The oral microbiome of treated and untreated chronic HCV infection: A preliminary study.

OBJECTIVES: Chronic hepatitis C virus (HCV) infection is a debilitating disease that is lately treated using direct-acting antivirals (DAAs). Changes in the oral microbiome were detected in other liver diseases; however, oral microbiome was never investigated in patients having chronic HCV infection, whether pre- or post-treatment. MATERIALS AND METHODS: This case-control preliminary study enrolled three equal groups: Group (I): untreated HCV patients; group (II): HCV patients who achieved viral clearance after DAA administration; and group (III): healthy controls. For each participant, a buccal swab was harvested and its 16S rRNA was sequenced. RESULTS: The oral microbiome of chronic HCV patients had a significantly distinct bacterial community compared to healthy controls, characterized by high diversity and abundance of certain pathogenic species. These changes resemble that of oral lichen planus patients. After treatment by DAAs, the oral microbiome shifted to a community with partial similarity to both the diseased and the healthy ones. CONCLUSIONS: Chronic HCV is associated with dysbiotic oral microbiome having abundant pathogenic bacteria. With HCV clearance by DAAs, the oral microbiome shifts to approach the healthy composition.

ZnO Nanorods Coated Single-Mode-Multimode-Single-Mode Optical Fiber Sensor for VOC Biomarker Detection.

This work demonstrated a ZnO-coated optical fiber sensor for the detection of a volatile organic compound (VOC) biomarker for diabetes for detecting isopropanol (IPA) markers. A coreless silica fiber (CSF) was connected to a single-mode fiber (SMF) at both ends to achieve a SMF-CSF-SMF structure. CSF is the sensing region where multimode interference (MMI) generates higher light interaction at the interface between the fiber and sensing medium, leading to enhanced sensitivity. Optimization of the CSF length was conducted numerically to attain the highest possible coupling efficiency at the output. Surface functionalization was achieved via hydrothermal growth of ZnO nanorods directly onto the CSF at low temperatures. The optical fiber-based sensor was successfully fabricated and tested with 20%, 40%, 60%, 80%, and 100% of IPA. The sensor response was recorded using an optical spectrometer and analyzed for sensor sensitivity. The fabricated sensor shows the potential to detect isopropanol with the sensitivity of 0.053 nm/%IPA vapor. Further improvement of the sensor sensitivity and selectivity is also proposed for future work.

Single-step 3D-printed integrated optical system and its implementation for a sensing application using digital light processing technology.

This study proposes a single-step integrated optical fabrication scheme utilizing a 3D printer using digital light processing technology. Strong light confinement in the fabricated structure is realized through the introduction of an elevated (tower-shaped) waveguide in a transparent photosensitive resin (PX-8880). The fabrication is optimized to maximize light confinement through varying the dimensions of the guiding region and the tower structure. Benefiting from the surface roughness produced by the slicing process in the 3D printing (50 µm resolution), the fabricated structure was tested for vapor sensing. Obvious intensity dynamics have been reported due to the change of the optical scattering due to the presence of vapor as well as polymer vapor interaction. Though the reported response time is long, further optimization can lead to practical operation time.

An Analytical Model for Describing the Power Coupling Ratio between Multimode Fibers with Transverse Displacement and Angular Misalignment in an Optical Fiber Bend Sensor.

The power coupling ratio between step-index multimode fibers caused by combined transversal and angular misalignment is calculated. A theoretical description of the coupling efficiency between two optical fibers based on geometrical optics is provided. The theoretical calculations are collaborated by experiments, determining the power coupling ratio between three output fibers with an axial offset and angular misalignment with a single input fiber. The calculation results are in good agreement with experimental results obtained using a previously fabricated optical fiber sensor for monitoring physiological parameters in clinical environments. The theoretical results are particularly beneficial for optimizing the design of optical fiber bending sensors that are based on power coupling loss (intensity) as the measurement interrogation requires either axial displacement, angular misalignment, or both.

Transformation optics based on unitary vectors and Fermat's principle for arbitrary spatial transformation design.

A methodology of designing an arbitrary transformation using transformation optics (TO) based on unitary vectors and Fermat's principle is presented. The TO equation is derived in terms of grid coordinates. The geometry of the transformed space is stored in the grid coordinates rather than the transformation functions. This allows the crafting of an arbitrary transformation by combining several transformation templates together. The touch interface is employed to intuitively apply the transformations. The resulting material parameters are calculated from the proposed method and verified using the anisotropic finite-difference frequency-domain method. Five examples are presented to demonstrate the capability of this method.

Optimization of a horizontal slot waveguide biosensor to detect DNA hybridization.

A full-vectorial H-field formulation-based finite element approach is used to optimize a biosensor structure incorporating a horizontal slot waveguide. It is designed to detect DNA hybridization through the change of the effective index of the waveguide structure. The key parameters, such as normalized power confinement, power density, change in effective index, and sensitivity are presented by optimizing the device parameters of the slot waveguide. It is shown here that a 90.0 µm long compact Mach-Zehnder section can be designed with horizontal slot waveguide to detect DNA hybridization and for a ring resonator arrangement a sensitivity of 893.5 nm/RIU is obtained.

Simultaneous dispersion measurements of multiple fiber modes using virtual reference interferometry.

We present the simultaneous measurement of first and second order dispersion in short length (< 1 m) few mode fibers (polarization and transverse) using virtual reference interferometry. This technique generates results equivalent to balanced spectral interferometry, without the complexity associated with physical balancing. This is achieved by simulating a virtual reference with a group delay equal to that of the physical interferometer. The amplitude modulation that results from mixing the interferograms, generated in both the unbalanced interferometer and the virtual reference, is equivalent to the first order interference that would be produced by physical balancing. The advantages of the technique include speed, simplicity, convenience and the capability for simultaneous measurement of multiple modes. The theoretical framework is first developed and then verified experimentally.

Characterizing short dispersion-length fiber via dispersive virtual reference interferometry.

The ability to characterize fibers with near-zero dispersion-length products is of considerable practical interest. We introduce dispersive virtual reference interferometry (DVRI) as a technique for the characterization of short length (<1m) fibers with near-zero disperison-length. DVRI has an accuracy equivalent to standard balanced spectral interferometry (on the order of 10(−3) ps and 10(−5) ps/nm for the group delay and dispersion-length measurements respectively) but does not require wide spectral bandwidths or multiple spectral scans. Following experimental validation, the DVRI technique is used to characterize a 23.3-cm erbium-doped gain fiber (dispersion-length product <0.002 ps/nm), using a tunable laser with a bandwidth of 145 nm. Furthermore, the dispersion in a 28.6-cm commercial dispersion shifted fiber is characterized across the zero-dispersion wavelength and the zero-disperison-wavelength and slope were determined to be 1566.7 nm and 8.57 × 10(−5) ps/(nm2∙m) with a precision of ± 0.2 nm and ± 0.06 × 10(−5) ps/(nm2∙m), respectively.

Realization of a polymer nanowire optical transducer by using the nanoimprint technique.

An optical transducer using an integrated optics polymer nanowire is proposed. The nanoimprint technique is used to fabricate an OrmoComp nanowire with 1.0 µm width and 0.5 µm height, but the resulting sidewalls are not perfectly vertical. Maximum sensitivity is achieved by enhancing the evanescent field in the cladding region. The possible mode fields and power confinement of the nanowire are studied with respect to their structural dimensions, the operating wavelength, and the cladding material by using the H-field finite element method. The attenuation coefficient is extracted and calculated over the different cladding media, specifically air, water, and glycerol solution. It is observed that the scattering caused due to the surface roughness is the dominant effect that provides a larger attenuation coefficient.

Stability and photocurrent enhancement of photodetectors by using core/shell structured CsPbBr3/TiO2 quantum dots and 2D materials.

Ultra-stable CsPbBr3 perovskite quantum dots (QDs) were prepared, and the performance of the photodetector fabricated from them was enhanced by 2D material incorporation. This multi-component photodetector appears to have good stability in the ambient utilization environment. All inorganic CsPbBr3 QDs are potential candidates for application in photodetection devices. However, QDs have several issues such as defects on the QD surface, degradation under environmental conditions, and unfavorable carrier mobility limiting the high performance of the photodetectors. This work addresses these issues by fabricating a core/shell structure and introducing 2D materials (MXenes, Ti3C2Tx) into the device. Here, three types of photodetectors with QDs only, QDs with a core/shell structure, and QDs with a core/shell structure and MXenes are fabricated for systematic study. The CsPbBr3/TiO2 photodetector demonstrated a two times photocurrent enhancement compared to bare QDs and had good device stability after TiO2 shell coating. After introducing Ti3C2Tx into CsPbBr3/TiO2, a significant photocurrent enhancement from nanoampere (nA) to microampere (µA) was observed, revealing that MXenes can improve the photoelectric response of perovskite materials significantly. Higher photocurrent can avoid signal interference from environmental noise for better practical feasibility. This study provides a systematic understanding of the photocurrent conversion of perovskite quantum dots that is beneficial in advancing optoelectronic device integration, especially for flexible wearable device applications.

Optical fiber-based sensor for in situ monitoring of cadmium sulfide thin-film growth.

This work presents a scheme for in situ monitoring of thin-film growth. A fiber-optic sensor based on Fabry-Perot interferometric technique has been established for the first time to monitor in situ growth of thin films. This was applied for determining thickness of cadmium sulfide (CdS) thin films during growth. The fabrication process of CdS film was carried out in 30 mM cadmium acetate and thioacetamide solution at 60°C temperature. The estimated thickness determined during the growth was verified by scanning electron microscopy. This study shows that in situ measurement of the thickness of thin films is feasible by this new technique, and a close match of the estimated thickness was achieved.

Chromatic dispersion measurements using a virtually referenced interferometer.

We present a technique for measuring the chromatic dispersion of short-length (<1 m) optical devices using unbalanced spectral interferometry and a virtual reference path. The technique combines the speed and ease of measurement of unbalanced spectral interferometry with the accuracy of balanced spectral interferometry. We demonstrate measurement accuracy for group delay and the dispersion-length product of ~10(-3) ps/m (<0.0001% relative error) and ~10(-5) ps/m (<0.5% relative error), respectively. Measurement precision is demonstrated to be ~10(-5) ps/m (<0.15% relative deviation). We validate the technique via measurement of well-known dispersion standards.

Polarization-independent on-axis light coupler for surface plasmon resonance using a concentric chirped grating.

A novel on-axis one-element polarization-independent light in- and out-coupling mechanism for surface plasmon resonance (SPR) is proposed. The system utilizes an integrated high-NA concentric chirped grating to both focus the incident light on the metallic film and collimate the reflected beam onto a CCD array to extract the SPR signal. With NA up to 1.47, a broad sensing dynamic range from n=1 to 1.35 can be achieved. An analytical model is implemented to demonstrate the dependency of the radial location of the resonances on the detecting substance and its sensitivity to the change of the refractive index. The model shows a trend similar to rigorous ray-tracing calculations.

Draft genome sequence of Clostridium jeddahense EE-R19 isolated from an anaerobic digester.

OBJECTIVES: Clostridium species of the order Clostridiales are mostly strictly anaerobic rod-shaped bacteria. They can be detected in a variety of environments, including the intestines of humans and animals, soil, water, and biogas reactors. Species of the genus Clostridium are widely used in various biotechnological processes, but several of them have been identified as significant human pathogens. Therefore, investigation at the genome level is necessary to provide valuable information about the ecology, genetics, and phylogenetic diversity of various Clostridium species. DATA DESCRIPTION: In the present study, we report the whole genome sequence of Clostridium jeddahense strain EE-R19, which was isolated from a mesophilic anaerobic digester. The draft genome of C. jeddahense EE-R19 consisted of 59 contigs (> 500 bp), which amounted to 3,562,974 with an overall G + C content of 51.79%. The whole genome shotgun project of C. jeddahense EE-R19 has been deposited at DDBJ/ENA/GenBank under the accession number JAAVNF000000000.

Draft genome sequence of Bacillus sp. EE-W1 isolated from a biogas reactor.

OBJECTIVES: The genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data may be useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics. DATA DESCRIPTION: Here, we present the draft genome sequence of Bacillus sp. strain EE-W1 isolated from a biogas reactor, Kazan, Russia. The assembled genome size was 5,769,164 bp, with a GC content 35.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession WIPE00000000.

Ochratoxin A detection in coffee by competitive inhibition assay using chitosan-based surface plasmon resonance compact system.

This study demonstrates the evaluation of ochratoxin A (OTA) in coffee on compact surface plasmon resonance (SPR) biosensors based on crosslinked chitosan and carboxymethyl chitosan nanomatrix substrates. Ochratoxin A is a toxic secondary metabolite widely produced by Aspergillus and Penicillium fungi and requires regular quantification and detection in food samples. The gold coated SPR chips were synthesized with chitosan and carboxymethyl chitosan through spin coating technique. The SPR nanomatrix chips were used for the immobilization of ochratoxin A-bovine serum albumin (OTA-BSA) conjugate to develop a competitive inhibition immunoassay. The monoclonal ochratoxin A antibodies (mAb-OTA) were used as biological receptors for the detection of OTA in buffer and coffee samples. The limit of detection (LOD) in coffee for chitosan (CS) and carboxymethyl chitosan (CMC) substrates was 5.7 ng/mL and 3.8 ng/mL, respectively. Compact surface plasmon resonance (SPR) system based on chitosan-based (CS-AU) nanomatrix substrates provides a platform for the detection of ochratoxin A with high sensitivity, accuracy, ease-of-use and cost-effectiveness. This compact SPR system can be used at farm and industrial levels for the detection of OTA in food matrices.

A Validation Study of a Polymer Optical Fiber Sensor for Monitoring Lumbar Spine Movement.

This study aims to investigate the validity and reliability of a novel plastic optical fiber (POF) sensor, which was developed to measure the angles of flexion, extension and lateral bend at the lumbar region. The angles of flexion, extension and lateral bend for a standing position were measured simultaneously using both the novel POF sensor of this investigation and the commercial Biometrics goniometer instrument. Each movement had two steps of bending which were 10° and 20° based on inclinometer readings. The POF sensor had good intra-rater reliability (Intraclass correlation coefficient, ICC = 0.61 to 0.83). Bland⁻Altman plots were used to study the agreement using these two sensors. There were proportional differences and bias between the POF sensor and Biometrics goniometer, as the zero points did not lie in the percentage difference region in the Bland⁻Altman plots. The proportional difference between these two likely reflects the different sizes and thus, measurement regions of the two sensors. There was also strong correlation between the two sensors (r > 0.77). Hence, the POF sensor could be of potential utility in measuring lumbar range of motion (ROM) in a manner which is minimally invasive, and where discrete sections of the spine are under specific investigation.

Draft genome sequence data and analysis of Brachybacterium sp. strain EE-P12 isolated from a laboratory-scale anaerobic reactor.

The species of the genus Brachybacterium belonging to the family Dermabacteraceae within the phylum Actinobacteria are gram-positive, facultatively anaerobic or aerobic, nonmotile and nonsporeforming bacteria. Cells of Brachybacterium spp. vary in shape from coccoid forms (stationary phase) to rods (exponential phase). Brachybacterium species can be isolated from numerous sources such as poultry deep litter, human gut, soil, food products. Here we describe the draft genome sequence of Brachybacterium sp. EE-P12 that was isolated from a laboratory-scale anaerobic digester. The genome sequencing generated 3,964,988 bp, with a G+C content of 72.2%. This draft genome data has been deposited at DDBJ/ENA/GenBank under the accession number QXCP00000000 (https://www.ncbi.nlm.nih.gov/nuccore/QXCP00000000).

Draft genome sequence of Staphylococcus sp. EZ-P03 isolated from a mesophilic anaerobic digester.

OBJECTIVES: Staphylococcus species of the family Staphylococcaceae are facultatively anaerobic Gram-positive cocci growing in clusters, pairs and occasionally in short chains. Staphylococci can be detected in different environments. They are common commensals, but some can also cause infections in humans. Hence, their investigation is required to understand ecology and genetics and to create an opportunity for comparative studies. DATA DESCRIPTION: In this study, we report the determination of a draft genome sequence of Staphylococcus sp. strain EZ-P03 which was isolated from anaerobically digested chicken waste materials. The draft genome of Staphylococcus sp. EZ-P03 constituted a total of 62 contigs (> 500 bp) amounting to 2,689,358 bp with a G+C content of 37.3% and a N50 contig size of 126,562 bp. The whole genome shotgun project of Staphylococcus sp. strain EZ-P03 has been deposited at DDBJ/ENA/GenBank under the accession number QPMO00000000.

Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae).

The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.