Light propagation in two-dimensional and three-dimensional slabs of reflective colloidal particles in solution: The effect of interfaces and interparticle correlations.

The propagation of light across 2D and 3D slabs of reflective colloidal particles in a fluidlike state has been investigated by simulation. The colloids are represented as hard spheres with and without an attractive square-well tail. Representative configurations of particles have been generated by Monte Carlo. The path of rays entering the slab normal to its planar surface has been determined by exact geometric scattering conditions, assuming that particles are macroscopic spheres fully reflective at the surface of their hard-core potential. The analysis of light paths provides the transmission and reflection coefficients, the mean-free path, the average length of transmitted and reflected paths, the distribution of scattering events across the slab, the angular spread of the outcoming rays as a function of dimensionality, and thermodynamic state. The results highlight the presence of a sizable population of very long paths, which play an important role in random lasing from solutions of metal particles in an optically active fluid. The output power spectrum resulting from the stimulated emission amplification decays asymptotically as an inverse power law. The present study goes beyond the standard approach based on a random walk confined between two planar interfaces and parametrized in terms of the mean-free path and scattering matrix. Here, instead, the mean-free path, the correlation among scattering events, and memory effects are not assumed a priori, but emerge from the underlying statistical mechanics model of interacting particles. In this way the dependence of properties on the thermodynamic state, the effect of particle-particle and particle-interface correlations and of spatial inhomogeneity, and memory effects are accounted for in a transparent way. Moreover, the approach joins smoothly the ballistic regime of light propagation at low density with the diffusive regime at high density of scattering centers. These properties are exploited to investigate the effect of weak polydispersivity and of large density fluctuations at the critical point of the model with the attractive potential tail.

Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behavior.

Cetaceans are fully aquatic mammals that descended from terrestrial ancestors, an iconic evolutionary transition characterized by adaptations for underwater foraging via breath-hold diving. Although the evolutionary history of this specialized behavior is challenging to reconstruct, coevolving sensory systems may offer valuable clues. The dim-light visual pigment, rhodopsin, which initiates phototransduction in the rod photoreceptors of the eye, has provided insight into the visual ecology of depth in several aquatic vertebrate lineages. Here, we use ancestral sequence reconstruction and protein resurrection experiments to quantify light-activation metrics in rhodopsin pigments from ancestors bracketing the cetacean terrestrial-to-aquatic transition. By comparing multiple reconstruction methods on a broadly sampled cetartiodactyl species tree, we generated highly robust ancestral sequence estimates. Our experimental results provide direct support for a blue-shift in spectral sensitivity along the branch separating cetaceans from terrestrial relatives. This blue-shift was 14 nm, resulting in a deep-sea signature (λmax = 486 nm) similar to many mesopelagic-dwelling fish. We also discovered that the decay rates of light-activated rhodopsin increased in ancestral cetaceans, which may indicate an accelerated dark adaptation response typical of deeper-diving mammals. Because slow decay rates are thought to help sequester cytotoxic photoproducts, this surprising result could reflect an ecological trade-off between rod photoprotection and dark adaptation. Taken together, these ancestral shifts in rhodopsin function suggest that some of the first fully aquatic cetaceans could dive into the mesopelagic zone (>200 m). Moreover, our reconstructions indicate that this behavior arose before the divergence of toothed and baleen whales.

Transcutaneous electrical stimulation as a resistance force in lingual exercise: A preliminary proof-of-concept study.

BACKGROUND: Limited knowledge exists regarding whether transcutaneous electrical stimulation (TES)-based exercise can improve the lingual pressure generation. OBJECTIVES: To compare the effect of submental TES with two different pulse durations (PD) coupled with isometric lingual exercises on lingual pressure measures. METHODS: Twenty-eight healthy volunteers were divided into two submental TES groups: short PD (300 µs) and long PD (700 µs). The Iowa Oral Performance Instrument (IOPI) was used for lingual pressure measurements and exercise. In total, participants attended six exercise sessions 3 days per week for 2 consecutive weeks. Maximum and swallowing lingual pressures were measured 1 h following each exercise session and 3 days after the final session to assess any detraining effect. Data were analysed using repeated measure ANOVA. RESULTS: Mean maximum lingual pressure change was significantly greater in TES with short PD versus the long PD condition following the first week of exercise. Following the 2-week exercise, a significant increase was found in mean maximum lingual pressure for short and long PD conditions compared with the baseline. However, no significant difference was found between PD conditions for maximum lingual pressure. Likewise, no significant differences in swallowing lingual pressure were found compared with the baseline or across the two TES conditions. CONCLUSION: Although short PD induced greater gain in maximum lingual pressure than the long PD after week 1, the enhanced effect faded after week 2, leading to a comparable increase in maximum lingual pressure for both groups. However, increased gain in maximum lingual pressure was not transferred to lingual pressure during swallowing.

Clinical Swallowing Profile Change in HNC Patients Treated with C/RT.

OBJECTIVES/HYPOTHESIS: To demonstrate utility of the Mann Assessment of Swallowing Ability-Cancer (MASA-C) to describe change in swallowing ability in a cohort of HNC patients from pre-C/RT to post-C/RT to follow up at 3 months post-C/RT. An exploratory analysis compared patients treated with radiotherapy (RT) only to patients treated with chemoradiation (CRT). STUDY DESIGN: Prospective Cohort. METHODS: The MASA-C and Functional Oral Intake Scale (FOIS) were completed on 85 HNC patients within the first 5 days of CRT initiation, at the completion of C/RT (6 weeks), and 3 months after completion of C/RT. MASA-C total scores and clinical profiles were used to describe change in swallowing performance at each time point. RESULTS: MASA-C and FOIS scores were significantly lower at 6 weeks and 3 months compared to baseline. Patients treated with CRT demonstrated more frequent and more severe dysphagia. Post C/RT items demonstrating the most deterioration included taste, diet level, oral mucosa, saliva, weight loss, and pharyngeal functions. Significant recovery was observed between 6 weeks and 3 months on both the MASA-C and FOIS. MASA-C items revealing the greatest recovery included taste, diet level, oral mucosa, tongue movement, weight loss, oral transit, voice, and pharyngeal phase. Few significant differences were noted between RT and CRT cases at 3 months. CONCLUSIONS: Swallowing functions deteriorate significantly following C/RT with incomplete recovery at 3 months. Few differences were noted between RT and CRT treated patients at 3 months. Clinical profiling with the MASA-C provides a standard, simple method to document swallow function change over time in these patients. LEVEL OF EVIDENCE: 2 Laryngoscope, 131:E1873-E1880, 2021.

Comparative Validity of the American Speech-Language-Hearing Association's National Outcomes Measurement System, Functional Oral Intake Scale, and G-Codes to Mann Assessment of Swallowing Ability Scores for Dysphagia.

Background The American Speech-Language-Hearing Association (ASHA) advocates using the National Outcomes Measurement System (NOMS) scales to assist speech-language pathologists (SLPs) in the mandated assigning of "functional limitation levels" and G-Code for Medicare Part B claims. Unfortunately, not all SLPs have access to this tool, and it is unclear how other common outcome measurement scales relate to ASHA NOMS or G-Codes. To explore the utility of other scales in reporting Centers for Medicare & Medicaid Services G-Codes, we conducted a comparative validity study comparing ASHA NOMS Dysphagia Scale, Functional Oral Intake Scale (FOIS), and Mann Assessment of Swallowing Ability to G-Codes on a sample of 105 patients who had stroke. Method Nine SLP student researchers trained to criterion on the NOMS and FOIS blindly and independently scored 105 stroke cases with dysphagia de-identified from a past study. Three graduate SLP clinicians independently assigned G-Codes. Data from the student researchers and Mann Assessment of Swallowing Ability scores were compared for admission and discharge from subacute rehabilitation. Analysis included intraclass correlation for reliability, Spearman correlation for comparative validity, and area under the receiver operating characteristic curve to compare the validity and discriminatory utility of measures in classifying dysphagia. Results Strong correlations (> .6) were noted between all measures at baseline, particularly FOIS and NOMS coding ( r = .919). At discharge, superior performance by the FOIS (area under the receiver operating characteristic curve = 0.819) was demonstrated. Code missingness was higher for the NOMS than the other scales. Discussion All 3 clinical dysphagia tools demonstrate acceptable validity in supporting G-Code designation to stroke cases. The FOIS demonstrated superior validity and utility across time points. The NOMS Dysphagia Scale was significantly affected by data missingness due to the multiconstruct nature of the tool.

Evolution of nonspectral rhodopsin function at high altitudes.

High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.

An experimental comparison of human and bovine rhodopsin provides insight into the molecular basis of retinal disease.

Rhodopsin is the visual pigment that mediates dim-light vision in vertebrates and is a model system for the study of retinal disease. The majority of rhodopsin experiments are performed using bovine rhodopsin; however, recent evidence suggests that significant functional differences exist among mammalian rhodopsins. In this study, we identify differences in both thermal decay and light-activated retinal release rates between bovine and human rhodopsin and perform mutagenesis studies to highlight two clusters of substitutions that contribute to these differences. We also demonstrate that the retinitis pigmentosa-associated mutation G51A behaves differently in human rhodopsin compared to bovine rhodopsin and determine that the thermal decay rate of an ancestrally reconstructed mammalian rhodopsin displays an intermediate phenotype compared to the two extant pigments.

Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin.

Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.

A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics.

Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates.

Biology and Conservation of the Taiwanese Humpback Dolphin, Sousa chinensis taiwanensis.

The humpback dolphins of the eastern Taiwan Strait were first discovered scientifically in 2002 and since then have received much research attention. We reviewed all information published in peer-reviewed scientific journals on these dolphins and where appropriate and available, peer-reviewed scientific workshop reports and graduate theses were also examined. Recent evidence demonstrated that this population warranted recognition as a subspecies, Sousa chinensis taiwanensis. It is found in a highly restricted and linear strip of coastal waters along central western Taiwan. Numbering fewer than 80 individuals and declining, five main threats (fisheries interactions, habitat loss and degradation, loss of freshwater to estuaries within their habitat, air and water pollution, and noise) threaten the future existence of this subspecies. These dolphins have cultural and religious importance and boast the highest level of legal protection for wildlife in Taiwan. However, despite enormous efforts by local and international non-governmental groups urging immediate conservation actions, there have been no real government efforts to mitigate any existing threats; instead, some of these threats have worsened. Based on recent studies, we suggest the IUCN Red List status be revised to Critically Endangered CR 2a(ii); D for the subspecies.

Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment.

Cetaceans have undergone a remarkable evolutionary transition that was accompanied by many sensory adaptations, including modification of the visual system for underwater environments. Recent sequencing of cetacean genomes has made it possible to begin exploring the molecular basis of these adaptations. In this study we use in vitro expression methods to experimentally characterize the first step of the visual transduction cascade, the light activation of rhodopsin, for the killer whale. To investigate the spectral effects of amino acid substitutions thought to correspond with absorbance shifts relative to terrestrial mammals, we used the orca gene as a background for the first site-directed mutagenesis experiments in a cetacean rhodopsin. The S292A mutation had the largest effect, and was responsible for the majority of the spectral difference between killer whale and bovine (terrestrial) rhodopsin. Using codon-based likelihood models, we also found significant evidence for positive selection in cetacean rhodopsin sequences, including on spectral tuning sites we experimentally mutated. We then investigated patterns of ecological divergence that may be correlated with rhodopsin functional variation by using a series of clade models that partitioned the data set according to phylogeny, habitat, and foraging depth zone. Only the model partitioning according to depth was significant. This suggests that foraging dives might be a selective regime influencing cetacean rhodopsin divergence, and our experimental results indicate that spectral tuning may be playing an adaptive role in this process. Our study demonstrates that combining computational and experimental methods is crucial for gaining insight into the selection pressures underlying molecular evolution.

Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes.

BACKGROUND: Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed genes are thought to experience stronger selection pressures on synonymous codons. This should result in codon usage bias even in species with relatively low effective population sizes, like mammals, where synonymous site selection is thought to be weak. Here we use phylogenetic codon-based likelihood models to explore patterns of codon usage bias in a dataset of 18 mammalian rhodopsin sequences, the protein mediating the first step in vision in the eye, and one of the most highly expressed genes in vertebrates. We use these patterns to infer selection pressures on key translational mechanisms including polypeptide elongation, protein folding, mRNA stability, and splicing. RESULTS: Overall, patterns of selection in mammalian rhodopsin appear to be correlated with post-transcriptional and translational processes. We found significant evidence for selection at synonymous sites using phylogenetic mutation-selection likelihood models, with C-ending codons found to have the highest relative fitness, and to be significantly more abundant at conserved sites. In general, these codons corresponded with the most abundant tRNAs in mammals. We found significant differences in codon usage bias between rhodopsin loops versus helices, though there was no significant difference in mean synonymous substitution rate between these motifs. We also found a significantly higher proportion of GC-ending codons at paired sites in rhodopsin mRNA secondary structure, and significantly lower synonymous mutation rates in putative exonic splicing enhancer (ESE) regions than in non-ESE regions. CONCLUSIONS: By focusing on a single highly expressed gene we both distinguish synonymous codon selection from mutational effects and analytically explore underlying functional mechanisms. Our results suggest that codon bias in mammalian rhodopsin arises from selection to optimally balance high overall translational speed, accuracy, and proper protein folding, especially in structurally complicated regions. Selection at synonymous sites may also be contributing to mRNA stability and splicing efficiency at exonic-splicing-enhancer (ESE) regions. Our results highlight the importance of investigating highly expressed genes in a broader phylogenetic context in order to better understand the evolution of synonymous substitutions.