Interferometric biosensing platform for multiplexed digital detection of viral pathogens and biomarkers

Thesis (Ph.D.)--Boston UniversityLabel-free optical biosensors have been established as proven tools for monitoring specific biomolecular interactions. However, compact and robust embodiments of such instruments have yet to be introduced in order to provide sensitive, quantitative, and high-throughput biosensing for low-cost research and clinical applications. Here we present the interferometric reflectance-imaging sensor (IRIS). IRIS allows sensitive label free analysis using an inexpensive and durable multi-color LED illumination source on a silicon based surface. IRIS monitors biomolecular interaction through measurement of biomass addition to the sensor's surface. We demonstrate the capability of this system to dynamically monitor antigen-antibody interactions with a noise floor of 5.2 pg/mm^2 and DNA single mismatch detection under isothermal melting conditions in an array format. Ensemble detection of binding events using IRIS did not provide the sensitivity needed for detection of infectious disease and biomarkers at clinically relevant concentrations. Therefore, a new approach was adapted to the IRIS platform that allowed the detection and identification of individual nanoparticles on the sensor's surface. The new detection method was te1med single-particle IRIS (SP-IRIS). We developed two detection modalities for SP-IRIS. The first modality is when the target is a nanoparticle such as a virus. We verified that SP-IRIS can accurately detect and size individual viral particles. Then we demonstrated that single nanoparticle counting and sizing methodology on SP-IRIS leads to a specific and sensitive virus sensor that can be multiplexed. Finally, we developed an assay for the detection of Ebola and Marburg. A detection limit of 3 x 10^3 PFU/ml was demonstrated for vesicular stomatitis virus (VSV) pseudotyped with Ebola or Marburg virus glycoprotein. We have demonstrated that virus detection can be done in human whole blood directly without the need for sample preparation. The second modality of SP-IRIS we developed was single molecule counting of biomarkers utilizing a sandwich assay with detection probes labeled with gold nanoparticles. We demonstrated the use of single molecule counting in a nucleic acid assay for melanoma biomarker detection. We showed that a single molecule counting assay can lead to detection limits in the attomolar range. The improved sensitivity of IRIS utilizing single nanoparticle detection holds promise for a simple and low-cost technology for rapid virus detection and multiplexed molecular screening for clinical applications

Study of the transition from conduction to injection in an electrohydrodynamic flow in blade-plane geometry

A dielectric fluid can be set into motion with the help of electric forces, mainly Coulomb force. This phenomenon, called electroconvection, can be induced by electrohydrodynamic conduction, injection, and induction. Conduction is based on the dissociation/recombination phenomenon, generates heterocharge layers, and occurs for low electric field values. Injection produces homocharge layers in the electrode vicinity and requires stronger electric fields to be initiated. This study is an experimental observation of the transition from conduction to injection of a dielectric liquid in blade-plane geometry using Particle Image Velocimetry. In addition, the electric current is measured to completely understand the flow behavior

A digital microarray using interferometric detection of plasmonic nanorod labels

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and dynamic range of traditional fluorescence microarrays compared to other techniques have been the technology's Achilles' Heel, and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ('digital') regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about three orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10x objective lens. This approach does not require any chemical enhancement such as silver deposition, and scans arrays with a throughput similar to commercial fluorescence devices. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about one million directly from a single scan

A digital microarray using interferometric detection of plasmonic nanorod labels

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and dynamic range of traditional fluorescence microarrays compared to other techniques have been the technology's Achilles' Heel, and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ('digital') regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about three orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10x objective lens. This approach does not require any chemical enhancement such as silver deposition, and scans arrays with a throughput similar to commercial fluorescence devices. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about one million directly from a single scan.First author draf

Digital microarrays: single-molecule readout with interferometric detection of plasmonic nanorod labels

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology’s Achilles’ heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule (“digital”) regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform’s primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique’s simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.The authors wish to thank Oguzhan Avci and Jacob Trueb for thoughtful comments and suggestions regarding numerical optimization of the optical system. This work was funded in part by a research contract with ASELSAN, Inc. and the Wallace H. Coulter Foundation 2010 Coulter Translational Award. (ASELSAN, Inc.; Wallace H. Coulter Foundation Coulter Translational Award)Accepted manuscrip

Robotic Control Using Model Based Meta Adaption

In machine learning, meta-learning methods aim for fast adaptability to unknown tasks using prior knowledge. Model-based meta-reinforcement learning combines reinforcement learning via world models with Meta Reinforcement Learning (MRL) for increased sample efficiency. However, adaption to unknown tasks does not always result in preferable agent behavior. This paper introduces a new Meta Adaptation Controller (MAC) that employs MRL to apply a preferred robot behavior from one task to many similar tasks. To do this, MAC aims to find actions an agent has to take in a new task to reach a similar outcome as in a learned task. As a result, the agent will adapt quickly to the change in the dynamic and behave appropriately without the need to construct a reward function that enforces the preferred behavior

Treatment Strategies in Colorectal Cancer

Colorectal cancer is known to be one of the most commonly diagnosed cancers worldwide. It maintains a high mortality rate despite the newest methodological therapeutic approaches adopted in various academic establishments. The treatment modalities in colorectal cancer follow the degree of disease progression based on staging information. Earliest the cancer is diagnosed, the highest the possibility to be cured. Different strategies are being involved in treating colorectal cancer, starting from simple endoscopic polypectomy to remove a potential malignant polyp, to wider surgical intervention to get rid of a primary unmetastasized tumor, to other concomitant radio-chemotherapy combinations to reduce a bulky tumor rendering it operable, ending in more sophisticated chemotherapeutical regimens combined with targeted drugs to shrink the metastatic lesions and prolong survival rate. Different new treatments are being investigated with a sole aim to preserve the patient’s quality of life and extend life span

Polarization enhanced interferometric imaging

https://patentimages.storage.googleapis.com/1e/21/aa/dee6cbdf9a3542/US11428626.pdfPublished versio

Error models and error correction for incremental encoders of servo drives

Um die hohen Anforderungen bezüglich Dynamik, und Genauigkeit bei Anwendungen von Servoantrieben erfüllen zu können, benötigt der Servoregler hochaufgelöste Lage- und Drehzahlsignale. Diese werden heutzutage überwiegend mit Hilfe von Sinus-Cosinus-Lagegebern realisiert. In der Praxis weisen die Gebersignale jedoch systematische Fehler und Rauschanteile auf. Die systematischen Fehler können grundsätzlich in zwei Kategorien eingeteilt werden: Feinlagefehler und Groblagefehler. Wenn sich das Drehzahlsignal regelungstechnisch im Rückkopplungszweig befindet, wirkt ihr Fehlersignal wie ein zusätzlicher Sollwert. Als Folge können Geräusche und Drehzahlschwankungen entstehen. In dieser Arbeit sind neue Verfahren zur Korrektur der systematischen und stochastischen Fehler entwickelt und untersucht worden, mit denen die Qualität der Korrekturverfahren konstant im gesamten Drehzahlbereich des Servomotors ist, insbesondere bei hohen Geschwindigkeiten. Die Hardware, die mit einer Kombination der DSP- und FPGA-Technik aufgebaut ist, wird für das Identifizieren der systematischen Fehler und für die Verifizierung der Korrekturverfahren eingesetzt. Um eine gleichförmige Bewegung während des Identifizierens der systematischen Fehler zu erreichen, wurde der verwendete AC-Motor mit einer zusätzlichen Schwungmasse an der Motorwelle versehen. Für die Unterdrückung der Groblage- und Feinlagefehler wurde ein zweistufiges Korrekturverfahren untersucht. Die Kompensation der beiden Fein- und Groblagefehler erfolgt durch die gleichen Korrekturtabellen im gesamten Drehzahlbereich. Um die Qualität der Korrekturverfahren bei den hohen Geschwindigkeitsbereichen bzw. die Änderungen systematischer Feinlagefehler mit der Geschwindigkeit verfolgen zu können, werden Multi-Tabellengestützte Verfahren oder Korrekturfunktion eingesetzt. Weiterhin ist ein neues Verfahren zur Unterdrückung des zufälligen Fehlers entwickelt worden. Dieses Verfahren basiert auf der linearen Regression für die Gesamtlage des Motors. Die Effektivität der untersuchten Korrekturverfahren wurde mit dem geschlossenen Geschwindigkeitsregelkreis geprüft. Somit ist das Gleichlaufverhalten im gesamten Drehzahlbereich deutlich verbessert worden. Bei den praktischen Versuchen wird ein Standard-Servo-Asynchronmotor mit optischem Drehgeber verwendet. Die Ergebnisse wurden durch einen Vergleich der gemessenen systematischen Fehler und des Geschwindigkeitssignals mit und ohne Korrekturverfahren dargestellt.In high performance servo applications the optical encoder is the standard sensor for acquiring high-resolution position and speed signals. In reality, the encoder signals contain systematic errors in addition to superimposed stochastic noise. The systematic errors are classified into two types: coarse and fine position errors. If these errors are not compensated and the speed signal is used as a feedback for the speed control loop, the controller will try to smooth out these errors, thus generating acoustic noise or speed fluctuations. In this thesis, new methods are proposed to compensate the systematic error and reduce stochastic noise with the same performance over the whole speed range of the servomotor especially at high speeds. A hardware based on FPGA and DSP was developed in order to identify the process of the systematic error and to verify the proposed correction methods of the systematic error und stochastic noise. In order to have a uniform motion during the identification of the error, the AC motor is equipped with an additional large inertia (flywheel). Two correction stages are proposed for coarse and fine position errors correction. Compensation of the two errors was performed using the same lookup tables over the whole speed range. To improve the performance at high speeds and for tracking the changes of the fine error as the speed is increased, several correction tables or an error correction function for the fine error were developed. Furthermore, a novel approach to reduce the stochastic noise was proposed. This approach is based on linear regression for the high resolution position. The performance of the proposed correction methods has been proved using a closed speed loop, and the results show an improved smooth running over the whole speed range. The experimental results are based on an induction servomotor, which is equipped with an optical encoder. A comparison between the systematic errors and the speed signal with and without error correction were investigated