Survival Analysis as a Basis for Testing Hypotheses when Using Quantitative Ordinal Scale Disease Severity Data.

Disease severity in plant pathology is often measured by the amount of a plant or plant part that exhibits disease symptoms. This is typically assessed using a numerical scale, which allows a standardized, convenient, and quick method of rating. These scales, known as quantitative ordinal scales (QOS), divide the percentage scale into a predetermined number of intervals. There are various ways to analyze these ordinal data, with traditional methods involving the use of midpoint conversion to represent the interval. However, this may not be precise enough, as it is only an estimate of the true value. In this case, the data may be considered interval-censored, meaning that we have some knowledge of the value but not an exact measurement. This type of uncertainty is known as censoring, and techniques that address censoring, such as survival analysis (SA), use all available information and account for this uncertainty. To investigate the pros and cons of using SA with QOS measurements, we conducted a simulation based on three pathosystems. The results showed that SA almost always outperformed midpoint conversion with data analyzed using a t test, particularly when data were not normally distributed. Midpoint conversion is currently a standard procedure. In certain cases, the midpoint approach required a 400% increase in sample size to achieve the same power as the SA method. However, as the mean severity increases, fewer additional samples are needed (approximately an additional 100%), regardless of the assessment method used. Based on these findings, we conclude that SA is a valuable method for enhancing the power of hypothesis testing when analyzing QOS severity data. Future research should investigate the wider use of survival analysis techniques in plant pathology and their potential applications in the discipline.

Robustness and stability of doubly periodic patterns of the focusing nonlinear Schrödinger equation.

The nonlinear Schrödinger equation possesses doubly periodic solutions expressible in terms of the Jacobi elliptic functions. Such solutions can be realized through doubly periodic patterns observed in experiments in fluid mechanics and optics. Stability and robustness of these doubly periodic wave profiles in the focusing regime are studied computationally by using two approaches. First, linear stability is considered by Floquet theory. Growth will occur if the eigenvalues of the monodromy matrix are of a modulus larger than unity. This is verified by numerical simulations with input patterns of different periods. Initial patterns associated with larger eigenvalues will disintegrate faster due to instability. Second, formation of these doubly periodic patterns from a tranquil background is scrutinized. Doubly periodic profiles are generated by perturbing a continuous wave with one Fourier mode, with or without the additional presence of random noise. Effects of varying phase difference, perturbation amplitude, and randomness are studied. Varying the phase angle has a dramatic influence. Periodic patterns will only emerge if the perturbation amplitude is not too weak. The growth of higher-order harmonics, as well as the formation of breathers and repeating patterns, serve as a manifestation of the classical problem of Fermi-Pasta-Ulam-Tsingou recurrence.

Quantitative Ordinal Scale Estimates of Plant Disease Severity: Comparing Treatments Using a Proportional Odds Model.

Studies in plant pathology, agronomy, and plant breeding requiring disease severity assessment often use quantitative ordinal scales (i.e., a special type of ordinal scale that uses defined numeric ranges); a frequently used example of such a scale is the Horsfall-Barratt scale. Parametric proportional odds models (POMs) may be used to analyze the ratings obtained from quantitative ordinal scales directly, without converting ratings to percent area affected using range midpoints of such scales (currently a standard procedure). Our aim was to evaluate the performance of the POM for comparing treatments using ordinal estimates of disease severity relative to two alternatives, the midpoint conversions (MCs) and nearest percent estimates (NPEs). A simulation method was implemented and the parameters of the simulation estimated using actual disease severity data from the field. The criterion for comparison of the three approaches was the power of the hypothesis test (the probability to reject the null hypothesis when it is false). Most often, NPEs had superior performance. The performance of the POM was never inferior to using the MC at severity <40%. Especially at low disease severity (≤10%), the POM was superior to using the MC method. Thus, for early onset of disease or for comparing treatments with severities <40%, the POM is preferable for analyzing disease severity data based on quantitative ordinal scales when comparing treatments and at severities >40% is equivalent to other methods.

Disease Severity Estimates-Effects of Rater Accuracy and Assessment Methods for Comparing Treatments.

Assessment of disease severity is required for several purposes in plant pathology; most often, the estimates are made visually. It is established that visual estimates can be inaccurate and unreliable. The ramifications of biased or imprecise estimates by raters have not been fully explored using empirical data, partly because of the logistical difficulties involved in different raters assessing the same leaves for which actual disease has been measured in a replicated experiment with multiple treatments. In this study, nearest percent estimates (NPEs) of Septoria leaf blotch (SLB) on leaves of winter wheat from nontreated and fungicide-treated plots were assessed in both 2006 and 2007 by four raters and compared with assumed actual values measured using image analysis. Lin's concordance correlation (LCC, ρc) was used to assess agreement between the two approaches. NPEs were converted to Horsfall-Barratt (HB) midpoints and were compared with actual values. The estimates of SLB severity from fungicide-treated and nontreated plots were analyzed using generalized linear mixed modeling to ascertain effects of rater using both the NPE and HB values. Rater 1 showed good accuracy (ρc = 0.986 to 0.999), while raters 3 and 4 were less accurate (ρc = 0.205 to 0.936). Conversion to the HB scale had little effect on bias but reduced numerically both precision and accuracy for most raters on most assessment dates (precision, r = -0.001 to -0.132; and accuracy, ρc = -0.003 to -0.468). Interrater reliability was also reduced slightly by conversion of estimates to HB midpoint values. Estimates of mean SLB severity were significantly different between image analysis and raters 2, 3, and 4, and there were frequently significant differences among raters (F = 151 to 1,260, P = 0.001 to P < 0.0001). Only on 26 June 2007 did conversion to the HB scale change the means separation ranking of rater estimates. Nonetheless, image analysis and all raters were able to differentiate control and treated-plot treatments (F = 116 to 1,952, P = 0.002 to P < 0.0001, depending on date and rater). Conversion of NPEs to the HB scale tended to reduce F values slightly (2006: NPEs, F = 116 to 276, P = 0.002 to 0.0005; and, for the HB-converted values, F = 101 to 270, P = 0.002 to 0.0005; 2007: NPEs, F = 164 to 1,952, P = 0.001 to P < 0.0001; and, for HB-converted values, F = 126 to 1,633, P = 0.002 to P < 0.0001). The results reaffirm the need for accurate and reliable disease assessment to minimize over- or underestimates compared with actual disease, and the data we present support the view that, where multiple raters are deployed, they should be assigned in a manner to reduce any potential effect of rater differences on the analysis.

Graphene enhanced evanescent field in microfiber multimode interferometer for highly sensitive gas sensing.

Graphene based new physics phenomena are leading to a variety of stimulating graphene-based photonic devices. In this study, the enhancement of surface evanescent field by graphene cylindrical cladding is observed, for the first time, by using a graphene-coated microfiber multi-mode interferometer (GMMI). It is found theoretically and experimentally that the light transmitting in the fiber core is efficiently dragged by the graphene, hence significantly enhancing the evanescent fields, and subsequently improving the sensitivity of the hybrid waveguide. The experimental results for gas sensing verified the theoretical prediction, and ultra-high sensitivities of ~0.1 ppm for NH(3) gas detection and ~0.2 ppm for H(2)O vapor detection are achieved, which could be used for trace analysis. The enhancement of surface evanescent field induced by graphene may pave a new way for developing novel graphene-based all-fiber devices with compactness, low cost, and temperature immunity.

Graphene Bragg gratings on microfiber.

Graphene Bragg gratings (GBGs) on microfiber are proposed and investigated in this paper. Numerical analysis and simulated results show that the mode distribution, transmission loss, and central wavelength of the GBG are controllable by changing the diameter of the microfiber or the refractive index of graphene. Such type of GBGs with tunability may find important applications in optical fiber communication and sensing as all-fiber in-line devices.

Graphene-coated microfiber Bragg grating for high-sensitivity gas sensing.

A graphene coated microfiber Bragg grating (GMFBG) for gas sensing is reported in this Letter. Taking advantage of the surface field enhancement and gas absorption of a GMFBG, we demonstrate an ultrasensitive approach to detect the concentration of chemical gas. The obtained sensitivities are 0.2 and 0.5 ppm for NH3 and xylene gas, respectively, which are tens of times higher than that of a GMFBG without graphene for tiny gas concentration change detection. Experimental results indicate that the GMFBG-based NH3 gas sensor has fast response due to its highly compact structure. Such a miniature fiber-optic element may find applications in high sensitivity gas sensing and trace analysis.

Graphene-based D-shaped fiber multicore mode interferometer for chemical gas sensing.

In this Letter, a graphene-coated D-shaped fiber (GDF) chemical gas sensor is proposed and demonstrated. Taking advantage of both the graphene-induced evanescent field enhancement and the in-fiber multimode interferometer, the GDF shows very high sensitivity for polar gas molecule adsorptions. An extinction ratio of up to 28 dB within the free spectrum range of ~30 nm in the transmission spectrum is achieved. The maximum sensitivities for NH3 and H2O gas detections are ~0.04 and ~0.1 ppm, respectively. A hybrid sensing scheme with such compactness, high sensitivity, and online monitoring capabilities may pave the way for others to explore a series of graphene-based lab-on-fiber devices for biochemical sensing.

Experiences that matter in bipolar disorder: a qualitative study using the capability, comfort and calm framework.

BACKGROUND: When assessing the value of an intervention in bipolar disorder, researchers and clinicians often focus on metrics that quantify improvements to core diagnostic symptoms (e.g., mania). Providers often overlook or misunderstand the impact of treatment on life quality and function. We wanted to better characterize the shared experiences and obstacles of bipolar disorder within the United States from the patient's perspective. METHODS: We recruited 24 individuals diagnosed with bipolar disorder and six caretakers supporting someone with the condition. Participants were involved in treatment or support services for bipolar disorder in central Texas. As part of this qualitative study, participants discussed their everyday successes and obstacles related to living with bipolar disorder during personalized, open-ended interviews. Audio files were transcribed, and Nvivo software processed an initial thematic analysis. We then categorized themes into bipolar disorder-related obstacles that limit the patient's capability (i.e., function), comfort (i.e., relief from suffering) and calm (i.e., life disruption) (Liu et al., FebClin Orthop 475:315-317, 2017; Teisberg et al., MayAcad Med 95:682-685, 2020). We then discuss themes and suggest practical strategies that might improve the value of care for patients and their families. RESULTS: Issues regarding capability included the struggle to maintain identity, disruptions to meaningful employment, relationship loss and the unpredictable nature of bipolar disorder. Comfort related themes included the personal perception of diagnosis, social stigma and medication issues. Calm themes included managing dismissive doctors, finding the right psychotherapist and navigating financial burdens. CONCLUSIONS: Qualitative data from patients with bipolar disorder helps identify gaps in care or practical limitations to treatment. When we listen to these individuals, it is clear that treatments must also address the unmet psychosocial impacts of the condition to improve patient care, capability and calm.

Validity and severity thresholds for the depression subscale of the affective self rating scale: An equipercentile equating study using classical test theory.

BACKGROUND: The Affective Symptoms Scale (ASRS) is a unique instrument designed to separately measure depressive and manic symptoms in mood disorders. We validated the ASRS against the Patient Health Questionnaire (PHQ-9) and the Quick Inventory of Depressive Symptomatology (QIDS-16). METHODS: A retrospective study of 258 patients who completed the PHQ-9, QIDS-16 and ASRS as part of routine clinical care. To establish meaningful clinical thresholds for the depression subscale of the ASRS, it was equated with the QIDS and the PHQ-9. RESULTS: The depression subscale of the ASRS had significant positive correlations with the QIDS-16 and the PHQ-9 (respectively, r= 0.8, t[253] = 19.8, p < 0.001, and r= 0.8, t[245] = 28.2, p < 0.001). The equipercentile equating method with the PHQ-9 indicated that the thresholds corresponded to ASRS depression subscale scores of 5.4, 10.6, 16.1, and 23. Equating with the QIDS indicated that thresholds corresponded to ASRS depression subscale scores of 5.1, 11, 18.4, and 27.5. LIMITATIONS: Limitations include a small sample size that did not allow more detailed statistical analysis, such as Item Response Theory. The population is a heterogenous population at a university outpatient setting. CONCLUSIONS: The ASRS depression subscale significantly correlated with the PHQ-9 and QIDS-16. Our proposed threshold scores for the ASRS are 5, 11, 16 and 23 to indicated mild, moderate, severe and very severe depression respectively.

Pulse propagation in a decoupled two-core fiber.

It is known that a decoupled two-core fiber can prevent monochromatic light at a specific wavelength (the decoupling wavelength) launched into one core from coupling to the other core. In this paper, we show that a pulse at the decoupling wavelength launched into one core of such a fiber inevitably splits into two pairs of pulses propagating in the two cores along the fiber. The minimum distance required for pulse splitting to be visible is inversely proportional to the coupling-coefficient dispersion in the fiber and linearly proportional to the pulse width. It would take only several centimeters of a recently demonstrated decoupled two-core photonic-bandgap fiber to observe the pulse-splitting effect with a 100-fs pulse. We also study the effects of self-phase modulation on the pulse propagation dynamics in a decoupled two-core fiber in both the normal and anomalous dispersion regimes.

Refractive-index sensor based on long-range surface plasmon mode excitation with long-period waveguide grating.

We propose a refractive-index sensor that operates on the principle of exciting the long-range surface plasmon mode of a metal-coated waveguide with a long-period grating formed in the waveguide, where the wavelength at which the mode excitation occurs serves as a measure of the refractive index of the external medium. We analyze the sensor with a coupled-mode theory and highlight the effects of the waveguide parameters on the loss of the surface plasmon mode and the performance of the sensor. Our results show that the sensor can provide a sharp resonance for high precision measurements and a high sensitivity comparable to that of an optimized bulk prism-based surface plasmon sensor. Our sensor also offers much flexibility in the choice of waveguide parameters for different applications.

CO2 laser writing of long-period fiber grating in photonic crystal fiber under tension.

We demonstrate that the efficiency of CO(2) laser writing of long-period fiber gratings in a solid-core photonic crystal fiber (PCF) can be enhanced greatly by applying tension to the fiber during the writing process through the mechanism of frozen-in viscoelasticity. Using this mechanism, we are able to write strong gratings in PCFs with a dosage of CO(2) laser radiation low enough not to cause any significant fiber structure deformation.

All-fiber bandwidth-tunable band-rejection filter based on a composite grating induced by CO2 laser pulses.

We propose an all-fiber band-rejection filter with a tunable bandwidth, which is realized by putting a normal long-period fiber grating in series with a rotary long-period fiber grating written in a twisted single-mode fiber by CO(2) laser pulses. Bandwidth tuning is achieved by applying torsion to the composite grating. Our experimental filter shows a bandwidth tuning of approximately 16.3 nm at a rejection level of approximately 15 dB and a polarization-dependent loss lower than approximately 0.9 dB.

Temporal programming of chloroplast and cytoplasmic ribosomal RNA transcription in the synchronous cell cycle of Chlamydomonas reinhardtii.

Approximately 90% of the Chlamydomonas reinhardtii chloroplast and cytoplasmic rRNAs was transcribed in the nuclear G1 phase, which occurred during the light period under an alternating light-dark synchronization regime of 12 h each. The remaining 10% of chloroplast and cytoplasmic rRNAs was transcribed from its respective DNAs in the dark period, in the midst of an apparent turnover of a transcription appeared to be prokaryotic in sophistication. The transcription was not interrupted during chloroplast DNA synthesis which occurred during the light period. However, transcription of the nuclear DNA was repressed severely during the nuclear S phase in the dark period. The patterns of incorporation of 32P into chloroplast and cytoplasmic rRNA species in the cell cycle were similar to those of the actual rRNA synthesis as measured optically. However, the quantity of 32P incorporation per unit amount of rRNA synthesized varied considerably during the cell cycle, increasing in all rRNA's during the dark period. 32P incorporation data obtained from continuous and pulse 32P-labeling experiments also revealed a turnover of a small amount of both cytoplasmic and chloroplast rRNAs at the end of the S phase. The 32P incorporation into cytoplasmic and chloroplast rRNAs was well matched temporally with the 32P incorporation into their corresponding ribosomes, indicating that the newly synthesized rRNA molecules are utilized without delay throughout the cell cycle in the assembly of ribosomes.

Electro-optic long-period waveguide gratings in lithium niobate.

We report electro-optic (EO) long-period waveguide gratings (LPWGs) fabricated in a special lithium-niobate (LiNbO3) waveguide structure. The waveguide consists of a clad core formed with a two-step proton-exchange process and a thin cover layer created by an additional reverse proton-exchange process for the restoration of the EO strength of the waveguide. Using several LPWG samples, we demonstrate experimentally the effects of using different cladding modes and waveguide parameters on the grating performance. One of our 10-mm long samples shows a 27-dB rejection band at a driving voltage of 95 V with a center wavelength tunable thermally at a sensitivity of -0.4 nm/degrees C. Our analysis of the theoretical limit of the efficiency of such an EO grating suggests room for significant further improvement by optimizing the waveguide and electrode designs. The LiNbO(3) LPWG provides an EO control of the grating strength and a thermo-optic control of the operating wavelength and thus opens up many new opportunities for high-speed applications, such as dynamic optical filtering and optical intensity modulation.

Laser-micromachined Fabry-Perot optical fiber tip sensor for high-resolution temperature-independent measurement of refractive index.

We propose and demonstrate a Fabry-Perot (F-P) optical fiber tip sensor for high-resolution refractive-index measurement fabricated by using 157-nm laser micromachining, for the first time to our knowledge. The sensor head consists of a short air F-P cavity near the tip of a single-mode fiber and the fiber tip. The external refractive index is determined according to the maximum fringe contrast of the interference fringes in the reflective spectrum of the sensor. Such a sensor can provide temperature-independent measurement of practically any refractive index larger than that of air and offers a refractive-index resolution of ~4 x 10(-5) in its linear operating range. The experimental data agree well with the theoretical results.

Widely tunable long-period waveguide grating couplers.

We demonstrate experimentally two widely tunable optical couplers formed with parallel long-period polymer waveguide gratings. One of the couplers consists of two parallel gratings and shows a peak coupling efficiency of ~34%. The resonance wavelength of the coupler can be tuned thermally with a sensitivity of 4.7 nm/ degrees C. The experimental results agree well with the coupled-mode analysis. The other coupler consists of an array of ten widely separated gratings. A peak coupling efficiency of ~11% is obtained between the two best matched gratings in the array and the resonance wavelength can be tuned thermally with a sensitivity of -3.8 nm/ degrees C. These couplers have the potential to be further developed into practical broadband add/drop multiplexers and signal dividers.

Genetics of Chlamydomonas reinhardtii diploids. I. Isolation and characterization and meiotic segregation pattern of a homozygous diploid.

A strain of Chlamydomonas reinhardtii has been investigated which, when mated with known wild-types, produces very few viable germination products and transmits its Mendelian markers to more than half of those products. Cytogenetic observations, fluorometric measurements of DNA and genetic data all suggest that the strain, d mt-ery-M3a sr-u-1 is a stable homozygous diploid. This strain has twice as many nuclear chromatin bodies at metaphase and twice as much DNA as its haploid progenitor, and the phenotypes of its meiotic progeny are consistent with predictions based on triploid meiosis. Data from crosses involving d mt-ery-M3a sr-u-1 and from crosses involving hybrid diploids indicate that the frequency of second division segregation increases in triploid zygotes and that mitotic segregation following triploid meiosis is a frequent event which may more often result from mitotic recombination than from chromosome loss.

Genetics of Chlamydomonas reinhardtii diploids. II. The effects of diploidy and aneuploidy on the transmission of non-Mendelian markers.

The transmission of two non-Mendelian drug resistance markers has been studied in crosses of Chlamydomonas reinhardtii involving diploids and aneuploids with different mating type genotypes. Under normal laboratory conditions for gametogenesis, mating and zygote maturation, the transmission pattern of the non-Mendelian markers sr-u-1 (resistance to streptomycin) and spr-u-1-27-3 (resistance to spectinomycin) is primarily determined by the mating type genotypes of the parental cells. Our results confirm and expand an earlier observation suggesting that an apparent codominant function of the female (mt+) allele in regulating chloroplast gene transmission in meiosis appears to be distinct and separate from its recessive function in regulating mating behavior. The chloroplast DNA complement (as indexed by the number of extranuclear DNA-containing bodies) may exert a secondary effect on the transmission of these markers. Within a mating type group (mt+/mt- or mt-/mt-) a cell line with more chloroplast DNA tended to transmit its non-Mendelian markers more frequently than a cell line with less chloroplast DNA.