up. Most frequent overall ocular events of particular interest were retinal pigment epithelial tears (27 patients; <1%) and intraocular pressure-related events (12 patients; <0.3%). Most frequent non-ocular event of particular interest was stroke (19 patients; 0.4%); annual incidence of stroke was low across all registries (0.0–0.5%). Conclusions Ranibizumab demonstrated favourable 1-year safety profile for NV-AMD in this routine clinical practice sample, consistent with previous reported trial data. Additional data from a larger patient population are needed to better describe the long-term safety profile of ranibizumab in routine clinical practice and further evaluate risk for infrequent but serious events in ‘real-life’ settings. The 5-year LUMINOUS prospective observational study will address this need. PMID:23850682

Improving laboratory results turnaround time by reducing pre analytical phase.

PubMed

Khalifa, Mohamed; Khalid, Parwaiz

2014-01-01

Laboratory turnaround time is considered one of the most important indicators of work efficiency in hospitals, physicians always need timely results to take effective clinical decisions especially in the emergency department where these results can guide physicians whether to admit patients to the hospital, discharge them home or do further investigations. A retrospective data analysis study was performed to identify the effects of ER and Lab staff training on new routines for sample collection and transportation on the pre-analytical phase of turnaround time. Renal profile tests requested by the ER and performed in 2013 has been selected as a sample, and data about 7,519 tests were retrieved and analyzed to compare turnaround time intervals before and after implementing new routines. Results showed significant time reduction on "Request to Sample Collection" and "Collection to In Lab Delivery" time intervals with less significant improvement on the analytical phase of the turnaround time.

Design and implementation of a controlled clinical trial to evaluate the effectiveness and efficiency of routine opt-out rapid human immunodeficiency virus screening in the emergency department.

PubMed

Haukoos, Jason S; Hopkins, Emily; Byyny, Richard L; Conroy, Amy A; Silverman, Morgan; Eisert, Sheri; Thrun, Mark; Wilson, Michael; Boyett, Brian; Heffelfinger, James D

2009-08-01

In 2006, the Centers for Disease Control and Prevention (CDC) released revised recommendations for performing human immunodeficiency virus (HIV) testing in health care settings, including implementing routine rapid HIV screening, the use of an integrated opt-out consent, and limited prevention counseling. Emergency departments (EDs) have been a primary focus of these efforts. These revised CDC recommendations were primarily based on feasibility studies and have not been evaluated through the application of rigorous research methods. This article describes the design and implementation of a large prospective controlled clinical trial to evaluate the CDC's recommendations in an ED setting. From April 15, 2007, through April 15, 2009, a prospective quasi-experimental equivalent time-samples clinical trial was performed to compare the clinical effectiveness and efficiency of routine (nontargeted) opt-out rapid HIV screening (intervention) to physician-directed diagnostic rapid HIV testing (control) in a high-volume urban ED. In addition, three nested observational studies were performed to evaluate the cost-effectiveness and patient and staff acceptance of the two rapid HIV testing methods. This article describes the rationale, methodologies, and study design features of this program evaluation clinical trial. It also provides details regarding the integration of the principal clinical trial and its nested observational studies. Such ED-based trials are rare, but serve to provide valid comparisons between testing approaches. Investigators should consider similar methodology when performing future ED-based health services research.

Preanalytical influence of pneumatic tube delivery system on results of routine biochemistry and haematology analysis.

PubMed

Petit, Morgane; Mine, Louis; Pascreau, Tiffany; Brouzes, Chantal; Majoux, Sandrine; Borgel, Delphine; Beaudeux, Jean-Louis; Lasne, Dominique; Hennequin, Carole

2017-12-01

Pneumatic tube delivery system (PTS) enables to reduce considerably turnaround times. The aim of the study was to assess the influence of the PTS on the quality of routine biochemical and hematological tests in our laboratory. Blood samples from 6 hospitalized patients and 8 healthy volunteers were analyzed. Blood samples were delivered to the laboratory by a PTS and by a human courier. We performed the following analysis: ionized calcium, sodium, potassium, lactate deshydrogenase (LDH), aspartate aminotransferase (ASAT), arterial blood gas, complete blood count and coagulation test as prothrombin time, activated partial thromboplastin time, factors V and VIII. Results were compared between the both method of transport according to the recommendation of the Société française de biologie clinique and the French committee for accreditation (SH-GTA01, norme NF ISO 5275-6). The hemolysis index of plasma was similar between the groups and no morphological differences were found on blood cells. For three samples, when delivered by PTS, LDH levels (two samples) and neutrophil polynuclear count (one sample) were above the recommended guidelines compared to those delivered by courier. Conversely, LDH levels and FVIII were below in two samples delivered by PTS. LDH levels, PNN count or factor VIII can be affected by PTS without the clinical interpretation being modified. We concluded that the PTS can be used to transport blood samples for routine biochemical and hematological analysis in our hospital.

Prosthetists' perceptions and use of outcome measures in clinical practice: Long-term effects of focused continuing education.

PubMed

Hafner, Brian J; Spaulding, Susan E; Salem, Rana; Morgan, Sara J; Gaunaurd, Ignacio; Gailey, Robert

2017-06-01

Continuing education is intended to facilitate clinicians' skills and knowledge in areas of practice, such as administration and interpretation of outcome measures. To evaluate the long-term effect of continuing education on prosthetists' confidence in administering outcome measures and their perceptions of outcomes measurement in clinical practice. Pretest-posttest survey methods. A total of 66 prosthetists were surveyed before, immediately after, and 2 years after outcomes measurement education and training. Prosthetists were grouped as routine or non-routine outcome measures users, based on experience reported prior to training. On average, prosthetists were just as confident administering measures 1-2 years after continuing education as they were immediately after continuing education. In all, 20% of prosthetists, initially classified as non-routine users, were subsequently classified as routine users at follow-up. Routine and non-routine users' opinions differed on whether outcome measures contributed to efficient patient evaluations (79.3% and 32.4%, respectively). Both routine and non-routine users reported challenges integrating outcome measures into normal clinical routines (20.7% and 45.9%, respectively). Continuing education had a long-term impact on prosthetists' confidence in administering outcome measures and may influence their clinical practices. However, remaining barriers to using standardized measures need to be addressed to keep practitioners current with evolving practice expectations. Clinical relevance Continuing education (CE) had a significant long-term impact on prosthetists' confidence in administering outcome measures and influenced their clinical practices. In all, approximately 20% of prosthetists, who previously were non-routine outcome measure users, became routine users after CE. There remains a need to develop strategies to integrate outcome measurement into routine clinical practice.

First evaluation of automated specimen inoculation for wound swab samples by use of the Previ Isola system compared to manual inoculation in a routine laboratory: finding a cost-effective and accurate approach.

PubMed

Mischnik, Alexander; Mieth, Markus; Busch, Cornelius J; Hofer, Stefan; Zimmermann, Stefan

2012-08-01

Automation of plate streaking is ongoing in clinical microbiological laboratories, but evaluation for routine use is mostly open. In the present study, the recovery of microorganisms from the Previ Isola system plated polyurethane (PU) swab samples is compared to manually plated control viscose swab samples from wounds according to the CLSI procedure M40-A (quality control of microbiological transport systems). One hundred twelve paired samples (224 swabs) were analyzed. In 80/112 samples (71%), concordant culture results were obtained with the two methods. In 32/112 samples (29%), CFU recovery of microorganisms from the two methods was discordant. In 24 (75%) of the 32 paired samples with a discordant result, Previ Isola plated PU swabs were superior. In 8 (25%) of the 32 paired samples with a discordant result, control viscose swabs were superior. The quality of colony growth on culture media for further investigations was superior with Previ Isola inoculated plates compared to manual plating techniques. Gram stain results were concordant between the two methods in 62/112 samples (55%). In 50/112 samples (45%), the results of Gram staining were discordant between the two methods. In 34 (68%) of the 50 paired samples with discordant results, Gram staining of PU swabs was superior to that of control viscose swabs. In 16 (32%) of the 50 paired samples, Gram staining of control viscose swabs was superior to that of PU swabs. We report the first clinical evaluation of Previ Isola automated specimen inoculation for wound swab samples. This study suggests that use of an automated specimen inoculation system has good results with regard to CFU recovery, quality of Gram staining, and accuracy of diagnosis.

First Evaluation of Automated Specimen Inoculation for Wound Swab Samples by Use of the Previ Isola System Compared to Manual Inoculation in a Routine Laboratory: Finding a Cost-Effective and Accurate Approach

PubMed Central

Mieth, Markus; Busch, Cornelius J.; Hofer, Stefan; Zimmermann, Stefan

2012-01-01

Automation of plate streaking is ongoing in clinical microbiological laboratories, but evaluation for routine use is mostly open. In the present study, the recovery of microorganisms from the Previ Isola system plated polyurethane (PU) swab samples is compared to manually plated control viscose swab samples from wounds according to the CLSI procedure M40-A (quality control of microbiological transport systems). One hundred twelve paired samples (224 swabs) were analyzed. In 80/112 samples (71%), concordant culture results were obtained with the two methods. In 32/112 samples (29%), CFU recovery of microorganisms from the two methods was discordant. In 24 (75%) of the 32 paired samples with a discordant result, Previ Isola plated PU swabs were superior. In 8 (25%) of the 32 paired samples with a discordant result, control viscose swabs were superior. The quality of colony growth on culture media for further investigations was superior with Previ Isola inoculated plates compared to manual plating techniques. Gram stain results were concordant between the two methods in 62/112 samples (55%). In 50/112 samples (45%), the results of Gram staining were discordant between the two methods. In 34 (68%) of the 50 paired samples with discordant results, Gram staining of PU swabs was superior to that of control viscose swabs. In 16 (32%) of the 50 paired samples, Gram staining of control viscose swabs was superior to that of PU swabs. We report the first clinical evaluation of Previ Isola automated specimen inoculation for wound swab samples. This study suggests that use of an automated specimen inoculation system has good results with regard to CFU recovery, quality of Gram staining, and accuracy of diagnosis. PMID:22692745

Detection of Cryptic Genospecies Misidentified as Haemophilus influenzae in Routine Clinical Samples by Assessment of Marker Genes fucK, hap, and sodC▿

PubMed Central

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”). PMID:19535530

Utility of routine psychological screening in the childhood cancer survivor clinic.

PubMed

Recklitis, Christopher; O'Leary, Tara; Diller, Lisa

2003-03-01

This study examined the utility of routine psychologic screening in a childhood cancer survivor clinic by evaluating patient acceptance, comparing subjects' symptoms to normative data, examining the utility of specific tests, and identifying risk factors associated with psychological distress. During their annual clinic visit, 101 adult survivors of childhood cancer (median age, 25 years) completed the Symptom Checklist 90 Revised (SCL-90), as well as the Short Form 36 (SF-36), Beck Depression Inventory (BDI), and one additional suicide question. Psychological distress was operationally defined according to the published SCL-90 clinical case rule, classifying subjects with a consistent pattern of symptom elevations as clinical cases. The majority of subjects (80%) completed the screening in less than 30 minutes and reported little (15%) or no (84%) distress. Sixty-four percent believed it would help "very much" or "moderately" in getting to know them, and 35% thought it would help "slightly." On the SCL-90, 32 subjects (31.7%) had a positive screen, indicating significant psychological distress. All subjects with clinically significant symptoms on the BDI and SF-36 Mental Health Scale were cases on the SCL-90 (case-positive). Suicidal symptoms were reported in 13.9% of the sample, all of whom were SCL-90 cases. In a logistic regression model, subjects' dissatisfaction with physical appearance, poor physical health, and treatment with cranial radiation were associated with psychological distress. Results demonstrate that routine psychological screening can be successfully integrated into the cancer survivor clinic and may be effective in identifying those survivors with significant distress who require further evaluation.

Assessment of pituitary micro-lesions using 3D sampling perfection with application-optimized contrasts using different flip-angle evolutions.

PubMed

Wang, Jing; Wu, Yue; Yao, Zhenwei; Yang, Zhong

2014-12-01

The aim of this study was to explore the value of three-dimensional sampling perfection with application-optimized contrasts using different flip-angle evolutions (3D-SPACE) sequence in assessment of pituitary micro-lesions. Coronal 3D-SPACE as well as routine T1- and dynamic contrast-enhanced (DCE) T1-weighted images of the pituitary gland were acquired in 52 patients (48 women and four men; mean age, 32 years; age range, 17-50 years) with clinically suspected pituitary abnormality at 3.0 T, retrospectively. The interobserver agreement of assessment results was analyzed with K-statistics. Qualitative analyses were compared using Wilcoxon signed-rank test. There was good interobserver agreement of the independent evaluations for 3D-SPACE images (k = 0.892), fair for routine MR images (k = 0.649). At 3.0 T, 3D-SPACE provided significantly better images than routine MR images in terms of the boundary of pituitary gland, definition of pituitary lesions, and overall image quality. The evaluation of pituitary micro-lesions using combined routine and 3D-SPACE MR imaging was superior to that using only routine or 3D-SPACE imaging. The 3D-SPACE sequence can be used for appropriate and successful evaluation of the pituitary gland. We suggest 3D-SPACE sequence to be a powerful supplemental sequence in MR examinations with suspected pituitary micro-lesions.

Elemental analysis of urinary calculi by laser induced plasma spectroscopy.

PubMed

Fang, Xiao; Ahmad, S Rafi; Mayo, Mike; Iqbal, Syed

2005-12-01

Laser induced plasma spectroscopy (LIPS) has been applied to analyse and identify elemental constituents of urinary calculi. Measurements on seven different urinary stone samples were conducted and the concentrations of some key elemental species were estimated. The elements detected with the present system were: Calcium, Magnesium, Sodium, Samarium, Potassium and Lead. Absolute concentrations of the species were derived from pre-calibration of the system for each element. Their concentrations were found to be widely different in different samples. It was observed that the samples containing a significant amount of lead have large proportion of calcium. It has been established that LIPS would allow real time clinic measurements of elemental contents and the concentrations in the biomaterials without sample preparation. The technique has the potential for routine clinic applications in urological disorder diagnosis.

Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization.

PubMed

Botling, Johan; Micke, Patrick

2011-01-01

Access to high-quality fresh frozen tissue is critical for translational cancer research and molecular -diagnostics. Here we describe a workflow for the collection of frozen solid tissue samples derived from fresh human patient specimens after surgery. The routines have been in operation at Uppsala University Hospital since 2001. We have integrated cryosection and histopathologic examination of each biobank sample into the biobank manual. In this way, even small, macroscopically ill-defined lesions can be -procured without a diagnostic hazard due to the removal of uncharacterized tissue from a clinical -specimen. Also, knowledge of the histomorphology of the frozen tissue sample - tumor cell content, stromal components, and presence of necrosis - is pivotal before entering a biobank case into costly molecular profiling studies.

Laboratory maintenance of Treponema denticola.

PubMed

Fenno, J Christopher

2005-10-01

This unit describes the methods, media, and equipment necessary for routine laboratory culture and handling of the anaerobic oral spirochete Treponema denticola. Topics discussed include nutrient requirements, recommended media formulations, and expected growth kinetics, as well as methods and equipment necessary to maintain anaerobic conditions. An additional protocol on isolation of T. denticola from clinical samples is included.

Preoperative Hand Decontamination in Ophthalmic Surgery: A Comparison of the Removal of Bacteria from Surgeons' Hands by Routine Antimicrobial Scrub versus an Alcoholic Hand Rub.

PubMed

Forer, Yaara; Block, Colin; Frenkel, Shahar

2017-09-01

The goal of this experiment was to evaluate and compare the antimicrobial efficacy of routine preoperative hand washing using commercial medicated sponge brushes versus an alcoholic hand rub, by comparing bacterial growth on ophthalmic surgeons' hands after application of each of these methods. Twenty ophthalmic surgeons were recruited at the Hadassah-Hebrew University Medical Center in Jerusalem, Israel. Samples were collected twice from the hands of each surgeon after hand decontamination using two different protocols during routine surgical practice. The routine preparation consisted of a 3-minute surgical scrub using commercial brush-sponges incorporating either 4% chlorhexidine gluconate (CHG) or 1% povidone-iodine (PVP-I) formulations with detergent, followed by drying the hands with a sterile towel, while the 70% ethanol solution was applied for 60-seconds and allowed to air dry. Half of the group was randomly assigned to provide samples first after the routine method and the alcoholic solution a week later, and the other half of the group was sampled in the reverse order. Viable counts of bacteria were evaluated using a modified glove juice method. Bacterial colonies were enumerated after incubation for 24 hours and expressed as colony forming units (CFU)/mL for each pair of hands. Geometric mean counts were 1310 and 39 CFU/mL, in the routine and alcohol rub groups, respectively, representing a mean log 10 reduction in 1.53. The difference between the paired bacterial counts for the routine versus the alcohol rub was statistically significant (p < 0.0001). There was no statistically significant difference between log 10 reductions for CHG and PVP-I (p = 0.97). This study provides evidence that an alcohol rub protocol is more effective in reducing bacterial counts on hands than routine surgical hand preparation with PVP-I and CHG in a population of practicing ophthalmic surgeons in the operative clinical setting. Thus, it provides a safe alternative as a preoperative hand disinfection method.

Virological Diagnosis of Central Nervous System Infections by Use of PCR Coupled with Mass Spectrometry Analysis of Cerebrospinal Fluid Samples

PubMed Central

Lévêque, Nicolas; Legoff, Jérôme; Mengelle, Catherine; Mercier-Delarue, Séverine; N'guyen, Yohan; Renois, Fanny; Tissier, Fabien; Simon, François; Izopet, Jacques

2014-01-01

Viruses are the leading cause of central nervous system (CNS) infections, ahead of bacteria, parasites, and fungal agents. A rapid and comprehensive virologic diagnostic testing method is needed to improve the therapeutic management of hospitalized pediatric or adult patients. In this study, we assessed the clinical performance of PCR amplification coupled with electrospray ionization-time of flight mass spectrometry analysis (PCR-MS) for the diagnosis of viral CNS infections. Three hundred twenty-seven cerebrospinal fluid (CSF) samples prospectively tested by routine PCR assays between 2004 and 2012 in two university hospital centers (Toulouse and Reims, France) were retrospectively analyzed by PCR-MS analysis using primers targeted to adenovirus, human herpesviruses 1 to 8 (HHV-1 to -8), polyomaviruses BK and JC, parvovirus B19, and enteroviruses (EV). PCR-MS detected single or multiple virus infections in 190 (83%) of the 229 samples that tested positive by routine PCR analysis and in 10 (10.2%) of the 98 samples that tested negative. The PCR-MS results correlated well with herpes simplex virus 1 (HSV-1), varicella-zoster virus (VZV), and EV detection by routine PCR assays (kappa values [95% confidence intervals], 0.80 [0.69 to 0.92], 0.85 [0.71 to 0.98], and 0.84 [0.78 to 0.90], respectively), whereas a weak correlation was observed with Epstein-Barr virus (EBV) (0.34 [0.10 to 0.58]). Twenty-six coinfections and 16 instances of uncommon neurotropic viruses (HHV-7 [n = 13], parvovirus B19 [n = 2], and adenovirus [n = 1]) were identified by the PCR-MS analysis, whereas only 4 coinfections had been prospectively evidenced using routine PCR assays (P < 0.01). In conclusion, our results demonstrated that PCR-MS analysis is a valuable tool to identify common neurotropic viruses in CSF (with, however, limitations that were identified regarding EBV and EV detection) and may be of major interest in better understanding the clinical impact of multiple or neglected viral neurological infections. PMID:24197874

Advance Care Planning: Understanding Clinical Routines and Experiences of Interprofessional Team Members in Diverse Health Care Settings.

PubMed

Arnett, Kelly; Sudore, Rebecca L; Nowels, David; Feng, Cindy X; Levy, Cari R; Lum, Hillary D

2017-12-01

Interprofessional health care team members consider advance care planning (ACP) to be important, yet gaps remain in systematic clinical routines to support ACP. A clearer understanding of the interprofessional team members' perspectives on ACP clinical routines in diverse settings is needed. One hundred eighteen health care team members from community-based clinics, long-term care facilities, academic clinics, federally qualified health centers, and hospitals participated in a 35-question, cross-sectional online survey to assess clinical routines, workflow processes, and policies relating to ACP. Respondents were 53% physicians, 18% advanced practice nurses, 11% nurses, and 18% other interprofessional team members including administrators, chaplains, social workers, and others. Regarding clinical routines, respondents reported that several interprofessional team members play a role in facilitating ACP (ie, physician, social worker, nurse, others). Most (62%) settings did not have, or did not know of, policies related to ACP documentation. Only 14% of settings had a patient education program. Two-thirds of the respondents said that addressing ACP is a high priority and 85% felt that nonphysicians could have ACP conversations with appropriate training. The clinical resources needed to improve clinical routines included training for providers and staff, dedicated staff to facilitate ACP, and availability of patient/family educational materials. Although interprofessional health care team members consider ACP a priority and several team members may be involved, clinical settings lack systematic clinical routines to support ACP. Patient educational materials, interprofessional team training, and policies to support ACP clinical workflows that do not rely solely on physicians could improve ACP across diverse clinical settings.

Performance of a real-time PCR assay in routine bovine mastitis diagnostics compared with in-depth conventional culture.

PubMed

Hiitiö, Heidi; Riva, Rauna; Autio, Tiina; Pohjanvirta, Tarja; Holopainen, Jani; Pyörälä, Satu; Pelkonen, Sinikka

2015-05-01

Reliable identification of the aetiological agent is crucial in mastitis diagnostics. Real-time PCR is a fast, automated tool for detecting the most common udder pathogens directly from milk. In this study aseptically taken quarter milk samples were analysed with a real-time PCR assay (Thermo Scientific PathoProof Mastitis Complete-12 Kit, Thermo Fisher Scientific Ltd.) and by semi-quantitative, in-depth bacteriological culture (BC). The aim of the study was to evaluate the diagnostic performance of the real-time PCR assay in routine use. A total of 294 quarter milk samples from routine mastitis cases were cultured in the national reference laboratory of Finland and examined with real-time PCR. With BC, 251 out of 294 (85.7%) of the milk samples had at least one colony on the plate and 38 samples were considered contaminated. In the PCR mastitis assay, DNA of target species was amplified in 244 samples out of 294 (83.0%). The most common bacterial species detected in the samples, irrespective of the diagnostic method, was the coagulase negative staphylococci (CNS) group (later referred as Staphylococcus spp.) followed by Staphylococcus aureus. Sensitivity (Se) and specificity (Sp) for the PCR assay to provide a positive Staph. aureus result was 97.0 and 95.8% compared with BC. For Staphylococcus spp., the corresponding figures were 86.7 and 75.4%. Our results imply that PCR performed well as a diagnostic tool to detect Staph. aureus but may be too nonspecific for Staphylococcus spp. in routine use with the current cut-off Ct value (37.0). Using PCR as the only microbiological method for mastitis diagnostics, clinical relevance of the results should be carefully considered before further decisions, for instance antimicrobial treatment, especially when minor pathogens with low amount of DNA have been detected. Introducing the concept of contaminated samples should also be considered.

Effect of pre-milking teat disinfection on clinical mastitis incidence in a dairy herd in Northern Queensland, Australia.

PubMed

Rowe, S M; Tranter, W P; Laven, R A

2018-03-01

To determine if a pre-milking teat disinfection protocol would reduce the incidence of clinical mastitis by greater than 50%. Two pre-milking routines were compared in a natural exposure trial. Cows from a single dairy herd were randomly assigned to control (n = 246) and experimental (pre-milking teat disinfection [PMTD]; n = 244) groups. For cows in the control group, the pre-milking routine involved minimal teat-washing, except for cows with wet teat contamination. For cows in the PMTD group, the pre-milking routine involved washing of all teats, dipping with a commercial 0.1% available iodine solution, allowing a minimum of 30 s contact time and then drying of the teats using disposable paper towel. Clinical cases encountered during the trial were recorded and pathogens were isolated from milk samples using standard laboratory methods. The effect of PMTD was determined using multivariable binary logistic regression. Multiparous animals in the PMTD group had higher odds of experiencing clinical mastitis overall and of experiencing clinical mastitis caused by environmental pathogens (odds ratio (OR) 1.97 and 4.11, 95% confidence interval (CI) 1.15-3.38 and 1.49-11.3, respectively). In primiparous animals, pre-milking teat disinfection did not reduce the odds of clinical mastitis by greater than 50% (OR 1.31, 95%CI 0.52-3.29). In this herd, PMTD increased the odds of clinical mastitis. The effectiveness of PMTD to prevent clinical mastitis in pasture-based systems is likely to vary greatly between herds. We therefore recommend against the wholesale use of this practice on Australian farms. © 2018 Australian Veterinary Association.

Microbiological Assessment of Bile and Corresponding Antibiotic Treatment: A Strobe-Compliant Observational Study of 1401 Endoscopic Retrograde Cholangiographies.

PubMed

Rupp, Christian; Bode, Konrad; Weiss, Karl Heinz; Rudolph, Gerda; Bergemann, Janine; Kloeters-Plachky, Petra; Chahoud, Fadi; Stremmel, Wolfgang; Gotthardt, Daniel Nils; Sauer, Peter

2016-03-01

The aim of this study was to determine the antibiotic susceptibility profiles of bacteria in bile samples and to analyze the clinical relevance of the findings as only limited information about risk factors for elevated frequence of bacterial and fungal strains in routinely collected bile samples has been described so far.A prospective cohort study at a tertiary care center was conducted. Seven hundred forty-four patients underwent 1401 endoscopic retrograde cholangiographies (ERCs) as indicated by liver transplantation (427/1401), primary sclerosing cholangitis (222/1401), choledocholithiasis only (153/1401), obstruction due to malignancy (366/1401), or other conditions (233/1401). Bile samples for microbiological analysis were obtained in all patients.The 71.6% (823/1150) samples had a positive microbiological finding, and 57% (840/1491) of the bacterial isolates were gram-positive. The main species were Enterococcus spp (33%; 494/1491) and Escherichia coli (12%; 179/1491). Of the samples, 53.8% had enteric bacteria and 24.7% had Candida spp; both were associated with clinical and laboratory signs of cholangitis (C-reactive proteins 35.0 ± 50.1 vs 44.8 ± 57.6; 34.5 ± 51.2 vs 52.9 ± 59.7; P < 0.001), age, previous endoscopic intervention, and immunosuppression. Multi-resistant (MR) strains were found in 11.3% of all samples and were associated with clinical and laboratory signs of cholangitis, previous intervention, and immunocompromised status. In subgroup analysis, strain-specific antibiotic therapy based on bile sampling was achieved in 56.3% (89/158) of the patients. In cases with a positive bile culture and available blood culture, blood cultures were positive in 29% of cases (36/124), and 94% (34/36) of blood cultures had microbial species identical to the bile cultures.Bactobilia and fungobilia can usually be detected by routine microbiological sampling, allowing optimized, strain-specific antibiotic treatment. Previous endoscopic intervention, clinical and laboratory signs of cholangitis, and age are independent risk factors. MR bacteria and fungi are an evolving problem in cholangitis, especially in immunocompromised patients.

Microbiological Assessment of Bile and Corresponding Antibiotic Treatment

PubMed Central

Rupp, Christian; Bode, Konrad; Weiss, Karl Heinz; Rudolph, Gerda; Bergemann, Janine; Kloeters-Plachky, Petra; Chahoud, Fadi; Stremmel, Wolfgang; Gotthardt, Daniel Nils; Sauer, Peter

2016-01-01

Abstract The aim of this study was to determine the antibiotic susceptibility profiles of bacteria in bile samples and to analyze the clinical relevance of the findings as only limited information about risk factors for elevated frequence of bacterial and fungal strains in routinely collected bile samples has been described so far. A prospective cohort study at a tertiary care center was conducted. Seven hundred forty-four patients underwent 1401 endoscopic retrograde cholangiographies (ERCs) as indicated by liver transplantation (427/1401), primary sclerosing cholangitis (222/1401), choledocholithiasis only (153/1401), obstruction due to malignancy (366/1401), or other conditions (233/1401). Bile samples for microbiological analysis were obtained in all patients. The 71.6% (823/1150) samples had a positive microbiological finding, and 57% (840/1491) of the bacterial isolates were gram-positive. The main species were Enterococcus spp (33%; 494/1491) and Escherichia coli (12%; 179/1491). Of the samples, 53.8% had enteric bacteria and 24.7% had Candida spp; both were associated with clinical and laboratory signs of cholangitis (C-reactive proteins 35.0 ± 50.1 vs 44.8 ± 57.6; 34.5 ± 51.2 vs 52.9 ± 59.7; P < 0.001), age, previous endoscopic intervention, and immunosuppression. Multi-resistant (MR) strains were found in 11.3% of all samples and were associated with clinical and laboratory signs of cholangitis, previous intervention, and immunocompromised status. In subgroup analysis, strain-specific antibiotic therapy based on bile sampling was achieved in 56.3% (89/158) of the patients. In cases with a positive bile culture and available blood culture, blood cultures were positive in 29% of cases (36/124), and 94% (34/36) of blood cultures had microbial species identical to the bile cultures. Bactobilia and fungobilia can usually be detected by routine microbiological sampling, allowing optimized, strain-specific antibiotic treatment. Previous endoscopic intervention, clinical and laboratory signs of cholangitis, and age are independent risk factors. MR bacteria and fungi are an evolving problem in cholangitis, especially in immunocompromised patients. PMID:26962768

Informed, advance refusals of treatment by people with severe mental illness in a randomised controlled trial of joint crisis plans: demand, content and correlates.

PubMed

Henderson, Claire; Farrelly, Simone; Flach, Clare; Borschmann, Rohan; Birchwood, Max; Thornicroft, Graham; Waheed, Waquas; Szmukler, George

2017-11-24

In the UK, crisis planning for mental health care should acknowledge the right to make an informed advance treatment refusal under the Mental Capacity Act 2005. Our aims were to estimate the demand for such treatment refusals within a sample of service users who had had a recent hospital admission for psychosis or bipolar disorder, and to examine the relationship between refusals, and service user characteristics. To identify refusals we conducted content analysis of Joint Crisis Plans, which are plans formulated by service users and their clinical team with involvement from an external facilitator, and routine care plans in sub-samples from a multi-centre randomised controlled trial of Joint Crisis Plans (plus routine mental health care) versus routine care alone (CRIMSON) in England. Factors hypothesised to be associated with refusals were identified using the trial data collected through baseline interviews of service users and clinicians and collection of routine clinical data. Ninety-nine of 221 (45%) of the Joint Crisis Plans contained a treatment refusal compared to 10 of 424 (2.4%) baseline routine care plans. No Joint Crisis Plans recorded disagreement with refusals on the part of clinicians. Among those with completed Joint Crisis Plans, adjusted analyses indicated a significant association between treatment refusals and perceived coercion at baseline (odds ratio = 1.21, 95% CI 1.02-1.43), but not with baseline working alliance or a past history of involuntary admission. We demonstrated significant demand for written treatment refusals in line with the Mental Capacity Act 2005, which had not previously been elicited by the process of treatment planning. Future treatment/crisis plans should incorporate the opportunity for service users to record a treatment refusal during the drafting of such plans. ISRCTN11501328 Registered 13th March 2008.

Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler's murine encephalomyelitis virus and rat theilovirus.

PubMed

Yuan, Wen; Wang, Jing; Xu, Fengjiao; Huang, Bihong; Lian, Yuexiao; Rao, Dan; Yin, Xueqin; Wu, Miaoli; Zhu, Yujun; Zhang, Yu; Huang, Ren; Guo, Pengju

2016-10-01

Theiler's murine encephalomyelitis virus (TMEV) and rat theilovirus (RTV), the member of the genus Cardiovirus, are widespread in laboratory mice and rats, and are potential contaminants of biological materials. Cardioviruses infection may cause serious complications in biomedical research. To improve the efficiency of routine screening for Cardioviruses infection, a duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection and differentiation of TMEV and RTV. The duplex assay was specific for reference strains of TMEV and RTV, and no cross-reaction was found with seven other rodent viruses. The limits of detection of both TMEV and RTV were 4×10(1) copies RNA/reaction. Reproducibility was estimated using standard dilutions, with coefficients of variation <3.1%. 439 clinical samples were evaluated by both duplex real-time RT-PCR and conventional RT-PCR. For 439 clinical samples，95 samples were positive for TMEV and 72 samples were positive for RTV using duplex real-time RT-PCR approach, whereas only 77 samples were positive for TMEV and 66 samples were positive for RTV when conventional RT-PCR was applied. Mixed infections were found in 20 samples when analyzed by conventional RT-PCR whereas 30 samples were found to be mixed infection when duplex real-time RT-PCR was applied. This duplex assay provides a useful tool for routine health monitoring and screening of contaminated biological materials of these two viruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of the BD Vacutainer(®) RST blood collection tube for routine chemistry analytes: clinical significance of differences and stability study.

PubMed

Kocijancic, Marija; Cargonja, Jelena; Delic-Knezevic, Alma

2014-01-01

Preanalytical variables account for most of laboratory errors. There is a wide range of factors that affect the reliability of laboratory report. Most convenient sample type for routine laboratory analysis is serum. BD Vacutainer(®) Rapid Serum Tube (RST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) blood collection tube provides rapid clotting time allowing fast serum separation. Our aim was to evaluate the comparability of routine chemistry parameters in BD Vacutainer(®) RST blood collection tube in reference with the BD Vacutainer(®) Serum Separating Tubes II Advance Tube (SST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). Blood specimens were collected from 90 participants for evaluation on its results, clotting time and stability study of six routine biochemistry parameters: glucose (Glu), aspartate aminotransferase (AST), alanine aminotransferase (ALT), calcium (Ca), lactate dehidrogenase (LD) and potassium (K) measured with Olympus AU2700 analyzer (Beckman Coulter, Tokyo, Japan). The significance of the differences between samples was assessed by paired t-test or Wilcoxon Matched-Pairs Rank test after checking for normality. Clotting process was significantly shorter in the RSTs compared to SSTs (2.49 min vs. 19.47 min, respectively; P < 0.001). There was a statistically significant difference between the RST and SST II tubes for glucose, calcium and LD (P < 0.001). Differences for glucose and LD were also clinically significant. Analyte stability studies showed that all analytes were stable for 24 h at 4 °C. Most results (except LD and glucose) from RST are comparable with those from SST. In addition, RST tube provides shorter clotting time.

Validation and long-term evaluation of a modified on-line chiral analytical method for therapeutic drug monitoring of (R,S)-methadone in clinical samples.

PubMed

Ansermot, Nicolas; Rudaz, Serge; Brawand-Amey, Marlyse; Fleury-Souverain, Sandrine; Veuthey, Jean-Luc; Eap, Chin B

2009-08-01

Matrix effects, which represent an important issue in liquid chromatography coupled to mass spectrometry or tandem mass spectrometry detection, should be closely assessed during method development. In the case of quantitative analysis, the use of stable isotope-labelled internal standard with physico-chemical properties and ionization behaviour similar to the analyte is recommended. In this paper, an example of the choice of a co-eluting deuterated internal standard to compensate for short-term and long-term matrix effect in the case of chiral (R,S)-methadone plasma quantification is reported. The method was fully validated over a concentration range of 5-800 ng/mL for each methadone enantiomer with satisfactory relative bias (-1.0 to 1.0%), repeatability (0.9-4.9%) and intermediate precision (1.4-12.0%). From the results obtained during validation, a control chart process during 52 series of routine analysis was established using both intermediate precision standard deviation and FDA acceptance criteria. The results of routine quality control samples were generally included in the +/-15% variability around the target value and mainly in the two standard deviation interval illustrating the long-term stability of the method. The intermediate precision variability estimated in method validation was found to be coherent with the routine use of the method. During this period, 257 trough concentration and 54 peak concentration plasma samples of patients undergoing (R,S)-methadone treatment were successfully analysed for routine therapeutic drug monitoring.

Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy

PubMed Central

Zhao, Yongxin; Bucur, Octavian; Irshad, Humayun; Chen, Fei; Weins, Astrid; Stancu, Andreea L.; Oh, Eun-Young; DiStasio, Marcello; Torous, Vanda; Glass, Benjamin; Stillman, Isaac E.; Schnitt, Stuart J.; Beck, Andrew H.; Boyden, Edward S.

2017-01-01

Expansion microscopy (ExM), a method for improving the resolution of light microscopy by physically expanding the specimen, has not been applied to clinical tissue samples. Here we report a clinically optimized form of ExM that supports nanoscale imaging of human tissue specimens that have been fixed with formalin, embedded in paraffin, stained with hematoxylin and eosin (H&E), and/or fresh frozen. The method, which we call expansion pathology (ExPath), converts clinical samples into an ExM-compatible state, then applies an ExM protocol with protein anchoring and mechanical homogenization steps optimized for clinical samples. ExPath enables ~70 nm resolution imaging of diverse biomolecules in intact tissues using conventional diffraction-limited microscopes, and standard antibody and fluorescent DNA in situ hybridization reagents. We use ExPath for optical diagnosis of kidney minimal-change disease, which previously required electron microscopy (EM), and demonstrate high-fidelity computational discrimination between early breast neoplastic lesions that to date have challenged human judgment. ExPath may enable the routine use of nanoscale imaging in pathology and clinical research. PMID:28714966

Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy.

PubMed

Zhao, Yongxin; Bucur, Octavian; Irshad, Humayun; Chen, Fei; Weins, Astrid; Stancu, Andreea L; Oh, Eun-Young; DiStasio, Marcello; Torous, Vanda; Glass, Benjamin; Stillman, Isaac E; Schnitt, Stuart J; Beck, Andrew H; Boyden, Edward S

2017-08-01

Expansion microscopy (ExM), a method for improving the resolution of light microscopy by physically expanding a specimen, has not been applied to clinical tissue samples. Here we report a clinically optimized form of ExM that supports nanoscale imaging of human tissue specimens that have been fixed with formalin, embedded in paraffin, stained with hematoxylin and eosin, and/or fresh frozen. The method, which we call expansion pathology (ExPath), converts clinical samples into an ExM-compatible state, then applies an ExM protocol with protein anchoring and mechanical homogenization steps optimized for clinical samples. ExPath enables ∼70-nm-resolution imaging of diverse biomolecules in intact tissues using conventional diffraction-limited microscopes and standard antibody and fluorescent DNA in situ hybridization reagents. We use ExPath for optical diagnosis of kidney minimal-change disease, a process that previously required electron microscopy, and we demonstrate high-fidelity computational discrimination between early breast neoplastic lesions for which pathologists often disagree in classification. ExPath may enable the routine use of nanoscale imaging in pathology and clinical research.

Infection Control Measures in Private Dental Clinics in Lebanon

PubMed Central

Sfeir, Charles

2017-01-01

Purpose Evaluate infection control knowledge, attitude, and practice in Lebanese private dental clinics. Materials and Methods A survey including 46 questions related to routine safety procedures was sent to 1150 Lebanese dentists between July 1st and 2nd, 2015. The study sample was selected from the database of registered dentists based on a proportional random sampling ensuring equitable representation of the 5 geographic regions of Lebanon. A subset of 29 questions was used to generate an overall score of compliance (excellent, good, fair, and poor). Comparisons according to gender, type, region, and years of practice were performed. Results 417 dentists returned the completed questionnaires. 96% expressed concern about infection transmission, 90.6% were vaccinated against Hepatitis B, and 61.8% asked routinely about patients medical history. Only 43% used protective eyewear. Although most dentists (65%) used autoclaves, dry heat was still used. Significant correlations were found between gender and use of personal protective equipment. Less compliance was shown by clinicians with fewer years of experience. In the overall compliance questionnaire, the mean percentage of correct answers was roughly 54% with <5% of the practitioners scoring “excellent.” Conclusions. The study found inadequacy of compliance in private Lebanese dental clinics necessitating improved educational training and sustained monitoring by regulatory bodies. PMID:28642792

Cardiac peptide stability, aprotinin and room temperature: importance for assessing cardiac function in clinical practice.

PubMed

Buckley, M G; Marcus, N J; Yacoub, M H

1999-12-01

Brain natriuretic peptide (BNP), atrial natriuretic peptide (ANP) and N-terminal ANP are good research indices of the severity of heart failure. The stability of these peptides at room temperature has become an important factor in assessing their use as indicators of cardiac function in routine clinical practice. Inhibitors such as aprotinin are routinely added in the blood collection process, but may provide no benefit in sample collection and routine clinical practice. We assessed the stability of BNP, ANP and N-terminal ANP in blood samples collected in either the presence or the absence of the protease inhibitor aprotinin. Blood, either with or without aprotinin, was processed immediately (initial; 0 h) and after blood samples had been left for 3 h, 2 days or 3 days at room temperature. These times were chosen to reflect processing in a hospital outpatient clinic (2-3 h), or when posted from general practice (2-3 days). Initial plasma BNP, ANP and N-terminal ANP levels in the absence of aprotinin were 28.2+/-5.4, 44.2+/-7.9 and 1997+/-608 pg/ml respectively, and were not significantly different from initial values in the presence of aprotinin (29.0+/-5.9, 45.2+/-8.0 and 2009+/-579 pg/ml respectively). After 3 h at room temperature, there was a significant fall in ANP in the absence of aprotinin (36. 7+/-7.9 pg/ml; P<0.005), but not in the presence of aprotinin (41. 2+/-7.6 pg/ml). Both BNP and N-terminal ANP were unchanged in either the absence (BNP, 27.6+/-5.5 pg/ml; N-terminal ANP, 2099+/-613 pg/ml) or the presence (BNP, 29.4+/-5.6 pg/ml; N-terminal ANP, 1988+/-600 pg/ml) of aprotinin. After 2 days at room temperature, ANP had fallen significantly in both the absence (16.9+/-3.4 pg/ml) and the presence (24.0+/-5.0 pg/ml) of aprotinin compared with initial values, and there was a significant difference in ANP levels in the absence and presence of aprotinin (P<0.001). ANP levels had decreased further after 3 days at room temperature, to 11.9+/-3.4 pg/ml (no aprotinin) and 20.3+/-5.0 pg/ml (aprotinin added); these values were significantly different (P=0.002). In contrast, there was no change in the levels of BNP or N-terminal ANP after 2 or 3 days at room temperature, in either the absence or the presence of aprotinin. These studies indicate that aprotinin adds little benefit to the stability of cardiac peptides at room temperature. Blood samples for BNP and N-terminal ANP measurement used as a test of heart function in hospital clinics and by general practitioners in the community could be taken into blood tubes containing only EDTA as anticoagulant and without the additional step of adding the routinely used inhibitor aprotinin.

Isavuconazole Concentration in Real-world Practice: Consistency with Results from Clinical Trials.

PubMed

Andes, David; Kovanda, Laura; Desai, A; Kitt, Theresa; Zhao, M; Walsh, Thomas J

2018-05-07

Clinical use of voriconazole, posaconazole, and itraconazole revealed the need for therapeutic drug monitoring (TDM) of plasma concentrations of these antifungal agents. This need for TDM was not evident from clinical trials of these drugs. In order to establish if this requirement also applies to isavuconazole, we examined the plasma concentrations of 283 samples receiving isavuconazole in clinical practice and compared the values to those from clinical trials. The concentration distributions from real-world use and clinical trials were nearly identical (>1 μg/mL in 90% of patients). These findings suggest that routine TDM may not be required for isavuconazole in most instances. Copyright © 2018 American Society for Microbiology.

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

PubMed Central

Welker, Martin; Pincus, David; Charrier, Jean-Philippe; Girard, Victoria

2017-01-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement. PMID:28840984

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

PubMed

van Belkum, Alex; Welker, Martin; Pincus, David; Charrier, Jean Philippe; Girard, Victoria

2017-11-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement. © The Korean Society for Laboratory Medicine.

Fully automated atlas-based hippocampal volumetry for detection of Alzheimer's disease in a memory clinic setting.

PubMed

Suppa, Per; Anker, Ulrich; Spies, Lothar; Bopp, Irene; Rüegger-Frey, Brigitte; Klaghofer, Richard; Gocke, Carola; Hampel, Harald; Beck, Sacha; Buchert, Ralph

2015-01-01

Hippocampal volume is a promising biomarker to enhance the accuracy of the diagnosis of dementia due to Alzheimer's disease (AD). However, whereas hippocampal volume is well studied in patient samples from clinical trials, its value in clinical routine patient care is still rather unclear. The aim of the present study, therefore, was to evaluate fully automated atlas-based hippocampal volumetry for detection of AD in the setting of a secondary care expert memory clinic for outpatients. One-hundred consecutive patients with memory complaints were clinically evaluated and categorized into three diagnostic groups: AD, intermediate AD, and non-AD. A software tool based on open source software (Statistical Parametric Mapping SPM8) was employed for fully automated tissue segmentation and stereotactical normalization of high-resolution three-dimensional T1-weighted magnetic resonance images. Predefined standard masks were used for computation of grey matter volume of the left and right hippocampus which then was scaled to the patient's total grey matter volume. The right hippocampal volume provided an area under the receiver operating characteristic curve of 84% for detection of AD patients in the whole sample. This indicates that fully automated MR-based hippocampal volumetry fulfills the requirements for a relevant core feasible biomarker for detection of AD in everyday patient care in a secondary care memory clinic for outpatients. The software used in the present study has been made freely available as an SPM8 toolbox. It is robust and fast so that it is easily integrated into routine workflow.

Automated measurement of carbohydrate-deficient transferrin using the Bio-Rad %CDT by the HPLC test on a Variant HPLC system: evaluation and comparison with other routine procedures.

PubMed

Schellenberg, François; Mennetrey, Louise; Girre, Catherine; Nalpas, Bertrand; Pagès, Jean Christophe

2008-01-01

In this study, we evaluated the new %CDT by the HPLC method (Bio-Rad, Germany) on a Varianttrade mark HPLC system (Bio-Rad), checked the correlation with well-known methods and calculated the diagnostic value of the test. Intra-run and day-to-day precision values were calculated for samples with extreme serum transferrin concentrations, high trisialotransferrin and interfering conditions (haemolysed, lactescent and icteric samples). The method was compared with two routine procedures, the %CDT TIA (Bio-Rad, Hercules, CA, USA) and the Capillarystrade mark CDT (Sebia, France). A total of 350 clinical sera samples were used for a case-control study. Precision values were better in high CDT and medium CDT pools than in low CDT pools. The serum transferrin concentration had no effect on CDT measurement, except in samples with serum transferrin <1 g/L. Haemolysis was the only interfering situation. The method showed high correlation (r(2) > 0.95) with the two other methods (%CDT TIA and CZE %CDT). The global predictive value of the test was >0.90 at 1.9% cut-off. These results demonstrate that the %CDT by the HPLC test is suitable for CDT routine measurement; the results from the high-throughput Varianttrade mark system are well correlated with other methods and are of high diagnostic value.

Development and accuracy of quantitative real-time polymerase chain reaction assays for detection and quantification of enterotoxigenic Escherichia coli (ETEC) heat labile and heat stable toxin genes in travelers' diarrhea samples.

PubMed

Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

2014-01-01

Enterotoxigenic Escherichia coli (ETEC), the leading bacterial pathogen of travelers' diarrhea, is routinely detected by an established DNA hybridization protocol that is neither sensitive nor quantitative. Quantitative real-time polymerase chain reaction (qPCR) assays that detect the ETEC toxin genes eltA, sta1, and sta2 in clinical stool samples were developed and tested using donor stool inoculated with known quantities of ETEC bacteria. The sensitivity of the qPCR assays is 89%, compared with 22% for the DNA hybridization assay, and the limits of detection are 10,000-fold lower than the DNA hybridization assays performed in parallel. Ninety-three clinical stool samples, previously characterized by DNA hybridization, were tested using the new ETEC qPCR assays. Discordant toxin profiles were observed for 22 samples, notably, four samples originally typed as ETEC negative were ETEC positive. The qPCR assays are unique in their sensitivity and ability to quantify the three toxin genes in clinical stool samples.

Implementing a laboratory automation system: experience of a large clinical laboratory.

PubMed

Lam, Choong Weng; Jacob, Edward

2012-02-01

Laboratories today face increasing pressure to automate their operations as they are challenged by a continuing increase in workload, need to reduce expenditure, and difficulties in recruitment of experienced technical staff. Was the implementation of a laboratory automation system (LAS) in the Clinical Biochemistry Laboratory at Singapore General Hospital successful? There is no simple answer, so the following topics comparing and contrasting pre- and post-LAS have been explored: turnaround time (TAT), laboratory errors, and staff satisfaction. The benefits and limitations of LAS from the laboratory experience were also reviewed. The mean TAT for both stat and routine samples decreased post-LAS (30% and 13.4%, respectively). In the 90th percentile TAT chart, a 29% reduction was seen in the processing of stat samples on the LAS. However, no significant difference in the 90th percentile TAT was observed with routine samples. It was surprising to note that laboratory errors increased post-LAS. Considerable effort was needed to overcome the initial difficulties associated with adjusting to a new system, new software, and new working procedures. Although some of the known advantages and limitations of LAS have been validated, the claimed benefits such as improvements in TAT, laboratory errors, and staff morale were not evident in the initial months.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

PubMed

Alcaide, F; Amlerová, J; Bou, G; Ceyssens, P J; Coll, P; Corcoran, D; Fangous, M-S; González-Álvarez, I; Gorton, R; Greub, G; Hery-Arnaud, G; Hrábak, J; Ingebretsen, A; Lucey, B; Marekoviċ, I; Mediavilla-Gradolph, C; Monté, M R; O'Connor, J; O'Mahony, J; Opota, O; O'Reilly, B; Orth-Höller, D; Oviaño, M; Palacios, J J; Palop, B; Pranada, A B; Quiroga, L; Rodríguez-Temporal, D; Ruiz-Serrano, M J; Tudó, G; Van den Bossche, A; van Ingen, J; Rodriguez-Sanchez, B

2018-06-01

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Detection of BRAF V600 Mutations in Melanoma: Evaluation of Concordance between the Cobas® 4800 BRAF V600 Mutation Test and the Methods Used in French National Cancer Institute (INCa) Platforms in a Real-Life Setting

PubMed Central

Mourah, Samia; Denis, Marc G.; Narducci, Fabienne Escande; Solassol, Jérôme; Merlin, Jean-Louis; Sabourin, Jean-Christophe; Scoazec, Jean-Yves; Ouafik, L’Houcine; Emile, Jean-François; Heller, Remy; Souvignet, Claude; Bergougnoux, Loïc; Merlio, Jean-Philippe

2015-01-01

Vemurafenib is approved for the treatment of metastatic melanoma in patients with BRAF V600 mutation. In pivotal clinical trials, BRAF testing has always been done with the approved cobas 4800 BRAF test. In routine practice, several methods are available and are used according to the laboratories usual procedures. A national, multicenter, non-interventional study was conducted with prospective and consecutive collection of tumor samples. A parallel evaluation was performed in routine practice between the cobas 4800 BRAF V600 mutation test and home brew methods (HBMs) of 12 national laboratories, labelled and funded by the French National Cancer Institute (INCa). For 420 melanoma samples tested, the cobas method versus HBM showed a high concordance (93.3%; kappa = 0.86) in BRAF V600 genotyping with similar mutation rates (34.0% versus 35.7%, respectively). Overall, 97.4% and 98.6% of samples gave valid results using the cobas and HBM, respectively. Of the 185 samples strictly fulfilling the cobas guidelines, the concordance rate was even higher (95.7%; kappa = 0.91; 95%CI [0.85; 0.97]). Out of the 420 samples tested, 28 (6.7%) showed discordance between HBM and cobas. This prospective study shows a high concordance rate between the cobas 4800 BRAF V600 test and home brew methods in the routine detection of BRAF V600E mutations. PMID:25789737

Using routinely recorded data in the UK to assess outcomes in a randomised controlled trial: The Trials of Access.

PubMed

Powell, G A; Bonnett, L J; Tudur-Smith, C; Hughes, D A; Williamson, P R; Marson, A G

2017-08-23

In the UK, routinely recorded data may benefit prospective studies including randomised controlled trials (RCTs). In an on-going study, we aim to assess the feasibility of access and agreement of routinely recorded clinical and non-clinical data compared to data collected during a RCT using standard prospective methods. This paper will summarise available UK routinely recorded data sources and discuss our experience with the feasibility of accessing routinely recorded data for participants of a RCT before finally proposing recommendations for improving the access and implementation of routinely recorded data in RCTs. Setting: the case study RCT is the Standard and New Antiepileptic Drugs II (SANAD II) trial, a pragmatic, UK, multicentre, phase IV RCT assessing the clinical and cost-effectiveness of antiepileptic drug treatments for newly diagnosed epilepsy. 98 participants have provided written consent to permit the request of routinely recorded data. Study procedures: routinely recorded clinical and non-clinical data were identified and data requested through formal applications from available data holders for the duration that participants have been recruited into SANAD II. The feasibility of accessing routinely recorded data during a RCT is assessed and recommendations for improving access proposed. Secondary-care clinical and socioeconomic data is recorded on a national basis and can be accessed, although there are limitations in the application process. Primary-care data are recorded by a number of organisations on a de-identified basis but access for specific individuals has not been feasible. Access to data recorded by non-clinical sources, including The Department for Work and Pensions and The Driving and Vehicle Licensing Agency, was not successful. Recommendations discussed include further research to assess the attributes of routinely recorded data, an assessment of public perceptions and the development of strategies to collaboratively improve access to routinely recorded data for research. International Standard Randomised Controlled Trials, ISRCTN30294119 . Registered on 3 July 2012. EudraCT No: 2012-001884-64. Registered on 9 May 2012.

Integrated Blood Barcode Chips

PubMed Central

Fan, Rong; Vermesh, Ophir; Srivastava, Alok; Yen, Brian K.H.; Qin, Lidong; Ahmad, Habib; Kwong, Gabriel A.; Liu, Chao-Chao; Gould, Juliane; Hood, Leroy; Heath, James R.

2008-01-01

Blood comprises the largest version of the human proteome1. Changes of plasma protein profiles can reflect physiological or pathological conditions associated with many human diseases, making blood the most important fluid for clinical diagnostics2-4. Nevertheless, only a handful of plasma proteins are utilized in routine clinical tests. This is due to a host of reasons, including the intrinsic complexity of the plasma proteome1, the heterogeneity of human diseases and the fast kinetics associated with protein degradation in sampled blood5. Simple technologies that can sensitively sample large numbers of proteins over broad concentration ranges, from small amounts of blood, and within minutes of sample collection, would assist in solving these problems. Herein, we report on an integrated microfluidic system, called the Integrated Blood Barcode Chip (IBBC). It enables on-chip blood separation and the rapid measurement of a panel of plasma proteins from small quantities of blood samples including a fingerprick of whole blood. This platform holds potential for inexpensive, non-invasive, and informative clinical diagnoses, particularly, for point-of-care. PMID:19029914

Irregular analytical errors in diagnostic testing - a novel concept.

PubMed

Vogeser, Michael; Seger, Christoph

2018-02-23

In laboratory medicine, routine periodic analyses for internal and external quality control measurements interpreted by statistical methods are mandatory for batch clearance. Data analysis of these process-oriented measurements allows for insight into random analytical variation and systematic calibration bias over time. However, in such a setting, any individual sample is not under individual quality control. The quality control measurements act only at the batch level. Quantitative or qualitative data derived for many effects and interferences associated with an individual diagnostic sample can compromise any analyte. It is obvious that a process for a quality-control-sample-based approach of quality assurance is not sensitive to such errors. To address the potential causes and nature of such analytical interference in individual samples more systematically, we suggest the introduction of a new term called the irregular (individual) analytical error. Practically, this term can be applied in any analytical assay that is traceable to a reference measurement system. For an individual sample an irregular analytical error is defined as an inaccuracy (which is the deviation from a reference measurement procedure result) of a test result that is so high it cannot be explained by measurement uncertainty of the utilized routine assay operating within the accepted limitations of the associated process quality control measurements. The deviation can be defined as the linear combination of the process measurement uncertainty and the method bias for the reference measurement system. Such errors should be coined irregular analytical errors of the individual sample. The measurement result is compromised either by an irregular effect associated with the individual composition (matrix) of the sample or an individual single sample associated processing error in the analytical process. Currently, the availability of reference measurement procedures is still highly limited, but LC-isotope-dilution mass spectrometry methods are increasingly used for pre-market validation of routine diagnostic assays (these tests also involve substantial sets of clinical validation samples). Based on this definition/terminology, we list recognized causes of irregular analytical error as a risk catalog for clinical chemistry in this article. These issues include reproducible individual analytical errors (e.g. caused by anti-reagent antibodies) and non-reproducible, sporadic errors (e.g. errors due to incorrect pipetting volume due to air bubbles in a sample), which can both lead to inaccurate results and risks for patients.

Application of the FICTION technique for the simultaneous detection of immunophenotype and chromosomal abnormalities in routinely fixed, paraffin wax embedded bone marrow trephines

PubMed Central

Korać, P; Jones, M; Dominis, M; Kušec, R; Mason, D Y; Banham, A H; Ventura, R A

2005-01-01

The use of interphase fluorescence in situ hybridisation (FISH) to study cytogenetic abnormalities in routinely fixed paraffin wax embedded tissue has become commonplace over the past decade. However, very few studies have applied FISH to routinely fixed bone marrow trephines (BMTs). This may be because of the acid based decalcification methods that are commonly used during the processing of BMTs, which may adversely affect the suitability of the sample for FISH analysis. For the first time, this report describes the simultaneous application of FISH and immunofluorescent staining (the FICTION technique) to formalin fixed, EDTA decalcified and paraffin wax embedded BMTs. This technique allows the direct correlation of genetic abnormalities to immunophenotype, and therefore will be particularly useful for the identification of genetic abnormalities in specific tumour cells present in BMTs. The application of this to routine clinical practice will assist diagnosis and the detection of minimal residual disease. PMID:16311361

SPIRIT: Systematic Planning of Intelligent Reuse of Integrated Clinical Routine Data. A Conceptual Best-practice Framework and Procedure Model.

PubMed

Hackl, W O; Ammenwerth, E

2016-01-01

Secondary use of clinical routine data is receiving an increasing amount of attention in biomedicine and healthcare. However, building and analysing integrated clinical routine data repositories are nontrivial, challenging tasks. As in most evolving fields, recognized standards, well-proven methodological frameworks, or accurately described best-practice approaches for the systematic planning of solutions for secondary use of routine medical record data are missing. We propose a conceptual best-practice framework and procedure model for the systematic planning of intelligent reuse of integrated clinical routine data (SPIRIT). SPIRIT was developed based on a broad literature overview and further refined in two case studies with different kinds of clinical routine data, including process-oriented nursing data from a large hospital group and high-volume multimodal clinical data from a neurologic intensive care unit. SPIRIT aims at tailoring secondary use solutions to specific needs of single departments without losing sight of the institution as a whole. It provides a general conceptual best-practice framework consisting of three parts: First, a secondary use strategy for the whole organization is determined. Second, comprehensive analyses are conducted from two different viewpoints to define the requirements regarding a clinical routine data reuse solution at the system level from the data perspective (BOTTOM UP) and at the strategic level from the future users perspective (TOP DOWN). An obligatory clinical context analysis (IN BETWEEN) facilitates refinement, combination, and integration of the different requirements. The third part of SPIRIT is dedicated to implementation, which comprises design and realization of clinical data integration and management as well as data analysis solutions. The SPIRIT framework is intended to be used to systematically plan the intelligent reuse of clinical routine data for multiple purposes, which often was not intended when the primary clinical documentation systems were implemented. SPIRIT helps to overcome this gap. It can be applied in healthcare institutions of any size or specialization and allows a stepwise setup and evolution of holistic clinical routine data reuse solutions.

Comparison of five automated hematology analyzers in a university hospital setting: Abbott Cell-Dyn Sapphire, Beckman Coulter DxH 800, Siemens Advia 2120i, Sysmex XE-5000, and Sysmex XN-2000.

PubMed

Bruegel, Mathias; Nagel, Dorothea; Funk, Manuela; Fuhrmann, Petra; Zander, Johannes; Teupser, Daniel

2015-06-01

Various types of automated hematology analyzers are used in clinical laboratories. Here, we performed a side-by-side comparison of five current top of the range routine hematology analyzers in the setting of a university hospital central laboratory. Complete blood counts (CBC), differentials, reticulocyte and nucleated red blood cell (NRBC) counts of 349 patient samples, randomly taken out of routine diagnostics, were analyzed with Cell-Dyn Sapphire (Abbott), DxH 800 (Beckman Coulter), Advia 2120i (Siemens), XE-5000 and XN-2000 (Sysmex). Inter-instrument comparison of CBCs including reticulocyte and NRBC counts and investigation of flagging quality in relation to microscopy were performed with the complete set of samples. Inter-instrument comparison of five-part differential was performed using samples without atypical cells in blood smear (n=292). Automated five-part differentials and NRBCs were additionally compared with microscopy. The five analyzers showed a good concordance for basic blood count parameters. Correlations between instruments were less well for reticulocyte counts, NRBCs, and differentials. The poorest concordance for NRBCs with microscopy was observed for Advia 2120i (Kendall's τb=0.37). The highest flagging sensitivity for blasts was observed for XN-2000 (97% compared to 65%-76% for other analyzers), whereas overall specificity was comparable between different instruments. To the best of our knowledge, this is the most comprehensive side-by-side comparison of five current top of the range routine hematology analyzers. Variable analyzer quality and parameter specific limitations must be considered in defining laboratory algorithms in clinical practice.

Next-Generation Genotyping by Digital PCR to Detect and Quantify the BRAF V600E Mutation in Melanoma Biopsies.

PubMed

Lamy, Pierre-Jean; Castan, Florence; Lozano, Nicolas; Montélion, Cécile; Audran, Patricia; Bibeau, Frédéric; Roques, Sylvie; Montels, Frédéric; Laberenne, Anne-Claire

2015-07-01

The detection of the BRAF V600E mutation in melanoma samples is used to select patients who should respond to BRAF inhibitors. Different techniques are routinely used to determine BRAF status in clinical samples. However, low tumor cellularity and tumor heterogeneity can affect the sensitivity of somatic mutation detection. Digital PCR (dPCR) is a next-generation genotyping method that clonally amplifies nucleic acids and allows the detection and quantification of rare mutations. Our aim was to evaluate the clinical routine performance of a new dPCR-based test to detect and quantify BRAF mutation load in 47 paraffin-embedded cutaneous melanoma biopsies. We compared the results obtained by dPCR with high-resolution melting curve analysis and pyrosequencing or with one of the allele-specific PCR methods available on the market. dPCR showed the lowest limit of detection. dPCR and allele-specific amplification detected the highest number of mutated samples. For the BRAF mutation load quantification both dPCR and pyrosequencing gave similar results with strong disparities in allele frequencies in the 47 tumor samples under study (from 0.7% to 79% of BRAF V600E mutations/sample). In conclusion, the four methods showed a high degree of concordance. dPCR was the more-sensitive method to reliably and easily detect mutations. Both pyrosequencing and dPCR could quantify the mutation load in heterogeneous tumor samples. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry.

PubMed

La Scola, Bernard; Raoult, Didier

2009-11-25

With long delays observed between sampling and availability of results, the usefulness of blood cultures in the context of emergency infectious diseases has recently been questioned. Among methods that allow quicker bacterial identification from growing colonies, matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF) mass spectrometry was demonstrated to accurately identify bacteria routinely isolated in a clinical biology laboratory. In order to speed up the identification process, in the present work we attempted bacterial identification directly from blood culture bottles detected positive by the automate. We prospectively analysed routine MALDI-TOF identification of bacteria detected in blood culture by two different protocols involving successive centrifugations and then lysis by trifluoroacetic acid or formic acid. Of the 562 blood culture broths detected as positive by the automate and containing one bacterial species, 370 (66%) were correctly identified. Changing the protocol from trifluoroacetic acid to formic acid improved identification of Staphylococci, and overall correct identification increased from 59% to 76%. Lack of identification was observed mostly with viridans streptococci, and only one false positive was observed. In the 22 positive blood culture broths that contained two or more different species, only one of the species was identified in 18 samples, no species were identified in two samples and false species identifications were obtained in two cases. The positive predictive value of bacterial identification using this procedure was 99.2%. MALDI-TOF MS is an efficient method for direct routine identification of bacterial isolates in blood culture, with the exception of polymicrobial samples and viridans streptococci. It may replace routine identification performed on colonies, provided improvement for the specificity of blood culture broths growing viridans streptococci is obtained in the near future.

Clinical Neuropathology practice news 1-2014: Pyrosequencing meets clinical and analytical performance criteria for routine testing of MGMT promoter methylation status in glioblastoma

PubMed Central

Preusser, Matthias; Berghoff, Anna S.; Manzl, Claudia; Filipits, Martin; Weinhäusel, Andreas; Pulverer, Walter; Dieckmann, Karin; Widhalm, Georg; Wöhrer, Adelheid; Knosp, Engelbert; Marosi, Christine; Hainfellner, Johannes A.

2014-01-01

Testing of the MGMT promoter methylation status in glioblastoma is relevant for clinical decision making and research applications. Two recent and independent phase III therapy trials confirmed a prognostic and predictive value of the MGMT promoter methylation status in elderly glioblastoma patients. Several methods for MGMT promoter methylation testing have been proposed, but seem to be of limited test reliability. Therefore, and also due to feasibility reasons, translation of MGMT methylation testing into routine use has been protracted so far. Pyrosequencing after prior DNA bisulfite modification has emerged as a reliable, accurate, fast and easy-to-use method for MGMT promoter methylation testing in tumor tissues (including formalin-fixed and paraffin-embedded samples). We performed an intra- and inter-laboratory ring trial which demonstrates a high analytical performance of this technique. Thus, pyrosequencing-based assessment of MGMT promoter methylation status in glioblastoma meets the criteria of high analytical test performance and can be recommended for clinical application, provided that strict quality control is performed. Our article summarizes clinical indications, practical instructions and open issues for MGMT promoter methylation testing in glioblastoma using pyrosequencing. PMID:24359605

Improved procedure for determination of flucytosine in human blood plasma by high-pressure liquid chromatography.

PubMed Central

Schwertschlag, U; Nakata, L M; Gal, J

1984-01-01

Several high-pressure liquid chromatography procedures for the determination of flucytosine in serum or plasma have appeared. Some of these suffer from significant disadvantages, and none was applicable in our routine clinical therapeutic-drug-monitoring laboratory. A new high-pressure liquid chromatography assay for flucytosine was therefore developed. A 100-microliter sample of plasma was treated with an aqueous 5-iodocytosine internal-standard solution, and the mixture was deproteinized with trichloroacetic acid. A portion of the protein-free supernatant was diluted with 0.1 M ammonium phosphate, and an aliquot of the resulting solution was injected into the high-pressure liquid chromatography system. Chromatography was performed on a strong-cation-exchange column with a mobile phase containing aqueous ammonium phosphate, phosphoric acid, methanol, and acetonitrile. Detection was at 254 nm. The assay was shown to be linear in the 10 to 200-micrograms/ml drug-concentration range. Forty other drugs were tested for potential interference with the assay, and none was found. For routine use, a single-point working standard containing 75 micrograms of flucytosine per ml was used, giving intraassay coefficients of variation at 50 and 150 micrograms/ml of 1.8 and 2.3% respectively, whereas the day-to-day coefficient of variation at 50 micrograms/ml was 10.0%. Advantages of the procedure include the small sample size, the use of a convenient and reliable internal standard, speed, and simplicity. The assay is highly suitable for routine clinical drug-analysis laboratories. PMID:6508261

The Effectiveness of Online Cognitive Behavioral Treatment in Routine Clinical Practice

PubMed Central

Ruwaard, Jeroen; Lange, Alfred; Schrieken, Bart; Dolan, Conor V.; Emmelkamp, Paul

2012-01-01

Context Randomized controlled trails have identified online cognitive behavioral therapy as an efficacious intervention in the management of common mental health disorders. Objective To assess the effectiveness of online CBT for different mental disorders in routine clinical practice. Design An uncontrolled before-after study, with measurements at baseline, posttest, 6-week follow-up, and 1-year follow-up. Participants & Setting 1500 adult patients (female: 67%; mean age: 40 years) with a GP referral for psychotherapy were treated at a Dutch online mental health clinic for symptoms of depression (n = 413), panic disorder (n = 139), posttraumatic stress (n = 478), or burnout (n = 470). Interventions Manualized, web-based, therapist-assisted CBT, of which the efficacy was previously demonstrated in a series of controlled trials. Standardized duration of treatment varied from 5 weeks (online CBT for Posttraumatic stress) to 16 weeks (online CBT for Depression). Main Outcome Measures Validated self-report questionnaires of specific and general psychopathology, including the Beck Depression Inventory, the Impact of Event Scale, the Panic Disorder Severity Scale-Self Report, the Oldenburg Burnout Inventory, and the Depression Anxiety Stress Scales. Results Treatment adherence was 71% (n = 1071). Study attrition was 21% at posttest, 33% at 6-week FU and 65% at 1-year FU. Mixed-model repeated measures regression identified large short-term reductions in all measures of primary symptoms (d = 1.9±0.2 to d = 1.2±0.2; P<.001), which sustained up to one year after treatment. At posttest, rates of reliable improvement and recovery were 71% and 52% in the completer sample (full sample: 55%/40%). Patient satisfaction was high. Conclusions Results suggest that online therapist-assisted CBT may be as effective in routine practice as it is in clinical trials. Although pre-treatment withdrawal and long-term outcomes require further study, results warrant continued implementation of online CBT. PMID:22792217

A time-motion study of cardiovascular disease risk factor screening integrated into HIV clinic visits in Swaziland.

PubMed

Palma, Anton M; Rabkin, Miriam; Simelane, Samkelo; Gachuhi, Averie B; McNairy, Margaret L; Nuwagaba-Biribonwoha, Harriet; Bongomin, Pido; Okello, Velephi N; Bitchong, Raymond A; El-Sadr, Wafaa M

2018-03-01

Screening of modifiable cardiovascular disease (CVD) risk factors is recommended but not routinely provided for HIV-infected patients, especially in low-resource settings. Potential concerns include limited staff time and low patient acceptability, but little empirical data exists. As part of a pilot study of screening in a large urban HIV clinic in Swaziland, we conducted a time-motion study to assess the impact of screening on patient flow and HIV service delivery and exit interviews to assess patient acceptability. A convenience sample of patients ≥40 years of age attending routine HIV clinic visits was screened for hypertension, diabetes, hyperlipidemia and tobacco smoking. We observed HIV visits with and without screening and measured time spent on HIV and CVD risk factor screening activities. We compared screened and unscreened patients on total visit time and time spent receiving HIV services using Wilcoxon rank-sum tests. A separate convenience sample of screened patients participated in exit interviews to assess their satisfaction with screening. We observed 172 patient visits (122 with CVD risk factor screening and 50 without). Screening increased total visit time from a median (range) of 4 minutes (2 to 11) to 15 minutes (9 to 30) (p < 0.01). Time spent on HIV care was not affected: 4 (2 to 10) versus 4 (2 to 11) (p = 0.57). We recruited 126 patients for exit interviews, all of whom indicated that they would recommend screening to others. Provision of CVD risk factor screening more than tripled the length of routine HIV clinic visits but did not reduce the time spent on HIV services. Programme managers need to take longer visit duration into account in order to effectively integrate CVD risk factor screening and counselling into HIV programmes. © 2018 The Authors. Journal of the International AIDS Society published by John Wiley & sons Ltd on behalf of the International AIDS Society.

Validation of a single-platform method for hematopoietic CD34+ stem cells enumeration according to accreditation procedure.

PubMed

Massin, Frédéric; Huili, Cai; Decot, Véronique; Stoltz, Jean-François; Bensoussan, Danièle; Latger-Cannard, Véronique

2015-01-01

Stem cells for autologous and allogenic transplantation are obtained from several sources including bone marrow, peripheral blood or cord blood. Accurate enumeration of viable CD34+ hematopoietic stem cells (HSC) is routinely used in clinical settings, especially to monitor progenitor cell mobilization and apheresis. The number of viable CD34+ HSC has also been shown to be the most critical factor in haematopoietic engraftment. The International Society for Cellular Therapy actually recommends the use of single-platform flow cytometry system using 7-AAD as a viability dye. In a way to move routine analysis from a BD FACSCaliburTM instrument to a BD FACSCantoTM II, according to ISO 15189 standard guidelines, we define laboratory performance data of the BDTM Stem Cell Enumeration (SCE) kit on a CE-IVD system including a BD FACSCanto II flow cytometer and the BD FACSCantoTM Clinical Software. InterQCTM software, a real time internet laboratory QC management system developed by VitroTM and distributed by Becton DickinsonTM, was also tested to monitor daily QC data, to define the internal laboratory statistics and to compare them to external laboratories. Precision was evaluated with BDTM Stem Cell Control (high and low) results and the InterQC software, an internet laboratory QC management system by Vitro. This last one drew Levey-Jennings curves and generated numeral statistical parameters allowing detection of potential changes in the system performances as well as interlaboratory comparisons. Repeatability, linearity and lower limits of detection were obtained with routine samples from different origins. Agreement evaluation between BD FACSCanto II system versus BD FACSCalibur system was tested on fresh peripheral blood, freeze-thawed apheresis, fresh bone marrow and fresh cord blood samples. Instrument's measure and staining repeatability clearly evidenced acceptable variability on the different samples tested. Intra- and inter-laboratory CV in CD34+ cell absolute count are consistent and reproducible. Linearity analysis, established between 2 and 329 cells/μl showed a linear relation between expected counts and measured counts (R2=0.97). Linear regression and Bland-Altman representations showed an excellent correlation on samples from different sources between the two systems and allowed the transfer of routine analysis from BD FACSCalibur to BD FACSCanto II. The BD SCE kit provides an accurate measure of the CD34 HSC, and can be used in daily routine to optimize the enumeration of hematopoietic CD34+ stem cells by flow cytometry. Moreover, the InterQC system seems to be a very useful tool for laboratory daily quality monitoring and thus for accreditation.

Photoacoustic spectroscopic differences between normal and malignant thyroid tissues

NASA Astrophysics Data System (ADS)

Li, Li; Xie, Wengming; Li, Hui

2012-12-01

The thyroid is one of the main endocrine glands of human body, which plays a crucial role in the body's metabolism. Thyroid cancer mortality ranks only second to ovarian cancer in endocrine cancer. Routine diagnostic methods of thyroid diseases in present clinic exist misdiagnosis and missed diagnosis to varying degrees. Those lead to miss the best period of cancer treatment--early. Photoacoustic spectroscopy technology is a new tool, which provides an effective and noninvasive way for biomedical materials research, being highly sensitive and without sample pretreatment. In this paper, we use photoacoustic spectroscopy technology (PAST) to detect the absorption spectrum between normal and malignant thyroid tissues. The result shows that the photoacoustic spectroscopy technology (PAST) could differentiate malignant thyroid tissue from normal thyroid tissue very well. This technique combined with routine diagnostic methods has the potential to increase the diagnostic accuracy in clinical thyroid cancer diagnosis.

The Genetic Counseling Video Project (GCVP): Models of Practice

PubMed Central

Roter, D.; Ellington, L.; Erby, L. Hamby; Larson, S.; W, Dudley

2009-01-01

Genetic counseling is conceptualized as having both “teaching” and “counseling” functions; however, little is known about how these functions are articulated in routine practice. This study addresses the question by documenting, on videotape, the practices of a national sample of prenatal and cancer genetic counselors (GCs) providing routine pretest counseling to simulated clients (SCs). 177 GCs recruited at two annual conferences of the National Society of Genetic Counselors (NSGC) were randomly assigned to counsel one of six female SCs of varying ethnicity, with or without a spouse, in their specialty. 152 videotapes were coded with the Roter Interaction Analysis System (RIAS) and both GCs and SCs completed evaluative questionnaires. Two teaching and two counseling patterns of practice emerged from cluster analysis. The teaching patterns included: (1) Clinical teaching (31%) characterized by low psychosocial, emotional and facilitative talk, high levels of clinical exchange, and high verbal dominance; and (2) Psycho-educational teaching (27%) characterized by high levels of both clinical and psychosocial exchange, low levels of emotional and facilitative talk, and higher verbal dominance. The counseling patterns included: (1) Supportive counseling (33%) characterized by low psychosocial and clinical exchange, high levels of emotional and facilitative talk, and low verbal dominance; and (2) Psychosocial counseling (9%) with high emotional and facilitative talk, low clinical and high psychosocial exchange, and the lowest verbal dominance. SCs ratings of satisfaction with communication, the counselor’s affective demeanor, and the counselor’s use of nonverbal skills were highest for the counseling model sessions. Both the teaching and counseling models seem to be represented in routine practice and predict variation in client satisfaction. PMID:16941666

Evaluating the Responsiveness to Therapeutic Change with Routine Outcome Monitoring: A Comparison of the Symptom Questionnaire-48 (SQ-48) with the Brief Symptom Inventory (BSI) and the Outcome Questionnaire-45 (OQ-45).

PubMed

Carlier, Ingrid V E; Kovács, Viktória; van Noorden, Martijn S; van der Feltz-Cornelis, Christina; Mooij, Nanda; Schulte-van Maaren, Yvonne W M; van Hemert, Albert M; Zitman, Frans G; Giltay, Erik J

2017-01-01

Assessment of psychological distress is important, because it may help to monitor treatment effects and predict treatment outcomes. We previously developed the 48-item Symptom Questionnaire (SQ-48) as a public domain self-report psychological distress instrument and showed good internal consistency as well as good convergent and divergent validity among clinical and non-clinical samples. The present study, conducted among psychiatric outpatients in a routine clinical setting, describes additional psychometric properties of the SQ-48. The primary focus is on responsiveness to therapeutic change, which to date has been rarely examined within psychiatry or clinical psychology. Since a questionnaire should also be stable when no clinically important change occurs, we also examined test-retest reliability within a test-retest design before treatment (n = 43). A pre-treatment/post-treatment design was used for responsiveness to therapeutic change, comparing the SQ-48 with two internationally widely used instruments: the Brief Symptom Inventory (n = 97) and the Outcome Questionnaire-45 (n = 109). The results showed that the SQ-48 has excellent test-retest reliability and good responsiveness to therapeutic change, without significant differences between the questionnaires in terms of responsiveness. In sum, the SQ-48 is a psychometrically sound public domain self-report instrument that can be used for routine outcome monitoring, as a benchmark tool or for research purposes. Copyright © 2015 John Wiley & Sons, Ltd. Key Practitioner Message The SQ-48 is developed as a public domain self-report questionnaire, in line with growing efforts to develop clinical instruments that are free of charge. The SQ-48 has excellent test-retest reliability and good responsiveness to therapeutic change or patient progress. There were no significant differences in terms of responsiveness between the SQ-48 and BSI or OQ-45. The SQ-48 can be used as a routine evaluation outcome measure for quality assurance in clinical practice. Providing feedback on patient progress via outcome measures could contribute to the enhancement of treatment outcomes. Copyright © 2015 John Wiley & Sons, Ltd.

Detection of Cryptosporidium and Giardia in clinical laboratories in Europe--a comparative study.

PubMed

Manser, M; Granlund, M; Edwards, H; Saez, A; Petersen, E; Evengard, B; Chiodini, P

2014-01-01

To determine the routine diagnostic methods used and compare the performance in detection of oocysts of Cryptosporidium species and cysts of Giardia intestinalis in faecal samples by European specialist parasitology laboratories and European clinical laboratories. Two sets of seven formalin-preserved faecal samples, one containing cysts of Giardia intestinalis and the other, containing oocysts of Cryptosporidium, were sent to 18 laboratories. Participants were asked to examine the specimens using their routine protocol for detecting these parasites and state the method(s) used. Eighteen laboratories answered the questionnaire. For detection of Giardia, 16 of them used sedimentation/concentration followed by light microscopy. Using this technique the lower limit of detection of Giardia was 17.2 cysts/mL of faeces in the best performing laboratories. Only three of 16 laboratories used fluorescent-conjugated antibody-based microscopy. For detection of Cryptosporidium acid-fast staining was used by 14 of the 17 laboratories that examined the samples. With this technique the lower limit of detection was 976 oocysts/mL of faeces. Fluorescent-conjugated antibody-based microscopy was used by only five of the 17 laboratories. There was variation in the lower limit of detection of cysts of Giardia and oocysts of Cryptosporidium between laboratories using the same basic microscopic methods. Fluorescent-conjugated antibody-based microscopy was not superior to light microscopy under the conditions of this study. There is a need for a larger-scale multi-site comparison of the methods used for the diagnosis of these parasites and the development of a Europe-wide laboratory protocol based upon its findings. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Impact of Different Visual Field Testing Paradigms on Sample Size Requirements for Glaucoma Clinical Trials.

PubMed

Wu, Zhichao; Medeiros, Felipe A

2018-03-20

Visual field testing is an important endpoint in glaucoma clinical trials, and the testing paradigm used can have a significant impact on the sample size requirements. To investigate this, this study included 353 eyes of 247 glaucoma patients seen over a 3-year period to extract real-world visual field rates of change and variability estimates to provide sample size estimates from computer simulations. The clinical trial scenario assumed that a new treatment was added to one of two groups that were both under routine clinical care, with various treatment effects examined. Three different visual field testing paradigms were evaluated: a) evenly spaced testing, b) United Kingdom Glaucoma Treatment Study (UKGTS) follow-up scheme, which adds clustered tests at the beginning and end of follow-up in addition to evenly spaced testing, and c) clustered testing paradigm, with clusters of tests at the beginning and end of the trial period and two intermediary visits. The sample size requirements were reduced by 17-19% and 39-40% using the UKGTS and clustered testing paradigms, respectively, when compared to the evenly spaced approach. These findings highlight how the clustered testing paradigm can substantially reduce sample size requirements and improve the feasibility of future glaucoma clinical trials.

Validity of Targeted Next-Generation Sequencing in Routine Care for Identifying Clinically Relevant Molecular Profiles in Non-Small-Cell Lung Cancer: Results of a 2-Year Experience on 1343 Samples.

PubMed

Legras, Antoine; Barritault, Marc; Tallet, Anne; Fabre, Elizabeth; Guyard, Alice; Rance, Bastien; Digan, William; Pecuchet, Nicolas; Giroux-Leprieur, Etienne; Julie, Catherine; Jouveshomme, Stéphane; Duchatelle, Véronique; Giraudet, Véronique; Gibault, Laure; Cazier, Alain; Pastre, Jean; Le Pimpec-Barthes, Françoise; Laurent-Puig, Pierre; Blons, Hélène

2018-05-19

Theranostic assays are based on single-gene testing, but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single-gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated. NGS performance was assessed following guidelines. TaqMan probes and NGS were compared for their ability to detect EGFR and KRAS mutations, and NGS mutation profiles were analyzed on a large series of non-small-cell lung cancers (n = 1343). The R 2 correlation between expected and measured allelic ratio, using commercial samples, was >0.96. Mutation detection threshold was 2% for 10 ng of DNA input. κ Scores for TaqMan versus NGS were 0.99 (95% CI, 0.97-1.00) for EGFR and 0.98 (95% CI, 0.97-1.00) for KRAS after exclusion of rare EGFR (n = 40) and KRAS (n = 60) mutations. NGS identified 693 and 292 mutations in validated and potential oncogenic drivers, respectively. Significant associations were found between EGFR and PI3KCA or CTNNB1 and between KRAS and STK11. Potential oncogenic driver mutations or gene amplifications were more frequent in validated oncogenic driver nonmutated samples. This work is a proof of concept that targeted NGS is accessible in routine screening, including large screening, at reasonable cost. Clinical data should be collected and implemented in specific databases to make molecular data meaningful for direct patients' benefit. Copyright © 2018. Published by Elsevier Inc.

[Considering the role of the PCR method in routine diagnosis of toxoplasmosis in peripheral blood tests in immunocompetent patients].

PubMed

Cermáková, Zuzana; Prásil, Petr; Valenta, Zbynek; Förstl, Miroslav; Plísková, Lenka; Bolehovská, Radka

2009-08-01

Infections caused by pathogenic protozoan Toxoplasma gondii in our geographic area is the most frequent parasitic infection; Czech Republic declares seroprevalence approx. 30 %. Diagnosis of toxoplasmosis is mostly based on serological methods are used (EIA IgM, IgA, IgE, IgG and avidity in IgG, Western Blot, complement fixation). According to positive results of these tests diagnosis of acute toxoplasmosis is established. In our retrospective study we tried to evaluate results of T. gondii DNA positivity from blood samples by PCR compared with positive markers of acute infection in patients before specific therapy was initiated. In accordance with literature we concluded, that in routine examination of immunocompetent outpatients of Clinic of Infectious Diseases from the moment of 4 weeks after lymphatic nodes swelling protozoan DNA detection in blood sample is not possible.

Systematic Reviews Published in Emergency Medicine Journals Do Not Routinely Search Clinical Trials Registries: A Cross-Sectional Analysis.

PubMed

Keil, Lukas G; Platts-Mills, Timothy F; Jones, Christopher W

2015-10-01

Publication bias compromises the validity of systematic reviews. This problem can be addressed in part through searching clinical trials registries to identify unpublished studies. This study aims to determine how often systematic reviews published in emergency medicine journals include clinical trials registry searches. We identified all systematic reviews published in the 6 highest-impact emergency medicine journals between January 1 and December 31, 2013. Systematic reviews that assessed the effects of an intervention were further examined to determine whether the authors described searching a clinical trials registry and whether this search identified relevant unpublished studies. Of 191 articles identified through PubMed search, 80 were confirmed to be systematic reviews. Our sample consisted of 41 systematic reviews that assessed a specific intervention. Eight of these 41 (20%) searched a clinical trials registry. For 4 of these 8 reviews, the registry search identified at least 1 relevant unpublished study. Systematic reviews published in emergency medicine journals do not routinely include searches of clinical trials registries. By helping authors identify unpublished trial data, the addition of registry searches may improve the validity of systematic reviews. Copyright © 2014 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

Single molecule targeted sequencing for cancer gene mutation detection.

PubMed

Gao, Yan; Deng, Liwei; Yan, Qin; Gao, Yongqian; Wu, Zengding; Cai, Jinsen; Ji, Daorui; Li, Gailing; Wu, Ping; Jin, Huan; Zhao, Luyang; Liu, Song; Ge, Liangjin; Deem, Michael W; He, Jiankui

2016-05-19

With the rapid decline in cost of sequencing, it is now affordable to examine multiple genes in a single disease-targeted clinical test using next generation sequencing. Current targeted sequencing methods require a separate step of targeted capture enrichment during sample preparation before sequencing. Although there are fast sample preparation methods available in market, the library preparation process is still relatively complicated for physicians to use routinely. Here, we introduced an amplification-free Single Molecule Targeted Sequencing (SMTS) technology, which combined targeted capture and sequencing in one step. We demonstrated that this technology can detect low-frequency mutations using artificially synthesized DNA sample. SMTS has several potential advantages, including simple sample preparation thus no biases and errors are introduced by PCR reaction. SMTS has the potential to be an easy and quick sequencing technology for clinical diagnosis such as cancer gene mutation detection, infectious disease detection, inherited condition screening and noninvasive prenatal diagnosis.

South African families raising children with autism spectrum disorders: relationship between family routines, cognitive appraisal and family quality of life.

PubMed

Schlebusch, L; Samuels, A E; Dada, S

2016-05-01

The purpose of this study was to investigate the relationship between family routines, cognitive appraisal of the impact of autism spectrum disorders (ASD) on the family and family quality of life (FQOL) in families raising children with ASD in South Africa. A sample of 180 families of young children with ASD who were receiving disability-related services in the Gauteng province of South Africa completed a self-administered survey. Structural equation modelling was used to examine the direct relationship between the regularity of family routines and FQOL, and the mediating effect of cognitive appraisal on this relationship. The results suggested a direct, positive relationship between the regularity of family routines and families' satisfaction with their FQOL. Furthermore, cognitive appraisal of the impact of ASD on the family mediated this relationship in a partial manner. A higher frequency of regular family routines was strongly associated with a higher satisfaction level of FQOL. Also, cognitive appraisal of the impact of ASD acted as a mechanism through which the regularity of family routines influenced FQOL. We discuss the research and clinical implications of these findings. © 2016 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

The place of information and communication technology-mediated consultations in primary care: GPs' perspectives.

PubMed

Hanna, Lisa; May, Carl; Fairhurst, Karen

2012-06-01

New information and communication technologies such as email and text messaging have been shown to be useful in some aspects of primary care service delivery. Little is known about Scottish GPs' attitudes towards the adoption of these technologies as routine consultation tools. To explore GPs' perceptions of the potential place of new non-face-to-face consultation technologies in the routine delivery of primary care; to explore GPs' perceived barriers to the introduction of these technologies and to identify the processes by which GPs feel that new consultation technologies could be incorporated into routine primary care. Qualitative interview study: 20 in-depth semi-structured interviews carried out with maximum variation sample of GPs across Scotland. Whilst the face-to-face consultation was seen as central to much of the clinical and diagnostic work of primary care, many GPs were conditionally willing to consider using new technologies in the future, particularly to carry out administrative or less complex tasks and therefore maximize practice efficiency and patient convenience. Key considerations were access to appropriate training, IT support and medico-legal guidance. GPs are conditionally willing to use new consultation media if clinically appropriate and if medico-legal and technical support is available.

Genetic analysis of milk β-hydroxybutyrate and its association with fat-to-protein ratio, body condition score, clinical ketosis, and displaced abomasum in early first lactation of Canadian Holsteins.

PubMed

Koeck, A; Jamrozik, J; Schenkel, F S; Moore, R K; Lefebvre, D M; Kelton, D F; Miglior, F

2014-11-01

The aim of this study was to estimate genetic parameters for milk β-hydroxybutyrate (BHBA) in early first lactation of Canadian Holstein cows and to examine its genetic association with indicators of energy balance (fat-to-protein ratio and body condition score) and metabolic diseases (clinical ketosis and displaced abomasum). Data for milk BHBA recorded between 5 and 100 d in milk was obtained from Valacta (Sainte-Anne-de-Bellevue, Québec, Canada), the Canadian Dairy Herd Improvement organization responsible for Québec and Atlantic provinces. Test-day milk samples were analyzed by mid-infrared spectrometry using previously developed calibration equations for milk BHBA. Test-day records of fat-to-protein ratio were obtained from the routine milk recording scheme. Body condition score records were available from the routine type classification system. Data on clinical ketosis and displaced abomasum recorded by producers were available from the national dairy cattle health system in Canada. Data were analyzed using linear animal models. Heritability estimates for milk BHBA at different stages of early lactation were between 0.14 and 0.29. Genetic correlations between milk BHBA were higher between adjacent lactation intervals and decreased as intervals were further apart. Correlations between breeding values for milk BHBA and routinely evaluated traits revealed that selection for lower milk BHBA in early lactation would lead to an improvement of several health and fertility traits, including SCS, calving to first service, number of services, first service to conception, and days open. Also, lower milk BHBA was associated with a longer herd life, better conformation, and better feet and legs. A higher genetic merit for milk yield was associated with higher milk BHBA, and, therefore, a greater susceptibility to hyperketonemia. Milk BHBA at the first test-day was moderately genetically correlated with fat-to-protein ratio (0.49), body condition score (-0.35), and clinical ketosis (0.48), whereas the genetic correlation with displaced abomasum was near zero (0.07). Milk BHBA can be routinely analyzed in milk samples at test days, and, therefore, provides a practical tool for breeding cows less susceptible to hyperketonemia. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Are patients open to elective re-sampling of their glioblastoma? A new way of assessing treatment innovations.

PubMed

Mir, Taskia; Dirks, Peter; Mason, Warren P; Bernstein, Mark

2014-10-01

This is a qualitative study designed to examine patient acceptability of re-sampling surgery for glioblastoma multiforme (GBM) electively post-therapy or at asymptomatic relapse. Thirty patients were selected using the convenience sampling method and interviewed. Patients were presented with hypothetical scenarios including a scenario in which the surgery was offered to them routinely and a scenario in which the surgery was in a clinical trial. The results of the study suggest that about two thirds of the patients offered the surgery on a routine basis would be interested, and half of the patients would agree to the surgery as part of a clinical trial. Several overarching themes emerged, some of which include: patients expressed ethical concerns about offering financial incentives or compensation to the patients or surgeons involved in the study; patients were concerned about appropriate communication and full disclosure about the procedures involved, the legalities of tumor ownership and the use of the tumor post-surgery; patients may feel alone or vulnerable when they are approached about the surgery; patients and their families expressed immense trust in their surgeon and indicated that this trust is a major determinant of their agreeing to surgery. The overall positive response to re-sampling surgery suggests that this procedure, if designed with all the ethical concerns attended to, would be welcomed by most patients. This approach of asking patients beforehand if a treatment innovation is acceptable would appear to be more practical and ethically desirable than previous practice.

Prevalence of human herpes virus types 1-7 in the semen of men attending an infertility clinic and correlation with semen parameters.

PubMed

Neofytou, Eirini; Sourvinos, George; Asmarianaki, Maria; Spandidos, Demetrios A; Makrigiannakis, Antonios

2009-06-01

To determine the prevalence of herpes viruses in the semen of an asymptomatic male cohort with and without infertility problems and its association with altered semen parameters. A prospective randomized study. Medical school and IVF clinic. One hundred seventy-two male patients undergoing routine semen analysis: 80 with normal semen parameters (control group) and 92 with abnormal semen parameters. Semen samples were collected by masturbation. The DNA from the Herpesviridae family (herpes simplex virus 1 [HSV-1], herpes simplex virus 2 [HSV-2], Varicella zoster virus [VZV], Epstein-Barr virus [EBV], cytomegalovirus [CMV], human herpes virus type 6 [HHV-6], human herpes virus type 7 [HHV-7]) and routine semen parameters. Viral DNA was detected in 143/172 (83.1%) of the total samples for at least one herpes virus: HSV-1, 2.5%; VZV, 1.2%; EBV, 45%; CMV, 62.5%; HHV-6, 70%; HHV-7, 0% in the normal semen samples and HSV-1, 2.1%; VZV, 3.2%; EBV, 39.1%; CMV, 56.5%; HHV-6, 66.3%; HHV-7, 0% in the abnormal semen samples. No association was found between the presence of viral DNA and semen parameters. Interestingly, a statistical significance between leukocytospermia and the presence of EBV DNA was observed. The DNA of herpes viruses is frequently detected in the semen of asymptomatic fertile and infertile male patients. Further studies are required to investigate the role of herpes viruses in male factor infertility.

Porous Silicon Antibody Microarrays for Quantitative Analysis: Measurement of Free and Total PSA in Clinical Plasma Samples

PubMed Central

Tojo, Axel; Malm, Johan; Marko-Varga, György; Lilja, Hans; Laurell, Thomas

2014-01-01

The antibody microarrays have become widespread, but their use for quantitative analyses in clinical samples has not yet been established. We investigated an immunoassay based on nanoporous silicon antibody microarrays for quantification of total prostate-specific-antigen (PSA) in 80 clinical plasma samples, and provide quantitative data from a duplex microarray assay that simultaneously quantifies free and total PSA in plasma. To further develop the assay the porous silicon chips was placed into a standard 96-well microtiter plate for higher throughput analysis. The samples analyzed by this quantitative microarray were 80 plasma samples obtained from men undergoing clinical PSA testing (dynamic range: 0.14-44ng/ml, LOD: 0.14ng/ml). The second dataset, measuring free PSA (dynamic range: 0.40-74.9ng/ml, LOD: 0.47ng/ml) and total PSA (dynamic range: 0.87-295ng/ml, LOD: 0.76ng/ml), was also obtained from the clinical routine. The reference for the quantification was a commercially available assay, the ProStatus PSA Free/Total DELFIA. In an analysis of 80 plasma samples the microarray platform performs well across the range of total PSA levels. This assay might have the potential to substitute for the large-scale microtiter plate format in diagnostic applications. The duplex assay paves the way for a future quantitative multiplex assay, which analyses several prostate cancer biomarkers simultaneously. PMID:22921878

Collection fluid helps preservation in voided urine cytology.

PubMed

Raistrick, J; Shambayati, B; Dunsmuir, W

2008-04-01

Degenerative change caused by delay in processing contributes to false-negative and false-positive diagnosis of urothelial carcinoma in cytology. The aim of the study was to see if the use of a collection fluid for urine samples made a significant difference to urine cytology diagnosis, and if one was better suited for routine use in the hospital laboratory. Three cell collection fluids were evaluated by analysing the preservation and degeneration of cells in urine samples, as was the routine preparation which did not use a collection fluid. In the design study 50 voided urine specimens were taken at random from the hospital haematuria clinic. Three commercially available collection fluids cytolyt, cytospin and cytoRich Blue and the hospital's routine conventional preparation of urine were compared. The degree of degeneration, and so preservation, was assessed by a table of chosen criteria; then ranked and analysed by Friedman's nonparametric test, at P = 0.05. A second table showing the cell content of each slide was also made. These showed no significant diagnostic difference between the collection fluids, but there was a significant difference between the collection fluids and the routine preparation. Minor differences that do not affect diagnosis, such as crystals and ghost red blood cells, were noted in cytospin and cytoRich Blue. It is recommended that a collection fluid is used. This choice should be made after health and safety issues and cost are considered.

Innovative electrochemical approach for an early detection of microRNAs.

PubMed

Lusi, E A; Passamano, M; Guarascio, P; Scarpa, A; Schiavo, L

2009-04-01

The recent findings of circulating cell-free tissue specific microRNAs in the systemic circulation and the potential of their use as specific markers of disease highlight the need to make microRNAs testing a routine part of medical care. At the present time, microRNAs are detected by long and laborious techniques such as Northern blot, RT-PCR, and microarrays. The originality of our work consists in performing microRNAs detection through an electrochemical genosensor using a label-free method. We were able to directly detect microRNAs without the need of PCR and a labeling reaction. The test is simple, very fast and ultrasensitive, with a detection limit of 0.1 pmol. Particularly feasible for a routine microRNAs detection in serum and other biological samples, our technical approach would be of great scientific value and become a common method for simple miRNAs routine detection in both clinical and research settings.

Plasma myelin basic protein assay using Gilford enzyme immunoassay cuvettes.

PubMed

Groome, N P

1981-10-01

The assay of myelin basic protein in body fluids has potential clinical importance as a routine indicator of demyelination. Preliminary details of a competitive enzyme immunoassay for this protein have previously been published by the author (Groome, N. P. (1980) J. Neurochem. 35, 1409-1417). The present paper now describes the adaptation of this assay for use on human plasma and various aspects of routine data processing. A commercially available cuvette system was found to have advantages over microtitre plates but required a permuted arrangement of sample replicates for consistent results. For dose interpolation, the standard curve could be fitted to a three parameter non-linear equation by regression analysis or linearised by the logit/log transformation.

Non-invasive assessment of liver fibrosis

PubMed Central

Papastergiou, Vasilios; Tsochatzis, Emmanuel; Burroughs, Andrew K.

2012-01-01

The presence and degree of hepatic fibrosis is crucial in order to make therapeutic decisions and predict clinical outcomes. Currently, the place of liver biopsy as the standard of reference for assessing liver fibrosis has been challenged by the increasing awareness of a number of drawbacks related to its use (invasiveness, sampling error, inter-/intraobserver variability). In parallel with this, noninvasive assessment of liver fibrosis has experienced explosive growth in recent years and a wide spectrum of noninvasive methods ranging from serum assays to imaging techniques have been developed. Some are validated methods, such as the Fibrotest/ Fibrosure and transient elastography in Europe, and are gaining a growing role in routine clinical practice, especially in chronic hepatitis C. Large-scale validation is awaited in the setting of other chronic liver diseases. However, noninvasive tests used to detect significant fibrosis and cirrhosis, the two major clinical endpoints, are not yet at a level of performance suitable for routine diagnostic tests, and there is still no perfect surrogate or method able to completely replace an optimal liver biopsy. This article aims to review current noninvasive tests for the assessment of liver fibrosis and the perspectives for their rational use in clinical practice. PMID:24714123

Routine health insurance data for scientific research: potential and limitations of the Agis Health Database.

PubMed

Smeets, Hugo M; de Wit, Niek J; Hoes, Arno W

2011-04-01

Observational studies performed within routine health care databases have the advantage of their large size and, when the aim is to assess the effect of interventions, can offer a completion to randomized controlled trials with usually small samples from experimental situations. Institutional Health Insurance Databases (HIDs) are attractive for research because of their large size, their longitudinal perspective, and their practice-based information. As they are based on financial reimbursement, the information is generally reliable. The database of one of the major insurance companies in the Netherlands, the Agis Health Database (AHD), is described in detail. Whether the AHD data sets meet the specific requirements to conduct several types of clinical studies is discussed according to the classification of the four different types of clinical research; that is, diagnostic, etiologic, prognostic, and intervention research. The potential of the AHD for these various types of research is illustrated using examples of studies recently conducted in the AHD. HIDs such as the AHD offer large potential for several types of clinical research, in particular etiologic and intervention studies, but at present the lack of detailed clinical information is an important limitation. Copyright © 2011 Elsevier Inc. All rights reserved.

The Validity of a New Structured Assessment of Gastrointestinal Symptoms Scale (SAGIS) for Evaluating Symptoms in the Clinical Setting.

PubMed

Koloski, N A; Jones, M; Hammer, J; von Wulffen, M; Shah, A; Hoelz, H; Kutyla, M; Burger, D; Martin, N; Gurusamy, S R; Talley, N J; Holtmann, G

2017-08-01

The clinical assessments of patients with gastrointestinal symptoms can be time-consuming, and the symptoms captured during the consultation may be influenced by a variety of patient and non-patient factors. To facilitate standardized symptom assessment in the routine clinical setting, we developed the Structured Assessment of Gastrointestinal Symptom (SAGIS) instrument to precisely characterize symptoms in a routine clinical setting. We aimed to validate SAGIS including its reliability, construct and discriminant validity, and utility in the clinical setting. Development of the SAGIS consisted of initial interviews with patients referred for the diagnostic work-up of digestive symptoms and relevant complaints identified. The final instrument consisted of 22 items as well as questions on extra intestinal symptoms and was given to 1120 consecutive patients attending a gastroenterology clinic randomly split into derivation (n = 596) and validation datasets (n = 551). Discriminant validity along with test-retest reliability was assessed. The time taken to perform a clinical assessment with and without the SAGIS was recorded along with doctor satisfaction with this tool. Exploratory factor analysis conducted on the derivation sample suggested five symptom constructs labeled as abdominal pain/discomfort (seven items), gastroesophageal reflux disease/regurgitation symptoms (four items), nausea/vomiting (three items), diarrhea/incontinence (five items), and difficult defecation and constipation (2 items). Confirmatory factor analysis conducted on the validation sample supported the initially developed five-factor measurement model ([Formula: see text], p < 0.0001, χ 2 /df = 4.6, CFI = 0.90, TLI = 0.88, RMSEA = 0.08). All symptom groups demonstrated differentiation between disease groups. The SAGIS was shown to be reliable over time and resulted in a 38% reduction of the time required for clinical assessment. The SAGIS instrument has excellent psychometric properties and supports the clinical assessment of and symptom-based categorization of patients with a wide spectrum of gastrointestinal symptoms.

Clinical utility of an automated instrument for gram staining single slides.

PubMed

Baron, Ellen Jo; Mix, Samantha; Moradi, Wais

2010-06-01

Gram stains of 87 different clinical samples were prepared by the laboratory's conventional methods (automated or manual) and by a new single-slide-type automated staining instrument, GG&B AGS-1000. Gram stains from either heat- or methanol-fixed slides stained with the new instrument were easy to interpret, and results were essentially the same as those from the methanol-fixed slides prepared as a part of the routine workflow. This instrument is well suited to a rapid-response laboratory where Gram stain requests are commonly received on a stat basis.

Laboratory diagnosis of gestational diabetes: An in silico investigation into the effects of pre-analytical processing on the diagnostic sensitivity and specificity of the oral glucose tolerance test.

PubMed

Mansell, Erin; Lunt, Helen; Docherty, Paul

2017-06-01

Delayed separation of red cells from plasma causes pre analytical glucose loss, which in turn results in an under-diagnosis of GDM (gestational diabetes) based on the OGTT (oral glucose tolerance test). In silico investigations may help laboratory decision making, when exploring pragmatic improvements to sample processing. Late pregnancy 0, 1 and 2h 75g OGTT values were obtained from two distinct populations of pregnant women: 1. Values derived from the HAPO (Hyperglycemia and Adverse Pregnancy Outcome) Study and 2. New Zealand women identified as at higher risk of GDM by their caregivers, undergoing OGTT during routine antenatal care. In both populations studied, in silico modelling focussed on the effects of pre-analytical delays in plasma separation, when using fluoride collection tubes. Using a model that 'batched' samples from the three OGTT collection times, diagnostic sensitivity was estimated as follows: 66.1% for HAPO research population and 48.4% for the 1305 women receiving routine antenatal care. If samples were not batched, but processed shortly after each blood sample was collected, then sensitivity increased to 81%. Exploration of a range of clinical and laboratory scenarios using in silico modelling, showed that delaying the processing of pregnancy OGTT samples, using batched sample collection into fluoride tubes, causes unacceptable loss of GDM diagnostic sensitivity across two distinct population groups. This modelling approach will hopefully provide information that helps with final decision making around improved laboratory processing techniques. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Children and adolescents referred for treatment of anxiety disorders: differences in clinical characteristics.

PubMed

Waite, Polly; Creswell, Cathy

2014-01-01

Reports of the clinical characteristics of children and adolescents with anxiety disorders are typically based on community populations or from clinical samples with exclusion criterion applied. Little is known about the clinical characteristics of children and adolescents routinely referred for treatment for anxiety disorders. Furthermore, children and adolescents are typically treated as one homogeneous group although they may differ in ways that are clinically meaningful. A consecutive series of children (n=100, aged 6-12 years) and adolescents (n=100, aged 13-18 years), referred to a routine clinical service, were assessed for anxiety and comorbid disorders, school refusal and parental symptoms of psychopathology. Children with a primary anxiety disorder were significantly more likely to be diagnosed with separation anxiety disorder than adolescents. Adolescents with a primary anxiety disorder had significantly higher self and clinician rated anxiety symptoms and had more frequent primary diagnoses of social anxiety disorder, diagnoses and symptoms of mood disorders, and irregular school attendance. Childhood and adolescence were considered categorically as distinct, developmental periods; in reality changes would be unlikely to occur in such a discrete manner. The finding that children and adolescents with anxiety disorders have distinct clinical characteristics has clear implications for treatment. Simply adapting treatments designed for children to make the materials more 'adolescent-friendly' is unlikely to sufficiently meet the needs of adolescents. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: intact cell vs. extraction method.

PubMed

Ferreira, L; Sánchez-Juanes, F; Muñoz-Bellido, J L; González-Buitrago, J M

2011-07-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a fast and reliable technology for the identification of microorganisms with proteomics approaches. Here, we compare an intact cell method and a protein extraction method before application on the MALDI plate for the direct identification of microorganisms in both urine and blood culture samples from clinical microbiology laboratories. The results show that the intact cell method provides excellent results for urine and is a good initial method for blood cultures. The extraction method complements the intact cell method, improving microorganism identification from blood culture. Thus, we consider that MALDI-TOF MS performed directly on urine and blood culture samples, with the protocols that we propose, is a suitable technique for microorganism identification, as compared with the routine methods used in the clinical microbiology laboratory. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Detection and genotyping of rubella virus from exanthematous patients suspected of having measles using reverse transcription-PCR.

PubMed

Yasui, Yoshihiro; Mori, Yoshio; Adachi, Hirokazu; Kobayashi, Shinichi; Yamashita, Teruo; Minagawa, Hiroko

2014-01-01

Between July 2012 and March 2013, a total of 133 clinical specimens from 47 patients suspected of having measles were collected for virological surveillance in Aichi Prefecture, Japan. Facing the rubella epidemic, the reverse transcription (RT)-PCR protocol for measles virus (MeV) was modified to simultaneously detect rubella virus (RUBV) in these clinical specimens. As a result, 30 specimens from 15 patients were positive for RUBV and 8 specimens from 3 patients were positive for MeV. The RUBV genotype analysis for the samples from 13 patients revealed 12 samples as 2B and 1 sample as 1E. The results provided additional evidence for the difficulty in the diagnosis of exanthematous diseases based on clinical manifestations alone and the necessity of virological diagnosis to maintain the accuracy of case-based surveillance. Furthermore, the results indicated that the modified RT-PCR protocol could be useful as a routine procedure to simultaneously detect MeV and RUBV in clinical specimens of patients suspected of having exanthematous disease caused by these viruses.

Nano-plasmonic exosome diagnostics

PubMed Central

Im, Hyungsoon; Shao, Huilin; Weissleder, Ralph; Castro, Cesar M.; Lee, Hakho

2015-01-01

Exosomes have emerged as a promising biomarker. These vesicles abound in biofluids and harbor molecular constituents from their parent cells, thereby offering a minimally-invasive avenue for molecular analyses. Despite such clinical potential, routine exosomal analysis, particularly the protein assay, remains challenging, due to requirements for large sample volumes and extensive processing. We have been developing miniaturized systems to facilitate clinical exosome studies. These systems can be categorized into two components: microfluidics for sample preparation and analytical tools for protein analyses. In this report, we review a new assay platform, nano-plasmonic exosome (nPLEX), in which sensing is based on surface plasmon resonance to achieve label-free exosome detection. Looking forward, we also discuss some potential challenges and improvements in exosome studies. PMID:25936957

The Clinical Ethnographic Interview: A user-friendly guide to the cultural formulation of distress and help seeking

PubMed Central

Arnault, Denise Saint; Shimabukuro, Shizuka

2013-01-01

Transcultural nursing, psychiatry, and medical anthropology have theorized that practitioners and researchers need more flexible instruments to gather culturally relevant illness experience, meaning, and help seeking. The state of the science is sufficiently developed to allow standardized yet ethnographically sound protocols for assessment. However, vigorous calls for culturally adapted assessment models have yielded little real change in routine practice. This paper describes the conversion of the Diagnostic and Statistical Manual IV, Appendix I Outline for Cultural Formulation into a user-friendly Clinical Ethnographic Interview (CEI), and provides clinical examples of its use in a sample of highly distressed Japanese women. PMID:22194348

Limited utility of routine surveillance imaging for classical Hodgkin lymphoma patients in first complete remission.

PubMed

Pingali, Sai Ravi; Jewell, Sarah W; Havlat, Luiza; Bast, Martin A; Thompson, Jonathan R; Eastwood, Daniel C; Bartlett, Nancy L; Armitage, James O; Wagner-Johnston, Nina D; Vose, Julie M; Fenske, Timothy S

2014-07-15

The objective of this study was to compare the outcomes of patients with classical Hodgkin lymphoma (cHL) who achieved complete remission with frontline therapy and then underwent either clinical surveillance or routine surveillance imaging. In total, 241 patients who were newly diagnosed with cHL between January 2000 and December 2010 at 3 participating tertiary care centers and achieved complete remission after first-line therapy were retrospectively analyzed. Of these, there were 174 patients in the routine surveillance imaging group and 67 patients in the clinical surveillance group, based on the intended mode of surveillance. In the routine surveillance imaging group, the intended plan of surveillance included computed tomography and/or positron emission tomography scans; whereas, in the clinical surveillance group, the intended plan of surveillance was clinical examination and laboratory studies, and scans were obtained only to evaluate concerning signs or symptoms. Baseline patient characteristics, prognostic features, treatment records, and outcomes were collected. The primary objective was to compare overall survival for patients in both groups. For secondary objectives, we compared the success of second-line therapy and estimated the costs of imaging for each group. After 5 years of follow-up, the overall survival rate was 97% (95% confidence interval, 92%-99%) in the routine surveillance imaging group and 96% (95% confidence interval, 87%-99%) in the clinical surveillance group (P = .41). There were few relapses in each group, and all patients who relapsed in both groups achieved complete remission with second-line therapy. The charges associated with routine surveillance imaging were significantly higher than those for the clinical surveillance strategy, with no apparent clinical benefit. Clinical surveillance was not inferior to routine surveillance imaging in patients with cHL who achieved complete remission with frontline therapy. Routine surveillance imaging was associated with significantly increased estimated imaging charges. © 2014 American Cancer Society.

Comparative antibiogram of coagulase-negative Staphylococci (CNS) associated with subclinical and clinical mastitis in dairy cows.

PubMed

Bansal, B K; Gupta, D K; Shafi, T A; Sharma, S

2015-03-01

The present study was planned to determine the in vitro antibiotic susceptibility of coagulase-negative Staphylococci (CNS) strains isolated from clinical and subclinical cases of mastitis in dairy cows. Antibiotic sensitivity profile will be helpful to recommend early therapy at the field level prior to availability of CST results. The milk samples from cases of clinical mastitis received in Mastitis Laboratory, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana and those of subclinical mastitis collected during routine screening of state dairy farms, were subjected to microbial culture. Identification of CNS organisms was done by standard biochemical tests. Antibiotic sensitivity testing, based on 30 antibiotics belonging to 12 groups, was done on 58 randomly selected CNS isolates (clinical isolates: 41, subclinical isolates: 17). Isolates were highly susceptible to chloramphenicol (98.3%), gentamicin (93.1%), streptomycin (91.4%), linezolid (91.4%), ceftixozime (87.9%), cloxacillin (86.2%), clotrimazole (86.2%), bacitracin (86.2%), enrofloxacin (84.5%) and ceftrioxone + tazobactum (70.7%), while resistance was observed against amoxicillin (77.6%), penicillin (75.9%), ampicillin (74.1%) and cefoperazone (51.7%). Overall, isolates from clinical cases of mastitis had a higher resistance than subclinical isolates. CNS isolates were susceptible to chloramphenicol, gentamicin and streptomycin, while higher resistance was recorded against routinely used penicillin group.

The Genetic Counseling Video Project (GCVP): models of practice.

PubMed

Roter, D; Ellington, L; Erby, L Hamby; Larson, S; Dudley, W

2006-11-15

Genetic counseling is conceptualized as having both "teaching" and "counseling" functions; however, little is known about how these functions are articulated in routine practice. This study addresses the question by documenting, on videotape, the practices of a national sample of prenatal and cancer genetic counselors (GCs) providing routine pre-test counseling to simulated clients (SCs). One hundred and seventy-seven GCs recruited at two annual conferences of the National Society of Genetic Counselors (NSGC) were randomly assigned to counsel one of six female SCs of varying ethnicity, with or without a spouse, in their specialty. One hundred and fifty-two videotapes were coded with the Roter Interaction Analysis System (RIAS) and both GCs and SCs completed evaluative questionnaires. Two teaching and two counseling patterns of practice emerged from cluster analysis. The teaching patterns included: (1) clinical teaching (31%) characterized by low psychosocial, emotional and facilitative talk, high levels of clinical exchange, and high verbal dominance; and (2) psycho-educational teaching (27%) characterized by high levels of both clinical and psychosocial exchange, low levels of emotional and facilitative talk, and higher verbal dominance. The counseling patterns included: (1) supportive counseling (33%) characterized by low psychosocial and clinical exchange, high levels of emotional and facilitative talk, and low verbal dominance; and (2) psychosocial counseling (9%) with high emotional and facilitative talk, low clinical and high psychosocial exchange, and the lowest verbal dominance. SCs ratings of satisfaction with communication, the counselor's affective demeanor, and the counselor's use of non-verbal skills were highest for the counseling model sessions. Both the teaching and counseling models seem to be represented in routine practice and predict variation in client satisfaction, affective demeanor, and nonverbal effectiveness. (c) 2006 Wiley-Liss, Inc.

Continuous blood pressure monitoring via non-invasive radial artery applanation tonometry and invasive arterial catheter demonstrates good agreement in patients undergoing colon carcinoma surgery.

PubMed

Sun, Jing; Chen, Hanjian; Zheng, Jun; Mao, Bin; Zhu, Shengmei; Feng, Jingyi

2017-12-01

Radial artery applanation tonometry (RAAT) has been developed and utilized for continuous arterial pressure monitoring. However, evidence is lacking to clinically verify the RAAT technology and identify appropriate patient groups before routine clinical use. This study aims to evaluate the RAAT technology by comparing systolic blood pressure (SBP), mean blood pressure (MBP) and diastolic blood pressure (DBP) values in patients undergoing colon carcinoma surgery. Blood Pressure (BP) values obtained via RAAT (TL-300, Tensys Medical Inc., San Diego, CA, USA) and conventional arterial catheterization from 30 colon carcinoma surgical patients were collected and compared via Bland-Atman method, linear regression and 4-quadrant plot concordance analysis. For SBPs, MBPs and DBPs, means of the differences (±standard deviation; 95% limits of agreement) were -0.9 (±7.6; -15.7 to 13.9) mmHg, 3.1 (±6.5; -9.6 to 15.8) mmHg and 4.3 (±7.4; -10.3 to 18.8) mmHg, respectively. Linear regression coefficients of determination were 0.8706 for SBPs, 0.8353 for MBPs and 0.6858 for DBPs. Four-quadrant concordance correlation coefficients were 0.8740, 0.8522 and 0.7108 for SBPs, MBPs and DBPs, respectively. A highly selected patient collective undergoing colon carcinoma surgery was studied. BP measurements obtained via the TL-300 had clinically acceptable agreement with that acquired invasively using an arterial catheter. For use in clinical routine, it is necessary to take measures for improvement regarding movement artifacts and dilution of noise. A large sample size of patients under various conditions is also needed to further evaluate the RAAT technology before clinically routine use.

Preanalytical management: serum vacuum tubes validation for routine clinical chemistry.

PubMed

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Picheth, Geraldo; Guidi, Gian Cesare

2012-01-01

The validation process is essential in accredited clinical laboratories. Aim of this study was to validate five kinds of serum vacuum tubes for routine clinical chemistry laboratory testing. Blood specimens from 100 volunteers in five different serum vacuum tubes (Tube I: VACUETTE, Tube II: LABOR IMPORT, Tube III: S-Monovette, Tube IV: SST and Tube V: SST II) were collected by a single, expert phlebotomist. The routine clinical chemistry tests were analyzed on cobas 6000 module. The significance of the differences between samples was assessed by paired Student's t-test after checking for normality. The level of statistical significance was set at P < 0.005. Finally, the biases from Tube I, Tube II, Tube III, Tube IV and Tube V were compared with the current desirable quality specifications for bias (B), derived from biological variation. Basically, our validation will permit the laboratory or hospital managers to select the brand's vacuum tubes validated according him/her technical or economical reasons, in order to perform the following laboratory tests: glucose, total cholesterol, high density lipoprotein-cholesterol, triglycerides, total protein, albumin, blood urea nitrogen, uric acid, alkaline phosphatise, aspartate aminotransferase, gamma-glutamyltransferase, lactate dehydrogenase, creatine kinase, total bilirubin, direct bilirubin, calcium, iron, sodium and potassium. On the contrary special attention will be required if the laboratory already performs creatinine, amylase, phosphate and magnesium determinations and the quality laboratory manager intend to change the serum tubes. We suggest that laboratory management should both standardize the procedures and frequently evaluate the quality of in vitro diagnostic devices.

Preanalytical management: serum vacuum tubes validation for routine clinical chemistry

PubMed Central

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Picheth, Geraldo; Guidi, Gian Cesare

2012-01-01

Introduction The validation process is essential in accredited clinical laboratories. Aim of this study was to validate five kinds of serum vacuum tubes for routine clinical chemistry laboratory testing. Materials and methods: Blood specimens from 100 volunteers in five diff erent serum vacuum tubes (Tube I: VACUETTE®, Tube II: LABOR IMPORT®, Tube III: S-Monovette®, Tube IV: SST® and Tube V: SST II®) were collected by a single, expert phlebotomist. The routine clinical chemistry tests were analyzed on cobas® 6000 module. The significance of the diff erences between samples was assessed by paired Student’s t-test after checking for normality. The level of statistical significance was set at P < 0.005. Finally, the biases from Tube I, Tube II, Tube III, Tube IV and Tube V were compared with the current desirable quality specifications for bias (B), derived from biological variation. Results and conclusions: Basically, our validation will permit the laboratory or hospital managers to select the brand’s vacuum tubes validated according him/her technical or economical reasons, in order to perform the following laboratory tests: glucose, total cholesterol, high density lipoprotein-cholesterol, triglycerides, total protein, albumin, blood urea nitrogen, uric acid, alkaline phosphatise, aspartate aminotransferase, gamma-glutamyltransferase, lactate dehydrogenase, creatine kinase, total bilirubin, direct bilirubin, calcium, iron, sodium and potassium. On the contrary special attention will be required if the laboratory already performs creatinine, amylase, phosphate and magnesium determinations and the quality laboratory manager intend to change the serum tubes. We suggest that laboratory management should both standardize the procedures and frequently evaluate the quality of in vitro diagnostic devices. PMID:22838184

Validation of the Complexity INdex in SARComas prognostic signature on formalin-fixed, paraffin-embedded, soft tissue sarcomas.

PubMed

Le Guellec, S; Lesluyes, T; Sarot, E; Valle, C; Filleron, T; Rochaix, P; Valentin, T; Pérot, G; Coindre, J-M; Chibon, F

2018-05-31

Prediction of metastatic outcome in sarcomas is challenging for clinical management since they are aggressive and carry a high metastatic risk. A 67-gene expression signature, the Complexity INdex in SARComas (CINSARC), has been identified as a better prognostic factor than the reference pathological grade. Since it cannot be applied easily in standard laboratory practice, we assessed its prognostic value using nanoString on formalin-fixed, paraffin-embedded (FFPE) blocks to evaluate its potential in clinical routine practice and guided therapeutic management. A code set consisting of 67 probes derived from the 67 genes of the CINSARC signature was built and named NanoCind®. To compare the performance of RNA-seq and nanoString (NanoCind®), we used expressions of various sarcomas (n=124, frozen samples) using both techniques and compared predictive values based on CINSARC risk groups and clinical annotations. We also used nanoString on FFPE blocks (n=67) and matching frozen and FFPE samples (n=45) to compare their level of agreement. Metastasis-free survival and agreement values in classification groups were evaluated. CINSARC strongly predicted metastatic outcome using nanoString on frozen samples (HR = 2.9, 95% CI 1.23-6.82) with similar risk-group classifications (86%). While more than 50% of FFPE blocks were not analyzable by RNA-seq owing to poor RNA quality, all samples were analyzable with nanoString. When similar (risk-group) classifications were measured with frozen tumors (RNA-seq) compared to FFPE blocks (84% agreement), the CINSARC signature was still a predictive factor of metastatic outcome with nanoString on FFPE samples (HR = 4.43, 95% CI 1.25-15.72). CINSARC is a material-independent prognostic signature for metastatic outcome in sarcomas and outperforms histological grade. Unlike RNA-seq, nanoString is not influenced by the poor quality of RNA extracted from FFPE blocks. The CINSARC signature can potentially be used in combination with nanoString (NanoCind®) in routine clinical practice on FFPE blocks to predict metastatic outcome.

The correlation between the number of eligible patients in routine clinical practice and the low recruitment level in clinical trials: a retrospective study using electronic medical records.

PubMed

Sumi, Eriko; Teramukai, Satoshi; Yamamoto, Keiichi; Satoh, Motohiko; Yamanaka, Kenya; Yokode, Masayuki

2013-12-11

A number of clinical trials have encountered difficulties enrolling a sufficient number of patients upon initiating the trial. Recently, many screening systems that search clinical data warehouses for patients who are eligible for clinical trials have been developed. We aimed to estimate the number of eligible patients using routine electronic medical records (EMRs) and to predict the difficulty of enrolling sufficient patients prior to beginning a trial. Investigator-initiated clinical trials that were conducted at Kyoto University Hospital between July 2004 and January 2011 were included in this study. We searched the EMRs for eligible patients and calculated the eligible EMR patient index by dividing the number of eligible patients in the EMRs by the target sample size. Additionally, we divided the trial eligibility criteria into corresponding data elements in the EMRs to evaluate the completeness of mapping clinical manifestation in trial eligibility criteria into structured data elements in the EMRs. We evaluated the correlation between the index and the accrual achievement with Spearman's rank correlation coefficient. Thirteen of 19 trials did not achieve their original target sample size. Overall, 55% of the trial eligibility criteria were mapped into data elements in EMRs. The accrual achievement demonstrated a significant positive correlation with the eligible EMR patient index (r = 0.67, 95% confidence interval (CI), 0.42 to 0.92). The receiver operating characteristic analysis revealed an eligible EMR patient index cut-off value of 1.7, with a sensitivity of 69.2% and a specificity of 100.0%. Our study suggests that the eligible EMR patient index remains exploratory but could be a useful component of the feasibility study when planning a clinical trial. Establishing a step to check whether there are likely to be a sufficient number of eligible patients enables sponsors and investigators to concentrate their resources and efforts on more achievable trials.

The clinical utility of the Cornell Scale for Depression in Dementia as a routine assessment in nursing homes.

PubMed

Jeon, Yun-Hee; Li, Zhicheng; Low, Lee-Fay; Chenoweth, Lynn; O'Connor, Daniel; Beattie, Elizabeth; Liu, Zhixin; Brodaty, Henry

2015-08-01

To examine the clinical utility of the Cornell Scale for Depression in Dementia (CSDD) in nursing homes. 14 nursing homes in Sydney and Brisbane, Australia. 92 residents with a mean age of 85 years. Consenting residents were assessed by care staff for depression using the CSDD as part of their routine assessment. Specialist clinicians conducted assessment of depression using the Semi-structured Clinical Diagnostic Interview for DSM-IV-TR Axis I Disorders for residents without dementia or the Provisional Diagnostic Criteria for Depression in Alzheimer Disease for residents with dementia to establish expert clinical diagnoses of depression. The diagnostic performance of the staff completed CSDD was analyzed against expert diagnosis using receiver operating characteristic (ROC) curves. The CSDD showed low diagnostic accuracy, with areas under the ROC curve being 0.69, 0.68 and 0.70 for the total sample, residents with dementia and residents without dementia, respectively. At the standard CSDD cutoff score, the sensitivity and specificity were 71% and 59% for the total sample, 69% and 57% for residents with dementia, and 75% and 61% for residents without dementia. The Youden index (for optimizing cut-points) suggested different depression cutoff scores for residents with and without dementia. When administered by nursing home staff the clinical utility of the CSDD is highly questionable in identifying depression. The complexity of the scale, the time required for collecting relevant information, and staff skills and knowledge of assessing depression in older people must be considered when using the CSDD in nursing homes. Copyright © 2015 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

Incorrect diagnosis of Clostridium difficile infection in a university hospital in Japan.

PubMed

Mori, Nobuaki; Yoshizawa, Sadako; Saga, Tomoo; Ishii, Yoshikazu; Murakami, Hinako; Iwata, Morihiro; Collins, Deirdre A; Riley, Thomas V; Tateda, Kazuhiro

2015-10-01

Physicians often fail to suspect Clostridium difficile infection (CDI) and many microbiology laboratories use suboptimal diagnostic techniques. To estimate the extent of and reasons for incorrect diagnosis of CDI in Japan, we investigated toxigenic C. difficile isolated from all stool culture samples and clinical course. Over a 12-month period in 2010, all stool culture samples (n = 975) submitted from inpatients in a university hospital in Japan were cultured for C. difficile and routine microbiological testing was conducted. In total, 177 C. difficile isolates were recovered, and 127 isolates were toxigenic. Among the toxin-A-positive/toxin-B-positive isolates, 12 were also positive for the binary toxin gene. However, clinically important ribotypes, such as 027 and 078, were not identified. A total of 58 (45.7%) cases with toxigenic C. difficile had unformed stool, and the incidence CDI was 1.6 cases per 10,000 patient-days. Of these 58 cases, 40 were not diagnosed in routine testing due to a lack of clinical suspicion (24.1%, 14/58) or a negative C. difficile toxin assay result (44.8%, 26/58). A stool toxin assay was performed in 54 patients (78.2%, 54/69) who did not have unformed stool. The present study demonstrated that a significant number of CDI cases in Japan might be overlooked or misdiagnosed in clinical practice due to a lack of clinical suspicion and limitations of microbiological testing for CDI in Japan. Providing education to promote awareness of CDI among physicians is important to improve the accuracy of diagnosis in Japan. Copyright © 2015 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Three Rounds of External Quality Assessment in France to Evaluate the Performance of 28 Platforms for Multiparametric Molecular Testing in Metastatic Colorectal and Non-Small Cell Lung Cancer.

PubMed

Dequeker, Elisabeth M C; Keppens, Cleo; Egele, Caroline; Delen, Sofie; Lamy, Aude; Lemoine, Antoinette; Sabourin, Jean-Christophe; Andrieu, Catherine; Ligtenberg, Marjolijn; Fetique, Dominique; Tops, Bastiaan; Descarpentries, Clotilde; Blons, Hélène; Denoux, Yves; Aube, Cécile; Penault-Llorca, Frederique; Hofman, Paul; Leroy, Karen; Le Marechal, Cédric; Doucet, Laurent; Duranton-Tanneur, Valérie; Pedeutour, Florence; Soubeyran, Isabelle; Côté, Jean-François; Emile, Jean-François; Vignaud, Jean-Michel; Monhoven, Nathalie; Haddad, Véronique; Laurent-Puig, Pierre; van Krieken, Han; Nowak, Frederique; Lonchamp, Etienne; Bellocq, Jean-Pierre; Rouleau, Etienne

2016-03-01

Personalized medicine has gained increasing importance in clinical oncology, and several clinically important biomarkers are implemented in routine practice. In an effort to guarantee high quality of molecular testing in France, three subsequent external quality assessment rounds were organized at the initiative of the National Cancer Institute between 2012 and 2014. The schemes included clinically relevant biomarkers for metastatic colorectal (KRAS, NRAS, BRAF, PIK3CA, microsatellite instability) and non-small cell lung cancer (EGFR, KRAS, BRAF, PIK3CA, ERBB2), and they represent the first multigene/multicancer studies throughout Europe. In total, 56 laboratories coordinated by 28 regional molecular centers participated in the schemes. Laboratories received formalin-fixed, paraffin-embedded samples and were asked to use routine methods for molecular testing to predict patient response to targeted therapies. They were encouraged to return results within 14 calendar days after sample receipt. Both genotyping and reporting were evaluated separately. During the three external quality assessment rounds, mean genotype scores were all above the preset standard of 90% for all biomarkers. Participants were mainly challenged in case of rare insertions or deletions. Assessment of the written reports showed substantial progress between the external quality assessment schemes on multiple criteria. Several essential elements such as the clinical interpretation of test results and the reason for testing still require improvement by continued external quality assessment education. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Diagnosis of cysticercosis in endemic regions. The Cysticercosis Working Group in Peru.

PubMed

Garcia, H H; Martinez, M; Gilman, R; Herrera, G; Tsang, V C; Pilcher, J B; Diaz, F; Verastegui, M; Gallo, C; Porras, M

1991-08-31

Taenia solium cysticercosis is a frequent cause of neurological disease in developing countries. Specific diagnosis of cysticercosis is difficult. We obtained serum and/or CSF samples from 204 consecutive patients admitted to a neurological ward in Lima, Peru, and looked for antibodies specific for T solium with the enzyme-linked immunoelectrotransfer blot (EITB) assay. 21 (12%) of 173 serum samples from these patients were EITB-positive. In contrast, only 2 (1.5%) of 135 patients attending a public endoscopy clinic and 1 (1%) of 88 patients attending a private endoscopy clinic were seropositive. 1 (1%) of 98 pregnant women living in a Lima shanty town was EITB-positive. 15 (58%) of 26 neurology patients diagnosed clinically as having cysticercosis were seronegative. Routine screening by EITB of all patients with neurological symptoms from areas of endemic cysticercosis would avoid misdiagnosis of this common and treatable disease.

Diagnosis of cysticercosis in endemic regions

PubMed Central

Garcia, H. H.; Martinez, M.; Gilman, R.; Herrera, G.; Tsang, V. C. W.; Pilcher, J. B.; Diaz, F.; Verastegui, M.; Gallo, C.; Porras, M.; Alvarado, M.; Naranjo, J.; Miranda, E.

2010-01-01

Taenia solium cysticercosis is a frequent cause of neurological disease in developing countries. Specific diagnosis of cysticercosis is difficult. We obtained serum and/or CSF samples from 204 consecutive patients admitted to a neurological ward in Lima, Peru, and looked for antibodies specific for T solium with the enzyme-linked immunoelectrotransfer blot (EITB) assay. 21 (12%) of 173 serum samples from these patients were EITB-positive. In contrast only 2 (1·5%) of 135 patients attending a public endoscopy clinic and 1 (1%) of 88 patients attending a private endoscopy clinic were seropositive. 1 (1%) of 98 pregnant women living in a Lima shanty town was EITB-positive. 15 (58%) of 26 neurology patients diagnosed clinically as having cysticercosis were seronegative. Routine screening by EITB of all patients with neurological symptoms from areas of endemic cysticercosis would avoid misdiagnosis of this common and treatable disease. PMID:1678809

Detection of sexually transmitted pathogens in patients with chronic prostatitis/chronic pelvic pain: a prospective clinical study.

PubMed

Papeš, Dino; Pasini, Miram; Jerončić, Ana; Vargović, Martina; Kotarski, Viktor; Markotić, Alemka; Škerk, Višnja

2017-05-01

In <10% of patients with prostatitis syndrome, a causative uropathogenic organism can be detected. It has been shown that certain organisms that cause sexually transmitted infections can also cause chronic bacterial prostatitis, which can be hard to diagnose and treat appropriately because prostatic samples obtained by prostatic massage are not routinely tested to detect them. We conducted a clinical study to determine the prevalence of Chlamydia, mycoplasma, and trichomonas infection in 254 patients that were previously diagnosed and treated for chronic prostatitis/chronic pelvic pain syndrome due to negative urethral swab, urine, and prostate samples. Urethral swabs and standard Meares-Stamey four-glass tests were done. Detailed microbiological analysis was conducted to detect the above organisms. Thirty-five (13.8%) patients had positive expressed prostatic secretions/VB3 samples, of which 22 (10.1%) were sexually transmitted organisms that were not detected on previous tests.

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis.

PubMed

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-05-09

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform's performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.

Stability of 35 biochemical and immunological routine tests after 10 hours storage and transport of human whole blood at 21°C.

PubMed

Henriksen, Linda O; Faber, Nina R; Moller, Mette F; Nexo, Ebba; Hansen, Annebirthe B

2014-10-01

Suitable procedures for transport of blood samples from general practitioners to hospital laboratories are requested. Here we explore routine testing on samples stored and transported as whole blood in lithium-heparin or serum tubes. Blood samples were collected from 106 hospitalized patients, and analyzed on Architect c8000 or Advia Centaur XP for 35 analytes at base line, and after storage and transport of whole blood in lithium-heparin or serum tubes at 21 ± 1°C for 10 h. Bias and imprecision (representing variation from analysis and storage) were calculated from values at baseline and after storage, and differences tested by paired t-tests. Results were compared to goals set by the laboratory. We observed no statistically significant bias and results within the goal for imprecision between baseline samples and 10-h samples for albumin, alkaline phosphatase, antitrypsin, bilirubin, creatinine, free triiodothyronine, γ-glutamyl transferase, haptoglobin, immunoglobulin G, lactate dehydrogenase, prostate specific antigen, total carbon dioxide, and urea. Alanine aminotransferase, amylase, C-reactive protein, calcium, cholesterol, creatine kinase, ferritin, free thyroxine, immunoglobulin A, immunoglobulin M, orosomucoid, sodium, transferrin, and triglycerides met goals for imprecision, though they showed a minor, but statistically significant bias in results after storage. Cobalamin, folate, HDL-cholesterol, iron, phosphate, potassium, thyroid stimulating hormone and urate warranted concern, but only folate and phosphate showed deviations of clinical importance. We conclude that whole blood in lithium-heparin or serum tubes stored for 10 h at 21 ± 1°C, may be used for routine analysis without restrictions for all investigated analytes but folate and phosphate.

Stability and reproducibility of a single-sample urinary C-peptide/creatinine ratio and its correlation with 24-h urinary C-peptide.

PubMed

McDonald, Tim J; Knight, Bridget A; Shields, Beverley M; Bowman, Pamela; Salzmann, Maurice B; Hattersley, Andrew T

2009-11-01

C-peptide measurement in blood or 24-h urine samples provides useful information regarding endogenous insulin secretion, but problems related to the rapid degradation of C-peptide in blood and difficulty of 24-h urine collection have limited widespread routine clinical use of this test. We assessed the feasibility of measuring urinary C-peptide (UCP) with correction for creatinine concentration in single urine samples. We analyzed UCP using a routine electrochemiluminescence immunoassay in samples from 21 healthy volunteers. We investigated the stability of UCP with different preservatives and storage conditions and compared the reproducibility of urinary C-peptide/creatinine ratio (UCPCR) in first- and second-void fasting urines, then assessed correlations with 24-h collections. UCPCR was unchanged at room temperature for 24 h and at 4 degrees C for 72 h even in the absence of preservative. UCPCR collected in boric acid was stable at room temperature for 72 h. UCPCR remained stable after 7 freeze-thaw cycles but decreased with freezer storage time and dropped to 82%-84% of baseline by 90 days at -20 degrees C. Second-void fasting UCPCRs were lower than first-void (median 0.78 vs 1.31, P = 0.0003) and showed less variation (CV 33% vs 52%), as second-void UCPCRs were not influenced by evening food-related insulin secretion. Second-void fasting UCPCR was highly correlated with 24-h UCP (r = 0.8, P = 0.00006). Second-void fasting UCPCR is a reproducible measure that correlates well with 24-h UCP in normal samples. The 3-day stability of UCPCR at room temperature greatly increases its potential clinical utility.

Detection of IDH1 R132H mutation in acute myeloid leukemia by mutation-specific immunohistochemistry.

PubMed

Byers, Richard; Hornick, Jason L; Tholouli, Eleni; Kutok, Jeffery; Rodig, Scott J

2012-01-01

IDH1 mutations are present but are uncommon in acute myeloid leukemia (AML) and although prognostically favorable in gliomas their clinical significance in AML is unclear. Some have associated IDH1 mutations with inferior outcome, whereas others found no association with prognosis. Complicating these analyses is the need to sequence IDH1 from leukemic blasts, which is technically challenging and not yet routine. Mutation-specific antibodies enable robust, cost-effective detection of mutations in routine biopsy samples. Immunohistochemistry for the R132H mutation-specific antibody was performed in a tissue microarray containing 159 cases of AML, detecting the R132H mutation in 7 cases (4.4%). Positivity was associated with intermediate risk cytogenetics. Our results demonstrate an association between the R132H IDH1 mutation and intermediate risk cytogenetics in AML, suggesting that R132H IDH1 mutation may be associated with improved clinical outcome and demonstrate the feasibility of using mutation-specific antibodies to genotype and subclassify AML.

Establishing an EGFR mutation screening service for non-small cell lung cancer - sample quality criteria and candidate histological predictors.

PubMed

Leary, Alexandra F; Castro, David Gonzalez de; Nicholson, Andrew G; Ashley, Sue; Wotherspoon, Andrew; O'Brien, Mary E R; Popat, Sanjay

2012-01-01

EGFR screening requires good quality tissue, sensitivity and turn-around time (TAT). We report our experience of routine screening, describing sample type, TAT, specimen quality (cellularity and DNA yield), histopathological description, mutation result and clinical outcome. Non-small cell lung cancer (NSCLC) sections were screened for EGFR mutations (M+) in exons 18-21. Clinical, pathological and screening outcome data were collected for year 1 of testing. Screening outcome alone was collected for year 2. In year 1, 152 samples were tested, most (72%) were diagnostic. TAT was 4.9 days (95%confidence interval (CI)=4.5-5.5). EGFR-M+ prevalence was 11% and higher (20%) among never-smoking women with adenocarcinomas (ADCs), but 30% of mutations occurred in current/ex-smoking men. EGFR-M+ tumours were non-mucinous ADCs and 100% thyroid transcription factor (TTF1+). No mutations were detected in poorly differentiated NSCLC-not otherwise specified (NOS). There was a trend for improved overall survival (OS) among EGFR-M+ versus EGFR-M- patients (median OS=78 versus 17 months). In year 1, test failure rate was 19%, and associated with scant cellularity and low DNA concentrations. However 75% of samples with poor cellularity but representative of tumour were informative and mutation prevalence was 9%. In year 2, 755 samples were tested; mutation prevalence was 13% and test failure only 5.4%. Although samples with low DNA concentration (<2 ng/μL) had more test failures (30% versus 3.9% for [DNA]>2.2 ng/μL), the mutation rate was 9.2%. Routine epidermal growth factor receptor (EGFR) screening using diagnostic samples is fast and feasible even on samples with poor cellularity and DNA content. Mutations tend to occur in better-differentiated non-mucinous TTF1+ ADCs. Whether these histological criteria may be useful to select patients for EGFR testing merits further investigation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Computer-based intervention in HIV clinical care setting improves antiretroviral adherence: the LifeWindows Project.

PubMed

Fisher, Jeffrey D; Amico, K Rivet; Fisher, William A; Cornman, Deborah H; Shuper, Paul A; Trayling, Cynthia; Redding, Caroline; Barta, William; Lemieux, Anthony F; Altice, Frederick L; Dieckhaus, Kevin; Friedland, Gerald

2011-11-01

We evaluated the efficacy of LifeWindows, a theory-based, computer-administered antiretroviral (ARV) therapy adherence support intervention, delivered to HIV + patients at routine clinical care visits. 594 HIV + adults receiving HIV care at five clinics were randomized to intervention or control arms. Intervention vs. control impact in the intent-to-treat sample (including participants whose ARVs had been entirely discontinued, who infrequently attended care, or infrequently used LifeWindows) did not reach significance. Intervention impact in the On Protocol sample (328 intervention and control arm participants whose ARVs were not discontinued, who attended care and were exposed to LifeWindows regularly) was significant. On Protocol intervention vs. control participants achieved significantly higher levels of perfect 3-day ACTG-assessed adherence over time, with sensitivity analyses maintaining this effect down to 70% adherence. This study supports the utility of LifeWindows and illustrates that patients on ARVs who persist in care at clinical care sites can benefit from adherence promotion software.

Clinical Outcome of Degenerative Mitral Regurgitation: Critical Importance of Echocardiographic Quantitative Assessment in Routine Practice.

PubMed

Antoine, Clemence; Benfari, Giovanni; Michelena, Hector I; Malouf, Joseph F; Nkomo, Vuyisile T; Thapa, Prabin; Enriquez-Sarano, Maurice

2018-05-31

Background -Echocardiographic quantitation of degenerative mitral regurgitation (DMR) is recommended whenever possible in clinical guidelines but is criticized and its scalability to routine clinical practice doubted. We hypothesized that echocardiographic DMR quantitation, performed in routine clinical practice by multiple practitioners predicts independently long-term survival, and thus is essential to DMR management. Methods -We included patients diagnosed with isolated mitral-valve-prolapse 2003-2011 and any degree of MR quantified by any physician/sonographer in routine clinical practice. Clinical/echocardiographic data acquired at diagnosis were retrieved electronically. Endpoint was mortality under medical treatment analyzed by Kaplan-Meir method and Proportional-Hazard models. Results -The cohort included 3914 patients (55% male) aged 62±17 years, with left ventricular ejection fraction (LVEF) 63±8% and routinely measured effective regurgitant orifice area (EROA) 19[0-40] mm 2 During follow-up (6.7±3.1 years) 696 patients died under medical management and 1263 underwent mitral surgery. In multivariate analysis, routinely measured EROA was associated with mortality (adjusted-hazard-ratio 1.19[1.13-1.24] p<0.0001 per-10mm 2 ) independently of LVEF and end-systolic diameter, symptoms and age/comorbidities. The association between routinely measured EROA and mortality persisted with competitive risk modeling (adjusted hazard-ratio 1.15[1.10-1.20] per 10mm 2 p<0.0001), or in patients without guideline-based Class I/II surgical triggers (adjusted hazard ratio 1.19[1.10-1.28] per 10mm 2 p<0.0001) and in all subgroups examined (all p<0.01). Spline curve analysis showed that, compared with general population mortality, excess mortality appears for moderate DMR (EROA ≥20mm 2 ) becomes notable ≥EROA 30mm 2 and steadily increases with higher EROA levels, > 40 mm 2 threshold. Conclusions -Echocardiographic DMR quantitation is scalable to routine practice and is independently associated with clinical outcome. Routinely measured EROA is strongly associated with long-term survival under medical treatment. Excess mortality vs. the general population appears in the "moderate" DMR range and steadily increases with higher EROA. Hence, individual EROA values should be integrated into therapeutic considerations, additionally to categorical DMR grading.

Prospective evaluation of a high multiplexing real-time polymerase chain reaction array for the rapid identification and characterization of bacteria causative of nosocomial pneumonia from clinical specimens: a proof-of-concept study.

PubMed

Roisin, S; Huang, T-D; de Mendonça, R; Nonhoff, C; Bogaerts, P; Hites, M; Delaere, B; Hamels, S; de Longueville, F; Glupczynski, Y; Denis, O

2018-01-01

The purpose of this study was evaluation of the VAPChip assay based on the "Rapid-Array-PCR-technology" which targets 13 respiratory pathogens and 24 β-lactam resistance genes directly on respiratory clinical specimens. The first step included analysis of 45 respiratory specimens in order to calibrate and determine the threshold for target genes. The second prospective step involved 85 respiratory samples from patients suspected of nosocomial pneumonia collected in two academic hospitals over an 8-month period. Results of the VAPChip assay were compared to routine methods. The first step showed a large proportion of positive signals for H. influenzae and/or S. pneumoniae. For identification, discrepancies were observed in seven samples. Thresholds were adapted and two probes were re-designed to create a new version of the cartridge. In the second phase, sensitivity and specificity of the VAPchip for bacterial identification were 72.9% and 99.1%, respectively. Seventy (82%) pathogens were correctly identified by both methods. Nine pathogens detected by the VAPChip were culture negative and 26 pathogens identified by culture were VAPChip negative. For resistance mechanisms, 11 probes were positive without identification of pathogens with an antimicrobial-susceptibility testing compatible by culture. However, the patient's recent microbiological history was able to explain most of these positive signals. The VAPChip assay simultaneously detects different pathogens and resistance mechanisms directly from clinical samples. This system seems very promising but the extraction process needs to be automated for routine implementation. This kind of rapid point-of-care automated platform permitting a syndromic approach will be the future challenge in the management of infectious diseases.

Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic Alterations in Solid Tumors.

PubMed

Paasinen-Sohns, Aino; Koelzer, Viktor H; Frank, Angela; Schafroth, Julian; Gisler, Aline; Sachs, Melanie; Graber, Anne; Rothschild, Sacha I; Wicki, Andreas; Cathomas, Gieri; Mertz, Kirsten D

2017-03-01

Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Influence of centrifugation conditions on the results of 77 routine clinical chemistry analytes using standard vacuum blood collection tubes and the new BD-Barricor tubes

PubMed Central

Cadamuro, Janne; Mrazek, Cornelia; Leichtle, Alexander B.; Kipman, Ulrike; Felder, Thomas K.; Wiedemann, Helmut; Oberkofler, Hannes; Fiedler, Georg M.; Haschke-Becher, Elisabeth

2017-01-01

Introduction Although centrifugation is performed in almost every blood sample, recommendations on duration and g-force are heterogeneous and mostly based on expert opinions. In order to unify this step in a fully automated laboratory, we aimed to evaluate different centrifugation settings and their influence on the results of routine clinical chemistry analytes. Materials and methods We collected blood from 41 healthy volunteers into BD Vacutainer PST II-heparin-gel- (LiHepGel), BD Vacutainer SST II-serum-, and BD Vacutainer Barricor heparin-tubes with a mechanical separator (LiHepBar). Tubes were centrifuged at 2000xg for 10 minutes and 3000xg for 7 and 5 minutes, respectively. Subsequently 60 and 21 clinical chemistry analytes were measured in plasma and serum samples, respectively, using a Roche COBAS instrument. Results High sensitive Troponin T, pregnancy-associated plasma protein A, ß human chorionic gonadotropin and rheumatoid factor had to be excluded from statistical evaluation as many of the respective results were below the measuring range. Except of free haemoglobin (fHb) measurements, no analyte result was altered by the use of shorter centrifugation times at higher g-forces. Comparing LiHepBar to LiHepGel tubes at different centrifugation setting, we found higher lactate-dehydrogenase (LD) (P = 0.003 to < 0.001) and lower bicarbonate values (P = 0.049 to 0.008) in the latter. Conclusions Serum and heparin samples may be centrifuged at higher speed (3000xg) for a shorter amount of time (5 minutes) without alteration of the analytes tested in this study. When using LiHepBar tubes for blood collection, a separate LD reference value might be needed. PMID:29187797

Influence of centrifugation conditions on the results of 77 routine clinical chemistry analytes using standard vacuum blood collection tubes and the new BD-Barricor tubes.

PubMed

Cadamuro, Janne; Mrazek, Cornelia; Leichtle, Alexander B; Kipman, Ulrike; Felder, Thomas K; Wiedemann, Helmut; Oberkofler, Hannes; Fiedler, Georg M; Haschke-Becher, Elisabeth

2018-02-15

Although centrifugation is performed in almost every blood sample, recommendations on duration and g-force are heterogeneous and mostly based on expert opinions. In order to unify this step in a fully automated laboratory, we aimed to evaluate different centrifugation settings and their influence on the results of routine clinical chemistry analytes. We collected blood from 41 healthy volunteers into BD Vacutainer PST II-heparin-gel- (LiHepGel), BD Vacutainer SST II-serum-, and BD Vacutainer Barricor heparin-tubes with a mechanical separator (LiHepBar). Tubes were centrifuged at 2000xg for 10 minutes and 3000xg for 7 and 5 minutes, respectively. Subsequently 60 and 21 clinical chemistry analytes were measured in plasma and serum samples, respectively, using a Roche COBAS instrument. High sensitive Troponin T, pregnancy-associated plasma protein A, ß human chorionic gonadotropin and rheumatoid factor had to be excluded from statistical evaluation as many of the respective results were below the measuring range. Except of free haemoglobin (fHb) measurements, no analyte result was altered by the use of shorter centrifugation times at higher g-forces. Comparing LiHepBar to LiHepGel tubes at different centrifugation setting, we found higher lactate-dehydrogenase (LD) (P = 0.003 to < 0.001) and lower bicarbonate values (P = 0.049 to 0.008) in the latter. Serum and heparin samples may be centrifuged at higher speed (3000xg) for a shorter amount of time (5 minutes) without alteration of the analytes tested in this study. When using LiHepBar tubes for blood collection, a separate LD reference value might be needed.

Hematology, plasma biochemistry, and tissue enzyme activities of invasive red lionfish captured off North Carolina, USA.

PubMed

Anderson, E T; Stoskopf, M K; Morris, J A; Clarke, E O; Harms, C A

2010-12-01

The red lionfish Pterois volitans is important not only in the aquarium trade but also as an invasive species in the western Atlantic. Introduced to waters off the southeastern coast of the United States, red lionfish have rapidly spread along much of the East Coast and throughout Bermuda, the Bahamas, and much of the Caribbean. Hematology and plasma biochemistry were evaluated in red lionfish captured from the offshore waters of North Carolina to establish baseline parameters for individual and population health assessment. Blood smears were evaluated for total and differential white blood cell counts, and routine clinical biochemical profiles were performed on plasma samples. To improve the interpretive value of routine plasma biochemistry profiles, tissue enzyme activities (alkaline phosphatase [ALP], alanine aminotransferase [ALT], aspartate aminotransferase [AST], gamma-glutamyl transferase [GGT], lactate dehydrogenase [LD], and creatine kinase [CK]) were analyzed from liver, kidney, skeletal muscle, gastrointestinal tract, and heart tissues from five fish. The hematological and plasma biochemical values were similar to those of other marine teleosts except that the estimated white blood cell counts were much lower than those routinely found in many species. The tissue enzyme activity findings suggest that plasma LD, CK, and AST offer clinical relevance in the assessment of red lionfish.

Technical note: Preservation of Trichomonas vaginalis viability in urine for laboratorial diagnosis by the wet mount examination.

PubMed

da Silva Dias, Mariana; Menezes, Camila Braz; Tasca, Tiana

2016-11-01

This study compared preservative solutions at different temperatures aiming to improve the wet mount for trichomoniasis diagnosis. The glucose-saline pH6.0 solution preserved the trophozoites up to 6h. The urine samples preservation is crucial for diagnosis and we suggest this solution as part of the clinical laboratorial routine. Copyright © 2016 Elsevier B.V. All rights reserved.

[Identification of occult disseminated tumor cells by recombinant herpes simplex virus expressing GFP (HSV(GFP))].

PubMed

Han, Xiang-ping; Shi, Gui-lan; Wang, Cheng-feng; Li, Jie; Zhang, Jian-wei; Zhang, Yu; Zhang, Shu-ren; Liu, Bin-lei

2012-12-01

To develop a novel rapid protocol for the detection of occult disseminated tumor cells by a recombinant herpes simplex virus expressing GFP (HSV(GFP)). Tumor cells of seven cell lines were exposed to HSV(GFP) and then examined for GFP expression by fluorescence microscopy. Various numbers of tumor cells (10, 100, 1000, 10 000) were mixed into 2 ml human whole blood, separated with lymphocytes separation medium, exposed to HSV(GFP), incubated at 37°C for 6 - 24 h and then counted for the number of green cells under the fluorescence microscope. Some clinical samples including peripheral blood, pleural effusion, ascites, spinal fluid from tumor-bearing patients were screened using this protocol in parallel with routine cytological examination. HSV(GFP) was able to infect all 7 tumor cell lines indicating that the HSV(GFP) can be used to detect different types of tumor cells. The detection sensitivity was 10 cancer cells in 2 ml whole blood. In the clinical samples, there were 4/15 positive by routine cytological examination but 11/15 positive by HSV(GFP), indicating a higher sensitivity of this new protocol. Recombinant herpes simplex virus-mediated green fluorescence is a simple and sensitive technique for the identification of occult disseminated cancer cells including circulating tumor cells (CTCs).

Prevalent emm types and superantigen gene patterns of group A Streptococcus in Thailand.

PubMed

Paveenkittiporn, W; Nozawa, T; Dejsirilert, S; Nakagawa, I; Hamada, S

2016-03-01

Group A Streptococcus (GAS) are globally distributed bacterial pathogens. We examined the emm genotypes, which are important indicators of virulence, of 349 clinical GAS isolates collected using two surveillance systems, i.e. Invasive Bacterial Infection Surveillance (IBIS) from 2010 to 2011 (234 isolates) and routine surveillance of clinically isolated bacteria from various hospitals during 1996-2011 (115 isolates) in Thailand. The major emm genotypes in IBIS samples were emm44 (12·0%), emm104 (6·8%), emm22 (5·6%), and emm81 (5·6%), whereas only one isolate (0·4%) had the emm1 genotype, which is significantly more common in invasive cases in the Western world. In samples collected during routine surveillance, emm238 (10·4%), emm44 (8·7%), and emm165 (7·0%) were dominant. The major superantigen gene profiles were similar between the groups, and 30·1% of isolates did not possess the phage-encoded superantigens (speA, speC, speH, speI, speK, speL, speM, ssa). Although most isolates exhibited limited gene profiles, emm44 isolates had highly variable gene profiles (15 patterns). We conclude that emm44 is the predominant GAS genotype in Thailand, and isolates varied in superantigen gene profiles.

High diagnostic yield by CSF-PCR for entero- and herpes simplex viruses and TBEV serology in adults with acute aseptic meningitis in Stockholm.

PubMed

Franzen-Rohl, Elisabeth; Larsson, Kenny; Skoog, Eva; Tiveljung-Lindell, Annika; Grillner, Lena; Aurelius, Elisabeth; Glimåker, Martin

2008-01-01

Acute aseptic meningitis (AAM) affects 10-20/100,000 inhabitants per years in Sweden. Up to the beginning of the 1980s the diagnoses were made by virus isolation and/or determination of viral antibodies in serum. The development of PCR for detection of viruses in CSF samples has increased the sensitivity and diagnostic efficiency considerably. We investigated the aetiology of AAM and the diagnostic efficiency in an adult population in Stockholm, using a limited first-line combination of microbiological assays. CSF and serum samples, consecutively collected in 419 patients with clinical symptoms of AAM in northern Stockholm during 1999-2004, were included. PCR assays for herpes simplex virus (HSV) DNA and enterovirus (EV) RNA in the CSF as well as ELISA for IgM in serum to tick-borne encephalitis virus (TBEV) were performed routinely. A viral diagnosis was obtained in 255 of the 419 cases (62%) with these routinely performed assays. Clinical findings in combination with additional diagnostic tests resulted in an overall aetiological yield of 72%. EV was the major causative agent (27%) followed by TBEV (21%) and HSV-2 (19%). We conclude that consistent use of CSF-PCR for EV and HSV and TBEV serology established a diagnosis in the majority of AAM patients.

Practical way to develop 10-color flow cytometry protocols for the clinical laboratory

NASA Astrophysics Data System (ADS)

Tárnok, Attila; Bocsi, Jozsef

2010-02-01

The latest development of commercial routine flow cytometers (FCM) is that they are equipped with three (blue, red, violet) or more lasers and many PMT detectors. Nowadays routine clinical instruments are capable of detecting 10 or more fluorescence colors simultaneously. Thereby, presenting opportunities for getting detailed information on the single cell level for cytomics and systems biology for improve diagnostics and monitoring of patients. The University Leipzig, Germany) recently started a cluster of excellence to study the molecular background of life style and environment associated diseases, enrolling 25000 individuals (LIFE). To this end the most comprehensive FCM protocol has to be developed for this study. We aimed to optimize fluorochrome and antibody combinations to the characteristics of the instrument for successful 10-color FCM. Systematic review of issues related to sampling, preparation, instrument settings, spillover and compensation matrix, reagent performance, and general principles of panel construction was performed. 10-color FCM enables for increased accuracy in cell subpopulation identification, the ability to obtain detailed information from blood specimens, improved laboratory efficiency, and the means to consistently detect major and rare cell populations. Careful attention to details of instrument and reagent performance allows for the development of panels suitable for screening of samples from healthy and diseased donors. The characteristics of this technique are particularly well suited for the analysis of broad human population cohorts and have the potential to reach the everyday practice in a standardized way for the clinical laboratory.

Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: Retrospective validation and prospective audit in the UK National Health Service.

PubMed

Hamblin, Angela; Wordsworth, Sarah; Fermont, Jilles M; Page, Suzanne; Kaur, Kulvinder; Camps, Carme; Kaisaki, Pamela; Gupta, Avinash; Talbot, Denis; Middleton, Mark; Henderson, Shirley; Cutts, Anthony; Vavoulis, Dimitrios V; Housby, Nick; Tomlinson, Ian; Taylor, Jenny C; Schuh, Anna

2017-02-01

Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing. We validated a 46-gene hotspot cancer panel assay allowing multiple gene testing from small diagnostic biopsies. From 1 January 2013 to 31 December 2013, solid tumour samples (including non-small-cell lung carcinoma [NSCLC], colorectal carcinoma, and melanoma) were sequenced in the context of the UK National Health Service from 351 consecutively submitted prospective cases for which treating clinicians thought the patient had potential to benefit from more extensive genetic analysis. Following histological assessment, tumour-rich regions of formalin-fixed paraffin-embedded (FFPE) sections underwent macrodissection, DNA extraction, NGS, and analysis using a pipeline centred on Torrent Suite software. With a median turnaround time of seven working days, an integrated clinical report was produced indicating the variants detected, including those with potential diagnostic, prognostic, therapeutic, or clinical trial entry implications. Accompanying phenotypic data were collected, and a detailed cost analysis of the panel compared with single gene testing was undertaken to assess affordability for routine patient care. Panel sequencing was successful for 97% (342/351) of tumour samples in the prospective cohort and showed 100% concordance with known mutations (detected using cobas assays). At least one mutation was identified in 87% (296/342) of tumours. A locally actionable mutation (i.e., available targeted treatment or clinical trial) was identified in 122/351 patients (35%). Forty patients received targeted treatment, in 22/40 (55%) cases solely due to use of the panel. Examination of published data on the potential efficacy of targeted therapies showed theoretically actionable mutations (i.e., mutations for which targeted treatment was potentially appropriate) in 66% (71/107) and 39% (41/105) of melanoma and NSCLC patients, respectively. At a cost of £339 (US$449) per patient, the panel was less expensive locally than performing more than two or three single gene tests. Study limitations include the use of FFPE samples, which do not always provide high-quality DNA, and the use of "real world" data: submission of cases for sequencing did not always follow clinical guidelines, meaning that when mutations were detected, patients were not always eligible for targeted treatments on clinical grounds. This study demonstrates that more extensive tumour sequencing can identify mutations that could improve clinical decision-making in routine cancer care, potentially improving patient outcomes, at an affordable level for healthcare providers.

Patterns of preventive practice in New Brunswick

PubMed Central

Battista, Renaldo N.; Palmer, Cynthia S.; Marchand, Beatrice M.; Spitzer, Walter O.

1985-01-01

A survey of active general practitioners was conducted in New Brunswick to ascertain their patterns of preventive practice with respect to cancer of four anatomic sites: the breast, the cervix, the colon and rectum, and the lung. Ninety-two percent of the physicians reported that they taught breast self-examination to their female patients, 98% that they performed breast examinations, 98% that they did Papanicolaou smears routinely, and 97% that they provided counselling against smoking. Few of the physicians reported that they submitted women aged 50 to 59 years to annual mammography (3%) or examined stool samples from asymptomatic patients over 44 years of age for occult blood (20%). Many (77%) said they still routinely performed chest roentgenography for early detection of lung cancer; an estimated 49% of the physicians said they performed cytologic screening of sputum samples for the same purpose. Preventive practices, when used, were usually carried out during major encounters with patients, such as general check-ups. The potential for prevention through this clinically based approach is still largely unrealized. PMID:3986725

Analysis of serum angiotensin-converting enzyme.

PubMed

Muller, B R

2002-09-01

Serum angiotensin-converting enzyme (SACE) levels are influenced by genetic polymorphism. Interpretation of serum levels with the appropriate genotypic reference range improves the diagnostic sensitivity of the assay for sarcoidosis. SACE assays are performed by a large number of routine clinical laboratories. However, there is no external quality assessment (EQA) for SACE other than an informal regional scheme. This showed analytical performance of SACE assays to be poor, with a diversity of reference ranges, leading to widely disparate clinical classification of EQA samples. Genetic polymorphism combined with poor analytical performance suggest that perhaps SACE assays should revert to being the province of specialized laboratories.

Clinical Utility of an Automated Instrument for Gram Staining Single Slides ▿

PubMed Central

Baron, Ellen Jo; Mix, Samantha; Moradi, Wais

2010-01-01

Gram stains of 87 different clinical samples were prepared by the laboratory's conventional methods (automated or manual) and by a new single-slide-type automated staining instrument, GG&B AGS-1000. Gram stains from either heat- or methanol-fixed slides stained with the new instrument were easy to interpret, and results were essentially the same as those from the methanol-fixed slides prepared as a part of the routine workflow. This instrument is well suited to a rapid-response laboratory where Gram stain requests are commonly received on a stat basis. PMID:20410348

Pulmonary nodules: effect of adaptive statistical iterative reconstruction (ASIR) technique on performance of a computer-aided detection (CAD) system-comparison of performance between different-dose CT scans.

PubMed

Yanagawa, Masahiro; Honda, Osamu; Kikuyama, Ayano; Gyobu, Tomoko; Sumikawa, Hiromitsu; Koyama, Mitsuhiro; Tomiyama, Noriyuki

2012-10-01

To evaluate the effects of ASIR on CAD system of pulmonary nodules using clinical routine-dose CT and lower-dose CT. Thirty-five patients (body mass index, 22.17 ± 4.37 kg/m(2)) were scanned by multidetector-row CT with tube currents (clinical routine-dose CT, automatically adjusted mA; lower-dose CT, 10 mA) and X-ray voltage (120 kVp). Each 0.625-mm-thick image was reconstructed at 0%-, 50%-, and 100%-ASIR: 0%-ASIR is reconstructed using only the filtered back-projection algorithm (FBP), while 100%-ASIR is reconstructed using the maximum ASIR and 50%-ASIR implies a blending of 50% FBP and ASIR. CAD output was compared retrospectively with the results of the reference standard which was established using a consensus panel of three radiologists. Data were analyzed using Bonferroni/Dunn's method. Radiation dose was calculated by multiplying dose-length product by conversion coefficient of 0.021. The consensus panel found 265 non-calcified nodules ≤ 30 mm (ground-glass opacity [GGO], 103; part-solid, 34; and solid, 128). CAD sensitivity was significantly higher at 100%-ASIR [clinical routine-dose CT, 71% (overall), 49% (GGO); lower-dose CT, 52% (overall), 67% (solid)] than at 0%-ASIR [clinical routine-dose CT, 54% (overall), 25% (GGO); lower-dose CT, 36% (overall), 50% (solid)] (p<0.001). Mean number of false-positive findings per examination was significantly higher at 100%-ASIR (clinical routine-dose CT, 8.5; lower-dose CT, 6.2) than at 0%-ASIR (clinical routine-dose CT, 4.6; lower-dose CT, 3.5; p<0.001). Effective doses were 10.77 ± 3.41 mSv in clinical routine-dose CT and 2.67 ± 0.17 mSv in lower-dose CT. CAD sensitivity at 100%-ASIR on lower-dose CT is almost equal to that at 0%-ASIR on clinical routine-dose CT. ASIR can increase CAD sensitivity despite increased false-positive findings. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Evaluation of the Abbott RealTime HCV assay for quantitative detection of hepatitis C virus RNA.

PubMed

Michelin, Birgit D A; Muller, Zsofia; Stelzl, Evelyn; Marth, Egon; Kessler, Harald H

2007-02-01

The Abbott RealTime HCV assay for quantitative detection of HCV RNA has recently been introduced. In this study, the performance of the Abbott RealTime HCV assay was evaluated and compared to the COBAS AmpliPrep/COBAS TaqMan HCV test. Accuracy, linearity, interassay and intra-assay variations were determined, and a total of 243 routine clinical samples were investigated. When accuracy of the new assay was tested, the majority of results were found to be within +/-0.5 log(10) unit of the results obtained by reference laboratories. Determination of linearity resulted in a quasilinear curve up to 1.0 x 10(6)IU/ml. The interassay variation ranged from 15% to 32%, and the intra-assay variation ranged from 5% to 8%. When clinical samples were tested by the Abbott RealTime HCV assay and the results were compared with those obtained by the COBAS AmpliPrep/COBAS TaqMan HCV test, the results for 93% of all samples with positive results by both tests were found to be within +/-1.0 log(10) unit. The viral loads for all patients measured by the Abbott and Roche assays showed a high correlation (R(2)=0.93); quantitative results obtained by the Abbott assay were found to be lower than those obtained by the Roche assay. The Abbott RealTime HCV assay proved to be suitable for use in the routine diagnostic laboratory. The time to results was similar for both of the assays.

Exposure of hospital workers to airborne antineoplastic agents

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

deWerk Neal, A.; Wadden, R.A.; Chiou, W.L.

Practices for handling antineoplastic drugs were surveyed, and ambient-air sampling for four antineoplastic agents was conducted in outpatient oncology clinics. A questionnaire was administered in 1981 to the nurse or pharmacist in charge of drug preparation at 10 hospital oncology clinics. At three sites, air samples were collected during working hours in medication-preparation rooms and nearby offices. The air-sampling pumps contained filters at breathing-zone height; room air was drawn through each filter for 40 hours. Extracts from the filters were assayed by high-performance liquid chromatography (HPLC) for fluorouracil and cyclophosphamide in seven sets of samples and methotrexate and doxorubicin inmore » five sets of samples. Mass spectrometry (MS) was used to confirm detection of fluorouracil. Total use of each monitored drug was recorded at each site. Nine clinics had no ventilation hood, and drugs were prepared by nurses in eight clinics. Routine use of gloves (three clinics) and masks (one clinic) was uncommon, and wastes were disposed of in uncovered receptacles in four of the clinics. Eating and drinking occurred in seven of the preparation rooms. At the main air-sampling site, fluorouracil (0.12-82.26 ng/cu m) was detected in air during 200 of the 320 hours monitored. Cyclophosphamide (370 ng/cu m) was present during 80 hours. In the two other sites, fluorouracil was detected by HPLC but not confirmed by MS, and no cyclophosphamide was detected. No detectable amounts of methotrexate and doxorubicin were present. Fluorouracil was the most frequently used drug, and cyclophosphamide was second. Results suggest that personnel handling antineoplastic drugs are subject to potential systemic absorption of these agents by inhalation.« less

Automatic patient dose registry and clinical audit on line for mammography.

PubMed

Ten, J I; Vano, E; Sánchez, R; Fernandez-Soto, J M

2015-07-01

The use of automatic registry systems for patient dose in digital mammography allows clinical audit and patient dose analysis of the whole sample of individual mammography exposures while fulfilling the requirements of the European Directives and other international recommendations. Further parameters associated with radiation exposure (tube voltage, X-ray tube output and HVL values for different kVp and target/filter combinations, breast compression, etc.) should be periodically verified and used to evaluate patient doses. This study presents an experience in routine clinical practice for mammography using automatic systems. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Proteomic analysis allows for early detection of potential markers of metabolic impairment in very young obese children

PubMed Central

2014-01-01

Background Early diagnosis of initial metabolic derangements in young obese children could influence their management; however, this impairment is frequently not overt, but subtle and undetectable by routinely used clinical assays. Our aim was to evaluate the ability of serum proteomic analysis to detect these incipient metabolic alterations in comparison to standard clinical methods and to identify new candidate biomarkers. Methods A cross-sectional study of fasting serum samples from twenty-two prepubertal, Caucasian obese (OB; 9.22 ± 1.93 years; 3.43 ± 1.08 BMI-SDS) and twenty-one lean controls (C; 8.50 ± 1.98 years; -0.48 ± 0.81 BMI-SDS) and a prospective study of fasting serum samples from twenty prepubertal, Caucasian obese children (11 insulin resistant [IR]) before (4.77 ± 1.30 BMI-SDS) and after weight reduction (2.57 ± 1.29 BMI-SDS) by conservative treatment in a reference hospital (Pros-OB) was performed. Proteomic analysis (two-dimension-eletrophoresis + mass spectrometry analysis) of serum and comparative evaluation of the sensitivity of routinely used assays in the clinics to detect the observed differences in protein expression level, as well as their relationship with anthropometric features, insulin resistance indexes, lipid profile and adipokine levels were carried out. Results Study of the intensity data from proteomic analysis showed a decrease of several isoforms of apolipoprotein-A1, apo-J/clusterin, vitamin D binding protein, transthyretin in OBvs. C, with some changes in these proteins being enhanced by IR and partially reversed after weight loss. Expression of low molecular weight isoforms of haptoglobin was increased in OB, enhanced in IR and again decreased after weight loss, being positively correlated with serum interleukin-6 and NAMPT/visfatin levels. After statistical correction for multiple comparisons, significance remained for a single isoform of low MW haptoglobin (OB vs. C and IR vs. non-IR) and Apo A1 (IR vs. non-IR). Assays routinely used in the clinical setting (ELISA/kinetic nephelometry), only partially confirmed the changes observed by proteomic analysis (ApoA1 and haptoglobin). Conclusion Proteomic analysis can allow for the identification of potential new candidate biomarkers as a complement to routinely used assays to detect initial changes in serum markers of inflammation and lipid metabolism impairment in young obese children. PMID:24949022

Family physicians believe the placebo effect is therapeutic but often use real drugs as placebos.

PubMed

Kermen, Rachel; Hickner, John; Brody, Howard; Hasham, Irma

2010-10-01

Few national data exist on physicians' use of and beliefs about placebos in routine health care. We mailed a 22-question, confidential survey about placebo use and beliefs to a random sample of 1,000 members of the American Academy of Family Physicians. A total of 412 of 970 (43%) eligible physicians responded, and 56% of respondents said they had used a placebo in clinical practice. Forty percent of respondents had used an antibiotic as a placebo, and 11% had used inert substances. The most common reason for prescribing placebos was "after unjustified demand for medication." Eighty-five percent of respondents believed placebos can have both psychological and physical benefits. The majority (61%) recommended a placebo over offering no treatment, while 8% said clinical placebo use should be categorically prohibited. Nearly all respondents believed a number of routine clinical practices promote the placebo effect. Many US family physicians use placebos and generally believe the placebo effect has both psychological and physical benefits. Physicians recognize the broader application of the placebo effect but they commonly use active medication as placebos. The responses to this survey raise important questions about the appropriate use of placebos and the therapeutic value of the placebo effect in clinical practice.

Oral candidiasis as clinical manifestation of HIV/AIDS infection in Airlangga University hospital patients

NASA Astrophysics Data System (ADS)

Putranti, A.; Asmarawati, T. P.; Rachman, B. E.; Hadi, U.; Nasronudin

2018-03-01

The purpose of this study was to determine the characteristics of HIV/AIDS patients with oral candidiasis as its clinical manifestation at Airlangga University Hospital Surabaya. This is a descriptive analytic research with cross-sectional design using Chi-Square statistic test. Samples of this study consist of 34 patients using total sampling methods. Those patients were all HIV/AIDS infected patients with oral candidiasis clinical manifestations, who were admitted to Airlangga University Hospital Surabaya from January 2016 to September 2017. Results showed that mostly HIV/AIDS patients with oral candidiasis are male (79.4%), old age (40-75years) total amounted to 58.8%, heterosexual as main risk factor (70%), clinical stadium mostly in stage IV (61.8%), 26% of patients with chronic diarrhea and 56% with pulmonary TB, clinical stages of patients have a significant relation to the incidence of oral candidiasis infection (p=0.024). The most common oral lesions found in people with HIV are Candidiasis. The best management is through routine dental examination and dental precautions to maintain health and achieve a better quality of life.

Quantitative comparison of DNA methylation assays for biomarker development and clinical applications.

PubMed

2016-07-01

DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.

Implementation of Health Information Technology in Routine Care for Fibromyalgia: Pilot Study.

PubMed

Sparks, Toni; Kawi, Jennifer; Menzel, Nancy Nivison; Hartley, Kendall

2016-02-01

Fibromyalgia management remains complicated and challenging. Health information technology is an evidence-based, nonpharmacological self and symptom management strategy, but few studies have evaluated its feasibility for managing fibromyalgia patients in clinical practice. FibroGuide is an example of an evidence-based, interactive, and computer-based program comprised of 10 educational modules on fibromyalgia. Study aims were to: (1) develop a process for implementing FibroGuide into the routine care of patients with fibromyalgia, (2) evaluate the overall impact on fibromyalgia before and after a 12-week implementation, and (3) assess patient perspectives on using FibroGuide health information technology to assist in self-management. In this pilot study, 35 participants with fibromyalgia were recruited from an Advanced Practice Registered Nurse's outpatient clinic. Using a descriptive design, quantitative data analysis was employed to address study aims. Based on data collection pre- and post-intervention using paired samples testing, a statistically significant change (p = .017) was observed in overall fibromyalgia impact (improved symptom severity, activity, and function). Majority felt that FibroGuide was helpful as part of their routine care, and nearly half reported that it assisted in their self-management. Although 65% noted that technology was an effective and efficient way to receive education for fibromyalgia management, 57% preferred talking to healthcare providers. Larger longitudinal studies are needed on the use of health information technology in fibromyalgia, evaluating both statistical and clinical significance, while decreasing barriers to participant use for this promising adjunct to clinical management. Providers need to be well educated on supporting self-management strategies and health information technology. Copyright © 2016 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

An evaluation of the effectiveness of psychological therapy in reducing general psychological distress for adults with autism spectrum conditions and comorbid mental health problems.

PubMed

Blainey, Sarah H; Rumball, Freya; Mercer, Louise; Evans, Lauren Jayne; Beck, Alison

2017-11-01

To investigate the effectiveness of psychological therapy in reducing psychological distress for adults with autism spectrum conditions (ASC) and co-morbid mental health conditions in routine clinical practice. To explore the effect of individual characteristics and service factors on change in general distress. In a specialist psychological therapies service for adults with ASC, the Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM) self-report questionnaire of psychological distress is completed by clients at start and end of therapy. Change over time and reliable and clinical change was assessed for 81 of a total of 122 clients (66.4%). Factors which may influence change over time were explored using available clinical information. Overall, there was a significant reduction in CORE-OM score during therapy with a small effect size. Most clients showed an improvement in psychological distress over therapy (75.4% improved, with 36.9% of these showing reliable changes). Significant and comparable reductions from pre-therapy to post-therapy were seen across the sample, showing that individual differences did not mediate therapy effectiveness. CORE-OM scores mediate the association between age of ASD diagnosis and hours of therapeutic input required, with greater age at diagnosis and higher distress associated with longer therapy duration. Our preliminary findings suggest that psychological therapy may be effective in reducing general distress for clients with ASC and co-morbid mental health conditions and should be routinely offered. Individuals who are diagnosed with ASD in adulthood are likely to require a longer course of therapy when their general distress scores are high. Copyright © 2017 John Wiley & Sons, Ltd.

Assessment of anaerobic blood cultures in pediatric oncology patients.

PubMed

Monsonís Cabedo, Manuel; Rives Solá, Susana; Noguera-Julian, Antoni; Urrea Ayala, Mireia; Cruz Martinez, Ofelia; Gené Giralt, Amadeu

2017-01-01

The routine use of a single aerobic bottle for blood culture in pediatric patients has become commonplace, as anaerobic bacteria are not frequently involved in clinically significant infections. The aim of this study was to assess the usefulness of routinely performing anaerobic blood cultures in pediatric oncology patients. Prospective study was conducted on pediatric (<18 years) patients affected with febrile syndrome after receiving chemotherapy for hematological or solid malignancies. Samples were inoculated into pediatric aerobic and standard anaerobic bottles (BacT/Alert automatic system). Strains were considered clinically significant, or deemed as contaminants, depending on isolation circumstances and clinical criteria. A total of 876 blood cultures from 228 patients were processed during the 21-month study period (January 2014 to September 2015). Baseline diagnosis included 143 solid tumors and 67/18 cases of leukemia/lymphoma. Bacterial growth was detected in 90 (10.2%) blood cultures for 95 different isolates, of which 62 (7.1%)/63 isolates were considered clinically significant. Among the latter, 38 (60.3%) microorganisms grew in both aerobic and anaerobic bottles, 18 (28.6%) only in aerobic bottles, and 7 (11.1%) only in anaerobic bottles. Gram-negative bacilli (33; 52.4%), mainly from the Enterobacteriaceae family, were the most frequently isolated microorganisms. Overall, only 3 out of 90 isolates (3.3%) were strict anaerobes (Propionibacterium acnes), and all of them were deemed contaminants. Strict anaerobes did not cause significant infections in febrile pediatric oncology patients, and anaerobic blood culture bottles offered no additional advantages over aerobic media. Our results suggest that routine blood cultures should be solely processed in aerobic media in this group of patients. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Acceptability of unsupervised HPV self-sampling using written instructions.

PubMed

Waller, J; McCaffery, K; Forrest, S; Szarewski, A; Cadman, L; Austin, J; Wardle, J

2006-01-01

The study measured the acceptability of self-sampling for human papillomavirus (HPV) testing in the context of cervical cancer screening. Women carried out self-sampling unsupervised, using a written instruction sheet. Participants were women attending either a family planning clinic or a primary care trust for routine cervical screening. Women (n = 902) carried out self-sampling for HPV testing and then a clinician did a routine cervical smear and HPV test. Immediately after having the two tests, participants completed a measure of acceptability for both tests, and answered questions about ease of using the instruction sheet and willingness to use self-sampling in the future. The majority of women found self-sampling more acceptable than the clinician-administered test, but there was a lack of confidence that the test had been done correctly. Significant demographic differences in attitudes were found, with married women having more favourable attitudes towards self-sampling than single women, and Asian women having more negative attitudes than women in other ethnic groups. Intention to use self-sampling in the future was very high across all demographic groups. Self-sampling for HPV testing was highly acceptable in this large and demographically diverse sample, and women were able to carry out the test alone, using simple written instructions. Consistent with previous studies, women were concerned about doing the test properly and this issue will need to be addressed if self-sampling is introduced. More work is needed to see whether the demographic differences we found are robust and to identify reasons for lower acceptability among single women and those from Asian background.

Next-Generation Proteomics and Its Application to Clinical Breast Cancer Research.

PubMed

Mardamshina, Mariya; Geiger, Tamar

2017-10-01

Proteomics technology aims to map the protein landscapes of biological samples, and it can be applied to a variety of samples, including cells, tissues, and body fluids. Because the proteins are the main functional molecules in the cells, their levels reflect much more accurately the cellular phenotype and the regulatory processes within them than gene levels, mutations, and even mRNA levels. With the advancement in the technology, it is possible now to obtain comprehensive views of the biological systems and to study large patient cohorts in a streamlined manner. In this review we discuss the technological advancements in mass spectrometry-based proteomics, which allow analysis of breast cancer tissue samples, leading to the first large-scale breast cancer proteomics studies. Furthermore, we discuss the technological developments in blood-based biomarker discovery, which provide the basis for future development of assays for routine clinical use. Although these are only the first steps in implementation of proteomics into the clinic, extensive collaborative work between these worlds will undoubtedly lead to major discoveries and advances in clinical practice. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Nurses' Lived Experience of Working with Nursing Students in Clinical Wards: a Phenomenological Study

PubMed Central

Parvan, Kobra; Shahbazi, Shahla; Ebrahimi, Hossein; Valizadeh, Susan; Rahmani, Azad; Jabbarzadeh Tabrizi, Faranak; Esmaili, Fariba

2018-01-01

Introduction: Despite being aware of the importance of nurses’ role in providing clinical training to nursing students, studies show that sufficient research has not yet been conducted on the experience of clinical nurses who are engaged in training nursing students outside their normal working hours. The present study aim to describe the experience of these nurses who are training outside their routine working hours. Methods: This study was conducted using descriptive-phenomenology method. Twelve nurses was participated in this research. Data were collected using purposive sampling method and face to face interviews based on nurses’ real life experience of students’ learning in clinical settings through answering open-ended questions. Spiegel burg analysis method was used to analyze the data. Results: The result of data analysis was the derivation of four themes and eight sub-themes. Themes included "nurses as teaching sources", "changes in the balance of doing routine tasks", "professional enthusiasm", and "nurses as students' professional socialization source of inspiration". Sub-themes included "efficient education", "poor education", "support", "interference in the role," "self-efficacy development", "inner satisfaction", "positive imaging" and "being a model". Conclusion: It is necessary that academic centers plan for teaching nurses working on a contractual basis in the field of the evaluation method and various methods of teaching. The findings also suggested the development of individual self-efficacy in clinical nurses who train students. PMID:29637056

Searching CINAHL did not add value to clinical questions posed in NICE guidelines.

PubMed

Beckles, Zosia; Glover, Sarah; Ashe, Joanna; Stockton, Sarah; Boynton, Janette; Lai, Rosalind; Alderson, Philip

2013-09-01

This study aims to quantify the unique useful yield from the Cumulative Index to Nursing and Allied Health Literature (CINAHL) database to National Institute for Health and Clinical Excellence (NICE) clinical guidelines. A secondary objective is to investigate the relationship between this yield and different clinical question types. It is hypothesized that the unique useful yield from CINAHL is low, and this database can therefore be relegated to selective rather than routine searching. A retrospective sample of 15 NICE guidelines published between 2005 and 2009 was taken. Information on clinical review question type, number of references, and reference source was extracted. Only 0.33% (95% confidence interval: 0.01-0.64%) of references per guideline were unique to CINAHL. Nursing- or allied health (AH)-related questions were nearly three times as likely to have references unique to CINAHL as non-nursing- or AH-related questions (14.89% vs. 5.11%), and this relationship was found to be significant (P<0.05). No significant relationship was found between question type and unique CINAHL yield for drug-related questions. The very low proportion of references unique to CINAHL strongly suggests that this database can be safely relegated to selective rather than routine searching. Nursing- and AH-related questions would benefit from selective searching of CINAHL. Copyright © 2013 Elsevier Inc. All rights reserved.

The British Association for Sexual Health and HIV 2016 UK national audit and survey of clinic policies in relation to risk assessment, HIV testing and follow-up.

PubMed

Bhaduri, S; Curtis, H; McClean, H; Sullivan, A K

2018-01-01

This national audit of 142 clinics demonstrated that the majority of clinics surveyed had policies and agreed clinical practice for alcohol and recreational drug enquiry, as well as documentation of HIV test refusal, although this was not the case in 24% of clinics as regards alcohol usage, 21% of clinics as regards recreational drugs use and 43% of clinics as regards chemsex usage. Regarding management of HIV test refusal, there was no policy or agreed practice in 13% of clinics with respect to men having sex with men (MSM) attenders, and in 18% of clinics for heterosexual attenders. Seventy percent of clinics had HIV point of care tests (POCT) available. Recommendations include: all clinics should have a policy of routine enquiry about alcohol, recreational drugs and chemsex, all clinics should record reasons for HIV test refusal and all clinics should provide testing alternatives to improve uptake, e.g. point of care testing or home sampling.

Best practices for veterinary toxicologic clinical pathology, with emphasis on the pharmaceutical and biotechnology industries.

PubMed

Tomlinson, Lindsay; Boone, Laura I; Ramaiah, Lila; Penraat, Kelley A; von Beust, Barbara R; Ameri, Mehrdad; Poitout-Belissent, Florence M; Weingand, Kurt; Workman, Heather C; Aulbach, Adam D; Meyer, Dennis J; Brown, Diane E; MacNeill, Amy L; Bolliger, Anne Provencher; Bounous, Denise I

2013-09-01

The purpose of this paper by the Regulatory Affairs Committee (RAC) of the American Society for Veterinary Clinical Pathology (ASVCP) is to review the current regulatory guidances (eg, guidelines) and published recommendations for best practices in veterinary toxicologic clinical pathology, particularly in the pharmaceutical and biotechnology industries, and to utilize the combined experience of ASVCP RAC to provide updated recommendations. Discussion points include (1) instrumentation, validation, and sample collection, (2) routine laboratory variables, (3) cytologic laboratory variables, (4) data interpretation and reporting (including peer review, reference intervals and statistics), and (5) roles and responsibilities of clinical pathologists and laboratory personnel. Revision and improvement of current practices should be in alignment with evolving regulatory guidance documents, new technology, and expanding understanding and utility of clinical pathology. These recommendations provide a contemporary guide for the refinement of veterinary toxicologic clinical pathology best practices. © 2013 American Society for Veterinary Clinical Pathology.

K(3)EDTA Vacuum Tubes Validation for Routine Hematological Testing.

PubMed

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Poli, Giovanni; Solero, Giovanni Pietro; Picheth, Geraldo; Guidi, Gian Cesare

2012-01-01

Background and Objective. Some in vitro diagnostic devices (e.g, blood collection vacuum tubes and syringes for blood analyses) are not validated before the quality laboratory managers decide to start using or to change the brand. Frequently, the laboratory or hospital managers select the vacuum tubes for blood collection based on cost considerations or on relevance of a brand. The aim of this study was to validate two dry K(3)EDTA vacuum tubes of different brands for routine hematological testing. Methods. Blood specimens from 100 volunteers in two different K(3)EDTA vacuum tubes were collected by a single, expert phlebotomist. The routine hematological testing was done on Advia 2120i hematology system. The significance of the differences between samples was assessed by paired Student's t-test after checking for normality. The level of statistical significance was set at P < 0.05. Results and Conclusions. Different brand's tubes evaluated can represent a clinically relevant source of variations only on mean platelet volume (MPV) and platelet distribution width (PDW). Basically, our validation will permit the laboratory or hospital managers to select the brand's vacuum tubes validated according to him/her technical or economical reasons for routine hematological tests.

K3EDTA Vacuum Tubes Validation for Routine Hematological Testing

PubMed Central

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Poli, Giovanni; Solero, Giovanni Pietro; Picheth, Geraldo; Guidi, Gian Cesare

2012-01-01

Background and Objective. Some in vitro diagnostic devices (e.g, blood collection vacuum tubes and syringes for blood analyses) are not validated before the quality laboratory managers decide to start using or to change the brand. Frequently, the laboratory or hospital managers select the vacuum tubes for blood collection based on cost considerations or on relevance of a brand. The aim of this study was to validate two dry K3EDTA vacuum tubes of different brands for routine hematological testing. Methods. Blood specimens from 100 volunteers in two different K3EDTA vacuum tubes were collected by a single, expert phlebotomist. The routine hematological testing was done on Advia 2120i hematology system. The significance of the differences between samples was assessed by paired Student's t-test after checking for normality. The level of statistical significance was set at P < 0.05. Results and Conclusions. Different brand's tubes evaluated can represent a clinically relevant source of variations only on mean platelet volume (MPV) and platelet distribution width (PDW). Basically, our validation will permit the laboratory or hospital managers to select the brand's vacuum tubes validated according to him/her technical or economical reasons for routine hematological tests. PMID:22888448

Accuracy of the HumaSensplus point-of-care uric acid meter using capillary blood obtained by fingertip puncture.

PubMed

Fabre, Stéphanie; Clerson, Pierre; Launay, Jean-Marie; Gautier, Jean-François; Vidal-Trecan, Tiphaine; Riveline, Jean-Pierre; Platt, Adam; Abrahamsson, Anna; Miner, Jeffrey N; Hughes, Glen; Richette, Pascal; Bardin, Thomas

2018-05-02

The uric acid (UA) level in patients with gout is a key factor in disease management and is typically measured in the laboratory using plasma samples obtained after venous puncture. This study aimed to assess the reliability of immediate UA measurement with capillary blood samples obtained by fingertip puncture with the HumaSens plus point-of-care meter. UA levels were measured using both the HumaSens plus meter in the clinic and the routine plasma UA method in the biochemistry laboratory of 238 consenting diabetic patients. HumaSens plus capillary and routine plasma UA measurements were compared by linear regression, Bland-Altman plots, intraclass correlation coefficient (ICC), and Lin's concordance coefficient. Values outside the dynamic range of the meter, low (LO) or high (HI), were analyzed separately. The best capillary UA thresholds for detecting hyperuricemia were determined by receiver operating characteristic (ROC) curves. The impact of potential confounding factors (demographic and biological parameters/treatments) was assessed. Capillary and routine plasma UA levels were compared to reference plasma UA measurements by liquid chromatography-mass spectrometry (LC-MS) for a subgroup of 67 patients. In total, 205 patients had capillary and routine plasma UA measurements available. ICC was 0.90 (95% confidence interval (CI) 0.87-0.92), Lin's coefficient was 0.91 (0.88-0.93), and the Bland-Altman plot showed good agreement over all tested values. Overall, 17 patients showed values outside the dynamic range. LO values were concordant with plasma values, but HI values were considered uninterpretable. Capillary UA thresholds of 299 and 340 μmol/l gave the best results for detecting hyperuricemia (corresponding to routine plasma UA thresholds of 300 and 360 μmol/l, respectively). No significant confounding factor was found among those tested, except for hematocrit; however, this had a negligible influence on the assay reliability. When capillary and routine plasma results were discordant, comparison with LC-MS measurements showed that plasma measurements had better concordance: capillary UA, ICC 0.84 (95% CI 0.75-0.90), Lin's coefficient 0.84 (0.77-0.91); plasma UA, ICC 0.96 (0.94-0.98), Lin's coefficient 0.96 (0.94-0.98). UA measurements with the HumaSens plus meter were reasonably comparable with those of the laboratory assay. The meter is easy to use and may be useful in the clinic and in epidemiologic studies.

HIV and STI Prevalence among Female Sex Workers in Côte d'Ivoire: Why Targeted Prevention Programs Should Be Continued and Strengthened

PubMed Central

Vuylsteke, Bea; Semdé, Gisèle; Sika, Lazare; Crucitti, Tania; Ettiègne Traoré, Virginie; Buvé, Anne; Laga, Marie

2012-01-01

Objective To assess condom use and prevalence of STIs and HIV among female sex workers (FSWs), as part of a comprehensive monitoring and evaluation plan of a nationwide sex worker prevention project in Côte d'Ivoire. Design and Methods Cross sectional surveys were conducted among FSWs attending five project clinics in Abidjan and San Pedro (2007), and in Yamoussoukro and Gagnoa (2009). A standardized questionnaire was administered in a face-to-face interview, which included questions on socio-demographic characteristics, sexual behaviour and condom use. After the interview, the participants were asked to provide samples for STI and HIV testing. Results A total of 1110 FSWs participated in the surveys. There were large differences in socio-demographic and behavioural characteristics between FSW coming for the first time as compared to FSW coming on a routine visit. The prevalence of N. gonorrhoeae or C.trachomatis was 9.1%, 11.8% among first vs. 6.9% routine attendees (p = 0.004). The overall HIV prevalence was 26.6%, it was lower among first time attendees (17.5% as compared to 33.9% for routine attendees, p<0.001). The HIV prevalence among first attendees was also lower than the proportion of HIV positive tests from routine testing and counselling services in the same clinics. Conclusions The results show a relatively high STI and HIV prevalence among FSWs in different cities in Côte d'Ivoire. In the light of these results, prevention efforts should continue to focus on FSWs in the country. PMID:22403685

Advanced flight design systems subsystem performance models. Sample model: Environmental analysis routine library

NASA Technical Reports Server (NTRS)

Parker, K. C.; Torian, J. G.

1980-01-01

A sample environmental control and life support model performance analysis using the environmental analysis routines library is presented. An example of a complete model set up and execution is provided. The particular model was synthesized to utilize all of the component performance routines and most of the program options.

Post-standardization of routine creatinine assays: are they suitable for clinical applications.

PubMed

Jassam, Nuthar; Weykamp, Cas; Thomas, Annette; Secchiero, Sandra; Sciacovelli, Laura; Plebani, Mario; Thelen, Marc; Cobbaert, Christa; Perich, Carmen; Ricós, Carmen; Paula, Faria A; Barth, Julian H

2017-05-01

Introduction Reliable serum creatinine measurements are of vital importance for the correct classification of chronic kidney disease and early identification of kidney injury. The National Kidney Disease Education Programme working group and other groups have defined clinically acceptable analytical limits for creatinine methods. The aim of this study was to re-evaluate the performance of routine creatinine methods in the light of these defined limits so as to assess their suitability for clinical practice. Method In collaboration with the Dutch External Quality Assurance scheme, six frozen commutable samples, with a creatinine concentration ranging from 80 to 239  μmol/L and traceable to isotope dilution mass spectrometry, were circulated to 91 laboratories in four European countries for creatinine measurement and estimated glomerular filtration rate calculation. Two out of the six samples were spiked with glucose to give high and low final concentrations of glucose. Results Results from 89 laboratories were analysed for bias, imprecision (%CV) for each creatinine assay and total error for estimated glomerular filtration rate. The participating laboratories used analytical instruments from four manufacturers; Abbott, Beckman, Roche and Siemens. All enzymatic methods in this study complied with the National Kidney Disease Education Programme working group recommended limits of bias of 5% above a creatinine concentration of 100  μmol/L. They also did not show any evidence of interference from glucose. In addition, they also showed compliance with the clinically recommended %CV of ≤4% across the analytical range. In contrast, the Jaffe methods showed variable performance with regard to the interference of glucose and unsatisfactory bias and precision. Conclusion Jaffe-based creatinine methods still exhibit considerable analytical variability in terms of bias, imprecision and lack of specificity, and this variability brings into question their clinical utility. We believe that clinical laboratories and manufacturers should work together to phase out the use of relatively non-specific Jaffe methods and replace them with more specific methods that are enzyme based.

Ultrasound transducer function: annual testing is not sufficient.

PubMed

Mårtensson, Mattias; Olsson, Mats; Brodin, Lars-Åke

2010-10-01

The objective was to follow-up the study 'High incidence of defective ultrasound transducers in use in routine clinical practice' and evaluate if annual testing is good enough to reduce the incidence of defective ultrasound transducers in routine clinical practice to an acceptable level. A total of 299 transducers were tested in 13 clinics at five hospitals in the Stockholm area. Approximately 7000-15,000 ultrasound examinations are carried out at these clinics every year. The transducers tested in the study had been tested and classified as fully operational 1 year before and since then been in normal use in the routine clinical practice. The transducers were tested with the Sonora FirstCall Test System. There were 81 (27.1%) defective transducers found; giving a 95% confidence interval ranging from 22.1 to 32.1%. The most common transducer errors were 'delamination' of the ultrasound lens and 'break in the cable' which together constituted 82.7% of all transducer errors found. The highest error rate was found at the radiological clinics with a mean error rate of 36.0%. There was a significant difference in error rate between two observed ways the clinics handled the transducers. There was no significant difference in the error rates of the transducer brands or the transducers models. Annual testing is not sufficient to reduce the incidence of defective ultrasound transducers in routine clinical practice to an acceptable level and it is strongly advisable to create a user routine that minimizes the handling of the transducers.

Applying metabolomics to cardiometabolic intervention studies and trials: past experiences and a roadmap for the future.

PubMed

Rankin, Naomi J; Preiss, David; Welsh, Paul; Sattar, Naveed

2016-10-01

Metabolomics and lipidomics are emerging methods for detailed phenotyping of small molecules in samples. It is hoped that such data will: (i) enhance baseline prediction of patient response to pharmacotherapies (beneficial or adverse); (ii) reveal changes in metabolites shortly after initiation of therapy that may predict patient response, including adverse effects, before routine biomarkers are altered; and( iii) give new insights into mechanisms of drug action, particularly where the results of a trial of a new agent were unexpected, and thus help future drug development. In these ways, metabolomics could enhance research findings from intervention studies. This narrative review provides an overview of metabolomics and lipidomics in early clinical intervention studies for investigation of mechanisms of drug action and prediction of drug response (both desired and undesired). We highlight early examples from drug intervention studies associated with cardiometabolic disease. Despite the strengths of such studies, particularly the use of state-of-the-art technologies and advanced statistical methods, currently published studies in the metabolomics arena are largely underpowered and should be considered as hypothesis-generating. In order for metabolomics to meaningfully improve stratified medicine approaches to patient treatment, there is a need for higher quality studies, with better exploitation of biobanks from randomized clinical trials i.e. with large sample size, adjudicated outcomes, standardized procedures, validation cohorts, comparison witth routine biochemistry and both active and control/placebo arms. On the basis of this review, and based on our research experience using clinically established biomarkers, we propose steps to more speedily advance this area of research towards potential clinical impact. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) for rapid identification of micro-organisms in the routine clinical microbiology laboratory.

PubMed

Wattal, C; Oberoi, J K; Goel, N; Raveendran, R; Khanna, S

2017-05-01

The study evaluates the utility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) Vitek MS for identification of microorganisms in the routine clinical microbiology laboratory. From May 2013 to April 2014, microbial isolates recovered from various clinical samples were identified by Vitek MS. In case of failure to identify by Vitek MS, the isolate was identified using the Vitek 2 system (bioMerieux, France) and serotyping wherever applicable or otherwise by nucleic acid-mediated methods. All the moulds were identified by Lactophenol blue mounts, and mycobacterial isolates were identified by molecular identification systems including AccuProbe (bioMerieux, France) or GenoType Mycobacterium CM (Hain Lifescience, Germany). Out of the 12,003 isolates, the Vitek MS gave a good overall ID at the genus and or species level up to 97.7% for bacterial isolates, 92.8% for yeasts and 80% for filamentous fungi. Of the 26 mycobacteria tested, only 42.3% could be identified using the Saramis RUO (Research Use Only) database. VITEK MS could not identify 34 of the 35 yeast isolates identified as C. haemulonii by Vitek 2. Subsequently, 17 of these isolates were identified as Candida auris (not present in the Vitek MS database) by 18S rRNA sequencing. Using these strains, an in-house superspectrum of C. auris was created in the VITEK MS database. Use of MALDI-TOF MS allows a rapid identification of aerobic bacteria and yeasts in clinical practice. However, improved sample extraction protocols and database upgrades with inclusion of locally representative strains is required, especially for moulds.

Multilocus sequence typing of Trichomonas vaginalis clinical samples from Amsterdam, the Netherlands

PubMed Central

van der Veer, C; Himschoot, M; Bruisten, S M

2016-01-01

Objectives In this cross-sectional epidemiological study we aimed to identify molecular profiles for Trichomonas vaginalis and to determine how these molecular profiles were related to patient demographic and clinical characteristics. Setting Molecular typing methods previously identified two genetically distinct subpopulations for T. vaginalis; however, few molecular epidemiological studies have been performed. We now increased the sensitivity of a previously described multilocus sequence typing (MLST) tool for T. vaginalis by using nested PCR. This enabled the typing of direct patient samples. Participants From January to December 2014, we collected all T. vaginalis positive samples as detected by routine laboratory testing. Samples from patients either came from general practitioners offices or from the sexually transmitted infections (STI) clinic in Amsterdam. Epidemiological data for the STI clinic patients were retrieved from electronic patient files. Primary and secondary outcome measures The primary outcome was the success rate of genotyping direct T. vaginalis positive samples. The secondary outcome was the relation between T. vaginalis genotypes and risk factors for STI. Results All 7 MLST loci were successfully typed for 71/87 clinical samples. The 71 typed samples came from 69 patients, the majority of whom were women (n=62; 90%) and half (n=34; 49%) were STI clinic patients. Samples segregated into a two population structure for T. vaginalis representing genotypes I and II. Genotype I was most common (n=40; 59.7%). STI clinic patients infected with genotype II reported more sexual partners in the preceding 6 months than patients infected with genotype I (p=0.028). No other associations for gender, age, ethnicity, urogenital discharge or co-occurring STIs with T. vaginalis genotype were found. Conclusions MLST with nested PCR is a sensitive typing method that allows typing of direct (uncultured) patient material. Genotype II is possibly more prevalent in high-risk sexual networks. PMID:27737887

Multilocus sequence typing of Trichomonas vaginalis clinical samples from Amsterdam, the Netherlands.

PubMed

van der Veer, C; Himschoot, M; Bruisten, S M

2016-10-13

In this cross-sectional epidemiological study we aimed to identify molecular profiles for Trichomonas vaginalis and to determine how these molecular profiles were related to patient demographic and clinical characteristics. Molecular typing methods previously identified two genetically distinct subpopulations for T. vaginalis; however, few molecular epidemiological studies have been performed. We now increased the sensitivity of a previously described multilocus sequence typing (MLST) tool for T. vaginalis by using nested PCR. This enabled the typing of direct patient samples. From January to December 2014, we collected all T. vaginalis positive samples as detected by routine laboratory testing. Samples from patients either came from general practitioners offices or from the sexually transmitted infections (STI) clinic in Amsterdam. Epidemiological data for the STI clinic patients were retrieved from electronic patient files. The primary outcome was the success rate of genotyping direct T. vaginalis positive samples. The secondary outcome was the relation between T. vaginalis genotypes and risk factors for STI. All 7 MLST loci were successfully typed for 71/87 clinical samples. The 71 typed samples came from 69 patients, the majority of whom were women (n=62; 90%) and half (n=34; 49%) were STI clinic patients. Samples segregated into a two population structure for T. vaginalis representing genotypes I and II. Genotype I was most common (n=40; 59.7%). STI clinic patients infected with genotype II reported more sexual partners in the preceding 6 months than patients infected with genotype I (p=0.028). No other associations for gender, age, ethnicity, urogenital discharge or co-occurring STIs with T. vaginalis genotype were found. MLST with nested PCR is a sensitive typing method that allows typing of direct (uncultured) patient material. Genotype II is possibly more prevalent in high-risk sexual networks. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

The evaluation of a positive direct antiglobulin test (autocontrol) in pretransfusion testing revisited.

PubMed

Judd, W J; Barnes, B A; Steiner, E A; Oberman, H A; Averill, D B; Butch, S H

1986-01-01

Direct antiglobulin tests (DATs) using anti-IgG were performed on 65,049 blood samples from prospective transfusion recipients; 3570 tests (5.49%) were positive. Using criteria published previously (primarily excluding patients not transfused within the preceding 14 days), 778 samples from other than neonatal patients were selected for further evaluation. Eluates that did not react were obtained on 518 (66.6%) of these samples. Warm-reactive autoantibodies were apparent in 192 eluates, while 16 contained drug-related antibodies, anti-A or anti-B from prior transfusion with ABO mismatched blood components, or anti-D passively acquired from immune serum globulin. Fifty-two eluates contained alloantibodies; however, in only six of these cases did the corresponding serum lack unexpected alloantibodies, as determined by routine pretransfusion studies. Three additional weakly reactive clinically significant alloantibodies were detected solely through additional serum tests performed on DAT-positive samples. On the basis of these findings, the DAT had a low predictive value when used to detect the early manifestations of an immune response to recently transfused red cells. Elimination of the autocontrol from routine pretransfusion testing, therefore, carries minimal risk to patients yet will undoubtedly contribute to the containment of health care costs. Moreover, the risk is lower than that associated with the elimination of the antiglobulin crossmatch.

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

PubMed Central

Fisher, Kevin E.; Zhang, Linsheng; Wang, Jason; Smith, Geoffrey H.; Newman, Scott; Schneider, Thomas M.; Pillai, Rathi N.; Kudchadkar, Ragini R.; Owonikoko, Taofeek K.; Ramalingam, Suresh S.; Lawson, David H.; Delman, Keith A.; El-Rayes, Bassel F.; Wilson, Malania M.; Sullivan, H. Clifford; Morrison, Annie S.; Balci, Serdar; Adsay, N. Volkan; Gal, Anthony A.; Sica, Gabriel L.; Saxe, Debra F.; Mann, Karen P.; Hill, Charles E.; Khuri, Fadlo R.; Rossi, Michael R.

2017-01-01

We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines. PMID:26801070

Fasting Is Not Routinely Required for Determination of a Lipid Profile: Clinical and Laboratory Implications Including Flagging at Desirable Concentration Cutpoints-A Joint Consensus Statement from the European Atherosclerosis Society and European Federation of Clinical Chemistry and Laboratory Medicine.

PubMed

Nordestgaard, Børge G; Langsted, Anne; Mora, Samia; Kolovou, Genovefa; Baum, Hannsjörg; Bruckert, Eric; Watts, Gerald F; Sypniewska, Grazyna; Wiklund, Olov; Borén, Jan; Chapman, M John; Cobbaert, Christa; Descamps, Olivier S; von Eckardstein, Arnold; Kamstrup, Pia R; Pulkki, Kari; Kronenberg, Florian; Remaley, Alan T; Rifai, Nader; Ros, Emilio; Langlois, Michel

2016-07-01

To critically evaluate the clinical implications of the use of non-fasting rather than fasting lipid profiles and to provide guidance for the laboratory reporting of abnormal non-fasting or fasting lipid profiles. Extensive observational data, in which random non-fasting lipid profiles have been compared with those determined under fasting conditions, indicate that the maximal mean changes at 1-6 h after habitual meals are not clinically significant [+0.3 mmol/L (26 mg/dL) for triglycerides; -0.2 mmol/L (8 mg/dL) for total cholesterol; -0.2 mmol/L (8 mg/dL) for LDL cholesterol; +0.2 mmol/L (8 mg/dL) for calculated remnant cholesterol; -0.2 mmol/L (8 mg/dL) for calculated non-HDL cholesterol]; concentrations of HDL cholesterol, apolipoprotein A1, apolipoprotein B, and lipoprotein(a) are not affected by fasting/non-fasting status. In addition, non-fasting and fasting concentrations vary similarly over time and are comparable in the prediction of cardiovascular disease. To improve patient compliance with lipid testing, we therefore recommend the routine use of non-fasting lipid profiles, whereas fasting sampling may be considered when non-fasting triglycerides are >5 mmol/L (440 mg/dL). For non-fasting samples, laboratory reports should flag abnormal concentrations as triglycerides ≥2 mmol/L (175 mg/dL), total cholesterol ≥5 mmol/L (190 mg/dL), LDL cholesterol ≥3 mmol/L (115 mg/dL), calculated remnant cholesterol ≥0.9 mmol/L (35 mg/dL), calculated non-HDL cholesterol ≥3.9 mmol/L (150 mg/dL), HDL cholesterol ≤1 mmol/L (40 mg/dL), apolipoprotein A1 ≤1.25 g/L (125 mg/dL), apolipoprotein B ≥1.0 g/L (100 mg/dL), and lipoprotein(a) ≥50 mg/dL (80th percentile); for fasting samples, abnormal concentrations correspond to triglycerides ≥1.7 mmol/L (150 mg/dL). Life-threatening concentrations require separate referral for the risk of pancreatitis when triglycerides are >10 mmol/L (880 mg/dL), for homozygous familial hypercholesterolemia when LDL cholesterol is >13 mmol/L (500 mg/dL), for heterozygous familial hypercholesterolemia when LDL cholesterol is >5 mmol/L (190 mg/dL), and for very high cardiovascular risk when lipoprotein(a) >150 mg/dL (99th percentile). We recommend that non-fasting blood samples be routinely used for the assessment of plasma lipid profiles. Laboratory reports should flag abnormal values on the basis of desirable concentration cutpoints. Non-fasting and fasting measurements should be complementary but not mutually exclusive. © 2016 American Association for Clinical Chemistry.

Introducing automation to the molecular diagnosis of Trypanosoma cruzi infection: A comparative study of sample treatments, DNA extraction methods and real-time PCR assays.

PubMed

Abras, Alba; Ballart, Cristina; Llovet, Teresa; Roig, Carme; Gutiérrez, Cristina; Tebar, Silvia; Berenguer, Pere; Pinazo, María-Jesús; Posada, Elizabeth; Gascón, Joaquim; Schijman, Alejandro G; Gállego, Montserrat; Muñoz, Carmen

2018-01-01

Polymerase chain reaction (PCR) has become a useful tool for the diagnosis of Trypanosoma cruzi infection. The development of automated DNA extraction methodologies and PCR systems is an important step toward the standardization of protocols in routine diagnosis. To date, there are only two commercially available Real-Time PCR assays for the routine laboratory detection of T. cruzi DNA in clinical samples: TCRUZIDNA.CE (Diagnostic Bioprobes Srl) and RealCycler CHAG (Progenie Molecular). Our aim was to evaluate the RealCycler CHAG assay taking into account the whole process. We assessed the usefulness of an automated DNA extraction system based on magnetic particles (EZ1 Virus Mini Kit v2.0, Qiagen) combined with a commercially available Real-Time PCR assay targeting satellite DNA (SatDNA) of T. cruzi (RealCycler CHAG), a methodology used for routine diagnosis in our hospital. It was compared with a well-known strategy combining a commercial DNA isolation kit based on silica columns (High Pure PCR Template Preparation Kit, Roche Diagnostics) with an in-house Real-Time PCR targeting SatDNA. The results of the two methodologies were in almost perfect agreement, indicating they can be used interchangeably. However, when variations in protocol factors were applied (sample treatment, extraction method and Real-Time PCR), the results were less convincing. A comprehensive fine-tuning of the whole procedure is the key to successful results. Guanidine EDTA-blood (GEB) samples are not suitable for DNA extraction based on magnetic particles due to inhibition, at least when samples are not processed immediately. This is the first study to evaluate the RealCycler CHAG assay taking into account the overall process, including three variables (sample treatment, extraction method and Real-Time PCR). Our findings may contribute to the harmonization of protocols between laboratories and to a wider application of Real-Time PCR in molecular diagnostic laboratories associated with health centers.

Determining health personnel's application trends of new guidelines for preoperative fasting: findings from a survey.

PubMed

Karadağ, Mevlüde; Pekin İşeri, Ozge

2014-06-01

For over a century, the discontinuation of oral food intake preoperatively after midnight has been routinely applied. Although routine fasting during the night before elective surgery has been abandoned by many modern centers, preoperative fasting after midnight continues as a routine practice. The purpose of this study was to determine trends in health personnel's application of new guidelines for preoperative fasting. The research sample of this descriptive study consisted of 73 nurses and physicians who were working in the surgical clinics during the time when the study was conducted and who agreed to participate in the study. The data of the study were collected using a questionnaire designed by the researchers. Of the health personnel included in the study group, 43.8% routinely kept adult patients fasting after midnight, 34.2% discontinued solid food intake 8 hours preoperatively, 5.5% discontinued solid food intake 6 hours preoperatively, and 34.2% discontinued the intake of clear and particulate liquids 4 to 8 hours preoperatively. Compliance of the American Society of Anesthesiologists' "2-4-6-8 rule" by health staff was very low. This study was carried out in a hospital and based on the statements of health staff. Therefore, the findings of the study are suggestive in nature and cannot be generalized. We recommend that the study should be conducted with larger sample groups and that actual preoperative fasting periods of the patients should be determined. Copyright © 2014 American Society of PeriAnesthesia Nurses. Published by Elsevier Inc. All rights reserved.

Uniform data collection in routine clinical practice in cardiovascular patients for optimal care, quality control and research: The Utrecht Cardiovascular Cohort.

PubMed

Asselbergs, Folkert W; Visseren, Frank Lj; Bots, Michiel L; de Borst, Gert J; Buijsrogge, Marc P; Dieleman, Jan M; van Dinther, Baukje Gf; Doevendans, Pieter A; Hoefer, Imo E; Hollander, Monika; de Jong, Pim A; Koenen, Steven V; Pasterkamp, Gerard; Ruigrok, Ynte M; van der Schouw, Yvonne T; Verhaar, Marianne C; Grobbee, Diederick E

2017-05-01

Background Cardiovascular disease remains the major contributor to morbidity and mortality. In routine care for patients with an elevated cardiovascular risk or with symptomatic cardiovascular disease information is mostly collected in an unstructured manner, making the data of limited use for structural feedback, quality control, learning and scientific research. Objective The Utrecht Cardiovascular Cohort (UCC) initiative aims to create an infrastructure for uniform registration of cardiovascular information in routine clinical practice for patients referred for cardiovascular care at the University Medical Center Utrecht, the Netherlands. This infrastructure will promote optimal care according to guidelines, continuous quality control in a learning healthcare system and creation of a research database. Methods The UCC comprises three parts. UCC-1 comprises enrolment of all eligible cardiovascular patients in whom the same information will be collected, based on the Dutch cardiovascular management guideline. A sample of UCC-1 will be invited for UCC-2. UCC-2 involves an enrichment through extensive clinical measurements with emphasis on heart failure, cerebral ischaemia, arterial aneurysms, diabetes mellitus and elevated blood pressure. UCC-3 comprises on-top studies, with in-depth measurements in smaller groups of participants typically based on dedicated project grants. All participants are followed up for morbidity and mortality through linkage with national registries. Conclusion In a multidisciplinary effort with physicians, patients and researchers the UCC sets a benchmark for a learning cardiovascular healthcare system. UCC offers an invaluable resource for future high quality care as well as for first-class research for investigators.

Clustering of self-organizing map identifies five distinct medulloblastoma subgroups.

PubMed

Cao, Changjun; Wang, Wei; Jiang, Pucha

2016-01-01

Medulloblastoma is one the most malignant paediatric brain tumours. Molecular subgrouping these medulloblastomas will not only help identify specific cohorts for certain treatment but also improve confidence in prognostic prediction. Currently, there is a consensus of the existences of four distinct subtypes of medulloblastoma. We proposed a novel bioinformatics method, clustering of self-organizing map, to determine the subgroups and their molecular diversity. Microarray expression profiles of 46 medulloblastoma samples were analysed and five clusters with distinct demographics, clinical outcome and transcriptional profiles were identified. The previously reported Wnt subgroup was identified as expected. Three other novel subgroups were proposed for later investigation. Our findings underscore the value of SOM clustering for discovering the medulloblastoma subgroups. When the suggested subdivision has been confirmed in large cohorts, this method should serve as a part of routine classification of clinical samples.

Microfluidic Sample Preparation for Diagnostic Cytopathology

PubMed Central

Mach, Albert J.; Adeyiga, Oladunni B.; Di Carlo, Dino

2014-01-01

The cellular components of body fluids are routinely analyzed to identify disease and treatment approaches. While significant focus has been placed on developing cell analysis technologies, tools to automate the preparation of cellular specimens have been more limited, especially for body fluids beyond blood. Preparation steps include separating, concentrating, and exposing cells to reagents. Sample preparation continues to be routinely performed off-chip by technicians, preventing cell-based point-of-care diagnostics, increasing the cost of tests, and reducing the consistency of the final analysis following multiple manually-performed steps. Here, we review the assortment of biofluids for which suspended cells are analyzed, along with their characteristics and diagnostic value. We present an overview of the conventional sample preparation processes for cytological diagnosis. We finally discuss the challenges and opportunities in developing microfluidic devices for the purpose of automating or miniaturizing these processes, with particular emphases on preparing large or small volume samples, working with samples of high cellularity, automating multi-step processes, and obtaining high purity subpopulations of cells. We hope to convey the importance of and help identify new research directions addressing the vast biological and clinical applications in preparing and analyzing the array of available biological fluids. Successfully addressing the challenges described in this review can lead to inexpensive systems to improve diagnostic accuracy while simultaneously reducing overall systemic healthcare costs. PMID:23380972

Application of Digital Image Analysis to Determine Pancreatic Islet Mass and Purity in Clinical Islet Isolation and Transplantation

PubMed Central

Wang, Ling-jia; Kissler, Hermann J; Wang, Xiaojun; Cochet, Olivia; Krzystyniak, Adam; Misawa, Ryosuke; Golab, Karolina; Tibudan, Martin; Grzanka, Jakub; Savari, Omid; Grose, Randall; Kaufman, Dixon B; Millis, Michael; Witkowski, Piotr

2015-01-01

Pancreatic islet mass, represented by islet equivalent (IEQ), is the most important parameter in decision making for clinical islet transplantation. To obtain IEQ, the sample of islets is routinely counted manually under a microscope and discarded thereafter. Islet purity, another parameter in islet processing, is routinely acquired by estimation only. In this study, we validated our digital image analysis (DIA) system developed using the software of Image Pro Plus for islet mass and purity assessment. Application of the DIA allows to better comply with current good manufacturing practice (cGMP) standards. Human islet samples were captured as calibrated digital images for the permanent record. Five trained technicians participated in determination of IEQ and purity by manual counting method and DIA. IEQ count showed statistically significant correlations between the manual method and DIA in all sample comparisons (r >0.819 and p < 0.0001). Statistically significant difference in IEQ between both methods was found only in High purity 100μL sample group (p = 0.029). As far as purity determination, statistically significant differences between manual assessment and DIA measurement was found in High and Low purity 100μL samples (p<0.005), In addition, islet particle number (IPN) and the IEQ/IPN ratio did not differ statistically between manual counting method and DIA. In conclusion, the DIA used in this study is a reliable technique in determination of IEQ and purity. Islet sample preserved as a digital image and results produced by DIA can be permanently stored for verification, technical training and islet information exchange between different islet centers. Therefore, DIA complies better with cGMP requirements than the manual counting method. We propose DIA as a quality control tool to supplement the established standard manual method for islets counting and purity estimation. PMID:24806436

[Optimization of blood gas analysis in intensive care units : Reduction of preanalytical errors and improvement of workflow].

PubMed

Kieninger, M; Zech, N; Mulzer, Y; Bele, S; Seemann, M; Künzig, H; Schneiker, A; Gruber, M

2015-05-01

Point of care testing with blood gas analysis (BGA) is an important factor for intensive care medicine. Continuous efforts to optimize workflow, improve safety for the staff and avoid preanalytical mistakes are important and should reflect quality management standards. In a prospective observational study it was investigated whether the implementation of a new system for BGA using labeled syringes and automated processing of the specimens leads to improvements compared to the previously used procedure. In a 4-week test period the time until receiving the final results of the BGA with the standard method used in the clinical routine (control group) was compared to the results in a second 4-week test period using the new labeled syringes and automated processing of the specimens (intervention group). In addition, preanalytical mistakes with both systems were checked during routine daily use. Finally, it was investigated whether a delay of 10 min between taking and analyzing the blood samples alters the results of the BGA. Preanalytical errors were frequently observed in the control group where non-deaerated samples were recorded in 87.3 % but in the intervention group almost all samples (98.9 %) were correctly deaerated. Insufficient homogenization due to omission of manual pivoting was seen in 83.2 % in the control group and in 89.9 % in the intervention group; however, in the intervention group the samples were homogenized automatically during the further analytical process. Although a survey among the staff revealed a high acceptance of the new system and a subjective improvement of workflow, a measurable gain in time after conversion to the new procedure could not be seen. The mean time needed for a complete analysis process until receiving the final results was 244 s in the intervention group and 201 s in the control group. A 10-min delay between taking and analyzing the blood samples led to a significant and clinically relevant elevation of the values for partial pressure of oxygen (pO2) in both groups compared to the results when analyzing the samples immediately (118.4 vs. 148.6 mmHg in the control group and 115.3 vs. 123.7 mmHg in the intervention group). When using standard syringes the partial pressure of carbon dioxide (pCO2) was significantly lower (40.5 vs. 38.3 mmHg) whereas no alterations were seen when using the labeled syringes. The implementation of a new BGA system with labeled syringes and automated processing of the specimens was possible without any difficulties under daily clinical routine conditions in this 10-bed intensive care unit (ICU). A gain of time could not be measured but a reduction in preanalytical errors using the labeled syringes with automated processing was found. Delayed analysis of blood samples can lead to significant changes in pO2 and pCO2 depending on the type of syringe used.

Generalizability of Evidence-Based Assessment Recommendations for Pediatric Bipolar Disorder

PubMed Central

Jenkins, Melissa M.; Youngstrom, Eric A.; Youngstrom, Jennifer Kogos; Feeny, Norah C.; Findling, Robert L.

2013-01-01

Bipolar disorder is frequently clinically diagnosed in youths who do not actually satisfy DSM-IV criteria, yet cases that would satisfy full DSM-IV criteria are often undetected clinically. Evidence-based assessment methods that incorporate Bayesian reasoning have demonstrated improved diagnostic accuracy, and consistency; however, their clinical utility is largely unexplored. The present study examines the effectiveness of promising evidence-based decision-making compared to the clinical gold standard. Participants were 562 youth, ages 5-17 and predominantly African American, drawn from a community mental health clinic. Research diagnoses combined semi-structured interview with youths’ psychiatric, developmental, and family mental health histories. Independent Bayesian estimates relied on published risk estimates from other samples discriminated bipolar diagnoses, Area Under Curve=.75, p<.00005. The Bayes and confidence ratings correlated rs =.30. Agreement about an evidence-based assessment intervention “threshold model” (wait/assess/treat) had K=.24, p<.05. No potential moderators of agreement between the Bayesian estimates and confidence ratings, including type of bipolar illness, were significant. Bayesian risk estimates were highly correlated with logistic regression estimates using optimal sample weights, r=.81, p<.0005. Clinical and Bayesian approaches agree in terms of overall concordance and deciding next clinical action, even when Bayesian predictions are based on published estimates from clinically and demographically different samples. Evidence-based assessment methods may be useful in settings that cannot routinely employ gold standard assessments, and they may help decrease rates of overdiagnosis while promoting earlier identification of true cases. PMID:22004538

[Use of PubMed to improve evidence-based medicine in routine urological practice].

PubMed

Rink, M; Kluth, L A; Shariat, S F; Chun, F K; Fisch, M; Dahm, P

2013-03-01

Applying evidence-based medicine in daily clinical practice is the basis of patient-centered medicine and knowledge of accurate literature acquisition skills is necessary for informed clinical decision-making. PubMed is an easy accessible, free bibliographic database comprising over 21 million citations from the medical field, life-science journals and online books. The article summarizes the effective use of PubMed in routine urological clinical practice based on a common case scenario. This article explains the simple use of PubMed to obtain the best search results with the highest evidence. Accurate knowledge about the use of PubMed in routine clinical practice can improve evidence-based medicine and also patient treatment.

Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers.

PubMed

Rantalainen, Mattias; Klevebring, Daniel; Lindberg, Johan; Ivansson, Emma; Rosin, Gustaf; Kis, Lorand; Celebioglu, Fuat; Fredriksson, Irma; Czene, Kamila; Frisell, Jan; Hartman, Johan; Bergh, Jonas; Grönberg, Henrik

2016-11-30

Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data. Non-routine biomarkers, including mutations in BRCA1, BRCA2 and ERBB2(HER2), and additional clinically actionable somatic alterations were also investigated. Concordance with routine diagnostic biomarkers was high for ER status (AUC = 0.95;AUC(replication) = 0.97) and HER2 status (AUC = 0.97;AUC(replication) = 0.92). The transcriptomic grade model enabled classification of histological grade 1 and histological grade 3 tumors with high accuracy (AUC = 0.98;AUC(replication) = 0.94). Clinically actionable mutations in BRCA1, BRCA2 and ERBB2(HER2) were detected in 5.5% of patients, while 53% had genomic alterations matching ongoing or concluded breast cancer studies. Sequencing-based molecular profiling can be applied as an alternative to histopathology to determine ER and HER2 status, in addition to providing improved tumor grading and clinically actionable mutations and molecular subtypes. Our results suggest that sequencing-based breast cancer diagnostics in a near future can replace routine biomarkers.

Predicting the evolution of low back pain patients in routine clinical practice: results from a registry within the Spanish National Health Service.

PubMed

Kovacs, Francisco M; Seco, Jesús; Royuela, Ana; Corcoll Reixach, Josep; Abraira, Víctor

2012-11-01

The Spanish National Health Service (SNHS) is a tax-funded public organization that provides free health care to every resident in Spain. To develop models for predicting the evolution of low back pain (LBP) in routine clinical practice within SNHS. Analysis of a prospective registry in routine clinical practice, in 17 centers across SNHS. Patient sample includes 4,477 acute and chronic LBP patients treated in primary and hospital care. Pain and disability, measured through validated instruments. Patients treated for LBP were assessed at baseline and 3 months later. Data gathered were the following: sex, age, employment status, duration of pain, severity of LBP, pain down to the leg (LP) and disability, history of lumbar surgery, diagnostic procedures undertaken, imaging findings, and treatments used throughout the study period. Three separate multivariate logistic regression models were developed for predicting a clinically relevant improvement in LBP, LP, and disability at 3 months. In total, 4,261 patients (95.2%) attended follow-up. For all the models, calibration was reasonable and the area under the receiver operating characteristic curve was ≥0.640. For LBP, LP, and disability, factors associated with a higher probability of improvement at 3 months were the following: not having undergone lumbar surgery, higher baseline scores for the corresponding variable, lower ones for the rest, and being treated with neuroreflexotherapy. Additional factors were the following: for LBP, shorter pain duration; for LP, not undergoing electromyography; and for disability, shorter pain duration, not being diagnosed with disc degeneration, and being treated with muscle relaxants and not opioids. A prospective registry can be used for developing predictive models to quantify the odds that a given LBP patient will experience a clinically relevant improvement. This may empower patients for an informed shared decision making. Copyright © 2012 Elsevier Inc. All rights reserved.

Nonculture molecular techniques for diagnosis of bacterial disease in animals: a diagnostic laboratory perspective.

PubMed

Cai, H Y; Caswell, J L; Prescott, J F

2014-03-01

The past decade has seen remarkable technical advances in infectious disease diagnosis, and the pace of innovation is likely to continue. Many of these techniques are well suited to pathogen identification directly from pathologic or clinical samples, which is the focus of this review. Polymerase chain reaction (PCR) and gene sequencing are now routinely performed on frozen or fixed tissues for diagnosis of bacterial infections of animals. These assays are most useful for pathogens that are difficult to culture or identify phenotypically, when propagation poses a biosafety hazard, or when suitable fresh tissue is not available. Multiplex PCR assays, DNA microarrays, in situ hybridization, massive parallel DNA sequencing, microbiome profiling, molecular typing of pathogens, identification of antimicrobial resistance genes, and mass spectrometry are additional emerging technologies for the diagnosis of bacterial infections from pathologic and clinical samples in animals. These technical advances come, however, with 2 caveats. First, in the age of molecular diagnosis, quality control has become more important than ever to identify and control for the presence of inhibitors, cross-contamination, inadequate templates from diagnostic specimens, and other causes of erroneous microbial identifications. Second, the attraction of these technologic advances can obscure the reality that medical diagnoses cannot be made on the basis of molecular testing alone but instead through integrated consideration of clinical, pathologic, and laboratory findings. Proper validation of the method is required. It is critical that veterinary diagnosticians understand not only the value but also the limitations of these technical advances for routine diagnosis of infectious disease.

Quantitative data on the magnitude of the systemic inflammatory response and its effect on micronutrient status based on plasma measurements.

PubMed

Duncan, Andrew; Talwar, Dinesh; McMillan, Donald C; Stefanowicz, Fiona; O'Reilly, Denis St J

2012-01-01

Plasma concentrations of several trace elements and vitamins decrease because of the systemic inflammatory response. Thus, low values do not necessarily indicate deficiency. The magnitude of this effect on plasma micronutrient concentrations was investigated to provide guidance on the interpretation of routine clinical results. Between 2001 and 2011, the results (2217 blood samples from 1303 patients) of routine micronutrient screens (plasma zinc, copper, selenium, and vitamins A, B-6, C, and E) and all vitamin D results (4327 blood samples from 3677 patients) were extracted from the laboratory database. C-reactive protein concentrations were measured as a marker of the severity of inflammation and categorized into 6 groups; for each group, plasma micronutrient concentrations and percentage changes were calculated. Except for copper and vitamin E, all plasma micronutrient concentrations decreased with increasing severities of the acute inflammatory response. For selenium and vitamins B-6 and C, this occurred with only slightly increased C-reactive protein concentrations of 5 to 10 mg/L. For each micronutrient, the change in plasma concentrations varied markedly from patient to patient. The magnitude of the effect was greatest for selenium and vitamins A, B-6, C, and D, for which the median plasma concentrations decreased by >40%. The clinical interpretation of plasma micronutrients can be made only with knowledge of the degree of inflammatory response. A reliable clinical interpretation can be made only if the C-reactive protein is <20 mg/L (plasma zinc), <10 mg/L (plasma selenium and vitamins A and D), or <5 mg/L (vitamins B-6 and C).

[Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics].

PubMed

Nagy, Erzsébet; Abrók, Marianna; Bartha, Noémi; Bereczki, László; Juhász, Emese; Kardos, Gábor; Kristóf, Katalin; Miszti, Cecilia; Urbán, Edit

2014-09-21

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures.

Raman spectroscopic studies on bacteria

NASA Astrophysics Data System (ADS)

Maquelin, Kees; Choo-Smith, Lin-P'ing; Endtz, Hubert P.; Bruining, Hajo A.; Puppels, Gerwin J.

2000-11-01

Routine clinical microbiological identification of pathogenic micro-organisms is largely based on nutritional and biochemical tests. Laboratory results can be presented to a clinician after 2 - 3 days for most clinically relevant micro- organisms. Most of this time is required to obtain pure cultures and enough biomass for the tests to be performed. In the case of severely ill patients, this unavoidable time delay associated with such identification procedures can be fatal. A novel identification method based on confocal Raman microspectroscopy will be presented. With this method it is possible to obtain Raman spectra directly from microbial microcolonies on the solid culture medium, which have developed after only 6 hours of culturing for most commonly encountered organisms. Not only does this technique enable rapid (same day) identifications, but also preserves the sample allowing it to be double-checked with traditional tests. This, combined with the speed and minimal sample handling indicate that confocal Raman microspectroscopy has much potential as a powerful new tool in clinical diagnostic microbiology.

How Postpartum Women With Depressive Symptoms Manage Sleep Disruption and Fatigue.

PubMed

Doering, Jennifer J; Sims, Dauphne A; Miller, Donald D

2017-04-01

Postpartum sleep and fatigue have bidirectional relationships with depressive symptoms and challenge women's everyday functioning. The everyday process of managing postpartum sleep and fatigue in the context of depressive symptoms remains unexplored. We conducted a grounded theory study with a sample of 19 women who screened positive on the Postpartum Depression Screening Scale (PDSS™) Short Form at 3 weeks postpartum. Women completed semi-structured in-home interviews and the full PDSS and Modified Fatigue Symptoms Checklist at 1, 3, and 6 months postpartum. The sample was on average 27 years old, with 2.8 children, and 63% were African-American. They described a basic social process of Finding a Routine Together, during which women's experiences with their infants progressed from Retreating at month 1 toward Finding a New Normal at month 6. In their work to Find a Routine Together, mothers' patterns of change over time were continuous, gradual, or prolonged. Their progress was influenced by depressive symptoms, social support, work and daycare, stability in social circumstances, and underlying stressors. This study's findings suggest the need to allocate resources and tailor interventions to meet the needs of women who are most vulnerable to the health effects of ongoing persistent severe fatigue, disordered sleep, and sub-clinical and clinical levels of depressive symptoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Acknowledging and allocating responsibility for clinical inertia in the management of Type 2 diabetes in primary care: a qualitative study.

PubMed

Zafar, A; Stone, M A; Davies, M J; Khunti, K

2015-03-01

Failure to intensify treatment in patients with Type 2 diabetes with suboptimal blood glucose control has been termed clinical inertia and has been shown to contribute to poorer patient outcomes. We aimed to identify and explore perceptions about clinical inertia from the perspective of primary healthcare providers. A qualitative study was conducted in Leicestershire and Northamptonshire, UK. Purposive sampling was based on healthcare providers working in primary care settings with 'higher' and 'lower' target achievement based on routine data. Twenty semi-structured interviews were conducted, face-to-face or by telephone. Thematic analysis was informed by the constant comparative approach. An important broad theme that emerged during the analysis was related to attribution and explanation of responsibility for clinical inertia. This included general willingness to accept a degree of responsibility for clinical inertia. In some cases, however, participants had inaccurate perceptions about levels of target achievement in their primary care centres, as indicated by routine data. Participants sought to lessen their own sense of accountability by highlighting patient-level barriers such as comorbidities and human fallibility, and also system-level barriers, particularly time constraints. Perceptions about ways of addressing the problem of clinical inertia were not seen as straightforward, further emphasizing a complex and cumulative pattern of barriers. In order to understand and address the problem of clinical inertia, provider, patient- and system-level barriers should be considered together rather than as separate issues. Acknowledgement of responsibility should be regarded positively as a motivator for change. © 2014 The Authors. Diabetic Medicine © 2014 Diabetes UK.

Expanding sexually transmitted infection screening among women and men engaging in transactional sex: the feasibility of field-based self-collection.

PubMed

Roth, A M; Rosenberger, J G; Reece, M; Van Der Pol, B

2013-04-01

Routine screening is a key component of sexually transmitted infection (STI) prevention and control; however, traditional programmes often fail to effectively reach men and women in hidden communities. To reduce prevalence, we must understand the programmatic features that would encourage utilization of services among asymptomatic individuals. Using incentivized snowball sampling, 44 women and men recently engaging in transactional sex were recruited (24 women, 20 men); median age 37 years. Respondents were offered the opportunity to collect genital, oropharyngeal and rectal samples for STI testing and completed a face-to-face interview about their experience with self-obtained sampling. Interviews were analysed using qualitative methods. Participants were unaware of potential risk for STI, but found self-sampling in non-clinical settings to be acceptable and preferable to clinic-based testing. All participants collected genital specimens; 96% and 4% collected oropharyngeal and rectal specimens, respectively. The burden of disease in this population was high: 38% tested positive for at least one STI. We detected multiple concomitant infections. Incorporating field collection of self-obtained samples into STI control programmes may increase utilization among high-risk populations unlikely to access clinic-based services. High infection rates indicate that individuals engaging in transactional sex would benefit from, and be responsive to, community-based self-sampling for STI screening.

Determination of Minimum Training Sample Size for Microarray-Based Cancer Outcome Prediction–An Empirical Assessment

PubMed Central

Cheng, Ningtao; Wu, Leihong; Cheng, Yiyu

2013-01-01

The promise of microarray technology in providing prediction classifiers for cancer outcome estimation has been confirmed by a number of demonstrable successes. However, the reliability of prediction results relies heavily on the accuracy of statistical parameters involved in classifiers. It cannot be reliably estimated with only a small number of training samples. Therefore, it is of vital importance to determine the minimum number of training samples and to ensure the clinical value of microarrays in cancer outcome prediction. We evaluated the impact of training sample size on model performance extensively based on 3 large-scale cancer microarray datasets provided by the second phase of MicroArray Quality Control project (MAQC-II). An SSNR-based (scale of signal-to-noise ratio) protocol was proposed in this study for minimum training sample size determination. External validation results based on another 3 cancer datasets confirmed that the SSNR-based approach could not only determine the minimum number of training samples efficiently, but also provide a valuable strategy for estimating the underlying performance of classifiers in advance. Once translated into clinical routine applications, the SSNR-based protocol would provide great convenience in microarray-based cancer outcome prediction in improving classifier reliability. PMID:23861920

The quality of clinical maternal and neonatal healthcare - a strategy for identifying 'routine care signal functions'.

PubMed

Brenner, Stephan; De Allegri, Manuela; Gabrysch, Sabine; Chinkhumba, Jobiba; Sarker, Malabika; Muula, Adamson S

2015-01-01

A variety of clinical process indicators exists to measure the quality of care provided by maternal and neonatal health (MNH) programs. To allow comparison across MNH programs in low- and middle-income countries (LMICs), a core set of essential process indicators is needed. Although such a core set is available for emergency obstetric care (EmOC), the 'EmOC signal functions', a similar approach is currently missing for MNH routine care evaluation. We describe a strategy for identifying core process indicators for routine care and illustrate their usefulness in a field example. We first developed an indicator selection strategy by combining epidemiological and programmatic aspects relevant to MNH in LMICs. We then identified routine care process indicators meeting our selection criteria by reviewing existing quality of care assessment protocols. We grouped these indicators into three categories based on their main function in addressing risk factors of maternal or neonatal complications. We then tested this indicator set in a study assessing MNH quality of clinical care in 33 health facilities in Malawi. Our strategy identified 51 routine care processes: 23 related to initial patient risk assessment, 17 to risk monitoring, 11 to risk prevention. During the clinical performance assessment a total of 82 cases were observed. Birth attendants' adherence to clinical standards was lowest in relation to risk monitoring processes. In relation to major complications, routine care processes addressing fetal and newborn distress were performed relatively consistently, but there were major gaps in the performance of routine care processes addressing bleeding, infection, and pre-eclampsia risks. The identified set of process indicators could identify major gaps in the quality of obstetric and neonatal care provided during the intra- and immediate postpartum period. We hope our suggested indicators for essential routine care processes will contribute to streamlining MNH program evaluations in LMICs.

The Quality of Clinical Maternal and Neonatal Healthcare – A Strategy for Identifying ‘Routine Care Signal Functions’

PubMed Central

Brenner, Stephan; De Allegri, Manuela; Gabrysch, Sabine; Chinkhumba, Jobiba; Sarker, Malabika; Muula, Adamson S.

2015-01-01

Background A variety of clinical process indicators exists to measure the quality of care provided by maternal and neonatal health (MNH) programs. To allow comparison across MNH programs in low- and middle-income countries (LMICs), a core set of essential process indicators is needed. Although such a core set is available for emergency obstetric care (EmOC), the ‘EmOC signal functions’, a similar approach is currently missing for MNH routine care evaluation. We describe a strategy for identifying core process indicators for routine care and illustrate their usefulness in a field example. Methods We first developed an indicator selection strategy by combining epidemiological and programmatic aspects relevant to MNH in LMICs. We then identified routine care process indicators meeting our selection criteria by reviewing existing quality of care assessment protocols. We grouped these indicators into three categories based on their main function in addressing risk factors of maternal or neonatal complications. We then tested this indicator set in a study assessing MNH quality of clinical care in 33 health facilities in Malawi. Results Our strategy identified 51 routine care processes: 23 related to initial patient risk assessment, 17 to risk monitoring, 11 to risk prevention. During the clinical performance assessment a total of 82 cases were observed. Birth attendants’ adherence to clinical standards was lowest in relation to risk monitoring processes. In relation to major complications, routine care processes addressing fetal and newborn distress were performed relatively consistently, but there were major gaps in the performance of routine care processes addressing bleeding, infection, and pre-eclampsia risks. Conclusion The identified set of process indicators could identify major gaps in the quality of obstetric and neonatal care provided during the intra- and immediate postpartum period. We hope our suggested indicators for essential routine care processes will contribute to streamlining MNH program evaluations in LMICs. PMID:25875252

Diagnostic accuracy of a two-item Drug Abuse Screening Test (DAST-2).

PubMed

Tiet, Quyen Q; Leyva, Yani E; Moos, Rudolf H; Smith, Brandy

2017-11-01

Drug use is prevalent and costly to society, but individuals with drug use disorders (DUDs) are under-diagnosed and under-treated, particularly in primary care (PC) settings. Drug screening instruments have been developed to identify patients with DUDs and facilitate treatment. The Drug Abuse Screening Test (DAST) is one of the most well-known drug screening instruments. However, similar to many such instruments, it is too long for routine use in busy PC settings. This study developed and validated a briefer and more practical DAST for busy PC settings. We recruited 1300 PC patients in two Department of Veterans Affairs (VA) clinics. Participants responded to a structured diagnostic interview. We randomly selected half of the sample to develop and the other half to validate the new instrument. We employed signal detection techniques to select the best DAST items to identify DUDs (based on the MINI) and negative consequences of drug use (measured by the Inventory of Drug Use Consequences). Performance indicators were calculated. The two-item DAST (DAST-2) was 97% sensitive and 91% specific for DUDs in the development sample and 95% sensitive and 89% specific in the validation sample. It was highly sensitive and specific for DUD and negative consequences of drug use in subgroups of patients, including gender, age, race/ethnicity, marital status, educational level, and posttraumatic stress disorder status. The DAST-2 is an appropriate drug screening instrument for routine use in PC settings in the VA and may be applicable in broader range of PC clinics. Published by Elsevier Ltd.

Morphological and biochemical characterization of the aetiological agents of white piedra.

PubMed

Magalhães, Alba Regina; Mondino, Silvia Susana Bona de; Silva, Manuela da; Nishikawa, Marilia Martins

2008-12-01

The Trichosporon genus is constituted by many species, of which Trichosporon ovoides and Trichosporon inkin are the causative agents of white piedra. They can cause nodules in genital hair or on the scalp. At present, Brazilian laboratory routines generally do not include the identification of the species of Trichosporon genus, which, although morphologically and physiologically distinct, present many similarities, making the identification difficult. The aim of this study was to identify the aetiological agents at the species level of white piedra from clinical specimens. Therefore, both the macro and micro morphology were studied, and physiological tests were performed. Trichosporon spp. was isolated from 10 clinical samples; T. ovoides was predominant, as it was found in seven samples, while T. inkin was identified just in two samples. One isolate could not be identified at the species level. T. inkin was identified for the first time as a white piedra agent in the hair shaft on child under the age of 10.

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis

PubMed Central

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-01-01

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis. PMID:27157697

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis

NASA Astrophysics Data System (ADS)

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-05-01

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.

Detection of herpes simplex virus and varicella-zoster virus in clinical swabs: frequent inhibition of PCR as determined by internal controls.

PubMed

Bezold, G; Volkenandt, M; Gottlöber, P; Peter, R U

2000-12-01

PCR-based detection of microorganisms is widely used for diagnostic purposes. Most routine PCR applications do not control for inhibition of PCR, thus leading to false-negative results. One hundred eighteen swab samples obtained from skin and mucosa were investigated for the presence of herpes simplex virus (HSV), varicella-zoster virus (VZV), and the control gene betaglobin by internally controlled PCR with purified and unpurified DNA in parallel. With unpurified DNA, inhibition of PCR was detected in 23% of betaglobin PCRs, 25% of VZV PCRs, and 16% of HSV PCRs versus 3% each for purified DNA. Approximately 20% of the samples with positive results for HSV or VZV had negative or inhibited results using unpurified DNA. These results indicate that PCR from clinical swab specimens should be performed exclusively with internal controls because the positive control alone cannot exclude PCR inhibition in individual samples. Purification of DNA will decrease, but not exclude, PCR inhibition.

Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: Retrospective validation and prospective audit in the UK National Health Service

PubMed Central

Kaur, Kulvinder; Camps, Carme; Kaisaki, Pamela; Gupta, Avinash; Talbot, Denis; Middleton, Mark; Henderson, Shirley; Cutts, Anthony; Vavoulis, Dimitrios V.; Housby, Nick; Taylor, Jenny C.; Schuh, Anna

2017-01-01

Background Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing. Methods and findings We validated a 46-gene hotspot cancer panel assay allowing multiple gene testing from small diagnostic biopsies. From 1 January 2013 to 31 December 2013, solid tumour samples (including non-small-cell lung carcinoma [NSCLC], colorectal carcinoma, and melanoma) were sequenced in the context of the UK National Health Service from 351 consecutively submitted prospective cases for which treating clinicians thought the patient had potential to benefit from more extensive genetic analysis. Following histological assessment, tumour-rich regions of formalin-fixed paraffin-embedded (FFPE) sections underwent macrodissection, DNA extraction, NGS, and analysis using a pipeline centred on Torrent Suite software. With a median turnaround time of seven working days, an integrated clinical report was produced indicating the variants detected, including those with potential diagnostic, prognostic, therapeutic, or clinical trial entry implications. Accompanying phenotypic data were collected, and a detailed cost analysis of the panel compared with single gene testing was undertaken to assess affordability for routine patient care. Panel sequencing was successful for 97% (342/351) of tumour samples in the prospective cohort and showed 100% concordance with known mutations (detected using cobas assays). At least one mutation was identified in 87% (296/342) of tumours. A locally actionable mutation (i.e., available targeted treatment or clinical trial) was identified in 122/351 patients (35%). Forty patients received targeted treatment, in 22/40 (55%) cases solely due to use of the panel. Examination of published data on the potential efficacy of targeted therapies showed theoretically actionable mutations (i.e., mutations for which targeted treatment was potentially appropriate) in 66% (71/107) and 39% (41/105) of melanoma and NSCLC patients, respectively. At a cost of £339 (US$449) per patient, the panel was less expensive locally than performing more than two or three single gene tests. Study limitations include the use of FFPE samples, which do not always provide high-quality DNA, and the use of “real world” data: submission of cases for sequencing did not always follow clinical guidelines, meaning that when mutations were detected, patients were not always eligible for targeted treatments on clinical grounds. Conclusions This study demonstrates that more extensive tumour sequencing can identify mutations that could improve clinical decision-making in routine cancer care, potentially improving patient outcomes, at an affordable level for healthcare providers. PMID:28196074

Opinions and practices of healthcare professionals on assessment of disease associated malnutrition in children: Results from an international survey.

PubMed

Huysentruyt, Koen; Hulst, Jessie; Bian, Feifei; Shamir, Raanan; White, Melinda; Galera-Martinez, Raphael; Morais-Lopez, Anna; Kansu, Aydan; Gerasimidis, Konstantinos

2018-04-05

Lack of consensus on clinical indicators for the assessment of pediatric disease associated malnutrition (DAM) may explain its under-recognition in clinical practice. This study surveyed the opinions of health professionals (HP) on clinical indicators of DAM and barriers impeding routine nutritional screening in children. Web-based questionnaire survey (April 2013-August 2015) in Australia, Belgium, Israel, Spain, The Netherlands, Turkey and UK. There were 937 questionnaires returned via local professional associations, of which 693 respondents fulfilled the inclusion criteria and were included in the final analysis; 315 pediatric gastroenterologists and 378 pediatric dieticians. The most important clinical indicators of DAM were ongoing weight loss (80.4%), increased energy/nutrient losses (73.0%), suboptimal energy/macronutrient intake (68.6%), a high nutritional risk condition (67.2%) and increased energy/nutrient requirements (66.2%). These findings were consistent across countries and professions. The most common approach to screen for DAM was assessment of weight changes (85%), followed by the usage of growth charts (77-80%). Common perceived barriers for routine nutritional screening/assessment were low staff awareness (47.5%), no local policy or guidelines (33.4%) and lack of time to screen (33.4%). HP who routinely assess and treat children with DAM identified ongoing weight loss, increased losses, increased requirements, low intake and high nutritional risk conditions as the most important clinical indicators of DAM. These clinical indicators should now serve as a basis to form clinical-based criteria for the identification of DAM in routine clinical practice. Low awareness, lack of guidelines or local policy and lack of resources were the most important barriers of routine screening. Copyright © 2018 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

The clinical value of daily routine chest radiographs in a mixed medical-surgical intensive care unit is low.

PubMed

Graat, Marleen E; Choi, Goda; Wolthuis, Esther K; Korevaar, Johanna C; Spronk, Peter E; Stoker, Jaap; Vroom, Margreeth B; Schultz, Marcus J

2006-02-01

The clinical value of daily routine chest radiographs (CXRs) in critically ill patients is unknown. We conducted this study to evaluate how frequently unexpected predefined major abnormalities are identified with daily routine CXRs, and how often these findings lead to a change in care for intensive care unit (ICU) patients. This was a prospective observational study conducted in a 28-bed, mixed medical-surgical ICU of a university hospital. Over a 5-month period, 2,457 daily routine CXRs were done in 754 consecutive ICU patients. The majority of these CXRs did not reveal any new predefined major finding. In only 5.8% of daily routine CXRs (14.3% of patients) was one or more new and unexpected abnormality encountered, including large atelectases (24 times in 20 patients), large infiltrates (23 in 22), severe pulmonary congestion (29 in 25), severe pleural effusion (13 in 13), pneumothorax/pneumomediastinum (14 in 13), and malposition of the orotracheal tube (32 in 26). Fewer than half of the CXRs with a new and unexpected finding were ultimately clinically relevant; in only 2.2% of all daily routine CXRs (6.4% of patients) did these radiologic abnormalities result in a change to therapy. Subgroup analysis revealed no differences between medical and surgical patients with regard to the incidence of new and unexpected findings on daily routine CXRs and the effect of new and unexpected CXR findings on daily care. In the ICU, daily routine CXRs seldom reveal unexpected, clinically relevant abnormalities, and they rarely prompt action. We propose that this diagnostic examination be abandoned in ICU patients.

panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.

PubMed

Povysil, Gundula; Tzika, Antigoni; Vogt, Julia; Haunschmid, Verena; Messiaen, Ludwine; Zschocke, Johannes; Klambauer, Günter; Hochreiter, Sepp; Wimmer, Katharina

2017-07-01

Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy-number variations (CNVs) in addition to single-nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics. © 2017 The Authors. Human Mutation published by Wiley Periodicals, Inc.

panelcn.MOPS: Copy‐number detection in targeted NGS panel data for clinical diagnostics

PubMed Central

Povysil, Gundula; Tzika, Antigoni; Vogt, Julia; Haunschmid, Verena; Messiaen, Ludwine; Zschocke, Johannes; Klambauer, Günter; Wimmer, Katharina

2017-01-01

Abstract Targeted next‐generation‐sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy‐number variations (CNVs) in addition to single‐nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user‐friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state‐of‐the‐art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user‐selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user‐friendliness rendering it highly suitable for routine clinical diagnostics. PMID:28449315

Quantification and clinical application of carboplatin in plasma ultrafiltrate.

PubMed

Downing, Kim; Jensen, Berit Packert; Grant, Sue; Strother, Matthew; George, Peter

2017-05-10

Carboplatin is a chemotherapy drug used in a variety of cancers with the primary toxicity being exposure-dependant myelosuppression. We present the development and validation of a simple, robust inductively coupled plasma mass spectrometry (ICP-MS) method to measure carboplatin in plasma ultrafiltrate. Plasma ultrafiltrates samples were prepared using Amicon Ultra 30,000da cut-off filters and then diluted with ammonia EDTA before ICP-MS analysis. The assay was validated in the range 0.19-47.5mg/L carboplatin in ultrafiltrate. The assay was linear (r 2 >0.9999), accurate (<6% bias, 12% bias at LLOQ) and precise (intra- and inter-day precision of <3% coefficient of variation). No matrix effects were observed between plasma ultrafiltrate and aqueous platinum calibrators and recovery was complete. The assay was applied to 10 clinical samples from patients receiving carboplatin. Incurred sample reanalysis showed reproducible values over 3 analysis days (<6% CV). As plasma stability prior to ultrafiltration has been a major concern in previous clinical studies this was studied extensively at room temperature (22°C) over 24h. Carboplatin was found to be stable in both spiked plasma (n=3) and real patient samples (n=10) at room temperature for up to 8h before ultrafiltration. This makes routine measurement of carboplatin concentrations in clinical settings feasible. Copyright © 2017 Elsevier B.V. All rights reserved.

Diagnostic accuracy of routine blood examinations and CSF lactate level for post-neurosurgical bacterial meningitis.

PubMed

Zhang, Yang; Xiao, Xiong; Zhang, Junting; Gao, Zhixian; Ji, Nan; Zhang, Liwei

2017-06-01

To evaluate the diagnostic accuracy of routine blood examinations and Cerebrospinal Fluid (CSF) lactate level for Post-neurosurgical Bacterial Meningitis (PBM) at a large sample-size of post-neurosurgical patients. The diagnostic accuracies of routine blood examinations and CSF lactate level to distinguish between PAM and PBM were evaluated with the values of the Area Under the Curve of the Receiver Operating Characteristic (AUC -ROC ) by retrospectively analyzing the datasets of post-neurosurgical patients in the clinical information databases. The diagnostic accuracy of routine blood examinations was relatively low (AUC -ROC <0.7). The CSF lactate level achieved rather high diagnostic accuracy (AUC -ROC =0.891; CI 95%, 0.852-0.922). The variables of patient age, operation duration, surgical diagnosis and postoperative days (the interval days between the neurosurgery and examinations) were shown to affect the diagnostic accuracy of these examinations. The variables were integrated with routine blood examinations and CSF lactate level by Fisher discriminant analysis to improve their diagnostic accuracy. As a result, the diagnostic accuracy of blood examinations and CSF lactate level was significantly improved with an AUC -ROC value=0.760 (CI 95%, 0.737-0.782) and 0.921 (CI 95%, 0.887-0.948) respectively. The PBM diagnostic accuracy of routine blood examinations was relatively low, whereas the accuracy of CSF lactate level was high. Some variables that are involved in the incidence of PBM can also affect the diagnostic accuracy for PBM. Taking into account the effects of these variables significantly improves the diagnostic accuracies of routine blood examinations and CSF lactate level. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Empiric antibiotic treatment for urinary tract infection in preschool children: susceptibilities of urine sample isolates.

PubMed

Butler, Christopher C; O'Brien, Kathryn; Wootton, Mandy; Pickles, Timothy; Hood, Kerenza; Howe, Robin; Waldron, Cherry-Ann; Thomas-Jones, Emma; Dudley, Jan; Van Der Voort, Judith; Rumsby, Kate; Little, Paul; Downing, Harriet; Harman, Kim; Hay, Alastair D

2016-04-01

Antibiotic treatment recommendations based on susceptibility data from routinely submitted urine samples may be biased because of variation in sampling, laboratory procedures and inclusion of repeat samples, leading to uncertainty about empirical treatment. To describe and compare susceptibilities of Escherichia coli cultured from routinely submitted samples, with E. coli causing urinary tract infection (UTI) from a cohort of systematically sampled, acutely unwell children. Susceptibilities of 1458 E. coli isolates submitted during the course of routine primary care for children <5 years (routine care samples), compared to susceptibilities of 79 E. coli isolates causing UTI from 5107 children <5 years presenting to primary care with an acute illness [systematic sampling: the Diagnosis of Urinary Tract infection in Young children (DUTY) cohort]. The percentage of E. coli sensitive to antibiotics cultured from routinely submitted samples were as follows: amoxicillin 45.1% (95% confidence interval: 42.5-47.7%); co-amoxiclav using the lower systemic break point (BP) 86.6% (84.7-88.3%); cephalexin 95.1% (93.9-96.1%); trimethoprim 74.0% (71.7-76.2%) and nitrofurantoin 98.2% (97.4-98.8%). The percentage of E. coli sensitive to antibiotics cultured from systematically sampled DUTY urines considered to be positive for UTI were as follows: amoxicillin 50.6% (39.8-61.4%); co-amoxiclav using the systemic BP 83.5% (73.9-90.1%); co-amoxiclav using the urinary BP 94.9% (87.7-98.4%); cephalexin 98.7% (93.2-99.8%); trimethoprim 70.9% (60.1-80.0%); nitrofurantoin 100% (95.3-100.0%) and ciprofloxacin 96.2% (89.4-98.7%). Escherichia coli susceptibilities from routine and systematically obtained samples were similar. Most UTIs in preschool children remain susceptible to nitrofurantoin, co-amoxiclav and cephalexin. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Series: Pragmatic trials and real world evidence: Paper 8. Data collection and management.

PubMed

Meinecke, Anna-Katharina; Welsing, Paco; Kafatos, George; Burke, Des; Trelle, Sven; Kubin, Maria; Nachbaur, Gaelle; Egger, Matthias; Zuidgeest, Mira

2017-11-01

Pragmatic trials can improve our understanding of how treatments will perform in routine practice. In a series of eight papers, the GetReal Consortium has evaluated the challenges in designing and conducting pragmatic trials and their specific methodological, operational, regulatory, and ethical implications. The present final paper of the series discusses the operational and methodological challenges of data collection in pragmatic trials. A more pragmatic data collection needs to balance the delivery of highly accurate and complete data with minimizing the level of interference that data entry and verification induce with clinical practice. Furthermore, it should allow for the involvement of a representative sample of practices, physicians, and patients who prescribe/receive treatment in routine care. This paper discusses challenges that are related to the different methods of data collection and presents potential solutions where possible. No one-size-fits-all recommendation can be given for the collection of data in pragmatic trials, although in general the application of existing routinely used data-collection systems and processes seems to best suit the pragmatic approach. However, data access and privacy, the time points of data collection, the level of detail in the data, and the lack of a clear understanding of the data-collection process were identified as main challenges for the usage of routinely collected data in pragmatic trials. A first step should be to determine to what extent existing health care databases provide the necessary study data and can accommodate data collection and management. When more elaborate or detailed data collection or more structured follow-up is required, data collection in a pragmatic trial will have to be tailor-made, often using a hybrid approach using a dedicated electronic case report form (eCRF). In this case, the eCRF should be kept as simple as possible to reduce the burden for practitioners and minimize influence on routine clinical practice. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Implementation of cognitive therapy for PTSD in routine clinical care: effectiveness and moderators of outcome in a consecutive sample.

PubMed

Ehlers, Anke; Grey, Nick; Wild, Jennifer; Stott, Richard; Liness, Sheena; Deale, Alicia; Handley, Rachel; Albert, Idit; Cullen, Deborah; Hackmann, Ann; Manley, John; McManus, Freda; Brady, Francesca; Salkovskis, Paul; Clark, David M

2013-11-01

Trauma-focused psychological treatments are recommended as first-line treatments for Posttraumatic Stress Disorder (PTSD), but clinicians may be concerned that the good outcomes observed in randomized controlled trials (RCTs) may not generalize to the wide range of traumas and presentations seen in clinical practice. This study investigated whether Cognitive Therapy for PTSD (CT-PTSD) can be effectively implemented into a UK National Health Service Outpatient Clinic serving a defined ethnically mixed urban catchment area. A consecutive sample of 330 patients with PTSD (age 17-83) following a wide range of traumas were treated by 34 therapists, who received training and supervision in CT-PTSD. Pre and post treatment data (PTSD symptoms, anxiety, depression) were collected for all patients, including dropouts. Hierarchical linear modeling investigated candidate moderators of outcome and therapist effects. CT-PTSD was well tolerated and led to very large improvement in PTSD symptoms, depression and anxiety. The majority of patients showed reliable improvement/clinically significant change: intent-to-treat: 78.8%/57.3%; completer: 84.5%/65.1%. Dropouts and unreliable attenders had worse outcome. Statistically reliable symptom exacerbation with treatment was observed in only 1.2% of patients. Treatment gains were maintained during follow-up (M=280 days, n=220). Few of the selection criteria used in some RCTs, demographic, diagnostic and trauma characteristics moderated treatment outcome, and only social problems and needing treatment for multiple traumas showed unique moderation effects. There were no random effects of therapist on symptom improvement, but therapists who were inexperienced in CT-PTSD had more dropouts than those with greater experience. The results support the effectiveness of CT-PTSD and suggest that trauma-focused cognitive behavior therapy can be successfully implemented in routine clinical services treating patients with a wide range of traumas. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Methodology and lessons-learned from the efficacy clinical trial of the pentavalent rotavirus vaccine in Bangladesh.

PubMed

Zaman, K; Yunus, M; El Arifeen, Shams; Azim, Tasnim; Faruque, A S G; Huq, Ehsanul; Hossain, Ilias; Luby, Stephen P; Victor, John C; Dallas, Michael J; Lewis, Kristen D C; Rivers, Stephen B; Steele, A Duncan; Neuzil, Kathleen M; Ciarlet, Max; Sack, David A

2012-04-27

An efficacy clinical trial with pentavalent rotavirus vaccine (PRV), RotaTeq(®), was conducted at Matlab field site of ICDDR,B, Bangladesh from March 2007 to March 2009. The methodology, including operation logistics, and lessons-learned are described in this report. Vaccination was organized at 41 fixed-site clinics twice/month. A total of 1136 infants were randomized 1:1 to receive 3 doses of PRV/placebo at approximately 6-, 10-, and 14-weeks of age with routine vaccines of the Expanded Programme on Immunization (EPI) schedule. Twelve field-workers routinely visited study participants for safety and efficacy follow-up. The study was conducted following good clinical practices and maintaining cold-chain requirements. There were no temperature deviations of clinical vaccine supplies. Data entry was done using the source documents to a central database developed by the sponsor which was linked to web. Among enrolled infants, 1128 (99.3%) received 3 doses of PRV/placebo and efficacy follow-up was conducted for a median of 554 days. For the evaluation of immunogenicity, blood samples were collected from 150 participants predose 1 and from 147 (98%) of the same participants post dose 3. Stool samples were collected from 778 (99.9%) acute gastroenteritis episodes among children who reported to diarrhoea treatment centres. Thirty-nine serious adverse events, including 6 deaths, occurred among study participants. The efficacy of PRV against severe rotavirus gastroenteritis was 42.7% through the entire follow-up period; serum anti-rotavirus IgA response was 78.1%. Inclement weather, difficult transportation, and movement of study participants were some of the challenges identified. This is the first vaccine trial in rural Bangladesh with online data entry. The study was well accepted in the community and was completed successfully. Copyright © 2011 Elsevier Ltd. All rights reserved.

Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine.

PubMed

Han, Yanxi; Li, Jinming

2017-10-26

In this era of precision medicine, molecular biology is becoming increasingly significant for the diagnosis and therapeutic management of non-small cell lung cancer. The specimen as the primary element of the whole testing flow is particularly important for maintaining the accuracy of gene alteration testing. Presently, the main sample types applied in routine diagnosis are tissue and cytology biopsies. Liquid biopsies are considered as the most promising alternatives when tissue and cytology samples are not available. Each sample type possesses its own strengths and weaknesses, pertaining to the disparity of sampling, preparation and preservation procedures, the heterogeneity of inter- or intratumors, the tumor cellularity (percentage and number of tumor cells) of specimens, etc., and none of them can individually be a "one size to fit all". Therefore, in this review, we summarized the strengths and weaknesses of different sample types that are widely used in clinical practice, offered solutions to reduce the negative impact of the samples and proposed an optimized strategy for choice of samples during the entire diagnostic course. We hope to provide valuable information to laboratories for choosing optimal clinical specimens to achieve comprehensive functional genomic landscapes and formulate individually tailored treatment plans for NSCLC patients that are in advanced stages.

Prospective validation of a blood-based 9-miRNA profile for early detection of breast cancer in a cohort of women examined by clinical mammography.

PubMed

Lyng, Maria B; Kodahl, Annette R; Binder, Harald; Ditzel, Henrik J

2016-12-01

Mammography is the predominant screening method for early detection of breast cancer, but has limitations and could be rendered more accurate by combination with a blood-based biomarker profile. Circulating microRNAs (miRNAs) are increasingly recognized as strong biomarkers, and we previously developed a 9-miRNA profile using serum and LNA-based qPCR that effectively stratified patients with early stage breast cancer vs. healthy women. To further develop the test into routine clinical practice, we collected serum of women examined by clinical mammography (N = 197) according to standard operational procedures (SOPs) of the Danish Cancer Biobank. The performance of the circulating 9-miRNA profile was analyzed in 116 of these women, including 36 with breast cancer (aged 50-74), following a standardized protocol that mimicked a routine clinical set-up. We confirmed that the profile is significantly different between women with breast cancer and controls (p-value <0.0001), with an AUC of 0.61. Significantly, one woman whose 9-miRNA profile predicted a 73% probability of having breast cancer indeed developed the disease within one year despite being categorized as clinically healthy at the time of blood sample collection and mammography. We propose that this miRNA profile combined with mammography will increase the overall accuracy of early detection of breast cancer. Copyright © 2016 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

CONCEPTUAL AND METHODOLOGICAL ISSUES IN DESIGNING A RANDOMIZED CONTROLLED TREATMENT TRIAL FOR GERIATRIC BIPOLAR DISORDER: GERI-BD

PubMed Central

Young, Robert C.; Schulberg, Herbert C.; Gildengers, Ariel G.; Sajatovic, Martha; Mulsant, Benoit H.; Gyulai, Laszlo; Beyer, John; Marangell, Lauren; Kunik, Mark; Have, Thomas Ten; Bruce, Martha L.; Gur, Ruben; Marino, Patricia; Evans, Jovier D.; Reynolds, Charles F.; Alexopoulos, George S.

2010-01-01

Aim This report considers the conceptual and methodological concerns confronting clinical investigators seeking to generate knowledge regarding the tolerability and benefits of pharmacotherapy in geriatric bipolar (BP) patients. Method There is continuing need for evidence-based guidelines derived from randomized controlled trials that will enhance drug treatment of geriatric BP patients. We, therefore, present the complex conceptual and methodological choices encountered in designing a multi-site clinical trial and the decisions reached by the investigators with the intention that study findings are pertinent to, and can facilitate, routine treatment decisions. Results Guided by a literature review and input from peers, the tolerability and anti-manic effect of lithium and valproate were judged to be the key mood stabilizers to investigate with regard to treating BP I manic, mixed and hypomanic states. The patient selection criteria are intended to generate a sample that experiences common treatment needs but which also represents the variety of older patients seen in university-based clinical settings. The clinical protocol guides titratation of lithium and valproate to target serum concentrations, with lower levels allowed when necessitated by limited tolerability. The protocol emphasizes initial monotherapy. However, augmentation with risperidone is permitted after three weeks when indicated by operational criteria. Conclusions A randomized controlled trial that both investigates commonly prescribed mood stabilizers and maximizes patient participation can meaningfully address high priority clinical concerns directly relevant to the routine pharmacologic treatment of geriatric BP patients. PMID:20148867

An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences.

PubMed

Gerritsen, K E H; Olieslagers, T I; Groeneweg, M; Voorter, C E M; Tilanus, M G J

2014-11-01

The functional relevance of human leukocyte antigen (HLA) class I allele polymorphism beyond exons 2 and 3 is difficult to address because more than 70% of the HLA class I alleles are defined by exons 2 and 3 sequences only. For routine application on clinical samples we improved and validated the HLA sequence-based typing (SBT) approach based on RNA templates, using either a single locus-specific or two overlapping group-specific polymerase chain reaction (PCR) amplifications, with three forward and three reverse sequencing reactions for full length sequencing. Locus-specific HLA typing with RNA SBT of a reference panel, representing the major antigen groups, showed identical results compared to DNA SBT typing. Alleles encountered with unknown exons in the IMGT/HLA database and three samples, two with Null and one with a Low expressed allele, have been addressed by the group-specific RNA SBT approach to obtain full length coding sequences. This RNA SBT approach has proven its value in our routine full length definition of alleles. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Non-Antibody Universal Detection of Protein Phosphorylation Using pIMAGO

PubMed Central

Iliuk, Anton B.; Tao, W. Andy

2015-01-01

With recent technical advances, important signaling pathways have continuously been discovered and dissected in many biological events. The vast majority of these signaling pathways involve reversible protein phosphorylation, and the dynamics of phosphorylation provides important mechanisms on how signaling networks function and interact. With a variety of research projects using lab models or clinical samples, a simple and reliable phosphorylation assay is highly desirable for routine detection of phosphorylation in sample mixtures. The protocols in this article describe the general procedure for a new non-antibody strategy for phosphorylation assay, termed pIMAGO (phospho-imaging). This novel design takes advantage of not only the unique properties of the soluble nanoparticles, but also of the multiple functionality of the molecule, allowing for highly selective, sensitive and quantitative assessment of protein phosphorylation without the use of either radioactive isotopes or limited phosphospecific antibodies. It also offers the capability for multiplexed detection of phosphorylation and total protein amount simultaneously. The described procedures allow for straightforward and routine detection and quantitation of general phosphorylation on any site of any protein in Western Blot and ELISA formats. PMID:25727060

Doubling immunochemistry laboratory testing efficiency with the cobas e 801 module while maintaining consistency in analytical performance.

PubMed

Findeisen, P; Zahn, I; Fiedler, G M; Leichtle, A B; Wang, S; Soria, G; Johnson, P; Henzell, J; Hegel, J K; Bendavid, C; Collet, N; McGovern, M; Klopprogge, K

2018-06-04

The new immunochemistry cobas e 801 module (Roche Diagnostics) was developed to meet increasing demands on routine laboratories to further improve testing efficiency, while maintaining high quality and reliable data. During a non-interventional multicenter evaluation study, the overall performance, functionality and reliability of the new module was investigated under routine-like conditions. It was tested as a dedicated immunochemistry system at four sites and as a consolidator combined with clinical chemistry at three sites. We report on testing efficiency and analytical performance of the new module. Evaluation of sample workloads with site-specific routine request patterns demonstrated increased speed and almost doubled throughput (maximal 300 tests per h), thus revealing that one cobas e 801 module can replace two cobas e 602 modules while saving up to 44% floor space. Result stability was demonstrated by QC analysis per assay throughout the study. Precision testing over 21 days yielded excellent results within and between labs, and, method comparison performed versus the cobas e 602 module routine results showed high consistency of results for all assays under study. In a practicability assessment related to performance and handling, 99% of graded features met (44%) or even exceeded (55%) laboratory expectations, with enhanced reagent management and loading during operation being highlighted. By nearly doubling immunochemistry testing efficiency on the same footprint as a cobas e 602 module, the new module has a great potential to further consolidate and enhance laboratory testing while maintaining high quality analytical performance with Roche platforms. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Surveillance for cancer recurrence in long-term young breast cancer survivors randomly selected from a statewide cancer registry.

PubMed

Jones, Tarsha; Duquette, Debra; Underhill, Meghan; Ming, Chang; Mendelsohn-Victor, Kari E; Anderson, Beth; Milliron, Kara J; Copeland, Glenn; Janz, Nancy K; Northouse, Laurel L; Duffy, Sonia M; Merajver, Sofia D; Katapodi, Maria C

2018-05-01

This study examined clinical breast exam (CBE) and mammography surveillance in long-term young breast cancer survivors (YBCS) and identified barriers and facilitators to cancer surveillance practices. Data collected with a self-administered survey from a statewide, randomly selected sample of YBCS diagnosed with invasive breast cancer or ductal carcinoma in situ younger than 45 years old, stratified by race (Black vs. White/Other). Multivariate logistic regression models identified predictors of annual CBEs and mammograms. Among 859 YBCS (n = 340 Black; n = 519 White/Other; mean age = 51.0 ± 5.9; diagnosed 11.0 ± 4.0 years ago), the majority (> 85%) reported an annual CBE and a mammogram. Black YBCS in the study were more likely to report lower rates of annual mammography and more barriers accessing care compared to White/Other YBCS. Having a routine source of care, confidence to use healthcare services, perceived expectations from family members and healthcare providers to engage in cancer surveillance, and motivation to comply with these expectations were significant predictors of having annual CBEs and annual mammograms. Cost-related lack of access to care was a significant barrier to annual mammograms. Routine source of post-treatment care facilitated breast cancer surveillance above national average rates. Persistent disparities regarding access to mammography surveillance were identified for Black YBCS, primarily due to lack of access to routine source of care and high out-of-pocket costs. Public health action targeting cancer surveillance in YBCS should ensure routine source of post-treatment care and address cost-related barriers. Clinical Trials Registration Number: NCT01612338.

Clinical Supervision of Mental Health Professionals Serving Youth: Format and Microskills.

PubMed

Bailin, Abby; Bearman, Sarah Kate; Sale, Rafaella

2018-03-21

Clinical supervision is an element of quality assurance in routine mental health care settings serving children; however, there is limited scientific evaluation of its components. This study examines the format and microskills of routine supervision. Supervisors (n = 13) and supervisees (n = 20) reported on 100 supervision sessions, and trained coders completed observational coding on a subset of recorded sessions (n = 57). Results indicate that microskills shown to enhance supervisee competency in effectiveness trials and experiments were largely absent from routine supervision, highlighting potential missed opportunities to impart knowledge to therapists. Findings suggest areas for quality improvement within routine care settings.

Clinical outcome of subchromosomal events detected by whole‐genome noninvasive prenatal testing

PubMed Central

Helgeson, J.; Wardrop, J.; Boomer, T.; Almasri, E.; Paxton, W. B.; Saldivar, J. S.; Dharajiya, N.; Monroe, T. J.; Farkas, D. H.; Grosu, D. S.

2015-01-01

Abstract Objective A novel algorithm to identify fetal microdeletion events in maternal plasma has been developed and used in clinical laboratory‐based noninvasive prenatal testing. We used this approach to identify the subchromosomal events 5pdel, 22q11del, 15qdel, 1p36del, 4pdel, 11qdel, and 8qdel in routine testing. We describe the clinical outcomes of those samples identified with these subchromosomal events. Methods Blood samples from high‐risk pregnant women submitted for noninvasive prenatal testing were analyzed using low coverage whole genome massively parallel sequencing. Sequencing data were analyzed using a novel algorithm to detect trisomies and microdeletions. Results In testing 175 393 samples, 55 subchromosomal deletions were reported. The overall positive predictive value for each subchromosomal aberration ranged from 60% to 100% for cases with diagnostic and clinical follow‐up information. The total false positive rate was 0.0017% for confirmed false positives results; false negative rate and sensitivity were not conclusively determined. Conclusion Noninvasive testing can be expanded into the detection of subchromosomal copy number variations, while maintaining overall high test specificity. In the current setting, our results demonstrate high positive predictive values for testing of rare subchromosomal deletions. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd. PMID:26088833

NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics.

PubMed

Tsang, Hin-Fung; Xue, Vivian Weiwen; Koh, Su-Pin; Chiu, Ya-Ming; Ng, Lawrence Po-Wah; Wong, Sze-Chuen Cesar

2017-01-01

Formalin-fixed, paraffin-embedded (FFPE) tissue sample is a gold mine of resources for molecular diagnosis and retrospective clinical studies. Although molecular technologies have expanded the range of mutations identified in FFPE samples, the applications of existing technologies are limited by the low nucleic acids yield and poor extraction quality. As a result, the routine clinical applications of molecular diagnosis using FFPE samples has been associated with many practical challenges. NanoString technologies utilize a novel digital color-coded barcode technology based on direct multiplexed measurement of gene expression and offer high levels of precision and sensitivity. Each color-coded barcode is attached to a single target-specific probe corresponding to a single gene which can be individually counted without amplification. Therefore, NanoString is especially useful for measuring gene expression in degraded clinical specimens. Areas covered: This article describes the applications of NanoString technologies in molecular diagnostics and challenges associated with its applications and the future development. Expert commentary: Although NanoString technology is still in the early stages of clinical use, it is expected that NanoString-based cancer expression panels would play more important roles in the future in classifying cancer patients and in predicting the response to therapy for better personal therapeutic care.

Cell-block procedure in endoscopic ultrasound-guided-fine-needle-aspiration of gastrointestinal solid neoplastic lesions

PubMed Central

Ieni, Antonio; Barresi, Valeria; Todaro, Paolo; Caruso, Rosario Alberto; Tuccari, Giovanni

2015-01-01

In the present review we have analyzed the clinical applications of endoscopic ultrasound-guided-fine-needle-aspiration (EUS-FNA) and the methodological aspects obtained by cell-block procedure (CBP) in the diagnostic approach to the gastrointestinal neoplastic pathology. CBP showed numerous advantages in comparison to the cytologic routine smears; in particular, better preservation of cell architecture, achievement of routine haematoxylin-eosin staining equivalent to histological slides and possibility to perform immunohistochemistry or molecular analyses represented the most evident reasons to choose this method. Moreover, by this approach, the differential diagnosis of solid gastrointestinal neoplasias may be more easily achieved and the background of contaminant non-neoplastic gastrointestinal avoided. Finally, biological samples collected by EUS-FNA CBP-assisted should be investigated in order to identify and quantify further potential molecular markers. PMID:26322154

Diagnostic accuracy, incremental yield and prognostic value of Determine TB-LAM for routine diagnostic testing for tuberculosis in HIV-infected patients requiring acute hospital admission in South Africa: a prospective cohort.

PubMed

Lawn, Stephen D; Kerkhoff, Andrew D; Burton, Rosie; Schutz, Charlotte; Boulle, Andrew; Vogt, Monica; Gupta-Wright, Ankur; Nicol, Mark P; Meintjes, Graeme

2017-03-21

We previously reported that one-third of HIV-positive adults requiring medical admission to a South African district hospital had laboratory-confirmed tuberculosis (TB) and that almost two-thirds of cases could be rapidly diagnosed using Xpert MTB/RIF-testing of concentrated urine samples obtained on the first day of admission. Implementation of urine-based, routine, point-of-care TB screening is an attractive intervention that might be facilitated by use of a simple, low-cost diagnostic tool, such as the Determine TB-LAM lateral-flow rapid test for HIV-associated TB. Sputum, urine and blood samples were systematically obtained from unselected HIV-positive adults within 24 hours of admission to a South African township hospital. Additional clinical samples were obtained during hospitalization as clinically indicated. TB was defined by the detection of Mycobacterium tuberculosis in any sample using Xpert MTB/RIF or liquid culture. The diagnostic yield, accuracy and prognostic value of urine-lipoarabinomannan (LAM) testing were determined, but urine-LAM results did not inform treatment decisions. Consecutive HIV-positive adult acute medical admissions not already receiving TB treatment (n = 427) were enrolled regardless of clinical presentation or symptoms. TB was diagnosed in 139 patients (TB prevalence 32.6%; median CD4 count 80 cells/μL). In the first 24 hours of admission, sputum (spot and/or induced) samples were obtained from 37.0% of patients and urine samples from 99.5% of patients (P < 0.001). The diagnostic yields from these specimens were 19.4% (n = 27/139) for sputum-microscopy, 26.6% (n = 37/139) for sputum-Xpert, 38.1% (n = 53/139) for urine-LAM and 52.5% (n = 73/139) for sputum-Xpert/urine-LAM combined (P < 0.01). Corresponding yields among patients with CD4 counts <100 cells/μL were 18.9%, 24.3%, 55.4% and 63.5%, respectively (P < 0.01). The diagnostic yield of urine-LAM was unrelated to respiratory symptoms, and LAM assay specificity (using a grade-2 cut-off) was 98.9% (274/277; 95% confidence interval [CI] 96.9-99.8). Among TB cases, positive urine-LAM status was strongly associated with mortality at 90 days (adjusted hazard ratio 4.20; 95% CI 1.50-11.75). Routine testing for TB in newly admitted HIV-positive adults using Determine TB-LAM to test urine provides major incremental diagnostic yield with very high specificity when used in combination with sputum testing and has important utility among those without respiratory TB symptoms and/or unable to produce sputum. The assay also rapidly identifies individuals with a poor prognosis.

Identification of genus Acinetobacter: Standardization of in-house PCR and its comparison with conventional phenotypic methods.

PubMed

Kulkarni, Sughosh S; Madalgi, Radhika; Ajantha, Ganavalli S; Kulkarni, Raghavendra D

2017-01-01

Acinetobacter is grouped under nonfermenting Gram-negative bacilli. It is increasingly isolated from pathological samples. The ability of this genus to acquire drug resistance and spread in the hospital settings is posing a grave problem in healthcare. Specific treatment protocols are advocated for Acinetobacter infections. Hence, rapid identification and drug susceptibility profiling are critical in the management of these infections. To standardize an in-house polymerase chain reaction (PCR) for identification of genus Acinetobacter and to compare PCR with two protocols for its phenotypic identification. A total of 96 clinical isolates of Acinetobacter were included in the study. An in-house PCR for genus level identification of Acinetobacter was standardized. All the isolates were phenotypically identified by two protocols. The results of PCR and phenotypic identification protocols were compared. The in-house PCR standardized was highly sensitive and specific for the genus Acinetobacter . There was 100% agreement between the phenotypic and molecular identification of the genus. The preliminary identification tests routinely used in clinical laboratories were also in complete agreement with phenotypic and molecular identification. The in-house PCR for genus level identification is specific and sensitive. However, it may not be essential for routine identification as the preliminary phenotypic identification tests used in the clinical laboratory reliably identify the genus Acinetobacter .

Impact of routine real-time PCR testing of imported malaria over 4 years of implementation in a clinical laboratory.

PubMed

Shokoples, Sandra; Mukhi, Shamir N; Scott, Allison N; Yanow, Stephanie K

2013-06-01

In clinical laboratories, diagnosis of imported malaria is commonly performed by microscopy. However, the volume of specimens is generally low and maintaining proficiency in reading blood smears, particularly at the species level, is challenging in this setting. To address this problem, the Provincial Laboratory for Public Health (ProvLab) in Alberta, Canada, implemented real-time PCR for routine confirmation of all smear-positive samples in the province. Here we report our experience over a 4-year period (2008 to 2012) with this new diagnostic algorithm. While detection of Plasmodium falciparum by microscopy alone was accurate, real-time PCR served as an important adjunct to microscopy for the identification of non-falciparum species. In 18% of cases, the result was reported as non-falciparum or the species could not be identified by microscopy alone, and in all cases, the species was resolved by real-time PCR. In another 4% of cases, the species was misidentified by microscopy. To enhance surveillance for malaria, we integrated our demographic, clinical, and laboratory data into a new system developed by the Canadian Network for Public Health Intelligence, called the Malaria System for Online Surveillance (SOS). Using this application, we characterized our patient populations and travel history to identify risk factors associated with malaria infection abroad.

Assessment on Experimental Bacterial Biofilms and in Clinical Practice of the Efficacy of Sampling Solutions for Microbiological Testing of Endoscopes

PubMed Central

Aumeran, C.; Thibert, E.; Chapelle, F. A.; Hennequin, C.; Lesens, O.

2012-01-01

Opinions differ on the value of microbiological testing of endoscopes, which varies according to the technique used. We compared the efficacy on bacterial biofilms of sampling solutions used for the surveillance of the contamination of endoscope channels. To compare efficacy, we used an experimental model of a 48-h Pseudomonas biofilm grown on endoscope internal tubing. Sampling of this experimental biofilm was performed with a Tween 80-lecithin-based solution, saline, and sterile water. We also performed a randomized prospective study during routine clinical practice in our hospital sampling randomly with two different solutions the endoscopes after reprocessing. Biofilm recovery expressed as a logarithmic ratio of bacteria recovered on bacteria initially present in biofilm was significantly more effective with the Tween 80-lecithin-based solution than with saline solution (P = 0.002) and sterile water (P = 0.002). There was no significant difference between saline and sterile water. In the randomized clinical study, the rates of endoscopes that were contaminated with the Tween 80-lecithin-based sampling solution and the saline were 8/25 and 1/25, respectively (P = 0.02), and the mean numbers of bacteria recovered were 281 and 19 CFU/100 ml (P = 0.001), respectively. In conclusion, the efficiency and therefore the value of the monitoring of endoscope reprocessing by microbiological cultures is dependent on the sampling solutions used. A sampling solution with a tensioactive action is more efficient than saline in detecting biofilm contamination of endoscopes. PMID:22170930

An independent validation of a gene expression signature to differentiate malignant melanoma from benign melanocytic nevi.

PubMed

Clarke, Loren E; Flake, Darl D; Busam, Klaus; Cockerell, Clay; Helm, Klaus; McNiff, Jennifer; Reed, Jon; Tschen, Jaime; Kim, Jinah; Barnhill, Raymond; Elenitsas, Rosalie; Prieto, Victor G; Nelson, Jonathan; Kimbrell, Hillary; Kolquist, Kathryn A; Brown, Krystal L; Warf, M Bryan; Roa, Benjamin B; Wenstrup, Richard J

2017-02-15

Recently, a 23-gene signature was developed to produce a melanoma diagnostic score capable of differentiating malignant and benign melanocytic lesions. The primary objective of this study was to independently assess the ability of the gene signature to differentiate melanoma from benign nevi in clinically relevant lesions. A set of 1400 melanocytic lesions was selected from samples prospectively submitted for gene expression testing at a clinical laboratory. Each sample was tested and subjected to an independent histopathologic evaluation by 3 experienced dermatopathologists. A primary diagnosis (benign or malignant) was assigned to each sample, and diagnostic concordance among the 3 dermatopathologists was required for inclusion in analyses. The sensitivity and specificity of the score in differentiating benign and malignant melanocytic lesions were calculated to assess the association between the score and the pathologic diagnosis. The gene expression signature differentiated benign nevi from malignant melanoma with a sensitivity of 91.5% and a specificity of 92.5%. These results reflect the performance of the gene signature in a diverse array of samples encountered in routine clinical practice. Cancer 2017;123:617-628. © 2016 American Cancer Society. © 2016 Myriad Genetics, Inc. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society.

Does Intraoperative Systematic Bacterial Sampling During Complete Cytoreductive Surgery (CRS) with Hyperthermic Intraoperative Peritoneal Chemotherapy (HIPEC) Influence Postoperative Treatment? A New Predictive Factor for Postoperative Abdominal Infectious Complications.

PubMed

Dazza, Marie; Schwarz, Lilian; Coget, Julien; Frebourg, Noelle; Wood, Gregory; Huet, Emmanuel; Bridoux, Valérie; Veber, Benoit; Tuech, Jean-Jacques

2016-12-01

Cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) is an emerging curative treatment option for patients with peritoneal carcinomatosis. It has a long-term survival benefit but is associated with high rates of morbidity, ranging from 12 % to 65 %, mainly due to infectious complications. We sought to evaluate the clinical relevance of routine intraoperative bacteriological sampling following CRS/HIPEC. Between November 2010 and December 2014, every patients receiving CRS/HIPEC were included. Three samples were routinely collected from standardized locations for intraperitoneal rinsing liquid bacteriological analysis (RLBA) after completion of HIPEC. The clinical and surgical features, bacteriological results, and short-term outcomes were retrospectively reviewed. The overall mortality and morbidity rates were 5 and 45 %, respectively. Among the 75 included patients, 40 % (n = 30) had at least one positive bacterial culture. Risk factors for a positive culture were colorectal resection (adjusted hazard ratio [HR] = 3.072, 95 % CI 1.843-8.004; p = 0.009) and blood loss >1000 mL (HR = 4.272, 95 % CI 1.080-18.141; p = 0.031). Among 26 (35 %) patients with abdominal infectious complications, 13 (17 %) experienced isolated complications. A positive RLBA result was independently associated with abdominal infectious complications (HR = 5.108, 95 % CI 1.220-16.336; p = 0.024) and isolated abdominal infectious complications (HR = 4.199, 95 % CI 1.064-15.961; p = 0.04). Forty percent of the RLBA samples obtained following CRS/HIPEC tested positive for bacteria. Bacterial sampling of rinsing liquid should be systematically performed. An aggressive and immediate antibiotic strategy needs to be evaluated.

Towards a routine application of Top-Down approaches for label-free discovery workflows.

PubMed

Schmit, Pierre-Olivier; Vialaret, Jerome; Wessels, Hans J C T; van Gool, Alain J; Lehmann, Sylvain; Gabelle, Audrey; Wood, Jason; Bern, Marshall; Paape, Rainer; Suckau, Detlev; Kruppa, Gary; Hirtz, Christophe

2018-03-20

Thanks to proteomics investigations, our vision of the role of different protein isoforms in the pathophysiology of diseases has largely evolved. The idea that protein biomarkers like tau, amyloid peptides, ApoE, cystatin, or neurogranin are represented in body fluids as single species is obviously over-simplified, as most proteins are present in different isoforms and subjected to numerous processing and post-translational modifications. Measuring the intact mass of proteins by MS has the advantage to provide information on the presence and relative amount of the different proteoforms. Such Top-Down approaches typically require a high degree of sample pre-fractionation to allow the MS system to deliver optimal performance in terms of dynamic range, mass accuracy and resolution. In clinical studies, however, the requirements for pre-analytical robustness and sample size large enough for statistical power restrict the routine use of a high degree of sample pre-fractionation. In this study, we have investigated the capacities of current-generation Ultra-High Resolution Q-Tof systems to deal with high complexity intact protein samples and have evaluated the approach on a cohort of patients suffering from neurodegenerative disease. Statistical analysis has shown that several proteoforms can be used to distinguish Alzheimer disease patients from patients suffering from other neurodegenerative disease. Top-down approaches have an extremely high biological relevance, especially when it comes to biomarker discovery, but the necessary pre-fractionation constraints are not easily compatible with the robustness requirements and the size of clinical sample cohorts. We have demonstrated that intact protein profiling studies could be run on UHR-Q-ToF with limited pre-fractionation. The proteoforms that have been identified as candidate biomarkers in the-proof-of concept study are derived from proteins known to play a role in the pathophysiology process of Alzheimer disease. Copyright © 2017 Elsevier B.V. All rights reserved.

Diagnostic utility and cost-effectiveness of reflex bacterial culture for the detection of urinary tract infection in dogs with low urine specific gravity.

PubMed

Tivapasi, Musavenga T; Hodges, Joanne; Byrne, Barbara A; Christopher, Mary M

2009-09-01

Urinary tract infections (UTIs) may be subclinical or difficult to detect in dilute urine as sediment abnormalities may not be observed. In our laboratory, bacterial culture is automatically performed (reflex culture) on samples with urine specific gravity (USG)< or =1.013 to increase the likelihood of detecting infection. The value of routine culture of dilute urine, however, has not been fully assessed. The purpose of this retrospective study was to evaluate the frequency of positive bacterial cultures and analyze the diagnostic utility and cost-effectiveness of culture compared with routine sediment examination for detecting UTI in dilute urine specimens from dogs. Urinalysis and concurrent aerobic bacterial culture results were obtained from the electronic medical record system at the University of California-Davis Veterinary Medical Teaching Hospital for samples with USG< or =1.013 analyzed from July 1998 through January 2005. Urine collection method, presence of leukocytes and bacteria, bacterial culture results, and clinical diagnosis were recorded. Cost-effectiveness of reflex culture, based on low USG as the sole criterion, was evaluated. Of 1264 urine specimens, 106 (8.4%) had positive bacterial cultures. Using culture as the gold standard, sediment evaluation had a diagnostic sensitivity of 58.5% and specificity of 98.3% (diagnostic accuracy 94.9%). An additional cost of $60 per patient was incurred, leading to average annual costs of $11,668 for reflex bacterial cultures of all samples with low USG, regardless of collection method. Within our study population, 10 urine samples needed to be cultured for each true positive result. The sensitivity of urine sediment evaluation is low for UTI in dilute urine samples; however, reflex bacterial culture does not appear to be cost-effective in dogs with USG< or =1.013 in the absence of active urine sediment or high clinical suspicion for UTI.

[Applications of MALDI-TOF-MS in clinical microbiology laboratory].

PubMed

Carbonnelle, Etienne; Nassif, Xavier

2011-10-01

For twenty years, mass spectrometry (MS) has emerged as a particularly powerful tool for analysis and characterization of proteins in research. It is only recently that this technology, especially MALDI-TOF-MS (Matrix Assisted Laser Desorption Ionization Time-Of-Flight) has entered the field of routine microbiology. This method has proven to be reliable and safe for the identification of bacteria, yeasts, filamentous fungi and dermatophytes. MALDI-TOF-MS is a rapid, precise and cost-effective method for identification, compared to conventional phenotypic techniques or molecular biology. Its ability to analyse whole microorganisms with few sample preparation has greatly reduced the time to identification (1-2 min). Furthermore, this technology can be used to identify bacteria directly from clinical samples as blood culture bottles or urines. Future applications will be developed in order to provide direct information concerning virulence or resistance protein markers. © 2011 médecine/sciences – Inserm / SRMS.

High-Performance 3D Compressive Sensing MRI Reconstruction Using Many-Core Architectures.

PubMed

Kim, Daehyun; Trzasko, Joshua; Smelyanskiy, Mikhail; Haider, Clifton; Dubey, Pradeep; Manduca, Armando

2011-01-01

Compressive sensing (CS) describes how sparse signals can be accurately reconstructed from many fewer samples than required by the Nyquist criterion. Since MRI scan duration is proportional to the number of acquired samples, CS has been gaining significant attention in MRI. However, the computationally intensive nature of CS reconstructions has precluded their use in routine clinical practice. In this work, we investigate how different throughput-oriented architectures can benefit one CS algorithm and what levels of acceleration are feasible on different modern platforms. We demonstrate that a CUDA-based code running on an NVIDIA Tesla C2050 GPU can reconstruct a 256 × 160 × 80 volume from an 8-channel acquisition in 19 seconds, which is in itself a significant improvement over the state of the art. We then show that Intel's Knights Ferry can perform the same 3D MRI reconstruction in only 12 seconds, bringing CS methods even closer to clinical viability.

Negative symptoms in schizophrenia: a study in a large clinical sample of patients using a novel automated method.

PubMed

Patel, Rashmi; Jayatilleke, Nishamali; Broadbent, Matthew; Chang, Chin-Kuo; Foskett, Nadia; Gorrell, Genevieve; Hayes, Richard D; Jackson, Richard; Johnston, Caroline; Shetty, Hitesh; Roberts, Angus; McGuire, Philip; Stewart, Robert

2015-09-07

To identify negative symptoms in the clinical records of a large sample of patients with schizophrenia using natural language processing and assess their relationship with clinical outcomes. Observational study using an anonymised electronic health record case register. South London and Maudsley NHS Trust (SLaM), a large provider of inpatient and community mental healthcare in the UK. 7678 patients with schizophrenia receiving care during 2011. Hospital admission, readmission and duration of admission. 10 different negative symptoms were ascertained with precision statistics above 0.80. 41% of patients had 2 or more negative symptoms. Negative symptoms were associated with younger age, male gender and single marital status, and with increased likelihood of hospital admission (OR 1.24, 95% CI 1.10 to 1.39), longer duration of admission (β-coefficient 20.5 days, 7.6-33.5), and increased likelihood of readmission following discharge (OR 1.58, 1.28 to 1.95). Negative symptoms were common and associated with adverse clinical outcomes, consistent with evidence that these symptoms account for much of the disability associated with schizophrenia. Natural language processing provides a means of conducting research in large representative samples of patients, using data recorded during routine clinical practice. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Dental technician pneumoconiosis mimicking lung cancer.

PubMed

Uyar, Meral; Sokucu, Oral; Sanli, Maruf; Filiz, Ayten; Ali Ikidag, Mehmet; Feridun Isik, Ahmet; Bakir, Kemal

2015-09-01

A 47-year-old man was referred for assessment of bilateral lymph node enlargement identified on a routine chest radiograph. Positron emission tomography showed high standardized uptake values (SUVmax: 20.5) in right supraclavicular, right intercostal, and multiple mediastinal lymph nodes. Biopsy samples obtained from the right upper and left lower paratracheal nodes by mediastinoscopy revealed granulomatous inflammation. Clinical and laboratory findings indicated a diagnosis of dental technician pneumoconiosis. The patient is alive and well 3 years after diagnosis. This case highlights the importance of obtaining an occupational history.

X-ray vector radiography imaging for biomedical applications

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

Potdevin, Guillaume; Malecki, Andreas; Biernath, Thomas

The non-invasive estimation of fracture risk in osteoporosis remains a challenge in the clinical routine and is mainly based on an assessment of bone density by dual X-ray absorption (DXA) although bone micro-architecture is known to play an important role for bone fragility. Here we report on 'X-ray vector Radiography' measurements able to provide a direct bone microstructure diagnostics on human bone samples, which we compare qualitatively and quantitatively with numerical analysis of high resolution radiographs.

Performance of two strategies for urgent ANCA and anti-GBM analysis in vasculitis.

PubMed

de Joode, Anoek A E; Roozendaal, Caroline; van der Leij, Marcel J; Bungener, Laura B; Sanders, Jan Stephan F; Stegeman, Coen A

2014-02-01

In anti-neutrophil cytoplasmic antibodies (ANCA) associated small vessel vasculitis (AAV), rapid testing for ANCA and anti-glomerular basement membrane (GBM) antibodies may be beneficial for therapeutic purpose. We analysed the diagnostic performance of two rapid ANCA and anti-GBM test methods in 260 patients with suspected AAV. Between January 2004 and November 2010, we analysed 260 samples by qualitative Dotblot (Biomedical Diagnostics); retrospective analysis followed with directly coated highly sensitive automated Phadia ELiA and ELiA anti-GBM. Results were related to the final clinical diagnosis and compared with routine capture ELISA. Seventy-four patients had a final diagnosis of AAV (n=62) or anti-GBM disease (n=12). Both Dotblot and ELiA detected all 12 cases of anti-GBM disease; 2 false positive results were found. Dotblot detected ANCA in 56 of 62 AAV patients (sensitivity 90%, NPV 97%), and showed 5 false positives (specificity 97%, PPV 90%). The Phadia ELiA anti-PR3(s) or anti-MPO(s) was positive in 57 of 62 AAV patients (sensitivity 92%, NPV 97%), and had 5 false positives (specificity 97%, PPV 88%). Routine capture ELISA was equally accurate (sensitivity 94%, specificity 97%, PPV 88%, NPV 98%). The Dotblot and Phadia ELiA on anti-GBM, anti-PR3(s) and anti-MPO(s) performed excellently; results were almost identical to routine ELISA. When suspicion of AAV or anti-GBM disease is high and diagnosis is urgently needed, both tests are very powerful for rapid serological diagnosis. Further studies have to confirm the test performances in samples routinely presented for ANCA testing and in follow-up of positive patients. Copyright © 2013 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

Comparison of routine urinalysis and urine Gram stain for detection of bacteriuria in dogs.

PubMed

Way, Leilani Ireland; Sullivan, Lauren A; Johnson, Valerie; Morley, Paul S

2013-01-01

To determine the utility of performing urine Gram stain for detection of bacteriuria compared to routine urine sediment examination and bacterial aerobic urine culture. Prospective, observational study. University teaching hospital. Urine samples acquired via cystocentesis through convenience sampling from 103 dogs presenting to a tertiary referral institution. All samples underwent routine urinalysis, including sediment examination, as well as urine Gram stain and quantitative bacterial aerobic urine culture. The urine Gram stain demonstrated improved sensitivity (96% versus 76%), specificity (100% versus 77%), positive predictive value (100% versus 83%), and negative predictive value (93% versus 69%) when identifying bacteriuria, compared to routine urine sediment examination. The urine Gram stain is highly sensitive and specific when detecting the presence of bacteria in canine urine samples. Gram staining should be considered when bacteriuria is highly suspected and requires rapid identification while bacterial culture is pending. © Veterinary Emergency and Critical Care Society 2013.

Modified scoring criteria for the RBANS figures.

PubMed

Duff, Kevin; Leber, W R; Patton, Doyle E; Schoenberg, Mike R; Mold, James W; Scott, James G; Adams, Russell L

2007-01-01

Visual construction and memory tasks are routinely used in neuropsychological assessment, but their subjective scoring criteria can negatively affect the reliability of these instruments. The current study examined the standard scoring criteria for the Figure Copy and Recall subtests of the RBANS and compared them to a modified set of scoring criteria in two samples. In both a large community dwelling sample of older adults and in a mixed clinical sample, the original scoring criteria consistently led to lower scores than the modified criteria. Inter-rater reliability was high for the modified scoring criteria, and no age effects were found with the modified scoring criteria. In both samples, the modified scoring criteria led to Figure Copy scores that more closely approximated other performances on the RBANS compared to the standard criteria, whereas both scoring systems led to plausible Figure Recall scores. Despite these results, the present study cannot identify one scoring criterion as the "better," but only points out the significant differences between them. Such differences can have important clinical implications, and practitioners and researchers who utilize the RBANS with patient samples should be cautious when interpreting low scores on Figure Copy and Recall if the standard criteria are used.

A Systematic Evaluation of Blood Serum and Plasma Pre-Analytics for Metabolomics Cohort Studies

PubMed Central

Jobard, Elodie; Trédan, Olivier; Postoly, Déborah; André, Fabrice; Martin, Anne-Laure; Elena-Herrmann, Bénédicte; Boyault, Sandrine

2016-01-01

The recent thriving development of biobanks and associated high-throughput phenotyping studies requires the elaboration of large-scale approaches for monitoring biological sample quality and compliance with standard protocols. We present a metabolomic investigation of human blood samples that delineates pitfalls and guidelines for the collection, storage and handling procedures for serum and plasma. A series of eight pre-processing technical parameters is systematically investigated along variable ranges commonly encountered across clinical studies. While metabolic fingerprints, as assessed by nuclear magnetic resonance, are not significantly affected by altered centrifugation parameters or delays between sample pre-processing (blood centrifugation) and storage, our metabolomic investigation highlights that both the delay and storage temperature between blood draw and centrifugation are the primary parameters impacting serum and plasma metabolic profiles. Storing the blood drawn at 4 °C is shown to be a reliable routine to confine variability associated with idle time prior to sample pre-processing. Based on their fine sensitivity to pre-analytical parameters and protocol variations, metabolic fingerprints could be exploited as valuable ways to determine compliance with standard procedures and quality assessment of blood samples within large multi-omic clinical and translational cohort studies. PMID:27929400

Chemistry and haematology sample rejection and clinical impact in a tertiary laboratory in Cape Town.

PubMed

Jacobsz, Lourens A; Zemlin, Annalise E; Roos, Mark J; Erasmus, Rajiv T

2011-10-14

Recent publications report that up to 70% of total laboratory errors occur in the pre-analytical phase. Identification of specific problems highlights pre-analytic processes susceptible to errors. The rejection of unsuitable samples can lead to delayed turnaround time and affect patient care. A retrospective audit was conducted investigating the rejection rate of routine blood specimens received at chemistry and haematology laboratories over a 2-week period. The reasons for rejection and potential clinical impact of these rejections were investigated. Thirty patient files were randomly selected and examined to assess the impact of these rejections on clinical care. A total of 32,910 specimens were received during the study period, of which 481 were rejected, giving a rejection rate of 1.46%. The main reasons for rejection were inappropriate clotting (30%) and inadequate sample volume (22%). Only 51.7% of rejected samples were repeated and the average time for a repeat sample to reach the laboratory was about 5 days (121 h). Of the repeated samples, 5.1% had results within critical values. Examination of patient folders showed that in 40% of cases the rejection of samples had an impact on patient care. The evaluation of pre-analytical processes in the laboratory, with regard to sample rejection, allowed one to identify problem areas where improvement is necessary. Rejected samples due to factors out of the laboratory's control had a definite impact on patient care and can thus affect customer satisfaction. Clinicians should be aware of these factors to prevent such rejections.

Genetic antimicrobial susceptibility testing in Gram-negative sepsis - impact on time to results in a routine laboratory.

PubMed

Kommedal, Øyvind; Aasen, Johanne Lind; Lindemann, Paul Christoffer

2016-07-01

Diagnostic testing of positive blood cultures is among the most critical tasks performed by clinical microbiology laboratories, and the total analysis time from sampling to results should be kept as short as possible. By providing identification of pelleted bacteria directly from positive blood-cultures, MALDI-TOF MS opens for relatively low-complex species-adjusted genetic susceptibility testing from the same bacterial pellet. In our lab routine, we prospectively evaluated a rapid in-house real-time PCR targeting the most common aminoglycoside and cephalosporin resistance genes in Escherichia coli and Klebsiella pneumoniae and measured time to preliminary susceptibility reporting for 138 samples. The results were compared to direct phenotypic susceptibility testing with interpretation after 6 h and overnight incubation respectively. Results from the genetic susceptibility testing were available for 69.5% (96/138) of the positive blood cultures within 24 h after sample collection. No phenotypic susceptibility results were available at this time. Compared to overnight direct susceptibility testing, the average time from sample collection to preliminary susceptibility reporting was reduced with 43%, from 45 h and 5 min to 25 h and 44 min, providing an earlier adjustment of antimicrobial therapy for 12 patients. Minor logistic adjustments have the potential to save yet another 4 h. © 2016 APMIS. Published by John Wiley & Sons Ltd.

Methods to improve routine bioassay monitoring for freshly separated, poorly transported plutonium

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

Bihl, D.E.; Lynch, T.P.; Carbaugh, E.H.

1988-09-01

Several human cases involving inhalation of plutonium oxide at Hanford have shown clearance half-times from the lung that are much longer than the 500-day half-time recommended for class Y plutonium in Publication 30 of the International Commission on Radiological Protection(ICRP). The more tenaciously retained material is referred to as super class Y plutonium. The ability to detect super class Y plutonium by current routine bioassay measurements is shown to be poor. Pacific Northwest Laboratory staff involved in the Hanford Internal Dosimetry Program investigated four methods to se if improvements in routine monitoring of workers for fresh super class Y plutoniummore » are feasible. The methods were lung counting, urine sampling, fecal sampling, and use of diethylenetriaminepentaacetate (DTPA) to enhance urinary excretion. Use of DTPA was determined to be not feasible. Routine fecal sampling was found to be feasible but not recommended. Recommendations were made to improve the detection level for routine annual urinalysis and routine annual lung counting. 12 refs., 9 figs., 7 tabs.« less

Transcutaneous bilirubinometry reduces the need for blood sampling in neonates with visible jaundice.

PubMed

Mishra, S; Chawla, D; Agarwal, R; Deorari, A K; Paul, V K; Bhutani, V K

2009-12-01

We determined usefulness of transcutaneous bilirubinometry to decrease the need for blood sampling to assay serum total bilirubin (STB) in the management of jaundiced healthy Indian neonates. Newborns, > or =35 weeks' gestation, with clinical evidence of jaundice were enrolled in an institutional approved randomized clinical trial. The severity of hyperbilirubinaemia was determined by two non-invasive methods: i) protocol-based visual assessment of bilirubin (VaB) and ii) transcutaneous bilirubin (TcB) determination (BiliCheck). By a random allocation, either method was used to decide the need for blood sampling, which was defined to be present if assessed STB by allocated method exceeded 80% of hour-specific threshold values for phototherapy (2004 AAP Guidelines). A total of 617 neonates were randomized to either TcB (n = 314) or VaB (n = 303) groups with comparable gestation, birth weight and postnatal age. Need for blood sampling to assay STB was 34% lower (95% CI: 10% to 51%) in the TcB group compared with VaB group (17.5% vs 26.4% assessments; risk difference: -8.9%, 95% CI: -2.4% to -15.4%; p = 0.008). Routine use of transcutaneous bilirubinometry compared with systematic visual assessment of bilirubin significantly reduced the need for blood sampling to assay STB in jaundiced term and late-preterm neonates. (ClinicalTrials.gov number, NCT00653874).

Evaluation of health alerts from an early illness warning system in independent living.

PubMed

Rantz, Marilyn J; Scott, Susan D; Miller, Steven J; Skubic, Marjorie; Phillips, Lorraine; Alexander, Greg; Koopman, Richelle J; Musterman, Katy; Back, Jessica

2013-06-01

Passive sensor networks were deployed in independent living apartments to monitor older adults in their home environments to detect signs of impending illness and alert clinicians so they can intervene and prevent or delay significant changes in health or functional status. A retrospective qualitative deductive content analysis was undertaken to refine health alerts to improve clinical relevance to clinicians as they use alerts in their normal workflow of routine care delivery to older adults. Clinicians completed written free-text boxes to describe actions taken (or not) as a result of each alert; they also rated the clinical significance (relevance) of each health alert on a scale of 1 to 5. Two samples of the clinician's written responses to the health alerts were analyzed after alert algorithms had been adjusted based on results of a pilot study using health alerts to enhance clinical decision-making. In the first sample, a total of 663 comments were generated by seven clinicians in response to 385 unique alerts; there are more comments than alerts because more than one clinician rated the same alert. The second sample had a total of 142 comments produced by three clinicians in response to 88 distinct alerts. The overall clinical relevance of the alerts, as judged by the content of the qualitative comments by clinicians for each alert, improved from 33.3% of the alerts in the first sample classified as clinically relevant to 43.2% in the second. The goal is to produce clinically relevant alerts that clinicians find useful in daily practice. The evaluation methods used are described to assist others as they consider building and iteratively refining health alerts to enhance clinical decision making.

Public health facility resource availability and provider adherence to first antenatal guidelines in a low resource setting in Accra, Ghana.

PubMed

Amoakoh-Coleman, Mary; Agyepong, Irene Akua; Kayode, Gbenga A; Grobbee, Diederick E; Klipstein-Grobusch, Kerstin; Ansah, Evelyn K

2016-09-21

Lack of resources has been identified as a reason for non-adherence to clinical guidelines. Our aim was to describe public health facility resource availability in relation to provider adherence to first antenatal visit guidelines. A cross-sectional analysis of the baseline data of a prospective cohort study on adherence to first antenatal care visit guidelines was carried out in 11 facilities in the Greater Accra Region of Ghana. Provider adherence was studied in relation to health facility resource availability such as antenatal workload for clinical staffs, routine antenatal drugs, laboratory testing, protocols, ambulance and equipment. Eleven facilities comprising 6 hospitals (54.5 %), 4 polyclinics (36.4 %) and 1 health center were randomly sampled. Complete provider adherence to first antenatal guidelines for all the 946 participants was 48.1 % (95 % CI: 41.8-54.2 %), varying significantly amongst the types of facilities, with highest rate in the polyclinics. Average antenatal workload per month per clinical staff member was higher in polyclinics compared to the hospitals. All facility laboratories were able to conduct routine antenatal tests. Most routine antenatal drugs were available in all facilities except magnesium sulphate and sulphadoxine-pyrimethamine which were lacking in some. Antenatal service protocols and equipment were also available in all facilities. Although antenatal workload varies across different facility types in the Greater Accra region, other health facility resources that support implementation of first antenatal care guidelines are equally available in all the facilities. These factors therefore do not adequately account for the low and varying proportions of complete adherence to guidelines across facility types. Providers should be continually engaged for a better understanding of the barriers to their adherence to these guidelines.

How concerns for bisphosphonate-induced osteonecrosis of the jaw affect clinical practice among dentists: a study from the South Texas Oral Health Network

PubMed Central

Gonzales, Cara B.; Young, Veronica; Ketchum, Norma S.; Bone, Jamie; Oates, Thomas W.; Mungia, Rahma

2015-01-01

Bisphosphonate-induced osteonecrosis of the jaw (BONJ) represents a growing concern for dentists and patients, in that it may alter clinical care. This study assesses the knowledge and perceptions of practicing dentists in relation to the risk of BONJ and how their knowledge and perceptions influence their decisions when developing treatment plans. For this study, a sample of dentists (n = 93) in South Texas completed a 38-item survey about BONJ knowledge and perception and their current clinical practices for patients undergoing bisphosphonate therapy. Knowledge score groupings reflected differences between low-knowledge and high-knowledge dentists in terms of their behavior concerning medical history, alternative treatments offered, and routine blood testing for patients on bisphosphonate therapy. PMID:25734289

Determination of Zn/Cu ratio and oligoelements in serum samples by total reflection X-ray fluorescence spectrometry for cancer diagnosis

NASA Astrophysics Data System (ADS)

Marcó P., L. M.; Jiménez, E.; Hernández C., E. A.; Rojas, A.; Greaves, E. D.

2001-11-01

The method of quantification using the Compton peak as an internal standard, developed in a previous work, was applied to the routine determination of Fe, Cu, Zn and Se in serum samples from normal individuals and cancer patients by total reflection X-ray fluorescence spectrometry. Samples were classified according to age and sex of the donor, in order to determine reference values for normal individuals. Results indicate that the Zn/Cu ratio and the Cu concentration could prove to be useful tools for cancer diagnosis. Significant differences in these parameters between the normal and cancer group were found for all age ranges. The multielemental character of the technique, coupled with the small amounts of sample required and the short analysis time make it a valuable tool in clinical analysis.

Case report of unexplained hypocalcaemia in a slightly haemolysed sample.

PubMed

Cornes, Michael

2017-06-15

The case presented highlights a common pre-analytical problem identified in the laboratory that was initially missed. It concerns a young, generally healthy adult patient with no significant medical history and no significant family history. They presented with common flu like symptoms to their primary care clinician who considered this was most likely a viral problem that would pass with time. The clinician, however, did some routine bloods to reassure the patient despite a lack of clinical indication. When the sample was analysed the sample was haemolysed with strikingly low calcium. This led to the patient being called into hospital for urgent repeat investigations, all of which turned out to be within normal ranges. On further investigation the original sample was found to be contaminated. This result would normally have been flagged but was missed due to the complication of haemolysis.

Evidence and resources to implement Pharmacogenetic Knowledge for Precision Medicine

PubMed Central

Caudle, Kelly E.; Gammal, Roseann S.; Whirl-Carrillo, Michelle; Hoffman, James M.; Relling, Mary V.; Klein, Teri E.

2016-01-01

Purpose Implementation of pharmacogenetics into clinical practice has been relatively slow despite substantial scientific progress over the last decade. One barrier that inhibits uptake of pharmacogenetics into routine clinical practice is the lack of knowledge of how to translate a genetic test into a clinical action based on current evidence. The purpose of this paper is to describe the current state of pharmacogenetic evidence and evidence-based resources that facilitate the uptake of pharmacogenetics into clinical practice. Summary Controversy exists over the required evidence threshold needed for routine clinical implementation of pharmacogenetics. Large randomized controlled trials are not clinically feasible or necessary for many pharmacogenetic applications. Online resources exist like the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Pharmacogenomics Knowledgebase (PharmGKB) that provide freely available, evidence-based resources that facilitate the translation of genetic laboratory test results into actionable prescribing recommendations for specific drugs. Conclusion Resources provided by organizations such as CPIC and PharmGKB that use standardized approaches to evaluate the literature and provide clinical guidance are essential for the implementation of pharmacogenetics into routine clinical practice. PMID:27864205

Short structured general mental health in service training programme in Kenya improves patient health and social outcomes but not detection of mental health problems - a pragmatic cluster randomised controlled trial

PubMed Central

2013-01-01

Trial design A pragmatic cluster randomised controlled trial. Methods Participants: Clusters were primary health care clinics on the Ministry of Health list. Clients were eligible if they were aged 18 and over. Interventions: Two members of staff from each intervention clinic received the training programme. Clients in both intervention and control clinics subsequently received normal routine care from their health workers. Objective: To examine the impact of a mental health inservice training on routine detection of mental disorder in the clinics and on client outcomes. Outcomes: The primary outcome was the rate of accurate routine clinic detection of mental disorder and the secondary outcome was client recovery over a twelve week follow up period. Randomisation: clinics were randomised to intervention and control groups using a table of random numbers. Blinding: researchers and clients were blind to group assignment. Results Numbers randomised: 49 and 50 clinics were assigned to intervention and control groups respectively. 12 GHQ positive clients per clinic were identified for follow up. Numbers analysed: 468 and 478 clients were followed up for three months in intervention and control groups respectively. Outcome: At twelve weeks after training of the intervention group, the rate of accurate routine clinic detection of mental disorder was greater than 0 in 5% versus 0% of the intervention and control groups respectively, in both the intention to treat analysis (p = 0.50) and the per protocol analysis (p =0.50). Standardised effect sizes for client improvement were 0.34 (95% CI = (0.01,0.68)) for the General Health Questionnaire, 0.39 ((95% CI = (0.22, 0.61)) for the EQ and 0.49 (95% CI = (0.11,0.87)) for WHODAS (using ITT analysis); and 0.43 (95% CI = (0.09,0.76)) for the GHQ, 0.44 (95% CI = (0.22,0.65)) for the EQ and 0.58 (95% CI = (0.18,0.97)) for WHODAS (using per protocol analysis). Harms: None identified. Conclusion The training programme did not result in significantly improved recorded diagnostic rates of mental disorders in the routine clinic consultation register, but did have significant effects on patient outcomes in routine clinical practice. Trial registration International Standard Randomised Controlled Trial Number Register ISRCTN53515024. PMID:24188964

Ethnographic study of ICT-supported collaborative work routines in general practice.

PubMed

Swinglehurst, Deborah; Greenhalgh, Trisha; Myall, Michelle; Russell, Jill

2010-12-29

Health informatics research has traditionally been dominated by experimental and quasi-experimental designs. An emerging area of study in organisational sociology is routinisation (how collaborative work practices become business-as-usual). There is growing interest in the use of ethnography and other in-depth qualitative approaches to explore how collaborative work routines are enacted and develop over time, and how electronic patient records (EPRs) are used to support collaborative work practices within organisations. Following Feldman and Pentland, we will use 'the organisational routine' as our unit of analysis. In a sample of four UK general practices, we will collect narratives, ethnographic observations, multi-modal (video and screen capture) data, documents and other artefacts, and analyse these to map and compare the different understandings and enactments of three common routines (repeat prescribing, coding and summarising, and chronic disease surveillance) which span clinical and administrative spaces and which, though 'mundane', have an important bearing on quality and safety of care. In a detailed qualitative analysis informed by sociological theory, we aim to generate insights about how complex collaborative work is achieved through the process of routinisation in healthcare organisations. Our study offers the potential not only to identify potential quality failures (poor performance, errors, failures of coordination) in collaborative work routines but also to reveal the hidden work and workarounds by front-line staff which bridge the model-reality gap in EPR technologies and via which "automated" safety features have an impact in practice.

Ethnographic study of ICT-supported collaborative work routines in general practice

PubMed Central

2010-01-01

Background Health informatics research has traditionally been dominated by experimental and quasi-experimental designs. An emerging area of study in organisational sociology is routinisation (how collaborative work practices become business-as-usual). There is growing interest in the use of ethnography and other in-depth qualitative approaches to explore how collaborative work routines are enacted and develop over time, and how electronic patient records (EPRs) are used to support collaborative work practices within organisations. Methods/design Following Feldman and Pentland, we will use 'the organisational routine' as our unit of analysis. In a sample of four UK general practices, we will collect narratives, ethnographic observations, multi-modal (video and screen capture) data, documents and other artefacts, and analyse these to map and compare the different understandings and enactments of three common routines (repeat prescribing, coding and summarising, and chronic disease surveillance) which span clinical and administrative spaces and which, though 'mundane', have an important bearing on quality and safety of care. In a detailed qualitative analysis informed by sociological theory, we aim to generate insights about how complex collaborative work is achieved through the process of routinisation in healthcare organisations. Discussion Our study offers the potential not only to identify potential quality failures (poor performance, errors, failures of coordination) in collaborative work routines but also to reveal the hidden work and workarounds by front-line staff which bridge the model-reality gap in EPR technologies and via which "automated" safety features have an impact in practice. PMID:21190583

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles.

PubMed

Kitchen, Robert R; Sabine, Vicky S; Sims, Andrew H; Macaskill, E Jane; Renshaw, Lorna; Thomas, Jeremy S; van Hemert, Jano I; Dixon, J Michael; Bartlett, John M S

2010-02-24

Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data.

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles

PubMed Central

2010-01-01

Background Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. Results A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. Conclusion In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data. PMID:20181233

Fasting is not routinely required for determination of a lipid profile: clinical and laboratory implications including flagging at desirable concentration cut-points-a joint consensus statement from the European Atherosclerosis Society and European Federation of Clinical Chemistry and Laboratory Medicine.

PubMed

Nordestgaard, Børge G; Langsted, Anne; Mora, Samia; Kolovou, Genovefa; Baum, Hannsjörg; Bruckert, Eric; Watts, Gerald F; Sypniewska, Grazyna; Wiklund, Olov; Borén, Jan; Chapman, M John; Cobbaert, Christa; Descamps, Olivier S; von Eckardstein, Arnold; Kamstrup, Pia R; Pulkki, Kari; Kronenberg, Florian; Remaley, Alan T; Rifai, Nader; Ros, Emilio; Langlois, Michel

2016-07-01

To critically evaluate the clinical implications of the use of non-fasting rather than fasting lipid profiles and to provide guidance for the laboratory reporting of abnormal non-fasting or fasting lipid profiles. Extensive observational data, in which random non-fasting lipid profiles have been compared with those determined under fasting conditions, indicate that the maximal mean changes at 1-6 h after habitual meals are not clinically significant [+0.3 mmol/L (26 mg/dL) for triglycerides; -0.2 mmol/L (8 mg/dL) for total cholesterol; -0.2 mmol/L (8 mg/dL) for LDL cholesterol; +0.2 mmol/L (8 mg/dL) for calculated remnant cholesterol; -0.2 mmol/L (8 mg/dL) for calculated non-HDL cholesterol]; concentrations of HDL cholesterol, apolipoprotein A1, apolipoprotein B, and lipoprotein(a) are not affected by fasting/non-fasting status. In addition, non-fasting and fasting concentrations vary similarly over time and are comparable in the prediction of cardiovascular disease. To improve patient compliance with lipid testing, we therefore recommend the routine use of non-fasting lipid profiles, while fasting sampling may be considered when non-fasting triglycerides >5 mmol/L (440 mg/dL). For non-fasting samples, laboratory reports should flag abnormal concentrations as triglycerides ≥2 mmol/L (175 mg/dL), total cholesterol ≥5 mmol/L (190 mg/dL), LDL cholesterol ≥3 mmol/L (115 mg/dL), calculated remnant cholesterol ≥0.9 mmol/L (35 mg/dL), calculated non-HDL cholesterol ≥3.9 mmol/L (150 mg/dL), HDL cholesterol ≤1 mmol/L (40 mg/dL), apolipoprotein A1 ≤1.25 g/L (125 mg/dL), apolipoprotein B ≥1.0 g/L (100 mg/dL), and lipoprotein(a) ≥50 mg/dL (80th percentile); for fasting samples, abnormal concentrations correspond to triglycerides ≥1.7 mmol/L (150 mg/dL). Life-threatening concentrations require separate referral when triglycerides >10 mmol/L (880 mg/dL) for the risk of pancreatitis, LDL cholesterol >13 mmol/L (500 mg/dL) for homozygous familial hypercholesterolaemia, LDL cholesterol >5 mmol/L (190 mg/dL) for heterozygous familial hypercholesterolaemia, and lipoprotein(a) >150 mg/dL (99th percentile) for very high cardiovascular risk. We recommend that non-fasting blood samples be routinely used for the assessment of plasma lipid profiles. Laboratory reports should flag abnormal values on the basis of desirable concentration cut-points. Non-fasting and fasting measurements should be complementary but not mutually exclusive. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Cardiology.

Fasting is not routinely required for determination of a lipid profile: clinical and laboratory implications including flagging at desirable concentration cut-points—a joint consensus statement from the European Atherosclerosis Society and European Federation of Clinical Chemistry and Laboratory Medicine

PubMed Central

Nordestgaard, Børge G.; Langsted, Anne; Mora, Samia; Kolovou, Genovefa; Baum, Hannsjörg; Bruckert, Eric; Watts, Gerald F.; Sypniewska, Grazyna; Wiklund, Olov; Borén, Jan; Chapman, M. John; Cobbaert, Christa; Descamps, Olivier S.; von Eckardstein, Arnold; Kamstrup, Pia R.; Pulkki, Kari; Kronenberg, Florian; Remaley, Alan T.; Rifai, Nader; Ros, Emilio; Langlois, Michel

2016-01-01

Abstract Aims To critically evaluate the clinical implications of the use of non-fasting rather than fasting lipid profiles and to provide guidance for the laboratory reporting of abnormal non-fasting or fasting lipid profiles. Methods and results Extensive observational data, in which random non-fasting lipid profiles have been compared with those determined under fasting conditions, indicate that the maximal mean changes at 1–6 h after habitual meals are not clinically significant [+0.3 mmol/L (26 mg/dL) for triglycerides; −0.2 mmol/L (8 mg/dL) for total cholesterol; −0.2 mmol/L (8 mg/dL) for LDL cholesterol; +0.2 mmol/L (8 mg/dL) for calculated remnant cholesterol; −0.2 mmol/L (8 mg/dL) for calculated non-HDL cholesterol]; concentrations of HDL cholesterol, apolipoprotein A1, apolipoprotein B, and lipoprotein(a) are not affected by fasting/non-fasting status. In addition, non-fasting and fasting concentrations vary similarly over time and are comparable in the prediction of cardiovascular disease. To improve patient compliance with lipid testing, we therefore recommend the routine use of non-fasting lipid profiles, while fasting sampling may be considered when non-fasting triglycerides >5 mmol/L (440 mg/dL). For non-fasting samples, laboratory reports should flag abnormal concentrations as triglycerides ≥2 mmol/L (175 mg/dL), total cholesterol ≥5 mmol/L (190 mg/dL), LDL cholesterol ≥3 mmol/L (115 mg/dL), calculated remnant cholesterol ≥0.9 mmol/L (35 mg/dL), calculated non-HDL cholesterol ≥3.9 mmol/L (150 mg/dL), HDL cholesterol ≤1 mmol/L (40 mg/dL), apolipoprotein A1 ≤1.25 g/L (125 mg/dL), apolipoprotein B ≥1.0 g/L (100 mg/dL), and lipoprotein(a) ≥50 mg/dL (80th percentile); for fasting samples, abnormal concentrations correspond to triglycerides ≥1.7 mmol/L (150 mg/dL). Life-threatening concentrations require separate referral when triglycerides >10 mmol/L (880 mg/dL) for the risk of pancreatitis, LDL cholesterol >13 mmol/L (500 mg/dL) for homozygous familial hypercholesterolaemia, LDL cholesterol >5 mmol/L (190 mg/dL) for heterozygous familial hypercholesterolaemia, and lipoprotein(a) >150 mg/dL (99th percentile) for very high cardiovascular risk. Conclusion We recommend that non-fasting blood samples be routinely used for the assessment of plasma lipid profiles. Laboratory reports should flag abnormal values on the basis of desirable concentration cut-points. Non-fasting and fasting measurements should be complementary but not mutually exclusive. PMID:27122601

Standardization and quantification in FDG-PET/CT imaging for staging and restaging of malignant disease.

PubMed

Gámez-Cenzano, Cristina; Pino-Sorroche, Francisco

2014-04-01

There is a growing interest in using quantification in FDG-PET/CT in oncology, especially for evaluating response to therapy. Complex full quantitative procedures with blood sampling and dynamic scanning have been clinically replaced by the use of standardized uptake value measurements that provide an index of regional tracer uptake normalized to the administered dose of FDG. Some approaches have been proposed for assessing quantitative metabolic response, such as EORTC and PERCIST criteria in solid tumors. When using standardized uptake value in clinical routine and multicenter trials, standardization of protocols and quality control procedures of instrumentation is required. Copyright © 2014 Elsevier Inc. All rights reserved.

Different EGFR gene mutations in two patients with synchronous multiple lung cancers: A case report

PubMed Central

Sakai, Hiroki; Kimura, Hiroyuki; Tsuda, Masataka; Wakiyama, Yoichi; Miyazawa, Tomoyuki; Marushima, Hideki; Kojima, Koji; Hoshikawa, Masahiro; Takagi, Masayuki; Nakamura, Haruhiko

2017-01-01

Routine clinical and pathological evaluations to determine the relationship between different lesions are often not completely conclusive. Interestingly, detailed genetic analysis of tumor samples may provide important additional information and identify second primary lung cancers. In the present study, we report cases of two synchronous lung adenocarcinomas composed of two distinct pathological subtypes with different EGFR gene mutations: a homozygous deletion in exon 19 of the papillary adenocarcinoma subtype and a point mutation of L858R in exon 21 of the tubular adenocarcinoma. The present report highlights the clinical importance of molecular cancer biomarkers to guide management decisions in cases involving multiple lung tumors. PMID:29090842

Contamination with HIV antibody may be responsible for false positive results in specimens tested on automated platforms running HIV 4th generation assays in a region of high HIV prevalence.

PubMed

Hardie, Diana Ruth; Korsman, Stephen N; Hsiao, Nei-Yuan; Morobadi, Molefi Daniel; Vawda, Sabeehah; Goedhals, Dominique

2017-01-01

In South Africa where the prevalence of HIV infection is very high, 4th generation HIV antibody/p24 antigen combo immunoassays are the tests of choice for laboratory based screening. Testing is usually performed in clinical pathology laboratories on automated analysers. To investigate the cause of false positive results on 4th generation HIV testing platforms in public sector laboratories, the performance of two automated platforms was compared in a clinical pathology setting, firstly on routine diagnostic specimens and secondly on known sero-negative samples. Firstly, 1181 routine diagnostic specimens were sequentially tested on Siemens and Roche automated 4th generation platforms. HIV viral load, western blot and follow up testing were used to determine the true status of inconclusive specimens. Subsequently, known HIV seronegative samples from a single donor were repeatedly tested on both platforms and an analyser was tested for surface contamination with HIV positive serum to identify how suspected specimen contamination could be occurring. Serial testing of diagnostic specimens yielded 163 weakly positive or discordant results. Only 3 of 163 were conclusively shown to indicate true HIV infection. Specimen contamination with HIV antibody was suspected, based on the following evidence: the proportion of positive specimens increased on repeated passage through the analysers; viral loads were low or undetectable and western blots negative or indeterminate on problem specimens; screen negative, 2nd test positive specimens tested positive when reanalysed on the screening assay; follow up specimens (where available) were negative. Similarly, an increasing number of known negative specimens became (repeatedly) sero-positive on serial passage through one of the analysers. Internal and external analyser surfaces were contaminated with HIV serum, evidence that sample splashes occur during testing. Due to the extreme sensitivity of these assays, contamination with minute amounts of HIV antibody can cause a negative sample to test positive. Better contamination control measures are needed on analysers used in clinical pathology environments, especially in regions where HIV sero-prevalence is high.

A Survey of Attitudes towards the Clinical Application of Systemic Inflammation Based Prognostic Scores in Cancer.

PubMed

Watt, David G; Roxburgh, Campbell S; White, Mark; Chan, Juen Zhik; Horgan, Paul G; McMillan, Donald C

2015-01-01

The systemic inflammatory response (SIR) plays a key role in determining nutritional status and survival of patients with cancer. A number of objective scoring systems have been shown to have prognostic value; however, their application in routine clinical practice is not clear. The aim of the present survey was to examine the range of opinions internationally on the routine use of these scoring systems. An online survey was distributed to a target group consisting of individuals worldwide who have reported an interest in systemic inflammation in patients with cancer. Of those invited by the survey (n = 238), 65% routinely measured the SIR, mainly for research and prognostication purposes and clinically for allocation of adjuvant therapy or palliative chemotherapy. 40% reported that they currently used the Glasgow Prognostic Score/modified Glasgow Prognostic Score (GPS/mGPS) and 81% reported that a measure of systemic inflammation should be incorporated into clinical guidelines, such as the definition of cachexia. The majority of respondents routinely measured the SIR in patients with cancer, mainly using the GPS/mGPS for research and prognostication purposes. The majority reported that a measure of the SIR should be adopted into clinical guidelines.

Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.

PubMed

Velayati, Ali Akbar; Farnia, Parissa; Mozafari, Mohadese; Malekshahian, Donya; Seif, Shima; Rahideh, Snaz; Mirsaeidi, Mehdi

2014-01-01

While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran. A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations. Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (P<0.05). Out of 5314 positive clinical samples for mycobacteria, 175 (3.2%) isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078) in 2004 to 3.8% (39 out of 1005) in 2014 (P = 0.0001). The major clinical isolates were M. simiae (51; 29.1%), M. kansasii (26; 14.8%), M. chelonae (28; 16%), and M. fortuitum (13; 7.4%). Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.

Non-invasive prenatal testing (NIPT): Europe's first multicenter post-market clinical follow-up study validating the quality in clinical routine.

PubMed

Flöck, Anne; Tu, Ngoc-Chi; Rüland, Anna; Holzgreve, Wolfgang; Gembruch, Ulrich; Geipel, Annegret

2017-11-01

Non-invasive prenatal tests (NIPT) for the determination of fetal aneuploidies from maternal blood are firmly established in clinical routine. For the first time, the accuracy of an NIPT for the determination of trisomies 21, 18 and 13 in singleton pregnancies was assessed by means of a prospective German-wide multicenter post-market clinical follow-up study, to reliably evaluate the quality in clinical routine. The study covered the indications for testing, the test results, the rate of invasive diagnostics and the pregnancy outcome. 2232 cases were tested for trisomy 21. Of these, 1946 cases were additionally examined for trisomy 18 and 13. Sensitivity and specificity for trisomy 21 (43/43) and for trisomy 13 (2/2) were 100%, for trisomy 18 the sensitivity was 80% (4/5) with a specificity of 99.8%. Three false-positive results for trisomy 18 were observed (FPR 0.15%). The no-call rate was 0.5%. In this subgroup, 27.3% (3/11) aneuploidies were diagnosed. The rate of invasive procedures was 2.6%. NIPT provides a very high quality for the fetal trisomies 21, 13 and 18 in clinical routine. The results support the recommendation that NIPT should be offered after genetic counseling and only in conjunction with a qualified ultrasound examination.

Performance of Copan WASP for Routine Urine Microbiology

PubMed Central

Quiblier, Chantal; Jetter, Marion; Rominski, Mark; Mouttet, Forouhar; Böttger, Erik C.; Keller, Peter M.

2015-01-01

This study compared a manual workup of urine clinical samples with fully automated WASPLab processing. As a first step, two different inocula (1 and 10 μl) and different streaking patterns were compared using WASP and InoqulA BT instrumentation. Significantly more single colonies were produced with the10-μl inoculum than with the 1-μl inoculum, and automated streaking yielded significantly more single colonies than manual streaking on whole plates (P < 0.001). In a second step, 379 clinical urine samples were evaluated using WASP and the manual workup. Average numbers of detected morphologies, recovered species, and CFUs per milliliter of all 379 urine samples showed excellent agreement between WASPLab and the manual workup. The percentage of urine samples clinically categorized as positive or negative did not differ between the automated and manual workflow, but within the positive samples, automated processing by WASPLab resulted in the detection of more potential pathogens. In summary, the present study demonstrates that (i) the streaking pattern, i.e., primarily the number of zigzags/length of streaking lines, is critical for optimizing the number of single colonies yielded from primary cultures of urine samples; (ii) automated streaking by the WASP instrument is superior to manual streaking regarding the number of single colonies yielded (for 32.2% of the samples); and (iii) automated streaking leads to higher numbers of detected morphologies (for 47.5% of the samples), species (for 17.4% of the samples), and pathogens (for 3.4% of the samples). The results of this study point to an improved quality of microbiological analyses and laboratory reports when using automated sample processing by WASP and WASPLab. PMID:26677255

Statistical Design for Biospecimen Cohort Size in Proteomics-based Biomarker Discovery and Verification Studies

PubMed Central

Skates, Steven J.; Gillette, Michael A.; LaBaer, Joshua; Carr, Steven A.; Anderson, N. Leigh; Liebler, Daniel C.; Ransohoff, David; Rifai, Nader; Kondratovich, Marina; Težak, Živana; Mansfield, Elizabeth; Oberg, Ann L.; Wright, Ian; Barnes, Grady; Gail, Mitchell; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Boja, Emily S.

2014-01-01

Protein biomarkers are needed to deepen our understanding of cancer biology and to improve our ability to diagnose, monitor and treat cancers. Important analytical and clinical hurdles must be overcome to allow the most promising protein biomarker candidates to advance into clinical validation studies. Although contemporary proteomics technologies support the measurement of large numbers of proteins in individual clinical specimens, sample throughput remains comparatively low. This problem is amplified in typical clinical proteomics research studies, which routinely suffer from a lack of proper experimental design, resulting in analysis of too few biospecimens to achieve adequate statistical power at each stage of a biomarker pipeline. To address this critical shortcoming, a joint workshop was held by the National Cancer Institute (NCI), National Heart, Lung and Blood Institute (NHLBI), and American Association for Clinical Chemistry (AACC), with participation from the U.S. Food and Drug Administration (FDA). An important output from the workshop was a statistical framework for the design of biomarker discovery and verification studies. Herein, we describe the use of quantitative clinical judgments to set statistical criteria for clinical relevance, and the development of an approach to calculate biospecimen sample size for proteomic studies in discovery and verification stages prior to clinical validation stage. This represents a first step towards building a consensus on quantitative criteria for statistical design of proteomics biomarker discovery and verification research. PMID:24063748

Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.

PubMed

Skates, Steven J; Gillette, Michael A; LaBaer, Joshua; Carr, Steven A; Anderson, Leigh; Liebler, Daniel C; Ransohoff, David; Rifai, Nader; Kondratovich, Marina; Težak, Živana; Mansfield, Elizabeth; Oberg, Ann L; Wright, Ian; Barnes, Grady; Gail, Mitchell; Mesri, Mehdi; Kinsinger, Christopher R; Rodriguez, Henry; Boja, Emily S

2013-12-06

Protein biomarkers are needed to deepen our understanding of cancer biology and to improve our ability to diagnose, monitor, and treat cancers. Important analytical and clinical hurdles must be overcome to allow the most promising protein biomarker candidates to advance into clinical validation studies. Although contemporary proteomics technologies support the measurement of large numbers of proteins in individual clinical specimens, sample throughput remains comparatively low. This problem is amplified in typical clinical proteomics research studies, which routinely suffer from a lack of proper experimental design, resulting in analysis of too few biospecimens to achieve adequate statistical power at each stage of a biomarker pipeline. To address this critical shortcoming, a joint workshop was held by the National Cancer Institute (NCI), National Heart, Lung, and Blood Institute (NHLBI), and American Association for Clinical Chemistry (AACC) with participation from the U.S. Food and Drug Administration (FDA). An important output from the workshop was a statistical framework for the design of biomarker discovery and verification studies. Herein, we describe the use of quantitative clinical judgments to set statistical criteria for clinical relevance and the development of an approach to calculate biospecimen sample size for proteomic studies in discovery and verification stages prior to clinical validation stage. This represents a first step toward building a consensus on quantitative criteria for statistical design of proteomics biomarker discovery and verification research.

Hemato-biochemical alterations and urinalysis in dogs suffering from benign prostatic hyperplasia

PubMed Central

Das, M. R.; Patra, R. C.; Das, R. K.; Rath, P. K.; Mishra, B. P.

2017-01-01

Aim: The study was designed to evaluate the hemato-biochemical alterations, urinalysis along with histomorphological and histological changes of prostate glands in dogs affected with benign prostatic hyperplasia (BPH) in and around Bhubaneswar, Odisha, India. Materials and Methods: In toto, 445 dogs presented to the Teaching Veterinary Clinical Complex of the College of Veterinary Sciences and Animal Husbandry, one Government Veterinary Hospital and two pet clinics in and around Bhubaneswar screened for the presence of BPH. Most of the 57 dogs were 6 years and above as reported by the owners. Only 57 dogs found positive for BPH basing on the presence of typical clinical signs subjected for a detailed hemato-biochemical study. Most of the 57 dogs were 6 years and above as reported by the owners. Routine and microscopic urinalyses were done as per the routine procedure. Histomorphological evaluations of prostate glands were done through manual rectal palpation. Histological examinations of prostate tissue sections of two dead dogs were conducted with routine hematoxylin and eosin stain. Results: The study revealed about 12.8% (57/445) of dogs was suffering from BPH. Typical clinical signs - such as passing small thin tape-shaped feces, holding tail away from backward, tenesmus, and straining during urination and defecation - were seen in most of the cases. Urine samples of affected dogs were positive for glucose, occult blood, and protein. A significant decrease in lymphocytes and increase in eosinophil counts in dogs with BPH was recorded. Serum biochemical analysis showed a nonsignificant increase in creatinine and blood urea nitrogen with a significant decrease in total protein, albumin, globulin, A:G ratio. Histology of prostate glands collected during postmortem was characterized by fibrosis of prostate gland, and hyperplasia of the acinar epithelium. Conclusions: High rate of the prevalence of BPH in dogs poses an alarming condition which if diagnosed at an early stage can certainly prolong the longevity of the dogs. PMID:28435196

Comparison of smartphone application-based vital sign monitors without external hardware versus those used in clinical practice: a prospective trial.

PubMed

Alexander, John C; Minhajuddin, Abu; Joshi, Girish P

2017-08-01

Use of healthcare-related smartphone applications is common. However, there is concern that inaccurate information from these applications may lead patients to make erroneous healthcare decisions. The objective of this study is to study smartphone applications purporting to measure vital sign data using only onboard technology compared with monitors used routinely in clinical practice. This is a prospective trial comparing correlation between a clinically utilized vital sign monitor (Propaq CS, WelchAllyn, Skaneateles Falls, NY, USA) and four smartphone application-based monitors Instant Blood Pressure, Instant Blood Pressure Pro, Pulse Oximeter, and Pulse Oximeter Pro. We performed measurements of heart rate (HR), systolic blood pressures (SBP), diastolic blood pressure (DBP), and oxygen saturation (SpO 2 ) using standard monitor and four smartphone applications. Analysis of variance was used to compare measurements from the applications to the routine monitor. The study was completed on 100 healthy volunteers. Comparison of routine monitor with the smartphone applications shows significant differences in terms of HR, SpO 2 and DBP. The SBP values from the applications were not significantly different from those from the routine monitor, but had wide limits of agreement signifying a large degree of variation in the compared values. The degree of correlation between monitors routinely used in clinical practice and the smartphone-based applications studied is insufficient to recommend clinical utilization. This lack of correlation suggests that the applications evaluated do not provide clinically meaningful data. The inaccurate data provided by these applications can potentially contribute to patient harm.

Use of structured musculoskeletal examination routines in undergraduate medical education and postgraduate clinical practice - a UK survey.

PubMed

Baker, Kenneth F; Jandial, Sharmila; Thompson, Ben; Walker, David; Taylor, Ken; Foster, Helen E

2016-10-21

Structured examination routines have been developed as educational resources for musculoskeletal clinical skills teaching, including Gait-Arms-Legs-Spine (GALS), Regional Examination of the Musculoskeletal System (REMS) and paediatric GALS (pGALS). In this study, we aimed to assess the awareness and use of these examination routines in undergraduate medical teaching in UK medical schools and UK postgraduate clinical practice. Electronic questionnaires were distributed to adult and paediatric musculoskeletal teaching leads at UK medical schools and current UK doctors in training. Responses were received from 67 tutors representing teaching at 22/33 [67 %] of all UK medical schools, and 70 trainee doctors across a range of postgraduate training specialities. There was widespread adoption, at responding medical schools, of the adult examination routines within musculoskeletal teaching (GALS: 14/16 [88 %]; REMS: 12/16 [75 %]) and assessment (GALS: 13/16 [81 %]; REMS: 12/16 [75 %]). More trainees were aware of GALS (64/70 [91 %]) than REMS (14/67 [21 %]). Of the 39 trainees who used GALS in their clinical practice, 35/39 [90 %] reported that it had improved their confidence in musculoskeletal examination. Of the 17/22 responding medical schools that included paediatric musculoskeletal examination within their curricula, 15/17 [88 %] used the pGALS approach and this was included within student assessment at 4 medical schools. We demonstrate the widespread adoption of these examination routines in undergraduate education and significant uptake in postgraduate clinical practice. Further study is required to understand their impact upon clinical performance.

Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

PubMed

Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

2014-11-28

Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical review of diagnostic and procedure codes. The four distinct methods identifying complication from codified data offer great potential in generating new evidence on the quality and safety of new procedures using routine data. However the most robust method, using the methodology recommended by the NHS Classification Service, was the least frequently used, highlighting that much valuable observational data is being ignored.

High risk of false positive results in a widely used diagnostic test for detection of the porcine reproductive and respiratory syndrome virus (PRRSV).

PubMed

Fetzer, C; Pesch, S; Ohlinger, V F

2006-06-15

During 2003 and 2004, increasing numbers of positive PRRSV RT-PCR results were reported from herds negative for PRRSV infection. Interestingly, three herds represent nucleus herds with no animal contacts from outside and without clinical symptoms of PRRS until now. Since these positive results that were obtained using a PCR protocol adapted to routine laboratory conditions could not be reproduced with other PRRSV specific RT-PCRs, controlled negative and positive samples were used to examine this phenomenon. A RT-PCR assay for detection and differential diagnosis of the European and North American genotypes of the porcine reproductive and respiratory syndrome virus (PRRSV) according to the method previously published by Oleksiewicz et al. [Oleksiewicz, M.B., Botner, A., Madsen, K.G., Storgaard, T., 1998. Sensitive detection and typing of porcine reproductive and respiratory syndrome virus by RT-PCR amplification of whole viral genes. Vet. Microbiol. 64, 7-22] was investigated in parallel to another recently published method [Pesch, S., 2003. Etablierung einer Nachweismethode für die zwei Genotypen von dem porcine reproductive and respiratory syndrome virus (PRRSV) und ein Beitrag zu seiner molekularen Epidemiologie. Thesis, Institute of Virology, Faculty of Veterinary Medicine, University of Leipzig]. A panel of 228 clinical samples sent in for PRRSV routine diagnostics served as test panel. It was found that both methods have similar analytical sensitivity. However, the primers published by Oleksiewicz were shown to yield a very high proportion of false positive results under routine diagnostic laboratory conditions, i.e. they resulted in RT-PCR products with non-PRRSV sequences, that were indistinguishable from truly positive reagents in standard gel electrophoresis settings. The reason for and possible implications of this finding as well as the risk of modifying published methods without control are discussed.

Same-Day Identification and Antimicrobial Susceptibility Testing of Bacteria in Positive Blood Culture Broths Using Short-Term Incubation on Solid Medium with the MicroFlex LT, Vitek-MS, and Vitek2 Systems

PubMed Central

Ha, Jihye; Han, Geum Hee; Kim, Myungsook; Lee, Kyungwon

2018-01-01

Background Early and appropriate antibiotic treatment improves the clinical outcome of patients with septicemia; therefore, reducing the turn-around time for identification (ID) and antimicrobial susceptibility test (AST) results is essential. We established a method for rapid ID and AST using short-term incubation of positive blood culture broth samples on solid media, and evaluated its performance relative to that of the conventional method using two rapid ID systems and a rapid AST method. Methods A total of 254 mono-microbial samples were included. Positive blood culture samples were incubated on blood agar plates for six hours and identified by the MicroFlex LT (Bruker Daltonics) and Vitek-MS (bioMeriéux) systems, followed by AST using the Vitek2 System (bioMeriéux). Results The correct species-level ID rates were 82.3% (209/254) and 78.3% (199/254) for the MicroFlex LT and Vitek-MS platforms, respectively. For the 1,174 microorganism/antimicrobial agent combinations tested, the rapid AST method showed total concordance of 97.8% (1,148/1,174) with the conventional method, with a very major error rate of 0.5%, major error rate of 0.7%, and minor error rate of 1.0%. Conclusions Routine implementation of this short-term incubation method could provide ID results on the day of blood culture-positivity detection and one day earlier than the conventional AST method. This simple method will be very useful for rapid ID and AST of bacteria from positive blood culture bottles in routine clinical practice. PMID:29401558

Same-Day Identification and Antimicrobial Susceptibility Testing of Bacteria in Positive Blood Culture Broths Using Short-Term Incubation on Solid Medium with the MicroFlex LT, Vitek-MS, and Vitek2 Systems.

PubMed

Ha, Jihye; Hong, Sung Kuk; Han, Geum Hee; Kim, Myungsook; Yong, Dongeun; Lee, Kyungwon

2018-05-01

Early and appropriate antibiotic treatment improves the clinical outcome of patients with septicemia; therefore, reducing the turn-around time for identification (ID) and antimicrobial susceptibility test (AST) results is essential. We established a method for rapid ID and AST using short-term incubation of positive blood culture broth samples on solid media, and evaluated its performance relative to that of the conventional method using two rapid ID systems and a rapid AST method. A total of 254 mono-microbial samples were included. Positive blood culture samples were incubated on blood agar plates for six hours and identified by the MicroFlex LT (Bruker Daltonics) and Vitek-MS (bioMeriéux) systems, followed by AST using the Vitek2 System (bioMeriéux). The correct species-level ID rates were 82.3% (209/254) and 78.3% (199/254) for the MicroFlex LT and Vitek-MS platforms, respectively. For the 1,174 microorganism/antimicrobial agent combinations tested, the rapid AST method showed total concordance of 97.8% (1,148/1,174) with the conventional method, with a very major error rate of 0.5%, major error rate of 0.7%, and minor error rate of 1.0%. Routine implementation of this short-term incubation method could provide ID results on the day of blood culture-positivity detection and one day earlier than the conventional AST method. This simple method will be very useful for rapid ID and AST of bacteria from positive blood culture bottles in routine clinical practice. © The Korean Society for Laboratory Medicine

Generalizability of Pharmacologic and Psychotherapy Clinical Trial Results for Posttraumatic Stress Disorder to Community Samples.

PubMed

Franco, Silvia; Hoertel, Nicolas; McMahon, Kibby; Wang, Shuai; Rodríguez-Fernández, Jorge Mario; Peyre, Hugo; Limosin, Frédéric; Blanco, Carlos

2016-08-01

The present study sought to quantify the generalizability of pharmacologic and psychotherapy clinical trial results in individuals with a DSM-IV diagnosis of posttraumatic stress disorder (PTSD) to a large representative community sample. Data were derived from the 2004-2005 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), a large nationally representative sample of the adult US population. We applied a standard set of exclusion criteria representative of pharmacologic and psychotherapy clinical trials to all adults with a DSM-IV diagnosis of PTSD in the previous 12 months (n = 1,715) and then to a subsample of participants seeking treatment (n = 366). Our aim was to assess how many participants with PTSD would fulfill typical eligibility criteria. We found that more than 6 of 10 respondents from the overall PTSD sample and more than 7 of 10 respondents seeking treatment for PTSD would have been excluded by 1 exclusion criterion or more in a typical pharmacologic trial. In contrast, about 2 of 10 participants in the full sample and about 3 of 10 participants seeking treatment for PTSD would have been excluded in a typical psychotherapy efficacy trial. We found that psychotherapy trial results may be applied to most patients with PTSD in routine clinical practice. The designers of pharmacologic clinical trials should carefully consider the trade-offs between the application of each exclusion criterion and its impact on representativeness. Specification a priori of the goals of the study, better justification for each exclusion criterion, and estimation of the proportion of individuals ineligible for the trial would assist study design. Developing integrated forms of pharmacotherapy and psychotherapy that simultaneously target commonly overlapping psychiatric disorders may yield more informative results for mental health care providers and research funding agencies. © Copyright 2016 Physicians Postgraduate Press, Inc.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

PubMed Central

Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A. Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David; Bento, Celeste; Bignell, Patricia; Blair, Edward; Buckle, Veronica J; Bull, Katherine; Cais, Ondrej; Cario, Holger; Chapel, Helen; Copley, Richard R; Cornall, Richard; Craft, Jude; Dahan, Karin; Davenport, Emma E; Dendrou, Calliope; Devuyst, Olivier; Fenwick, Aimée L; Flint, Jonathan; Fugger, Lars; Gilbert, Rodney D; Goriely, Anne; Green, Angie; Greger, Ingo H.; Grocock, Russell; Gruszczyk, Anja V; Hastings, Robert; Hatton, Edouard; Higgs, Doug; Hill, Adrian; Holmes, Chris; Howard, Malcolm; Hughes, Linda; Humburg, Peter; Johnson, David; Karpe, Fredrik; Kingsbury, Zoya; Kini, Usha; Knight, Julian C; Krohn, Jonathan; Lamble, Sarah; Langman, Craig; Lonie, Lorne; Luck, Joshua; McCarthy, Davis; McGowan, Simon J; McMullin, Mary Frances; Miller, Kerry A; Murray, Lisa; Németh, Andrea H; Nesbit, M Andrew; Nutt, David; Ormondroyd, Elizabeth; Oturai, Annette Bang; Pagnamenta, Alistair; Patel, Smita Y; Percy, Melanie; Petousi, Nayia; Piazza, Paolo; Piret, Sian E; Polanco-Echeverry, Guadalupe; Popitsch, Niko; Powrie, Fiona; Pugh, Chris; Quek, Lynn; Robbins, Peter A; Robson, Kathryn; Russo, Alexandra; Sahgal, Natasha; van Schouwenburg, Pauline A; Schuh, Anna; Silverman, Earl; Simmons, Alison; Sørensen, Per Soelberg; Sweeney, Elizabeth; Taylor, John; Thakker, Rajesh V; Tomlinson, Ian; Trebes, Amy; Twigg, Stephen RF; Uhlig, Holm H; Vyas, Paresh; Vyse, Tim; Wall, Steven A; Watkins, Hugh; Whyte, Michael P; Witty, Lorna; Wright, Ben; Yau, Chris; Buck, David; Humphray, Sean; Ratcliffe, Peter J; Bell, John I; Wilkie, Andrew OM; Bentley, David; Donnelly, Peter; McVean, Gilean

2015-01-01

To assess factors influencing the success of whole genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases across a broad spectrum of disorders in whom prior screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritisation. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease causing variants in 21% of cases, rising to 34% (23/68) for Mendelian disorders and 57% (8/14) in trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, though only four were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis, but also highlight many outstanding challenges. PMID:25985138

Annotation of Sequence Variants in Cancer Samples: Processes and Pitfalls for Routine Assays in the Clinical Laboratory.

PubMed

Lee, Lobin A; Arvai, Kevin J; Jones, Dan

2015-07-01

As DNA sequencing of multigene panels becomes routine for cancer samples in the clinical laboratory, an efficient process for classifying variants has become more critical. Determining which germline variants are significant for cancer disposition and which somatic mutations are integral to cancer development or therapy response remains difficult, even for well-studied genes such as BRCA1 and TP53. We compare and contrast the general principles and lines of evidence commonly used to distinguish the significance of cancer-associated germline and somatic genetic variants. The factors important in each step of the analysis pipeline are reviewed, as are some of the publicly available annotation tools. Given the range of indications and uses of cancer sequencing assays, including diagnosis, staging, prognostication, theranostics, and residual disease detection, the need for flexible methods for scoring of variants is discussed. The usefulness of protein prediction tools and multimodal risk-based or Bayesian approaches are highlighted. Using TET2 variants encountered in hematologic neoplasms, several examples of this multifactorial approach to classifying sequence variants of unknown significance are presented. Although there are still significant gaps in the publicly available data for many cancer genes that limit the broad application of explicit algorithms for variant scoring, the elements of a more rigorous model are outlined. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Surveillance of emerging drugs of abuse in Hong Kong: validation of an analytical tool.

PubMed

Tang, Magdalene H Y; Ching, C K; Tse, M L; Ng, Carol; Lee, Caroline; Chong, Y K; Wong, Watson; Mak, Tony W L

2015-04-01

To validate a locally developed chromatography-based method to monitor emerging drugs of abuse whilst performing regular drug testing in abusers. Cross-sectional study. Eleven regional hospitals, seven social service units, and a tertiary level clinical toxicology laboratory in Hong Kong. A total of 972 drug abusers and high-risk individuals were recruited from acute, rehabilitation, and high-risk settings between 1 November 2011 and 31 July 2013. A subset of the participants was of South Asian ethnicity. In total, 2000 urine or hair specimens were collected. Proof of concept that surveillance of emerging drugs of abuse can be performed whilst conducting routine drug of abuse testing in patients. The method was successfully applied to 2000 samples with three emerging drugs of abuse detected in five samples: PMMA (paramethoxymethamphetamine), TFMPP [1-(3-trifluoromethylphenyl)piperazine], and methcathinone. The method also detected conventional drugs of abuse, with codeine, methadone, heroin, methamphetamine, and ketamine being the most frequently detected drugs. Other findings included the observation that South Asians had significantly higher rates of using opiates such as heroin, methadone, and codeine; and that ketamine and cocaine had significantly higher detection rates in acute subjects compared with the rehabilitation population. This locally developed analytical method is a valid tool for simultaneous surveillance of emerging drugs of abuse and routine drug monitoring of patients at minimal additional cost and effort. Continued, proactive surveillance and early identification of emerging drugs will facilitate prompt clinical, social, and legislative management.

Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation.

PubMed

Trtkova, Jitka; Pavlicek, Petr; Ruskova, Lenka; Hamal, Petr; Koukalova, Dagmar; Raclavsky, Vladislav

2009-11-10

Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD). Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification. A simple fully automated algorithm based on normalized melting data identified 80% of the isolates correctly. When this algorithm was supplemented by semi-automated matching of decisive peaks in first derivative plots, 87% of the isolates were identified correctly. However, a computer-aided visual matching of derivative plots showed the best performance with average 98.3% of the accurately identified isolates, almost matching the 99.4% performance of traditional RAPD fingerprinting. Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance.

Comparison of the Effects of Benson Muscle Relaxation and Nature Sounds on the Fatigue in Patients With Heart Failure: A Randomized Controlled Clinical Trial.

PubMed

Seifi, Leila; Najafi Ghezeljeh, Tahereh; Haghani, Hamid

This study was conducted with the aim of comparing the effects of Benson muscle relaxation and nature sounds on fatigue in patients with heart failure. Fatigue and exercise intolerance as prevalent symptoms experienced by patients with heart failure can cause the loss of independence in the activities of daily living. It can also damage self-care and increase dependence to others, which subsequently can reduce the quality of life. This randomized controlled clinical trial was conducted in an urban area of Iran in 2016. Samples were consisted of 105 hospitalized patients with heart failure chosen using a convenience sampling method. They were assigned to relaxation, nature sounds, and control groups using a randomized block design. In addition to routine care, the Benson muscle relaxation and nature sounds groups received interventions in mornings and evenings twice a day for 20 minutes within 3 consecutive days. A 9-item questionnaire was used to collect data regarding fatigue before and after the interventions. Relaxation and nature sounds reduced fatigue in patients with heart failure in comparison to the control group. However, no statistically significant difference was observed between the interventions. Benson muscle relaxation and nature sounds are alternative methods for the reduction of fatigue in patients with heart failure. They are inexpensive and easy to be administered and upon patients' preferences can be used by nurses along with routine nursing interventions.

Multisite tumor sampling enhances the detection of intratumor heterogeneity at all different temporal stages of tumor evolution.

PubMed

Erramuzpe, Asier; Cortés, Jesús M; López, José I

2018-02-01

Intratumor heterogeneity (ITH) is an inherent process of tumor development that has received much attention in previous years, as it has become a major obstacle for the success of targeted therapies. ITH is also temporally unpredictable across tumor evolution, which makes its precise characterization even more problematic since detection success depends on the precise temporal snapshot at which ITH is analyzed. New and more efficient strategies for tumor sampling are needed to overcome these difficulties which currently rely entirely on the pathologist's interpretation. Recently, we showed that a new strategy, the multisite tumor sampling, works better than the routine sampling protocol for the ITH detection when the tumor time evolution was not taken into consideration. Here, we extend this work and compare the ITH detections of multisite tumor sampling and routine sampling protocols across tumor time evolution, and in particular, we provide in silico analyses of both strategies at early and late temporal stages for four different models of tumor evolution (linear, branched, neutral, and punctuated). Our results indicate that multisite tumor sampling outperforms routine protocols in detecting ITH at all different temporal stages of tumor evolution. We conclude that multisite tumor sampling is more advantageous than routine protocols in detecting intratumor heterogeneity.

Phylogenetic characterisation of circulating, clinical influenza isolates from Bali, Indonesia: preliminary report from the BaliMEI project.

PubMed

Adisasmito, W; Budayanti, S N; Aisyah, D N; Gallo Cassarino, T; Rudge, J W; Watson, S J; Kozlakidis, Z; Smith, G J D; Coker, R

2017-08-23

Human influenza represents a major public health concern, especially in south-east Asia where the risk of emergence and spread of novel influenza viruses is particularly high. The BaliMEI study aims to conduct a five year active surveillance and characterisation of influenza viruses in Bali using an extensive network of participating healthcare facilities. Samples were collected during routine diagnostic treatment in healthcare facilities. In addition to standard clinical and molecular methods for influenza typing, next generation sequencing and subsequent de novo genome assembly were performed to investigate the phylogeny of the collected patient samples. The samples collected are characteristic of the seasonally circulating influenza viruses with indications of phylogenetic links to other samples characterised in neighbouring countries during the same time period. There were some strong phylogenetic links with sequences from samples collected in geographically proximal regions, with some of the samples from the same time-period resulting to small clusters at the tree-end points. However this work, which is the first of its kind completely performed within Indonesia, supports the view that the circulating seasonal influenza in Bali reflects the strains circulating in geographically neighbouring areas as would be expected to occur within a busy regional transit centre.

Clinical evaluation of the new Roche platform of serological and molecular cytomegalovirus-specific assays in the diagnosis and prognosis of congenital cytomegalovirus infection.

PubMed

Chiereghin, Angela; Pavia, Claudia; Gabrielli, Liliana; Piccirilli, Giulia; Squarzoni, Diego; Turello, Gabriele; Gibertoni, Dino; Simonazzi, Giuliana; Capretti, Maria Grazia; Lanari, Marcello; Lazzarotto, Tiziana

2017-10-01

Clinical evaluation of the Elecsys ® CMV IgM, IgG, IgG Avidity and COBAS AmpliPrep/COBAS TaqMan CMV (COBAS CMV) assays (Roche Diagnostics AG) in the diagnosis and prognosis of congenital CMV infection was performed. In this study, 150 preselected clinical samples (50 primary infection sera, 50 amniotic fluid [AF] and 50 newborn urine) were processed using Roche serological/molecular CMV-specific tests. Results were compared with those obtained by routine assays (comparator assays). The Elecsys ® CMV IgM and IgG assays showed a perfect agreement (100%) with the comparator assays. Using the combination of the Elecsys ® CMV IgM and IgG Avidity assays results, a primary infection was identified in 100% of cases. Inappropriate avidity CMV IgG values in two samples with very low IgG values (<6 AU/mL) were observed. COBAS CMV assay showed an agreement equal to 98% and 100% with comparator assays by processing AF and urine samples, respectively. Among AF with quantitative results, Lin's concordance correlation was 0.933 and comparator-COBAS CMV assays gave CMV-DNA loads differing by <0.5 log 10 DNA. Finally, higher CMV-DNA levels in AF samples were associated with a symptomatic outcome (p=0.003). The Roche CMV-specific assays compared well with the comparator assays, thus providing to be suitable for clinical use. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of Cobas Integra 800 under simulated routine conditions in six laboratories.

PubMed

Redondo, Francisco L; Bermudez, Pilar; Cocco, Claudio; Colella, Francesca; Graziani, Maria Stella; Fiehn, Walter; Hierla, Thomas; Lemoël, Gisèle; Belliard, AnneMarie; Manene, Dieudonne; Meziani, Mourad; Liebel, Maryann; McQueen, Matthew J; Stockmann, Wolfgang

2003-03-01

The new selective access analyser Cobas Integra 800 from Roche Diagnostics was evaluated in an international multicentre study at six sites. Routine simulation experiments showed good performance and full functionality of the instrument and provocation of anomalous situations generated no problems. The new features on Cobas Integra 800, namely clot detection and dispensing control, worked according to specifications. The imprecision of Cobas Integra 800 fulfilled the proposed quality specifications regarding imprecision of analytical systems for clinical chemistry with few exceptions. Claims for linearity, drift, and carry-over were all within the defined specifications, except urea linearity. Interference exists in some cases, as could be expected due to the chemistries applied. Accuracy met the proposed quality specifications, except in some special cases. Method comparisons with Cobas Integra 700 showed good agreement; comparisons with other analysis systems yielded in several cases explicable deviations. Practicability of Cobas Integra 800 met or exceeded the requirements for more than 95% of all attributes rated. The strong points of the new analysis system were reagent handling, long stability of calibration curves, high number of tests on board, compatibility of the sample carrier to other Roche systems, and the sample integrity check for more reliable analytical results. The improvement of the workflow offered by the 5-position rack and STAT handling like on Cobas Integra 800 makes the instrument attractive for further consolidation in the medium-sized laboratory, for dedicated use of special analytes, and/or as back-up in the large routine laboratory.

A Real-World Setting Study: Which Glucose Meter Could Be the Best for POCT Use? An Easy and Applicable Protocol During the Hospital Routine.

PubMed

Mancini, Alessio; Esposto, Giampaolo; Manfrini, Silvana; Rilli, Silvia; Tinti, Gessica; Carta, Giuseppe; Petrolati, Laura; Vidali, Matteo; Barocci, Simone

2018-05-01

The aim of this retrospective study is to evaluate the reliability and robustness of six glucose meters for point-of-care testing in our wards using a brand-new protocol. During a 30-days study period a total of 50 diabetes patients were subjected to venous blood sampling and glucose meter blood analysis. The results of six glucose meters were compared with our laboratory reference assay. GlucoMen Plus (Menarini) with the 82% of acceptable results was the most robust glucose meter. Even if the Passing-Bablok analysis demonstrates the presence of constant systematic errors and the Bland-Altman test highlighted a possible overestimation, the surveillance error grid analysis showed that this glucose meter can be used safely. We proved that portable glucose meters are not always reliable in routinely clinical settings.

[Serological diagnosis of whooping cough using immunoblot methods].

PubMed

Lochman, I; Pokorná, L; Mertová, H

2017-01-01

The aim of this study was to challenge the conclusion presented in the current recommendations of the EU Perstrain Group (European group of reference laboratories) [17] that immunoblotting methods are not appropriate serological methods for the diagnosis of pertussis because their results cannot be quantified. To consider benefits of these methods for the diagnosis of Bordetella infections was another aim of this work. The residual sera from routine testing intended for disposal and results of routine tests for Bordetella infections performed in Spadia Lab in 2015 and 2016 were used in this study. The test samples were anonymized. Standard commercial ELISA and immunoblot kits were used for analyses. Using the TestLine Clinical Diagnostics Company kits, we have shown that, contrary to the conclusion of the EU Perstrain Group, quantification of the immunoblot results is possible and that these methods can improve the diagnosis of Bordetella infections, ultimately making it more effective.

Possible Rickettsia massiliae Infection in Greece: an Imported Case.

PubMed

Chochlakis, Dimosthenis; Bongiorni, Christine; Partalis, Nikolaos; Tselentis, Yannis; Psaroulaki, Anna

2016-07-22

Tick-borne rickettsioses are endemic in Greece; however, until recently, only Rickettsia typhi and R. conorii were tested routinely in human samples arriving at the National Reference Center. During the last few years, the identification of different rickettsia species in ticks led to the introduction of other spotted fever group rickettsiae in routine analysis. Under the new scheme, R. massiliae is now tested routinely in human samples; herein, we describe a human case of this infection.

Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma

PubMed Central

Ramkissoon, Shakti H.; Bi, Wenya Linda; Schumacher, Steven E.; Ramkissoon, Lori A.; Haidar, Sam; Knoff, David; Dubuc, Adrian; Brown, Loreal; Burns, Margot; Cryan, Jane B.; Abedalthagafi, Malak; Kang, Yun Jee; Schultz, Nikolaus; Reardon, David A.; Lee, Eudocia Q.; Rinne, Mikael L.; Norden, Andrew D.; Nayak, Lakshmi; Ruland, Sandra; Doherty, Lisa M.; LaFrankie, Debra C.; Horvath, Margaret; Aizer, Ayal A.; Russo, Andrea; Arvold, Nils D.; Claus, Elizabeth B.; Al-Mefty, Ossama; Johnson, Mark D.; Golby, Alexandra J.; Dunn, Ian F.; Chiocca, E. Antonio; Trippa, Lorenzo; Santagata, Sandro; Folkerth, Rebecca D.; Kantoff, Philip; Rollins, Barrett J.; Lindeman, Neal I.; Wen, Patrick Y.; Ligon, Azra H.; Beroukhim, Rameen; Alexander, Brian M.; Ligon, Keith L.

2015-01-01

Background Multidimensional genotyping of formalin-fixed paraffin-embedded (FFPE) samples has the potential to improve diagnostics and clinical trials for brain tumors, but prospective use in the clinical setting is not yet routine. We report our experience with implementing a multiplexed copy number and mutation-testing program in a diagnostic laboratory certified by the Clinical Laboratory Improvement Amendments. Methods We collected and analyzed clinical testing results from whole-genome array comparative genomic hybridization (OncoCopy) of 420 brain tumors, including 148 glioblastomas. Mass spectrometry–based mutation genotyping (OncoMap, 471 mutations) was performed on 86 glioblastomas. Results OncoCopy was successful in 99% of samples for which sufficient DNA was obtained (n = 415). All clinically relevant loci for glioblastomas were detected, including amplifications (EGFR, PDGFRA, MET) and deletions (EGFRvIII, PTEN, 1p/19q). Glioblastoma patients ≤40 years old had distinct profiles compared with patients >40 years. OncoMap testing reliably identified mutations in IDH1, TP53, and PTEN. Seventy-seven glioblastoma patients enrolled on trials, of whom 51% participated in targeted therapeutic trials where multiplex data informed eligibility or outcomes. Data integration identified patients with complete tumor suppressor inactivation, albeit rarely (5% of patients) due to lack of whole-gene coverage in OncoMap. Conclusions Combined use of multiplexed copy number and mutation detection from FFPE samples in the clinical setting can efficiently replace singleton tests for clinical diagnosis and prognosis in most settings. Our results support incorporation of these assays into clinical trials as integral biomarkers and their potential to impact interpretation of results. Limited tumor suppressor variant capture by targeted genotyping highlights the need for whole-gene sequencing in glioblastoma. PMID:25754088

Identification of a novel pathogenic Borrelia species causing Lyme borreliosis with unusually high spirochaetaemia: a descriptive study.

PubMed

Pritt, Bobbi S; Mead, Paul S; Johnson, Diep K Hoang; Neitzel, David F; Respicio-Kingry, Laurel B; Davis, Jeffrey P; Schiffman, Elizabeth; Sloan, Lynne M; Schriefer, Martin E; Replogle, Adam J; Paskewitz, Susan M; Ray, Julie A; Bjork, Jenna; Steward, Christopher R; Deedon, Alecia; Lee, Xia; Kingry, Luke C; Miller, Tracy K; Feist, Michelle A; Theel, Elitza S; Patel, Robin; Irish, Cole L; Petersen, Jeannine M

2016-05-01

Lyme borreliosis is the most common tick-borne disease in the northern hemisphere. It is a multisystem disease caused by Borrelia burgdorferi sensu lato genospecies and characterised by tissue localisation and low spirochaetaemia. In this study we aimed to describe a novel Borrelia species causing Lyme borreliosis in the USA. At the Mayo clinic, from 2003 to 2014, we tested routine clinical diagnostic specimens from patients in the USA with PCR targeting the oppA1 gene of B burgdorferi sensu lato. We identified positive specimens with an atypical PCR result (melting temperature outside of the expected range) by sequencing, microscopy, or culture. We collected Ixodes scapularis ticks from regions of suspected patient tick exposure and tested them by oppA1 PCR. 100 545 specimens were submitted by physicians for routine PCR from Jan 1, 2003 to Sept 30, 2014. From these samples, six clinical specimens (five blood, one synovial fluid) yielded an atypical oppA1 PCR product, but no atypical results were detected before 2012. Five of the six patients with atypical PCR results had presented with fever, four had diffuse or focal rash, three had symptoms suggestive of neurological inclusion, and two were admitted to hospital. The sixth patient presented with knee pain and swelling. Motile spirochaetes were seen in blood samples from one patient and cultured from blood samples from two patients. Among the five blood specimens, the median oppA1 copy number was 180 times higher than that in 13 specimens that tested positive for B burgdorferi sensu stricto during the same time period. Multigene sequencing identified the spirochaete as a novel B burgdorferi sensu lato genospecies. This same genospecies was detected in ticks collected at a probable patient exposure site. We describe a new pathogenic Borrelia burgdorferi sensu lato genospecies (candidatus Borrelia mayonii) in the upper midwestern USA, which causes Lyme borreliosis with unusually high spirochaetaemia. Clinicians should be aware of this new B burgdorferi sensu lato genospecies, its distinct clinical features, and the usefulness of oppA1 PCR for diagnosis. US Centers for Disease Control and Prevention Epidemiology and Laboratory Capacity for Infectious Diseases (ELC) Cooperative Agreement and Mayo Clinic Small Grant programme. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Contribution of the detection of IgA antibodies to the laboratory diagnosis of mumps in the population with a high vaccination coverage].

PubMed

Limberková, R; Smíšková, D; Havlíčková, M; Herrmannová, K; Lexová, P; Malý, M

2015-03-01

Serological diagnosis of epidemic mumps can be difficult in vaccinated persons, particularly due to the absence of specific IgM antibodies. The aim was to find whether adding the detection of IgA antibodies to the currently used routine serological diagnosis of mumps (detection of IgM and IgG antibodies in an acute serum sample) would make the serological diagnosis of mumps more effective in a population with a high vaccination coverage. At the same time, ELISA kits for the detection of early IgA and IgM antibodies against the mumps virus were compared and statistical analysis of the results was performed. Sixty-four acute sera from patients with laboratory confirmed diagnosis of mumps were included in the study. Clinical specimens were collected at the onset of clinical symptoms. To test the sera, the MASTAZYME ELISA Mumps IgA kit (MAST DIAGNOSTICA, Germany) with the MASTSORB sorbent (RF and IgG) and Enzygnost Anti-Parotitis-Virus/IgM kit (Siemens, Germany) were used. A panel of 121 acute sera with no epidemiological link to mumps virus served as specificity controls for the IgA assay. The epidemiological data were derived from the EPIDAT system. The level of agreement was assessed using the McNemara test and Cohen's coefficient kappa. The Stata 9.2 software (Stata Corp LP, College Station, USA) was used for statistical analysis. The detection of IgA and IgM antibodies against the mumps virus yielded concordant results in 50/64 acute sera, 32 positive and 18 negative, i.e. an agreement of 78.12 %. Of the remaining 14 samples, 13 were only IgA positive and one was only IgM positive. The controls showed non-specific IgA positivity in 5/121 samples which indicates a 96% specificity. The absence of specific IgM antibodies against mumps virus is relatively often seen in vaccinated indivi-duals; nevertheless, the test is routinely used in patients with suspected active infection. The test for IgA antibodies, which is not routinely performed, significantly increased the detection rate of the disease. Based on the results of the present study, it can be concluded that the combination of the anti-mumps IgM and IgA assays increased the effectiveness of the serological diagnosis at the onset of clinical symptoms from less than 52% to nearly 72%.

Nonoperative management of blunt renal trauma: Is routine early follow-up imaging necessary?

PubMed Central

Malcolm, John B; Derweesh, Ithaar H; Mehrazin, Reza; DiBlasio, Christopher J; Vance, David D; Joshi, Salil; Wake, Robert W; Gold, Robert

2008-01-01

Background There is no consensus on the role of routine follow-up imaging during nonoperative management of blunt renal trauma. We reviewed our experience with nonoperative management of blunt renal injuries in order to evaluate the utility of routine early follow-up imaging. Methods We reviewed all cases of blunt renal injury admitted for nonoperative management at our institution between 1/2002 and 1/2006. Data were compiled from chart review, and clinical outcomes were correlated with CT imaging results. Results 207 patients were identified (210 renal units). American Association for the Surgery of Trauma (AAST) grades I, II, III, IV, and V were assigned to 35 (16%), 66 (31%), 81 (39%), 26 (13%), and 2 (1%) renal units, respectively. 177 (84%) renal units underwent routine follow-up imaging 24–48 hours after admission. In three cases of grade IV renal injury, a ureteral stent was placed after serial imaging demonstrated persistent extravasation. In no other cases did follow-up imaging independently alter clinical management. There were no urologic complications among cases for which follow-up imaging was not obtained. Conclusion Routine follow-up imaging is unnecessary for blunt renal injuries of grades I-III. Grade IV renovascular injuries can be followed clinically without routine early follow-up imaging, but urine extravasation necessitates serial imaging to guide management decisions. The volume of grade V renal injuries in this study is not sufficient to support or contest the need for routine follow-up imaging. PMID:18768088

Exploring the environment of clinical baccalaureate nursing students' education in Iran; A qualitative descriptive study.

PubMed

Yousefy, Alireza; Yazdannik, Ahmad reza; Mohammadi, Sepideh

2015-12-01

Today's students are the nurses of tomorrow. They need appropriate clinical learning opportunities in order to shape their professional identity, attitudes and values. Despite undeniable progresses of nursing education in Iran, the quality of the clinical education in Iran is not favorable. There is a need to explore the environment of clinical baccalaureate nursing students' education for developing, maintaining and enhancing the quality of clinical program. This is a qualitative study and was conducted based on content analysis multimethod design. Data were collected by individual interviews, focus groups and direct observations. 54 nursing students and 8 clinical educators from the four geographically diverse universities in the Iran composed the study sample. A purposive sampling was used. Five themes were emerged from data analysis including; ambiguity in the nursing care role, routine-based nursing care, uncritical and dependent thinking climate, incompetency of clinical educators and patient education as important component of nursing. The findings of this study describe a clearer understanding of the real environment of the clinical education in Iran. All of themes that emerged from the study play an important role in student learning and nursing education. It is crucial to pay more attention to reconsider care concept as an operational component of nursing, maximize meaningful learning opportunities, reevaluate clinical instructor as role models and prepare effective operational plan to combine theoretical and evidence based knowledge with clinical practice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Standardization of a fluconazole bioassay and correlation of results with those obtained by high-pressure liquid chromatography.

PubMed Central

Rex, J H; Hanson, L H; Amantea, M A; Stevens, D A; Bennett, J E

1991-01-01

An improved bioassay for fluconazole was developed. This assay is sensitive in the clinically relevant range (2 to 40 micrograms/ml) and analyzes plasma, serum, and cerebrospinal fluid specimens; bioassay results correlate with results obtained by high-pressure liquid chromatography (HPLC). Bioassay and HPLC analyses of spiked plasma, serum, and cerebrospinal fluid samples (run as unknowns) gave good agreement with expected values. Analysis of specimens from patients gave equivalent results by both HPLC and bioassay. HPLC had a lower within-run coefficient of variation (less than 2.5% for HPLC versus less than 11% for bioassay) and a lower between-run coefficient of variation (less than 5% versus less than 12% for bioassay) and was more sensitive (lower limit of detection, 0.1 micrograms/ml [versus 2 micrograms/ml for bioassay]). The bioassay is, however, sufficiently accurate and sensitive for clinical specimens, and its relative simplicity, low sample volume requirement, and low equipment cost should make it the technique of choice for analysis of routine clinical specimens. PMID:1854166

Conditions of High Resolution Melting Analysis on the Cobas z480 Instrument for the Genotyping of VKORC1 in the Clinical Routine Laboratory.

PubMed

Paar, Christian; Hammerl, Verena; Blessberger, Hermann; Stekel, Herbert; Steinwender, Clemens; Berg, Jörg

2016-12-01

High resolution melting (HRM) of amplicons is a simple method for genotyping of single nucleotide polymorphisms (SNPs). Albeit many applications reported, HRM seems to be rarely used in clinical laboratories. The suitability of HRM-PCR for the clinical laboratory was investigated for genotyping of SNPs of the vitamin K epoxide reductase complex unit 1 gene. About 100 DNA samples were analyzed by two different HRM-PCRs on the Cobas z480 instrument and compared with a PCR with fluorescently labeled probes (HybProbe-PCR) on the LightCycler 2.0 instrument as reference. Reliable genotyping with 100% matching results was obtained, when the amplicon size was small (63 bp) and DNA input was limited by e.g., sample dilution with salt-free water. DNA extracted by differing methods may be used for genotyping by HRM-PCR. Compared with HybProbe-PCR, HRM-PCR on the Cobas z480 instrument allows for higher through-put, however, at the cost of a higher degree of laboratory standardization and a slower turnaround.

Routine production of [(18)f]flumazenil from iodonium tosylate using a sample pretreatment method: a 2.5-year production report.

PubMed

Moon, Byung Seok; Park, Jun Hyung; Lee, Hong Jin; Lee, Byung Chul; Kim, Sang Eun

2014-10-01

[(18)F]Flumazenil, which has the advantage of a longer half-life than [(11)C]flumazenil, is well known for determining of the central benzodiazepine receptor concentrations. However, [(18)F]flumazenil has not been widely used because fluctuating and relatively low yields render automatic production insufficient for routine and multicenter clinical trials. Here, we describe the results of a 2.5-year production study of [(18)F]flumazenil using an iodonium tosylate precursor, which allowed us to overcome the limitations of low and fluctuating radiochemical yields. We developed a clinically applicable production system by modifying a commercial synthesizer for the reliable and reproducible production of [(18)F]flumazenil for routine clinical studies. [(18)F]Flumazenil was prepared at 150 °C for 5 min in the presence of 4-methylphenyl-mazenil iodonium tosylate (4 mg), a radical scavenger (TEMPO, 1 mg), and [(18)F]KF/kryptofix 2.2.2 complex in N,N-dimethylformamide (1 ml). In the purification step, the final mixture was pretreated using different cartridges before performing high-performance liquid chromatography (HPLC) separation. Finally, we measured the radiochemical yield and performed quality-control assays on 94 batches. After carrying out additional purification before HPLC separation using a C18 plus Sep-Pak cartridge, the radiochemical yield of [(18)F]flumazenil increased from 34.4 ± 9.7 % (without the pretreatment, n = 24) to 53.4 ± 9.0 % (n = 94), and the lifetime of the semi-preparative column was five times that of the column without the C18 plus Sep-Pak cartridge. The mean-specific activity of [(18)F]flumazenil was 572 ± 116 GBq/μmol at the end of synthesis, and the radiochemical purity was more than 99 %, as determined by analytical HPLC and radio-TLC. [(18)F]Flumazenil prepared using this method satisfied all quality-control test standards and was highly stable for up to 6 h after preparation. The results of the 2.5-year production study using an iodonium tosylate precursor indicate that [(18)F]flumazenil has commercial and routine clinical applicability.

The gap between available knowledge and its use in clinical psychiatry.

PubMed

Munk-Jørgensen, P; Blanner Kristiansen, C; Uwawke, R; Larsen, J I; Okkels, N; Christiansen, B; Hjorth, P

2015-12-01

The time span between knowledge becoming available and its integration into daily clinical routine is lengthy. This phenomenon is explored in this study. We used the outcomes of our activities for investigating and strengthening the research-based activities to improve physical health in the routines of clinical psychiatric wards as examples for our analyses. The time span between new knowledge becoming available and its implementation into general clinical treatment is very long. However, a shortening of this time span is seen through active leadership backup and clinical research experience among psychiatrists and staff in the wards. In particular, the involvement of medical students interested in clinical research activities seems to have a positive impact. Academia needs to be re-implemented into clinical psychiatry. Staff with research experience is needed in all professions to increase evidence-based practice. Leaders must take responsibility for implementing new knowledge into the routines of the department and must support staff in these activities on a daily basis. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Understanding physical activity promotion in physiotherapy practice: A qualitative study.

PubMed

Lowe, Anna; Littlewood, Chris; McLean, Sionnadh

2018-06-01

Physical inactivity is a major public health issue and healthcare professionals are encouraged to promote physical activity during routine patient contacts in order to reduce non-communicable diseases and enhance individuals' quality of life. Little is known about physical activity promotion in physiotherapy practice in the UK. The aim of this study was to better understand physiotherapists' experience of physical activity promotion in clinical practice. A qualitative study was undertaken comprising 12 telephone interviews with participants using a quota sampling approach. The qualitative data was analysed using a thematic analysis approach and written up according to COREQ guidelines. Four themes were identified (1) Current physiotherapy practice (2) Barriers to, and facilitators of physical activity promotion, (3) Exercise or physical activity? and (4) Functional restoration versus general wellbeing. Physiotherapists use routine clinical contacts to discuss physical activity. However, brief interventions are not consistently used and no common framework to guide physical activity promotion was identified. Approaches appear to be inconsistent and informal and focus largely on short-term restoration of function rather than health promotion. There is scope to improve practice in line with current guidance to maximise potential impact on inactivity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Rapid identification of oral isolates of Aggregatibacter actinomycetemcomitans obtained from humans and primates by an ultrafast super convection based polymerase chain reaction

PubMed Central

Karched, M.; Furgang, D.; Sawalha, N.; Fine, D.H.

2017-01-01

Aggregatibacter actinomycetemcomitans is a Gram negative oral bacterium associated with localized aggressive periodontitis (LAP). Detection of A. actinomycetemcomitans in clinical samples is routinely done by PCR. Our aim was to develop a rapid and reliable PCR method that can be used as a chair-side tool to detect A. actinomycetemcomitans in clinical samples. Sensitivity and specificity assessment was performed on buccal and plaque samples obtained from 40 adolescents enrolled in an ongoing LAP study by comparing 20 A. actinomycetemcomitans-positive subjects and 20 who were negative. In a second study, A. actinomycetemcomitans presence was tested in oral samples from eighty-six primates that included rhesus monkeys, chimpanzees, marmosets, tamarins and baboons. All samples were processed for detection of A. actinomycetemcomitans by means of culture, conventional PCR (cPCR) and rapid PCR (rPCR) using a Super Convection based AmpXpress thermal cycler (AlphaHelix, Sweden). For human samples, culture, cPCR and rPCR showed perfect agreement. Using this method A. actinomycetemcomitans was detected in 27 of 32 rhesus monkeys, 4 of 8 chimpanzees and 1 of 34 marmosets. Rapidity of AmpXpress thermal cycler, combined with Ready-To-Go PCR beads (GE Life sciences), a quick DNA extraction kit (Epicentre Biotechnologies, Madison, Wisconsin, USA) and a bufferless fast agarose gel system, made it possible to obtain results on A. actinomycetemcomitans detection within 35 min. We conclude that AmpXpress fast PCR can be conveniently used as a chair-side tool for rapid detection of A. actinomycetemcomitans in clinical samples. PMID:22326236

UMTRA Project water sampling and analysis plan, Durango, Colorado. Revision 1

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

NONE

1995-09-01

Planned, routine ground water sampling activities at the US Department of Energy (DOE) Uranium Mill Tailings Remedial Action (UMTRA) Project site in Durango, Colorado, are described in this water sampling and analysis plan. The plan identifies and justifies the sampling locations, analytical parameters, detection limits, and sampling frequency for the routine monitoring stations at the site. The ground water data are used to characterize the site ground water compliance strategies and to monitor contaminants of potential concern identified in the baseline risk assessment (DOE, 1995a). Regulatory basis for routine ground water monitoring at UMTRA Project sites is derived from themore » US EPA regulations in 40 CFR Part 192 (1994) and EPA standards of 1995 (60 FR 2854). Sampling procedures are guided by the UMTRA Project standard operating procedures (SOP) (JEG, n.d.), the Technical Approach Document (TAD) (DOE, 1989), and the most effective technical approach for the site.« less

Benchmarking routine psychological services: a discussion of challenges and methods.

PubMed

Delgadillo, Jaime; McMillan, Dean; Leach, Chris; Lucock, Mike; Gilbody, Simon; Wood, Nick

2014-01-01

Policy developments in recent years have led to important changes in the level of access to evidence-based psychological treatments. Several methods have been used to investigate the effectiveness of these treatments in routine care, with different approaches to outcome definition and data analysis. To present a review of challenges and methods for the evaluation of evidence-based treatments delivered in routine mental healthcare. This is followed by a case example of a benchmarking method applied in primary care. High, average and poor performance benchmarks were calculated through a meta-analysis of published data from services working under the Improving Access to Psychological Therapies (IAPT) Programme in England. Pre-post treatment effect sizes (ES) and confidence intervals were estimated to illustrate a benchmarking method enabling services to evaluate routine clinical outcomes. High, average and poor performance ES for routine IAPT services were estimated to be 0.91, 0.73 and 0.46 for depression (using PHQ-9) and 1.02, 0.78 and 0.52 for anxiety (using GAD-7). Data from one specific IAPT service exemplify how to evaluate and contextualize routine clinical performance against these benchmarks. The main contribution of this report is to summarize key recommendations for the selection of an adequate set of psychometric measures, the operational definition of outcomes, and the statistical evaluation of clinical performance. A benchmarking method is also presented, which may enable a robust evaluation of clinical performance against national benchmarks. Some limitations concerned significant heterogeneity among data sources, and wide variations in ES and data completeness.

Vital Signs Screening for Alcohol Misuse in a Rural Primary Care Clinic: A Feasibility Study

ERIC Educational Resources Information Center

Seale, J. Paul; Guyinn, Monique R.; Matthews, Michael; Okosun, Ike; Dent, M. Marie

2008-01-01

Context: Alcohol misuse is more common in rural areas, and rural problem drinkers are less likely to seek alcohol treatment services. Rural clinics face unique challenges to implementing routine alcohol screening and intervention. Purpose: To assess the feasibility of using the single alcohol screening question (SASQ) during routine nursing vital…

Modifying the Clinical Outcomes in Routine Evaluation Measure for Use with People Who Have a Learning Disability

ERIC Educational Resources Information Center

Marshall, Keith; Willoughby-Booth, Simon

2007-01-01

There are few reliable self-report measures suitable for people with a learning disability in reporting psychological distress. This study examines the modification of the Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM), exploring its reliability, using two different presentation styles. One style included a sequencing task then…

Colorimetric DNAzyme Biosensor for Convenience Detection of Enterotoxin B Harboring Staphylococcus aureus from Food Samples.

PubMed

Mondal, Bhairab; N, Bhavanashri; Ramlal, Shylaja; Kingston, Joseph

2018-02-14

In the present study, a colorimetric DNAzymes biosensor strategy was devised in combination with immunomagnetic separation for rapid and easy detection of enterotoxin B harboring Staphylococcus aureus from food and clinical samples. The method employs immunocapture of S. aureus and amplification of seb gene by DNAzyme complementary sequence integrated forward primer and with specific reverse primer. The DNAzyme sequence integrated dsDNA PCR products when treated with hemin and TMB (3,3',5,5'-tetramethylbenzidine) in the presence of H 2 O 2 produce colorimetric signal. A linear relationship of optical signal with the initial template of seb was obtained which could be monitored by visually or spectrophotrometrically for qualitative and quantitative detection. The limit of detection for the assay was approximately 10 2 CFU/mL of seb gene harboring target. This method is convenient compared to gel based and ELISA systems. Further, spiking studies and analysis on natural samples emphasized the robustness and applicability of developed method. Altogether, the established assay could be a reliable alternative, low-cost, viable detection tool for the routine investigation of seb from food and clinical sources.

Development and Validation of Pathogen Environmental Monitoring Programs for Small Cheese Processing Facilities.

PubMed

Beno, Sarah M; Stasiewicz, Matthew J; Andrus, Alexis D; Ralyea, Robert D; Kent, David J; Martin, Nicole H; Wiedmann, Martin; Boor, Kathryn J

2016-12-01

Pathogen environmental monitoring programs (EMPs) are essential for food processing facilities of all sizes that produce ready-to-eat food products exposed to the processing environment. We developed, implemented, and evaluated EMPs targeting Listeria spp. and Salmonella in nine small cheese processing facilities, including seven farmstead facilities. Individual EMPs with monthly sample collection protocols were designed specifically for each facility. Salmonella was detected in only one facility, with likely introduction from the adjacent farm indicated by pulsed-field gel electrophoresis data. Listeria spp. were isolated from all nine facilities during routine sampling. The overall Listeria spp. (other than Listeria monocytogenes ) and L. monocytogenes prevalences in the 4,430 environmental samples collected were 6.03 and 1.35%, respectively. Molecular characterization and subtyping data suggested persistence of a given Listeria spp. strain in seven facilities and persistence of L. monocytogenes in four facilities. To assess routine sampling plans, validation sampling for Listeria spp. was performed in seven facilities after at least 6 months of routine sampling. This validation sampling was performed by independent individuals and included collection of 50 to 150 samples per facility, based on statistical sample size calculations. Two of the facilities had a significantly higher frequency of detection of Listeria spp. during the validation sampling than during routine sampling, whereas two other facilities had significantly lower frequencies of detection. This study provides a model for a science- and statistics-based approach to developing and validating pathogen EMPs.

Influence of centrifuge brake on residual platelet count and routine coagulation tests in citrated plasma.

PubMed

Daves, Massimo; Giacomuzzi, Katia; Tagnin, Enrico; Jani, Erika; Adcock Funk, Dorothy M; Favaloro, Emmanuel J; Lippi, Giuseppe

2014-04-01

Sample centrifugation is an essential step in the coagulation laboratory, as clotting tests are typically performed on citrated platelet (PLT) poor plasma (PPP). Nevertheless, no clear indication has been provided as to whether centrifugation of specimens should be performed with the centrifuge brake set to on or off. Fifty consecutive sodium citrate anticoagulated samples were collected and divided into two aliquots. The former was centrifuged as for Clinical Laboratory Standards Institute (CLSI) guidelines with the centrifuge brake set to on, whereas the latter was centrifuged again as for CLSI guidelines, but with the brake set to off. In the PPP of all samples, a PLT count was performed, followed by the analysis of activated partial thromboplastin time (APTT), prothrombin time (PT) and fibrinogen (FBG). The PLT count after samples centrifugation was substantially reduced, either with centrifuge brake set to on or off (5 ± 1 versus 3 ± 1 × 10/l; P = 0.009). The frequency of samples exceeding a PLT count less than 10 × 10/l was nearly double in samples centrifuged with the brake on than in those with the brake off (14 versus 8%; P < 0.01). Although no significant difference was found for APTT values, PT was slightly prolonged using the centrifuge brake set to on (mean bias 0.2 s; P < 0.001). FBG values were also significantly higher using the centrifuge brake set to on (mean bias 0.29 g/l; P < 0.001). The results of this study indicate that sample centrifugation for routine coagulation testing should be preferably performed with the centrifuge brake set to off for providing a better quality specimen.

Prevalence of anti-DFS70 antibodies in patients with and without systemic autoimmune rheumatic diseases.

PubMed

Shovman, Ora; Gilburd, Boris; Chayat, Chen; Amital, Howard; Langevitz, Pnina; Watad, Abdulla; Guy, Adi; Perez, Dolores; Azoulay, Danielle; Blank, Miri; Segal, Yael; Bentow, Chelsea; Mahler, Michael; Shoenfeld, Yehuda

2018-01-01

Autoantibodies to the dense fine speckled 70 (DFS70) antigen are common among antinuclear antibodies (ANA) positive healthy individuals (HI). We assessed the prevalence of anti-DFS70 antibodies in patients with and without ANA-associated rheumatic diseases (AARDs) by two methods: chemiluminescent immunoassay (CIA) and an indirect immunofluorescence (IIF) assay based on immunoadsorption for DFS70. Fifty-one ANA-positive sera samples from patients with confirmed clinical diagnosis of AARD, 92 samples from HI and 85 samples submitted to a reference laboratory for routine ANA testing were evaluated for the presence of anti-DFS70 antibodies. The samples were evaluated by QUANTA Flash DFS70 CIA using BIO-FLASH instrument and by NOVA Lite selected HEp-2 kit on NOVA View - an automated IIF system. Sera with DFS positive pattern were pre-absorbed with highly purified human DFS70 antigen, and then tested again. Twenty-four samples (10.5%) tested by QUANTA Flash DFS70 CIA were positive for anti-DFS70 antibodies. The prevalence of monospecific anti-DFS70 antibodies was significantly higher in healthy subjects than in patients with AARDs (10.9% vs. 1.9%, p=0.02). The frequency of anti-DFS70 antibodies in samples submitted for routine ANA testing was 15.2%. A very good agreement was found between CIA and the DFS pattern identified by the automated HEp-2 IIF (kappa=0.97). In 80% of the samples obtained from patients without AARDs, immunoadsorption effectively inhibited the anti-DFS70 antibodies. The data confirm that mono-specific anti-DFS70 antibodies are a strong discriminator between ANA positive HI and AARD patients, and their evaluation should be included in ANA testing algorithms.

Evaluation of the Roche LightMix Gastro parasites multiplex PCR assay detecting Giardia duodenalis, Entamoeba histolytica, cryptosporidia, Dientamoeba fragilis, and Blastocystis hominis.

PubMed

Friesen, J; Fuhrmann, J; Kietzmann, H; Tannich, E; Müller, M; Ignatius, R

2018-03-23

Multiplex PCR assays offer highly sensitive and specific tools for the detection of enteric pathogens. This prospective study aimed at comparing the novel Roche LightMix Modular Assay Gastro Parasites (LMAGP) detecting Giardia duodenalis, Entamoeba histolytica, Cryptosporidium spp., Blastocystishominis, and Dientamoebafragilis with routine laboratory procedures. Stool specimens (n = 1062 from 1009 patients) were consecutively examined by LMAGP, R-Biopharm Ridascreen enzyme immunoassays (EIAs) detecting G. duodenalis or E. histolytica/dispar, and microscopy of wet mounts. Discrepant results were analysed by in-house PCR. D. fragilis or B. hominis were detected by LMAGP in 131 (14.4%) and 179 (19.9%; 16 samples positive by microscopy; p < 0.0001) of 909 samples, respectively. Of 918 samples analysed for Cryptosporidium spp., six were positive by LMAGP (three could be confirmed by Kinyoun staining and one by in-house PCR). G. duodenalis was detected by LMAGP, EIA, or microscopy in 20, 16, or 9 of 1039 stool samples, respectively; all four samples missed by EIA were confirmed by in-house PCR. In total, 938 stool samples were analysed for E. histolytica/dispar. Nine of ten EIA-positive samples were negative by LMAGP but positive by in-house PCR for E. dispar. One E. histolytica infection (positive by both LMAGP and in-house PCR) was missed by EIA and microscopy. Parasites only detected by microscopy included Enterobius vermicularis eggs (n = 3) and apathogenic amoebae (n = 27). The data call for routine use of multiplex PCR assays for the detection of enteric protozoan parasites in laboratory diagnostics. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Interpersonal differentiation within depression diagnosis: relating interpersonal subgroups to symptom load and the quality of the early therapeutic alliance.

PubMed

Grosse Holtforth, Martin; Altenstein, David; Krieger, Tobias; Flückiger, Christoph; Wright, Aidan G C; Caspar, Franz

2014-01-01

We examined interpersonal problems in psychotherapy outpatients with a principal diagnosis of a depressive disorder in routine care (n=361). These patients were compared to a normative non-clinical sample and to outpatients with other principal diagnoses (n=959). Furthermore, these patients were statistically assigned to interpersonally defined subgroups that were compared regarding symptoms and the quality of the early alliance. The sample of depressive patients reported higher levels of interpersonal problems than the normative sample and the sample of outpatients without a principal diagnosis of depression. Latent Class Analysis identified eight distinct interpersonal subgroups, which differed regarding self-reported symptom load and the quality of the early alliance. However, therapists' alliance ratings did not differentiate between the groups. This interpersonal differentiation within the group of patients with a principal diagnosis of depression may add to a personalized psychotherapy based on interpersonal profiles.

Quantitative bioanalysis of strontium in human serum by inductively coupled plasma-mass spectrometry

PubMed Central

Somarouthu, Srikanth; Ohh, Jayoung; Shaked, Jonathan; Cunico, Robert L; Yakatan, Gerald; Corritori, Suzana; Tami, Joe; Foehr, Erik D

2015-01-01

Aim: A bioanalytical method using inductively-coupled plasma-mass spectrometry to measure endogenous levels of strontium in human serum was developed and validated. Results & methodology: This article details the experimental procedures used for the method development and validation thus demonstrating the application of the inductively-coupled plasma-mass spectrometry method for quantification of strontium in human serum samples. The assay was validated for specificity, linearity, accuracy, precision, recovery and stability. Significant endogenous levels of strontium are present in human serum samples ranging from 19 to 96 ng/ml with a mean of 34.6 ± 15.2 ng/ml (SD). Discussion & conclusion: Calibration procedures and sample pretreatment were simplified for high throughput analysis. The validation demonstrates that the method was sensitive, selective for quantification of strontium (88Sr) and is suitable for routine clinical testing of strontium in human serum samples. PMID:28031925

Protein electrophoresis in cranes with presumed insect bite.

PubMed

Hartup, Barry K; Schroeder, Carrie A

2006-06-01

Serum protein electrophoresis (SPE) has emerged as a potentially valuable diagnostic tool in avian medicine; yet, there is limited information regarding SPE in cranes. Since 2000, 20 cases of unilateral periocular or facial soft tissue swelling, blepharitis, feather loss, and ocular or nasal discharge attributed to insect bite hypersensitivity were observed in cranes from a captive breeding center. SPE may be useful for evaluating these lesions. The aim of this study was to characterize the inflammatory response in cranes with hypersensitivity reactions using SPE. Serum samples from 7 cranes diagnosed with hypersensitivity reactions were submitted to a diagnostic laboratory for agarose gel electrophoresis. Results were compared to those in control serum samples obtained from the same cranes during routine physical examination, when they were clinically healthy. Total protein and a- and g-globulin concentrations were significantly increased and albumin/globulin ratios were significantly decreased in serum samples from cranes with hypersensitivity lesions compared with control samples. Using SPE, we documented changes in protein fraction concentrations in cranes with clinical signs of hypersensitivity. The increase in alpha- and gamma-globulin concentrations suggested inflammation and antigenic stimulation, consistent with a Type I hypersensitivity reaction.

Mental Health and Substance Use Among Patients in a North Carolina HIV Clinic.

PubMed

Skalski, Linda M; Watt, Melissa H; MacFarlane, Jessica C; Proeschold-Bell, Rae Jean; Stout, Jason E; Sikkema, Kathleen J

2015-01-01

The HIV/AIDS epidemic is a significant public health concern in North Carolina, and previous research has pointed to elevated mental health distress and substance use among HIV-infected populations, which may impact patients' adherence to medications. The aims of this study were to describe the prevalence of mental health and substance use issues among patients of a North Carolina HIV clinic, to examine differences by demographic characteristics, and to examine factors associated with suboptimal adherence to HIV medications. This study was a secondary analysis of clinical data routinely collected through a health behavior questionnaire at a large HIV clinic in North Carolina. We analyzed data collected from February 2011 to August 2012. The sample included 1,398 patients. Overall, 12.2% of patients endorsed current symptomology indicative of moderate or severe levels of depression, and 38.6% reported receiving a psychiatric diagnosis at some point in their life. Additionally, 19.1% had indications of current problematic drinking, and 8.2% reported problematic drug use. Nearly one-quarter (22.1%) reported suboptimal adherence to HIV medications. Factors associated with poor adherence included racial/ethnic minority, age less than 35 years, and indications of moderate or severe depression. The questionnaire was not completed systematically in the clinic, which may limit generalizability, and self-reported measures may have introduced social desirability bias. Patients were willing to disclose mental health distress, substance use, and suboptimal medication adherence to providers, which highlights the importance of routinely assessing these behaviors during clinic visits. Our findings suggest that treating depression may be an effective strategy to improve adherence to HIV medications. ©2015 by the North Carolina Institute of Medicine and The Duke Endowment. All rights reserved.

Assessment of three frequently used blood glucose monitoring devices in clinical routine.

PubMed

Zueger, Thomas; Schuler, Vanessa; Stettler, Christoph; Diem, Peter; Christ, Emanuel R

2012-07-12

Self-monitoring of blood glucose plays an important role in the management of diabetes and has been shown to improve metabolic control. The use of blood glucose meters in clinical practice requires sufficient reliability to allow adequate treatment. Direct comparison of different blood glucose meters in clinical practice, independent of the manufactures is scarce. We, therefore, aimed to evaluate three frequently used blood glucose meters in daily clinical practice. Capillary blood glucose was measured simultaneous using the following glucose meters: Contour® (Bayer Diabetes Care, Zürich, Switzerland), Accu-Chek® aviva (Roche Diagnostics, Rotkreuz, Switzerland), Free-Style® lite (Abbott Diabetes Care, Baar, Switzerland). The reference method consisted of the HemoCue® Glucose 201+ System (HemoCue® AB, Ängelholm, Sweden) with plasma conversion. The devices were assessed by comparison of the Mean Absolute Relative Differences (MARD), the Clarke Error Grid Analysis (EGA) and the compliance with the International Organization of Standardization criteria (ISO 15197:2003). Capillary blood samples were obtained from 150 patients. MARD was 10.1 ± 0.65%, 7.0 ± 0.62% and 7.8 ± 0.48% for Contour®, Accu-Chek® and Free-Style®, respectively. EGA showed 99.3% (Contour®), 98.7% (Accu-Chek®) and 100% (Free-Style®) of all measurements in zone A and B (clinically acceptable). The ISO criteria were fulfilled by Accu-Chek® (95.3%) and Free-Style® (96%), but not by Contour® (92%). In the present study the three glucose meters provided good agreement with the reference and reliable results in daily clinical routine. Overall, the Free-Style® and Accu-Chek® device slightly outperformed the Contour® device.

Sexual networks: the integration of social and genetic data.

PubMed

Day, S; Ward, H; Ison, C; Bell, G; Weber, J

1998-12-01

New methods for studying sexual networks are presented, drawing upon routine procedures followed in genitourinary medicine clinics in the UK for tracing partners and identifying strains of infection. The routine social procedures were developed to incorporate a structured interview. The routine microbiological diagnosis of gonorrhoea was augmented by phenotyping and the development of new genetic techniques for the fine discrimination of gonococcal strains (opa-typing). Selected results from a study in Sheffield, UK show that each method has limitations, when conducted separately, but these are minimised when the methods are combined. Moreover, the use of simple and routine methods of data collection resolve issues of scale and sample that have beset other network studies, as they provide a means of covering a larger and defined population. Popular concepts about these methods are discussed in the conclusion. The integrated approach employed in our research raises questions both about social methods, 'of people who lie, particularly when they talk about sex', and about microbiological methods, 'of genes that tell the truth' and bypass what people say and think altogether. We argue that these stereotypes are misleading insofar as they suggest that genetic techniques can substitute for the social, and we suggest that even the finest discrimination of organisms at the genetic level will never obviate the need for their interpretation in the light of social data.

The impact of telemedicine in the postoperative care of the neurosurgery patient in an outpatient clinic: a unique perspective of this valuable resource in the developing world--an experience of more than 3000 teleconsultations.

PubMed

Dadlani, Ravi; Mani, Subramaniyan; A U, Jai Ganesh; Mohan, Dilip; Rajgopalan, Niranjana; Thakar, Sumit; Aryan, Saritha; Hegde, Alangar S

2014-01-01

Telemedicine has always been used as a teleconsultation tool in neurological emergencies (e.g., triage in head injuries, stroke, and cerebrovascular accidents). At Sri Sathya Sai Institute of Higher Medical Sciences, Bangalore, India, we have been operating two teleconsultation sessions per week for the postoperative patient population, addressing routine follow-up and semiemergent conditions in this cohort of patients. At our center more than 80% of the neurosurgical procedures are conducted in patients traveling more than 1500 km. Telemedicine as a routine tool in clinical medicine has significant financial and psychosocial benefits versus routine outpatient clinics. There are very few reports of telemedicine use in routine outpatient teleconsultations in the available neurosurgical literature; those that are present do not differentiate or analyze the use in routine versus emergency neurosurgery. We discuss the role of this underused resource in the developing countries and retrospectively analyze the clinical data in more than 1500 patients and 3000 teleconsultations during a period of 6 years. We address the financial implications, psychosocial factors, and several other factors that could make this relatively modest technology an indispensible tool in current neurosurgical practice, especially in a developing country like India. Copyright © 2014 Elsevier Inc. All rights reserved.

A new laboratory-based surveillance system (Respiratory DataMart System) for influenza and other respiratory viruses in England: results and experience from 2009 to 2012.

PubMed

Zhao, H; Green, H; Lackenby, A; Donati, M; Ellis, J; Thompson, C; Bermingham, A; Field, J; Sebastianpillai, P; Zambon, M; Watson, Jm; Pebody, R

2014-01-23

During the 2009 influenza A(H1N1) pandemic, a new laboratory-based virological sentinel surveillance system, the Respiratory DataMart System (RDMS), was established in a network of 14 Health Protection Agency (now Public Health England (PHE)) and National Health Service (NHS) laboratories in England. Laboratory results (both positive and negative) were systematically collected from all routinely tested clinical respiratory samples for a range of respiratory viruses including influenza, respiratory syncytial virus (RSV), rhinovirus, parainfluenza virus, adenovirus and human metapneumovirus (hMPV). The RDMS also monitored the occurrence of antiviral resistance of influenza viruses. Data from the RDMS for the 2009–2012 period showed that the 2009 pandemic influenza virus caused three waves of activity with different intensities during the pandemic and post pandemic periods. Peaks in influenza A(H1N1)pdm09 positivity (defined as number of positive samples per total number of samples tested) were seen in summer and autumn in 2009, with slightly higher peak positivity observed in the first post-pandemic season in 2010/2011. The influenza A(H1N1)pdm09 virus strain almost completely disappeared in the second postpandemic season in 2011/2012. The RDMS findings are consistent with other existing community-based virological and clinical surveillance systems. With a large sample size, this new system provides a robust supplementary mechanism, through the collection of routinely available laboratory data at minimum extra cost, to monitor influenza as well as other respiratory virus activity. A near real-time, daily reporting mechanism in the RDMS was established during the London 2012 Olympic and Paralympic Games. Furthermore, this system can be quickly adapted and used to monitor future influenza pandemics and other major outbreaks of respiratory infectious disease, including novel pathogens.

Automated processing, extraction and detection of herpes simplex virus types 1 and 2: A comparative evaluation of three commercial platforms using clinical specimens.

PubMed

Binnicker, Matthew J; Espy, Mark J; Duresko, Brian; Irish, Cole; Mandrekar, Jay

2017-04-01

Recently, automated platforms have been developed that can perform processing, extraction and testing for herpes simplex virus (HSV) nucleic acid on a single instrument. In this study, we compared three commercially-available systems; Aptima ® /Panther (Hologic, San Diego, CA), ARIES ® (Luminex Corporation, Austin, TX), and cobas ® 4800 (Roche Molecular Systems Inc, Pleasanton, CA) for the qualitative detection of HSV-1/2 in clinical samples. Two-hundred seventy-seven specimens (genital [n=193], dermal [n=84]) were submitted for routine HSV-1/2 real-time PCR by a laboratory developed test. Following routine testing, samples were also tested by the Aptima, ARIES, and cobas HSV-1/2 assays per the manufacturer's recommendations. Results were compared to a "consensus standard" defined as the result obtained from ≥3 of the 4 assays. Following testing of 277 specimens, the cobas and ARIES assays demonstrated a sensitivity of 100% for HSV-1 (61/61) and HSV-2 (55/55). The Aptima assays showed a sensitivity of 91.8% (56/61) for HSV-1 and 90.9% (50/55) for HSV-2. Percent specificities for HSV-1 were 96.2% (202/210) by cobas, 99.5% (209/210) by ARIES and 100% (236/236) by Aptima. For HSV-2, the specificities were 98.1% (211/215) by cobas, 99.5% (215/216) by ARIES and 100% (216/216) by Aptima. The turnaround time for testing 24 samples was 2.5h by the cobas 4800, 3.1h by Aptima/Panther, and 3.9h by ARIES. The three commercial systems can perform all current functions on a single platform, thereby improving workflow and potentially reducing errors associated with manual processing of samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Practical Considerations for Clinical PET/MR Imaging.

PubMed

Galgano, Samuel; Viets, Zachary; Fowler, Kathryn; Gore, Lael; Thomas, John V; McNamara, Michelle; McConathy, Jonathan

2018-01-01

Clinical PET/MR imaging is currently performed at a number of centers around the world as part of routine standard of care. This article focuses on issues and considerations for a clinical PET/MR imaging program, focusing on routine standard-of-care studies. Although local factors influence how clinical PET/MR imaging is implemented, the approaches and considerations described here intend to apply to most clinical programs. PET/MR imaging provides many more options than PET/computed tomography with diagnostic advantages for certain clinical applications but with added complexity. A recurring theme is matching the PET/MR imaging protocol to the clinical application to balance diagnostic accuracy with efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

Practical Considerations for Clinical PET/MR Imaging.

PubMed

Galgano, Samuel; Viets, Zachary; Fowler, Kathryn; Gore, Lael; Thomas, John V; McNamara, Michelle; McConathy, Jonathan

2017-05-01

Clinical PET/MR imaging is currently performed at a number of centers around the world as part of routine standard of care. This article focuses on issues and considerations for a clinical PET/MR imaging program, focusing on routine standard-of-care studies. Although local factors influence how clinical PET/MR imaging is implemented, the approaches and considerations described here intend to apply to most clinical programs. PET/MR imaging provides many more options than PET/computed tomography with diagnostic advantages for certain clinical applications but with added complexity. A recurring theme is matching the PET/MR imaging protocol to the clinical application to balance diagnostic accuracy with efficiency. Copyright © 2016 Elsevier Inc. All rights reserved.

Principles and clinical applications of liquid chromatography - tandem mass spectrometry for the determination of adrenal and gonadal steroid hormones.

PubMed

Kulle, A E; Welzel, M; Holterhus, P-M; Riepe, F G

2011-10-01

Liquid-chromatography - tandem mass spectrometry (LC-MS/MS) is becoming the method of choice for clinical steroid analysis. In most instances, it has the advantage of higher sensitivity, better reproducibility and greater specificity than commercial immunoassay techniques. The method requires only minimal sample preparation and a small sample volume. Furthermore, it has the potential to analyze multiple steroids simultaneously. Modern instruments guarantee high throughput, allowing an affordable price for the individual assay. All this makes LC-MS/MS an attractive method for use in a clinical setting. Reliable reference ranges for the detected analytes are the pre-requisite for their clinical use. If these are available, LC-MS/MS can find application in congenital disorders of steroid metabolism, such as congenital adrenal hyperplasia, disorders of sex development and disorders of salt homeostasis, as well as in acquired disorders of steroid metabolism, such as primary aldosteronism, Cushing's disease, Addison's disease, and hyperandrogenemia, as well as in psychiatric disease states such as depression or anxiety disorders. The principles of LC-MS/MS for steroid measurement, the pros and cons of LC-MS/MS compared with conventional immunoassays and the possible applications in clinical routine, with a special focus on pediatric endocrinology needs, are discussed here.

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

PubMed Central

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.

2015-01-01

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

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

PubMed

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. Copyright © 2016 Whale et al.

Unanticipated error in HbA(1c) measurement on the HLC-723 G7 analyzer.

PubMed

van den Ouweland, Johannes M W; de Keijzer, Marinus H; van Daal, Henny

2010-04-01

Investigation of falsely elevated HbA(1c) measurements on the HLC-723 G7 analyser. Comparison of HbA(1c) in blood samples that were diluted either in hemolysis reagent or water. HbA(1c) results became falsely elevated when samples were diluted in hemolysis reagent, but not in water. QC-procedures failed to detect this error as calibrator and QC samples were manually diluted in water, according to manufacturer's instructions, whereas patient samples were automatically diluted using hemolysing reagent. After replacement of the instruments' sample-loop and rotor seal comparable HbA(1c) results were obtained, irrespective of dilution with hemolysing reagent or water. This case illustrates the importance of treating calibrator and QC materials similar to routine patient samples in order to prevent unnoticed drift in patient HbA(1c) results. Copyright 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Long-term frozen storage of urine samples: a trouble to get PCR results in Schistosoma spp. DNA detection?

PubMed

Fernández-Soto, Pedro; Velasco Tirado, Virginia; Carranza Rodríguez, Cristina; Pérez-Arellano, José Luis; Muro, Antonio

2013-01-01

Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples' storage or conditions for handling and DNA preservation and extraction methods. We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patients urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template. Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA method of extraction used.

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures.

PubMed

Kohlmann, Rebekka; Hoffmann, Alexander; Geis, Gabriele; Gatermann, Sören

2015-01-01

Rapid identification of the causative microorganism is a key element in appropriate antimicrobial therapy of bloodstream infections. Whereas traditional analysis of positive blood cultures requires subculture over at least 16-24h prior to pathogen identification by, e.g. matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), sample preparation procedures enabling direct MALDI-TOF MS, i.e. without preceding subculture, are associated with additional effort and costs. Hence, we integrated an alternative MALDI-TOF MS approach in diagnostic routine using a short incubation on a solid medium. Positive blood cultures were routinely plated on chocolate agar plates and incubated for 4h (37 °C, 5% CO2). Subsequently, MALDI-TOF MS using a Microflex LT instrument (Bruker Daltonics) and direct smear method was performed once per sample. For successful identification of bacteria at species level, score cut-off values were used as proposed by the manufacturer (≥ 2.0) and in a modified form (≥ 1.5 for MALDI-TOF MS results referring to Gram-positive cocci and ≥ 1.7 for MALDI-TOF MS results referring to bacteria other than Gram-positive cocci). Further data analysis also included an assessment of the clinical impact of the MALDI-TOF MS result. Applying the modified score cut-off values, our approach led to an overall correct species identification in 69.5% with misidentification in 3.4% (original cut-offs: 49.2% and 1.8%, respectively); for Gram-positive cocci, correct identification in 68.4% (100% for Staphylococcus aureus and enterococci, 80% for beta-hemolytic streptococci), for Gram-negative bacteria, correct identification in 97.6%. In polymicrobial blood cultures, in 72.7% one of the pathogens was correctly identified. Results were not reliable for Gram-positive rods and yeasts. The approach was easy to implement in diagnostic routine. In cases with available clinical data and successful pathogen identification, in 51.1% our approach allowed an optimized treatment recommendation. MALDI-TOF MS following 4h pre-culture is a valuable tool for rapid pathogen identification from positive blood cultures, allowing easy integration in diagnostic routine and the opportunity of considerably earlier treatment adaptation. Copyright © 2015 Elsevier GmbH. All rights reserved.

Profile and microbiological isolates of asymptomatic bacteriuria among pregnant women in Abakaliki, Nigeria

PubMed Central

Onu, Fidelis Agwu; Ajah, Leonard Ogbonna; Ezeonu, Paul Olisaemeka; Umeora, Odidika Ugochukwu Joannes; Ibekwe, Perpetus Chudi; Ajah, Monique Iheoma

2015-01-01

Background Detecting and treating asymptomatic bacteriuria (ASB) prevents urinary tract infection and its consequences. The cost-effectiveness of routine screening for ASB in pregnancy is controversial. In populations with high prevalence, however, it is worthwhile and justifiable. Aim To determine the profile, prevalence, microbiological isolates, and risk factors of ASB among booking antenatal clinic attendees in Abakaliki, Nigeria. Materials and methods This was a cross-sectional study involving booking antenatal clinic attendees at the Federal Teaching Hospital, Abakaliki, who met the inclusion criteria. This study occurred between January and December, 2012. The midstream urine samples of these women were subjected to microscopy, culture, and sensitivity. Results A total of 300 randomly selected booking antenatal clinic attendees participated in the study; 74 of them had ASB, giving a prevalence of 24.7%. With the exception of rural residence, sociodemographic and obstetric characteristics did not influence the risk of ASB among the participants in this study. Staphylococcus aureus was the commonest organism isolated. The majority of the organisms were sensitive to ofloxacin and ceftriaxone. Conclusion There is a high prevalence of ASB among pregnant women in Abakaliki. With the exception of rural dwelling, sociodemographic and obstetric characteristics did not significantly influence the risk of ASB among these pregnant women. Therefore, routine ASB screening of pregnant women is recommended in our environment. PMID:26244027

The human false-negative rate of rescreening Pap tests. Measured in a two-arm prospective clinical trial.

PubMed

Renshaw, A A; Lezon, K M; Wilbur, D C

2001-04-25

Routine quality control rescreening often is used to calculate the false-negative rate (FNR) of gynecologic cytology. Theoretic analysis suggests that this is not appropriate, due to the high FNR of rescreening and the inability to actually measure it. The authors sought to determine the FNR of manual rescreening in a large, prospective, two-arm clinical trial using an analytic instrument in the evaluation. The results of the Autopap System Clinical Trial, encompassing 25,124 analyzed slides, were reviewed. The false-negative and false-positive rates at various thresholds were determined for routine primary screening, routine rescreening, Autopap primary screening, and Autopap rescreening by using a simple, standard methodology. The FNR of routine manual rescreening at the level of atypical squamous cells of undetermined significance (ASCUS) was 73%, more than 3 times the FNR of primary screening; 11 cases were detected. The FNR of Autopap rescreening was 34%; 80 cases were detected. Routine manual rescreening decreased the laboratory FNR by less than 1%; Autopap rescreening reduced the overall laboratory FNR by 5.7%. At the same time, the false-positive rate for Autopap screening was significantly less than that of routine manual screening at the ASCUS level (4.7% vs. 5.6%; P < 0.0001). Rescreening with the Autopap system remained more sensitive than manual rescreening at the low grade squamous intraepithelial lesions threshold (FNR of 58.8% vs. 100%, respectively), although the number of cases rescreened was low. Routine manual rescreening cannot be used to calculate the FNR of primary screening. Routine rescreening is an extremely ineffective method to detect error and thereby decrease a laboratory's FNR. The Autopap system is a much more effective way of detecting errors within a laboratory and reduces the laboratory's FNR by greater than 25%.

Measuring the Level of Agreement Between Cloacal Gram's Stains and Bacterial Cultures in Hispaniolan Amazon Parrots ( Amazona ventralis ).

PubMed

Evans, Erika E; Mitchell, Mark A; Whittington, Julia K; Roy, Alma; Tully, Thomas N

2014-12-01

Cloacal or fecal Gram's stains and bacterial cultures are routinely performed during avian physical examinations to assess the microbial flora of the gastrointestinal tract. Although cloacal or fecal Gram's stains and bacterial cultures are considered routine diagnostic procedures, the level of agreement between the individual tests has not been determined. To investigate the level of agreement between results from Gram's stain and bacterial culture when used to assess cloacal or fecal samples from psittacine birds, samples were taken from 21 clinically healthy Hispaniolan Amazon parrots ( Amazona ventralis ) and tested by Gram's stain cytology and bacterial culture. Most bacteria (97.2%) identified by Gram's stain were gram positive. However, gram-negative organisms were identified in 7 of 21 (33.3%; 95% confidence interval: 13.3%-53.3%) birds. Escherichia coli was the only gram-negative organism identified on culture. Agreement between results of Gram's stain and culture was fair (weighted κ = 0.27). The results of this study suggest that Gram's stains and bacterial culture may need to be performed with a parallel testing strategy to limit the likelihood of misclassifying the microbial flora of psittacine patients.

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast.

PubMed

Dhiman, Neelam; Hall, Leslie; Wohlfiel, Sherri L; Buckwalter, Seanne P; Wengenack, Nancy L

2011-04-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.

Clinical evaluation of cobas core anti-dsDNA EIA quant.

PubMed

González, Concepción; Guevara, Paloma; García-Berrocal, Belén; Alejandro Navajo, José; Manuel González-Buitrago, José

2004-01-01

The measurement of antibodies to double-stranded DNA (anti-dsDNA) is a useful tool for the diagnosis and monitoring of patients with connective tissue diseases, particularly systemic lupus erythematosus (SLE). The aim of the present study was to compare a new enzyme-linked immunosorbent assay (ELISA) for the measurement of anti-dsDNA antibodies, which uses purified double-stranded plasmid DNA as the antigen (anti-dsDNA EIA Quant; Roche Diagnostics, Mannheim, Germany), with an established ELISA. The clinical usefulness of this new ELISA was also assessed. We measured anti-dsDNA antibodies in 398 serum samples that were divided into four groups: 1). routine samples sent to our laboratory for an antinuclear antibody (ANA) test (n=229), 2). samples from blood donors (n=74), 3). samples from patients with SLE (n=48), and 4) samples from patients with other autoimmune diseases (n=47). The methods used were the Cobas Core Anti-dsDNA EIA Quant (Roche Diagnostics, Mannheim, Germany) and the Anti-dsDNA test (Gull Diagnostics, Bois d'Arcy, France). We obtained a kappa index and Spearman correlation coefficient in the comparative study, and sensitivity, specificity, predictive values, and likelihood ratios in the clinical study. The results obtained show a good agreement between the two methods in both the qualitative results (kappa=0.91) and the quantitative data (r=0.854). The best accuracy, predictive values, likelihood ratios, and correlation with active disease were obtained with the Roche anti-dsDNA assay. Copyright 2004 Wiley-Liss, Inc.

Broad-Range Detection of Microorganisms Directly from Bronchoalveolar Lavage Specimens by PCR/Electrospray Ionization-Mass Spectrometry

PubMed Central

Ullberg, Måns; Lüthje, Petra; Mölling, Paula; Strålin, Kristoffer

2017-01-01

The clinical demand on rapid microbiological diagnostic is constantly increasing. PCR coupled to electrospray ionization-mass spectrometry, PCR/ESI-MS, offers detection and identification of over 750 bacteria and Candida species directly from clinical specimens within 6 hours. In this study, we investigated the clinical performance of the IRIDICA BAC LRT Assay for detection of bacterial pathogens in 121 bronchoalveolar lavage (BAL) samples that were received consecutively at our bacterial laboratory for BAL culture. Commensal or pathogenic microorganisms were detected in 118/121 (98%) BAL samples by PCR/ESI-MS, while in 104/121 (86%) samples by routine culture (P<0.01). Detection of potentially pathogenic microorganisms by PCR/ESI-MS was evaluated in comparison with conventional culture-based or molecular methods. The agreement between positive findings was overall good. Most Staphylococcus aureus-positive PCR/ESI-MS results were confirmed by culture or species-specific PCR (27/33, 82%). The identity of Streptococcus pneumoniae could however be confirmed for only 6/17 (35%) PCR/ESI-MS-positive samples. Non-cultivable and fastidious pathogens, which were not covered by standard culture procedures were readily detected by PCR/ESI-MS, including Legionella pneumophila, Bordetella pertussis, Norcadia species and Mycoplasma pneumoniae. In conclusion, PCR/ESI-MS detected a broad range of potential pathogens with equal or superior sensitivity compared to conventional methods within few hours directly from BAL samples. This novel method might thus provide a relevant tool for diagnostics in critically ill patients. PMID:28085931

An evaluation of routine antenatal depression screening and psychosocial assessment in a regional private maternity setting in Australia.

PubMed

Kalra, Harish; Reilly, Nicole; Austin, Marie-Paule

2018-01-30

There is limited information relating to routine depression screening and psychosocial assessment programs in private maternity settings in Australia. To describe the psychosocial profile of a sample of private maternity patients who participated in a depression screening and psychosocial risk assessment program as part of routine antenatal care, and to explore women's experience of receiving this component of pregnancy care. We conducted a retrospective medical records audit of 455 consecutive women having a routine psychosocial assessment and referral. Assessment was undertaken using the Edinburgh Postnatal Depression Scale (EPDS) and the Antenatal Risk Questionnaire (ANRQ) for psychosocial risk; 101 women completed a feedback survey about their experience of receiving routine psychosocial care. Of the 87.7% of women who completed both EPDS and ANRQ, 4.3% scored 13 or more on the EPDS. On the ANRQ, 25.3% of women endorsed one risk factor, 11.6% two risk factors and 10.5% three or more risk factors. Elevated EPDS scores were associated with major stresses in the last 12 months, high trait anxiety and significant past mental health issue/s. Acceptability of depression screening and psychosocial risk assessment was high. This study highlights the need for, and acceptability of, depression and psychosocial assessment in the private maternity sector. These findings are particularly timely given the provision of new Medicare Benefits Scheme items for obstetricians to undertake psychosocial assessment (both antenatally and postnally) in line with recommended clinical best practice. © 2018 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates

EPA Science Inventory

Molecular methods, such as DNA barcoding, have the potential in enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biom...

Current role of ICP-MS in clinical toxicology and forensic toxicology: a metallic profile.

PubMed

Goullé, Jean-Pierre; Saussereau, Elodie; Mahieu, Loïc; Guerbet, Michel

2014-08-01

As metal/metalloid exposure is inevitable owing to its omnipresence, it may exert toxicity in humans. Recent advances in metal/metalloid analysis have been made moving from flame atomic absorption spectrometry and electrothermal atomic absorption spectrometry to the multi-elemental inductively coupled plasma (ICP) techniques as ICP atomic emission spectrometry and ICP-MS. ICP-MS has now emerged as a major technique in inorganic analytical chemistry owing to its flexibility, high sensitivity and good reproducibility. This in depth review explores the ICP-MS metallic profile in human toxicology. It is now routinely used and of great importance, in clinical toxicology and forensic toxicology to explore biological matrices, specifically whole blood, plasma, urine, hair, nail, biopsy samples and tissues.

[Freiburg keratoconus registry : Example of application of smart data for clinical research and inititial results].

PubMed

Lang, S J; Böhringer, D; Reinhard, T

2016-06-01

Keratoconus is a progressive corneal disease with thinning and scarring of the cornea. Diagnostic and treatment options are usually evaluated in large prospective or retrospective trials. Big data and smart data provide the possibility to analyze routine data for clinical research. In this article we report the generation of a monocentric keratoconus registry by means of computerized data analysis of routine data. This demonstrates the potential of clinical research by means of routine data. A "clinical data warehouse" was created from all available routine electronic data. At the time of first presentation, each eye was classified into one out of four categories: suspected, early disease, late disease and status postkeratoplasty. Through integration of multiple data sources the clinical course for each patient was documented in the registry. A total of 3681 eyes from 1841 patients were included. The median follow-up time was 0.54 years. Patient age was higher in the groups with more severe stages of keratoconus, the proportion of female patients was higher in the group of suspected keratoconus and patient age and male to female ratios showed statistically significant differences between the groups (p < 0.001). We were able to create a "clinical data warehouse" by linking multiple data sources and normalizing the data. With this tool we established a novel, monocentric keratoconus registry. Only the grading of disease severity and the exclusion of false positive results were carried out manually. In our opinion establishing a structured clinical data warehouse has a huge potential for clinical and retrospective studies and proves the value of the Smart Data concept.

Treatment of painful bone metastases in prostate and breast cancer patients with the therapeutic radiopharmaceutical rhenium-188-HEDP. Clinical benefit in a real-world study.

PubMed

Lange, Rogier; Overbeek, Floor; de Klerk, John M H; Pasker-de Jong, Pieternel C M; van den Berk, Alexandra M; Ter Heine, Rob; Rodenburg, Cees J; Kooistra, Anko; Hendrikse, N Harry; Bloemendal, Haiko J

2016-09-26

Rhenium-188-HEDP ((188)Re-HEDP) is an effective radiopharmaceutical for the palliative treatment of osteoblastic bone metastases. However, only limited data on its routine use are available and its effect on quality of life (QoL) has not been studied. Therefore, we evaluated the clinical benefit of (188)Re-HEDP in routine clinical care. Prostate or breast cancer patients with painful bone metastases receiving (188)Re-HEDP as a routine clinical procedure were eligible for evaluation. Clinical benefit was assessed in terms of efficacy and toxicity. Pain palliation and QoL were monitored using the visual analogue scale (VAS), corrected for opioid intake, and the EORTC QLQ-C30 Global health status/QoL-scale. Thrombocyte and leukocyte nadirs were used to assess haematological toxicity. 45 and 47 patients were evaluable for pain palliation and QoL, respectively. After a single injection of (188)Re-HEDP, the overall pain response rate was 69% and mean VAS-scores decreased relevantly and significantly (p < 0.05). Repeated treatment resulted in similar pain response. The overall QoL response rate was 68% and mean Global health status/QoL-scores increased relevantly and significantly. Haematological side effects were mild and transient. The clinically relevant response on pain and quality of life and the limited adverse events prove clinical benefit of treatment with (188)Re-HEDP and support its use in routine clinical care. Its effectiveness appears comparable to that of external beam radiotherapy.

Colon cleansing protocol in children: research conditions vs. clinical practice.

PubMed

Elitsur, Yoram; Balfaqih, Yaslam; Preston, Deborah

2018-04-01

 Colon preparation rates are the limiting factor for a successful diagnostic colonoscopy in children. Different colon cleansing protocols have been published for use in children. Unfortunately, the applicability of those published research protocols has not been formally evaluated in routine clinical practice. We investigated the success rate of our previously published colon cleansing protocol as utilized in our clinical practice.  This was a retrospective study. In the clinical practice, the colon cleansing protocol included PEG-3350 at a dose of 2 g/kg/day plus Dulcolax (Bisacodyl, Boehringer Ingelheim, TX USA) 5 mg/day for 2 days. Adequate colon preparation was graded between 1 - 5, as previously described, and grade ≥ 4.0 was considered an adequate preparation. Patients were instructed to complete a questionnaire that included PEG-3350 dose, number of stools per day, consistency of each stool, and side effects (vomiting, abdominal pain). Clinical and endoscopic results were compared between the protocol under research conditions and routine practice.  The success rate of the colon preparation in our clinical practice was similar to the results observed under our research protocol (75 % vs. 73.6 %). Moreover, the total number of stools, stool consistency, and the intubation rate of the terminal ileum were also similar. We concluded, that in our experience, the colon cleansing protocol used under research conditions was effective and appropriate for use in routine clinical practice.  We recommend testing each new protocol under the routine conditions of clinical practice to confirm its applicability for general practitioners.

Long-Term Frozen Storage of Urine Samples: A Trouble to Get PCR Results in Schistosoma spp. DNA Detection?

PubMed Central

Fernández-Soto, Pedro; Velasco Tirado, Virginia; Carranza Rodríguez, Cristina; Pérez-Arellano, José Luis; Muro, Antonio

2013-01-01

Background Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples’ storage or conditions for handling and DNA preservation and extraction methods. Methodology/Principal Findings We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patientś urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template. Conclusions/Significance Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA method of extraction used. PMID:23613907

FISH-in-CHIPS: A Microfluidic Platform for Molecular Typing of Cancer Cells.

PubMed

Perez-Toralla, Karla; Mottet, Guillaume; Tulukcuoglu-Guneri, Ezgi; Champ, Jérôme; Bidard, François-Clément; Pierga, Jean-Yves; Klijanienko, Jerzy; Draskovic, Irena; Malaquin, Laurent; Viovy, Jean-Louis; Descroix, Stéphanie

2017-01-01

Microfluidics offer powerful tools for the control, manipulation, and analysis of cells, in particular for the assessment of cell malignancy or the study of cell subpopulations. However, implementing complex biological protocols on chip remains a challenge. Sample preparation is often performed off chip using multiple manually performed steps, and protocols usually include different dehydration and drying steps that are not always compatible with a microfluidic format.Here, we report the implementation of a Fluorescence in situ Hybridization (FISH) protocol for the molecular typing of cancer cells in a simple and low-cost device. The geometry of the chip allows integrating the sample preparation steps to efficiently assess the genomic content of individual cells using a minute amount of sample. The FISH protocol can be fully automated, thus enabling its use in routine clinical practice.

Is heart rate variability better than routine vital signs for prehospital identification of major hemorrhage?

PubMed

Edla, Shwetha; Reisner, Andrew T; Liu, Jianbo; Convertino, Victor A; Carter, Robert; Reifman, Jaques

2015-02-01

During initial assessment of trauma patients, metrics of heart rate variability (HRV) have been associated with high-risk clinical conditions. Yet, despite numerous studies, the potential of HRV to improve clinical outcomes remains unclear. Our objective was to evaluate whether HRV metrics provide additional diagnostic information, beyond routine vital signs, for making a specific clinical assessment: identification of hemorrhaging patients who receive packed red blood cell (PRBC) transfusion. Adult prehospital trauma patients were analyzed retrospectively, excluding those who lacked a complete set of reliable vital signs and a clean electrocardiogram for computation of HRV metrics. We also excluded patients who did not survive to admission. The primary outcome was hemorrhagic injury plus different PRBC transfusion volumes. We performed multivariate regression analysis using HRV metrics and routine vital signs to test the hypothesis that HRV metrics could improve the diagnosis of hemorrhagic injury plus PRBC transfusion vs routine vital signs alone. As univariate predictors, HRV metrics in a data set of 402 subjects had comparable areas under receiver operating characteristic curves compared with routine vital signs. In multivariate regression models containing routine vital signs, HRV parameters were significant (P<.05) but yielded areas under receiver operating characteristic curves with minimal, nonsignificant improvements (+0.00 to +0.05). A novel diagnostic test should improve diagnostic thinking and allow for better decision making in a significant fraction of cases. Our findings do not support that HRV metrics add value over routine vital signs in terms of prehospital identification of hemorrhaging patients who receive PRBC transfusion. Published by Elsevier Inc.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology.

PubMed

Clark, Andrew E; Kaleta, Erin J; Arora, Amit; Wolk, Donna M

2013-07-01

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

PubMed Central

Clark, Andrew E.; Kaleta, Erin J.; Arora, Amit

2013-01-01

SUMMARY Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the “nuts and bolts” of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care. PMID:23824373

Underutilisation of routinely collected data in the HIV programme in Zambia: a review of quantitatively analysed peer-reviewed articles.

PubMed

Munthali, Tendai; Musonda, Patrick; Mee, Paul; Gumede, Sehlulekile; Schaap, Ab; Mwinga, Alwyn; Phiri, Caroline; Kapata, Nathan; Michelo, Charles; Todd, Jim

2017-06-13

The extent to which routinely collected HIV data from Zambia has been used in peer-reviewed published articles remains unexplored. This paper is an analysis of peer-reviewed articles that utilised routinely collected HIV data from Zambia within six programme areas from 2004 to 2014. Articles on HIV, published in English, listed in the Directory of open access journals, African Journals Online, Google scholar, and PubMed were reviewed. Only articles from peer-reviewed journals, that utilised routinely collected data and included quantitative data analysis methods were included. Multi-country studies involving Zambia and another country, where the specific results for Zambia were not reported, as well as clinical trials and intervention studies that did not take place under routine care conditions were excluded, although community trials which referred patients to the routine clinics were included. Independent extraction was conducted using a predesigned data collection form. Pooled analysis was not possible due to diversity in topics reviewed. A total of 69 articles were extracted for review. Of these, 7 were excluded. From the 62 articles reviewed, 39 focused on HIV treatment and retention in care, 15 addressed prevention of mother-to-child transmission, 4 assessed social behavioural change, and 4 reported on voluntary counselling and testing. In our search, no articles were found on condom programming or voluntary male medical circumcision. The most common outcome measures reported were CD4+ count, clinical failure or mortality. The population analysed was children in 13 articles, women in 16 articles, and both adult men and women in 33 articles. During the 10 year period of review, only 62 articles were published analysing routinely collected HIV data in Zambia. Serious consideration needs to be made to maximise the utility of routinely collected data, and to benefit from the funds and efforts to collect these data. This could be achieved with government support of operational research and publication of findings based on routinely collected Zambian HIV data.

Clinical outcomes and cost effectiveness of accelerated diagnostic protocol in a chest pain center compared with routine care of patients with chest pain.

PubMed

Asher, Elad; Reuveni, Haim; Shlomo, Nir; Gerber, Yariv; Beigel, Roy; Narodetski, Michael; Eldar, Michael; Or, Jacob; Hod, Hanoch; Shamiss, Arie; Matetzky, Shlomi

2015-01-01

The aim of this study was to compare in patients presenting with acute chest pain the clinical outcomes and cost-effectiveness of an accelerated diagnostic protocol utilizing contemporary technology in a chest pain unit versus routine care in an internal medicine department. Hospital and 90-day course were prospectively studied in 585 consecutive low-moderate risk acute chest pain patients, of whom 304 were investigated in a designated chest pain center using a pre-specified accelerated diagnostic protocol, while 281 underwent routine care in an internal medicine ward. Hospitalization was longer in the routine care compared with the accelerated diagnostic protocol group (p<0.001). During hospitalization, 298 accelerated diagnostic protocol patients (98%) vs. 57 (20%) routine care patients underwent non-invasive testing, (p<0.001). Throughout the 90-day follow-up, diagnostic imaging testing was performed in 125 (44%) and 26 (9%) patients in the routine care and accelerated diagnostic protocol patients, respectively (p<0.001). Ultimately, most patients in both groups had non-invasive imaging testing. Accelerated diagnostic protocol patients compared with those receiving routine care was associated with a lower incidence of readmissions for chest pain [8 (3%) vs. 24 (9%), p<0.01], and acute coronary syndromes [1 (0.3%) vs. 9 (3.2%), p<0.01], during the follow-up period. The accelerated diagnostic protocol remained a predictor of lower acute coronary syndromes and readmissions after propensity score analysis [OR = 0.28 (CI 95% 0.14-0.59)]. Cost per patient was similar in both groups [($2510 vs. $2703 for the accelerated diagnostic protocol and routine care group, respectively, (p = 0.9)]. An accelerated diagnostic protocol is clinically superior and as cost effective as routine in acute chest pain patients, and may save time and resources.

Clinical Outcomes and Cost Effectiveness of Accelerated Diagnostic Protocol in a Chest Pain Center Compared with Routine Care of Patients with Chest Pain

PubMed Central

Asher, Elad; Reuveni, Haim; Shlomo, Nir; Gerber, Yariv; Beigel, Roy; Narodetski, Michael; Eldar, Michael; Or, Jacob; Hod, Hanoch; Shamiss, Arie; Matetzky, Shlomi

2015-01-01

Aims The aim of this study was to compare in patients presenting with acute chest pain the clinical outcomes and cost-effectiveness of an accelerated diagnostic protocol utilizing contemporary technology in a chest pain unit versus routine care in an internal medicine department. Methods and Results Hospital and 90-day course were prospectively studied in 585 consecutive low-moderate risk acute chest pain patients, of whom 304 were investigated in a designated chest pain center using a pre-specified accelerated diagnostic protocol, while 281 underwent routine care in an internal medicine ward. Hospitalization was longer in the routine care compared with the accelerated diagnostic protocol group (p<0.001). During hospitalization, 298 accelerated diagnostic protocol patients (98%) vs. 57 (20%) routine care patients underwent non-invasive testing, (p<0.001). Throughout the 90-day follow-up, diagnostic imaging testing was performed in 125 (44%) and 26 (9%) patients in the routine care and accelerated diagnostic protocol patients, respectively (p<0.001). Ultimately, most patients in both groups had non-invasive imaging testing. Accelerated diagnostic protocol patients compared with those receiving routine care was associated with a lower incidence of readmissions for chest pain [8 (3%) vs. 24 (9%), p<0.01], and acute coronary syndromes [1 (0.3%) vs. 9 (3.2%), p<0.01], during the follow-up period. The accelerated diagnostic protocol remained a predictor of lower acute coronary syndromes and readmissions after propensity score analysis [OR = 0.28 (CI 95% 0.14–0.59)]. Cost per patient was similar in both groups [($2510 vs. $2703 for the accelerated diagnostic protocol and routine care group, respectively, (p = 0.9)]. Conclusion An accelerated diagnostic protocol is clinically superior and as cost effective as routine in acute chest pain patients, and may save time and resources. PMID:25622029

Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba.

PubMed

Alemán, Yoan; Vinken, Lore; Kourí, Vivian; Pérez, Lissette; Álvarez, Alina; Abrahantes, Yeissel; Fonseca, Carlos; Pérez, Jorge; Correa, Consuelo; Soto, Yudira; Schrooten, Yoeri; Vandamme, Anne-Mieke; Van Laethem, Kristel

2015-01-01

As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.

Automated saliva processing for LC-MS/MS: Improving laboratory efficiency in cortisol and cortisone testing.

PubMed

Antonelli, Giorgia; Padoan, Andrea; Artusi, Carlo; Marinova, Mariela; Zaninotto, Martina; Plebani, Mario

2016-04-01

The aim of this study was to implement in our routine practice an automated saliva preparation protocol for quantification of cortisol (F) and cortisone (E) by LC-MS/MS using a liquid handling platform, maintaining the previously defined reference intervals with the manual preparation. Addition of internal standard solution to saliva samples and calibrators and SPE on μ-elution 96-well plate were performed by liquid handling platform. After extraction, the eluates were submitted to LC-MS/MS analysis. The manual steps within the entire process were to transfer saliva samples in suitable tubes, to put the cap mat and transfer of the collection plate to the LC auto sampler. Transference of the reference intervals from the manual to the automated procedure was established by Passing Bablok regression on 120 saliva samples analyzed simultaneously with the two procedures. Calibration curves were linear throughout the selected ranges. The imprecision ranged from 2 to 10%, with recoveries from 95 to 116%. Passing Bablok regression demonstrated no significant bias. The liquid handling platform translates the manual steps into automated operations allowing for saving hands-on time, while maintaining assay reproducibility and ensuring reliability of results, making it implementable in our routine with the previous established reference intervals. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Evaluation of the Olympus AU-510 analyser.

PubMed

Farré, C; Velasco, J; Ramón, F

1991-01-01

The selective multitest Olympus AU-510 analyser was evaluated according to the recommendations of the Comision de Instrumentacion de la Sociedad Española de Quimica Clinica and the European Committee for Clinical Laboratory Standards. The evaluation was carried out in two stages: an examination of the analytical units and then an evaluation in routine work conditions. The operational characteristics of the system were also studied.THE FIRST STAGE INCLUDED A PHOTOMETRIC STUDY: dependent on the absorbance, the inaccuracy varies between +0.5% to -0.6% at 405 nm and from -5.6% to 10.6% at 340 nm; the imprecision ranges between -0.22% and 0.56% at 405 nm and between 0.09% and 2.74% at 340 nm. Linearity was acceptable, apart from a very low absorbance for NADH at 340 nm; and the imprecision of the serum sample pipetter was satisfactory.TWELVE SERUM ANALYTES WERE STUDIED UNDER ROUTINE CONDITIONS: glucose, urea urate, cholesterol, triglycerides, total bilirubin, creatinine, phosphate, iron, aspartate aminotransferase, alanine aminotransferase and gamma-glutamyl transferase.The within-run imprecision (CV%) ranged from 0.67% for phosphate to 2.89% for iron and the between-run imprecision from 0.97% for total bilirubin to 7.06% for iron. There was no carryover in a study of the serum sample pipetter. Carry-over studies with the reagent and sample pipetters shows some cross contamination in the iron assay.

Intensive educational efforts combined with external quality assessment improve the preanalytical phase in general practitioner offices and nursing homes.

PubMed

Sølvik, Una Ørvim; Bjelkarøy, Wenche Iren; Berg, Kari van den; Saga, Anne Lise; Hager, Helle Borgstrøm; Sandberg, Sverre

2017-10-26

Errors in the preanalytical phase in clinical laboratories affect patient safety. The aim of this study was to evaluate the effect of intensive educational efforts together with external quality assessment (EQA) of the preanalytical phase from 2013 to 2015 to improve patient identification in primary health care in Norway. In addition, routines for venous and capillary blood sampling were investigated. A preanalytical EQA was circulated in 2013 by the Norwegian Quality Improvement of Laboratory Examinations (Noklus) to general practitioner offices and nursing homes (n=2000) to obtain information about important issues to focus on before launching an intensive educational program with courses, posters and visits in 2013-2015. Preanalytical EQA surveys were further circulated in 2014 and 2015. The response rate varied between 42% and 55%. The percentages of participants asking for the patients' name and the Norwegian identification number increased from about 8% in 2013 to about 35% in 2015. The increase was similar for those participating in only one EQA survey and for those who participated in EQA surveys both in 2013 and 2015. Guidelines for venous and capillary blood sampling were not always followed. Educational efforts more than the preanalytical EQA influenced the actions and resulted in an increase in the percentages of participants that followed the guidelines for patient identification. Some aspects of blood sampling routines need improvement.

Reliability, standard error, and minimum detectable change of clinical pressure pain threshold testing in people with and without acute neck pain.

PubMed

Walton, David M; Macdermid, Joy C; Nielson, Warren; Teasell, Robert W; Chiasson, Marco; Brown, Lauren

2011-09-01

Clinical measurement. To evaluate the intrarater, interrater, and test-retest reliability of an accessible digital algometer, and to determine the minimum detectable change in normal healthy individuals and a clinical population with neck pain. Pressure pain threshold testing may be a valuable assessment and prognostic indicator for people with neck pain. To date, most of this research has been completed using algometers that are too resource intensive for routine clinical use. Novice raters (physiotherapy students or clinical physiotherapists) were trained to perform algometry testing over 2 clinically relevant sites: the angle of the upper trapezius and the belly of the tibialis anterior. A convenience sample of normal healthy individuals and a clinical sample of people with neck pain were tested by 2 different raters (all participants) and on 2 different days (healthy participants only). Intraclass correlation coefficient (ICC), standard error of measurement, and minimum detectable change were calculated. A total of 60 healthy volunteers and 40 people with neck pain were recruited. Intrarater reliability was almost perfect (ICC = 0.94-0.97), interrater reliability was substantial to near perfect (ICC = 0.79-0.90), and test-retest reliability was substantial (ICC = 0.76-0.79). Smaller change was detectable in the trapezius compared to the tibialis anterior. This study provides evidence that novice raters can perform digital algometry with adequate reliability for research and clinical use in people with and without neck pain.

Very poor agreement between routine outpatient clinic office and ambulatory blood pressure: time to improve an old hospital outpatient clinic routine?

PubMed

Reinhard, Mark; Poulsen, Per L; Christensen, Kent L

2016-12-01

We investigated the agreement between elevated outpatient clinic office blood pressure (OC-OBP) as measured in the daily routine in our University Hospital Cardiology Outpatient Clinic and subsequent awake ambulatory blood pressure (AABP). In all patients referred for ambulatory blood pressure monitoring from our Cardiology Outpatient Clinic, we identified OC-OBP and changes in medication in the period from 1 January 2014 to 15 September 2015. The AABP was used as a reference measurement for the OC-OBP. A total of 183 patients were included in the study. Their mean age was 62.1±14.0 years and 49% were women. The mean systolic OC-OBP was 166.8±17.9 mmHg and the difference between the mean systolic OC-OBP and AABP was 28.0±19.5 mmHg (P<0.001) with 95% limits of agreement from -10.2 to +66.3 mmHg. The difference in mean systolic OC-OBP and AABP was 18.6±14.7 mmHg in patients less than 45 years (n=21), 24.8±18.2 mmHg in patients 45-74 years (n=121) and 42.3±18.5 mmHg in patients more than or equal to 75 years (n=41). In 32 (17%) of the patients, the antihypertensive treatment was intensified before the AABP, but in nine (28%) of these patients, the antihypertensive treatment was reduced again after the AABP because of low blood pressure. Routine OC-OBP in a busy cardiology clinic agrees poorly with AABP and may lead to unnecessary treatment and pharmacologically induced symptomatic hypotension, particularly in elderly patients. The results of this study urgently call for alternative solutions to routine OC-OBP in hospital outpatient clinics.

Renal geology (quantitative renal stone analysis) by 'Fourier transform infrared spectroscopy'.

PubMed

Singh, Iqbal

2008-01-01

To prospectively determine the precise stone composition (quantitative analysis) by using infrared spectroscopy in patients with urinary stone disease presenting to our clinic. To determine an ideal method for stone analysis suitable for use in a clinical setting. After routine and a detailed metabolic workup of all patients of urolithiasis, stone samples of 50 patients of urolithiasis satisfying the entry criteria were subjected to the Fourier transform infrared spectroscopic analysis after adequate sample homogenization at a single testing center. Calcium oxalate monohydrate and dihydrate stone mixture was most commonly encountered in 35 (71%) followed by calcium phosphate, carbonate apatite, magnesium ammonium hexahydrate and xanthine stones. Fourier transform infrared spectroscopy allows an accurate, reliable quantitative method of stone analysis. It also helps in maintaining a computerized large reference library. Knowledge of precise stone composition may allow the institution of appropriate prophylactic therapy despite the absence of any detectable metabolic abnormalities. This may prevent and or delay stone recurrence.

Quantum cascade lasers (QCLs) in biomedical spectroscopy.

PubMed

Schwaighofer, Andreas; Brandstetter, Markus; Lendl, Bernhard

2017-10-02

Quantum cascade lasers (QCL) are the first room temperature semiconductor laser source for the mid-IR spectral region, triggering substantial development for the advancement of mid-IR spectroscopy. Mid-IR spectroscopy in general provides rapid, label-free and objective analysis, particularly important in the field of biomedical analysis. Due to their unique properties, QCLs offer new possibilities for development of analytical methods to enable quantification of clinically relevant concentration levels and to support medical diagnostics. Compared to FTIR spectroscopy, novel and elaborated measurement techniques can be implemented that allow miniaturized and portable instrumentation. This review illustrates the characteristics of QCLs with a particular focus on their benefits for biomedical analysis. Recent applications of QCL-based spectroscopy for analysis of a variety of clinically relevant samples including breath, urine, blood, interstitial fluid, and biopsy samples are summarized. Further potential for technical advancements is discussed in combination with future prospects for employment of QCL-based devices in routine and point-of-care diagnostics.

High-Performance 3D Compressive Sensing MRI Reconstruction Using Many-Core Architectures

PubMed Central

Kim, Daehyun; Trzasko, Joshua; Smelyanskiy, Mikhail; Haider, Clifton; Dubey, Pradeep; Manduca, Armando

2011-01-01

Compressive sensing (CS) describes how sparse signals can be accurately reconstructed from many fewer samples than required by the Nyquist criterion. Since MRI scan duration is proportional to the number of acquired samples, CS has been gaining significant attention in MRI. However, the computationally intensive nature of CS reconstructions has precluded their use in routine clinical practice. In this work, we investigate how different throughput-oriented architectures can benefit one CS algorithm and what levels of acceleration are feasible on different modern platforms. We demonstrate that a CUDA-based code running on an NVIDIA Tesla C2050 GPU can reconstruct a 256 × 160 × 80 volume from an 8-channel acquisition in 19 seconds, which is in itself a significant improvement over the state of the art. We then show that Intel's Knights Ferry can perform the same 3D MRI reconstruction in only 12 seconds, bringing CS methods even closer to clinical viability. PMID:21922017

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

Gunter, B.J.

An investigation was made of possible hazardous exposures to mercury and nitrous oxide at a dental clinic. Air samples were taken while the dentist and assistants used mercury amalgams. Nitrous-oxide was in use for over three hours. The air-sampling results revealed a range of nitrous-oxide concentrations in the room air from 30 to 220 parts per million (ppm). Mercury concentrations ranged from nondetectable to 0.009ppm, well below the evaluation criteria of 0.05ppm. The author concludes that a health hazard from excessive exposures to nitrous oxide exists, but mercury levels pose no health hazard in the clinic. The author recommends thatmore » the ventilation system should be adjusted each time nitrous oxide is going to be used. Routine maintenance checks should be performed on all anesthetic and suction equipment. The installation of a large fan on the roof of the building is suggested. Patients, particularly children, should be watched so that they do not play with the face mask during the administration of nitrous oxide.« less

Comparison of microbiological diagnosis of urinary tract infection in young children by routine health service laboratories and a research laboratory: Diagnostic cohort study.

PubMed

Birnie, Kate; Hay, Alastair D; Wootton, Mandy; Howe, Robin; MacGowan, Alasdair; Whiting, Penny; Lawton, Michael; Delaney, Brendan; Downing, Harriet; Dudley, Jan; Hollingworth, William; Lisles, Catherine; Little, Paul; O'Brien, Kathryn; Pickles, Timothy; Rumsby, Kate; Thomas-Jones, Emma; Van der Voort, Judith; Waldron, Cherry-Ann; Harman, Kim; Hood, Kerenza; Butler, Christopher C; Sterne, Jonathan A C

2017-01-01

To compare the validity of diagnosis of urinary tract infection (UTI) through urine culture between samples processed in routine health service laboratories and those processed in a research laboratory. We conducted a prospective diagnostic cohort study in 4808 acutely ill children aged <5 years attending UK primary health care. UTI, defined as pure/predominant growth ≥105 CFU/mL of a uropathogen (the reference standard), was diagnosed at routine health service laboratories and a central research laboratory by culture of urine samples. We calculated areas under the receiver-operator curve (AUC) for UTI predicted by pre-specified symptoms, signs and dipstick test results (the "index test"), separately according to whether samples were obtained by clean catch or nappy (diaper) pads. 251 (5.2%) and 88 (1.8%) children were classified as UTI positive by health service and research laboratories respectively. Agreement between laboratories was moderate (kappa = 0.36; 95% confidence interval [CI] 0.29, 0.43), and better for clean catch (0.54; 0.45, 0.63) than nappy pad samples (0.20; 0.12, 0.28). In clean catch samples, the AUC was lower for health service laboratories (AUC = 0.75; 95% CI 0.69, 0.80) than the research laboratory (0.86; 0.79, 0.92). Values of AUC were lower in nappy pad samples (0.65 [0.61, 0.70] and 0.79 [0.70, 0.88] for health service and research laboratory positivity, respectively) than clean catch samples. The agreement of microbiological diagnosis of UTI comparing routine health service laboratories with a research laboratory was moderate for clean catch samples and poor for nappy pad samples and reliability is lower for nappy pad than for clean catch samples. Positive results from the research laboratory appear more likely to reflect real UTIs than those from routine health service laboratories, many of which (particularly from nappy pad samples) could be due to contamination. Health service laboratories should consider adopting procedures used in the research laboratory for paediatric urine samples. Primary care clinicians should try to obtain clean catch samples, even in very young children.

Order in the Home: Family Routines Moderate the Impact of Financial Hardship

ERIC Educational Resources Information Center

Budescu, Mia; Taylor, Ronald D.

2013-01-01

The study examined whether frequency of adolescent reported family routines moderated the relation between caregivers' perceptions of financial resources and adolescents' behavioral and academic outcomes among a sample of inner-city African American families. The sample consisted of 115 adolescents (average age = 15.95) and their female caregivers…

Variations in achievement of evidence-based, high-impact quality indicators in general practice: An observational study

PubMed Central

West, Robert; Rushforth, Bruno; Stokes, Tim; Glidewell, Liz; Carder, Paul; Faulkner, Simon; Foy, Robbie

2017-01-01

Background There are widely recognised variations in the delivery and outcomes of healthcare but an incomplete understanding of their causes. There is a growing interest in using routinely collected ‘big data’ in the evaluation of healthcare. We developed a set of evidence-based ‘high impact’ quality indicators (QIs) for primary care and examined variations in achievement of these indicators using routinely collected data in the United Kingdom (UK). Methods Cross-sectional analysis of routinely collected, electronic primary care data from a sample of general practices in West Yorkshire, UK (n = 89). The QIs covered aspects of care (including processes and intermediate clinical outcomes) in relation to diabetes, hypertension, atrial fibrillation, myocardial infarction, chronic kidney disease (CKD) and ‘risky’ prescribing combinations. Regression models explored the impact of practice and patient characteristics. Clustering within practice was accounted for by including a random intercept for practice. Results Median practice achievement of the QIs ranged from 43.2% (diabetes control) to 72.2% (blood pressure control in CKD). Considerable between-practice variation existed for all indicators: the difference between the highest and lowest performing practices was 26.3 percentage points for risky prescribing and 100 percentage points for anticoagulation in atrial fibrillation. Odds ratios associated with the random effects for practices emphasised this; there was a greater than ten-fold difference in the likelihood of achieving the hypertension indicator between the lowest and highest performing practices. Patient characteristics, in particular age, gender and comorbidity, were consistently but modestly associated with indicator achievement. Statistically significant practice characteristics were identified less frequently in adjusted models. Conclusions Despite various policy and improvement initiatives, there are enduring inappropriate variations in the delivery of evidence-based care. Much of this variation is not explained by routinely collected patient or practice variables, and is likely to be attributable to differences in clinical and organisational behaviour. PMID:28704407

[Therapeutic monitoring: analytic, pharmacokinetic and clinical aspects].

PubMed

Marquet, P

1999-01-01

This paper gives an overview of present aspects and future prospects of therapeutic drug monitoring (TDM). The main aims of TDM are to avoid therapeutic failures due to bad compliance or too low dose of a given drug, as well as adverse or toxic effects due to an excessive dose. The therapeutic drugs frequently monitored depend on the country, but are generally few. For some of these drugs or for others, only patients at risk or belonging to particular sub-populations for a given drug, need TDM. A pre-analytical management is necessary, comprising a correct information of the physician, concerning the nature of the sample to collect and the clinical data necessary to the interpretation, as well as their recording; the control of the sample routing and storing conditions. Nowadays, drug analyses are essentially performed using immunochemical techniques, rapid and easy to operate but limited to a small number of drugs, and chromatographic methods, more specific and adaptable to almost any therapeutic drug and financially and technically more and more accessible. The interpretation of analytical results is a most important part of TDM, which requires knowledge of clinical data, precise collection time, co-administered treatments, and to dispose of a previously defined therapeutic range or target concentration, adapted to the population to which the patient belongs; the limitations of the analytical technique used must also be considered. Clinical pharmacokinetics is a further step in the use of analytical results, allowing the prediction of an efficient dose and administration schedule in one step, using a limited number of blood samples and generally a Bayesian estimation algorithm, readily available through commercial software dedicated to a few drugs in different reference populations. The pharmacokinetic characteristics of different populations and the validation of bayesian estimation have also been published for a number of drugs, sometimes by pharmaceutical companies following phase I and II clinical trials, even taking into account various physiopathological co-variables, but mostly by independent researchers using smaller populations. The efficiency and cost of routine TDM are questionable when it is prescribed with no clinical information or even no indication of administration and sampling times. On the contrary, several studies reported that clinical pharmacokinetics significantly improved patient outcome and were cost-saving, particularly in terms of duration of hospitalisation. The author's opinion is that TDM, in the near future, will be mainly dedicated to drugs used to treat life-threatening diseases, such as anti-HIV, anticancer and immunosuppressive drugs, and maybe also biotechnological peptides or proteins, because of cost considerations. TDM will probably also be used preferentially in target populations, characterised by higher risk or pharmacokinetic variability. Very sensitive, specific and partly automated separative techniques, such as liquid chromatography-tandem mass spectrometry, might become more common than immunochemical methods, owing to a higher flexibility and improved sample throughout. Clinical pharmacokinetics may spread to a larger number of drugs and patients, due to larger reference populations available, taking into account a number of co-variables, computerised data collection and simplified modelisation. Therefore, TDM will mainly be performed in hospitals, with an essentially clinical role for the pharmacists or pharmacologists involved and routine use of recent and efficient technologies for the TDM laboratory technical staff.

Diagnosis of Bubonic Plague by PCR in Madagascar under Field Conditions

PubMed Central

Rahalison, L.; Vololonirina, E.; Ratsitorahina, M.; Chanteau, S.

2000-01-01

The diagnostic value of a PCR assay that amplifies a 501-bp fragment of the Yersinia pestis caf1 gene has been determined in a reference laboratory with 218 bubo aspirates collected from patients with clinically suspected plague managed in a regional hospital in Madagascar. The culture of Y. pestis and the detection of the F1 antigen (Ag) by enzyme-linked immunosorbent assay (ELISA) were used as reference diagnostic methods. The sensitivity of PCR was 89% (57 of 64) for the Y. pestis-positive patients, and 80.7% (63 of 78) for the F1 Ag-positive patients. The specificity of PCR for the culture-, F1 Ag-, and antibody-negative patients (n = 105) was 100%. Because in Madagascar most patients with plague are managed and their clinical samples are collected in remote villages, the usefulness of PCR was evaluated for routine diagnostic use in the operational conditions of the control program. The sensitivity of PCR was 50% (25 of 50) relative to the results of culture and 35.2% (19 of 54) relative to the results of the F1 Ag immunocapture ELISA. The specificity of PCR under these conditions was 96%. In conclusion, the PCR method was found to be very specific but not as sensitive as culture or the F1 Ag detection method. The limitation in sensitivity may have been due to suboptimal field conditions and the small volumes of samples used for DNA extraction. This technique is not recommended as a routine diagnostic test for plague in Madagascar. PMID:10618097

Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis

NASA Astrophysics Data System (ADS)

Gallego, Sandra F.; Højlund, Kurt; Ejsing, Christer S.

2018-01-01

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MSALL technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133-148 [1]) to support in-depth structural elucidation of lipid molecules. [Figure not available: see fulltext.

Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis.

PubMed

Gallego, Sandra F; Højlund, Kurt; Ejsing, Christer S

2018-01-01

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MS ALL technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133-148 [1]) to support in-depth structural elucidation of lipid molecules. Graphical Abstract ᅟ.

Brief sexual histories and routine HIV/STD testing by medical providers.

PubMed

Lanier, Yzette; Castellanos, Ted; Barrow, Roxanne Y; Jordan, Wilbert C; Caine, Virginia; Sutton, Madeline Y

2014-03-01

Clinicians who routinely take patient sexual histories have the opportunity to assess patient risk for sexually transmitted diseases (STDs), including human immunodeficiency virus (HIV), and make appropriate recommendations for routine HIV/STD screenings. However, less than 40% of providers conduct sexual histories with patients, and many do not receive formal sexual history training in school. After partnering with a national professional organization of physicians, we trained 26 (US and US territory-based) practicing physicians (58% female; median age=48 years) regarding sexual history taking using both in-person and webinar methods. Trainings occurred during either a 6-h onsite or 2-h webinar session. We evaluated their post-training experiences integrating sexual histories during routine medical visits. We assessed use of sexual histories and routine HIV/STD screenings. All participating physicians reported improved sexual history taking and increases in documented sexual histories and routine HIV/STD screenings. Four themes emerged from the qualitative evaluations: (1) the need for more sexual history training; (2) the importance of providing a gender-neutral sexual history tool; (3) the existence of barriers to routine sexual histories/testing; and (4) unintended benefits for providers who were conducting routine sexual histories. These findings were used to develop a brief, gender-neutral sexual history tool for clinical use. This pilot evaluation demonstrates that providers were willing to utilize a sexual history tool in clinical practice in support of HIV/STD prevention efforts.

Upfront dilution of ferritin samples to reduce hook effect, improve turnaround time and reduce costs.

PubMed

Wu, Shu Juan; Hayden, Joshua A

2018-02-15

Sandwich immunoassays offer advantages in the clinical laboratory but can yield erroneously low results due to hook (prozone) effect, especially with analytes whose concentrations span several orders of magnitude such as ferritin. This study investigated a new approach to reduce the likelihood of hook effect in ferritin immunoassays by performing upfront, five-fold dilutions of all samples for ferritin analysis. The impact of this change on turnaround time and costs were also investigated. Ferritin concentrations were analysed in routine clinical practice with and without upfront dilutions on Siemens Centaur® XP (Siemens Healthineers, Erlang, Germany) immunoanalysers. In addition, one month of baseline data (1026 results) were collected prior to implementing upfront dilutions and one month of data (1033 results) were collected after implementation. Without upfront dilutions, hook effect was observed in samples with ferritin concentrations as low as 86,028 µg/L. With upfront dilutions, samples with ferritin concentrations as high as 126,050 µg/L yielded values greater than the measurement interval and would have been diluted until an accurate value was obtained. The implementation of upfront dilution of ferritin samples led to a decrease in turnaround time from a median of 2 hours and 3 minutes to 1 hour and 18 minutes (P = 0.002). Implementation of upfront dilutions of all ferritin samples reduced the possibility of hook effect, improved turnaround time and saved the cost of performing additional dilutions.

Contamination of the Clinical Microbiology Laboratory with Vancomycin-Resistant Enterococci and Multidrug- Resistant Enterobacteriaceae: Implications for Hospital and Laboratory Workers

PubMed Central

Collins, Susan M.; Hacek, Donna M.; Degen, Lisa A.; Wright, Marc O.; Noskin, Gary A.; Peterson, Lance R.

2001-01-01

We surveyed environmental surfaces in our clinical microbiology laboratory to determine the prevalence of vancomycin-resistant enterococci (VRE) and multidrug-resistant Enterobacteriaceae (MDRE) during a routine working day. From a total of 193 surfaces, VRE were present on 20 (10%) and MDRE were present on 4 (2%) of the surfaces tested. In a subsequent survey after routine cleaning, all of the 24 prior positive surfaces were found to be negative. Thus, those in the laboratory should recognize that many surfaces may be contaminated by resistant organisms during routine processing of patient specimens. PMID:11574615

An estimation of the clinical mastitis incidence per 100 cows per year based on routinely collected herd data.

PubMed

Santman-Berends, I M G A; Lam, T J G M; Keurentjes, J; van Schaik, G

2015-10-01

The aim of this study was to evaluate whether it was possible to (1) estimate the clinical mastitis incidence rate (CMI) for all Dutch dairy herds and (2) to detect farms with a high CMI based on routinely collected herd data. For this study, 240 dairy farms with a conventional milking system that participated in the milk recording program every 4 to 6 wk were randomly selected and agreed to participate. From the initial 240 herds, data of clinical mastitis (CM) registrations and routinely collected herd data of 227 herds were complete and could be used for analysis. Routinely collected herd data consisted of identification and registration records, antimicrobial usage, test-day records from the milk recording program, bulk tank milk (BTM) somatic cell count data and results of diagnostic tests on BTM samples. For each of the 227 herds, the CMI per 100 cows per year was calculated per quarter of the year and was combined with the available herd data. Two models were developed to predict the CMI for all dairy herds and to detect individual herds that belonged to the 25% herds with the highest CMI. Records of 156 (67%) herds were used for development of the models and the remaining 71 (33%) were used for validation. The model that estimated the CMI in all herds consisted of 11 explanatory variables. The observed and predicted averages of the validation herds were not significantly different. The model estimated a CMI per 100 cows per year of 32.5 cases (95% confidence interval=30.2-34.8), whereas the farmers registered 33.4 cases (95% confidence interval=29.5-37.4). The model that aimed at detecting individual herds with a high CMI contained 6 explanatory variables and could correctly classify 77% of all validation herds at the quarter-year level. The most important variables in the model were antibiotic usage for treating CM and BTM somatic cell count. In conclusion, models based on routinely collected herd data gave an accurate prediction of CMI for all Dutch dairy herds and could detect individual dairy herds with a high CMI. With these models it is possible to periodically monitor CMI both at the herd and at the national level, which is valuable for monitoring purposes and can motivate farmers to continuously improve udder health in their herds. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

BASHH 2016 UK national audit and survey of HIV testing, risk assessment and follow-up: case note audit.

PubMed

Bhaduri, Sumit; Curtis, Hilary; McClean, Hugo; Sullivan, Ann K

2018-01-01

This national audit demonstrated discrepancies between actual practice and that indicated by clinic policies following enquiry about alcohol, recreational drugs and chemsex use. Clinics were more likely to enquire about risk behaviour if this was clinic policy or routine practice. Previous testing was the most common reason for refusing HIV testing, although 33% of men who have sex with men had a prior test of more than three months ago. Of the group declining due to recent exposure in the window period, 21/119 cases had an exposure within the four weeks prior to presentation, but had a previous risk not covered by previous testing. Recommendations include provision of risk assessments for alcohol, recreational drug use and chemsex, documenting reasons for HIV test refusal, provision of HIV point-of-care testing, follow-up for cases at higher risk of HIV and advice about community testing or self-sampling/testing.

[Applications of MALDI-TOF technology in clinical microbiology].

PubMed

Suarez, S; Nassif, X; Ferroni, A

2015-02-01

Until now, the identification of micro-organisms has been based on the cultural and biochemical characteristics of bacterial and fungal species. Recently, Mass Spectrometry type Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF MS) was developed in clinical microbiology laboratories. This new technology allows identification of micro-organisms directly from colonies of bacteria and fungi within few minutes. In addition, it can be used to identify germs directly from positive blood culture bottles or directly from urine samples. Other ways are being explored to expand the use of MALDI-TOF in clinical microbiology laboratories. Indeed, some studies propose to detect bacterial antibiotic resistance while others compare strains within species for faster strain typing. The main objective of this review is to update data from the recent literature for different applications of MALDI-TOF technique in microbiological diagnostic routine. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Single-cell proteomics: potential implications for cancer diagnostics.

PubMed

Gavasso, Sonia; Gullaksen, Stein-Erik; Skavland, Jørn; Gjertsen, Bjørn T

2016-01-01

Single-cell proteomics in cancer is evolving and promises to provide more accurate diagnoses based on detailed molecular features of cells within tumors. This review focuses on technologies that allow for collection of complex data from single cells, but also highlights methods that are adaptable to routine cancer diagnostics. Current diagnostics rely on histopathological analysis, complemented by mutational detection and clinical imaging. Though crucial, the information gained is often not directly transferable to defined therapeutic strategies, and predicting therapy response in a patient is difficult. In cancer, cellular states revealed through perturbed intracellular signaling pathways can identify functional mutations recurrent in cancer subsets. Single-cell proteomics remains to be validated in clinical trials where serial samples before and during treatment can reveal excessive clonal evolution and therapy failure; its use in clinical trials is anticipated to ignite a diagnostic revolution that will better align diagnostics with the current biological understanding of cancer.

Clinical utility of the Rorschach with African Americans.

PubMed

Presley, G; Smith, C; Hilsenroth, M; Exner, J

2001-12-01

In this study we sought to identify Rorschach differences between African Americans and White Americans and to understand these differences within a social and cultural framework. Data from the Exner (1993) Comprehensive System normative sample (N = 700) was used to form a group of 44 African Americans and 44 White Americans matched for age, sex, education, and socioeconomic status. Twenty-three Rorschach variables were chosen a priori and group differences were analyzed. The only clinically significant difference found was that African Americans offered significantly less cooperative movement. This lower frequency of cooperative movement may suggest African Americans do not anticipate cooperative interactions with others as a routine event. This may reflect a shared feeling among African Americans that most members of our society are less likely to be sensitive to or responsive to their needs relative to others. However, the study demonstrates a striking similarity between the groups, supporting the clinical use of the Rorschach with African Americans.

A Xhosa language translation of the CORE-OM using South African university student samples.

PubMed

Campbell, Megan M; Young, Charles

2016-10-01

The translation of well established psychometric tools from English into Xhosa may assist in improving access to psychological services for Xhosa speakers. The aim of this study was to translate the Clinical Outcomes in Routine Evaluation - Outcome Measure (CORE-OM), a measure of general distress and dysfunction developed in the UK, into Xhosa for use at South African university student counselling centres. The CORE-OM and embedded CORE-10 were translated into Xhosa using a five-stage translation design. This design included (a) forward-translation, (b) back-translation, (c) committee approach, (d) qualitative piloting, and (e) quantitative piloting on South African university students. Clinical and general samples were drawn from English-medium South African universities. Clinical samples were generated from university student counselling centres. General student samples were generated through random stratified cluster sampling of full-time university students. Qualitative feedback from the translation process and results from quantitative piloting of the 34-item CORE-OM English and Xhosa versions supported the reduction of the scale to 10 items. This reduced scale is referred to as the South African CORE-10 (SA CORE-10). A measurement and structural model of the SA CORE-10 English version was developed and cross-validated using an English-speaking university student sample. Equivalence of this model with the SA CORE-10 Xhosa version was investigated using a first-language Xhosa-speaking university sample. Partial measurement equivalence was achieved at the metric level. The resultant SA CORE-10 Xhosa and English versions provide core measures of distress and dysfunction. Additional, culture- and language-specific domains could be added to increase sensitivity and specificity. © The Author(s) 2016.

The clinical impact of using complex molecular profiling strategies in routine oncology practice.

PubMed

Laes, Jean-François; Aftimos, Philippe; Barthelemy, Philippe; Bellmunt, Joaquim; Berchem, Guy; Camps, Carlos; Peñas, Ramón de Las; Finzel, Ana; García-Foncillas, Jesús; Hervonen, Petteri; Wahid, Ibrahim; Joensuu, Timo; Kathan, Louis; Kong, Anthony; Mackay, James; Mikropoulos, Christos; Mokbel, Kefah; Mouysset, Jean-Loup; Odarchenko, Sergey; Perren, Timothy J; Pienaar, Rika; Regonesi, Carlos; Alkhayyat, Shadi Salem; El Kinge, Abdul Rahman; Abulkhair, Omalkhair; Galal, Khaled Morsi; Ghanem, Hady; El Karak, Fadi; Garcia, Angel; Ghitti, Gregori; Sadik, Helen

2018-04-17

Molecular profiling and functional assessment of signalling pathways of advanced solid tumours are becoming increasingly available. However, their clinical utility in guiding patients' treatment remains unknown. Here, we assessed whether molecular profiling helps physicians in therapeutic decision making by analysing the molecular profiles of 1057 advanced cancer patient samples after failing at least one standard of care treatment using a combination of next-generation sequencing (NGS), immunohistochemistry (IHC) and other specific tests. The resulting information was interpreted and personalized treatments for each patient were suggested. Our data showed that NGS alone provided the oncologist with useful information in 10-50% of cases (depending on cancer type), whereas the addition of IHC/other tests increased extensively the usefulness of the information provided. Using internet surveys, we investigated how therapy recommendations influenced treatment choice of the oncologist. For patients who were still alive after the provision of the molecular information (76.8%), 60.4% of their oncologists followed report recommendations. Most treatment decisions (93.4%) were made based on the combination of NGS and IHC/other tests, and an approved drug- rather than clinical trial enrolment- was the main treatment choice. Most common reasons given by physicians to explain the non-adherence to recommendations were drug availability and cost, which remain barriers to personalised precision medicine. Finally, we observed that 27% of patients treated with the suggested therapies had an overall survival > 12 months. Our study demonstrates that the combination of NGS and IHC/other tests provides the most useful information in aiding treatment decisions by oncologists in routine clinical practice.

Impact of Routine Surveillance Imaging on Outcomes of Patients With Diffuse Large B-Cell Lymphoma After Autologous Hematopoietic Cell Transplantation.

PubMed

Epperla, Narendranath; Shah, Namrata; Hamadani, Mehdi; Richardson, Kristin; Kapke, Jonathan T; Patel, Asmita; Teegavarapu, Sravanthi P; Carrum, George; Hari, Parameswaran N; Pingali, Sai R; Karmali, Reem; Fenske, Timothy S

2016-12-01

For patients with relapsed or refractory diffuse large B-cell lymphoma (DLBCL), autologous hematopoietic cell transplantation (auto-HCT) is commonly used. After auto-HCT, DLBCL patients are often monitored with surveillance imaging. However, there is little evidence to support this practice. We performed a multicenter retrospective study of DLBCL patients who underwent auto-HCT (n = 160), who experienced complete remission after transplantation, and who then underwent surveillance imaging. Of these, only 45 patients experienced relapse after day +100 after auto-HCT, with relapse detected by routine imaging in 32 (71%) and relapse detected clinically in 13 (29%). Baseline patient characteristics were similar between the 2 groups. Comparing the radiographic and clinically detected relapse groups, the median time from diagnosis to auto-HCT (389 days vs. 621 days, P = .06) and the median follow-up after auto-HCT (2464 days vs. 1593 days P = .60) were similar. The median time to relapse after auto-HCT was 191 days in radiographically detected relapses compared to 492 days in clinically detected relapses (P = .35), and median postrelapse survival was 359 days in such patients compared to 123 days in patients with clinically detected relapse (P = .36). However, the median posttransplantation overall survival was not significantly different for patients with relapse detected by routine imaging versus relapse detected clinically (643 vs. 586 days, P = .68). A majority (71%) of DLBCL relapses after auto-HCT are detected by routine surveillance imaging. Overall, there appears to be limited utility for routine imaging after auto-HCT except in select cases where earlier detection and salvage therapy with allogeneic HCT is a potential option. Copyright © 2016 Elsevier Inc. All rights reserved.

[Clinical observation on external humeral epicondylitis treated with back-rotation traction].

PubMed

Fu, Rui-yang; Wang, Ya-ling; Gu, Zhong-zhong; Wang, Bao-hu; Zhu, Qi; Li, Ye; Wang, En-ping

2009-02-01

To evaluate the clinical effect of manipulation on external humeral epicondylitis, and to explore the functional mechanism and ideal treatment. Eighty-six patients who had been treated with acupuncture, obturation and needle-knife were divided into routine group and treatment group randomly. In routine group, there were 42 cases (male 13, female 29, means 40.8 years); and in treatment group there were 44 cases (male 16, female 28, means 41.2 years). There's no further treatment for the routine group after the therapy above, while the treatment group was added with back-rotation traction manipulation. Taking Verhaar therapy effect appraisal system of tennis-ball elbow to evaluate elbow function. After 7 days of therapy, the results were excellent in 13 cases, good in 16, fair in 4, poor in 9 in the routine group; and excellent in 38, good in 4 and fair in 2 in treatment group; and the effect in the treatment group were better than that of the routine group (P < 0.010). Half a year later, in the routine group 38 cases recurrenced and in the treatment group 10 cases recurrenced. Making manipulation after routine acupuncture, local obturation and needle-knife has active meaning to remove trauma inflammation, prevent re-conglutination, promote recovery and prevent recurrence.

Design and Validation of a Radio-Frequency Identification-Based Device for Routinely Assessing Gait Speed in a Geriatrics Clinic.

PubMed

Barry, Lisa C; Hatchman, Laura; Fan, Zhaoyan; Guralnik, Jack M; Gao, Robert X; Kuchel, George A

2018-05-01

To evaluate the feasibility, acceptability, and validity of a radio-frequency identification (RFID)-based system to measure gait speed in a clinical setting as a first step to using unobtrusive gait speed assessment in routine clinical care. Feasibility study comparing gait speed assessed using an RFID-based system with gait speed assessed using handheld stopwatch, the criterion standard. Outpatient geriatrics clinic at a Connecticut-based academic medical center. Clinic attendees who could walk independently with or without an assistive device (N=50) and healthcare providers (N=9). Gait speed was measured in twice using 2 methods each time before participants entered an examination room. Participants walked at their usual pace while gait speed was recorded simultaneously using the RFID-based system and a handheld stopwatch operated by a trained study investigator. After 2 trials, participants completed a brief survey regarding their experience. At the end of the study period, clinic healthcare providers completed a separate survey. Test-retest reliability of the RFID-based system was high (intraclass correlation coefficient = 0.953). The mean difference ± standard deviation in gait speed between the RFID-based system and the stopwatch was -0.003±0.035 m/s (p=.53) and did not differ significantly according to age, sex, or use of an assistive walking aid. Acceptability of the device was high, and 8 of 9 providers indicated that measuring gait speed using the RFID-based system should be a part of routine clinical care. RFID technology may offer a practical means of overcoming barriers to routine measurement of gait speed in real-world outpatient clinical settings. © 2018, Copyright the Authors Journal compilation © 2018, The American Geriatrics Society.

Addressing phenoconversion: the Achilles' heel of personalized medicine

PubMed Central

Shah, Rashmi R; Smith, Robert L

2015-01-01

Phenoconversion is a phenomenon that converts genotypic extensive metabolizers (EMs) into phenotypic poor metabolizers (PMs) of drugs, thereby modifying their clinical response to that of genotypic PMs. Phenoconversion, usually resulting from nongenetic extrinsic factors, has a significant impact on the analysis and interpretation of genotype-focused clinical outcome association studies and personalizing therapy in routine clinical practice. The high phenotypic variability or genotype–phenotype mismatch, frequently observed due to phenoconversion within the genotypic EM population, means that the real number of phenotypic PM subjects may be greater than predicted from their genotype alone, because many genotypic EMs would be phenotypically PMs. If the phenoconverted population with genotype–phenotype mismatch, most extensively studied for CYP2D6, is as large as the evidence suggests, there is a real risk that genotype-focused association studies, typically correlating only the genotype with clinical outcomes, may miss clinically strong pharmacogenetic associations, thus compromising any potential for advancing the prospects of personalized medicine. This review focuses primarily on co-medication-induced phenoconversion and discusses potential approaches to rectify some of the current shortcomings. It advocates routine phenotyping of subjects in genotype-focused association studies and proposes a new nomenclature to categorize study populations. Even with strong and reliable data associating patients' genotypes with clinical outcome(s), there are problems clinically in applying this knowledge into routine pharmacotherapy because of potential genotype–phenotype mismatch. Drug-induced phenoconversion during routine clinical practice remains a major public health issue. Therefore, the principal challenges facing personalized medicine, which need to be addressed, include identification of the following factors: (i) drugs that are susceptible to phenoconversion; (ii) co-medications that can cause phenoconversion; and (iii) dosage amendments that need to be applied during and following phenoconversion. PMID:24913012

[Comparison of the performance of the ECLusys anti-HCV reagent with the Lumipulse f and HISCL 2000-i HCVAb assays].

PubMed

Sugiura, Aya; Iwahara, Kunihiro; Suga, Yasuyuki; Uchiyama, Sachinori; Maekawa, Masato

2012-09-01

We compared the ECLusys Anti-HCV (ECL) reagent to the Lumipulse f (LPf) and HISCL (HIS) HCV assays. In a correlation test using 210 routine clinical specimens measured using the Lumipulse method (96 positive and 114 negative), most of the results were consistent for all specimens. In a dilution sensitivity test using three different routine positive specimens, the ECL assay enabled detection at higher levels of sensitivity than either the LPf or the HIS assay. Moreover, when the distribution of the cut-off index (C.O.I.) values of the routine LPf negative specimens were compared to those on the ECL and HIS assays, it was found that on the ECL assay, most of the specimens had cut-off index values < 0.1, indicating a more clear-cut distribution. In a specificity test using high RF positive specimens(n = 33), pregnancy specimens (n = 35), cytomegalovirus (CMV) antibody positive specimens (n = 36), and high M protein positive specimens (n = 21), the ECL assay yielded positive results for a CMV antibody positive specimen and three high M protein positive specimens. Further testing using samples from the same patients collected on different days than these four samples resulted in a second positive result for the CMV positive specimen, and single antigen measurement yielded a Core/NS3 positive result, as well, suggesting past infection. However, since negative results were obtained for the three M protein positive specimens, the possibility of this being a ECLusys non-specific reaction could not be ruled out. The above results confirmed that the ECL assay provides superior fundamental performance, and possesses test performance nearly identical to that of the existing measurement methods that are widely used at a large number of facilities, and would therefore be a suitable assay for use in routine HCV antibody screening.

Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease—Towards a Point-of-Care Test

PubMed Central

Beissner, Marcus; Phillips, Richard Odame; Battke, Florian; Bauer, Malkin; Badziklou, Kossi; Sarfo, Fred Stephen; Maman, Issaka; Rhomberg, Agata; Piten, Ebekalisai; Frimpong, Michael; Huber, Kristina Lydia; Symank, Dominik; Jansson, Moritz; Wiedemann, Franz Xaver; Banla Kere, Abiba; Herbinger, Karl-Heinz; Löscher, Thomas; Bretzel, Gisela

2015-01-01

Background As the major burden of Buruli ulcer disease (BUD) occurs in remote rural areas, development of point-of-care (POC) tests is considered a research priority to bring diagnostic services closer to the patients. Loop-mediated isothermal amplification (LAMP), a simple, robust and cost-effective technology, has been selected as a promising POC test candidate. Three BUD-specific LAMP assays are available to date, but various technical challenges still hamper decentralized application. To overcome the requirement of cold-chains for transport and storage of reagents, the aim of this study was to establish a dry-reagent-based LAMP assay (DRB-LAMP) employing lyophilized reagents. Methodology/Principal Findings Following the design of an IS2404 based conventional LAMP (cLAMP) assay suitable to apply lyophilized reagents, a lyophylization protocol for the DRB-LAMP format was developed. Clinical performance of cLAMP was validated through testing of 140 clinical samples from 91 suspected BUD cases by routine assays, i.e. IS2404 dry-reagent-based (DRB) PCR, conventional IS2404 PCR (cPCR), IS2404 qPCR, compared to cLAMP. Whereas qPCR rendered an additional 10% of confirmed cases and samples respectively, case confirmation and positivity rates of DRB-PCR or cPCR (64.84% and 56.43%; 100% concordant results in both assays) and cLAMP (62.64% and 52.86%) were comparable and there was no significant difference between the sensitivity of the assays (DRB PCR and cPCR, 86.76%; cLAMP, 83.82%). Likewise, sensitivity of cLAMP (95.83%) and DRB-LAMP (91.67%) were comparable as determined on a set of 24 samples tested positive in all routine assays. Conclusions/Significance Both LAMP formats constitute equivalent alternatives to conventional PCR techniques. Provided the envisaged availability of field friendly DNA extraction formats, both assays are suitable for decentralized laboratory confirmation of BUD, whereby DRB-LAMP scores with the additional advantage of not requiring cold-chains. As validation of the assays was conducted in a third-level laboratory environment, field based evaluation trials are necessary to determine the clinical performance at peripheral health care level. PMID:26566026

Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

PubMed

Gowrisankar, Sivakumar; Lerner-Ellis, Jordan P; Cox, Stephanie; White, Emily T; Manion, Megan; LeVan, Kevin; Liu, Jonathan; Farwell, Lisa M; Iartchouk, Oleg; Rehm, Heidi L; Funke, Birgit H

2010-11-01

Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

Diagnostic performances of clinical laboratory tests using Triton X-100 to reduce the biohazard associated with routine testing of Ebola virus-infected patients.

PubMed

Tempestilli, Massimo; Pucci, Luigia; Notari, Stefania; Di Caro, Antonino; Castilletti, Concetta; Rivelli, Maria Rosaria; Agrati, Chiara; Pucillo, Leopoldo Paolo

2015-11-01

Ebola virus, an enveloped virus, is the cause of the largest and most complex Ebola virus disease (EVD) outbreak in West Africa. Blood or body fluids of an infected person may represent a biohazard to laboratory workers. Laboratory tests of virus containing specimens should be conducted in referral centres at biosafety level 4, but based on the severity of clinical symptoms, basic laboratories might be required to execute urgent tests for patients suspected of EVD. The aim of this work was to compare the analytical performances of laboratory tests when Triton X-100, a chemical agent able to inactivate other enveloped viruses, was added to specimens. Results of clinical chemistry, coagulation and haematology parameters on samples before and after the addition of 0.1% (final concentration) of Triton X-100 and 1 h of incubation at room temperature were compared. Overall, results showed very good agreement by all statistical analyses. Triton X-100 at 0.1% did not significantly affect the results for the majority of the analytes tested. Triton X-100 at 0.1% can be used to reduce the biohazard in performing laboratory tests on samples from patients with EVD without affecting clinical decisions.

Quantification of hepatitis C virus RNA in serum by branched DNA-based signal amplification assays.

PubMed

Pawlotsky, J M; Martinot-Peignoux, M; Poveda, J D; Bastie, A; Le Breton, V; Darthuy, F; Rémiré, J; Erlinger, S; Dhumeaux, D; Marcellin, P

1999-05-01

The objective of the study was to compare the clinical sensitivity and specificity of versions 1.0 and 2.0 of the branched DNA (bDNA)-based hepatitis C virus (HCV) RNA quantification assay, and also to compare the values yielded by the two versions according to the HCV genotype. Serum samples from 268 patients tested routinely by a non-quantitative HCV RNA PCR assay (group A) were tested with version 2.0 of the bDNA assay. Samples from 342 HCV PCR-positive patients with chronic hepatitis C eligible for interferon treatment (group B) were tested with both version 1.0 and version 2.0 of the bDNA assay. Version 2.0 had a clinical sensitivity of 92% (95% confidence interval (CI): 87-97%) in group A and 89% (86-92%) in group B. In group B, the gain in sensitivity with bDNA 2.0 was 16% relative to bDNA 1.0 (P < 0.001). The log values of the two assays correlated with samples positive by both assays (r = 0.83, P < 0.0001), but the distribution of values was larger in samples containing HCV genotypes 2 and 3. The mean ratio of assay 2.0/assay 1.0 values was 1.69 +/- 1.44 (range: 0.33-13.43). The mean ratio was close to 1 with samples containing genotype 1 or 4, but ranged from 0.33 to more than 5. The mean ratio was close to 3 with samples containing genotype 2 or 3, and ranged from 0.5 to more than 13. HCV RNA levels were significantly lower in samples containing genotype 4 than in those containing other genotypes. Sera from 200 anti-HCV-negative, HCV RNA PCR-negative blood donors (group C), and from 164 anti-HCV-negative patients with symptoms of chronic liver disease (group D) were used to assess the clinical specificity of bDNA 2.0. In addition, samples with an HCV RNA titer between 0.2 (assay cutoff) and 0.5 MEq/ml from a group of 546 patients tested routinely for HCV RNA load by bDNA 2.0 (group E) were retested by bDNA 2.0 and by qualitative PCR. The specificity of bDNA 2.0 was 100% (98-100%) in group C and 99% (97-100%) in group D. Among the 41 samples from group E, 38 were positive by bDNA 2.0 retesting (36 were PCR-positive) and three were negative by bDNA 2.0 retesting (all were PCR-positive). It is concluded that version 2.0 of the bDNA assay is markedly more sensitive than version 1.0 and has a good specificity. In contrast with version 1.0, version 2.0 is not influenced by the HCV genotype. The relationship between values obtained with assays 1.0 and 2.0 on clinical specimens is not linear, indicating that HCV RNA titers cannot reliably be calculated from the results of version 1.0.

Feasibility and effectiveness of the implementation of a primary prevention programme for type 2 diabetes in routine primary care practice: a phase IV cluster randomised clinical trial

PubMed Central

2012-01-01

Background The objective of this study is to perform an independent evaluation of the feasibility and effectiveness of an educational programme for the primary prevention of type 2 diabetes (DM2) in high risk populations in primary care settings, implanted within the Basque Health Service - Osakidetza. Methods/design This is a prospective phase IV cluster clinical trial conducted under routine conditions in 14 primary health care centres of Osakidetza, randomly assigned to an intervention or control group. We will recruit a total sample of 1089 individuals, aged between 45 and 70 years old, without diabetes but at high risk of developing the condition (Finnish Diabetes Risk Score, FINDRISC ≥ 14) and follow them up for 2 years. Primary health care nursing teams of the intervention centres will implement DE-PLAN, a structured educational intervention program focused on changing healthy lifestyles (diet and physical activity); while the patients in the control centres will receive the usual care for the prevention and treatment of DM2 currently provided in Osakidetza. The effectiveness attributable to the programme will be assessed by comparing the changes observed in patients exposed to the intervention and those in the control group, with respect to the risk of developing DM2 and lifestyle habits. In terms of feasibility, we will assess indicators of population coverage and programme implementation. Discussion The aim of this study is to provide the scientific basis for disseminate the programme to the remaining primary health centres in Osakidetza, as a novel way of addressing prevention of DM2. The study design will enable us to gather information on the effectiveness of the intervention as well as the feasibility of implementing it in routine practice. Trial registration ClinicalTrials.gov NCT01365013 PMID:23158830

Effects of probiotic supplementation over 5 months on routine haematology and clinical chemistry measures in healthy active adults.

PubMed

Cox, A J; West, N P; Horn, P L; Lehtinen, M J; Koerbin, G; Pyne, D B; Lahtinen, S J; Fricker, P A; Cripps, A W

2014-11-01

Use of probiotic-containing foods and probiotic supplements is increasing; however, few studies document safety and tolerability in conjunction with defined clinical end points. This paper reports the effects of 150 days of supplementation with either a single- (Bifidobacterium animalis subsp. lactis Bl-04) or a double-strain (Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bi-07) probiotic on routine haematology and clinical chemistry measures in healthy active adults. Pre- to post-intervention changes in laboratory measures were determined and compared between supplement and placebo groups. Overall there were few differences in routine haematology and clinical chemistry measures between supplement and placebo groups post-intervention. Exceptions included plasma calcium (P=0.03) and urea (P=0.015); however, observed changes were small and within assay-specific laboratory reference ranges. These data provide evidence supporting the use of these probiotic supplements over a period of 5 months in healthy active adults without obvious safety or tolerability issues.

Mycobiome in the Lower Respiratory Tract – A Clinical Perspective

PubMed Central

Krause, Robert; Moissl-Eichinger, Christine; Halwachs, Bettina; Gorkiewicz, Gregor; Berg, Gabriele; Valentin, Thomas; Prattes, Jürgen; Högenauer, Christoph; Zollner-Schwetz, Ines

2017-01-01

Recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. Most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. Recently, also the mycobiome has gained attention. Lower respiratory tract (LRT) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., HIV infection, lung transplantation, and treatment at intensive care units) have been investigated with regard to possible involvement of mycobiome in development or progression of diseases. It has been shown that diversities of mycobiome in the LRT vary in different populations and conditions. It has been proposed that the mycobiome diversity associated with LRT can vary with different stages of diseases. Overall, Candida was the dominant fungal genus in LRT samples. In this review, we summarize the recent findings regarding the human LRT mycobiome from a clinical perspective focussing on characterization of investigated patient groups and healthy controls as well as sampling techniques. From these data, clinical implications for further studies or routine practice are drawn. To obtain clinically relevant answers efforts should be enhanced to collect well characterized and described patient groups as well as healthy individuals for comparative data analysis and to apply thorough sampling techniques. We need to proceed with elucidation of the role of mycobiota in healthy LRT and LRT diseases to hopefully improve patient care. PMID:28119685

Reference Intervals of Common Clinical Chemistry Analytes for Adults in Hong Kong.

PubMed

Lo, Y C; Armbruster, David A

2012-04-01

Defining reference intervals is a major challenge because of the difficulty in recruiting volunteers to participate and testing samples from a significant number of healthy reference individuals. Historical literature citation intervals are often suboptimal because they're be based on obsolete methods and/or only a small number of poorly defined reference samples. Blood donors in Hong Kong gave permission for additional blood to be collected for reference interval testing. The samples were tested for twenty-five routine analytes on the Abbott ARCHITECT clinical chemistry system. Results were analyzed using the Rhoads EP evaluator software program, which is based on the CLSI/IFCC C28-A guideline, and defines the reference interval as the 95% central range. Method specific reference intervals were established for twenty-five common clinical chemistry analytes for a Chinese ethnic population. The intervals were defined for each gender separately and for genders combined. Gender specific or combined gender intervals were adapted as appropriate for each analyte. A large number of healthy, apparently normal blood donors from a local ethnic population were tested to provide current reference intervals for a new clinical chemistry system. Intervals were determined following an accepted international guideline. Laboratories using the same or similar methodologies may adapt these intervals if deemed validated and deemed suitable for their patient population. Laboratories using different methodologies may be able to successfully adapt the intervals for their facilities using the reference interval transference technique based on a method comparison study.

Mycobiome in the Lower Respiratory Tract - A Clinical Perspective.

PubMed

Krause, Robert; Moissl-Eichinger, Christine; Halwachs, Bettina; Gorkiewicz, Gregor; Berg, Gabriele; Valentin, Thomas; Prattes, Jürgen; Högenauer, Christoph; Zollner-Schwetz, Ines

2016-01-01

Recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. Most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. Recently, also the mycobiome has gained attention. Lower respiratory tract (LRT) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., HIV infection, lung transplantation, and treatment at intensive care units) have been investigated with regard to possible involvement of mycobiome in development or progression of diseases. It has been shown that diversities of mycobiome in the LRT vary in different populations and conditions. It has been proposed that the mycobiome diversity associated with LRT can vary with different stages of diseases. Overall, Candida was the dominant fungal genus in LRT samples. In this review, we summarize the recent findings regarding the human LRT mycobiome from a clinical perspective focussing on characterization of investigated patient groups and healthy controls as well as sampling techniques. From these data, clinical implications for further studies or routine practice are drawn. To obtain clinically relevant answers efforts should be enhanced to collect well characterized and described patient groups as well as healthy individuals for comparative data analysis and to apply thorough sampling techniques. We need to proceed with elucidation of the role of mycobiota in healthy LRT and LRT diseases to hopefully improve patient care.

Can we improve partner notification rates through expedited partner therapy in the UK? Findings from an exploratory trial of Accelerated Partner Therapy (APT).

PubMed

Estcourt, Claudia; Sutcliffe, Lorna; Cassell, Jackie; Mercer, Catherine H; Copas, Andrew; James, Laura; Low, Nicola; Horner, Patrick; Clarke, Michael; Symonds, Merle; Roberts, Tracy; Tsourapas, Angelos; Johnson, Anne M

2012-02-01

To develop two new models of expedited partner therapy for the UK, and evaluate them for feasibility, acceptability and preliminary outcome estimates to inform the design of a randomised controlled trial (RCT). Two models of expedited partner therapy (APTHotline and APTPharmacy), known as 'Accelerated Partner Therapy' (APT) were developed. A non-randomised comparative study was conducted of the two APT models and routine partner notification (PN), in which the index patient chose the PN option for his/her partner(s) in two contrasting clinics. The proportion of contactable partners treated when routine PN was chosen was 42/117 (36%) and was significantly higher if either APT option was chosen: APTHotline 80/135 (59%), p=0.003; APTPharmacy 29/44 (66%) p=0.001. However, partner treatment was often achieved through other routes. Although 40-60% of partners in APT groups returned urine samples for sexually transmitted infection (STI) testing, almost none accessed HIV and syphilis testing. APT options appear to facilitate faster treatment of sex partners than routine PN. Preferences and recruitment rates varied between sites, related to staff satisfaction with existing routine PN; approach to consent; and possibly, characteristics of local populations. Both methods of APT were feasible and acceptable to many patients and led to higher rates of partner treatment than routine PN. Preferences and recruitment rates varied greatly between settings, suggesting that organisational and cultural factors may have an important impact on the feasibility of an RCT and on outcomes. Mindful of these factors, it is proposed that APT should now be evaluated in a cluster RCT.

Dose Adjustment for Normal Eating (DAFNE) in routine clinical practice: who benefits?

PubMed

Keen, A J A; Duncan, E; McKillop-Smith, A; Evans, N D; Gold, A E

2012-05-01

To explore the effectiveness of Dose Adjustment for Normal Eating in routine clinical practice in the UK. Participants were 124 adults with Type 1 diabetes who had completed a Dose Adjustment for Normal Eating course. Data were collected before the course and again 1 year later on a variety of biological, psychological and social measures. There were a range of significant benefits consistent with Dose Adjustment for Normal Eating aims, including: better control among those with baseline HbA(1c) ≥ 81 mmol/mol (9.6%) (z = -2.8, P = 0.004); reduced number of participants reporting severe hypoglycaemia (χ² = 4.27, P = 0.039); total eradication of diabetic ketoacidosis (χ² = 4.17, P = 0.041) and lower diabetes-related distress (z = -4.5, P < 0.001). The most deprived of the clinic population were significantly under-represented (χ² = 17.8, P = 0.001) and the levels of clinical depression were unusually low. These results indicate that Dose Adjustment for Normal Eating delivered in routine clinical practice is associated with a range of benefits and that certain clinical and psychosocial characteristics are associated with better outcomes. © 2011 The Authors. Diabetic Medicine © 2011 Diabetes UK.

Antimicrobial-resistant Klebsiella species isolated from free-range chicken samples in an informal settlement.

PubMed

Fielding, Burtram C; Mnabisa, Amanda; Gouws, Pieter A; Morris, Thureyah

2012-02-29

Sub-therapeutic doses of antimicrobial agents are administered routinely to poultry to aid growth and to prevent disease, with prolonged exposure often resulting in bacterial resistance. Crossover of antibiotic resistant bacteria from poultry to humans poses a risk to human health. In this study, 17 chicken samples collected from a vendor operating in an informal settlement in the Cape Town Metropolitan area, South Africa were screened for antimicrobial-resistant Gram-negative bacilli using the Kirby Bauer disk diffusion assay. IN TOTAL, SIX ANTIBIOTICS WERE SCREENED: ampicillin, ciprofloxacin, gentamicin, nalidixic acid, tetracycline and trimethoprim. Surprisingly, Klebsiella ozaenae was identified in 96 and K. rhinoscleromatis in 6 (n=102) of the samples tested. Interestingly, ∼40% of the isolated Klebsiella spp. showed multiple resistance to at least three of the six antibiotics tested. Klebsiella ozaenae and K. rhinoscleromatis cause clinical chronic rhinitis and are almost exclusively associated with people living in areas of poor hygiene.

Comparison of the Roche Cobas® 4800 HPV assay to Roche Amplicor for detection of high-risk human papillomavirus.

PubMed

Phillips, S; Cornall, A M; Machalek, D A; Garland, S M; Bateson, D; Garefalakis, M; Tabrizi, S N

2016-08-01

Roche Amplicor HPV (AMP) had previously been used for detection of high-risk human papillomavirus (HR-HPV) in epidemiological and clinical studies. As this assay is no longer available, we compared its performance using PreservCyt samples from women aged of 18-24 years attending for routine cervical cytology screening to Roche Cobas® 4800 (Cobas) to determine if subsequent studies could continue using the Cobas assay. Overall 507 samples were tested on Cobas and compared to previous AMP results, with discrepant samples tested on Roche Linear Array. Overall, agreement between the Cobas and AMP for the presence of HR HPV types was very high (κ = 0.81) (95 % CI: 0.76 - 0.87) with percentage agreement of 91.57 %. Cobas is comparable to AMP for the detection of HR-HPV types in a community recruited cohort of healthy women.

Impact of insomnia on self-perceived health in the elderly.

PubMed

Silva, Janiciene; Truzzi, Annibal; Schaustz, Fayanne; Barros, Roberta; Santos, Marisa; Laks, Jerson

2017-05-01

To investigate the association between self-perceived health, and sociodemographic and clinical factors in a sample of elderly outpatients in Rio de Janeiro. A sample of 345 elderly patients was assessed with an anamnesis, Lawton and Brody's Scale, Katz Index, Geriatric Depression Scale, Timed Up and Go Test, and Study of Osteoporotic Fracture Index. Logistic regression analyses were performed to investigate the predictors of self-perceived health. Risk of falls, frailty, functional performance on the Instrumental Activities of Daily Living, insomnia, and familial support were related to self-perceived health. Insomnia was the variable that strongly influenced self-perceived health (OR = 0.47, CI 95%: 0.28-0.80, p = 0.01) in our sample. The investigation of insomnia in the elderly should be routinely performed in primary care, because of the negative impact it imposes on the health of this population.

[Lactic acidosis in the postictal state].

PubMed

van Rooij, Femke J M; Admiraal-van de Pas, Yvonne

2015-01-01

Epilepsy is a neurological disorder with an annual incidence in the Netherlands of 30 per 100,000 people. We present two cases of a patient admitted to the emergency department upon experiencing a generalized seizure. In each case, severe metabolic lactic acidosis was identified through routine laboratory diagnostics. Based on their clinical presentation, we had no reasons to suspect another cause of this severe acidosis apart from the seizure. We repeated arterial blood sample one to two hours later and found that both pH and lactate were normalized. Severe lactic acidosis may occur in patients who experience seizures but otherwise do not require treatment. Taking an arterial blood sample from these patients in the emergency setting will be of limited value, because in most patients hyperlactatemia in the postictal state is self-limiting. In some patients, however, a persistent hyperlactatemia may indicate a serious underlying pathology. It is therefore advisable to repeat an arterial blood sample a few hours later.

Prevalence and Correlates of Suicidal Ideation in a Treatment-Seeking Sample of Violent Loss Survivors.

PubMed

Williams, Joah L; Eddinger, Jasmine R; Rynearson, Edward K; Rheingold, Alyssa A

2018-05-31

Family members grieving the traumatic death of a loved one, as in cases of homicide, suicide, and fatal accidents, are at risk for a number of trauma and bereavement-related mental health problems, including posttraumatic stress disorder (PTSD), depression, prolonged grief disorder, and suicidal ideation (SI). The purpose of this study was to examine the prevalence and correlates of SI among a sample of 130 treatment-seeking traumatically bereaved family members. Adults seeking treatment at two clinics on the US West Coast were assessed for SI, clinical outcomes, and death-related characteristics. Overall, 42% of traumatically bereaved family members endorsed some form of active or passive SI on the Beck Depression Inventory suicide item. The type of loss experienced (i.e., homicide, suicide, fatal accident) was not associated with SI. Although individuals with SI reported more severe symptoms across all clinical outcomes, avoidance (OR = 2.22) and depression (OR = 1.16) were uniquely associated with SI even after adjusting for PTSD-related intrusions and hyperarousal. Results should be interpreted in light of limitations associated with cross-sectional data and a single-item outcome of SI. Routine screening for SI should be standard practice for providers working with traumatically bereaved families.

High-resolution melting analysis of gyrA codon 84 and grlA codon 80 mutations conferring resistance to fluoroquinolones in Staphylococcus pseudintermedius isolates from canine clinical samples.

PubMed

Loiacono, Monica; Martino, Piera A; Albonico, Francesca; Dell'Orco, Francesca; Ferretti, Manuela; Zanzani, Sergio; Mortarino, Michele

2017-09-01

Staphylococcus pseudintermedius is an opportunistic pathogen of dogs and cats. A high-resolution melting analysis (HRMA) protocol was designed and tested on 42 clinical isolates with known fluoroquinolone (FQ) susceptibility and gyrA codon 84 and grlA codon 80 mutation status. The HRMA approach was able to discriminate between FQ-sensitive and FQ-resistant strains and confirmed previous reports that the main mutation site associated with FQ resistance in S. pseudintermedius is located at position 251 (Ser84Leu) of gyrA. Routine, HRMA-based FQ susceptibility profiles may be a valuable tool to guide therapy. The FQ resistance-predictive power of the assay should be tested in a significantly larger number of isolates.

[Post-mortem microbiology analysis].

PubMed

Fernández-Rodríguez, Amparo; Alberola, Juan; Cohen, Marta Cecilia

2013-12-01

Post-mortem microbiology is useful in both clinical and forensic autopsies, and allows a suspected infection to be confirmed. Indeed, it is routinely applied to donor studies in the clinical setting, as well as in sudden and unexpected death in the forensic field. Implementation of specific sampling techniques in autopsy can minimize the possibility of contamination, making interpretation of the results easier. Specific interpretation criteria for post-mortem cultures, the use of molecular diagnosis, and its fusion with molecular biology and histopathology have led to post-mortem microbiology playing a major role in autopsy. Multidisciplinary work involving microbiologists, pathologists, and forensic physicians will help to improve the achievements of post-mortem microbiology, prevent infectious diseases, and contribute to a healthier population. Crown Copyright © 2012. Published by Elsevier Espana. All rights reserved.

Blood sample collection and patient identification demand improvement: a questionnaire study of preanalytical practices in hospital wards and laboratories.

PubMed

Wallin, Olof; Söderberg, Johan; Van Guelpen, Bethany; Stenlund, Hans; Grankvist, Kjell; Brulin, Christine

2010-09-01

Scand J Caring Sci; 2010; 24; 581-591 
 Blood sample collection and patient identification demand improvement: a questionnaire study of preanalytical practices in hospital wards and laboratories   Most errors in venous blood testing result from human mistakes occurring before the sample reach the laboratory.   To survey venous blood sampling (VBS) practices in hospital wards and to compare practices with hospital laboratories.   Staff in two hospitals (all wards) and two hospital laboratories (314 respondents, response rate 94%), completed a questionnaire addressing issues relevant to the collection of venous blood samples for clinical chemistry testing.   The findings suggest that instructions for patient identification and the collection of venous blood samples were not always followed. For example, 79% of the respondents reported the undesirable practice (UDP) of not always using wristbands for patient identification. Similarly, 87% of the respondents noted the UDP of removing venous stasis after the sampling is finished. Compared with the ward staff, a significantly higher proportion of the laboratory staff reported desirable practices regarding the collection of venous blood samples. Neither education nor the existence of established sampling routines was clearly associated with VBS practices among the ward staff.   The results of this study, the first of its kind, suggest that a clinically important risk of error is associated with VBS in the surveyed wards. Most important is the risk of misidentification of patients. Quality improvement of blood sample collection is clearly needed, particularly in hospital wards. © 2009 The Authors. Journal compilation © 2009 Nordic College of Caring Science.

LC-MS-sMRM Method Development and Validation of Different Classes of Pain Panel Drugs and Analysis of Clinical Urine Samples.

PubMed

Athar Masood, M; Veenstra, Timothy D

2017-08-26

Urine Drug Testing (UDT) is an important analytical/bio-analytical technique that has inevitably become an integral and vital part of a testing program for diagnostic purposes. This manuscript presents a tailor-made LC-MS/MS quantitative assay method development and validation for a custom group of 33 pain panel drugs and their metabolites belonging to different classes (opiates, opioids, benzodiazepines, illicit, amphetamines, etc.) that are prescribed in pain management and depressant therapies. The LC-MS/MS method incorporates two experiments to enhance the sensitivity of the assay and has a run time of about 7 min. with no prior purification of the samples required and a flow rate of 0.7 mL/min. The method also includes the second stage metabolites for some drugs that belong to different classes but have first stage similar metabolic pathways that will enable to correctly identify the right drug or to flag the drug that might be due to specimen tampering. Some real case examples and difficulties in peak picking were provided with some of the analytes in subject samples. Finally, the method was deliberated with some randomly selected de-identified clinical subject samples, and the data evaluated from "direct dilute and shoot analysis" and after "glucuronide hydrolysis" were compared. This method is now used to run routinely more than 100 clinical subjects samples on a daily basis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Sodium citrate blood contamination by K2 -ethylenediaminetetraacetic acid (EDTA): impact on routine coagulation testing.

PubMed

Lima-Oliveira, G; Salvagno, G L; Danese, E; Favaloro, E J; Guidi, G C; Lippi, G

2015-06-01

The potential cross-contamination of additives between primary blood tubes is a well-known problem during sample collection. The aim of this study was to assess the impact of citrated blood contamination with different amounts of dipotassium ethylenediaminetetraacetic (K2 EDTA blood) on activated partial thromboplastin time (APTT), prothrombin time (PT), and fibrinogen. Blood was collected from 15 ostensibly healthy volunteers into four 0.109 m citrate blood tubes followed by one K2 EDTA blood tube. The citrate tubes of each subject were pooled and divided in five aliquots. The whole blood of the K2 EDTA tube was then added in scalar amounts to autologous citrated blood aliquots, to obtain K2 EDTA contamination ranging from 0% to 43%, and thus mimic potential pre-analytical contamination. A statistically and clinically significant prolongation was observed for both APTT and PT between 29% and 43% K2 EDTA contamination, whereas the decrease of fibrinogen values became statistically and clinically significant at 43% K2 EDTA contamination. The results of this investigation show that contamination of citrated blood with as much as 29% of K2 EDTA blood generates a significant bias in results of routine clotting assays. This has serious implications for patient safety and management. © 2014 John Wiley & Sons Ltd.

Awareness and implementation of the 2000 United States public health service tobacco dependence treatment guideline in a public hospital system.

PubMed

Moody-Thomas, Sarah; Horswell, Ronald; Celestin, Michael D; Dellinger, Amy B; Kaiser, Michael; Butler, Michael

2011-04-01

The 2000 United States Public Health Service (USPHS) clinical practice guideline, "Treating Tobacco Use and Dependence," recommends systems interventions to integrate the treatment of tobacco into routine health care. The Tobacco Control Initiative employed a systems approach to integrate evidence-based treatment for tobacco use into patient care practices in Louisiana's safety net health care system. The purpose of this study was to assess changes in awareness and implementation of the USPHS clinical practice guideline. Surveys were administered to a purposive sample of hospital personnel from key departments in the Louisiana State University system of public hospitals in 2003 (n = 24) and 2007 (n = 44). Perceptions of implementation success improved for 50 of 59 distinct survey items. Rasch scaling was used to assess overall (scaled) change and showed substantial improvement from 2003 to 2007 (P < 0.001). Survey items also were grouped into 6 logical key concept sets. Improvement occurred in perceptions for all 6 key concepts; however, not uniformly. Results of the 2003 and 2007 surveys illustrate the potential effectiveness of using a systems approach to integrate the assessment and treatment of tobacco use into routine care practices in a public health care delivery system that serves medically vulnerable populations.

Contraception services for incarcerated women: a national survey of correctional health providers.

PubMed

Sufrin, Carolyn B; Creinin, Mitchell D; Chang, Judy C

2009-12-01

Incarcerated women have had limited access to health care prior to their arrest. Although their incarceration presents an opportunity to provide them with health care, their reproductive health needs have been overlooked. We performed a cross-sectional study of a nationally representative sample of 950 correctional health providers who are members of the Academy of Correctional Health Providers. A total of 405 surveys (43%) were returned, and 286 (30%) were eligible for analysis. Most ineligible surveys were from clinicians at male-only facilities. Of eligible respondents, 70% reported some degree of contraception counseling for women at their facilities. Only 11% provided routine counseling prior to release. Seventy percent said that their institution had no formal policy on contraception. Thirty-eight percent of clinicians provided birth control methods at their facilities. Although the most frequently counseled and prescribed method was oral contraceptive pills, only 50% of providers rated their oral contraceptive counseling ability as good or very good. Contraception counseling was associated with working at a juvenile facility, and with screening for sexually transmitted infections. Contraception does not appear to be integrated into the routine delivery of clinical services to incarcerated women. Because the correctional health care system can provide important clinical and public health interventions to traditionally marginalized populations, services for incarcerated women should include access to contraception.

Qualitative Assessment of the Integration of HIV Services With Infant Routine Immunization Visits in Tanzania

PubMed Central

Wallace, Aaron; Kimambo, Sajida; Dafrossa, Lyimo; Rusibamayila, Neema; Rwebembera, Anath; Songoro, Juma; Arthur, Gilly; Luman, Elizabeth; Finkbeiner, Thomas; Goodson, James L.

2015-01-01

Background In 2009, a project was implemented in 8 primary health clinics throughout Tanzania to explore the feasibility of integrating pediatric HIV prevention services with routine infant immunization visits. Methods We conducted interviews with 64 conveniently sampled mothers of infants who had received integrated HIV and immunization services and 16 providers who delivered the integrated services to qualitatively identify benefits and challenges of the intervention midway through project implementation. Findings Mothers’ perceived benefits of the integrated services included time savings, opportunity to learn their child's HIV status and receive HIV treatment, if necessary. Providers’ perceived benefits included reaching mothers who usually would not come for only HIV testing. Mothers and providers reported similar challenges, including mothers’ fear of HIV testing, poor spousal support, perceived mandatory HIV testing, poor patient flow affecting confidentiality of service delivery, heavier provider workloads, and community stigma against HIV-infected persons; the latter a more frequent theme in rural compared with urban locations. Interpretation Future scale-up should ensure privacy of these integrated services received at clinics and community outreach to address stigma and perceived mandatory testing. Increasing human resources for health to address higher workloads and longer waiting times for proper patient flow is necessary in the long term. PMID:24326602

[Health services research the example of atopic dermatitis].

PubMed

Schmitt, J

2011-03-01

Within the past years, health services research projects have analyzed critically the management of atopic eczema (AE) in routine care, quantified the utility of controlling severe AE, and introduced an international standardization of core outcome measures for AE. With a prevalence of 16%, AE is the most frequent chronic condition at all among children and adolescents seeking medical care. Despite lower prevalence in adults, about 60% of patients with AE in routine care are adults. There is a clinically relevant comorbidity of AE and psychiatric conditions. Independent of patient's age and physician's medical discipline topical corticosteroids dominate outpatient treatment of AE. However, there is considerable heterogeneity in the management of AE between treating physicians. Despite a lack of clinical trials, systemic corticosteroids are most frequently prescribed for severe AE. In contrast, cyclosporine only plays a minor role in routine care of severe AE although its efficacy is well-documented in trials. This observation stimulated a head-to-head trial that indicated superiority of cyclosporine over prednisolone for severe adult AE. The control of severe AE has high priority from the perspective of the general population and from the patients' perspective. Competence of the treating physician, disease severity and patient's competence to adjust treatment to disease activity are the main determinants of patient satisfaction. Aiming for a better comparability of clinical trials and better translation of trial evidence into clinical practice, we conducted a Delphi exercise including clinical experts from 11 countries, editors of international dermatological journals, regulatory agencies, and patient representatives. The preliminary core set of outcome domains for eczema trials as defined by the panel included symptoms, physician-assessed clinical signs, and a measurement for long-term control of flares. Symptoms such as itching should be regularly assessed in clinical practice. The presented studies indicate that health services research not only describes and critically analyzes the effectiveness of routine clinical care, but is also translational research in that it may stimulate clinical trials and generate new, clinically relevant hypotheses for experimental studies.

Prevalence, aetiology and antibiotic sensitivity profile of asymptomatic bacteriuria isolates from pregnant women in selected antenatal clinic from Nairobi, Kenya.

PubMed

Ayoyi, Adelaide Ogutu; Kikuvi, Gideon; Bii, Christine; Kariuki, Samuel

2017-01-01

Asymptomatic bacteriuria (ASB) is the presence of bacteria in urine without apparent symptoms of urinary tract infections. The importance of asymptomatic bacteriuria lies in the insight it provides into symptomatic infections. To determine prevalence, bacterial isolates and Antibiotic Sensitivity Profile of asymptomatic bacterial urinary tract infection in pregnant women in selected clinics in Nairobi. This was a cross-sectional study involving women attending antenatal clinic at selected clinics of Nairobi County. The women who met the inclusion criteria were included in the study. The midstream urine samples of these women were subjected to microscopy, culture and sensitivity. A total of 1020 of women on their first antenatal clinic visit participated in the study; 219 of them had ASB, giving a prevalence of 21.5 % at 95% confidence level. Escherichia coli were the common organism isolated at 38.8%. The majority of the organisms were sensitive to imipenem and gentamycin. There is a high prevalence of ASB among pregnant women included in the study from the Nairobi county clinics. Therefore, routine ASB screening of pregnant women is recommended among the women attending antennal clinics in Nairobi county clinics.

Prevalence, aetiology and antibiotic sensitivity profile of asymptomatic bacteriuria isolates from pregnant women in selected antenatal clinic from Nairobi, Kenya

PubMed Central

Ayoyi, Adelaide Ogutu; Kikuvi, Gideon; Bii, Christine; Kariuki, Samuel

2017-01-01

Introduction Asymptomatic bacteriuria (ASB) is the presence of bacteria in urine without apparent symptoms of urinary tract infections. The importance of asymptomatic bacteriuria lies in the insight it provides into symptomatic infections. To determine prevalence, bacterial isolates and Antibiotic Sensitivity Profile of asymptomatic bacterial urinary tract infection in pregnant women in selected clinics in Nairobi. Methods This was a cross-sectional study involving women attending antenatal clinic at selected clinics of Nairobi County. The women who met the inclusion criteria were included in the study. The midstream urine samples of these women were subjected to microscopy, culture and sensitivity. Results A total of 1020 of women on their first antenatal clinic visit participated in the study; 219 of them had ASB, giving a prevalence of 21.5 % at 95% confidence level. Escherichia coli were the common organism isolated at 38.8%. The majority of the organisms were sensitive to imipenem and gentamycin. Conclusion There is a high prevalence of ASB among pregnant women included in the study from the Nairobi county clinics. Therefore, routine ASB screening of pregnant women is recommended among the women attending antennal clinics in Nairobi county clinics. PMID:28451019

Comparison of techniques for detecting antigens of Giardia lamblia and Cryptosporidium parvum in faeces.

PubMed Central

Tee, G H; Moody, A H; Cooke, A H; Chiodini, P L

1993-01-01

AIM--To compare the use of commercial monoclonal antibody test systems--the Giardia CEL IF test and the Crypto CEL IF test--for the detection of Giardia lamblia and Cryptosporidium parvum antigens in faeces with conventional techniques. METHODS--Sensitivity and specificity were evaluated using preparations of cysts of G lamblia and purified oocysts of C parvum. Evaluation of 59 random faecal samples passing through the Department of Clinical Parasitology, Hospital for Tropical Diseases, London, was carried out for both organisms. RESULTS--The fluorescence staining techniques proved more sensitive than other tests routinely used for diagnosis. PMID:8331181

Pharmacogenetic testing, informed consent and the problem of secondary information.

PubMed

Netzer, Christian; Biller-Andorno, Nikola

2004-08-01

Numerous benefits for patients have been predicted if prescribing decisions were routinely accompanied by pharmacogenetic testing. So far, little attention has been paid to the possibility that the routine application of this new technology could result in considerable harm to patients. This article emphasises that pharmacogenetic testing shares both the opportunities and the pitfalls with 'conventional' disease-genetic testing. It demonstrates that performing pharmacogenetic tests as well as interpreting the results are extraordinarily complex issues requiring a high level of expertise. It further argues that pharmacogenetic testing can have a huge impact on clinical decisions and may influence the therapeutic strategy as well as the clinical monitoring of a patient. This view challenges the predominant paradigm that pharmacogenetic testing will predict patients' responses to medicines, but that it will not provide any other significant disease-specific predictive information about the patient or family members. The article also questions published proposals to reduce the consent procedure for pharmacogenetic testing to a simple statement that the physician wishes to test a sample of the patient's DNA to see if a drug will be safe or whether it will work, and presents an alternative model that is better suited to protect patient's interests and to obtain meaningful informed consent. The paper concludes by outlining conditions for the application of pharmacogenetic testing in clinical practice in a way that can make full use of its potential benefits while minimising possible harm to patients and their families.

[The effect of donepezil in comparison with conventional treatment on cognitive functioning and the performance of the patient in a prospective cohort of patients with Alzheimer's disease treated in routine clinical practice in Spain].

PubMed

López-Pousa, S; Bermejo-Pareja, F; Frank, A; Hernández, F; León, T; Rejas-Gutiérrez, J

2010-11-16

Our aim was to perform a secondary analysis of a 12-month-long, non-blind, multi-centre prospective cost-of-illness study. The analysis assessed the effect of donepezil on cognitive functioning and the performance of patients with possible or probable Alzheimer's disease, compared to that of other drugs for dementia. A sample of 700 patients took part in the study (76.8 ± 6.6 years of age, 67.3% females): 600 (31.4% drug-naive) received donepezil and 100 (9% drug-naive) were given other drugs for dementia. The mean variations corrected by the baseline values and the centre of the total scores on the Folstein minimental test, the clinical dementia rating and Blessed dementia rating scales at 12 months were significantly lower in patients treated with donepezil: -1.23 ± 3.41 versus -2.26 ± 3.07 (p = 0.006), 0.20 ± 0.68 versus 0.39 ± 1.03 (p = 0.014) and 1.28 ± 3.31 versus 2.04 ± 2.84 (p = 0.027), respectively. This secondary analysis shows that the deterioration in the cognitive functioning and performance of patients with the passage of time is slower with donepezil than with other drugs for dementia in routine medical practice. Since these results were observed in a post hoc analysis, formal prospective clinical trials should be conducted to confirm these findings.

Internal quality control: best practice.

PubMed

Kinns, Helen; Pitkin, Sarah; Housley, David; Freedman, Danielle B

2013-12-01

There is a wide variation in laboratory practice with regard to implementation and review of internal quality control (IQC). A poor approach can lead to a spectrum of scenarios from validation of incorrect patient results to over investigation of falsely rejected analytical runs. This article will provide a practical approach for the routine clinical biochemistry laboratory to introduce an efficient quality control system that will optimise error detection and reduce the rate of false rejection. Each stage of the IQC system is considered, from selection of IQC material to selection of IQC rules, and finally the appropriate action to follow when a rejection signal has been obtained. The main objective of IQC is to ensure day-to-day consistency of an analytical process and thus help to determine whether patient results are reliable enough to be released. The required quality and assay performance varies between analytes as does the definition of a clinically significant error. Unfortunately many laboratories currently decide what is clinically significant at the troubleshooting stage. Assay-specific IQC systems will reduce the number of inappropriate sample-run rejections compared with the blanket use of one IQC rule. In practice, only three or four different IQC rules are required for the whole of the routine biochemistry repertoire as assays are assigned into groups based on performance. The tools to categorise performance and assign IQC rules based on that performance are presented. Although significant investment of time and education is required prior to implementation, laboratories have shown that such systems achieve considerable reductions in cost and labour.

Temporal trends in early clinical outcomes and health care resource utilization for liver transplantation in the United States.

PubMed

Scarborough, John E; Pietrobon, Ricardo; Marroquin, Carlos E; Tuttle-Newhall, Janet E; Kuo, Paul C; Collins, Bradley H; Desai, Dev M; Pappas, Theodore N

2007-01-01

Procedures such as liver transplantation, which entail large costs while benefiting only a small percentage of the population, are being increasingly scrutinized by third-party payors. The purpose of our study was to conduct a longitudinal analysis of the early clinical outcomes and health care resource utilization for liver transplantation in the United States. The Nationwide Inpatient Sample database was used to conduct a longitudinal analysis of the clinical outcome and resource utilization data for liver transplantation procedures in adult recipients performed in the United States over three time periods (Period I: 1988-1993; Period II: 1994-1998: Period III: 1999-2003). Compared to Period I, adult liver transplant recipients were more likely to be male, older, and non-White in Period III. Recipients were more likely to have at least one major comorbidity preoperatively than in Period I. The in-hospital mortality rate after liver transplantation decreased significantly from Period I to Period III, but the major intraoperative and postoperative complication rates increased over the same time period. Mean length of hospital stay decreased over the 15-year period, but the percentage of patients with a non-routine discharge status increased. Our findings indicate that the rate of postoperative complications and non-routine discharges after liver transplantation is increasing. However, these negative changes in the cost-outcomes relationship for liver transplantation are balanced by improving postoperative survival rates and reductions in the length of hospital stay.

Assessing the Risk Factors of Cyber and Mobile Phone Bullying Victimization in a Nationally Representative Sample of Singapore Youth.

PubMed

Holt, Thomas J; Fitzgerald, Sarah; Bossler, Adam M; Chee, Grace; Ng, Esther

2016-04-01

This study utilized routine activity theory to examine the relationships between online behaviors, target suitability, and cyber and mobile phone-based bullying victimization in a nationally representative sample of youth from nine schools across Singapore. Key measures in all three categories-access to technology, online routine behaviors, and target suitability-were significant predictors of both forms of bullying victimization. In particular, females and victims of physical bullying were more likely to experience both forms of victimization. Access to technology and online routine behaviors predicted cyber and mobile phone-based bullying victimization differently. These findings demonstrate that routine activity theory is a viable framework to understand online bullying in non-Western nations, consistent with the existing literature on Western nations. © The Author(s) 2014.

Measuring routine nursing service efficiency: a comparison of cost per patient day and data envelopment analysis models.

PubMed Central

Nunamaker, T R

1983-01-01

This article provides an illustrative application of Data Envelopment Analysis (DEA) methodology to the measurement of routine nursing service efficiency at a group of Wisconsin hospitals. The DEA efficiency ratings and cost savings estimates are then compared to those resulting from application of Medicare's routine cost limitation to the sample data. DEA is also used to determine if any changes in the potential for efficient operations occurred during the 1978-1979 period. Empirical results were representative of the fundamental differences existing between the DEA and cost per patient day approaches. No evidence was found to support the notion that the overall potential for efficient delivery of routine services by the sample institutions was greater in one year than another. PMID:6874357

Adoption of routine telemedicine in Norway: the current picture

PubMed Central

Zanaboni, Paolo; Knarvik, Undine; Wootton, Richard

2014-01-01

Background Telemedicine appears to be ready for wider adoption. Although existing research evidence is useful, the adoption of routine telemedicine in healthcare systems has been slow. Objective We conducted a study to explore the current use of routine telemedicine in Norway, at national, regional, and local levels, to provide objective and up-to-date information and to estimate the potential for wider adoption of telemedicine. Design A top-down approach was used to collect official data on the national use of telemedicine from the Norwegian Patient Register. A bottom-up approach was used to collect complementary information on the routine use of telemedicine through a survey conducted at the five largest publicly funded hospitals. Results Results show that routine telemedicine has been adopted in all health regions in Norway and in 68% of hospitals. Despite being widely adopted, the current level of use of telemedicine is low compared to the number of face-to-face visits. Examples of routine telemedicine can be found in several clinical specialties. Most services connect different hospitals in secondary care, and they are mostly delivered as teleconsultations via videoconference. Conclusions Routine telemedicine in Norway has been widely adopted, probably for geographical reasons, as in other settings. However, the level of use of telemedicine in Norway is rather low, and it has significant potential for further development as an alternative to face-to-face outpatient visits. This study is a first attempt to map routine telemedicine at regional, institutional, and clinical levels, and it provides useful information to understand the adoption of telemedicine in routine healthcare and to measure change in future updates. PMID:24433942

Clinical practice of analysis of anti-drug antibodies against interferon beta and natalizumab in multiple sclerosis patients in Europe: A descriptive study of test results

PubMed Central

Auer, Michael; Ryner, Malin; Hässler, Signe; Bachelet, Delphine; Mbogning, Cyprien; Warnke, Clemens; Buck, Dorothea; Hyldgaard Jensen, Poul Erik; Sievers, Claudia; Ingenhoven, Kathleen; Fissolo, Nicolas; Lindberg, Raija; Grummel, Verena; Donnellan, Naoimh; Comabella, Manuel; Montalban, Xavier; Kieseier, Bernd; Soelberg Sørensen, Per; Hartung, Hans-Peter; Derfuss, Tobias; Lawton, Andy; Sikkema, Dan; Pallardy, Marc; Hemmer, Bernhard; Deisenhammer, Florian; Broët, Philippe; Dönnes, Pierre; Davidson, Julie; Fogdell-Hahn, Anna

2017-01-01

Antibodies against biopharmaceuticals (anti-drug antibodies, ADA) have been a well-integrated part of the clinical care of multiple sclerosis (MS) in several European countries. ADA data generated in Europe during the more than 10 years of ADA monitoring in MS patients treated with interferon beta (IFNβ) and natalizumab have been pooled and characterized through collaboration within a European consortium. The aim of this study was to report on the clinical practice of ADA testing in Europe, considering the number of ADA tests performed and type of ADA assays used, and to determine the frequency of ADA testing against the different drug preparations in different countries. A common database platform (tranSMART) for querying, analyzing and storing retrospective data of MS cohorts was set up to harmonize the data and compare results of ADA tests between different countries. Retrospective data from six countries (Sweden, Austria, Spain, Switzerland, Germany and Denmark) on 20,695 patients and on 42,555 samples were loaded into tranSMART including data points of age, gender, treatment, samples, and ADA results. The previously observed immunogenic difference among the four IFNβ preparations was confirmed in this large dataset. Decreased usage of the more immunogenic preparations IFNβ-1a subcutaneous (s.c.) and IFNβ-1b s.c. in favor of the least immunogenic preparation IFNβ-1a intramuscular (i.m.) was observed. The median time from treatment start to first ADA test correlated with time to first positive test. Shorter times were observed for IFNβ-1b-Extavia s.c. (0.99 and 0.94 years) and natalizumab (0.25 and 0.23 years), which were introduced on the market when ADA testing was already available, as compared to IFNβ-1a i.m. (1.41 and 2.27 years), IFNβ-1b-Betaferon s.c. (2.51 and 1.96 years) and IFNβ-1a s.c. (2.11 and 2.09 years) which were available years before routine testing began. A higher rate of anti-IFNβ ADA was observed in test samples taken from older patients. Testing for ADA varies between different European countries and is highly dependent on the policy within each country. For drugs where routine monitoring of ADA is not in place, there is a risk that some patients remain on treatment for several years despite ADA positivity. For drugs where a strategy of ADA testing is introduced with the release of the drug, there is a reduced risk of having ADA positive patients and thus of less efficient treatment. This indicates that potential savings in health cost might be achieved by routine analysis of ADA. PMID:28170401

Clinical practice of analysis of anti-drug antibodies against interferon beta and natalizumab in multiple sclerosis patients in Europe: A descriptive study of test results.

PubMed

Link, Jenny; Ramanujam, Ryan; Auer, Michael; Ryner, Malin; Hässler, Signe; Bachelet, Delphine; Mbogning, Cyprien; Warnke, Clemens; Buck, Dorothea; Hyldgaard Jensen, Poul Erik; Sievers, Claudia; Ingenhoven, Kathleen; Fissolo, Nicolas; Lindberg, Raija; Grummel, Verena; Donnellan, Naoimh; Comabella, Manuel; Montalban, Xavier; Kieseier, Bernd; Soelberg Sørensen, Per; Hartung, Hans-Peter; Derfuss, Tobias; Lawton, Andy; Sikkema, Dan; Pallardy, Marc; Hemmer, Bernhard; Deisenhammer, Florian; Broët, Philippe; Dönnes, Pierre; Davidson, Julie; Fogdell-Hahn, Anna

2017-01-01

Antibodies against biopharmaceuticals (anti-drug antibodies, ADA) have been a well-integrated part of the clinical care of multiple sclerosis (MS) in several European countries. ADA data generated in Europe during the more than 10 years of ADA monitoring in MS patients treated with interferon beta (IFNβ) and natalizumab have been pooled and characterized through collaboration within a European consortium. The aim of this study was to report on the clinical practice of ADA testing in Europe, considering the number of ADA tests performed and type of ADA assays used, and to determine the frequency of ADA testing against the different drug preparations in different countries. A common database platform (tranSMART) for querying, analyzing and storing retrospective data of MS cohorts was set up to harmonize the data and compare results of ADA tests between different countries. Retrospective data from six countries (Sweden, Austria, Spain, Switzerland, Germany and Denmark) on 20,695 patients and on 42,555 samples were loaded into tranSMART including data points of age, gender, treatment, samples, and ADA results. The previously observed immunogenic difference among the four IFNβ preparations was confirmed in this large dataset. Decreased usage of the more immunogenic preparations IFNβ-1a subcutaneous (s.c.) and IFNβ-1b s.c. in favor of the least immunogenic preparation IFNβ-1a intramuscular (i.m.) was observed. The median time from treatment start to first ADA test correlated with time to first positive test. Shorter times were observed for IFNβ-1b-Extavia s.c. (0.99 and 0.94 years) and natalizumab (0.25 and 0.23 years), which were introduced on the market when ADA testing was already available, as compared to IFNβ-1a i.m. (1.41 and 2.27 years), IFNβ-1b-Betaferon s.c. (2.51 and 1.96 years) and IFNβ-1a s.c. (2.11 and 2.09 years) which were available years before routine testing began. A higher rate of anti-IFNβ ADA was observed in test samples taken from older patients. Testing for ADA varies between different European countries and is highly dependent on the policy within each country. For drugs where routine monitoring of ADA is not in place, there is a risk that some patients remain on treatment for several years despite ADA positivity. For drugs where a strategy of ADA testing is introduced with the release of the drug, there is a reduced risk of having ADA positive patients and thus of less efficient treatment. This indicates that potential savings in health cost might be achieved by routine analysis of ADA.

Norovirus GII.Pe Genotype: Tracking a Foodborne Outbreak on a Cruise Ship Through Molecular Epidemiology, Brazil, 2014.

PubMed

Morillo, Simone Guadagnucci; Luchs, Adriana; Cilli, Audrey; Ribeiro, Cibele Daniel; de Cássia Compagnoli Carmona, Rita; do Carmo Sampaio Tavares Timenetsky, Maria

2017-06-01

Norovirus (NoV) is recognized as the most common cause of foodborne outbreaks. In 2014, an outbreak of acute gastroenteritis occurred on a cruise ship in Brazil, and NoV became the suspected etiology. Here we present the molecular identification of the NoV strains and the use of sequence analysis to determine modes of virus transmission. Food (cream cheese, tuna salad, grilled fish, orange mousse, and vegetables soup) and clinical samples were analyzed by ELISA, conventional RT-PCR, qRT-PCR, and sequencing. Genogroup GII NoV was identified by ELISA and conventional RT-PCR in fecal samples from 5 of 12 patients tested (41.7%), and in the orange mousse food sample by conventional RT-PCR and qRT-PCR. Two fecal GII NoV samples and the orange mousse GII NoV sample were successfully genotyped as GII.Pe (ORF 1), revealed 98.0-98.8% identities among them, and shared phylogenetically distinct cluster. Establishing the source of a NoV outbreak can be a challenging task. In this report, the molecular analysis of the partial RdRp NoV gene provided a powerful tool for genotyping (GII.Pe) and tracking of outbreak-related samples. In addition, the same fast and simple extraction methods applied to clinical samples could be successfully used for complex food matrices, and have the potential to be introduced in routine laboratories for screening foods for presence of NoV.

Performance Evaluation of the Sysmex CS-5100 Automated Coagulation Analyzer.

PubMed

Chen, Liming; Chen, Yu

2015-01-01

Coagulation testing is widely applied clinically, and laboratories increasingly demand automated coagulation analyzers with short turn-around times and high-throughput. The purpose of this study was to evaluate the performance of the Sysmex CS-5100 automated coagulation analyzer for routine use in a clinical laboratory. The prothrombin time (PT), international normalized ratio (INR), activated partial thromboplastin time (APTT), fibrinogen (Fbg), and D-dimer were compared between the Sysmex CS-5100 and Sysmex CA-7000 analyzers, and the imprecision, comparison, throughput, STAT function, and performance for abnormal samples were measured in each. The within-run and between-run coefficients of variation (CV) for the PT, APTT, INR, and D-dimer analyses showed excellent results both in the normal and pathologic ranges. The correlation coefficients between the Sysmex CS-5100 and Sysmex CA-7000 were highly correlated. The throughput of the Sysmex CS-5100 was faster than that of the Sysmex CA-7000. There was no interference at all by total bilirubin concentrations and triglyceride concentrations in the Sysmex CS-5100 analyzer. We demonstrated that the Sysmex CS-5100 performs with satisfactory imprecision and is well suited for coagulation analysis in laboratories processing large sample numbers and icteric and lipemic samples.

Determination of rivaroxaban in patient's plasma samples by anti-Xa chromogenic test associated to High Performance Liquid Chromatography tandem Mass Spectrometry (HPLC-MS/MS).

PubMed

Derogis, Priscilla Bento Matos; Sanches, Livia Rentas; de Aranda, Valdir Fernandes; Colombini, Marjorie Paris; Mangueira, Cristóvão Luis Pitangueira; Katz, Marcelo; Faulhaber, Adriana Caschera Leme; Mendes, Claudio Ernesto Albers; Ferreira, Carlos Eduardo Dos Santos; França, Carolina Nunes; Guerra, João Carlos de Campos

2017-01-01

Rivaroxaban is an oral direct factor Xa inhibitor, therapeutically indicated in the treatment of thromboembolic diseases. As other new oral anticoagulants, routine monitoring of rivaroxaban is not necessary, but important in some clinical circumstances. In our study a high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method was validated to measure rivaroxaban plasmatic concentration. Our method used a simple sample preparation, protein precipitation, and a fast chromatographic run. It was developed a precise and accurate method, with a linear range from 2 to 500 ng/mL, and a lower limit of quantification of 4 pg on column. The new method was compared to a reference method (anti-factor Xa activity) and both presented a good correlation (r = 0.98, p < 0.001). In addition, we validated hemolytic, icteric or lipemic plasma samples for rivaroxaban measurement by HPLC-MS/MS without interferences. The chromogenic and HPLC-MS/MS methods were highly correlated and should be used as clinical tools for drug monitoring. The method was applied successfully in a group of 49 real-life patients, which allowed an accurate determination of rivaroxaban in peak and trough levels.

Filter paper saturated by urine sample in metabolic disorders detection by proton magnetic resonance spectroscopy.

PubMed

Blasco, Hélène; Garrigue, Marie-Ange; De Vos, Aymeric; Antar, Catherine; Labarthe, François; Maillot, François; Andres, Christian R; Nadal-Desbarats, Lydie

2010-02-01

NMR spectroscopy of urine samples is able to diagnose many inborn errors of metabolism (IEM). However, urinary metabolites have a poor stability, requiring special care for routine analysis (storage of urine at -20 or -80 degrees C, fast transport). The aim of our study was to investigate the reliability of dried urine filter paper for urine storage and transport and to evaluate the ability of NMR to detect several IEM using this method. Urine samples from five healthy subjects were analyzed by (1)H NMR following different storage conditions (-20 vs 4 degrees C vs dried on filter paper) and at different time points (24 h, 48 h, 96 h, and 7 days). Urine pattern of fresh urine was considered as a reference. We analyzed the conservation of some amino acids and organic acids using Bland and Altman plot with intraclass correlation coefficient determination. Then, we evaluated the use of filter paper to detect four different IEM (methylmalonic and isovaleric acidurias, ornithine transcarbamylase deficiency, and cystinuria). Analysis of urine samples from healthy subjects revealed a high stability of studied molecules (ICC > 0.8) even after 7 days of storage on filter paper. Moreover, an excellent preservation of metabolites specifically accumulated in IEM was observed when analysis of dried urine filter paper was compared to fresh urine (coefficient of variation < 15%). This preliminary study demonstrates that storage of dried urine on filter paper is reliable for (1)H NMR spectroscopy analysis. Preservation of urine molecules over time using that method is convenient for routine clinical practice.

How is the high vaginal swab used to investigate vaginal discharge in primary care and how do GPs' expectations of the test match the tests performed by their microbiology services?

PubMed

Noble, H; Estcourt, C; Ison, C; Goold, P; Tite, L; Carter, Y H

2004-06-01

To describe the management of vaginal discharge in general practice, with particular regard to the use of the high vaginal swab (HVS), and to compare GPs' expectations of this test with the processing and reporting undertaken by different laboratories. A postal questionnaire survey of 2146 GPs in the North Thames area and postal questionnaire study of the 22 laboratories serving the same GPs were carried out. GPs were asked how they would manage a young woman with vaginal discharge and what information they would like on an HVS report. Laboratories were asked how they would process and report on the HVS sample from the same patient. Response rate was 26%. 72% of GPs would take an HVS and 62% would refer on to a genitourinary medicine (GUM) clinic. 45% would offer empirical therapy and 47% of these would treat for candida initially. 75% of GPs routinely request "M,C&S" on HVS samples but 55% only want to be informed about specific pathogens. Routine processing of HVS samples varies widely between laboratories and 86% only report specific pathogens. 78% of GPs would like to be offered a suggested diagnosis on HVS reports, and 74% would like a suggested treatment. 43% of laboratories ever provide a diagnosis, and 14% provide a suggested treatment. GPs frequently manage vaginal discharge and most of them utilise the HVS. GPs' expectations of the test are not well matched to laboratory processing or reporting of the samples.

Use of Recombinant Antigens for Sensitive Serodiagnosis of American Tegumentary Leishmaniasis Caused by Different Leishmania Species.

PubMed

Sato, Camila Massae; Sanchez, Maria Carmen Arroyo; Celeste, Beatriz Julieta; Duthie, Malcolm S; Guderian, Jeffrey; Reed, Steven G; de Brito, Maria Edileuza Felinto; Campos, Marliane Batista; de Souza Encarnação, Helia Valeria; Guerra, Jorge; de Mesquita, Tirza Gabrielle Ramos; Pinheiro, Suzana Kanawati; Ramasawmy, Rajendranath; Silveira, Fernando Tobias; de Assis Souza, Marina; Goto, Hiro

2017-02-01

American tegumentary leishmaniasis (ATL) (also known as cutaneous leishmaniasis [CL]) is caused by various species of protozoa of the genus Leishmania The diagnosis is achieved on a clinical, epidemiological, and pathological basis, supported by positive parasitological exams and demonstration of leishmanin delayed-type hypersensitivity. Serological assays are not routinely used in the diagnosis because many are considered to have low sensitivity and the particular Leishmania species causing the disease can lead to variable performance. In the present study, we generated recombinant versions of two highly conserved Leishmania proteins, Leishmania (Viannia) braziliensis-derived Lb8E and Lb6H, and evaluated both in enzyme-linked immunosorbent assays (ELISA). Recombinant Lb6H (rLb6H) had better performance and reacted with 100.0% of the ATL and 89.4% of the VL samples. These reactions with rLb6H were highly specific (98.5%) when compared against those for samples from healthy control individuals. We then assessed rLb6H against sera from ATL patients infected with different species of Leishmania prevalent in Brazil [Leishmania (Leishmania) amazonensis, L (Viannia) braziliensis, and L (V) guyanensis] and samples from patients with other infectious diseases. In analyses of 500 sera, ELISA using rLb6H detected all 219 ATL samples (sensitivity of 100.0%) with an overall specificity of 93.9% (considering healthy individuals and other infectious diseases patients). Only a minority of samples from Chagas disease patients possessed antibodies against rLb6H, and all of these responses were low (with a highest reactivity index of 2.2). Taken together, our data support further evaluation of rLb6H and the potential for its routine use in the serological diagnosis of ATL. Copyright © 2017 Sato et al.

Exhaled breath condensate methods adapted from human studies using longitudinal metabolomics for predicting early health alterations in dolphins.

PubMed

Borras, Eva; Aksenov, Alexander A; Baird, Mark; Novick, Brittany; Schivo, Michael; Zamuruyev, Konstantin O; Pasamontes, Alberto; Parry, Celeste; Foutouhi, Soraya; Venn-Watson, Stephanie; Weimer, Bart C; Davis, Cristina E

2017-11-01

Monitoring health conditions is essential to detect early asymptomatic stages of a disease. To achieve this, blood, urine and breath samples are commonly used as a routine clinical diagnostic. These samples offer the opportunity to detect specific metabolites related to diseases and provide a better understanding of their development. Although blood samples are commonly used routinely to monitor health, the implementation of a relatively noninvasive technique, such as exhaled breath condensate (EBC) analysis, may further benefit the well-being of both humans and other animals. EBC analysis can be used to track possible physical or biochemical alterations caused by common diseases of the bottlenose dolphin (Tursiops truncatus), such as infections or inflammatory-mediated processes. We have used an untargeted metabolomic method with liquid chromatography-mass spectrometry analysis of EBC samples to determine biomarkers related to disease development. In this study, five dolphins under human care were followed up for 1 year. We collected paired blood, physical examination information, and EBC samples. We then statistically correlated this information to predict specific health alterations. Three dolphins provided promising case study information about biomarkers related to cutaneous infections, respiratory infections, dental disease, or hormonal changes (pregnancy). The use of complementary liquid chromatography platforms, with hydrophilic interaction chromatography and reverse-phased columns, allowed us to detect a wide spectrum of EBC biomarker compounds that could be related to these health alterations. Moreover, these two analytical techniques not only provided complementary metabolite information but in both cases they also provided promising diagnostic information for these health conditions. Graphical abstract Collection of the exhaled condensed breath from a bottlenose dolphin from U.S. Navy Marine Mammal Program (MMP).

Incidence and severity of self-reported chemotherapy side effects in routine care: A prospective cohort study

PubMed Central

Haas, Marion; Viney, Rosalie; Pearson, Sallie-Anne; Haywood, Philip; Brown, Chris; Ward, Robyn

2017-01-01

Aim Chemotherapy side effects are often reported in clinical trials; however, there is little evidence about their incidence in routine clinical care. The objective of this study was to describe the frequency and severity of patient-reported chemotherapy side effects in routine care across treatment centres in Australia. Methods We conducted a prospective cohort study of individuals with breast, lung or colorectal cancer undergoing chemotherapy. Side effects were identified by patient self-report. The frequency, prevalence and incidence rates of side effects were calculated by cancer type and grade, and cumulative incidence curves for each side effect computed. Frequencies of side effects were compared between demographic subgroups using chi-squared statistics. Results Side effect data were available for 449 eligible individuals, who had a median follow-up of 5.64 months. 86% of participants reported at least one side effect during the study period and 27% reported a grade IV side effect, most commonly fatigue or dyspnoea. Fatigue was the most common side effect overall (85%), followed by diarrhoea (74%) and constipation (74%). Prevalence and incidence rates were similar across side effects and cancer types. Age was the only demographic factor associated with the incidence of side effects, with older people less likely to report side effects. Conclusion This research has produced the first Australian estimates of self-reported incidence of chemotherapy side effects in routine clinical care. Chemotherapy side effects in routine care are common, continue throughout chemotherapy and can be serious. This work confirms the importance of observational data in providing clinical practice-relevant information to decision-makers. PMID:29016607

Incidence and severity of self-reported chemotherapy side effects in routine care: A prospective cohort study.

PubMed

Pearce, Alison; Haas, Marion; Viney, Rosalie; Pearson, Sallie-Anne; Haywood, Philip; Brown, Chris; Ward, Robyn

2017-01-01

Chemotherapy side effects are often reported in clinical trials; however, there is little evidence about their incidence in routine clinical care. The objective of this study was to describe the frequency and severity of patient-reported chemotherapy side effects in routine care across treatment centres in Australia. We conducted a prospective cohort study of individuals with breast, lung or colorectal cancer undergoing chemotherapy. Side effects were identified by patient self-report. The frequency, prevalence and incidence rates of side effects were calculated by cancer type and grade, and cumulative incidence curves for each side effect computed. Frequencies of side effects were compared between demographic subgroups using chi-squared statistics. Side effect data were available for 449 eligible individuals, who had a median follow-up of 5.64 months. 86% of participants reported at least one side effect during the study period and 27% reported a grade IV side effect, most commonly fatigue or dyspnoea. Fatigue was the most common side effect overall (85%), followed by diarrhoea (74%) and constipation (74%). Prevalence and incidence rates were similar across side effects and cancer types. Age was the only demographic factor associated with the incidence of side effects, with older people less likely to report side effects. This research has produced the first Australian estimates of self-reported incidence of chemotherapy side effects in routine clinical care. Chemotherapy side effects in routine care are common, continue throughout chemotherapy and can be serious. This work confirms the importance of observational data in providing clinical practice-relevant information to decision-makers.

Effect of On-Demand vs Routine Nebulization of Acetylcysteine With Salbutamol on Ventilator-Free Days in Intensive Care Unit Patients Receiving Invasive Ventilation: A Randomized Clinical Trial.

PubMed

van Meenen, David M P; van der Hoeven, Sophia M; Binnekade, Jan M; de Borgie, Corianne A J M; Merkus, Maruschka P; Bosch, Frank H; Endeman, Henrik; Haringman, Jasper J; van der Meer, Nardo J M; Moeniralam, Hazra S; Slabbekoorn, Mathilde; Muller, Marcella C A; Stilma, Willemke; van Silfhout, Bart; Neto, Ary Serpa; Ter Haar, Hans F M; Van Vliet, Jan; Wijnhoven, Jan Willem; Horn, Janneke; Juffermans, Nicole P; Pelosi, Paolo; Gama de Abreu, Marcelo; Schultz, Marcus J; Paulus, Frederique

2018-03-13

It remains uncertain whether nebulization of mucolytics with bronchodilators should be applied for clinical indication or preventively in intensive care unit (ICU) patients receiving invasive ventilation. To determine if a strategy that uses nebulization for clinical indication (on-demand) is noninferior to one that uses preventive (routine) nebulization. Randomized clinical trial enrolling adult patients expected to need invasive ventilation for more than 24 hours at 7 ICUs in the Netherlands. On-demand nebulization of acetylcysteine or salbutamol (based on strict clinical indications, n = 471) or routine nebulization of acetylcysteine with salbutamol (every 6 hours until end of invasive ventilation, n = 473). The primary outcome was the number of ventilator-free days at day 28, with a noninferiority margin for a difference between groups of -0.5 days. Secondary outcomes included length of stay, mortality rates, occurrence of pulmonary complications, and adverse events. Nine hundred twenty-two patients (34% women; median age, 66 (interquartile range [IQR], 54-75 years) were enrolled and completed follow-up. At 28 days, patients in the on-demand group had a median 21 (IQR, 0-26) ventilator-free days, and patients in the routine group had a median 20 (IQR, 0-26) ventilator-free days (1-sided 95% CI, -0.00003 to ∞). There was no significant difference in length of stay or mortality, or in the proportion of patients developing pulmonary complications, between the 2 groups. Adverse events (13.8% vs 29.3%; difference, -15.5% [95% CI, -20.7% to -10.3%]; P < .001) were more frequent with routine nebulization and mainly related to tachyarrhythmia (12.5% vs 25.9%; difference, -13.4% [95% CI, -18.4% to -8.4%]; P < .001) and agitation (0.2% vs 4.3%; difference, -4.1% [95% CI, -5.9% to -2.2%]; P < .001). Among ICU patients receiving invasive ventilation who were expected to not be extubated within 24 hours, on-demand compared with routine nebulization of acetylcysteine with salbutamol did not result in an inferior number of ventilator-free days. On-demand nebulization may be a reasonable alternative to routine nebulization. clinicaltrials.gov Identifier: NCT02159196.

Brief Sexual Histories and Routine HIV/STD Testing by Medical Providers

PubMed Central

Lanier, Yzette; Castellanos, Ted; Barrow, Roxanne Y.; Jordan, Wilbert C.; Caine, Virginia

2014-01-01

Abstract Clinicians who routinely take patient sexual histories have the opportunity to assess patient risk for sexually transmitted diseases (STDs), including human immunodeficiency virus (HIV), and make appropriate recommendations for routine HIV/STD screenings. However, less than 40% of providers conduct sexual histories with patients, and many do not receive formal sexual history training in school. After partnering with a national professional organization of physicians, we trained 26 (US and US territory-based) practicing physicians (58% female; median age=48 years) regarding sexual history taking using both in-person and webinar methods. Trainings occurred during either a 6-h onsite or 2-h webinar session. We evaluated their post-training experiences integrating sexual histories during routine medical visits. We assessed use of sexual histories and routine HIV/STD screenings. All participating physicians reported improved sexual history taking and increases in documented sexual histories and routine HIV/STD screenings. Four themes emerged from the qualitative evaluations: (1) the need for more sexual history training; (2) the importance of providing a gender-neutral sexual history tool; (3) the existence of barriers to routine sexual histories/testing; and (4) unintended benefits for providers who were conducting routine sexual histories. These findings were used to develop a brief, gender-neutral sexual history tool for clinical use. This pilot evaluation demonstrates that providers were willing to utilize a sexual history tool in clinical practice in support of HIV/STD prevention efforts. PMID:24564387

Systematic review of discharge coding accuracy

PubMed Central

Burns, E.M.; Rigby, E.; Mamidanna, R.; Bottle, A.; Aylin, P.; Ziprin, P.; Faiz, O.D.

2012-01-01

Introduction Routinely collected data sets are increasingly used for research, financial reimbursement and health service planning. High quality data are necessary for reliable analysis. This study aims to assess the published accuracy of routinely collected data sets in Great Britain. Methods Systematic searches of the EMBASE, PUBMED, OVID and Cochrane databases were performed from 1989 to present using defined search terms. Included studies were those that compared routinely collected data sets with case or operative note review and those that compared routinely collected data with clinical registries. Results Thirty-two studies were included. Twenty-five studies compared routinely collected data with case or operation notes. Seven studies compared routinely collected data with clinical registries. The overall median accuracy (routinely collected data sets versus case notes) was 83.2% (IQR: 67.3–92.1%). The median diagnostic accuracy was 80.3% (IQR: 63.3–94.1%) with a median procedure accuracy of 84.2% (IQR: 68.7–88.7%). There was considerable variation in accuracy rates between studies (50.5–97.8%). Since the 2002 introduction of Payment by Results, accuracy has improved in some respects, for example primary diagnoses accuracy has improved from 73.8% (IQR: 59.3–92.1%) to 96.0% (IQR: 89.3–96.3), P= 0.020. Conclusion Accuracy rates are improving. Current levels of reported accuracy suggest that routinely collected data are sufficiently robust to support their use for research and managerial decision-making. PMID:21795302

Making sense of the shadows: priorities for creating a learning healthcare system based on routinely collected data

PubMed Central

Deeny, Sarah R; Steventon, Adam

2015-01-01

Socrates described a group of people chained up inside a cave, who mistook shadows of objects on a wall for reality. This allegory comes to mind when considering ‘routinely collected data’—the massive data sets, generated as part of the routine operation of the modern healthcare service. There is keen interest in routine data and the seemingly comprehensive view of healthcare they offer, and we outline a number of examples in which they were used successfully, including the Birmingham OwnHealth study, in which routine data were used with matched control groups to assess the effect of telephone health coaching on hospital utilisation. Routine data differ from data collected primarily for the purposes of research, and this means that analysts cannot assume that they provide the full or accurate clinical picture, let alone a full description of the health of the population. We show that major methodological challenges in using routine data arise from the difficulty of understanding the gap between patient and their ‘data shadow’. Strategies to overcome this challenge include more extensive data linkage, developing analytical methods and collecting more data on a routine basis, including from the patient while away from the clinic. In addition, creating a learning health system will require greater alignment between the analysis and the decisions that will be taken; between analysts and people interested in quality improvement; and between the analysis undertaken and public attitudes regarding appropriate use of data. PMID:26065466

Design of the FemCure study: prospective multicentre study on the transmission of genital and extra-genital Chlamydia trachomatis infections in women receiving routine care.

PubMed

Dukers-Muijrers, Nicole H T M; Wolffs, Petra F G; Eppings, Lisanne; Götz, Hannelore M; Bruisten, Sylvia M; Schim van der Loeff, Maarten F; Janssen, Kevin; Lucchesi, Mayk; Heijman, Titia; van Benthem, Birgit H; van Bergen, Jan E; Morre, Servaas A; Herbergs, Jos; Kok, Gerjo; Steenbakkers, Mieke; Hogewoning, Arjan A; de Vries, Henry J; Hoebe, Christian J P A

2016-08-08

In women, anorectal infections with Chlamydia trachomatis (CT) are about as common as genital CT, yet the anorectal site remains largely untested in routine care. Anorectal CT frequently co-occurs with genital CT and may thus often be treated co-incidentally. Nevertheless, post-treatment detection of CT at both anatomic sites has been demonstrated. It is unknown whether anorectal CT may play a role in post-treatment transmission. This study, called FemCure, in women who receive routine treatment (either azithromycin or doxycycline) aims to understand the post-treatment transmission of anorectal CT infections, i.e., from their male sexual partner(s) and from and to the genital region of the same woman. The secondary objective is to evaluate other reasons for CT detection by nucleic acid amplification techniques (NAAT) such as treatment failure, in order to inform guidelines to optimize CT control. A multicentre prospective cohort study (FemCure) is set up in which genital and/or anorectal CT positive women (n = 400) will be recruited at three large Dutch STI clinics located in South Limburg, Amsterdam and Rotterdam. The women self-collect anorectal and vaginal swabs before treatment, and at the end of weeks 1, 2, 4, 6, 8, 10, and 12. Samples are tested for presence of CT-DNA (by NAAT), load (by quantitative polymerase chain reaction -PCR), viability (by culture and viability PCR) and CT type (by multilocus sequence typing). Sexual exposure is assessed by online self-administered questionnaires and by testing samples for Y chromosomal DNA. Using logistic regression models, the impact of two key factors (i.e., sexual exposure and alternate anatomic site of infection) on detection of anorectal and genital CT will be assessed. The FemCure study will provide insight in the role of anorectal chlamydia infection in maintaining the CT burden in the context of treatment, and it will provide practical recommendations to reduce avoidable transmission. Implications will improve care strategies that take account of anorectal CT. ClinicalTrials.gov Identifier: NCT02694497 .

Lost opportunities to identify and treat HIV-positive patients: results from a baseline assessment of provider-initiated HIV testing and counselling (PITC) in Malawi.

PubMed

Ahmed, Saeed; Schwarz, Monica; Flick, Robert J; Rees, Chris A; Harawa, Mwelura; Simon, Katie; Robison, Jeff A; Kazembe, Peter N; Kim, Maria H

2016-04-01

To assess implementation of provider-initiated testing and counselling (PITC) for HIV in Malawi. A review of PITC practices within 118 departments in 12 Ministry of Health (MoH) facilities across Malawi was conducted. Information on PITC practices was collected via a health facility survey. Data describing patient visits and HIV tests were abstracted from routinely collected programme data. Reported PITC practices were highly variable. Most providers practiced symptom-based PITC. Antenatal clinics and maternity wards reported widespread use of routine opt-out PITC. In 2014, there was approximately 1 HIV test for every 15 clinic visits. HIV status was ascertained in 94.3% (5293/5615) of patients at tuberculosis clinics, 92.6% (30,675/33,142) of patients at antenatal clinics and 49.4% (6871/13,914) of patients at sexually transmitted infection clinics. Reported challenges to delivering PITC included test kit shortages (71/71 providers), insufficient physical space (58/71) and inadequate number of HIV counsellors (32/71) while providers from inpatient units cited the inability to test on weekends. Various models of PITC currently exist at MoH facilities in Malawi. Only antenatal and maternity clinics demonstrated high rates of routine opt-out PITC. The low ratio of facility visits to HIV tests suggests missed opportunities for HIV testing. However, the high proportion of patients at TB and antenatal clinics with known HIV status suggests that routine PITC is feasible. These results underscore the need to develop clear, standardised PITC policy and protocols, and to address obstacles of limited health commodities, infrastructure and human resources. © 2016 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Bayesian estimation of test characteristics of real-time PCR, bacteriological culture and California mastitis test for diagnosis of intramammary infections with Staphylococcus aureus in dairy cattle at routine milk recordings.

PubMed

Mahmmod, Yasser S; Toft, Nils; Katholm, Jørgen; Grønbæk, Carsten; Klaas, Ilka C

2013-11-01

Danish farmers can order a real-time PCR mastitis diagnostic test on routinely taken cow-level samples from milk recordings. Validation of its performance in comparison to conventional mastitis diagnostics under field conditions is essential for efficient control of intramammary infections (IMI) with Staphylococcus aureus (S. aureus). Therefore, the objective of this study was to estimate the sensitivity (Se) and specificity (Sp) of real-time PCR, bacterial culture (BC) and California mastitis test (CMT) for the diagnosis of the naturally occurring IMI with S. aureus in routinely collected milk samples using latent class analysis (LCA) to avoid the assumption of a perfect reference test. Using systematic random sampling, a total of 609 lactating dairy cows were selected from 6 dairy herds with bulk tank milk PCR cycle threshold (Ct) value ≤39 for S. aureus. At routine milk recordings, automatically obtained cow-level (composite) milk samples were analyzed by PCR and at the same milking, 2436 quarter milk samples were collected aseptically for BC and CMT. Results showed that 140 cows (23%) were positive for S. aureus IMI by BC while 170 cows (28%) were positive by PCR. Estimates of Se and Sp for PCR were higher than test estimates of BC and CMT. SeCMT was higher than SeBC however, SpBC was higher than SpCMT. SePCR was 91%, while SeBC was 53%, and SeCMT was 61%. SpPCR was 99%, while SpBC was 89%, and SpCMT was 65%. In conclusion, PCR has a higher performance than the conventional diagnostic tests (BC and CMT) suggesting its usefulness as a routine test for accurate diagnosis of S. aureus IMI from dairy cows at routine milk recordings. The use of LCA provided estimates of the test characteristics for two currently diagnostic tests (BC, CMT) and a novel technique (real-time PCR) for diagnosing S. aureus IMI under field conditions at routine milk recordings in Denmark. Copyright © 2013 Elsevier B.V. All rights reserved.

Routine operation of an Elliott 903 computer in a clinical chemistry laboratory

PubMed Central

Whitby, L. G.; Simpson, D.

1973-01-01

Experience gained in the last four years concerning the capabilities and limitations of an 8K Elliott 903 (18-bit word) computer with magnetic tape backing store in the routine operation of a clinical chemistry laboratory is described. Designed as a total system, routine operation has latterly had to be confined to data acquisition and process control functions, due primarily to limitations imposed by the choice of hardware early in the project. In this final report of a partially successful experiment the opportunity is taken to review mistakes made, especially at the start of the project, to warn potential computer users of pitfalls to be avoided. PMID:4580240

Routine clinical heart examinations using SQUID magnetocardiography at University of Tsukuba Hospital

NASA Astrophysics Data System (ADS)

Inaba, T.; Nakazawa, Y.; Yoshida, K.; Kato, Y.; Hattori, A.; Kimura, T.; Hoshi, T.; Ishizu, T.; Seo, Y.; Sato, A.; Sekiguchi, Y.; Nogami, A.; Watanabe, S.; Horigome, H.; Kawakami, Y.; Aonuma, K.

2017-11-01

A 64-channel Nb-based DC-SQUID magnetocardiography (MCG) system was installed at the University of Tsukuba Hospital (UTH) in March 2007 after obtaining Japanese pharmaceutical approval and insurance reimbursement approval. In the period between 2008 and 2016, the total number of patients was 10 085. The heart diseases diagnosed in fetuses as well as adults are mainly atrial arrhythmia, abnormal repolarization, ventricular arrhythmia, and fetal arrhythmia. In most cases of insufficient diagnostic accuracy with electrocardiography, SQUID MCG precisely revealed these heart diseases as an abnormal electrical current distribution. Based on success in routine examinations, SQUID MCG is now an indispensable clinical instrument with diagnostic software tuned up during routine use at UTH.

Gender Differences During Toddlerhood in Autism Spectrum Disorder: A Prospective Community-Based Longitudinal Follow-Up Study.

PubMed

Lawson, Lauren P; Joshi, Rucha; Barbaro, Josephine; Dissanayake, Cheryl

2018-03-01

Relatively few studies have examined gender differences in infants and toddlers, and most focus on clinically referred samples or high-risk infant cohorts. The current study aimed to examine gender differences in early autism manifestations and cognitive development in a community-ascertained sample. In total, 46 males and 21 females with ASD were seen at approximately 24 and 48 months of age. No significant gender differences were observed on overall cognitive ability, verbal skills, non-verbal skills, overall autism severity, or restricted repetitive behaviours. However, females were found to exhibit more social communication impairments than males. These findings may indicate that female toddlers with less severe or different, social communication impairments may be more likely to be missed during routine surveillance during toddlerhood.

Ultra-sensitive high performance liquid chromatography-laser-induced fluorescence based proteomics for clinical applications.

PubMed

Patil, Ajeetkumar; Bhat, Sujatha; Pai, Keerthilatha M; Rai, Lavanya; Kartha, V B; Chidangil, Santhosh

2015-09-08

An ultra-sensitive high performance liquid chromatography-laser induced fluorescence (HPLC-LIF) based technique has been developed by our group at Manipal, for screening, early detection, and staging for various cancers, using protein profiling of clinical samples like, body fluids, cellular specimens, and biopsy-tissue. More than 300 protein profiles of different clinical samples (serum, saliva, cellular samples and tissue homogenates) from volunteers (normal, and different pre-malignant/malignant conditions) were recorded using this set-up. The protein profiles were analyzed using principal component analysis (PCA) to achieve objective detection and classification of malignant, premalignant and healthy conditions with high sensitivity and specificity. The HPLC-LIF protein profiling combined with PCA, as a routine method for screening, diagnosis, and staging of cervical cancer and oral cancer, is discussed in this paper. In recent years, proteomics techniques have advanced tremendously in life sciences and medical sciences for the detection and identification of proteins in body fluids, tissue homogenates and cellular samples to understand biochemical mechanisms leading to different diseases. Some of the methods include techniques like high performance liquid chromatography, 2D-gel electrophoresis, MALDI-TOF-MS, SELDI-TOF-MS, CE-MS and LC-MS techniques. We have developed an ultra-sensitive high performance liquid chromatography-laser induced fluorescence (HPLC-LIF) based technique, for screening, early detection, and staging for various cancers, using protein profiling of clinical samples like, body fluids, cellular specimens, and biopsy-tissue. More than 300 protein profiles of different clinical samples (serum, saliva, cellular samples and tissue homogenates) from healthy and volunteers with different malignant conditions were recorded by using this set-up. The protein profile data were analyzed using principal component analysis (PCA) for objective classification and detection of malignant, premalignant and healthy conditions. The method is extremely sensitive to detect proteins with limit of detection of the order of femto-moles. The HPLC-LIF combined with PCA as a potential proteomic method for the diagnosis of oral cancer and cervical cancer has been discussed in this paper. This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Analytical and clinical performance of the new Fujirebio 25-OH vitamin D assay, a comparison with liquid chromatography-tandem mass spectrometry (LC-MS/MS) and three other automated assays.

PubMed

Saleh, Lanja; Mueller, Daniel; von Eckardstein, Arnold

2016-04-01

We evaluated the analytical and clinical performance of the new Lumipulse® G 25-OH vitamin D assay from Fujirebio, and compared it to a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method and three other commercial automated assays. Total 25 hydroxy vitamin D (25(OH)D) levels were measured in 100 selected serum samples from our routine analysis with Fujirebio 25(OH)D assay. The results were compared with those obtained with LC-MS/MS and three other automated 25(OH)D assays (Abbott, Beckman, and Roche). The accuracy of each assay tested was evaluated against a Labquality reference serum panel for 25(OH)D (Ref!25OHD; University of Ghent). Intra- and inter-day imprecision of the Fujirebio 25(OH)D assay was <5%. Fujirebio 25(OH)D assay showed the highest correlation among the assays tested with the LC-MS/MS method (R=0.986). The mean relative bias obtained was -15.6% (Fujirebio), -12.7% (Beckman), -2.1% (Abbott) and 9.7% (Roche) as compared to LC-MS/MS. Comparison with the Labquality certified reference serum panel yielded a mean bias of -11.8% (Fujirebio), -14.1% (Beckman), 4.4% (Abbott) and 3.2% (Roche), respectively. Compared to LC-MS/MS, the sensitivity of different methods in detecting vitamin D insufficiency (<50 nmol/L) varied from 100% for the Fujirebio assay to 72.7% for Roche, and specificity ranged from 94.4% for Roche to 87.6% for Beckman. The Lumipulse G 25-OH vitamin D assay from Fujirebio demonstrated a good correlation with LC-MS/MS and some immunoassays. The performance of the assay is well-suited for routine 25(OH)D measurement in clinical serum samples. A correction for the observed negative bias vs. LC-MS/MS could be considered.

Perceived body weight, eating and exercise problems of different groups of women.

PubMed

Coker, Elise; Telfer, James; Abraham, Suzanne

2012-10-01

To compare prevalence of problems with body weight, eating and exercise (past or present) of female psychiatric inpatients with routine care, gynaecological and obstetric female outpatients, and eating disorder inpatients. One thousand and thirty-eight females aged 18-55 years from routine care (n=99), gynaecological (n=263) and obstetric (n=271) outpatient clinics, and eating disorder (n=223) and general psychiatric units (n=182) participated. Participants self-reported past or current problems with weight, eating and exercise using a short survey. A sub-sample of women completed the Eating and Exercise Examination (EEE) which includes the Quality of Life for Eating Disorders (QOL ED). The prevalence of self-reported problems controlling weight (52%), disordered eating and eating disorders (43%) for the psychiatric patients was significantly greater than for the routine care and gynaecological and obstetrics outpatients. The psychiatric group had a significantly higher mean body mass index (BMI) of 27.3 kg/m(2) (standard deviation (SD)=6.7) and prevalence of self-reported obesity (28%) than the other groups. Treatment of women with psychiatric problems should include assessment and concurrent attention to body weight, eating disorder and exercise problems in association with appropriate medical, psychiatric, psychological and medication treatment of their presenting disorder.

Chromosomal Microarray versus Karyotyping for Prenatal Diagnosis

PubMed Central

Wapner, Ronald J.; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C.; Eng, Christine M.; Zachary, Julia M.; Savage, Melissa; Platt, Lawrence D.; Saltzman, Daniel; Grobman, William A.; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S.; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N.; Thom, Elizabeth A.; Beaudet, Arthur L.; Ledbetter, David H.; Shaffer, Lisa G.; Jackson, Laird

2013-01-01

Background Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Methods Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. Results We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down’s syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. Conclusions In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.) PMID:23215555

Antibiotic Therapy in Comatose Mechanically Ventilated Patients Following Aspiration: Differentiating Pneumonia From Pneumonitis.

PubMed

Lascarrou, Jean Baptiste; Lissonde, Floriane; Le Thuaut, Aurélie; Bachoumas, Konstantinos; Colin, Gwenhael; Henry Lagarrigue, Matthieu; Vinatier, Isabelle; Fiancette, Maud; Lacherade, Jean Claude; Yehia, Aihem; Joret, Aurélie; Lebert, Christine; Bourdon, Sandra; Martin Lefèvre, Laurent; Reignier, Jean

2017-08-01

To determine the proportion of patients with documented bacterial aspiration pneumonia among comatose ICU patients with symptoms suggesting either bacterial aspiration pneumonia or non-bacterial aspiration pneumonitis. Prospective observational study. University-affiliated 30-bed ICU. Prospective cohort of 250 patients admitted to the ICU with coma (Glasgow Coma Scale score ≤ 8) and treated with invasive mechanical ventilation. None. The primary outcome was the proportion of patients with microbiologically documented bacterial aspiration pneumonia. Patients meeting predefined criteria for aspiration syndrome routinely underwent telescopic plugged catheter sampling during bronchoscopy before starting probabilistic antibiotic treatment. When cultures were negative, the antibiotic treatment was stopped. Of 250 included patients, 98 (39.2%) had aspiration syndrome, including 92 before mechanical ventilation discontinuation. Telescopic plugged catheter in these 92 patients showed bacterial aspiration pneumonia in 43 patients (46.7%). Among the remaining 49 patients, 16 continued to receive antibiotics, usually for infections other than pneumonia; of the 33 patients whose antibiotics were discontinued, only two subsequently showed signs of lung infection. In the six patients with aspiration syndrome after mechanical ventilation, and therefore without telescopic plugged catheter, antibiotic treatment was continued for 7 days. Mechanical ventilation duration, ICU length of stay, and mortality did not differ between the 43 patients with bacterial aspiration pneumonia and the 49 patients with non-bacterial aspiration pneumonitis. The 152 patients without aspiration syndrome did not receive antibiotics. Among comatose patients receiving mechanical ventilation, those without clinical, laboratory, or radiologic evidence of bacterial aspiration pneumonia did not require antibiotics. In those with suspected bacterial aspiration pneumonia, stopping empirical antibiotic therapy when routine telescopic plugged catheter sampling recovered no microorganisms was nearly always effective. This strategy may be a valid alternative to routine full-course antibiotic therapy. Only half the patients with suspected bacterial aspiration pneumonia had this diagnosis confirmed by telescopic plugged catheter sampling.

Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli.

PubMed

Christner, Martin; Trusch, Maria; Rohde, Holger; Kwiatkowski, Marcel; Schlüter, Hartmut; Wolters, Manuel; Aepfelbacher, Martin; Hentschke, Moritz

2014-01-01

In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.

A highly sensitive and versatile virus titration assay in the 96-well microplate format.

PubMed

Borisevich, V; Nistler, R; Hudman, D; Yamshchikov, G; Seregin, A; Yamshchikov, V

2008-02-01

This report describes a fast, reproducible, inexpensive and convenient assay system for virus titration in the 96-well format. The micromethod substantially increases assay throughput and improves the data reproducibility. A highly simplified variant of virus quantification is based on immunohistochemical detection of virus amplification foci obtained without use of agarose or semisolid overlays. It can be incorporated into several types of routine virological assays successfully replacing the laborious and time-consuming conventional methods based on plaque formation under semisolid overlays. The method does not depend on the development of CPE and can be accommodated to assay viruses with substantial differences in growth properties. The use of enhanced immunohistochemical detection enabled a five- to six-fold reduction of the total assay time. The micromethod was specifically developed to take advantage of multichannel pipettor use to simplify handling of a large number of samples. The method performs well with an inexpensive low-power binocular, thus offering a routine assay system usable outside of specialized laboratory setting, such as for testing of clinical or field samples. When used in focus reduction-neutralization tests (FRNT), the method accommodates very small volumes of immune serum, which is often a decisive factor in experiments involving small rodent models.

Acute Toxoplasma gondii infection in children with reactive hyperplasia of the cervical lymph nodes.

PubMed

Bilal, Jalal A; Alsammani, Mohamed A; Ahmed, Mohamed I

2014-07-01

To determine the seroprevalence of Toxoplasma gondii (T. gondii) in children with reactive hyperplasia of the cervical lymph nodes. This cross-sectional prospective study was conducted in Khartoum Children Emergency Hospital, Khartoum, Sudan between January 2010 and April 2011. Eighty children with cervical lymphadenopathy were selected using random sampling. Their lymph nodes were aspirated for cytology, and a blood sample was collected from all patients for routine laboratory analysis and T. gondii IgG and IgM antibodies. Among 80 children with cervical lymphadenopathy, 60 (75%) had non-specific reactive hyperplasia. The seroprevalence of T. gondii among children with cervical lymphadenopathy was 27.5% (n=22), and the seropositivity of acute T. gondii among those with reactive hyperplasia was 36.7% (n=22/60). Lymph nodes in the T. gondii positive group were mobile and warm (p<0.05). The clinical features and laboratory tests were insignificant predictors of acute T. gondii infection with reactive hyperplasia of the cervical lymph nodes. The prevalence of acute T. gondii infection is high among children with non-specific reactive hyperplasia of the cervical lymph nodes. Routine laboratory studies are not helpful in the diagnosis of T. gondii infection with reactive hyperplasia of the lymph nodes however, serological studies may be requested prior to invasive procedures.

Mass Spectrometry in Clinical Laboratory: Applications in Therapeutic Drug Monitoring and Toxicology.

PubMed

Garg, Uttam; Zhang, Yan Victoria

2016-01-01

Mass spectrometry (MS) has been used in research and specialized clinical laboratories for decades as a very powerful technology to identify and quantify compounds. In recent years, application of MS in routine clinical laboratories has increased significantly. This is mainly due to the ability of MS to provide very specific identification, high sensitivity, and simultaneous analysis of multiple analytes (>100). The coupling of tandem mass spectrometry with gas chromatography (GC) or liquid chromatography (LC) has enabled the rapid expansion of this technology. While applications of MS are used in many clinical areas, therapeutic drug monitoring, drugs of abuse, and clinical toxicology are still the primary focuses of the field. It is not uncommon to see mass spectrometry being used in routine clinical practices for those applications.

Prospective evaluation of the VITEK MS for the routine identification of bacteria and yeast in the clinical microbiology laboratory: assessment of accuracy of identification and turnaround time.

PubMed

Charnot-Katsikas, Angella; Tesic, Vera; Boonlayangoor, Sue; Bethel, Cindy; Frank, Karen M

2014-02-01

This study assessed the accuracy of bacterial and yeast identification using the VITEK MS, and the time to reporting of isolates before and after its implementation in routine clinical practice. Three hundred and sixty-two isolates of bacteria and yeast, consisting of a variety of clinical isolates and American Type Culture Collection strains, were tested. Results were compared with reference identifications from the VITEK 2 system and with 16S rRNA sequence analysis. The VITEK MS provided an acceptable identification to species level for 283 (78 %) isolates. Considering organisms for which genus-level identification is acceptable for routine clinical care, 315 isolates (87 %) had an acceptable identification. Six isolates (2 %) were identified incorrectly, five of which were Shigella species. Finally, the time for reporting the identifications was decreased significantly after implementation of the VITEK MS for a total mean reduction in time of 10.52 h (P<0.0001). Overall, accuracy of the VITEK MS was comparable or superior to that from the VITEK 2. The findings were also comparable to other studies examining the accuracy of the VITEK MS, although differences exist, depending on the diversity of species represented as well as on the versions of the databases used. The VITEK MS can be incorporated effectively into routine use in a clinical microbiology laboratory and future expansion of the database should provide improved accuracy for the identification of micro-organisms.

Clinical vs. structured interview on anxiety and affective disorders by primary care physicians. understanding diagnostic discordance.

PubMed

Balestrieri, Matteo; Baldacci, Sandra; Bellomo, Antonello; Bellantuono, Cesario; Conti, Luciano; Perugi, Giulio; Nardini, Marcello; Borbotti, Marco; Viegi, Giovanni

2007-01-01

To assess in a national sample the ability of GPs to detect psychiatric disorders using a clinical vs. a standardized interview and to characterize the patients that were falsely diagnosed with an anxiety or affective disorder. This is a national, cross-sectional, epidemiological survey, carried out by GPs on a random sample of their patients. The GPs were randomly divided into two groups. Apart from the routine clinical interview, the experimental group (group A) had to administer the Mini-International Neuropsychiatric Interview (MINI). Data was collected by 143 GPs. 17.2% of all patients had a clinical diagnosis of an affective disorder, and 25.4% a clinical diagnosis of an anxiety disorder. In group A, the number of clinical diagnoses was about twice that of MINI diagnoses for affective disorders and one and a half times that for anxiety disorders. The majority of clinical diagnoses were represented by MINI subsyndromal cases (52.3%). Females showed a higher OR of being over-detected by GPs with anxiety disorders or of not being diagnosed with an affective disorder. Being divorced/separated/widowed increased the OR of over-detection of affective and anxiety disorders. The OR of over-detection of an affective or an anxiety disorder was higher for individuals with a moderate to poor quality of life. In the primary care a gap exists between clinical and standardized interviews in the detection of affective and anxiety disorders. Some experiential and social factors can increase this tendency. The use of a psycho.

Evaluation of the Technicon Axon analyser.

PubMed

Martínez, C; Márquez, M; Cortés, M; Mercé, J; Rodriguez, J; González, F

1990-01-01

An evaluation of the Technicon Axon analyser was carried out following the guidelines of the 'Sociedad Española de Química Clínica' and the European Committee for Clinical Laboratory Standards.A photometric study revealed acceptable results at both 340 nm and 404 nm. Inaccuracy and imprecision were lower at 404 nm than at 340 nm, although poor dispersion was found at both wavelengths, even at low absorbances. Drift was negligible, the imprecision of the sample pipette delivery system was greater for small sample volumes, the reagent pipette delivery system imprecision was acceptable and the sample diluting system study showed good precision and accuracy.Twelve analytes were studied for evaluation of the analyser under routine working conditions. Satisfactory results were obtained for within-run imprecision, while coefficients of variation for betweenrun imprecision were much greater than expected. Neither specimenrelated nor specimen-independent contamination was found in the carry-over study. For all analytes assayed, when comparing patient sample results with those obtained in a Hitachi 737 analyser, acceptable relative inaccuracy was observed.

Tuberculosis screening in patients with HIV: An audit against UK national guidelines to assess current practice and the effectiveness of an electronic tuberculosis-screening prompt.

PubMed

Fox-Lewis, A; Brima, N; Muniina, P; Grant, A D; Edwards, S G; Miller, R F; Pett, S L

2016-09-01

A retrospective clinical audit was performed to assess if the British HIV Association 2011 guidelines on routine screening for tuberculosis in HIV are being implemented in a large UK urban clinic, and if a tuberculosis-screening prompt on the electronic patient record for new attendees was effective. Of 4658 patients attending during the inclusion period, 385 were newly diagnosed first-time attendees and routine tuberculosis screening was recommended in 165. Of these, only 6.1% of patients had a completed tuberculosis screening prompt, and 12.1% underwent routine tuberculosis screening. This audit represents the first published UK data on routine screening rates for tuberculosis in HIV and demonstrates low rates of tuberculosis screening despite an electronic screening prompt designed to simplify adherence to the national guideline. Reasons why tuberculosis screening rates were low, and the prompt ineffective, are unclear. A national audit is ongoing, and we await the results to see if our data reflect a lack of routine tuberculosis screening in HIV-infected patients at a national level. © The Author(s) 2016.

Diagnosis of central nervous system relapse of pediatric acute lymphoblastic leukemia: Impact of routine cytological CSF analysis at the time of intrathecal chemotherapy.

PubMed

Gassas, Adam; Krueger, Joerg; Alvi, Saima; Sung, Lillian; Hitzler, Johanne; Lieberman, Lani

2014-12-01

Despite the success of central nervous system (CNS) directed therapy in pediatric acute lymphoblastic leukemia (ALL), relapse involving the CNS continues to be observed in 5-10% of children when utilizing standard intrathecal prophylactic chemotherapy. While most pediatric ALL treatment protocols mandate regular lumbar punctures (LP) for the intrathecal injection of chemotherapy, the value of routine cytological analysis of cerebrospinal fluid (CSF) during therapy is unknown. Our objective was to assess the diagnostic value of routine CSF analysis during ALL therapy. To allow for at least 10 years of follow up from ALL diagnosis, children (0-18 years) with ALL diagnosed and treated at SickKids, Toronto, Canada between 1994-2004 were studied. Medical records of patients with CNS relapse were examined to determine whether CNS relapse was diagnosed based on cytology of a routinely obtained CSF sample, a CSF sample obtained because of signs and symptoms or a CSF sample obtained after the diagnosis of a bone marrow relapse. Of 494 children treated for ALL, 31 (6.6%) developed a relapse of ALL involving the CNS. Twenty-two had an isolated CNS relapse and nine had a combined bone marrow and CNS relapse. Among patients with isolated CNS relapse, 73% (16/22) were diagnosed based on routine CSF samples obtained from asymptomatic children. Conversely, 89% (8/9) of children with combined bone marrow and CNS relapse presented with symptoms and signs that prompted CSF examination. Routine CSF examination at the time of LP for intrathecal chemotherapy is useful in detecting CNS relapse. © 2014 Wiley Periodicals, Inc.

qPCR detection of Mycobacterium leprae in biopsies and slit skin smear of different leprosy clinical forms.

PubMed

Azevedo, Michelle de Campos Soriani; Ramuno, Natália Mortari; Fachin, Luciana Raquel Vincenzi; Tassa, Mônica; Rosa, Patrícia Sammarco; Belone, Andrea de Faria Fernandes; Diório, Suzana Madeira; Soares, Cleverson Teixeira; Garlet, Gustavo Pompermaier; Trombone, Ana Paula Favaro

Leprosy, whose etiological agent is Mycobacterium leprae, is a chronic infectious disease that mainly affects the skin and peripheral nervous system. The diagnosis of leprosy is based on clinical evaluation, whereas histopathological analysis and bacilloscopy are complementary diagnostic tools. Quantitative PCR (qPCR), a current useful tool for diagnosis of infectious diseases, has been used to detect several pathogens including Mycobacterium leprae. The validation of this technique in a robust set of samples comprising the different clinical forms of leprosy is still necessary. Thus, in this study samples from 126 skin biopsies (collected from patients on all clinical forms and reactional states of leprosy) and 25 slit skin smear of leprosy patients were comparatively analyzed by qPCR (performed with primers for the RLEP region of M. leprae DNA) and routine bacilloscopy performed in histological sections or in slit skin smear. Considering clinical diagnostic as the gold standard, 84.9% of the leprosy patients were qPCR positive in skin biopsies, resulting in 84.92% sensitivity, with 84.92 and 61.22% positive (PPV) and negative (NPV) predictive values, respectively. Concerning bacilloscopy of histological sections (BI/H), the sensitivity was 80.15% and the PPV and NPV were 80.15 and 44.44%, respectively. The concordance between qPCR and BI/H was 87.30%. Regarding the slit skin smear, 84% of the samples tested positive in the qPCR. Additionally, qPCR showed 100% specificity, since all samples from different mycobacteria, from healthy individuals, and from other granulomatous diseases presented negative results. In conclusion, the qPCR technique for detection of M. leprae using RLEP primers proved to be specific and sensitive, and qPCR can be used as a complementary test to diagnose leprosy irrespective of the clinical form of disease. Copyright © 2016 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

Comparison of microbiological diagnosis of urinary tract infection in young children by routine health service laboratories and a research laboratory: Diagnostic cohort study

PubMed Central

Birnie, Kate; Hay, Alastair D.; Wootton, Mandy; Howe, Robin; MacGowan, Alasdair; Whiting, Penny; Lawton, Michael; Delaney, Brendan; Downing, Harriet; Dudley, Jan; Hollingworth, William; Lisles, Catherine; Little, Paul; O’Brien, Kathryn; Pickles, Timothy; Rumsby, Kate; Thomas-Jones, Emma; Van der Voort, Judith; Waldron, Cherry-Ann; Harman, Kim; Hood, Kerenza; Butler, Christopher C.; Sterne, Jonathan A. C.

2017-01-01

Objectives To compare the validity of diagnosis of urinary tract infection (UTI) through urine culture between samples processed in routine health service laboratories and those processed in a research laboratory. Population and methods We conducted a prospective diagnostic cohort study in 4808 acutely ill children aged <5 years attending UK primary health care. UTI, defined as pure/predominant growth ≥105 CFU/mL of a uropathogen (the reference standard), was diagnosed at routine health service laboratories and a central research laboratory by culture of urine samples. We calculated areas under the receiver-operator curve (AUC) for UTI predicted by pre-specified symptoms, signs and dipstick test results (the “index test”), separately according to whether samples were obtained by clean catch or nappy (diaper) pads. Results 251 (5.2%) and 88 (1.8%) children were classified as UTI positive by health service and research laboratories respectively. Agreement between laboratories was moderate (kappa = 0.36; 95% confidence interval [CI] 0.29, 0.43), and better for clean catch (0.54; 0.45, 0.63) than nappy pad samples (0.20; 0.12, 0.28). In clean catch samples, the AUC was lower for health service laboratories (AUC = 0.75; 95% CI 0.69, 0.80) than the research laboratory (0.86; 0.79, 0.92). Values of AUC were lower in nappy pad samples (0.65 [0.61, 0.70] and 0.79 [0.70, 0.88] for health service and research laboratory positivity, respectively) than clean catch samples. Conclusions The agreement of microbiological diagnosis of UTI comparing routine health service laboratories with a research laboratory was moderate for clean catch samples and poor for nappy pad samples and reliability is lower for nappy pad than for clean catch samples. Positive results from the research laboratory appear more likely to reflect real UTIs than those from routine health service laboratories, many of which (particularly from nappy pad samples) could be due to contamination. Health service laboratories should consider adopting procedures used in the research laboratory for paediatric urine samples. Primary care clinicians should try to obtain clean catch samples, even in very young children. PMID:28199403