Machine learning at the edge for AI-enabled multiplexed pathogen detection

Multiplexed detection of biomarkers in real-time is crucial for sensitive and accurate diagnosis at the point of use. This scenario poses tremendous challenges for detection and identification of signals of varying shape and quality at the edge of the signal-to-noise limit. Here, we demonstrate a robust target identification scheme that utilizes a Deep Neural Network (DNN) for multiplex detection of single particles and molecular biomarkers. The model combines fast wavelet particle detection with Short-Time Fourier Transform analysis, followed by DNN identification on an AI-specific edge device (Google Coral Dev board). The approach is validated using multi-spot optical excitation of Klebsiella Pneumoniae bacterial nucleic acids flowing through an optofluidic waveguide chip that produces fluorescence signals of varying amplitude, duration, and quality. Amplification-free 3× multiplexing in real-time is demonstrated with excellent specificity, sensitivity, and a classification accuracy of 99.8%. These results show that a minimalistic DNN design optimized for mobile devices provides a robust framework for accurate pathogen detection using compact, low-cost diagnostic devices.

Optical trapping assisted label-free and amplification-free detection of SARS-CoV-2 RNAs with an optofluidic nanopore sensor

Ultrasensitive, versatile sensors for molecular biomarkers are a critical component of disease diagnostics and personalized medicine as the COVID-19 pandemic has revealed in dramatic fashion. Integrated electrical nanopore sensors can fill this need via label-free, direct detection of individual biomolecules, but a fully functional device for clinical sample analysis has yet to be developed. Here, we report amplification-free detection of SARS-CoV-2 RNAs with single molecule sensitivity from clinical nasopharyngeal swab samples on an electro-optofluidic chip. The device relies on optically assisted delivery of target carrying microbeads to the nanopore for single RNA detection after release. A sensing rate enhancement of over 2,000x with favorable scaling towards lower concentrations is demonstrated. The combination of target specificity, chip-scale integration and rapid detection ensures the practicality of this approach for COVID-19 diagnosis over the entire clinically relevant concentration range from 10⁴-10⁹ copies/mL.

Optofluidic Amplification-free Multiplex Detection of Viral Hemorrhagic Fevers

Infectious disease outbreaks such as Ebola and other Viral Hemorrhagic Fevers (VHF) require low-complexity, specific, and differentiated diagnostics as illustrated by the recent outbreak in the Democratic Republic of Congo. Here, we describe amplification-free spectrally multiplex detection of four different VHF total RNA samples using multi-spot excitation on a multimode interference waveguide platform along with combinatorial fluorescence labeling of target nucleic acids. In these experiments, we observed an average of 8-fold greater fluorescence signal amplitudes for the Ebola total RNA sample compared to three other total RNA samples: Lake Victoria Marburg Virus, Ravn Marburg Virus, and Crimean-Congo Hemorrhagic Fever. We have attributed this amplitude amplification to an increased amount of RNA during synthesis of soluble glycoprotein in infection. This hypothesis is confirmed by single molecule detection of the total RNA sample after heat-activated release from the carrier microbeads. From these experiments, we observed at least a 5.3x higher RNA mass loading on the Ebola carrier microbeads compared to the Lake Victoria Marburg carrier microbeads, which is consistent with the known production of soluble glycoprotein during infection.

3× multiplexed detection of antibiotic resistant plasmids with single molecule sensitivity

Bacterial pathogens resistant to antibiotics have become a serious health threat. Those species which have developed resistance against multiple drugs such as the carbapenems, are more lethal as these are last line therapy antibiotics. Current diagnostic tests for these resistance traits are based on singleplex target amplification techniques which can be time consuming and prone to errors. Here, we demonstrate a chip based optofluidic system with single molecule sensitivity for amplification-free, multiplexed detection of plasmids with genes corresponding to antibiotic resistance, within one hour. Rotating disks and microfluidic chips with functionalized polymer monoliths provided the upstream sample preparation steps to selectively extract these plasmids from blood spiked with E. coli DH5α cells. Waveguide-based spatial multiplexing using a multi-mode interference waveguide on an optofluidic chip was used for parallel detection of three different carbapenem resistance genes. These results point the way towards rapid, amplification-free, multiplex analysis of antibiotic-resistant pathogens.

On demand delivery and analysis of single molecules on a programmable nanopore-optofluidic device

Nanopore-based single nanoparticle detection has recently emerged as a vibrant research field with numerous high-impact applications. Here, we introduce a programmable optofluidic chip for nanopore-based particle analysis: feedback-controlled selective delivery of a desired number of biomolecules and integration of optical detection techniques on nanopore-selected particles. We demonstrate the feedback-controlled introduction of individual biomolecules, including 70S ribosomes, DNAs and proteins into a fluidic channel where the voltage across the nanopore is turned off after a user-defined number of single molecular insertions. Delivery rates of hundreds/min with programmable off-times of the pore are demonstrated using individual 70S ribosomes. We then use real-time analysis of the translocation signal for selective voltage gating of specific particles from a mixture, enabling selection of DNAs from a DNA-ribosome mixture. Furthermore, we report optical detection of nanopore-selected DNA molecules. These capabilities point the way towards a powerful research tool for high-throughput single-molecule analysis on a chip.

Buried Rib SiO2 Multimode Interference Waveguides for Optofluidic Multiplexing

Multimode interference (MMI) waveguides can be used to create wavelength-dependent spot patterns which enables simultaneous analyte detection on a single optofluidic chip, useful for disease diagnostics. The fidelity of such multi-spot patterns is important for high sensitivity and accurate target identification. Buried rib structures have been incorporated into these SiO₂-based waveguides to improve environmental stability. Through experiments and simulation, this letter explores design parameters for a buried MMI rib waveguide based on anti-resonant reflecting optical waveguides in order to produce high-fidelity spot patterns. Optimal rib heights and widths are reported in the context of available microfabrication etch technology and performance for an optimized biosensor is shown.

Optofluidic detection of Zika nucleic acid and protein biomarkers using multimode interference multiplexing

The recent massive Zika virus (ZIKV) outbreak illustrates the need for rapid and specific diagnostic techniques. Detecting ZIKV in biological samples poses unique problems: antibody detection of ZIKV is insufficient due to cross-reactivity of Zika antibodies with other flaviviruses, and nucleic acid and protein biomarkers for ZIKV are detectable at different stages of infection. Here, we describe a new optofluidic approach for the parallel detection of different molecular biomarkers using multimode interference (MMI) waveguides. We report differentiated, multiplex detection of both ZIKV biomarker types using multi-spot excitation at two visible wavelengths with over 98% fidelity by combining several analysis techniques.

Optimized ARROW-Based MMI Waveguides for High Fidelity Excitation Patterns for Optofluidic Multiplexing

Multimode interference (MMI) waveguides can be used for multiplexing and de-multiplexing optical signals. High fidelity, wavelength dependent multi-spot patterns from MMI waveguides are useful for sensitive and simultaneous identification of multiple targets in multiplexed fluorescence optofluidic biosensors. Through experiments and simulation, this paper explores design parameters for an MMI rib anti-resonant reflecting optical waveguide (ARROW) in order to produce high fidelity spot patterns at the liquid core biomarker excitation region. Width and etch depth of the single excitation rib waveguide used to excite the MMI waveguide are especially critical because they determine the size of the input optical mode which is imaged at the MMI waveguide's output. To increase optical throughput into the MMI waveguide when light is coupled in from an optical fiber, tapers in the waveguide width can be used for better mode matching.

Scalable Spatial-Spectral Multiplexing of Single-Virus Detection Using Multimode Interference Waveguides

Simultaneous detection of multiple pathogens and samples (multiplexing) is one of the key requirements for diagnostic tests in order to enable fast, accurate and differentiated diagnoses. Here, we introduce a novel, highly scalable, photonic approach to multiplex analysis with single virus sensitivity. A solid-core multimode interference (MMI) waveguide crosses multiple fluidic waveguide channels on an optofluidic chip to create multi-spot excitation patterns that depend on both the wavelength and location of the channel along the length of the MMI waveguide. In this way, joint spectral and spatial multiplexing is implemented that encodes both spatial and spectral information in the time dependent fluorescence signal. We demonstrate this principle by using two excitation wavelengths and three fluidic channels to implement a 6x multiplex assay with single virus sensitivity. High fidelity detection and identification of six different viruses from a standard influenza panel is reported. This multimodal multiplexing strategy scales favorably to large numbers of targets or large numbers of clinical samples. Further, since single particles are detected unbound in flow, the technique can be broadly applied to direct detection of any fluorescent target, including nucleic acids and proteins.

Multiplexed efficient on-chip sample preparation and sensitive amplification-free detection of Ebola virus

An automated microfluidic sample preparation multiplexer (SPM) has been developed and evaluated for Ebola virus detection. Metered air bubbles controlled by microvalves are used to improve bead-solution mixing thereby enhancing the hybridization of the target Ebola virus RNA with capture probes bound to the beads. The method uses thermally stable 4-formyl benzamide functionalized (4FB) magnetic beads rather than streptavidin coated beads with a high density of capture probes to improve the target capture efficiency. Exploiting an on-chip concentration protocol in the SPM and the single molecule detection capability of the antiresonant reflecting optical waveguide (ARROW) biosensor chip, a detection limit of 0.021pfu/mL for clinical samples is achieved without target amplification. This RNA target capture efficiency is two orders of magnitude higher than previous results using streptavidin beads and the limit of detection (LOD) improves 10×. The wide dynamic range of this technique covers the whole clinically applicable concentration range. In addition, the current sample preparation time is ~1h which is eight times faster than previous work. This multiplexed, miniaturized sample preparation microdevice establishes a key technology that intended to develop next generation point-of-care (POC) detection system.

On-chip wavelength multiplexed detection of cancer DNA biomarkers in blood

We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip. Specifically, we extract two types of melanoma biomarkers, mutated cell-free nucleic acids -BRAFV600E and NRAS, from whole blood. We detect and identify these two targets simultaneously using the spectral multiplexing approach with up to a 96% success rate. These results point the way toward a full front-to-back chip-based optofluidic compact system for high-performance analysis of complex biological samples.

Optimization of Y-splitting antiresonant reflecting optical waveguides-based rib waveguides

Antiresonant reflecting optical waveguide power splitters, designed for use around the 635-nm wavelength, are characterized for multiple split angles ranging from 0.5 deg to 9 deg. Theoretical expectations and simulations predict lowest transmission losses at this split junction for the lowest angles. This is confirmed by the experimental structures built in SiO₂ films on silicon substrates. A fabrication nonideality affects the achievable splitting angle. Design considerations are discussed based on tradeoffs between loss and the required length for a Y-splitter.

Signal-to-noise Enhancement in Optical Detection of Single Viruses with Multi-spot Excitation

We present fluorescence detection of single H1N1 viruses with enhanced signal to noise ratio (SNR) achieved by multi-spot excitation in liquid-core anti-resonant reflecting optical waveguides (ARROWs). Solid-core Y-splitting ARROW waveguides are fabricated orthogonal to the liquid-core section of the chip, creating multiple excitation spots for the analyte. We derive expressions for the SNR increase after signal processing, and analyze its dependence on signal levels and spot number. Very good agreement between theoretical calculations and experimental results is found. SNR enhancements up to 5x10⁴ are demonstrated.

Optofluidic wavelength division multiplexing for single-virus detection

Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context--the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine.

Optofluidic analysis system for amplification-free, direct detection of Ebola infection

The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

Optofluidic analysis system for amplification-free, direct detection of Ebola infection

The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

Glue ablation of a late-presentation urinary fistula after partial nephrectomy

Urinary fistula is an acknowledged complication of partial nephrectomy. We describe a case of a urinary fistula that failed to respond to conventional treatment and the subsequent use of percutaneous Hystoacryl glue to achieve its resolution.

Is the conservative management of chronic retention in men ever justified?

OBJECTIVE

To assess the outcome of men presenting with lower urinary tract symptoms (LUTS) associated with large postvoid residual urine volumes (PVR).

PATIENTS AND METHODS

The study included men presenting with LUTS and a PVR of > 250 mL who, because of significant comorbidity, a low symptom score or patient request, were managed conservatively and prospectively, and were followed with symptom assessment, serum creatinine levels, flow rates and renal ultrasonography. Patients were actively managed if there was a history of previous outflow tract surgery, prostate cancer, urethral strictures, neuropathy, elevated creatinine or hydronephrosis. In all, 93 men (mean age 70 years, range 40-84) with a median (range) PVR of 363 mL (250-700) were included in the study and followed for 5 (3-10) years. At presentation, the median maximum flow rate was 10.2 (3-30) mL/s and the voided volume 316 (89-714) mL.

RESULTS

The measured PVR remained stable in 47 (51%), reduced in 27 (29%) and increased in 19 (20%) patients; 31 patients (33%) went on to transurethral resection of the prostate after a median of 30 (10-120) months, because of serum creatinine elevation (two), acute retention (seven), increasing PVR (eight) and worsening symptoms (14). Of 31 patients 25 were available for evaluation after surgery; their median PVR was 159 (0-1000) mL, flow rate 18.4 (4-37) mL/s and voided volume 321 (90-653) mL. Symptoms were improved in all but five men. There was no difference in initial flow rate, voided volume or PVR between those who developed complications or went on to surgery and those who did not. Urinary tract infections (UTIs) occurred in five patients and two developed bladder stones.

CONCLUSIONS

Complications such as renal failure, acute retention and UTIs are uncommon in men with large, chronic PVRs. Conservative management for this group of patients is reasonable but outpatient review is prudent. There were no factors that could be used to predict those patients who eventually required surgery.

Cytoplasmic induction and over-expression of cyclooxygenase-2 in human prostate cancer: implications for prevention and treatment

OBJECTIVE

To assess the level and morphological distribution of cyclooxygenase (COX)-1 and -2 in human prostates and to determine any association with the Gleason grade of prostate cancer. Materials and methods The study comprised 30 samples from patients with benign prostatic hyperplasia (BPH) and 82 with prostate cancer. Immunohistochemistry was used to assess the expression of COX-1 and -2, and 13 samples were also assessed using immunoblotting (six BPH and seven cancers).

RESULTS

For both BPH and prostate cancer, COX-1 expression was primarily in the fibromuscular stroma, with variable weak cytoplasmic expression in glandular/neoplastic epithelial cells. In contrast, COX-2 expression differed markedly between BPH and cancer. In BPH there was membranous expression of COX-2 in luminal glandular cells and no stromal expression. In cancer the stromal expression of COX-2 was unaltered, but expression by tumour cells was significantly greater (P = 0.008), with a change in the staining pattern from membranous to cytoplasmic (P < 0.001). COX-2 expression was significantly higher in poorly differentiated than in well differentiated tumours (P < 0.001). These results were supported by immunoblotting, which showed similar levels of COX-1 in both BPH and cancer, but four times greater expression of COX-2 in cancer than in BPH.

CONCLUSION

This is the first study to assess the co-expression of COX-1 and COX-2 proteins in benign and malignant human prostates, and showed the induction and significantly greater expression of COX-2 in cancer, which was also associated with tumour grade. The regular use of nonsteroidal anti-inflammatory drugs is associated with a reduced incidence of cancers. The present results provide the basis for a potential role for COX-2 inhibitors in the prevention and treatment of prostate cancer.

Tanning and sunburn: knowledge, attitudes and behaviour of people in Great Britain

BACKGROUND

A representative sample of the British population was interviewed to identify the factors associated with sunburn and intention to tan, and the source from which people obtained their information about the risks of sun exposure.

METHODS

As part of its rolling Omnibus survey, the Office for National Statistics interviewed a randomly selected representative sample of 1858 adults (aged 16 or over) in Great Britain in October 1996. The analysis and interpretation of the resulting data form the basis of this study.

RESULTS

The response rate was just below 70 per cent. Forty-three per cent of men and 35 per cent of women reported sunburning in the 12 months to October 1996. Factors associated with sunburn were: being male, having a skin that tans with difficulty and being younger. Concerning 'intention to tan', 34 per cent of men and 39 per cent of women admitted trying. There were associations with having a skin that tans easily, and, less strongly, with being younger. There was a clear association between trying to tan and severity of sunburn. Most people identified television as their main source of information about the dangers of sun exposure, and the majority had seen the sunburn forecasts on weather reports. Comparison with a previous Omnibus sunburn survey from 1993 shows little change in the proportion of the population becoming sunburnt, but some increase in the proportion of men intending to tan.

CONCLUSIONS

The data allow an insight into current sun-related behaviour and whether there has been a change since 1993. Health promotion campaigns warning about the risk from the sun may have increased awareness, but have thus far failed to reduce the proportion becoming sunburnt. It is time to re-evaluate the thinking behind such programmes.

Contemporary results of radical radiotherapy for bladder transitional cell carcinoma in a district general hospital with cancer-centre status

OBJECTIVE

To assess the current efficacy and safety of definitive external beam radiotherapy (EBRT) in the treatment of invasive bladder transitional cell carcinoma (TCC) in a district general hospital with cancer-centre status.

PATIENTS AND METHODS

The case notes of all patients with bladder TCC undergoing EBRT with curative intent over an 8-year period (1988-95) were reviewed. Additional missing outcome data were collected.

RESULTS

In all, 120 patients (109 men; median age 70 years, range 34-90) underwent radical EBRT (40-65 Gy; fraction median=20) over the 8-year period. Staging, as assessed by examination under anaesthesia and computed tomography, was T1 in 16%, T2 in 43%, T3 in 38% and T4 in 3%. In 96 patients (80%) the tumour was poorly differentiated (G3). The overall morbidity at 12 months was 12%; proctitis occurred in nine patients (8%) and cystitis in five (4%). Sixty-seven patients (59%) developed a local recurrence and in 36 (30%) this was invasive. The overall median survival was 60 months. Thirty-three patients underwent salvage cystectomy with a subsequent median survival of 12.5 months.

CONCLUSION

Modern radical multifraction EBRT in invasive bladder TCC has a low morbidity, with an overall median survival of 5 years.

Do not catheterise your nephrectomies

A retrospective study of 100 consecutive nephrectomy patients showed a 20% catheterisation rate. Of the 11 carried out post-operatively only 4 were for urinary retention. The post-operative catheterisation rate for males was 7.1% and for females 2%. The rate of post-operative retention was 4.4%, which is much lower than that reported from other units. This rate of post-operative catheterisation for retention is so low that in spite of the very mild increase in complications compared with intra-operative catheterisation, the practice of routine prophylactic catheterisation of nephrectomy patients is unnecessary and cannot be recommended.

Indoramin in the treatment of prostatic bladder outflow obstruction

A series of 40 patients took part in a double-blind, placebo-controlled trial of indoramin in prostatic bladder outflow obstruction. Patients were assessed clinically and urodynamically before and after 4 weeks' treatment. Significant improvement was seen in nocturia, volume voided, flow rates and residual urine. The drug was well tolerated, although 7 patients on treatment and 7 on placebo noted side effects. These results suggest that indoramin may be a useful agent in the symptomatic management of bladder outflow obstruction.

Bilateral inguinal hernias: simultaneous or sequential repair?

Two hundred and forty four patients underwent either simultaneous bilateral inguinal hernia repair (n = 122) or unilateral inguinal hernia (n = 122) repair at a general hospital between January 1971 and December 1981. The two groups of patients were matched for age and sex. Both groups had a similar overall incidence of post-operative complications and in both groups the duration of post-operative stay and duration of operating time were similar. Chest infections developed in 12 patients after bilateral repair and in 3 patients after unilateral repair (P less than 0.02). All patients were assessed prospectively from 4 to 15 years after operation, when no significant difference in the number of recurrent hernias was found. Our results suggest that simultaneous bilateral inguinal herniorrhaphy is economical in terms of both operating time and duration of hospital stay, and that this economy is not bought at a cost of increased short term morbidity or long-term recurrence rate.