Coupled waveguide model for computing phase and transmission through nanopillar-based metasurfaces.

Dielectric metasurfaces are important in modern photonics due to their unique beam shaping capabilities. However, the standard tools for the computation of the phase and transmission through a nanopillar-based metasurface are either simple, approximating the properties of the surface by that of a single cylinder, or use full 3D numerical simulations. Here we introduce a new analytical model for computing metasurface properties which explicitly takes into account the effect of the lattice geometry. As an example we investigate silicon nanopillar-based metasurfaces, examining how the transmission properties depend on the presence of different modes in the unit cell of the metasurface array. We find that the new model outperforms the isolated cylinder model in predicting the phase, and gives excellent agreement with full numerical simulations when the fill fraction is moderate. Our model offers a waveguide perspective for comprehending metasurface properties, linking it to fiber optics and serving as a practical tool for future metasurface design.

Orders of magnitude loss reduction in photonic bandgap fibers by engineering the core surround.

We demonstrate how to reduce the loss in photonic bandgap fibers by orders of magnitude by varying the radius of the corner strands in the core surround. As a fundamental working principle we find that changing the corner strand radius can lead to backscattering of light into the fiber core. Selecting an optimal corner strand radius can thus reduce the loss of the fundamental core mode in a specific wavelength range by almost two orders of magnitude when compared to an unmodified cladding structure. Using the optimal corner radius for each transmission window, we observe the low-loss behavior for the first and second bandgaps, with the losses in the second bandgap being even lower than that of the first one. Our approach of reducing the confinement loss is conceptually applicable to all kinds of photonic bandgap fibers including hollow core and all-glass fibers as well as on-chip light cages. Therefore, our concept paves the way to low-loss light guidance in such systems with substantially reduced fabrication complexity.

Impact of sustained virologic response on risk of type 2 diabetes among hepatitis C patients in the United States.

Data regarding the impact of hepatitis C (HCV) therapy on incidence of type 2 diabetes mellitus are limited. We used the data from the longitudinal Chronic Hepatitis Cohort Study-drawn from four large US health systems-to investigate how response to HCV treatment impacts the risk of subsequent diabetes. Among HCV patients without a history of type 2 diabetes mellitus or hepatitis B, we investigated the incidence of type 2 diabetes from 12 weeks post-HCV treatment through December 2015. Cox proportional hazards models were used to test the effect of treatment status (sustained virologic response [SVR] or treatment failure) and baseline risk factors on the development of diabetes, considering any possible risk factor-by-SVR interactions, and death as a competing risk. Among 5127 patients with an average follow-up of 3.7 years, diabetes incidence was significantly lower among patients who achieved SVR (231/3748; 6.2%) than among patients with treatment failure (299/1379; 21.7%; adjusted hazard ratio [aHR] = 0.79; 95% CI: 0.65-0.96). Risk of diabetes was higher among African American and Asian American patients than White patients (aHR = 1.82 and 1.75, respectively; P < .05), and among Hispanic patients than non-Hispanics (aHR = 1.86). Patients with BMI ≥ 30 and 25-30 (demonstrated higher risk of diabetes aHR = 3.62 and 1.72, respectively; P < .05) than those with BMI < 25; patients with cirrhosis at baseline had higher risk than those without cirrhosis (aHR = 1.47). Among a large US cohort of patients treated for HCV, patients who achieved SVR demonstrated a substantially lower risk for the development of type 2 diabetes mellitus than patients with treatment failure.

Analytical mode normalization and resonant state expansion for bound and leaky modes in optical fibers - an efficient tool to model transverse disorder.

We adapt the resonant state expansion to optical fibers such as capillary and photonic crystal fibers. As a key requirement of the resonant state expansion and any related perturbative approach, we derive the correct analytical normalization for all modes of these fiber structures, including leaky modes that radiate energy perpendicular to the direction of propagation and have fields that grow with distance from the fiber core. Based on the normalized fiber modes, an eigenvalue equation is derived that allows for calculating the influence of small and large perturbations such as structural disorder on the guiding properties. This is demonstrated for two test systems: a capillary fiber and a photonic crystal fiber.

Analytic Mode Normalization for the Kerr Nonlinearity Parameter: Prediction of Nonlinear Gain for Leaky Modes.

Based on the resonant-state expansion with analytic mode normalization, we derive a general master equation for the nonlinear pulse propagation in waveguide geometries that is valid for bound and leaky modes. In the single-mode approximation, this equation transforms into the well-known nonlinear Schrödinger equation with a closed expression for the Kerr nonlinearity parameter. The expression for the Kerr nonlinearity parameter can be calculated on the minimal spatial domain that spans only across the regions of spatial inhomogeneities. It agrees with previous vectorial formulations for bound modes, while for leaky modes the Kerr nonlinearity parameter turns out to be a complex number with the imaginary part providing either nonlinear loss or even gain for the overall attenuating pulses. This nonlinear gain results in more intense pulse compression and stronger spectral broadening, which is demonstrated here on the example of liquid-filled capillary-type fibers.

Modern Breeding and Biotechnological Approaches to Enhance Carotenoid Accumulation in Seeds.

There is an increasing demand for carotenoids, which are fundamental components of the human diet, for example as precursors of vitamin A. Carotenoids are also potent antioxidants and their health benefits are becoming increasingly evident. Protective effects against prostate cancer and age-related macular degeneration have been proposed for lycopene and lutein/zeaxanthin, respectively. Additionally, ß-carotene, astaxanthin and canthaxanthin are high-value carotenoids used by the food industry as feed supplements and colorants. The production and consumption of these carotenoids from natural sources, especially from seeds, constitutes an important step towards fortifying the diet of malnourished people in developing nations. Therefore, attempts to metabolically manipulate ß-carotene production in plants have received global attention, especially after the generation of Golden Rice (Oryza sativa). The endosperms of Golden Rice seeds synthesize and accumulate large quantities of ß-carotene (provitamin A), yielding a characteristic yellow color in the polished grains. Classical breeding efforts have also focused in the development of cultivars with elevated seed carotenoid content, with maize and other cereals leading the way. In this communication we will summarize transgenic efforts and modern breeding strategies to fortify various crop seeds with nutraceutical carotenoids.

Using thermal boundary conditions to engineer the quantum state of a bulk magnet.

The degree of contact between a system and the external environment can alter dramatically its proclivity to quantum mechanical modes of relaxation. We show that controlling the thermal coupling of cubic-centimeter-sized crystals of the Ising magnet LiHo(x)Y(1-x)F4 to a heat bath can be used to tune the system between a glassy state dominated by thermal excitations over energy barriers and a state with the hallmarks of a quantum spin liquid. Application of a magnetic field transverse to the Ising axis introduces both random magnetic fields and quantum fluctuations, which can retard and speed the annealing process, respectively, thereby providing a mechanism for continuous tuning between the destination states. The nonlinear response of the system explicitly demonstrates quantum interference between internal and external relaxation pathways.

Higher all-cause hospitalization among patients with chronic hepatitis C: the Chronic Hepatitis Cohort Study (CHeCS), 2006-2013.

In the United States, hospitalization among patients with chronic hepatitis C virus (HCV) infection is high. The healthcare burden associated with hospitalization is not clearly known. We analysed data from the Chronic Hepatitis Cohort Study, an observational cohort of patients receiving care at four integrated healthcare systems, collected from 2006 to 2013 to determine all-cause hospitalization rates of patients with chronic HCV infection and the other health system patients. To compare the hospitalization rates, we selected two health system patients for each chronic HCV patient using their propensity score (PS). Propensity score matching was conducted by site, gender, race, age and household income to minimize differences attributable to these characteristics. We also compared primary reason for hospitalization between chronic HCV patients and the other health system patients. Overall, 10 131 patients with chronic HCV infection and 20 262 health system patients were selected from the 1 867 802 health system patients and were matched by PS. All-cause hospitalization rates were 27.4 (27.0-27.8) and 7.4 (7.2-7.5) per 100 persons-year (PY) for chronic HCV patients and for the other health system patients, respectively. Compared to health system patients, hospitalization rates were significantly higher by site, gender, age group, race and household income among chronic HCV patients (P < 0.001). Compared to health system patients, chronic HCV patients were more likely to be hospitalized from liver-related conditions (RR = 24.8, P < 0.001). Hence, patients with chronic HCV infection had approximately 3.7-fold higher all-cause hospitalization rate than other health system patients. These findings highlight the incremental costs and healthcare burden of patients with chronic HCV infection associated with hospitalization.

The validity of serum markers for fibrosis staging in chronic hepatitis B and C.

Assessment of liver fibrosis is critical for successful individualized disease management in persons with chronic hepatitis B (CHB) or chronic hepatitis C (CHC). We expanded and validated serum marker indices to provide accurate, reproducible and easily applied methods of fibrosis assessment. Liver biopsy results from over 284 CHB and 2304 CHC patients in the Chronic Hepatitis Cohort Study ('CHeCS') were mapped to a F0-F4 equivalent scale. APRI and FIB-4 scores within a 6-month window of biopsy were mapped to the same scale. A novel algorithm was applied to derive and validate optimal cut-offs for differentiating fibrosis levels. For the prediction of advanced fibrosis and cirrhosis, the FIB-4 score outperformed the other serum marker indices in the CHC cohort and was similar to APRI in the CHB cohort. The area under the receiver operating characteristic curves (AUROC) for FIB-4 in differentiating F3-F4 from F0-F2 was 0.86 (95% CI: 0.80-0.92) for CHB and 0.83 (95% CI: 0.81-0.85) for CHC. The suggested cut-offs based on FIB-4 model produced high positive predictive values [CHB: 90.0% for F0-F2, 100.0% for cirrhosis (F4); CHC: 89.7% for F0-F2; 82.9% for cirrhosis (F4)]. In this large observational cohort, FIB-4 predicted the upper and lower end of liver fibrosis stage (cirrhosis and F0-F2, respectively) with a high degree of accuracy in both CHB and CHC patients.

APRI and FIB-4 are good predictors of the stage of liver fibrosis in chronic hepatitis B: the Chronic Hepatitis Cohort Study (CHeCS).

We aim to determine the predictive ability of APRI, FIB-4 and AST/ALT ratio for staging of liver fibrosis and to differentiate significant fibrosis (F2-F4) from none to minimal fibrosis (F0-F1) in chronic hepatitis B (CHB). Liver biopsy results were mapped to an F0-4 equivalent fibrosis stage. Mean APRI and FIB-4 scores were significantly higher for each successive fibrosis level from F1 to F4 (P < 0.05). Based on optimized cut-offs, the AUROCs in distinguishing F2-F4 from F0 to F1 were 0.81 (0.76-0.87) for APRI, 0.81 (0.75-0.86) for FIB-4 and 0.56 (0.49-0.64) for AST/ALT ratio. APRI and FIB-4 distinguished F2-F4 from F0 to F1 with good sensitivity and specificity and can be useful for treatment decisions and monitoring progression of fibrosis.

Reflectivity enhanced refractive index sensor based on a fiber-integrated Fabry-Perot microresonator.

We discuss a fiber-integrated refractive index sensor with strongly improved detection performance. The resonator has been implemented by means of focused-ion beam milling of a step index fiber and shows a sensitivity of about 1.15µm/RIU. Coating the resonator walls led to a strongly improved mirror reflectivity by a factor of about 26. Design rules for device optimization and a detailed mathematical analysis are discussed, revealing that the sensor operates as an optimized Fabry-Perot resonator. We also show that the performance of such kind of Fabry-Perot sensors is, in general, limited by the detection limit function - a quantity depending on the cavitiy's finesse and on the measurement capabilities used.

Midinfrared frequency combs from coherent supercontinuum in chalcogenide and optical parametric oscillation.

We observe the coherence of the supercontinuum generated in a nanospike chalcogenide-silica hybrid waveguide pumped at 2 µm. The supercontinuum is shown to be coherent with the pump by interfering it with a doubly resonant optical parametric oscillator (OPO) that is itself coherent with the shared pump laser. This enables coherent locking of the OPO to the optically referenced pump frequency comb, resulting in a composite frequency comb with wavelengths from 1 to 6 µm.

Influencing surgical management in patients with carcinoma of the cervix using a T2- and ZOOM-diffusion-weighted endovaginal MRI technique.

BACKGROUND: Endovaginal MRI (evMRI) at 3.0-T with T2-weighted (T2-W) and ZOnal Oblique Multislice (ZOOM)-diffusion-weighted imaging (DWI) potentially improves the detection of stage Ia/Ib1 cervical cancer. We aimed to determine its sensitivity/specificity, document tumour-to-stromal contrast and establish the effect of imaging on surgical management. METHODS: Following ethical approval and written informed consent, 57 consecutive patients with suspected stage Ia/Ib1 cervical cancer underwent evMRI at 3.0-T using T2-W and ZOOM-DWI. Sensitivity/specificity were calculated against histopathology for two independent observers. Tumour-to-stromal contrast was determined on T2-W, and diffusion-weighted (b=800 s mm(-2)) images and apparent diffusion coefficients (ADCs) were recorded. In patients due for radical vaginal trachelectomy (RVT), change of surgical management based on imaging findings was documented. RESULTS: Sensitivity/specificity for detecting tumour was the following: reporting read 88.0/81.8%, anonymised read 92.0/81.8% (observer 1); 84.0/72.7% (observer2; median tumour volume=1.7 cm(3)). Intraobserver agreement was excellent (kappa=0.89) and the interobserver agreement was good (kappa=0.65). Tumour-to-stromal contrast was greater on ZOOM-DWI compared with T2-W images (3.35±2.36 vs 1.39±0.95; P<0.0004). Tumour and stromal ADCs were significantly different (P<0.00001). In 31 patients due for RVT, evMRI altered surgical management in 12 (38.7%) cases (10 cone-biopsy, 2 chemoradiotherapy). CONCLUSION: T2-W+ZOOM-DWI evMRI has high sensitivity/specificity for detecting stage Ia/Ib1 cervical tumours; in patients due for RVT, the surgical management was altered in ∼39%.

Mid-infrared supercontinuum generation in As2S3-silica "nano-spike" step-index waveguide.

Efficient generation of a broad-band mid-infrared supercontinuum spectrum is reported in an arsenic trisulphide waveguide embedded in silica. A chalcogenide "nano-spike", designed to transform the incident light adiabatically into the fundamental mode of a 2-mm-long uniform section 1 µm in diameter, is used to achieve high launch efficiencies. The nano-spike is fully encapsulated in a fused silica cladding, protecting it from the environment. Nano-spikes provide a convenient means of launching light into sub-wavelength scale waveguides. Ultrashort (65 fs, repetition rate 100 MHz) pulses at wavelength 2 µm, delivered from a Tm-doped fiber laser, are launched with an efficiency ~12% into the sub-wavelength chalcogenide waveguide. Soliton fission and dispersive wave generation along the uniform section result in spectral broadening out to almost 4 µm for launched energies of only 18 pJ. The spectrum generated will have immediate uses in metrology and infrared spectroscopy.

Excitation of a nanowire "molecule" in gold-filled photonic crystal fiber.

A pair of gold nanowires, incorporated into a photonic crystal fiber, acts as a plasmonic "molecule." Hybridized modes are excited at specific wavelengths by launching light into the glass core. The formation of bonding and antibonding solutions results in a modal splitting of more than 100 nm, even though the spatial separation between the wires is larger than 3 µm. The study provides insight into multiwire plasmonic devices with applications as polarizers or filters in near-field optics, nonlinear plasmonics, optical sensing, and telecommunications.

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies.

MOTIVATION: Next-generation sequencing presents several statistical challenges, with one of the most fundamental being determining an individual's genotype from multiple aligned short read sequences at a position. Some simple approaches for genotype calling apply fixed filters, such as calling a heterozygote if more than a specified percentage of the reads have variant nucleotide calls. Other genotype-calling methods, such as MAQ and SOAPsnp, are implementations of Bayes classifiers in that they classify genotypes using posterior genotype probabilities. RESULTS: Here, we propose a novel genotype-calling algorithm that, in contrast to the other methods, estimates parameters underlying the posterior probabilities in an adaptive way rather than arbitrarily specifying them a priori. The algorithm, which we call SeqEM, applies the well-known Expectation-Maximization algorithm to an appropriate likelihood for a sample of unrelated individuals with next-generation sequence data, leveraging information from the sample to estimate genotype probabilities and the nucleotide-read error rate. We demonstrate using analytic calculations and simulations that SeqEM results in genotype-call error rates as small as or smaller than filtering approaches and MAQ. We also apply SeqEM to exome sequence data in eight related individuals and compare the results to genotypes from an Illumina SNP array, showing that SeqEM behaves well in real data that deviates from idealized assumptions. CONCLUSION: SeqEM offers an improved, robust and flexible genotype-calling approach that can be widely applied in the next-generation sequencing studies. AVAILABILITY AND IMPLEMENTATION: Software for SeqEM is freely available from our website: www.hihg.org under Software Download.

Optofluidic refractive-index sensor in step-index fiber with parallel hollow micro-channel.

We present a simple refractive index sensor based on a step-index fiber with a hollow micro-channel running parallel to its core. This channel becomes waveguiding when filled with a liquid of index greater than silica, causing sharp dips to appear in the transmission spectrum at wavelengths where the glass-core mode phase-matches to a mode of the liquid-core. The sensitivity of the dip-wavelengths to changes in liquid refractive index is quantified and the results used to study the dynamic flow characteristics of fluids in narrow channels. Potential applications of this fiber microstructure include measuring the optical properties of liquids, refractive index sensing, biophotonics and studies of fluid dynamics on the nanoscale.

Pressure-assisted melt-filling and optical characterization of Au nano-wires in microstructured fibers.

We report a novel splicing-based pressure-assisted melt-filling technique for creating metallic nanowires in hollow channels in microstructured silica fibers. Wires with diameters as small as 120 nm (typical aspect ration 50:1) could be realized at a filling pressure of 300 bar. As an example we investigate a conventional single-mode step-index fiber with a parallel gold nanowire (wire diameter 510 nm) running next to the core. Optical transmission spectra show dips at wavelengths where guided surface plasmon modes on the nanowire phase match to the glass core mode. By monitoring the side-scattered light at narrow breaks in the nanowire, the loss could be estimated. Values as low as 0.7 dB/mm were measured at resonance, corresponding to those of an ultra-long-range eigenmode of the glass-core/nanowire system. By thermal treatment the hollow channel could be collapsed controllably, permitting creation of a conical gold nanowire, the optical properties of which could be monitored by side-scattering. The reproducibility of the technique and the high optical quality of the wires suggest applications in fields such as nonlinear plasmonics, near-field scanning optical microscope tips, cylindrical polarizers, optical sensing and telecommunications.

Supercontinuum generation in chalcogenide-silica step-index fibers.

We explore the use of a highly nonlinear chalcogenide-silica waveguide for supercontinuum generation in the near infrared. The structure was fabricated by a pressure-assisted melt-filling of a silica capillary fiber (1.6 µm bore diameter) with Ga4Ge21Sb10S65 glass. It was designed to have zero group velocity dispersion (for HE11 core mode) at 1550 nm. Pumping a 1 cm length with 60 fs pulses from an erbium-doped fiber laser results in the generation of octave-spanning supercontinuum light for pulse energies of only 60 pJ. Good agreement is obtained between the experimental results and theoretical predictions based on numerical solutions of the generalized nonlinear Schrödinger equation. The pressure-assisted melt-filling approach makes it possible to realize highly nonlinear devices with unusual combinations of materials. For example, we show numerically that a 1 cm long As2S3:silica step-index fiber with a core diameter of 1 µm, pumped by 60 fs pulses at 1550 nm, would generate a broadband supercontinuum out to 4 µm.

Evolving concepts in ventral hernia repair and physical therapy: prehabilitation, rehabilitation, and analogies to tendon reconstruction.

PURPOSE: The abdominal wall and musculoskeletal tendons share many anatomic, physiologic, and functional characteristics. This review aims to highlight these similar characteristics and to present a rationale why the treatment principles of successful musculoskeletal tendon reconstruction, including principles of surgical technique and physical therapy, can be used in the treatment of complex abdominal wall reconstruction or ventral hernia repair. METHODS: The MEDLINE/PubMed database was used to identify published literature relevant to the purpose of this review. CONCLUSIONS: There are several anatomical and functional similarities between the linea alba and musculoskeletal tendons. Because of this reason, many of the surgical principles for musculoskeletal tendon repair and ventral hernia repair overlap. Distribution of tension is the main driving principle for both procedures. Suture material and configuration are chosen to maximize tension distribution among the tissue edges, as seen in the standard of care multistrand repairs for musculoskeletal tendons, as well as in the small bites for laparotomy technique described in the STITCH trial. Physical therapy is also one of the mainstays of tendon repair, but surprisingly, is not routine in ventral hernia repair. The evidence surrounding physical therapy prehabilitation and rehabilitation protocols in other disciplines is significant. This review challenges the fact that these protocols are not routinely implemented for ventral hernia repair, and presents the rationale and feasibility for the routine practice of physical therapy in ventral hernia repair.