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.

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 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.

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.

Colonic mucormycosis in an immunocompetent patient with endocarditis.

Mucormycosis is a fatal opportunistic fungal infection. Rarely it can occur in immunocompetent patients. Here, we present a case of colonic mucormycosis in immunocompetent patients.

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.

Whole Genome Sequencing and Multiplex qPCR Methods to Identify Campylobacter jejuni Encoding cst-II or cst-III Sialyltransferase.

Campylobacter jejuni causes more than 2 million cases of gastroenteritis annually in the United States, and is also linked to the autoimmune sequelae Guillan-Barre syndrome (GBS). GBS often results in flaccid paralysis, as the myelin sheaths of nerve cells are degraded by the adaptive immune response. Certain strains of C. jejuni modify their lipooligosaccharide (LOS) with the addition of neuraminic acid, resulting in LOS moieties that are structurally similar to gangliosides present on nerve cells. This can trigger GBS in a susceptible host, as antibodies generated against C. jejuni can cross-react with gangliosides, leading to demyelination of nerves and a loss of signal transduction. The goal of this study was to develop a quantitative PCR (qPCR) method and use whole genome sequencing data to detect the Campylobacter sialyltransferase (cst) genes responsible for the addition of neuraminic acid to LOS. The qPCR method was used to screen a library of 89 C. jejuni field samples collected by the Food and Drug Administration Pacific Northwest Lab (PNL) as well as clinical isolates transferred to PNL. In silico analysis was used to screen 827 C. jejuni genomes in the FDA GenomeTrakr SRA database. The results indicate that a majority of C. jejuni strains could produce LOS with ganglioside mimicry, as 43.8% of PNL isolates and 46.9% of the GenomeTrakr isolates lacked the cst genes. The methods described in this study can be used by public health laboratories to rapidly determine whether a C. jejuni isolate has the potential to induce GBS. Based on these results, a majority of C. jejuni in the PNL collection and submitted to GenomeTrakr have the potential to produce LOS that mimics human gangliosides.

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.

Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance.

As the most prevalent bacterial cause of human gastroenteritis, food-borne Campylobacter infections pose a serious threat to public health. Whole Genome Sequencing (WGS) is a tool providing quick and inexpensive approaches for analysis of food-borne pathogen epidemics. Here we report the WGS and annotation of a Campylobacter coli strain, FNW20G12, which was isolated from milk in the United States in 1997 and carries multidrug resistance. The draft genome of FNW20G12 (DDBJ/ENA/GenBank accession number LWIH00000000) contains 1, 855,435 bp (GC content 31.4%) with 1902 annotated coding regions, 48 RNAs and resistance to aminoglycoside, beta-lactams, tetracycline, as well as fluoroquinolones. There are very few genome reports of C. coli from dairy products with multidrug resistance. Here the draft genome of FNW20G12, a C. coli strain isolated from raw milk, is presented to aid in the epidemiology study of C. coli antimicrobial resistance and role in foodborne outbreak.

Mediastinal pancreatic pseudocyst with hemorrhage and left gastric artery pseudoaneurysm, managed with left gastric artery embolization and placement of percutaneous trans-hepatic pseudocyst drainage.

Mediastinal pancreatic pseudocyst (MPP) is a rare, but known, complication of both acute and chronic pancreatitis. Most pseudocysts are associated with alcoholic pancreatitis. Recent advances in endoscopic techniques have shown promising results, with reduced chances of infection and recurrence than with percutaneous drainage, but limited availability restricts widespread use. Left gastric artery pseudoaneurysm with mediastinal pseudocyst has not been described in the literature to date. We report a successful resolution of hemorrhagic MPP with embolization of pseudoaneurysm and percutaneous trans-hepatic pseudocyst drainage.

Draft Genome Sequence of the Beer Spoilage Bacterium Megasphaera cerevisiae Strain PAT 1T.

The genus Megasphaera harbors important spoilage organisms that cause beer spoilage by producing off flavors, undesirable aroma, and turbidity. Megasphaera cerevisiae is mainly found in nonpasteurized low-alcohol beer. In this study, we report the draft genome of the type strain of the genus, M. cerevisiae strain PAT 1(T).

Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.

Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. The goal of this study was to analyze the C. jejuni F38011 strain, recovered from an individual with severe enteritis, at a genomic and proteomic level to gain insight into microbial processes. The C. jejuni F38011 genome is comprised of 1,691,939 bp, with a mol.% (G+C) content of 30.5%. PacBio sequencing coupled with REBASE analysis was used to predict C. jejuni F38011 genomic sites and enzymes that may be involved in DNA restriction-modification. A total of five putative methylation motifs were identified as well as the C. jejuni enzymes that could be responsible for the modifications. Peptides corresponding to the deduced amino acid sequence of the C. jejuni enzymes were identified using proteomics. This work sets the stage for studies to dissect the precise functions of the C. jejuni putative restriction-modification enzymes. Taken together, the data generated in this study contributes to our knowledge of the genomic content, methylation profile, and encoding capacity of C. jejuni.

Reducing Campylobacter jejuni colonization of poultry via vaccination.

Campylobacter jejuni is a leading bacterial cause of human gastrointestinal disease worldwide. While C. jejuni is a commensal organism in chickens, case-studies have demonstrated a link between infection with C. jejuni and the consumption of foods that have been cross-contaminated with raw or undercooked poultry. We hypothesized that vaccination of chickens with C. jejuni surface-exposed colonization proteins (SECPs) would reduce the ability of C. jejuni to colonize chickens, thereby reducing the contamination of poultry products at the retail level and potentially providing a safer food product for consumers. To test our hypothesis, we injected chickens with recombinant C. jejuni peptides from CadF, FlaA, FlpA, CmeC, and a CadF-FlaA-FlpA fusion protein. Seven days following challenge, chickens were necropsied and cecal contents were serially diluted and plated to determine the number of C. jejuni per gram of material. The sera from the chickens were also analyzed to determine the concentration and specificity of antibodies reactive against the C. jejuni SECPs. Vaccination of chickens with the CadF, FlaA, and FlpA peptides resulted in a reduction in the number of C. jejuni in the ceca compared to the non-vaccinated C. jejuni-challenged group. The greatest reduction in C. jejuni colonization was observed in chickens injected with the FlaA, FlpA, or CadF-FlaA-FlpA fusion proteins. Vaccination of chickens with different SECPs resulted in the production of C. jejuni-specific IgY antibodies. In summary, we show that the vaccination of poultry with individual C. jejuni SECPs or a combination of SECPs provides protection of chickens from C. jejuni colonization.

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.