Clinical laboratory analytics: Challenges and promise for an emerging discipline

The clinical laboratory is a major source of health care data. Increasingly these data are being integrated with other data to inform health system-wide actions meant to improve diagnostic test utilization, service efficiency, and “meaningful use.” The Academy of Clinical Laboratory Physicians and Scientists hosted a satellite meeting on clinical laboratory analytics in conjunction with their annual meeting on May 29, 2014 in San Francisco. There were 80 registrants for the clinical laboratory analytics meeting. The meeting featured short presentations on current trends in clinical laboratory analytics and several panel discussions on data science in laboratory medicine, laboratory data and its role in the larger healthcare system, integrating laboratory analytics, and data sharing for collaborative analytics. One main goal of meeting was to have an open forum of leaders that work with the “big data” clinical laboratories produce. This article summarizes the proceedings of the meeting and content discussed.

Trans-radial versus trans-femoral access in patients with end-stage liver disease undergoing cardiac catheterization

Cardiac catheterization has been increasingly utilized to evaluate coronary artery disease in patients with end stage liver disease (ESLD). It is known in other populations that radial access reduces access site complications;however, there is a paucity of data in ESLD patients. We investigated vascular and bleeding complications rates between trans-femoral and trans-radial cardiac catheterizations in this high risk population. In this retrospective cohort study, three hundred and thirty four ESLD patients were identified between August 2004 and December 2012 who had undergone trans-femoral (femoral group) or trans-radial (radial group) cardiac catheterizations at our institution. The radial group was not significantly different from the femoral group in age (p = 0.056), proportions of genders (p = 0.85), and weight (p = 0.19); however, compared to the femoral group, the radial group had significantly lower blood pressure (p < 0.0001), hemoglobin (10.4 ± 1.9 vs 11.1 ± 2.02 g/dL, p = 0.001), and hematocrit (30.3 ± 5.7% vs 32.6 ± 6.0%, p < 0.0006), and had a significantly higher INR (1.94 ± 1.16 vs 1.59 ± 0.62, p = 0.0001). In terms of vascular complications, the radial group had a significantly lower rate of pseudoaneurysms (0% vs 3.7%, p = 0.019) than the femoral group. While there were no bleeding complications in either group or differences in transfusion requirements, there was a significantly lower percentage drop in hematocrit in the radial group compared to the femoral group (5.4% vs 7.8%, p = 0.039). In conclusion, trans-radial catheterization is associated with lower rates of vascular access site complications compared to trans-femoral catheterization.

The successful implementation of a licensed data management interface between a Sunquest(®) laboratory information system and an AB SCIEX™ mass spectrometer

Background:

Interfacing complex laboratory equipment to laboratory information systems (LIS) has become a more commonly encountered problem in clinical laboratories, especially for instruments that do not have an interface provided by the vendor. Liquid chromatography-tandem mass spectrometry is a great example of such complex equipment, and has become a frequent addition to clinical laboratories. As the testing volume on such instruments can be significant, manual data entry will also be considerable and the potential for concomitant transcription errors arises. Due to this potential issue, our aim was to interface an AB SCIEX™ mass spectrometer to our Sunquest^® LIS.

Materials and Methods:

We licensed software for the data management interface from the University of Pittsburgh, but extended this work as follows: The interface was designed so that it would accept a text file exported from the AB SCIEX™ × 5500 QTrap^® mass spectrometer, pre-process the file (using newly written code) into the correct format and upload it into Sunquest^® via file transfer protocol.

Results:

The licensed software handled the majority of the interface tasks with the exception of converting the output from the Analyst^® software to the required Sunquest^® import format. This required writing of a “pre-processor” by one of the authors which was easily integrated with the supplied software.

Conclusions:

We successfully implemented the data management interface licensed from the University of Pittsburgh. Given the coding that was required to write the pre-processor, and alterations to the source code that were performed when debugging the software, we would suggest that before a laboratory decides to implement such an interface, it would be necessary to have a competent computer programmer available.

Decolorization of a mixture of textile dyes using Bjerkandera sp. BOL-13

The white-rot fungus Bjerkandera sp. BOL-13 was evaluated regarding decolorization of four textile dyes Reactive blue 21, Reactive black 5, Reactive orange 13 and Reactive yellow 206. Experiments were performed in batch and continuous modes. The total dye concentration in all experiments was 100 mg l(-1). The results of the batch experiments showed that the fungus decolorized all dyes but at different rates. There was, however, an increase in the ultraviolet (UV) absorbance when a medium with a low concentration of nitrogen was used. No increase in UV range was observed when the nitrogen concentration was increased. A continuous experiment was performed to study the decolorization of a mixture of three of the dyes Reactive blue 21, Reactive black 5 and Reactive orange 13. Scanning of inlet and outlet samples showed that the absorbance at the peaks in the visible range decreased by 60-66%. The UV absorbance of the outlet increased during the first days of operation after which it decreased again to reach the same level as the inlet. The hydraulic retention time in the reactor was 3 days. The medium containing the higher nitrogen concentration was used in the continuous experiment.

Creating a clinical video-conferencing facility in a security-constrained environment using open-source AccessGrid software and consumer hardware

The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components.

A code of professional ethical conduct for the American Medical Informatics Association: an AMIA Board of Directors approved white paper

The AMIA Board of Directors has decided to periodically publish AMIA's Code of Professional Ethical Conduct for its members in the Journal of the American Medical Informatics Association. The Code also will be available on the AMIA Web site at www.amia.org as it continues to evolve in response to feedback from the AMIA membership. The AMIA Board acknowledges the continuing work and dedication of the AMIA Ethics Committee. AMIA is the copyright holder of this work.

Sequential removal of heavy metals ions and organic pollutants using an algal-bacterial consortium

The residual algal-bacterial biomass from photosynthetically supported, organic pollutant biodegradation processes, in enclosed photobioreactors, was tested for its ability to accumulate Cu(II), Ni(II), Cd(II), and Zn(II). Salicylate was chosen as a model contaminant. The algal-bacterial biomass combined the high adsorption capacity of microalgae with the low cost of the residual biomass, which makes it an attractive biosorbent for environmental applications. Cu(II) was preferentially taken-up from the medium when the metals were present both separately and in combination. There was no observed competition for adsorption sites, which suggested that Cu(II), Ni(II), Cd(II), and Zn(II) bind to different sites and that active Ni(II), Cd(II) and Zn(II) binding groups were present at very low concentrations. Therefore, special focus was given to Cu(II) biosorption. Cu(II) biosorption by the algal-bacterial biomass was characterized by an initial fast cell surface adsorption followed by a slower metabolically driven uptake. pH, Cu(II), and algal-bacterial concentration significantly affected the biosorption capacity for Cu(II). Maximum Cu(II) adsorption capacities of 8.5+/-0.4 mg g-1 were achieved at an initial Cu(II) concentration of 20 mg l-1 and at pH 5 for the tested algal-bacterial biomass. These are consistent with values reported for other microbial sorbents under similar conditions. The desorption of Cu(II) from saturated biomass was feasible by elution with a 0.0125 M HCl solution. Simultaneous Cu(II) and salicylate removal in a continuous stirred tank photobioreactor was not feasible due to the high toxicity of Cu(II) towards the microbial culture. The introduction of an adsorption column, packed with the algal-bacterial biomass, prior to the photobioreactor reduced Cu(II) concentration, thereby allowing the subsequent salicylate biodegradation in the photobioreactor.

Degradation of toxaphene by Bjerkandera sp. strain BOL13 using waste biomass as a cosubstrate

The white-rot fungus Bjerkandera sp. strain BOL13 was capable of degrading toxaphene when supplied with wood chips, wheat husk or cane molasses as cosubstrates in batch culture experiments. Approximately 85% of toxaphene was removed when wheat husk was the main substrate. The production of lignin peroxidase was only stimulated when wheat husk was present in the liquid medium. Although xylanase was always detected, wheat husk supported the highest xylanase production. A negligible amount of beta-glucosidase and cellulase were found in the batch culture medium. To the best of our knowledge, this is the first reported case of toxaphene degradation by white-rot fungi.

The ability of white-rot fungi to degrade the endocrine-disrupting compound nonylphenol

Phanerochaete chrysosporium, Pleurotus ostreatus, Trametes versicolor and Bjerkandera sp. BOL13 were tested for their ability to degrade the endocrine-disrupting compound nonylphenol at an initial concentration of 100 mg l-1. The highest removals were achieved with T. versicolor and Bjerkandera sp. BOL13, which were able to degrade 97 mg l-1 and 99 mg l-1 of nonylphenol in 25 days of incubation, respectively. Nonylphenol removal was associated with the production of laccase by T. versicolor, but the levels of laccase, manganese peroxidase and lignin peroxidase produced by Bjerkandera sp. BOL13 were very low. At 14 degrees C, T. versicolor and Bjerkandera sp. BOL13 sustained the removal of 88 mg l-1 and 79 mg l-1 of nonylphenol, respectively. No pollutant removal was recorded at 4 degrees C, although both fungi could grow at this temperature in the absence of nonylphenol. A microtoxicity assay showed that the fungi produced compounds that were toxic to Vibrio fischerii; and thus a reduction in toxicity could not be correlated with nonylphenol metabolism. T. versicolor and Bjerkandera sp. BOL13 were capable of colonizing soil artificially contaminated with 430 mg kg-1 of nonylphenol. Only 1.3+/-0.1% of nonylphenol remained in the soil after 5 weeks of incubation.

Characteristics of educational software use in 106 clinical laboratories

The University of Washington, Seattle, has developed educational software for clinical laboratories. We used a 32-question survey to study software implementation. Of 106 clinical laboratories (response rate, 60%) that purchased the software and completed the survey, 89 laboratories (84%) that reported using the software formed the basis for the study. The most common software users were laboratory personnel, followed by medical technologist or medical laboratory technician students, residents, and medical students; the mean (SD) number of personnel categories using the software per laboratory was 1.8 (0.8). The most common reasons for use were initial instruction, cross-training, and competency assessment. The most frequent setting for software use was an area where laboratory testing occurred, followed by a dedicated training location, a location chosen by the employee, a classroom, and a distance learning mode. On a scale of 1 (poor) to 5 (excellent), the average satisfaction rating as an instructional tool was 4.4 and as a competency assessment tool, 4.2. Compared with laboratories in hospitals with 400 beds or fewer, laboratories in hospitals with more than 400 beds used the software for more categories of users (P = .008), had a higher proportion of laboratories using it for residents (P = .003), and had a higher proportion of laboratories with dedicated training areas (P = .02).