Interfacial Effect-Based Quantification of Droplet Isothermal Nucleic Acid Amplification for Bacterial Infection

Bacterial infection is a widespread problem in humans that can potentially lead to hospitalization and morbidity. The largest obstacle for physicians/clinicians is the time delay in accurately identifying infectious bacteria, especially their sub-species, in order to adequately treat and diagnose such infected patients. Loop-mediated amplification (LAMP) is a nucleic acid amplification method that has been widely used in diagnostic applications due to its simplicity of constant temperature, use of up to 4 to 6 primers (rendering it highly specific), and capability of amplifying low copies of target sequences. Use of interfacial effect-based monitoring is expected to dramatically shorten the time-to-results of nucleic acid amplification techniques. In this work, we developed a LAMP-based point-of-care platform for detection of bacterial infection, utilizing smartphone measurement of contact angle from oil-immersed droplet LAMP reactions. Whole bacteria (Escherichia coli O157:H7) were assayed in buffer as well as 5% diluted human whole blood. Monitoring of droplet LAMP reactions was demonstrated in a three-compartment, isothermal proportional-integrated-derived (PID)-controlled chip. Smartphone-captured images of droplet LAMP reactions, and their contact angles, were evaluated. Contact angle decreased substantially upon target amplification in both buffer and whole blood samples. In comparison, notarget control (NTC) droplets remained stable throughout the 30 min isothermal reactions. These results were explained by the pre-adsorption of plasma proteins to an oil-water interface (lowering contact angle), followed by time-dependent amplicon formation and their preferential adsorption to the plasma protein-occupied oil-water interface. Time-to-results was as fast as 5 min, allowing physicians to quickly make their decision for infected patients. The developed assay demonstrated quantification of bacteria concentration, with a limit-of-detection at 10(2) CFU/mu L for buffer samples, and binary target or no-target identification with a limit-of-detection at 10 CFU/mu L for 5% diluted whole blood samples.Cardiovascular Biomedical Engineering Training Grant from U.S. National Institutes of Health [T32HL007955]; W. L. Gore & Associates, Inc.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

High-carrier-density electron dynamics in low-temperature-grown GaAs

Pump-probe differential transmission measurements examine high-carrier-density phenomena in as-grown and annealed GaAs samples grown at temperatures from 210 to 270 °C. We observe trap saturation and Auger recombination, and accurately model the measurements on annealed samples with a simple two level rate equation, allowing us to extract the trapped-electron lifetimes. © 1997 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70634/2/APPLAB-70-24-3245-1.pd

Dephasing times in quantum dots due to elastic LO phonon-carrier collisions

Interpretation of experiments on quantum dot (QD) lasers presents a challenge: the phonon bottleneck, which should strongly suppress relaxation and dephasing of the discrete energy states, often seems to be inoperative. We suggest and develop a theory for an intrinsic mechanism for dephasing in QD's: second-order elastic interaction between quantum dot charge carriers and LO-phonons. The calculated dephasing times are of the order of 200 fs at room temperature, consistent with experiments. The phonon bottleneck thus does not prevent significant room temperature dephasing.Comment: 4 pages, 1 figure, accepted for Phys. Rev. Let

Visualisation of the oblique vein of the left atrium (vein of Marshall) using cardiac computed tomography: is the game worth the candle?

Background: The vein of Marshall (VoM) is a small vessel that descends obliquely on the back of the left atrium and ends in the coronary sinus near the area where the great cardiac vein continues into the coronary sinus.Aim: The aim of the study was to examine the frequency of occurrence and anatomical aspects as well as the possibility of visualising the VoM, including an evaluation of the quality of the visualisation, on computed tomography (CT).Methods: Three hundred patients aged 58.8 ± 11.5 years (111 women) were included into this single-centre study. Cardiac CT was performed in all patients. The search for the VoM was performed by two experienced researchers using two- and three-dimensional techniques. A dedicated Likert-based scale was used to evaluate the quality of the visualisations.Results: The VoM was found in 61 (20.33%) of 300 patients. Its average diameter was 1.72 ± 0.69 mm with no sex-related differences (men: 1.71 ± 0.69 mm; women: 1.73 ± 0.57 mm; p = 0.91). The average length of the vessel was 9.24 ± 7.58 mm. The VoM was more frequently (p = 0.01) visualised in the systolic phases (68.85% of cases) compared to the diastolic phases (27.86% of cases). Occasionally it was visualised in other phases (3.29%).Conclusions: Although it was possible to visualise the VoM using cardiac CT in about 20% of the population, this method of visualisation requires that special attention be paid to the quality of the images, especially in the systolic phases. Visualisation may be useful before certain electrophysiology procedures

How I do it: transapical cannulation for acute type-A aortic dissection

Aortic dissection is the most frequently diagnosed lethal disease of the aorta. Half of all patients with acute type-A aortic dissection die within 48 hours of presentation. There is still debate as to the optimal site of arterial cannulation for establishing cardiopulmonary bypass in patients with type-A aortic dissection

Molecular subtyping of bladder cancer using Kohonen self-organizing maps

Kohonen self-organizing maps (SOMs) are unsupervised Artificial Neural Networks (ANNs) that are good for low-density data visualization. They easily deal with complex and nonlinear relationships between variables. We evaluated molecular events that characterize high- and low-grade BC pathways in the tumors from 104 patients. We compared the ability of statistical clustering with a SOM to stratify tumors according to the risk of progression to more advanced disease. In univariable analysis, tumor stage (log rank P = 0.006) and grade (P < 0.001), HPV DNA (P < 0.004), Chromosome 9 loss (P = 0.04) and the A148T polymorphism (rs 3731249) in CDKN2A (P = 0.02) were associated with progression. Multivariable analysis of these parameters identified that tumor grade (Cox regression, P = 0.001, OR.2.9 (95% CI 1.6–5.2)) and the presence of HPV DNA (P = 0.017, OR 3.8 (95% CI 1.3–11.4)) were the only independent predictors of progression. Unsupervised hierarchical clustering grouped the tumors into discreet branches but did not stratify according to progression free survival (log rank P = 0.39). These genetic variables were presented to SOM input neurons. SOMs are suitable for complex data integration, allow easy visualization of outcomes, and may stratify BC progression more robustly than hierarchical clustering

Monitoring Cognitive and Emotional Processes Through Pupil and Cardiac Response During Dynamic Versus Logical Task

The paper deals with the links between physiological measurements and cognitive and emotional functioning. As long as the operator is a key agent in charge of complex systems, the definition of metrics able to predict his performance is a great challenge. The measurement of the physiological state is a very promising way but a very acute comprehension is required; in particular few studies compare autonomous nervous system reactivity according to specific cognitive processes during task performance and task related psychological stress is often ignored. We compared physiological parameters recorded on 24 healthy subjects facing two neuropsychological tasks: a dynamic task that require problem solving in a world that continually evolves over time and a logical task representative of cognitive processes performed by operators facing everyday problem solving. Results showed that the mean pupil diameter change was higher during the dynamic task; conversely, the heart rate was more elevated during the logical task. Finally, the systolic blood pressure seemed to be strongly sensitive to psychological stress. A better taking into account of the precise influence of a given cognitive activity and both workload and related task-induced psychological stress during task performance is a promising way to better monitor operators in complex working situations to detect mental overload or pejorative stress factor of error

The Challenge of Detection and Diagnosis of Fugacious Hardware Faults in VLSI Designs

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-38789-0_7Current integration scales are increasing the number and types of faults that embedded systems must face. Traditional approaches focus on dealing with those transient and permanent faults that impact the state or output of systems, whereas little research has targeted those faults being logically, electrically or temporally masked -which we have named fugacious. A fast detection and precise diagnosis of faults occurrence, even if the provided service is unaffected, could be of invaluable help to determine, for instance, that systems are currently under the influence of environmental disturbances like radiation, suffering from wear-out, or being affected by an intermittent fault. Upon detection, systems may react to adapt the deployed fault tolerance mechanisms to the diagnosed problem. This paper explores these ideas evaluating challenges and requirements involved, and provides an outline of potential techniques to be applied.This work has been funded by Spanish Ministry of Economy ARENES project (TIN2012-38308-C02-01)Espinosa García, J.; Andrés Martínez, DD.; Ruiz, JC.; Gil, P. (2013). The Challenge of Detection and Diagnosis of Fugacious Hardware Faults in VLSI Designs. En Dependable Computing. Springer. 76-87. https://doi.org/10.1007/978-3-642-38789-0_7S7687Narayanan, V., Xie, Y.: Reliability concerns in embedded systems design. IEEE Computer 1(39), 118–120 (2006)Hannius, O., Karlsson, J.: Impact of soft errors in a jet engine controller. In: Ortmeier, F., Daniel, P. (eds.) SAFECOMP 2012. LNCS, vol. 7612, pp. 223–234. Springer, Heidelberg (2012)Borkar, S.: Designing reliable systems from unreliable components: the challenges of transistor variability and degradation. IEEE Micro 25(6), 10–16 (2005)JEDEC: Measurement and reporting of alpha particle and terrestrial cosmic ray-induced soft errors in semiconductor devices. JEDEC Standard JESD89A. JEDEC (2006)Gracia-Moran, J., Gil-Tomas, D., Saiz-Adalid, L.J., Baraza, J.C., Gil-Vicente, P.J.: Experimental validation of a fault tolerant microcomputer system against intermittent faults. In: DSN, pp. 413–418 (2010)Constantinescu, C.: Intermittent faults and effects on reliability of integrated circuits. In: Proceedings of the 2008 Annual Reliability and Maintainability Symposium, pp. 370–374. IEEE Computer Society, Washington, DC (2008)Avizienis, A., Laprie, J.C., Randell, B., Landwehr, C.: Basic concepts and taxonomy of dependable and secure computing. IEEE Trans. Dependable Secur. Comput. 1, 11–33 (2004)Johnson, C., Holloway, C.: The dangers of failure masking in fault-tolerant software: Aspects of a recent in-flight upset event. In: 2007 2nd Institution of Engineering and Technology International Conference on System Safety, pp. 60–65 (October 2007)Bolchini, C., Salice, F., Sciuto, D.: Fault analysis for networks with concurrent error detection. IEEE Des. Test 15(4), 66–74 (1998)Goessel, M., Ocheretny, V., Sogomonyan, E., Marienfeld, D.: New Methods of Concurrent Checking (Frontiers in Electronic Testing), 1st edn. Springer Publishing Company, Incorporated (2008)Iyer, R.K., Rossetti, D.J.: A statistical load dependency model for cpu errors at slac. In: Twenty-Fifth International Symposium on Fault-Tolerant Computing, ‘Highlights from Twenty-Five Years’, p. 373 (June 1995)Dodd, P.E., Shaneyfelt, M.R., Felix, J.A., Schwank, J.R.: Production and propagation of single-event transients in high-speed digital logic ics. IEEE Transactions on Nuclear Science 51, 3278–3284 (2004)Nightingale, E.B., Douceur, J.R., Orgovan, V.: Cycles, cells and platters: an empirical analysisof hardware failures on a million consumer pcs. In: Proceedings of the Sixth Conference on Computer Systems, EuroSys 2011, pp. 343–356. ACM, New York (2011)Kimseng, K., Hoit, M., Tiwari, N., Pecht, M.: Physics-of-failure assessment of a cruise control module. Microelectronics Reliability 39(10), 1423–1444 (1999)Savir, J.: Detection of single intermittent faults in sequential circuits. IEEE Trans. Comput. 29(7), 673–678 (1980)Correcher, A., Garcia, E., Morant, F., Quiles, E., Rodriguez, L.: Intermittent failure dynamics characterization. IEEE Transactions on Reliability 61(3), 649–658 (2012)Sorensen, B., Kelly, G., Sajecki, A., Sorensen, P.: An analyzer for detecting intermittent faults in electronic devices. In: AUTOTESTCON 1994. IEEE Systems Readiness Technology Conference. ‘Cost Effective Support Into the Next Century’, Conference Proceedings, pp. 417–421 (September 1994)Sosnowski, J.: Transient fault tolerance in digital systems. IEEE Micro 14(1), 24–35 (1994)Bondavalli, A., Chiaradonna, S., Di Giandomenico, F., Grandoni, F.: Threshold-based mechanisms to discriminate transient from intermittent faults. IEEE Trans. Comput. 49(3), 230–245 (2000)Rashid, L., Pattabiraman, K., Gopalakrishnan, S.: Intermittent hardware errors and recovery: modelling and evaluation. In: International Conference on Quantitative Evaluation of Systems, QEST (2012)Touba, N.A., McCluskey, E.J.: Logic synthesis of multilevel circuits with concurrent error detection. IEEE Trans. CAD 16(7), 783–789 (1997)Nicolaidis, M., Manich, S., Figueras, J.: Achieving fault secureness in parity prediction arithmetic operators: General conditions and implementations. In: Proceedings of the 1996 European conference on Design and Test, EDTC 1996, pp. 186–193. IEEE Computer Society, Washington, DC (1996)Ko, S.B., Lo, J.C.: Efficient realization of parity prediction functions in fpgas. J. Electron. Test. 20(5), 489–499 (2004)D’Angelo, S., Sechi, G.R., Metra, C.: Transient and permanent fault diagnosis for fpga-based tmr systems. In: Proceedings of the 14th International Symposium on Defect and Fault-Tolerance in VLSI Systems, DFT 1999, pp. 330–338. IEEE Computer Society, Washington, DC (1999)Kim, C.: Detection and location of intermittent faults by monitoring carrier signal channel behavior of electrical interconnection system. In: Electric Ship Technologies Symposium, ESTS 2009, pp. 449–455. IEEE (April 2009