bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Activated Protein C Resistance With Factor V Leiden Testing by Molecular Assay
Authors: Perry William R , Pipe Steven W , Li Shih-Hon 
Published: September 2019

Abstract
Factor V Leiden (FVL) is a variant form of coagulation factor V that is the most common inherited risk factor for venous thromboembolism in people of European ancestry. FVL is associated with the missense mutation, p.R506Q, which encodes a FV protein resistant to cleavage by activated protein C (APC). Laboratory testing for FVL includes both phenotypic assays that assess APC resistance (APCR) and molecular assays that evaluate FVL genotype (FVLM) directly. Although APCR results are typically highly concordant with FVL genotype, discrepancies are known to occur and may result in inference of an incorrect FV genotype if only APCR testing is used. The objective of this study was to compare the results of these two testing methodologies and to identify potential explanations for discrepancies in results. Data were obtained by searching the electronic medical record of a large academic hospital for patients who underwent both APCR and FVLM testing from 2013 to 2018. APCR was evaluated using the ratio between two dilute Russell Viper Venom Time (DRVVT) tests, one preincubated with a protein C activator derived from A contortrix contortrix venom and the other with vehicle; the validated normal APCR ratio is ≥1.7. FVLM was performed by invader analysis utilizing fluorescence resonance energy transfer (FRET). In total, 424 patients underwent testing with both assays. Of 21 patients who had APCR assay clot times that exceeded the measurement range, all were FVLM negative, and 15 were anticoagulated during APCR testing. Of the 403 patients with reportable results for both tests, 385 (95.5%) patients had normal APCR and were FVLM negative. Of the 18 (4.5%) patients with discrepant results, 15 (3.7%) had an abnormally low APCR but were FVLM negative, and 3 (0.8%) had a normal APCR but were FVLM heterozygous. Among the 15 FVLM-negative patients with abnormal APCR <1.7, 11 (73.3%) were on warfarin with/out enoxaparin and had low protein S activity and/or low protein C activity. Of the 3 FVLM heterozygous patients with normal APCR, 1 was on apixaban. Our results demonstrated a high concordance between APCR phenotype and FVLM genotype. The concordance of APCR and FVLM may be limited in patients with low protein S or low protein C activity and those on a range of anticoagulant therapy.
Verification of a Novel Multiplex PCR Respiratory Virus Panel in a US Biocontainment Unit
Authors: Dean Christina L , Alvey Emily , Evans Crystal , Hill Charles , Burd Eileen , Kraft Colleen 
Published: September 2019

Abstract
Emerging infectious diseases carry unique logistical, financial, and clinical ramifications. Rapid diagnostic testing methods can alleviate some of these challenges by providing definitive diagnoses earlier in the clinical course, leading to appropriate targeted therapy, cost savings, and improved patient outcomes. The BioFire FilmArray Respiratory Panel 2 plus (RP2plus; bioMérieux, Marcy l’Etoile, France) is a multiplexed nucleic acid test for detection of Middle East respiratory syndrome coronavirus (MERS-CoV) and 14 common viral and 4 bacterial respiratory pathogens in nasopharyngeal swabs obtained from those meeting MERS-CoV epidemiological criteria. The aim of this study was to verify the FilmArray RP2plus for use in our biocontainment unit. Of note, the RP2plus is FDA approved but not currently available for sale in the United States. Eight patient samples were tested with known results (GenMark Respiratory Virus Panel [RVP] or Cepheid Xpert Flu/RSV). We had concordant results between the platforms for samples containing influenza A, respiratory syncytial virus (RSV), parainfluenza virus 2, rhinovirus, and a negative sample. We evaluated two influenza B samples from two different patients. The FilmArray RP2plus did not detect influenza B in one of the patient samples. The sample was exhausted and repeat testing could not be performed. A second rhinovirus sample was not detected by the RP2plus, but Coronavirus 229E was detected in this sample, a virus not detected by the RVP. The sample was repeated and again did not detect rhinovirus. Further investigation into this discrepancy revealed that rhinovirus was originally detected by RVP at a signal of 34.4 nA (repeat of 46.9 nA). The concordant rhinovirus sample had a signal of 226.7 nA by RVP, which was much higher than the discrepant sample. Because of the low signal by RVP in the discrepant sample, perhaps the viral load was below the limit of detection of the RP2plus. All other quality control sample pools passed verification testing, including day-to-day and operator variance. It is not uncommon for a person under investigation (PUI) for a highly communicable disease to be evaluated in our facility. The performance of the RP2plus test on clinical samples showed acceptable concordance with our current means of testing for respiratory pathogens. The RP2plus will eliminate challenges implicated in storing and transporting specimens to an off-site lab, facilitate quicker turnaround time, and streamline the often cumbersome, complex protocols and practices required to work up a serious communicable disease.
Differences of Ionized Calcium Concentrations in Continuous Renal Replacement Therapy Among Three Analyzers
Authors: Salehi Maryam , Bryksin Janetta , Cole Lisa , Connor Michael J , Posey Tammy , Guarner Jeannette 
Published: September 2019

Abstract

Continuous renal replacement therapy (CRRT) is a standard of care for critically ill patients according to the guidelines for Kidney Disease Improving Global Outcomes Clinical Practice. Within the CRRT dialysis instrument, blood requires anticoagulation with citrate with a goal to have ionized calcium (iCa) <0.4 mmol/L. In our hospital system, nephrologists who manage the therapy rotate through these hospitals, although in each of the hospitals, instruments that measure iCa are different. The objective of this study was to demonstrate the differences in measurement by these instruments.

Method
Twelve patient samples were drawn in triplicate and compared in the three different analyzers: RAPIDPoint, Nova Biomedical, and GEM4000 analyzers. One of the analyzers uses whole blood while the other two measure iCa in plasma. In one of the facilities, samples were spun, decapped, sent to the automated line outlet, and tested after having been exposed to air, and thus an experiment in another facility decapped the specimens for an hour and retested.

Results
Postfilter iCa measurements ranged from 0.18 to 0.64 mmol/L; however, range was different for each of the instruments: The Nova measurements averaged 0.55 mmol/L (range 0.42-0.64), the Rapid Point 0.36 (0.28-0.45), and the GEM 0.30 (0.18-0.39). The average difference between results of the Nova and GEM was 0.25 mmol/L, between Nova and RAPIDPoint 0.19 mmol/L, and GEM and RAPIDPoint 0.06 mmol/L. The differences between the values measured 1 hour after the sample had been decapped were negligible.

Conclusion
This study demonstrates inconsistency among instruments when measuring iCa in CRRT blood samples. The Nova analyzer tends to give higher results while the Rapid Point and GEM are lower and with values closer together. Currently, there is no reference material or reference method established for low iCa in CRRT samples. This study helped our clinicians understand the differences that occur between the different analyzers for low levels of iCa in CRRT blood samples.
Better Blood Bank Administration Review and Bridging Epic Using QUEries (BB-BARBEQUE)
Authors: Hsu Jim , Gowani Faaria , Duhon Daniel , Ipe Tina , Leveque Christopher , Salazar Eric 
Published: September 2019

Abstract
High-volume blood banks at academic hospitals and medical centers have increased demands for utilization review, which can be manual and laborious. Every blood bank’s utilization review program is unique and depends on available personnel, staffing, and access to electronic medical records. A standardized, automated workflow for utilization review can reduce error and subjectivity and maximize efficiency. A customizable query that can accommodate different product utilization review criteria and is compatible with mainstream EMRs such as Epic is a valuable clinical tool for many practice settings. Furthermore, an efficient workflow that minimizes manual technician review and reduces provider fatigue can provide increased cost savings while maintaining compliant utilization review practices.
Modern versions of Microsoft Excel, the most used data spreadsheet program worldwide, incorporate new features for data collation and analysis, namely, Power Query. Power Query enhances Excel’s capabilities for self-service Business Intelligence (BI). We introduce an approach for Better Blood Bank Administration Review and Bridging Epic using QUEries (BB-BARBEQUE) and demonstrate a preliminary version of the workflow that enables ordinary end users, such as pathology residents, to conduct utilization reviews more easily and efficiently. The workflow is designed to dynamically capture product utilization data that are generated through Epic SQL reporting into a user-friendly spreadsheet format. The data are filtered by using customizable queries to capture blood product requests that are most likely to yield actionable results. Our reviews included blood product requests for units of packed red blood cells, platelets, fresh-frozen plasma, and cryoprecipitate, as well as extensive associated metadata, including the ordering unit, patient identifiers, provider names, dates and times of product use and laboratory collection, and most recent laboratory values for hemoglobin, platelet count, INR, and fibrinogen.
We compare this approach to the previous, manual workflow. Incidences deemed inappropriate for product use are tracked and compared with both approaches, through a metric designed to evaluate the number of successful provider contacts, either through a form letter or telephone call. We also provide preliminary comparisons of technician time saved by adopting this procedure compared to the previous approach. Overall, we show that automation of key steps in the utilization review procedure can significantly increase efficiency while improving the end-user experience, and we demonstrate an end-user product that is translatable to many institutions using an Epic EMR backend.
Comparison of Serum Free Light Chain Assay and Urine Protein Electrophoresis for the Detection of Monoclonal Gammopathies
Authors: Huang Rongrong , Yi Xin 
Published: September 2019

Abstract
Laboratory detection of monoclonal immunoglobulins is essential for the diagnosis and monitoring of monoclonal gammopathies (MGs). In alignment with the recent effort from the College of American Pathologists (CAP) to develop evidence-based clinical practice guideline for laboratory detection and initial diagnosis of MGs, we retrospectively collected 1-year laboratory results from three tests, including serum protein electrophoresis (SPEP) with reflex to immunofixation (IFE), urine protein electrophoresis (UPEP) with reflex to immunofixation (IFE), and serum free light chain analysis (FLC), to identify the current ordering patterns from clinical care providers and analyze the diagnostic performances of these tests. From February 2018 to February 2019, there were a total of 5,614 SEPEs ordered with 19% reflexed for IFE. Among these, 70% were reported negative for SPEP without reflexing to IFE and 5% were reported negative after confirmation by IFE, with the rest being positive for monoclonal immunoglobulin(s) confirmed by either current or previous IFE results. Together with SPEP, FLC was ordered more often than UPEP (36% vs 19% of the total SPEP orders), with 12% of these having all three tests ordered. Using serum immunofixation results as a reference, we compared the diagnostic performance of UPEP and FLC as initial screening tools, with FLC considered abnormal if abnormal kappa/lambda ratio was accompanied with at least one elevated free light chain concentration. FLC had slightly higher sensitivity compared to UPEP (63% vs 56%) but with lower positive predictive value (69% vs 82%). When combining FLC with UPEP, the sensitivity increased to 79% with a positive predictive value of 71%. Interestingly, FLC and UPEP also showed various sensitivity in detecting specific type of free light chains, with FLC being positive in 81% of UPEP with detectable free kappa light chain, but only positive in 62% of UPEP with detectable free lambda light chain. Due to the reflex algorithm nature, those specimens with negative SPEP were not reflexed for IFE and therefore could not be used to assess the performance of FLC and UPEP. In summary, FLC was more frequently ordered than UPEP in addition to SPEP by our clinicians, although the majority of SPEPs were still ordered alone. In our practice, FLC and UPEP had comparable performance, with FLC showing slightly higher sensitivity but lower specificity. The current data did not support the replacement of one with the other, given that there was only 50% overlapping on positive identifications between FLC and UPEP. Further studies to include serum IFE for all specimens and clinical correlations would be beneficial to fully assess the diagnostic performance of FLC and UPEP, as well as their utilizations for various patient populations and clinical purpose.
The Burden of Add-On Orders in a Laboratory With Manual Processing
Authors: Barouqa Mohammad , Fecher Roger , Wolgast Lucia R , Forest Stefanie 
Published: September 2019

Abstract
In order to avoid additional blood draws for their patients, clinicians frequently order add-on tests on existing specimens in the laboratory. Manually processing these add-ons is problematic, utilizes tremendous resources, and raises concerns regarding specimen integrity. The objective of this study was to analyze add-on ordering patterns and assess the time and resources required to complete these orders. In this retrospective study conducted at a large, multisite, academic medical center, a report was generated from the laboratory information system (LIS) to identify all the add-on orders that were placed with details about the type of add-on test, which specimen it was added to, and location from where an add-on order was placed for a 2-month period (August 5 to October 4, 2018). The workflow was observed and financial cost was calculated. The laboratory received 5,658 add-on orders during the study period. By laboratory protocol, 859 tests were cancelled, leaving 4,799 tests to be processed. Add-on orders were most common for liver tests (7.48%), creatine kinase (6.35%), troponin (6.31%), vancomycin level (5.93%), thyroid-stimulating hormone (4.91%), magnesium (4.81%), and vitamin B12 (4.33%). The add-on orders were mainly generated for inpatient (74.07%) followed by emergency (17.79%) and outpatient departments (8.12%). The add-on request is placed by the clinical provider in the hospital information system (HIS) as a generic “Add-on Order” test, with free text to specify the test and specimen. A clerk in the laboratory uses the LIS-generated work list to electronically order the requested tests to the original specimen. Subsequently, a clerk must manually locate the original specimen and deliver it to the performing lab to run the add-on test. The median turnaround time from the provider placing the generic add-on order in the HIS to the lab placing the add-on in the LIS is 119 minutes. The median time for the provider to place an add-on after the initial order is 462 minutes. The average time needed to monitor the add-on work list, electronically place the add-on to the original order, and retrieve the sample for one test for a skilled senior statistical clerk is 7 minutes. The average number of add-on requests received daily is 71. Therefore, the daily time to process add-ons is 497 minutes (8.2 hours). Based on the hourly cost and fringe in the laboratory ($28.92/hour), these add-on tests cost $237/day in labor ($86,000/year). Our study demonstrates the significant cost and labor burden of add-on tests in a laboratory with manual processing. The laboratory is considering transitioning to direct provider ordering of add-ons to existing specimens using laboratory-defined rules in the HIS and moving to total laboratory automation with robotic specimen archival and retrieval to reduce the manual efforts, which would streamline the add-on workflow.
The Magnificent VWF SNPs and Where to Find Them: A Journey in Exon 28 of the Hispanic Population
Authors: Barouqa Mohammad , Choudhuri Jui , Fecher Roger , Jacob Jack , Sadeghi Saed , Gil Morayma Reyes 
Published: September 2019

Abstract
von Willebrand disease (VWD) is a common coagulation disorder with a prevalence of 0.1% to 1.0% manifesting as a wide spectrum of bleeding symptoms. Type 1 is diagnosed by confirming a quantitative decrease in VWF level, while type 3 has undetectable levels of VWF. Type 2 VWD variants are characterized by functional and binding defects. Initial diagnosis and follow-up depend mainly on measuring VWF protein and VWF activity and calculating the activity to protein ratio. Ristocetin cofactor activity (VWF:RCo) is the most widely used and gold standard activity assay. In our institute, we use a cutoff of VWF:RCo/VWF:Ag <0.7 to screen for possible type 2 VWD. However, the use of this ratio is flawed by the presence of specific SNPs (I1380V, N1435S, and D1472H) in the A1 domain, especially in African Americans. These SNPs lead to a decrease in ristocetin binding to VWF and hence decreased VWF:RCo/VWF:Ag ratio. In this retrospective study, we analyzed the levels of VWF:AG and VWF:RCo based on patients’ ethnicity using an in-house data mining software from 2011 to 2016. Then, we validated several exon 28 primers, kindly provided by Dr. Montgomery (Blood Center of Wisconsin), used to detect type 2 mutations and SNPs in African Americans. We excluded cases diagnosed as positive for VWD and included only cases rendered nondiagnostic of VWD following a comprehensive panel including multimers, collagen binding, and molecular studies when indicated. In our Hispanic population (n = 936), VWF:Ag was 138.9% and 117% (average and median) and VWF:RCo was 110.5% and 93.0% (average and median); 43.2% of Hispanics had VWF:RCo/VWF:Ag <0.7. In our African American population (n = 664), VWF:Ag was 163.0% and 138.5% (average and median) and VWF:RCo was 108.5% and 92.0% (average and median); 50.6% of the African American patients had VWF:RCo/VWF:Ag <0.7. Patients from Caucasian origins (n = 242) had VWF:Ag of 149.6% and 113.0% (average and median) and VWF:RCo of 137.6% and 116.0% (average and median), respectively; 30.9% of Caucasian patients had VWF:RCo/VWF:Ag of less than 0.7. We then selected four random Hispanic cases with VWF:RCo/VWF:Ag <0.5 as part of the validation study of exon 28 sequencing. Using a Sanger sequence assay, we found multiple benign/likely benign single-nucleotide polymorphisms (SNPs) at exon 28 that code for VWF antigen A1 domain. All four cases showed P.Thr1381Ala and P.Thr1547 = [OC1] polymorphism, three showed p.Val1565Leu polymorphism, and two showed p.Ala1555 = polymorphism. The statistical analysis of VWF:Ag/VWF:RCo levels from Hispanics shows a similar trend to African Americans with a high rate of cases with VWF:RCo/VWF:Ag <0.7 in comparison to Caucasians. However, the finding of SNPs and absence of known African American polymorphisms suggest that these SNPs may be the cause of decreased ristocetin binding in Hispanics. This study calls for ethnic-based considerations in VWD workflows.
An Optimized Assay for Assessing Platelet Dense Granule Secretion Using Diluted Whole Blood
Authors: Cho Joseph , Mikrut Krzysztof , Miller Jonathan 
Published: September 2019

Abstract
Assessment of dense granule secretion following agonist stimulation is an integral part of platelet function testing and can be performed in the clinical laboratory using lumi-aggregometry. A significant limitation of traditional lumi-aggregometry is the relatively large volume of blood required and the normal platelet counts needed to perform the assay, which often precludes usage of this test in pediatric and thrombocytopenic patients. By optimizing the luciferase-luciferin reaction with commercially available reagents and using a conventional lumi-aggregometer, we have developed a method that measures platelet dense granule secretion following agonist stimulation in diluted whole blood, at up to 10-fold dilutions. With the goal of developing a testing method independent of platelet count, the assay intentionally does not include specimen stirring. Direct comparison of the optimized reagents with the standard Chrono-lume reagent in 10-fold diluted whole blood showed an improved lower limit of detection for exogenously added ATP by at least one order of magnitude. We reproducibly observed dose-dependent responses in platelet ATP release using this assay upon stimulation with platelet agonists such as the thrombin receptor-activating peptide (TRAP) and the collagen receptor agonist convulxin. ATP release in 10-fold diluted whole blood, for example, was 168.6 ± 24.7 pmoles/107 platelets in response to 40 μM TRAP and 17.1 ± 2.9 pmoles/107 platelets in response to 1 nM convulxin (mean ± SEM, N = 6). Method comparisons of this assay were performed using 10-fold diluted whole blood without stirring, compared to standard methodology using undiluted platelet-rich plasma stirred at 1000 rpm. On concurrently run, matched specimens, ATP release in response to a series of agonists of varying stimulus intensity showed overall moderate concordance, with an r2 = 0.722. Based on ATP standard curves and the observed agonist responses to date, we are hopeful that this assay may prove capable of assessing platelet dense granule release in patient blood with platelet counts as low as 20,000/μL. Additionally, the assay requires less than 60 μL of whole blood per agonist with testing performed at two different agonist concentrations. The extended analytical range and robustness of the assay, with no need for centrifugation, offer promise that it may be useful for the assessment of platelet dense granule secretion in pediatric or thrombocytopenic patients who require assays amenable to limited blood volumes and low platelet counts.