Standardization of diagnostic biomarker concentrations in urine; the hematuria caveat

Sensitive and specific urinary biomarkers can improve patient outcomes in many diseases through informing early diagnosis. Unfortunately, to date, the accuracy and translation of diagnostic urinary biomarkers into clinical practice has been disappointing. We believe this may be due to inappropriate standardization of diagnostic urinary biomarkers. Our objective was therefore to characterize the effects of standardizing urinary levels of IL-6, IL-8, and VEGF using the commonly applied standards namely urinary creatinine, osmolarity and protein. First, we report results based on the biomarker levels measured in 120 hematuric patients, 80 with pathologically confirmed bladder cancer, 27 with confounding pathologies and 13 in whom no underlying cause for their hematuria was identified, designated “no diagnosis”. Protein levels were related to final diagnostic categories (p = 0.022, ANOVA). Osmolarity (mean = 529 mOsm; median = 528 mOsm) was normally distributed, while creatinine (mean = 10163 µmol/l, median = 9350 µmol/l) and protein (0.3297, 0.1155 mg/ml) distributions were not. When we compared AUROCs for IL-6, IL-8 and VEGF levels, we found that protein standardized levels consistently resulted in the lowest AUROCs. The latter suggests that protein standardization attenuates the “true” differences in biomarker levels across controls and bladder cancer samples. Second, in 72 hematuric patients; 48 bladder cancer and 24 controls, in whom urine samples had been collected on recruitment and at follow-up (median = 11 (1 to 20 months)), we demonstrate that protein levels were approximately 24% lower at follow-up (Bland Altman plots). There was an association between differences in individual biomarkers and differences in protein levels over time, particularly in control patients.

Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936.

In a European BIOMED-2 collaborative study, multiplex PCR assays have successfully been developed and standardized for the detection of clonally rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes and the chromosome aberrations t(11;14) and t(14;18). This has resulted in 107 different primers in only 18 multiplex PCR tubes: three VH-JH, two DH-JH, two Ig kappa (IGK), one Ig lambda (IGL), three TCR beta (TCRB), two TCR gamma (TCRG), one TCR delta (TCRD), three BCL1-Ig heavy chain (IGH), and one BCL2-IGH. The PCR products of Ig/TCR genes can be analyzed for clonality assessment by heteroduplex analysis or GeneScanning. The detection rate of clonal rearrangements using the BIOMED-2 primer sets is unprecedentedly high. This is mainly based on the complementarity of the various BIOMED-2 tubes. In particular, combined application of IGH (VH-JH and DH-JH) and IGK tubes can detect virtually all clonal B-cell proliferations, even in B-cell malignancies with high levels of somatic mutations. The contribution of IGL gene rearrangements seems limited. Combined usage of the TCRB and TCRG tubes detects virtually all clonal T-cell populations, whereas the TCRD tube has added value in case of TCRgammadelta(+) T-cell proliferations. The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease.

Physicochemical and mineralogical characteristics of soil/saprolite cores from a field research site, Tennessee

Site characterization is an essential initial step in determining the feasibility of remedial alternatives at hazardous waste sites. Physicochemical and mineralogical characterization of U-contaminated soils in deeply weathered saprolite at Area 2 of the DOE Field Research Center (FRC) site, Oak Ridge, TN, was accomplished to examine the feasibility of bioremediation. Concentrations of U in soil–saprolite (up to 291 mg kg–1 in oxalate-extractable Uo) were closely related to low pH (ca. 4–5), high effective cation exchange capacity without Ca (64.7–83.2 cmolc kg–1), amorphous Mn content (up to 9910 mg kg–1), and the decreased presence of relative clay mineral contents in the bulk samples (i.e., illite 2.5–12 wt. %, average 32 wt. %). The pH of the fill material ranged from 7.0 to 10.5, whereas the pH of the saprolite ranged from 4.5 to 8. Uranium concentration was highest (about 300 mg kg–1) at around 6 m below land surface near the saprolite–fill interface. The pH of ground water at Area 2 tended to be between 6 and 7 with U concentrations of about 0.9 to 1.7 mg L–1. These site specific characteristics of Area 2, which has lower U and nitrate contamination levels and more neutral ground water pH compared with FRC Areas 1 and 3 (ca. 5.5 and

Influence of the Graphical Levels of Detail of a Virtual Thrower on the Perception of the Movement

Virtual reality has a number of advantages for analyzing sports interactions such as the standardization of experimental conditions, stereoscopic vision, and complete control of animated humanoid movement. Nevertheless, in order to be useful for sports applications, accurate perception of simulated movement in the virtual sports environment is essential. This perception depends on parameters of the synthetic character such as the number of degrees of freedom of its skeleton or the levels of detail (LOD) of its graphical representation. This study focuses on the influence of this latter parameter on the perception of the movement. In order to evaluate it, this study analyzes the judgments of immersed handball goalkeepers that play against a graphically modified virtual thrower. Five graphical representations of the throwing action were defined: a textured reference level (L0), a nontextured level (L1), a wire-frame level (L2), a moving point light display (MLD) level with a normal-sized ball (L3), and a MLD level where the ball is represented by a point of light (L4). The results show that judgments made by goalkeepers in the L4 condition are significantly less accurate than in all the other conditions (p

Guidelines for the measurement of BCR-ABL1 transcripts in chronic myeloid leukaemia

Molecular testing for the BCR-ABL1 fusion gene by real time quantitative polymerase chain reaction (RT-qPCR) is the most sensitive routine approach for monitoring the response to therapy of patients with chronic myeloid leukaemia. In the context of tyrosine kinase inhibitor (TKI) therapy, the technique is most appropriate for patients who have achieved complete cytogenetic remission and can be used to define specific therapeutic milestones. To achieve this effectively, standardization of the laboratory procedures and the interpretation of results are essential. We present here consensus best practice guidelines for RT-qPCR testing, data interpretation and reporting that have been drawn up and agreed by a consortium of 21 testing laboratories in the United Kingdom and Ireland in accordance with the procedures of the UK Clinical Molecular Genetics Society.

Evaluation of sources of uncertainties in microtensile bond strength of dental adhesive system for different specimen geometries

Objective: The aim of this research is to use finite element analysis (FEA) to quantify the effect of the sample shape and the imperfections induced during the manufacturing process of samples on the bond strength and modes of failure of dental adhesive systems through microtensile test. Using the FEA prediction for individual parameters effect, estimation of expected variation and spread of the microtensile bond strength results for different sample geometries is made. Methods: The estimated stress distributions for three different sample shapes, hourglass, stick and dumbbell predicted by FEA are used to predict the strength for different fracture modes. Parameters such as the adhesive thickness, uneven interface of the adhesive and composite and dentin, misalignment of axis of loading, the existence of flaws such as induced cracks during shaping the samples or bubbles created during application of the adhesive are considered. Microtensile experiments are performed simultaneously to measure bond strength and modes of failure. These are compared with the FEA results. Results: The relative bonding strength and its standard deviation for the specimens with different geometries measured through the microtensile tests confirm the findings of the FEA. The hourglass shape samples show lower tensile bond strength and standard deviation compared to the stick and dumbbell shape samples. ANOVA analysis confirms no significant difference between dumbbell and stick geometry results, and major differences of these two geometries compared to hourglass shape measured values. Induced flaws in the adhesive and misalignment of the angle of application of load have significant effect on the microtensile bond strength. Using adhesive with higher modulus the differences between the bond strength of the three sample geometries increase. Significance: The result of the research clarifies the importance of the sample geometry chosen in measuring the bond strength. It quantifies the effect of the imperfections on the bond strength for each of the sample geometries through a systematic and all embracing study. The results explain the reasons of the large spread of the microtensile test results reported by various researchers working in different labs and the need for standardization of the test method and sample shape used in evaluation of the dentin-adhesive bonding system. © 2007 Academy of Dental Materials.

Characterization of a reference material for BCR-ABL (M-BCR) mRNA quantitation by real-time amplification assays:towards new standards for gene expression measurements

Monitoring of BCR-ABL transcripts has become established practice in the management of chronic myeloid leukemia. However, nucleic acid amplification techniques are prone to variations which limit the reliability of real-time quantitative PCR (RQ-PCR) for clinical decision making, highlighting the need for standardization of assays and reporting of minimal residual disease (MRD) data. We evaluated a lyophilized preparation of a leukemic cell line (K562) as a potential quality control reagent. This was found to be relatively stable, yielding comparable respective levels of ABL, GUS and BCR-ABL transcripts as determined by RQ-PCR before and after accelerated degradation experiments as well as following 5 years storage at -20 degrees C. Vials of freeze-dried cells were sent at ambient temperature to 22 laboratories on four continents, with RQ-PCR analyses detecting BCR-ABL transcripts at levels comparable to those observed in primary patient samples. Our results suggest that freeze-dried cells can be used as quality control reagents with a range of analytical instrumentations and could enable the development of urgently needed international standards simulating clinically relevant levels of MRD.

Assessment of Anaerobic Biodegradation of Aromatic Hydrocarbons: The Impact of Molecular Biology Approaches

One of the most cost effective methods of pollution remediation is through natural attenuation where the resident microorganisms are responsible for the breakdown of pollutants (Dou et al. 2008). Other forms of bioremediation - such as analogue enrichment, composting and bio-venting - also use the microbes already present in a contaminated site to enhance the remediation process. In order for these approaches to be successful, in an industrial setting, some form of monitoring needs to take place enabling conclusions to be drawn about the degradation processes occurring. In this review we look at some key molecular biology techniques that have the potential to act as a monitoring tool for industries dealing with contaminated land. 

EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations.

PCR-based immunoglobulin (Ig)/T-cell receptor (TCR) clonality testing in suspected lymphoproliferations has largely been standardized and has consequently become technically feasible in a routine diagnostic setting. Standardization of the pre-analytical and post-analytical phases is now essential to prevent misinterpretation and incorrect conclusions derived from clonality data. As clonality testing is not a quantitative assay, but rather concerns recognition of molecular patterns, guidelines for reliable interpretation and reporting are mandatory. Here, the EuroClonality (BIOMED-2) consortium summarizes important pre- and post-analytical aspects of clonality testing, provides guidelines for interpretation of clonality testing results, and presents a uniform way to report the results of the Ig/TCR assays. Starting from an immunobiological concept, two levels to report Ig/TCR profiles are discerned: the technical description of individual (multiplex) PCR reactions and the overall molecular conclusion for B and T cells. Collectively, the EuroClonality (BIOMED-2) guidelines and consensus reporting system should help to improve the general performance level of clonality assessment and interpretation, which will directly impact on routine clinical management (standardized best-practice) in patients with suspected lymphoproliferations.

Systematically Identifying Relevant Research : Case Study on Child Protection Social workers' Resilience

Context: The development of a consolidated knowledge base for social work requires rigorous approaches to identifying relevant research. Method: The quality of 10 databases and a web search engine were appraised by systematically searching for research articles on resilience and burnout in child protection social workers. Results: Applied Social Sciences Index and Abstracts, Social Services Abstracts and Social Sciences Citation Index (SSCI) had greatest sensitivity, each retrieving more than double than any other database. PsycINFO and Cumulative Index to Nursing and Allied Health (CINAHL) had highest precision. Google Scholar had modest sensitivity and good precision in relation to the first 100 items. SSCI, Google Scholar, Medline, and CINAHL retrieved the highest number of hits not retrieved by any other database. Conclusion: A range of databases is required for even modestly comprehensive searching. Advanced database searching methods are being developed but the profession requires greater standardization of terminology to assist in information retrieval.

Is the raised volume rapid thoracic compression technique ready for use in clinical trials in infants with cystic fibrosis?

The European Cystic Fibrosis Society Clinical Trial Network (ECFS-CTN) has established a Standardization Committee to undertake a rigorous evaluation of promising outcome measures with regard to use in multicentre clinical trials in cystic fibrosis (CF). The aim of this article is to present a review of literature on clinimetric properties of the infant raised-volume rapid thoracic compression (RVRTC) technique in the context of CF, to summarise the consensus amongst the group on feasibility and answer key questions regarding the promotion of this technique to surrogate endpoint status.

METHODS: A literature search (from 1985 onwards) identified 20 papers that met inclusion criteria of RVRTC use in infants with CF. Data were extracted and tabulated regarding repeatability, validity, correlation with other outcome measures, responsiveness and reference values. A working group discussed the tables and answered 4 key questions.

RESULTS: Overall, RVRTC in particular forced expiratory volume in 0.5s, showed good clinimetric properties despite presence of individual variability. Few studies showed a relationship between RVRTC and inflammation and infection, and to date, data remains limited regarding the responsiveness of RVRTC after an intervention. Concerns were raised regarding feasibility in multi-centre studies and availability of reference values.

CONCLUSION: The ECFS-CTN Working Group considers that RVRTC cannot be used as a primary outcome in clinical trials in infants with CF before universal standardization of this measurement is achieved and implementation of inter-institutional networking is in place. We advise its use currently in phase I/II trials and as a secondary endpoint in phase III studies. We emphasise the need for (1) more short-term variability and longitudinal 'natural history' studies, and (2) robust reference values for commercially available devices.

VentBase:Developing a consensus among stakeholders in the deep-sea regarding environmental impact assessment for deep-sea mining-A workshop report

Mining seafloor massive sulfides for metals is an emergent industry faced with environmental management challenges. These revolve largely around limits to our current understanding of biological variability in marine systems, a challenge common to all marine environmental management. VentBase was established as a forum where academic, commercial, governmental, and non-governmental stakeholders can develop a consensus regarding the management of exploitative activities in the deep-sea. Participants advocate a precautionary approach with the incorporation of lessons learned from coastal studies. This workshop report from VentBase encourages the standardization of sampling methodologies for deep-sea environmental impact assessment. VentBase stresses the need for the collation of spatial data and importance of datasets amenable to robust statistical analyses. VentBase supports the identification of set-asides to prevent the local extirpation of vent-endemic communities and for the post-extraction recolonization of mine sites. © 2013.