Implementation of automated reporting of estimated glomerular filtration rate among Veterans Affairs laboratories: a retrospective study.

BACKGROUND: Automated reporting of estimated glomerular filtration rate (eGFR) is a recent advance in laboratory information technology (IT) that generates a measure of kidney function with chemistry laboratory results to aid early detection of chronic kidney disease (CKD). Because accurate diagnosis of CKD is critical to optimal medical decision-making, several clinical practice guidelines have recommended the use of automated eGFR reporting. Since its introduction, automated eGFR reporting has not been uniformly implemented by U. S. laboratories despite the growing prevalence of CKD. CKD is highly prevalent within the Veterans Health Administration (VHA), and implementation of automated eGFR reporting within this integrated healthcare system has the potential to improve care. In July 2004, the VHA adopted automated eGFR reporting through a system-wide mandate for software implementation by individual VHA laboratories. This study examines the timing of software implementation by individual VHA laboratories and factors associated with implementation. METHODS: We performed a retrospective observational study of laboratories in VHA facilities from July 2004 to September 2009. Using laboratory data, we identified the status of implementation of automated eGFR reporting for each facility and the time to actual implementation from the date the VHA adopted its policy for automated eGFR reporting. Using survey and administrative data, we assessed facility organizational characteristics associated with implementation of automated eGFR reporting via bivariate analyses. RESULTS: Of 104 VHA laboratories, 88% implemented automated eGFR reporting in existing laboratory IT systems by the end of the study period. Time to initial implementation ranged from 0.2 to 4.0 years with a median of 1.8 years. All VHA facilities with on-site dialysis units implemented the eGFR software (52%, p<0.001). Other organizational characteristics were not statistically significant. CONCLUSIONS: The VHA did not have uniform implementation of automated eGFR reporting across its facilities. Facility-level organizational characteristics were not associated with implementation, and this suggests that decisions for implementation of this software are not related to facility-level quality improvement measures. Additional studies on implementation of laboratory IT, such as automated eGFR reporting, could identify factors that are related to more timely implementation and lead to better healthcare delivery.

Explosion in fume cupboard damages several laboratories

An explosion occurred in a busy university laboratory during a few minutes when it happened to be unoccupied. The explosion was puzzling since the laboratory was dedicated to geochemical work, such as digesting rock samples with stable, inorganic reagents. The only unstable substance knowingly stored or handled for this purpose, perchloric acid, was not in use on the day of the incident. The investigation was unable to reach an exact conclusion but did prove that a substantial organic contaminant, not on the laboratory inventory, must have been present

Collaborative artistic laboratories. Transfrontier spaces of cultural production

The appearance of the open code paradigm and the demands of social movements have permeated the ways in which today’s cultural institutions are organized. This article analyzes the birth of a new critical and cooperative spatiality and how it is transforming current modes of cultural research and production. It centers on the potential for establishing the new means of cooperation that are being tested in what are defined as collaborative artistic laboratories. These are hybrid spaces of research and creation based on networked and cooperative structures producing a new societal-technical body that forces us to reconsider the traditional organic conditions of the productive scenarios of knowledge and artistic practice.

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Guidance for laboratories performing molecular pathology for cancer patients

Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.

A mobile robot platform for open learning based on serious games and remote laboratories

Within the pedagogical community, Serious Games have arisen as a viable alternative to traditional course-based learning materials. Until now, they have been based strictly on software solutions. Meanwhile, research into Remote Laboratories has shown that they are a viable, low-cost solution for experimentation in an engineering context, providing uninterrupted access, low-maintenance requirements, and a heightened sense of reality when compared to simulations. This paper will propose a solution where both approaches are combined to deliver a Remote Laboratory-based Serious Game for use in engineering and school education. The platform for this system is the WebLab-Deusto Framework, already well-tested within the remote laboratory context, and based on open standards. The laboratory allows users to control a mobile robot in a labyrinth environment and take part in an interactive game where they must locate and correctly answer several questions, the subject of which can be adapted to educators' needs. It also integrates the Google Blockly graphical programming language, allowing students to learn basic programming and logic principles without needing to understand complex syntax.

Addressing software impact in the design of remote laboratories

Remote Laboratories or WebLabs constitute a first-order didactic resource in engineering faculties. However, in many cases, they lack a proper software design, both in the client and server side, which degrades their quality and academic usefulness. This paper presents the main characteristics of a Remote Laboratory, analyzes the software technologies to implement the client and server sides in a WebLab, and correlates these technologies with the characteristics to facilitate the selection of a technology to implement a WebLab. The results obtained suggest the adoption of a Service Oriented Laboratory Architecture-based approach for the design of future Remote Laboratories so that client-agnostic Remote Laboratories and Remote Laboratory composition are enabled. The experience with the real Remote Laboratory, WebLab-Deusto, is also presented.

Genotoxic effects in occupational exposure to formaldehyde: A study in anatomy and pathology laboratories and formaldehyde-resins production

ABSTRACT – Background: According to the Report on Carcinogens, formaldehyde ranks 25th in the overall U.S. chemical production, with more than 5 million tons produced each year. Given its economic importance and widespread use, many people are exposed to formaldehyde environmentally and/or occupationally. Presently, the International Agency for Research on Cancer classifies formaldehyde as carcinogenic to humans (Group 1), based on sufficient evidence in humans and in experimental animals. Manyfold in vitro studies clearly indicated that formaldehyde can induce genotoxic effects in proliferating cultured mammalian cells. Furthermore, some in vivo studies have found changes in epithelial cells and in peripheral blood lymphocytes related to formaldehyde exposure. Methods: A study was carried out in Portugal, using 80 workers occupationally exposed to formaldehyde vapours: 30 workers from formaldehyde and formaldehyde-based resins production factory and 50 from 10 pathology and anatomy laboratories. A control group of 85 non-exposed subjects was considered. Exposure assessment was performed by applying simultaneously two techniques of air monitoring: NIOSH Method 2541 and Photo Ionization Detection equipment with simultaneously video recording. Evaluation of genotoxic effects was performed by application of micronucleus test in exfoliated epithelial cells from buccal mucosa and peripheral blood lymphocytes. Results: Time-weighted average concentrations not exceeded the reference value (0.75 ppm) in the two occupational settings studied. Ceiling concentrations, on the other hand, were higher than reference value (0.3 ppm) in both. The frequency of micronucleus in peripheral blood lymphocytes and in epithelial cells was significantly higher in both exposed groups than in the control group (p < 0.001). Moreover, the frequency of micronucleus in peripheral blood lymphocytes was significantly higher in the laboratories group than in the factory workers (p < 0.05). A moderate positive correlation was found between duration of occupational exposure to formaldehyde (years of exposure) and micronucleus frequency in peripheral blood lymphocytes (r = 0.401; p < 0.001) and in epithelial cells (r = 0.209; p < 0.01). Conclusions: The population studied is exposed to high peak concentrations of formaldehyde with a long-term exposure. These two aspects, cumulatively, can be the cause of the observed genotoxic endpoint effects. The association of these cytogenetic effects with formaldehyde exposure gives important information to risk assessment process and may also be used to assess health risks for exposed worker

Supervisor-Student Relations: Examining the Spectrum of Conflicts of Interest in Bioscience Laboratories

Much attention has been given to financial conflicts of interest (COI) in bioscience research. Yet to date, surprisingly little attention has focused on other COIs that arise in supervisor-student relations. We examine a spectrum of related situations, ranging from standard graduate supervision through to dual relationships sometimes found in research with commercial potential. We illustrate some of the less-obvious factors that can bias supervisory judgment, and situate financial COI along a spectrum of forces that are deserving of recognition. We conclude by providing two sets of recommendations: one for individual supervisors, and the other for institutions and policy-makers.