bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrical conduction and dielectric relaxation mechanisms in the KNN-based ceramics
Authors: Wang Xiaozhi , Huan Yu , Wang Zhenxing , Lin Xiujuan , Huang Shifeng , Wei Tao , Li Longtu , Wang Xiaohui
Published: September 2019

Multilayer ceramic actuators with a base metal internal electrode are in great demand because of their high voltage-driven displacement. Thus, the piezoelectric materials should be sintered in low oxygen partial pressure. The (Li, Ta, Sb)-doped (K,Na)NbO3 (KNN)-based ceramics are heat-treated in O2, air, N2, and 99 vol. % N2/1 vol. % H2 mixture gas at 300 °C in this study to identify the predominant charge carriers by defect chemistry. By analyzing electrical conduction and dielectric relaxation mechanisms, the dominant charge carriers in the ceramics are electrons and oxygen vacancies at low (<450 °C) and high temperature (>500 °C), respectively. In addition, the defect concentration in the ceramics increases with the decreasing oxygen partial pressures, and the change is more evident in the presence of H2 gas. Correspondingly, the electrical properties slightly degrade with the decreasing oxygen partial pressure and severely degrade in the N2/H2 mixture gas. Therefore, the (Li, Ta, Sb)-doped KNN-based ceramics with an n-type conduction mechanism are difficult to sinter in a reducing atmosphere. In order to cofire with base metal electrodes, the p-type conduction should be designed by doping the KNN ceramic in the future for industrial application.
Multi-mode ionization instability induced striations in RF driven He/H2O atmospheric pressure plasma (APP) discharges
Authors: Kawamura E. , Lieberman M. A. , Lichtenberg A. J.
Published: September 2019

Previously [E. Kawamura et al., Plasma Sources Sci. Technol. 25, 054009 (2016) and E. Kawamura et al., J. Phys. D: Appl. Phys. 50, 145204 (2017)], one dimensional (1D) particle-in-cell (PIC) simulations of 1 to 4 mm gap, He/2%H2O atmospheric pressure plasma discharges showed an ionization instability resulting in bulk striations. Assuming that the ionization rate coefficient Kiz is related to the root mean square electric field E by Kiz ∝ Eq, a striation theory showed that q < 0 is a necessary condition for the instability. A local calculation yielded q > 0, implying that nonlocal electron kinetics are required for the instability. Wider gaps can fit in a wider range of wavelengths, resulting in multi-mode striations. Previously, we assumed a single mean q value for each discharge, and did not calculate q for each mode separately. Here, we develop a wavelength resolved global striation model and apply it to 1D PIC simulations of 4 mm gap discharges with input currents Jrf = 0.04 to 0.30 A/cm2. We first examine a base case at 0.23 A/cm2 and observe a mixture of unstable modes within a window of wavelengths λ. At shorter λ, the modes are suppressed by diffusion. At longer λ, we observe a transition to locality in which q becomes less negative with increasing λ, approaching its local positive value and stabilizing the modes. The window of unstable modes shifts to shorter λ with increasing Jrf, causing the modes to be suppressed by diffusion at higher Jrf. At lower Jrf, the decrease in bulk plasma density with decreasing Jrf suppresses the striations.
Xe laser-plasma EUV radiation source with a wavelength near 11 nm—Optimization and conversion efficiency
Authors: Kalmykov S. G. , Butorin P. S. , Sasin M. E.
Published: September 2019

Xe laser-produced plasma with a gas-jet target is considered a promising λ = 11.2-nm radiation source for a possible extension of the EUV (Extreme UltraViolet) lithography. EUV spectra of the plasma radiation obtained with the aid of both a grating spectrograph and Bragg mirrors are presented. The absorption of the EUV radiation in the cold peripheral gas has been eliminated in another experiment by means of irradiating the target with a wide defocused laser beam that resulted in an increase of the EUV output by an order of magnitude. In that experiment, the conversion efficiency at λ = 11.2 nm amounted to 3.9%.
Numerical simulation of ultrasonic field within the large-scale Al alloy melts treated by scalable sonotrodes
Authors: Peng Hao , Wang Ying , Jiang Ripeng , Li Xiaoqian , Li Ruiqing , Zhang Lihua
Published: September 2019

The single sonotrode-generated ultrasonic field cannot fully spread the whole volume of large-scale Al alloy melt. Then, the effective volume of Al alloy melt processed by ultrasound is very limited. Thus, single sonotrode does not completely satisfy the casting of large-scale Al alloys. Scalable power ultrasounds provide an alternative way for this dilemma. However, only the optimal configuration of scalable power ultrasounds lead to a high efficiency during casting. In the present work, numerical simulation of ultrasonic field within the large-scale Al alloy melts was carried out for three cases, i.e. single sonotrode, three parallel sonotrodes, and three non-parallel sonotrodes that were configured in various ways. Simulation work mainly focused on investigating (a) the three dimensional (3D) distribution of acoustic pressure under different configurations, (b) the 2D distribution of acoustic pressure along each sonotrode’s axis, (c) the 1D distribution of acoustic pressure along the central axis of large-scale Al alloy melts, and (d) the mean acoustic energy density and the cavitation zones as well. Meanwhile, the 3D dynamic evolution of acoustic pressure fields for different configurations was also analyzed in one cyclic vibration time. Compared with single sonotrode, three scalable sonotrodes (when configured in an appropriate way) enable to generate larger high-pressure zones, increase the mean acoustic energy density, and enlarge the volume fraction of potential cavitation zones. The present work raises insights for the configuration and optimization of scalable sonotrodes for casting the large-scale metallic materials, like Al alloy.
A first-principles study on transport properties of polyacene in zigzag graphene nanoribbon: Configuration, length and doping effects
Authors: Yang Zhixiong , Pan Jiangling , Cheng Xue , Xiong Xiang , Ouyang Fangping
Published: September 2019

Electronic transport properties of molecular junctions constructed by bridging a polyacene (PA) molecule between two zigzag graphene nanoribbons (ZGNR) are studied based on density functional theory and the nonequilibrium Green function method. It is found that the molecule-electrode coupling strength is related to the PA position with respect to the nanoribbon edge, which gives rise to the configuration dependency of transport properties. Negative differential resistance (NDR) is predicted in the junctions of which the PA molecule aligns with the inner part of the ZGNR. The on-set bias and current peak decrease as the PA molecule moves inward. The origin of NDR is presented by analyzing the transmission spectra, relative voltage-drop rate, and electron density difference of the junctions. The on-set bias is proportional to the energy of the resonance peak of the lowest unoccupied molecular orbital and can be tuned by the PA molecule length or by doping. This work provides a detailed discussion on PA-bridged ZGNR junctions, which may help to understand ZGNR-based molecular junctions and design negative differential resistance devices.
'…but I just prefer to treat everyone the same…': general practice receptionists talking about health inequities
Authors: Manhire-Heath Rowan , Cormack Donna , Wyeth Emma
Published: September 2019

General practice receptionists are positioned at the beginning of a patient’s journey within the healthcare system, yet their influence on a patient’s experience is unknown. The limited data on, and research involving, general practice receptionists both in New Zealand and internationally is evidence of this. This research undertook an exploration of the discourses used by a group of general practice receptionists in Wellington, New Zealand to discover how they talk about, and represent, health inequities. Eight in-depth semi-structured interviews were conducted, guided by Social Constructionism and Decolonising Theory. Three reoccurring patterns of discourse were identified: discourses about the social determinants of health; discourses about Māori culture and behaviour; and discourses about egalitarianism. Further, narratives that could be seen as deficit-focussed or victim-blaming were identified. Racism was not directly discussed by participants as a health determinant. The findings support the need for training guided by cultural safety and anti-racism principles to be available for all general practice receptionists.
Understanding homeowners' decisions to mitigate wildfire risk and create defensible space
Authors: Sisante Angelo M. , Taylor Michael H. , Rollins Kimberly S.
Published: September 2019

This article analyses homeowners’ decisions to undertake fire-safe investments and create defensible space on their property using a unique dataset from 35 wildland–urban interface communities in Nevada. The dataset combines homeowner information from a mail survey with their observed fire-safe investments obtained through parcel-level hazard assessments. We find that homeowners’ self-reported mitigation expenditures are driven by their subjective beliefs about their wildfire risk, whereas observed defensible space status is driven by their costs of investment. We develop a theoretical model of a homeowner’s fire-safe investment decision that accounts for our empirical results.
Significance of sunlight for organic matter degradation in aquatic systems
Authors: Hunting Ellard R , de Jong Sanne , Schrama Maarten
Published: September 2019

Degradation of organic matter (OM) is generally considered to be primarily governed by biotic factors in aquatic environments. However, a number of abiotic processes also play key roles in mediating OM-degradation. Sunlight can act as a principal abiotic driver of the degradation of terrestrial organic matter, but its importance for freshwater ecosystems and possible interactions with biotic drivers remains poorly understood. We carried out two microcosm experiments which focused on the role of sunlight on microbial and invertebrate-mediated OM degradation using two species of plant leaves and the aquatic invertebrate Asellus aquaticus. Results indicated that sunlight was the primary driver of leaf mass loss during the early stages of decomposition, whereas microbial communities had a negligible effect. Sunlight was observed to strongly affect invertebrate behavior as invertebrates avoided direct illumination. This alteration of behavior resulted in a reduction in the consumption of a leaf surrogate (DECOTAB) by A. aquaticus. Together, these results indicate that sunlight has the potential to strongly influence structural and functional attributes of shallow freshwater systems, and hence serve as an appraisal to consider sunlight as a significant direct and indirect physical driver governing OM degradation in shallow aquatic systems.
Shortened nuclear matrix attachment regions are sufficient for replication and maintenance of episomes in mammalian cells
Authors: Wang Xiao-Yin , Zhang Xi , Wang Tian-Yun , Jia Yan-Long , Xu Dan-Hua , Yi Dan-Dan
Published: September 2019

Matrix attachment regions (MARs) can mediate the replication of vector episomes in mammalian cells; however, the molecular mode of action remains unclear. Here, we assessed the characteristics of MARs and the mechanism that mediates episomal vector replication in mammalian cells. Five shortened subfragments of β-interferon MAR fragments were cloned and transferred into CHO cells, and transgene expression levels, presence of the gene, and the episomal maintenance mechanism were determined. Three shortened MAR derivatives (position 781–1320, 1201–1740, and 1621–2201) retained full MAR activity and mediated episomal vector replication. Moreover, the three shortened MARs showed higher transgene expression levels, greater efficiency in colony formation, and more persistent transgene expression compared with those of the original pEPI-1 plasmid, and three functional truncated MARs can bind to SAF-A MAR-binding protein. These results suggest that shortened MARs are sufficient for replication and maintenance of episomes in CHO cells.
Practical Cost Analysis of Genomic Data in the Cloud
Authors: Krumm Niklas , Hoffman Noah
Published: September 2019

Background

The growth of clinical NGS testing, together with new CAP checklist items stating that read-level (raw) NGS data must be retained for a minimum of 2 years, has prompted laboratories to reevaluate their NGS data storage solutions. In this context, cloud-based storage has several advantages, such as low per-GB prices, scalability, and minimal fixed costs; nonetheless, several perceived disadvantages, including increased complexity and security/regulatory considerations, have hindered adoption. Furthermore, despite the ostensibly simple usage-based pricing plans, practical cost analysis of cloud storage for NGS data storage is not straightforward.

Methods

We developed an easy-to-use tool designed specifically for cost and usage estimation for laboratories performing clinical NGS testing (https://ngscosts.info). Our tool enables quick exploration of dozens of storage options across three major cloud providers and provides complex cost and usage forecasts over 10- to 20-year timeframes. Parameters include current test volumes (and customizable file sizes), expected test volume growth rate, data compression techniques, data retention times across storage tiers, and case reaccess rates. Outputs include an easy-to-visualize chart of total data stored, yearly and lifetime costs, and a “cost per test” estimate.

Results

The per-GB storage prices among major cloud providers have dropped ~6 to 7× over the past 10 years; in addition, there currently exists an up to 20× price difference between storage tiers. Lower prices are typically offset by either increased access/transfer costs or slower retrieval rates. Two factors were found to markedly affect the average cost per test: (1) total file size, including the use of NGS-specific file compression techniques, and (2) storage tiers and rapid transfer to “cold” or archival storage. In contrast, some factors were not found to affect total costs, including costs associated with reaccess from archival storage tiers, and discounts associated with increased volumes.

When data from NGS testing were stored in “hot” storage for 1 year, then archived for 9 years, typical costs per exome were ~$3/test and genomes ranged from $40/test to $66/test, depending on compression algorithms used. Overall, reaccess of data from cold storage added 2% or less to the total cost per test (with an estimated reaccess rate of 10% of cases per year).

Conclusions

Steady declines in cloud storage pricing, as well as new options for storage and retrieval, make storing clinical NGS data on the cloud economical and friendly to laboratory workflows. Taken together, laboratories should not be concerned about reaccess costs but rather should focus on data compression techniques and archival storage tiers for long-term data. Our web-based tool makes it possible to explore and compare cloud storage solutions and provide forecasts specifically for clinical NGS laboratories.
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

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

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

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.
The (Un)Necessary Use of Short-Tandem-Repeat (STR) Testing on Bone Marrow Samples in Patients After 1 Year Postallogeneic Hematopoietic Stem Cell Transplant
Authors: Wooten Melanie , Sullivan Harold C , Jaye David
Published: September 2019

Allogeneic hematopoietic stem cell transplant (HSCT) patients at our institution are monitored at multiple time points posttransplant for neoplastic disorders by short-tandem-repeat (STR) testing of unfractionated bone marrow (BM) and BM biopsy evaluation (morphology, flow cytometry, genetics) to assess for engraftment, rejection, relapse risk, graft-versus-host disease, and disease relapse. Since there is some overlap in the information provided by STR and BM biopsies, we asked if and when this combined testing may be redundant. To answer this question, we compared results of STR and flow cytometry (a surrogate for BM biopsy evaluation) at different time points posttransplant. We identified 1,199 cases, between June 2011 and November 2018, from 410 patients in which STR testing on unfractionated BM samples had concurrent flow cytometry analysis (within 7 days of each other). STR testing was considered positive if ≥1% of recipient DNA was identified in the sample. Flow cytometry was considered positive if an aberrant population was identified that correlated with the patient’s prior diagnosis. Analysis included concordance/discordance rates as a function of time from transplant and relapse (if relapse had occurred) and potential reasons for discordance. The overall concordance rate between STR and flow cytometry was 93%, with a majority of cases (1,063) being STR(–)/Flow(–). Of all discordant cases, 75 of those were STR(+)/Flow(–); however, the majority of these cases (70%) demonstrated <5% of recipient DNA. Five cases of graft failure/rejection were identified with an average recipient DNA of 93% at <1 year from transplant. The eight cases identified as STR(–)/Flow(+) represented relapsed/residual disease diagnosed on average 565 days after transplant (aberrant population ranged from 1% to 6% of total events by flow cytometry). Focusing on cases ≥1 year from transplant (54% of all cases), the concordance rate between STR and flow cytometry increased to 98%, with only nine cases identified as STR(+)/Flow(–). Five of the nine cases had an average recipient DNA of 2% and no clinical or pathologic evidence of relapse with at least 490 days posttransplant follow-up. The other four cases were at time points either after pathologic relapse had already been confirmed, at 3 months prior to cytogenetic relapse, or at least 2 years prior to STR(+)/Flow(+) relapse. Our main findings include the following: (1) STR testing is critical for identifying graft failure/rejection within 1-year posttransplant, (2) flow cytometry is superior to STR at detecting late relapses with low-level disease, and (3) STR testing on BM samples from patients ≥1 year post-HSCT may be unnecessary, as in our experience the BM biopsy evaluation is sufficient to determine disease relapse. Lastly, financial analysis suggests that elimination of STR testing 1-year post-HSCT would lead to a significant cost-avoidance to our health care system.
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

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

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

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

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

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.
Nuclear Magnetic Resonance (NMR)–Based Serum Metabolic Profiles: Impact of Fasting Status
Authors: Smy Laura , Lee Megan , Biase Irene De , Genzen Jon , Yuzyuk Tatiana
Published: September 2019

Introduction

Measurement of lipoprotein subclass concentration (-c), particle number (-p), and size (-s) by nuclear magnetic resonance (NMR) has gained traction recently in the clinical laboratory due to associations between smaller lipid particle sizes and atherogenic risk, especially for LDL-p. Since patients may not comply with the clinician’s recommendation of fasting before sample collection, our objective was to evaluate the impact of fasting status on NMR-based lipid and amino acid determinations.

Methods

Fifty self-reported healthy participants were recruited using an internal review board-approved protocol: males (n = 25; 41.3 ± 10.5 years; BMI 27.7 ± 4.6 kg/m2) and females (n = 25; 35.6 ± 9.1 years; BMI 25.3 ± 5.4 kg/m2). Blood was collected after overnight fast and 4 hours after a high-fat meal. Samples were analyzed using the AXINON lipoFIT by NMR assay (Numares) with an Avance III NMR spectrometer and Ascend 600 MHz magnet (Bruker). This assay included measurements of triglycerides, total cholesterol, IDL-c, and LDL, HDL, VLDL concentrations; particle numbers; and sizes. Additionally, NMR-based glucose, alanine, valine, leucine, and isoleucine concentrations were acquired. Conventional lipid parameters were obtained using cobas 8000 chemistry system (Roche). Fasting and postprandial results were compared for significant differences.

Results

As expected, mean triglycerides increased after the meal (53%, P < .0001). Increases were also observed for VLDL-c (22%, P < .0001) and large VLDL-p (56%, P < .0001), as well as LDL-s, HDL-s, and VLDL-s (all <3.5%, P < .005). In contrast, LDL-p, small LDL-p, large LDL-p, HDL-p, small HDL-p, glucose, total cholesterol, and LDL, HDL, and IDL cholesterols demonstrated at most an 11% decrease (all P < .002). Valine, leucine, and isoleucine also increased after the meal (31%-46%, P < .0001 for all). Differences in individual lipids or amino acids were not sufficient to distinguish between fasting vs postprandial states, although incorporation of valine into a ratio with VLDL-c and LDL cholesterol (Valine*VLDL-c/LDL cholesterol) provided adequate differentiation (ROC analysis: AUC 0.91 [SD 0.03, P < .0001]). A cutoff of 75 for the ratio had a sensitivity of 88.9% (95% CI, 76.0%-96.3%) and specificity of 85.4% (95% CI, 72.2%-93.9%). Interference with NMR results occurred for three participants’ postprandial samples. These individuals had significantly higher fasting triglycerides, LDL-p, small LDL-p, large VLDL-p, VLDL-s, VLDL-c, IDL-c and lower LDL-s, and HDL-s compared to other participants.

Conclusions

The clinical impact on results from postprandial samples warrants further evaluation prior to accepting nonfasting samples for NMR analysis. Considering a subpar compliance with fasting, algorithms to differentiate fasting and postprandial specimens may be useful in identifying suboptimal specimens.
The Correlation Between DPYD*9A(c.85T>C) Genotype and Dihydropyrimidine Dehydrogenase Deficiency Phenotype in Patients With Gastrointestinal Malignancies Treated With Fluoropyrimidines
Authors: Maharjan Anu S , McMillin Gwendolyn , Khushman Moh’d , Patel Girijesh
Published: September 2019

Introduction

The correlation between DPYD*9A (c.85T>C) genotype and dihydropyrimidine dehydrogenase (DPD) deficiency phenotype is controversial. In a cohort of 28 patients, DPYD*9A was the most commonly diagnosed variant (46%) and there was a noticeable genotype-phenotype correlation. Here we genotyped a larger cohort of a mixed racial background to explore the incidence of DPYD*9A variant and to further study the genotype-phenotype correlation.

Methods

Genotyping for high-risk DPYD variants (DPYD*2A, DPYD*13, and DPYD*9B) and the DPYD*9A variant was performed on 113 patients with gastrointestinal malignancies (GI) treated with fluoropyrimidines, using TaqMan chemistry. The prevalence of different DPYD variants was further analyzed in 1,283 retrospective data from ARUP laboratories. Fluoropyrimidines-associated toxicity was graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events (v 5.0). Fisher’s exact test was used for statistical analysis.

Results

In total, 1,283 were retrospectively reviewed for DPYD variants. Four patients (0.31%) carried DPYD c.-1590T>C, 10 patients (0.55%) carried DPYD c.1679T>G (*13), 36 patients (2.8%) carried DPYD c.2846A>T, and 527 patients (41.1%) carried DPYD c.85T>C (*9A). In the GI cancer cohort, DPYD variants were identified in 61 patients (54%), showing similar prevalence as the retrospective analysis. Caucasians represented 54% and African Americans represented 43%. Twenty-eight patients (46%) were females. Heterozygous DPYD*9A was identified in 46 patients (41%) and homozygous DPYD*9A was identified in 11 patients (10%). DPYD*2A was identified in 3 patients and DPYD*9B was identified in 2 patients (one patient had double heterozygous *9A and *9B). Grade 3 to 4 toxicities were experienced in 26 patients with mutant DPYD*9A (3 patients had homozygous DPYD*9A) and in 20 patients with no identified DPYD mutation (P = .7035). In patients who received full-dose fluoropyrimidines (N = 85), grade 3 to 4 toxicities were experienced in 22 patients with mutant DPYD*9A (2 patients had homozygous DPYD*9A) and in 17 patients with no identified DPYD mutation (P = .8275).

Conclusion

In the GI cancer population, the DPYD*9A variant was identified in 54% of patients. The correlation between DPYD*9A variant and DPD clinical phenotype was not significant. The noticeable correlation that was previously reported is likely due to small sample size and selection bias.