High-speed RF spectral analysis using a Rayleigh backscattering speckle spectrometer.

Persistent wideband radio frequency (RF) surveillance and spectral analysis is increasingly important, driven by the proliferation of wireless communication and RADAR technology. However, conventional electronic approaches are limited by the ∼1 GHz bandwidth of real-time analog-to-digital converters (ADCs). While faster ADCs exist, high data rates prohibit continuous operation, limiting these approaches to acquiring short snapshots of the RF spectrum. In this work, we introduce an optical RF spectrum analyzer designed for continuous, wideband operation. Our approach encodes the RF spectrum as sidebands on an optical carrier and relies on a speckle spectrometer to measure these sidebands. To achieve the resolution and update rate required for RF analysis, we use Rayleigh backscattering in single-mode fiber to rapidly generate wavelength-dependent speckle patterns with MHz-level spectral correlation. We also introduce a dual-resolution scheme to mitigate the trade-off between resolution, bandwidth, and measurement rate. This optimized spectrometer design enables continuous, wideband (15 GHz) RF spectral analysis with MHz-level resolution and a fast update rate of 385 kHz. The entire system is constructed using fiber-coupled off-the-shelf-components, providing a powerful new approach for wideband RF detection and monitoring.

Architecture for integrated RF photonic downconversion of electronic signals.

Electronic analog to digital converters (ADCs) are running up against the well-known bit depth versus bandwidth trade off. Towards this end, radio frequency (RF) photonic-enhanced ADCs have been the subject of interest for some time. Optical frequency comb technology has been used as a workhorse underlying many of these architectures. Unfortunately, such designs must generally grapple with size, weight, and power (SWaP) concerns, as well as frequency ambiguity issues which threaten to obscure critical spectral information of detected RF signals. In this work, we address these concerns via an RF photonic downconverter with potential for easy integration and field deployment by leveraging a novel, to the best of our knowledge, hybrid microcomb/electro-optic comb design.

High-resolution wide-band optical frequency comb control using stimulated Brillouin scattering.

We introduce a technique to manipulate an optical frequency comb on a line-by-line basis using stimulated Brillouin scattering (SBS). The narrow-linewidth SBS process has been used to address individual lines in optical frequency combs, but previous demonstrations required a dedicated laser to modulate each comb tooth, prohibiting complete comb control. Here, we use a pair of frequency shifting fiber optic loops to generate both an optical frequency comb and a train of frequency-locked pulses that can be used to manipulate the comb via SBS. This approach enables control of the entire frequency comb using a single seed laser without active frequency locking. To demonstrate the versatility of this technique, we generate and manipulate a comb consisting of 50 lines with 200 MHz spacing. By using polarization pulling assisted SBS, we achieve a modulation depth of 30 dB. This represents a scalable approach to control large numbers of comb teeth with high resolution using standard fiber-optic components.

Impact of nonlinearity including bleaching in MUTC photodetectors on RF-modulated electro-optic frequency combs.

We use the drift-diffusion equations to calculate the responsivity of a modified uni-traveling carrier (MUTC) photodetector (PD) with a frequency comb input that is generated by a series of short optical pulses. We first use experimental results for the responsivity of the MUTC PD to obtain an empirical model of bleaching in pulsed mode. We incorporate our empirical bleaching model into a drift-diffusion model to calculate the impact of nonlinearity in an MUTC PD on RF-modulated electro-optic frequency combs. We quantify the nonlinearity using the second- and third-order intermodulation distortion powers (IMD2 and IMD3), from which we calculate the second- and third-order output intercept points (OIP2 and OIP3). In contrast to a continuous wave (CW) input for which there is a single IMD2 and IMD3 and hence a single OIP2 and OIP3, each comb line n has its own IMD2n, IMD3n, OIP2n, and OIP3n associated with it. We determine the IMD2n, IMD3n, OIP2n, and OIP3n, and we compare the results with and without bleaching. We find that the impact of bleaching is complex and, somewhat surprisingly, not always detrimental. The principal effect of bleaching is to lower the responsivity, which decreases the nonlinearity due to space charge. While bleaching always reduces the OIP2n and OIP3n, we find that bleaching leads to a decreased distortion-to-signal ratio for large n.

Comparison of the impact of nonlinearity in a p-i-n and an MUTC photodetector on electro-optic frequency combs.

We calculate the impact of nonlinearity in both a p-i-n photodetector (PD) and a modified uni-traveling carrier (MUTC) PD on an RF-modulated frequency comb generated using 100-fs optical pulses with a 50-MHz repetition rate. We take into account bleaching (nonlinear saturation) that is due to the high peak-to-average-power ratio and contributes to the device nonlinearity. Nonlinear impairment of an RF-modulated continuous wave is typically characterized by the second- and third-order intermodulation distortion products (IMD2 and IMD3). In contrast, an RF-modulated frequency comb must be characterized by a distinct IMD2n and IMD3n for each comb line n. We calculate IMD2n and IMD3n in both p-i-n and MUTC PDs and compare the results. We also calculate the ratio of the IMD2n power and the IMD3n power to the fundamental power Sin in both p-i-n and MUTC PDs. We find that nonlinear distortion has a greater impact at high frequencies in the MUTC PD than in the p-i-n PD.

Calculation of the impulse response and phase noise of a high-current photodetector using the drift-diffusion equations.

We describe a procedure to calculate the impulse response and phase noise of high-current photodetectors using the drift-diffusion equations while avoiding computationally expensive Monte Carlo simulations. We apply this procedure to a modified uni-traveling-carrier (MUTC) photodetector. In our approach, we first use the full drift-diffusion equations to calculate the steady-state photodetector parameters. We then perturb the generation rate as a function of time to calculate the impulse response. We next calculate the fundamental shot noise limit and cut-off frequency of the device. We find the contributions of the electron, hole, and displacement currents. We calculate the phase noise of an MUTC photodetector. We find good agreement with experimental and Monte Carlo simulation results. We show that phase noise is minimized by having an impulse response with a tail that is as small as possible. Since, our approach is much faster computationally than Monte Carlo simulations, we are able to carry out a broad parameter study to optimize the device performance. We propose a new optimized structure with less phase noise and reduced nonlinearity.

Interlaboratory validation of an improved method for detection of Cyclospora cayetanensis in produce using a real-time PCR assay.

A collaborative validation study was performed to evaluate the performance of a new U.S. Food and Drug Administration method developed for detection of the protozoan parasite, Cyclospora cayetanensis, on cilantro and raspberries. The method includes a sample preparation step in which oocysts are recovered from produce using an enhanced produce washing solution containing 0.1% Alconox and a commercially available method to disrupt the C. cayetanensis oocysts and extract DNA. A real-time PCR assay targeting the C. cayetanensis 18S rDNA gene with an internal amplification control to monitor PCR inhibition provides species-specific identification. Five laboratories blindly analyzed a total of 319 samples consisting of 25 g of cilantro or 50 g of raspberries which were either uninoculated or artificially contaminated with C. cayetanensis oocysts. Detection rates for cilantro inoculated with 200, 10, and 5 oocysts, were 100%, 80%, and 31%, respectively. For raspberries, the detection rates for samples inoculated with 200, 10, and 5 oocysts were 100%, 90% and 50%, respectively. All uninoculated samples, DNA blank extracts, and no-template PCR controls were negative. Reproducibility between laboratories and analysts was high and the method was shown to be an effective analytical tool for detection of C. cayetanensis in produce.

Simultaneous Identification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari with SmartCycler-Based Multiplex Quantitative Polymerase Chain Reaction.

BACKGROUND: Consumption of Campylobacter contaminated food or water is a leading cause of human acute gastroenteritis. Campylobacter jejuni, Campylobacter coli, and Campylobacter lari account for over 95% of total Campylobacter infections. A multiplex quantitative polymerase chain reaction (qPCR) for simultaneous identification of C. jejuni, C. coli, and C. lari was developed for use with the SmartCycler II system. MATERIALS AND METHODS: We evaluated and combined previously described primers and probes for Campylobacter detection, designed a new internal amplification control, and optimized the multiplex qPCR for the detection of C. jejuni, C. coli, and C. lari. RESULTS: This method was 100% specific when tested against a panel of 32 target Campylobacter strains and 31 non-Campylobacter reference strains. Furthermore, there was no cross-reactivity with seven strains from four nontarget Campylobacter species. The amplification efficiency of each target in this multiplex qPCR was over 90%, and each coefficient of linearity was greater than 0.99. With artificially mixed genomic DNA, this method detected as few as two, three, and two genome copies of C. jejuni, C. coli, and C. lari, respectively. This method was also able to detect these three Campylobacter species in artificially contaminated milk with a sensitivity of five spiked cells of each target per reaction. CONCLUSION: The three Campylobacter targets were simultaneously identified using artificially mixed genomic DNA and spiked raw milk. This SmartCycler-based multiplex qPCR is a rapid, specific, and sensitive method to identify C. jejuni, C. coli, and C. lari.

Broadband RF disambiguation in subsampled analog optical links via intentionally-introduced sampling jitter.

We introduce a novel technique for broadband RF disambiguation which exploits a known jitter imparted onto the sampling rate of an optical pulse source in a subsampled analog optical link. Coarse disambiguation to bandwidths equal to the sample rate is achieved using pure tones as example waveforms by comparing the amplitude of the jitter-induced sidebands relative to the measured signal within the fundamental Nyquist band (frep/2). This sampling technique allows for ultra-wideband signal recovery with a single measurement. In a first-of-its-kind photonics demonstration we show reliable disambiguation for signals with center frequencies spanning 1 MHz - 40 GHz.

Bias-dependent distortion in optical comb-based analog optical links.

We provide the first experimental demonstration of the impact of bias-frequency on second-order distortion in sampled analog optical links. We show proper selection of bias frequency yields >48 dB improvement in second-order distortion performance. In addition, we demonstrate that measurement of the average frequency of the optical comb may be used to determine the optimum bias frequency - without the need for involved radio-frequency distortion measurements.

Suppression of even-order photodiode distortions via predistortion linearization with a bias-shifted Mach-Zehnder modulator.

A new technique to cancel photodiode-induced even-order distortion in microwave photonic links is demonstrated. A single Mach-Zehnder modulator, biased slightly away from the quadrature point, is shown to suppress photodiode second-order intermodulation distortion in excess of 40 dB without affecting the fundamental power. The technique is theoretically described with supporting experimental results.

Case Report: Unveiling an Incidentally Diagnosed Extrapulmonary Small Cell Carcinoma of the Rectum.

Extrapulmonary small cell carcinoma (EPSCC) is a rare malignancy with distinct clinical and pathological characteristics. We present the case of a 72-year-old male diagnosed with EPSCC of the rectum during a routine screening colonoscopy. The patient was asymptomatic, and pathological examination revealed a rectal mass displaying features of small cell carcinoma (SCC) associated with tubular adenoma. The treatment comprised radiation therapy and cisplatin/etoposide chemotherapy. This case underscores the importance of considering EPSCC as a potential diagnosis in patients with rectal masses, necessitating further studies to optimize treatment strategies.

Campylobacter jejuni survival within human epithelial cells is enhanced by the secreted protein CiaI.

Although it is known that Campylobacter jejuni invade the cells that line the human intestinal tract, the bacterial proteins that enable this pathogen to survive within Campylobacter-containing vacuoles (CCV) have not been identified. Here, we describe the identification and characterization of a protein that we termed CiaI for Campylobacter invasion antigen involved in intracellular survival. We show that CiaI harbours an amino-terminal type III secretion sequence and is secreted from C. jejuni through the flagellar type III secretion system. In addition, the ciaI mutant was impaired in intracellular survival when compared with a wild-type strain, as judged by the gentamicin-protection assay. Fluorescence microscopy examination of epithelial cells infected with the C. jejuni ciaI mutant revealed that the CCV were more frequently co-localized with Cathepsin D (a lysosomal marker) than the CCV in cells infected with a C. jejuni wild-type strain. Ectopic expression of CiaI-GFP in epithelial cells yielded a punctate phenotype not observed with the other C. jejuni genes, and this phenotype was abolished by mutation of a dileucine motif located in the carboxy-terminus of the protein. Based on the data, we conclude that CiaI contributes to the ability of C. jejuni to survive within epithelial cells.

Rapid, field-deployable method for genotyping and discovery of single-nucleotide polymorphisms associated with drug resistance in Plasmodium falciparum.

Despite efforts to reduce malaria morbidity and mortality, drug-resistant parasites continue to evade control strategies. Recently, emphasis has shifted away from control and toward regional elimination and global eradication of malaria. Such a campaign requires tools to monitor genetic changes in the parasite that could compromise the effectiveness of antimalarial drugs and undermine eradication programs. These tools must be fast, sensitive, unambiguous, and cost-effective to offer real-time reports of parasite drug susceptibility status across the globe. We have developed and validated a set of genotyping assays using high-resolution melting (HRM) analysis to detect molecular biomarkers associated with drug resistance across six genes in Plasmodium falciparum. We improved on existing technical approaches by developing refinements and extensions of HRM, including the use of blocked probes (LunaProbes) and the mutant allele amplification bias (MAAB) technique. To validate the sensitivity and accuracy of our assays, we compared our findings to sequencing results in both culture-adapted lines and clinical isolates from Senegal. We demonstrate that our assays (i) identify both known and novel polymorphisms, (ii) detect multiple genotypes indicative of mixed infections, and (iii) distinguish between variants when multiple copies of a locus are present. These rapid and inexpensive assays can track drug resistance and detect emerging mutations in targeted genetic loci in P. falciparum. They provide tools for monitoring molecular changes associated with changes in drug response across populations and for determining whether parasites present after drug treatment are the result of recrudescence or reinfection in clinical settings.

Amino-terminal residues dictate the export efficiency of the Campylobacter jejuni filament proteins via the flagellum.

Bacterial flagella play an essential role in the pathogenesis of numerous enteric pathogens. The flagellum is required for motility, colonization, and in some instances, for the secretion of effector proteins. In contrast to the intensively studied flagella of Escherichia coli and Salmonella typhimurium, the flagella of Campylobacter jejuni, Helicobacter pylori and Vibrio cholerae are less well characterized and composed of multiple flagellin subunits. This study was performed to gain a better understanding of flagellin export from the flagellar type III secretion apparatus of C. jejuni. The flagellar filament of C. jejuni is comprised of two flagellins termed FlaA and FlaB. We demonstrate that the amino-termini of FlaA and FlaB determine the length of the flagellum and motility of C. jejuni. We also demonstrate that protein-specific residues in the amino-terminus of FlaA and FlaB dictate export efficiency from the flagellar type III secretion system (T3SS) of Yersinia enterocolitica. These findings demonstrate that key residues within the amino-termini of two nearly identical proteins influence protein export efficiency, and that the mechanism governing the efficiency of protein export is conserved among two pathogens belonging to distinct bacterial classes. These findings are of additional interest because C. jejuni utilizes the flagellum to export virulence proteins.

Impact of obesity in asthma: evidence from a large prospective disease management study.

BACKGROUND: asthma and obesity continue to have a significant effect on public health. It is widely accepted that obesity may be an independent risk factor for asthma and affect asthma severity and quality of life (QOL). OBJECTIVE: to examine the relationship between body mass index (BMI [calculated as weight in kilograms divided by height in meters squared]) and asthma severity, spirometry findings, health care utilization (HCU), and QOL. METHODS: this 12-month prospective randomized controlled trial comparing disease management with traditional care enrolled 902 patients (473 pediatric and 429 adults) representing an underserved population. Data collected at baseline and at 6-month intervals included demographics, asthma severity, medication use, spirometry findings, and HCU. The QOL was assessed using the pediatric and adult versions of the Asthma Quality of Life Questionnaire and the 36-Item Short Form Health Survey. All HCU was determined by means of patient interview and extensive medical record review. Data were analyzed using negative binomial regression and analysis of variance. RESULTS: in children, 45% were overweight/obese (17% with BMIs >85th percentile; 28% with BMIs ≥ 95th percentile). In adults, 58% were obese (BMIs ≥ 30). There was no relationship in children between BMI and severity of asthma, spirometry findings, QOL, or HCU. In adults, there was no relationship between BMI and asthma severity or HCU. Higher BMI was associated with a significant reduction in QOL (P < .001). The BMI had an inverse relationship with forced vital capacity but with no other spirometric values. CONCLUSIONS: obesity was not associated with worse asthma severity, spirometry findings, QOL, or HCU in children. In adults with asthma, obesity was associated with lower forced vital capacity and QOL but not with severity or HCU.

Comparison of MiSeq, MinION, and hybrid genome sequencing for analysis of Campylobacter jejuni.

The sequencing, assembly, and analysis of bacterial genomes is central to tracking and characterizing foodborne pathogens. The bulk of bacterial genome sequencing at the US Food and Drug Administration is performed using short-read Illumina MiSeq technology, resulting in highly accurate but fragmented genomic sequences. The MinION sequencer from Oxford Nanopore is an evolving technology that produces long-read sequencing data with low equipment cost. The goal of this study was to compare Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. Two reference strains and two field isolates of C. jejuni were sequenced using MiSeq and MinION, and the sequence data were assembled using the software programs SPAdes and Canu, respectively. Hybrid genome assembly was performed using the program Unicycler. Comparison of the C. jejuni 81-176 and RM1221 genome assemblies to the PacBio reference genomes revealed that the SPAdes assemblies had the most accurate nucleotide identity, while the hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate, containing many indels and substitutions that affected downstream analyses. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements such as rRNA and tRNA genes. The full genomes of both C. jejuni field isolates were completed and circularized using hybrid sequencing, and a plasmid was detected in one isolate. Continued development of nanopore sequencing technologies will likely enhance the accuracy of hybrid genome assemblies and enable public health laboratories to routinely generate complete circularized bacterial genome sequences.

Joint effects of common genetic variants from multiple genes and pathways on the risk of premature coronary artery disease.

OBJECTIVE: The aim of this study is to discover common variants in 6 lipid metabolic genes and construct and validate a genetic risk score (GRS) based on the joint effects of genetic variants in multiple genes from lipid and other pathobiologic pathways. BACKGROUND: Explaining the genetic basis of coronary artery disease (CAD) is incomplete. Discovery and aggregation of genetic variants from multiple pathways may advance this objective. METHODS: Premature CAD cases (n = 1,947) and CAD-free controls (n = 1,036) were selected from our angiographic registry. In a discovery phase, single nucleotide polymorphisms (SNPs) at 56 loci from internal discovery and external reports were tested for associations with biomarkers and CAD: 28 promising SNPs were then tested jointly for CAD associations, and a GRS consisting of SNPs contributing independently was constructed and validated in a replication set of familial cases and population-based controls (n = 1,320). RESULTS: Five variants contributed jointly to CAD prediction in a multigenic GRS model: odds ratio 1.24 (95% CI 1.16-1.33) per risk allele, P = 8.2 x 10(-11), adjusted OR 2.03 (1.53-2.70), fourth versus first quartile. 5-SNP genetic risk score had minor impact on area under the receiver operating characteristic curve (P > .05) but resulted in substantial net reclassification improvement: 0.16 overall, 0.28 in intermediate-risk patients (both P < .0001). GRS(5) predicted familial CAD with similar magnitude in the validation set. CONCLUSIONS: The Intermountain Healthcare's Coronary Genetics study demonstrates the ability of a multigenic, multipathway GRS to improve discrimination of angiographic CAD. Genetic risk scores promise to increase understanding of the genetic basis of CAD and improve identification of individuals at increased CAD risk.

An evaluation of nine genetic variants related to metabolism and mechanism of action of warfarin as applied to stable dose prediction.

Warfarin anticoagulation is complicated by the highly variable inter-individual response. Approximately 50% of the dose variability arises from clinical factors and variants in two genes, CYP2C9 (*2 and *3 variants) and VKORC1 -1173 C > T. We tested variants in five additional genes (EPHX1, PROC, APOE, CYP4F2, CALU and a new variant in VKORC1 in an attempt to further reduce the variability in predicted stable warfarin dose. Consecutive consenting outpatients requiring anticoagulation on stable warfarin dose (target INR 2-3) were genotyped; the association of SNP genotypes with stable warfarin dose was evaluated using the test of linear contrasts in analysis of variance (ANOVA). Study participants were 71 ± 13 years, 53% female, 85 ± 23 kg, body mass index 29 ± 7 kg/m(2). Genotypes were in Hardy-Weinberg equilibrium with the exception of VKORC1 -1639. Weekly stable dosages were 31.7 ± 13.9 mg/week; median: 30 mg/week, range: 11-70 mg/week. Significant associations with dose were seen for VKORC1 -1639 (P < 0.001), CYP2C9*2 (P = 0.005) and *3 (P = 0.003), the CYP4F2 SNP (P-trend = 0.00037), and VKORC1 3730 (p-trend = 0.042). In linear regression, age, sex, weight, and CYP2C9 *2 and *3 and VKORC1-1639 genotype explained 42% of variance. The addition of CYP4F2 genotype to the regression model increased the degree of variance explained to 47%. Addition of VKORC1 SNP -1639 to a model eliminated the association of VKORC1 3730 with warfarin dose (P-trend = 0.74), but -1639 remained highly significant. No impact on dose was observed for the other tested genetic variants.