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Search Results: 1 - 10 of 224086 matches for " Nira R. Pollock "
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A Disposable Microfluidic Virus Concentration Device Based on Evaporation and Interfacial Tension
Jane Yuqian Zhang,Madhumita Mahalanabis,Lena Liu,Jessie Chang,Nira R. Pollock,Catherine M. Klapperich
Diagnostics , 2013, DOI: 10.3390/diagnostics3010155
Abstract: We report a disposable and highly effective polymeric microfluidic viral sample concentration device capable of increasing the concentration of virus in a human nasopharyngeal specimen more than one order of magnitude in less than 30 min without the use of a centrifuge. The device is fabricated using 3D maskless xurography method using commercially available polymeric materials, which require no cleanroom operations. The disposable components can be fabricated and assembled in five minutes. The device can concentrate a few milliliters (mL) of influenza virus in solution from tissue culture or clinical nasopharyngeal swab specimens, via reduction of the fluid volume, to tens of microliters (mL). The performance of the device was evaluated by nucleic acid extraction from the concentrated samples, followed by a real-time quantitative polymerase chain reaction (qRT-PCR). The viral RNA concentration in each sample was increased on average over 10-fold for both cultured and patient specimens compared to the starting samples, with recovery efficiencies above 60% for all input concentrations. Highly concentrated samples in small fluid volumes can increase the downstream process speed of on-chip nucleic acid extraction, and result in improvements in the sensitivity of many diagnostic platforms that interrogate small sample volumes.
Microfluidic Chip for Molecular Amplification of Influenza A RNA in Human Respiratory Specimens
Qingqing Cao, Madhumita Mahalanabis, Jessie Chang, Brendan Carey, Christopher Hsieh, Ahjegannie Stanley, Christine A. Odell, Patricia Mitchell, James Feldman, Nira R. Pollock, Catherine M. Klapperich
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033176
Abstract: A rapid, low cost, accurate point-of-care (POC) device to detect influenza virus is needed for effective treatment and control of both seasonal and pandemic strains. We developed a single-use microfluidic chip that integrates solid phase extraction (SPE) and molecular amplification via a reverse transcription polymerase chain reaction (RT-PCR) to amplify influenza virus type A RNA. We demonstrated the ability of the chip to amplify influenza A RNA in human nasopharyngeal aspirate (NPA) and nasopharyngeal swab (NPS) specimens collected at two clinical sites from 2008–2010. The microfluidic test was dramatically more sensitive than two currently used rapid immunoassays and had high specificity that was essentially equivalent to the rapid assays and direct fluorescent antigen (DFA) testing. We report 96% (CI 89%,99%) sensitivity and 100% (CI 95%,100%) specificity compared to conventional (bench top) RT-PCR based on the testing of n = 146 specimens (positive predictive value = 100%(CI 94%,100%) and negative predictive value = 96%(CI 88%,98%)). These results compare well with DFA performed on samples taken during the same time period (98% (CI 91%,100%) sensitivity and 96%(CI 86%,99%) specificity compared to our gold standard testing). Rapid immunoassay tests on samples taken during the enrollment period were less reliable (49%(CI 38%,61%) sensitivity and 98%(CI 98%,100%) specificity). The microfluidic test extracted and amplified influenza A RNA directly from clinical specimens with viral loads down to 103 copies/ml in 3 h or less. The new test represents a major improvement over viral culture in terms of turn around time, over rapid immunoassay tests in terms of sensitivity, and over bench top RT-PCR and DFA in terms of ease of use and portability.
Challenges in the Development of an Immunochromatographic Interferon-Gamma Test for Diagnosis of Pleural Tuberculosis
Claudia M. Denkinger, Yatiraj Kalantri, Samuel G. Schumacher, Joy S. Michael, Deepa Shankar, Arvind Saxena, Natarajan Sriram, Thangakunam Balamugesh, Robert Luo, Nira R. Pollock, Madhukar Pai, Devasahayam J. Christopher
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0085447
Abstract: Existing diagnostic tests for pleural tuberculosis (TB) have inadequate accuracy and/or turnaround time. Interferon-gamma (IFNg) has been identified in many studies as a biomarker for pleural TB. Our objective was to develop a lateral flow, immunochromatographic test (ICT) based on this biomarker and to evaluate the test in a clinical cohort. Because IFNg is commonly present in non-TB pleural effusions in low amounts, a diagnostic IFNg-threshold was first defined with an enzyme-linked immunosorbent assay (ELISA) for IFNg in samples from 38 patients with a confirmed clinical diagnosis (cut-off of 300pg/ml; 94% sensitivity and 93% specificity). The ICT was then designed; however, its achievable limit of detection (5000pg/ml) was over 10-fold higher than that of the ELISA. After several iterations in development, the prototype ICT assay for IFNg had a sensitivity of 69% (95% confidence interval (CI): 50-83) and a specificity of 94% (95% CI: 81-99%) compared to ELISA on frozen samples. Evaluation of the prototype in a prospective clinical cohort (72 patients) on fresh pleural fluid samples, in comparison to a composite reference standard (including histopathological and microbiologic test results), showed that the prototype had 65% sensitivity (95% CI: 44-83) and 89% specificity (95% CI: 74-97). Discordant results were observed in 15% of samples if testing was repeated after one freezing and thawing step. Inter-rater variability was limited (3%; 1out of 32). In conclusion, despite an iterative development and optimization process, the performance of the IFNg ICT remained lower than what could be expected from the published literature on IFNg as a biomarker in pleural fluid. Further improvements in the limit of detection of an ICT for IFNg, and possibly combination of IFNg with other biomarkers such as adenosine deaminase, are necessary for such a test to be of value in the evaluation of pleural tuberculosis.
Field Evaluation of a Prototype Paper-Based Point-of-Care Fingerstick Transaminase Test
Nira R. Pollock, Sarah McGray, Donn J. Colby, Farzad Noubary, Huyen Nguyen, The Anh Nguyen, Sariah Khormaee, Sidhartha Jain, Kenneth Hawkins, Shailendra Kumar, Jason P. Rolland, Patrick D. Beattie, Nguyen V. Chau, Vo M. Quang, Cori Barfield, Kathy Tietje, Matt Steele, Bernhard H. Weigl
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0075616
Abstract: Monitoring for drug-induced liver injury (DILI) via serial transaminase measurements in patients on potentially hepatotoxic medications (e.g., for HIV and tuberculosis) is routine in resource-rich nations, but often unavailable in resource-limited settings. Towards enabling universal access to affordable point-of-care (POC) screening for DILI, we have performed the first field evaluation of a paper-based, microfluidic fingerstick test for rapid, semi-quantitative, visual measurement of blood alanine aminotransferase (ALT). Our objectives were to assess operational feasibility, inter-operator variability, lot variability, device failure rate, and accuracy, to inform device modification for further field testing. The paper-based ALT test was performed at POC on fingerstick samples from 600 outpatients receiving HIV treatment in Vietnam. Results, read independently by two clinic nurses, were compared with gold-standard automated (Roche Cobas) results from venipuncture samples obtained in parallel. Two device lots were used sequentially. We demonstrated high inter-operator agreement, with 96.3% (95% C.I., 94.3–97.7%) agreement in placing visual results into clinically-defined “bins” (<3x, 3–5x, and >5x upper limit of normal), >90% agreement in validity determination, and intraclass correlation coefficient of 0.89 (95% C.I., 0.87–0.91). Lot variability was observed in % invalids due to hemolysis (21.1% for Lot 1, 1.6% for Lot 2) and correlated with lots of incorporated plasma separation membranes. Invalid rates <1% were observed for all other device controls. Overall bin placement accuracy for the two readers was 84% (84.3%/83.6%). Our findings of extremely high inter-operator agreement for visual reading–obtained in a target clinical environment, as performed by local practitioners–indicate that the device operation and reading process is feasible and reproducible. Bin placement accuracy and lot-to-lot variability data identified specific targets for device optimization and material quality control. This is the first field study performed with a patterned paper-based microfluidic device and opens the door to development of similar assays for other important analytes.
Nonlinear dynamics of the additive-pulse modelocked laser
E. J. Mozdy,C. R. Pollock
Discrete Dynamics in Nature and Society , 1997, DOI: 10.1155/s1026022698000089
Abstract: We have modeled the additive-pulse modelocked (APM) laser with a set of four nonlinear difference equations, that describe the transit of optical pulses through the main cavity and through an external cavity containing a single-mode optical fiber. Simulating the system under several parameter variations, including fiber length, gain, and fiber coupling, we have observed period-doubling bifurcations into chaos. In addition, the model predicted large regimes of quasiperiodicity, and crisis transitions between different chaotic regions. We have used the method of nearest neighbors, Lyapunov exponents, and attractor reconstruction to characterize the chaotic regimes and the different types of bifurcations. We have included bandwidth-limiting and monitoring provisions to prevent non-physical solutions. To our knowledge, this is the first such characterization of chaos in the APM laser, as well as the first evidence of crisis behavior.
Upper-division student difficulties with the Dirac delta function
Bethany R. Wilcox,Steven J. Pollock
Physics , 2015, DOI: 10.1103/PhysRevSTPER.11.010108
Abstract: The Dirac delta function is a standard mathematical tool that appears repeatedly in the undergraduate physics curriculum in multiple topical areas including electrostatics, and quantum mechanics. While Dirac delta functions are often introduced in order to simplify a problem mathematically, students still struggle to manipulate and interpret them. To characterize student difficulties with the delta function at the upper-division level, we examined students' responses to traditional exam questions and a standardized conceptual assessment, and conducted think-aloud interviews. Our analysis was guided by an analytical framework that focuses on how students activate, construct, execute, and reflect on the Dirac delta function in the context of problem solving in physics. Here, we focus on student difficulties using the delta function to express charge distributions in the context of junior-level electrostatics. Common challenges included: invoking the delta function spontaneously, translating a description of a charge distribution into a mathematical expression using delta functions, integrating 3D or non-Cartesian delta function expressions, and recognizing that the delta function can have units. We also briefly discuss implications of these difficulties for instruction.
Coupled Multiple-response vs. Free-response Conceptual assessment: An Example from upper-division Physics
Bethany R. Wilcox,Steven J. Pollock
Physics , 2014, DOI: 10.1103/PhysRevSTPER.10.020124
Abstract: Free-response research-based assessments, like the Colorado Upper-division Electrostatics Diagnostic (CUE), provide rich, fine-grained information about students' reasoning. However, because of the difficulties inherent in scoring these assessments, the majority of the large-scale conceptual assessments in physics are multiple-choice. To increase the scalability and usability of the CUE, we set out to create a new version of the assessment that preserves the insights afforded by a free-response format while exploiting the logistical advantages of a multiple-choice assessment. We used our extensive database of responses to the free-response CUE to construct distractors for a new version where students can select multiple responses and receive partial credit based on the accuracy and consistency of their selections. Here, we describe the development of this modified CUE format, which we call coupled multiple-response (CMR), and present data from direct comparisons of both versions. We find that the two formats have the same average score and perform similarly on multiple measures of validity and reliability, suggesting that the new version is a potentially viable alternative to the original CUE for the purpose of large-scale research-based assessment. We also compare the details of student responses on each of the two versions. While the CMR version does not capture the full scope of potential student responses, nearly three-quarters of our students' responses to the free-response version contained one or more elements that matched options provided on the CMR version.
Student Difficulties with the Dirac Delta Function
Bethany R. Wilcox,Steven J. Pollock
Physics , 2014,
Abstract: The Dirac delta function is a standard mathematical tool used in multiple topical areas in the undergraduate physics curriculum. While Dirac delta functions are usually introduced in order to simplify a problem mathematically, students often struggle to manipulate and interpret them. To better understand student difficulties with the delta function at the upper-division level, we examined responses to traditional exam questions and conducted think-aloud interviews. Our analysis was guided by an analytical framework that focuses on how students activate, construct, execute, and reflect on the Dirac delta function in physics. Here, we focus on student difficulties using the delta function to express charge distributions in the context of junior-level electrostatics. Challenges included: invoking the delta function spontaneously, constructing two- and three-dimensional delta functions, integrating novel delta function expressions, and recognizing that the delta function can have units.
Multiple-choice Assessment for Upper-division Electricity and Magnetism
Bethany R. Wilcox,Steven J. Pollock
Physics , 2013,
Abstract: The Colorado Upper-division Electrostatics (CUE) diagnostic was designed as an open-ended assessment in order to capture elements of student reasoning in upper-division electrostatics. The diagnostic has been given for many semesters at several universities resulting in an extensive database of CUE responses. To increase the utility and scalability of the assessment, we used this database along with research on students' difficulties to create a multiple-choice version. The new version explores the viability of a novel test format where students select multiple responses and can receive partial credit based on the accuracy and consistency of their selections. This format was selected with the goal of preserving insights afforded by the open-ended format while exploiting the logistical advantages of a multiple-choice assessment. Here, we present examples of the questions and scoring of the multiple-choice CUE as well as initial analysis of the test's validity, item difficulty, discrimination, and overall consistency with the open-ended version.
Upper-division student difficulties with Separation of Variables
Bethany R. Wilcox,Steven J. Pollock
Physics , 2015, DOI: 10.1103/PhysRevSTPER.11.020131
Abstract: Separation of variables can be a powerful technique for solving many of the partial differential equations that arise in physics contexts. Upper-division physics students encounter this technique in multiple topical areas including electrostatics and quantum mechanics. To better understand the difficulties students encounter when utilizing the separation of variables technique, we examined students' responses to midterm exam questions and a standardized conceptual assessment, and conducted think-aloud, problem-solving interviews. Our analysis was guided by an analytical framework that focuses on how students activate, construct, execute, and reflect on the separation of variables technique when solving physics problems. Here we focus on student difficulties with separation of variables as a technique to solve Laplace's equation in both Cartesian and spherical coordinates in the context of junior-level electrostatics. Challenges include: recognizing when separation of variables is the appropriate tool; recalling/justifying the separated form of the potential and the need for the infinite sum; identifying implicit boundary conditions; and spontaneously reflecting on their solutions. Moreover, the type and frequency of errors was often different for SoV problems in Cartesian and spherical geometries. We also briefly discuss implication of these our findings for instruction.
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