Patterns and effects of gene flow on adaptation across spatial scales: implications for management.

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

Elucidating the interaction between stretch and stiffness using an agent-based spring network model of progressive pulmonary fibrosis.

Pulmonary fibrosis is a deadly disease that involves the dysregulation of fibroblasts and myofibroblasts, which are mechanosensitive. Previous computational models have succeeded in modeling stiffness-mediated fibroblasts behaviors; however, these models have neglected to consider stretch-mediated behaviors, especially stretch-sensitive channels and the stretch-mediated release of latent TGF-ß. Here, we develop and explore an agent-based model and spring network model hybrid that is capable of recapitulating both stiffness and stretch. Using the model, we evaluate the role of mechanical signaling in homeostasis and disease progression during self-healing and fibrosis, respectively. We develop the model such that there is a fibrotic threshold near which the network tends towards instability and fibrosis or below which the network tends to heal. The healing response is due to the stretch signal, whereas the fibrotic response occurs when the stiffness signal overpowers the stretch signal, creating a positive feedback loop. We also find that by changing the proportional weights of the stretch and stiffness signals, we observe heterogeneity in pathological network structure similar to that seen in human IPF tissue. The system also shows emergent behavior and bifurcations: whether the network will heal or turn fibrotic depends on the initial network organization of the damage, clearly demonstrating structure's pivotal role in healing or fibrosis of the overall network. In summary, these results strongly suggest that the mechanical signaling present in the lungs combined with network effects contribute to both homeostasis and disease progression.

Local fractal dimension of collagen detects increased spatial complexity in fibrosis.

Increase of collagen content and reorganization characterizes fibrosis but quantifying the latter remains challenging. Spatially complex structures are often analyzed via the fractal dimension; however, established methods for calculating this quantity either provide a single dimension for an entire object or a spatially distributed dimension that only considers binary images. These neglect valuable information related to collagen density in images of fibrotic tissue. We sought to develop a fractal analysis that can be applied to 3-dimensional (3D) images of fibrotic tissue. A fractal dimension map for each image was calculated by determining a single fractal dimension for a small area surrounding each image pixel, using fiber thickness as the third dimension. We found that this local fractal dimension increased with age and with progression of fibrosis regardless of collagen content. Our new method of distributed 3D fractal analysis can thus distinguish between changes in collagen content and organization induced by fibrosis.

Degeneracy in Intercalated Pb Phases under Buffer-Layer Graphene on SiC(0001) and Diffuse Moiré Spots in Surface Diffraction.

First-principles density functional theory (DFT) is used to analyze the stability of Pb intercalated phases under buffer layer graphene on SiC(0001) as a function of the supercell size, Pb coverage, and degree of Pb ordering. By comparing the chemical potentials of such two-dimensional Pb structures, we find that there is a family of structurally distinct thermodynamically preferred Pb subsurface configurations with minute stability differences. These differences are comparable to the thermal energies at about 450 °C, where the Pb intercalated phases are grown. High-resolution surface-diffraction experiments using Spot Profile Analysis Low-Energy Electron Diffraction (SPA-LEED) confirm this high degree of degeneracy of the Pb intercalated phases from broad, low-intensity moiré spots observed exclusively from intercalated Pb. The low intensity of the moiré spots implies the coexistence of structurally different subsurface Pb phases.

Semiclassical Husimi Distributions of Schur Vectors in Non-Hermitian Quantum Systems.

We construct a semiclassical phase-space density of Schur vectors in non-Hermitian quantum systems. Each Schur vector is associated to a single Planck cell. The Schur states are organized according to a classical norm landscape on phase space-a classical manifestation of the lifetimes which are characteristic of non-Hermitian systems. To demonstrate the generality of this construction we apply it to a highly nontrivial example: a PT-symmetric kicked rotor in the regimes of mixed and chaotic classical dynamics.

Multiscale stiffness of human emphysematous precision cut lung slices.

Emphysema is a debilitating disease that remodels the lung leading to reduced tissue stiffness. Thus, understanding emphysema progression requires assessing lung stiffness at both the tissue and alveolar scales. Here, we introduce an approach to determine multiscale tissue stiffness and apply it to precision-cut lung slices (PCLS). First, we established a framework for measuring stiffness of thin, disk-like samples. We then designed a device to verify this concept and validated its measuring capabilities using known samples. Next, we compared healthy and emphysematous human PCLS and found that the latter was 50% softer. Through computational network modeling, we discovered that this reduced macroscopic tissue stiffness was due to both microscopic septal wall remodeling and structural deterioration. Lastly, through protein expression profiling, we identified a wide spectrum of enzymes that can drive septal wall remodeling, which, together with mechanical forces, lead to rupture and structural deterioration of the emphysematous lung parenchyma.

Predicting alveolar ventilation heterogeneity in pulmonary fibrosis using a non-uniform polyhedral spring network model.

Pulmonary Fibrosis (PF) is a deadly disease that has limited treatment options and is caused by excessive deposition and cross-linking of collagen leading to stiffening of the lung parenchyma. The link between lung structure and function in PF remains poorly understood, although its spatially heterogeneous nature has important implications for alveolar ventilation. Computational models of lung parenchyma utilize uniform arrays of space-filling shapes to represent individual alveoli, but have inherent anisotropy, whereas actual lung tissue is isotropic on average. We developed a novel Voronoi-based 3D spring network model of the lung parenchyma, the Amorphous Network, that exhibits more 2D and 3D similarity to lung geometry than regular polyhedral networks. In contrast to regular networks that show anisotropic force transmission, the structural randomness in the Amorphous Network dissipates this anisotropy with important implications for mechanotransduction. We then added agents to the network that were allowed to carry out a random walk to mimic the migratory behavior of fibroblasts. To model progressive fibrosis, agents were moved around the network and increased the stiffness of springs along their path. Agents migrated at various path lengths until a certain percentage of the network was stiffened. Alveolar ventilation heterogeneity increased with both percent of the network stiffened, and walk length of the agents, until the percolation threshold was reached. The bulk modulus of the network also increased with both percent of network stiffened and path length. This model thus represents a step forward in the creation of physiologically accurate computational models of lung tissue disease.

Can the Remote Use of a Peak Flow Meter Predict Severity of Subglottic Stenosis and Surgical Timing?

OBJECTIVE: We aimed to assess the relationship between patient-performed and patient-reported peak flow meter (PFM) measurements with pulmonary function testing (PFT) and Dyspnea Index (DI) scores as a tool for monitoring Subglottic stenosis (SGS) disease progression remotely. METHODS: Thirty-five SGS patients were prospectively enrolled. Patients were given PFMs to report serial measurements from home. DI scores and PFT were recorded at serial clinic visits. Data were analyzed to determine the correlation between PFM measurements and PFT data. Pre-operative and post-operative PFM measurements, PFT, and DI scores were analyzed for patients who underwent operative intervention. Receiver operating characteristic (ROC) curves were created for PFM measurements, PFT data, and DI scores to predict the likelihood of surgery. RESULTS: PFM measurements had a "strong" correlation with the peak expiratory flow rate (PEFR), r = 0.78. Means of PEFR, PIFR, EDI, PFM measurements, and DI scores all significantly improved after the operative intervention (p ≤ 0.05). The area under the curve for ROC curves for DI scores, PFM measurements, and EDI were highest in our cohort with values of 0.896, 0.823, and 0.806, respectively. CONCLUSION: In our SGS cohort, PFM measurements correlate strongly with PEFR measurements. PFM measurements can adequately demonstrate disease progression and predict the need for surgery in this patient population. Together, DI scores and PFM measurements may be a useful tool to remotely follow patients with SGS and inform timing of in-person assessments. LEVEL OF EVIDENCE: 2 Laryngoscope, 133:628-633, 2023.

Breaking of Inversion Symmetry and Interlayer Electronic Coupling in Bilayer Graphene Heterostructure by Structural Implementation of High Electric Displacement Fields.

Controlling the interlayer coupling in two-dimensional (2D) materials generates novel electronic and topological phases. Its effective implementation is commonly done with a transverse electric field. However, phases generated by high displacement fields are elusive in this standard approach. Here, we introduce an exceptionally large displacement field by structural modification of a model system: AB-stacked bilayer graphene (BLG) on a SiC(0001) surface. We show that upon intercalation of gadolinium, electronic states in the top graphene layers exhibit a significant difference in the on-site potential energy, which effectively breaks the interlayer coupling between them. As a result, for energies close to the corresponding Dirac points, the BLG system behaves like two electronically isolated single graphene layers. This is proven by local scanning tunneling microscopy (STM)/spectroscopy, corroborated by density functional theory, tight binding, and multiprobe STM transport. The work presents metal intercalation as a promising approach for the synthesis of 2D graphene heterostructures with electronic phases generated by giant displacement fields.

Co-creating Digital Stories With UK-Based Stroke Survivors With the Aim of Synthesizing Collective Lessons From Individual Experiences of Interacting With Healthcare Professionals.

Background: Stroke survivor narratives can provide valuable insight into experiences of healthcare and beyond. There is need to further understand collective lessons from stroke survivor narratives, yet prior studies utilizing digital storytelling tend to not synthesize lessons from individual experiences. This study aims to develop a novel method to co-create digital stories with stroke survivors that will aim to synthesize and portray important collective lessons from individual stroke survivors' experiences of interacting with healthcare professionals. Methods: This study follows-up a qualitative study conducted with 30 stroke survivors exploring factors that help or hinder survivors to positively reconfigure their identity post-stroke. Five co-creation workshops were conducted with a subset of UK-based stroke survivors from this previous study. Participants were invited to join through: online workshops, an online bulletin board, and as an advisor. A four-stage workshop framework was developed through the integration of UK Design Council's Double Diamond method, digital storytelling strategies and the Behavior Change Wheel (BCW) framework for developing behavioral change interventions. Findings: Six online workshop participants (three male, three female; aged 33-63; time since stroke 2-16 years) co-created digital stories that share six collective lessons aimed at increasing empathy and encouraging behavior change in healthcare professionals (HCPs) working with stroke survivors. Online bulletin board participants (n = 1) and advisors (n = 5) supported the co-creation process. Collective lessons identified were: (1) Stroke has a variety of symptoms that must all be considered; (2) Stroke can affect anyone of any age and not just the elderly; (3) Assumptions should not be made about a survivor's lifestyle or habits; (4) It is important to acknowledge the person behind the stroke and ensure that they are communicated with and listened to; (5) Stroke survivors can often feel unprepared for the reality of life after stroke; (6) Adapting to life after stroke is a long-term process requiring long-term support. Conclusion: Stroke survivor stories highlighted preconceptions, attitudes and behaviors embedded within healthcare that negatively impacted their experiences and recovery. The novel methodology employed in this study enabled these stories to be synthesized into collective lessons to bring about improvements in these behaviors in future.

Comparison between the kinematics for kangaroo rat hopping on a solid versus sand surface.

In their natural habitats, animals move on a variety of substrates, ranging from solid surfaces to those that yield and flow (e.g. sand). These substrates impose different mechanical demands on the musculoskeletal system and may therefore elicit different locomotion patterns. The goal of this study is to compare bipedal hopping by desert kangaroo rats (Dipodomys deserti) on a solid versus granular substrate under speed-controlled conditions. To accomplish this goal, we developed a rotary treadmill, which is able to have different substrates or uneven surfaces. We video recorded six kangaroo rats hopping on a solid surface versus sand at the same speed (1.8 m s-1) and quantified the differences in the hopping kinematics between the two substrates. We found no significant differences in the hop period, hop length or duty cycle, showing that the gross kinematics on the two substrates were similar. This similarity was surprising given that sand is a substrate that absorbs mechanical energy. Measurements of the penetration resistance of the sand showed that the combination of the sand properties, toe-print area and kangaroo rat weight was probably the reason for the similarity.

Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.

We reassess progress in the field of biomolecular modeling and simulation, following up on our perspective published in 2011. By reviewing metrics for the field's productivity and providing examples of success, we underscore the productive phase of the field, whose short-term expectations were overestimated and long-term effects underestimated. Such successes include prediction of structures and mechanisms; generation of new insights into biomolecular activity; and thriving collaborations between modeling and experimentation, including experiments driven by modeling. We also discuss the impact of field exercises and web games on the field's progress. Overall, we note tremendous success by the biomolecular modeling community in utilization of computer power; improvement in force fields; and development and application of new algorithms, notably machine learning and artificial intelligence. The combined advances are enhancing the accuracy andscope of modeling and simulation, establishing an exemplary discipline where experiment and theory or simulations are full partners.

Nerve Growth Factor Is Responsible for Exercise-Induced Recovery of Septohippocampal Cholinergic Structure and Function.

Exercise has been shown to improve or rescue cognitive functioning in both humans and rodents, and the augmented actions of neurotrophins within the hippocampus and associated regions play a significant role in the improved neural plasticity. The septohippocampal circuit is modified by exercise. Beyond an enhancement of spatial working memory and a rescue of hippocampal activity-dependent acetylcholine (ACh) efflux, the re-emergence of the cholinergic/nestin neuronal phenotype within the medial septum/diagonal band (MS/dB) is observed following exercise (Hall and Savage, 2016). To determine which neurotrophin, brain-derived neurotrophic factor (BDNF) or nerve growth factor (NGF), is critical for exercise-induced cholinergic improvements, control and amnestic rats had either NGF or BDNF sequestered by TrkA-IgG or TrkB-IgG coated microbeads placed within the dorsal hippocampus. Hippocampal ACh release within the hippocampus during spontaneous alternation was measured and MS/dB cholinergic neuronal phenotypes were assessed. Sequestering NGF, but not BDNF, abolished the exercise-induced recovery of spatial working memory and ACh efflux. Furthermore, the re-emergence of the cholinergic/nestin neuronal phenotype within the MS/dB following exercise was also selectively dependent on the actions of NGF. Thus, exercise-induced enhancement of NGF within the septohippocampal pathway represents a key avenue for aiding failing septo-hippocampal functioning and therefore has significant potential for the recovery of memory and cognition in several neurological disorders.

Loud Music Exposure and Cochlear Synaptopathy in Young Adults: Isolated Auditory Brainstem Response Effects but No Perceptual Consequences.

The purpose of this study was to test the hypothesis that listeners with frequent exposure to loud music exhibit deficits in suprathreshold auditory performance consistent with cochlear synaptopathy. Young adults with normal audiograms were recruited who either did ( n = 31) or did not ( n = 30) have a history of frequent attendance at loud music venues where the typical sound levels could be expected to result in temporary threshold shifts. A test battery was administered that comprised three sets of procedures: (a) electrophysiological tests including distortion product otoacoustic emissions, auditory brainstem responses, envelope following responses, and the acoustic change complex evoked by an interaural phase inversion; (b) psychoacoustic tests including temporal modulation detection, spectral modulation detection, and sensitivity to interaural phase; and (c) speech tests including filtered phoneme recognition and speech-in-noise recognition. The results demonstrated that a history of loud music exposure can lead to a profile of peripheral auditory function that is consistent with an interpretation of cochlear synaptopathy in humans, namely, modestly abnormal auditory brainstem response Wave I/Wave V ratios in the presence of normal distortion product otoacoustic emissions and normal audiometric thresholds. However, there were no other electrophysiological, psychophysical, or speech perception effects. The absence of any behavioral effects in suprathreshold sound processing indicated that, even if cochlear synaptopathy is a valid pathophysiological condition in humans, its perceptual sequelae are either too diffuse or too inconsequential to permit a simple differential diagnosis of hidden hearing loss.

Gap Detection in School-Age Children and Adults: Center Frequency and Ramp Duration.

Purpose: The age at which gap detection becomes adultlike differs, depending on the stimulus characteristics. The present study evaluated whether the developmental trajectory differs as a function of stimulus frequency region or duration of the onset and offset ramps bounding the gap. Method: Thresholds were obtained for wideband noise (500-4500 Hz) with 4- or 40-ms raised-cosine ramps and for a 25-Hz-wide low-fluctuation narrowband noise centered on either 500 or 5000 Hz with 40-ms ramps. Stimuli were played continuously at 70 dB SPL, and the task was to indicate which of 3 intervals contained a gap. Listeners were 5.2- to 15.1-year-old children (n = 40) and adults (n = 10) with normal hearing. Results: Regardless of listener age, gap detection thresholds for the wideband noise tended to be lower when gaps were shaped using 4-ms rather than 40-ms ramps. Thresholds also tended to be lower for the low-fluctuation narrowband noise centered on 5000 Hz than 500 Hz. Performance reached adult levels after 11 years of age for all 4 stimuli. Maturation was not uniform across individuals, however; a subset of young children performed like adults, including some 5-year-olds. Conclusion: For these stimuli, the developmental trajectory was similar regardless of narrowband noise center frequency or wideband noise onset and offset ramp duration.

Membrane Protein Insertion into and Compatibility with Biomimetic Membranes.

Membrane protein and membrane protein-mimic functionalized materials are rapidly gaining interest across a wide range of applications, including drug screening, DNA sequencing, drug delivery, sensors, water desalination, and bioelectronics. In these applications, material performance is highly dependent on activity-per-protein and protein packing density in bilayer and bilayer-like structures collectively known as biomimetic membranes. However, a clear understanding of, and accurate tools to study these properties of biomimetic membranes does not exist. This paper presents methods to evaluate membrane protein compatibility with biomimetic membrane materials. The methods utilized provide average single protein activity, and for the first time, provide experimentally quantifiable measures of the chemical and physical compatibility between proteins (and their mimics) and membrane materials. Water transport proteins, rhodopsins, and artificial water channels are reconstituted into the full range of current biomimetic membrane matrices to evaluate the proposed platform. Compatibility measurement results show that both biological and artificial water channels tested largely preserve their single protein water transport rates in biomimetic membranes, while their reconstitution density is variable, leading to different overall membrane permeabilities. It is also shown that membrane protein insertion efficiency inversely correlates with both chemical and physical hydrophobicity mismatch between membrane protein and the membrane matrix.

Effect of response context and masker type on word recognition in school-age children and adults.

In adults, masked speech recognition improves with the provision of a closed set of response alternatives. The present study evaluated whether school-age children (5-13 years) benefit to the same extent as adults from a forced-choice context, and whether this effect depends on masker type. Experiment 1 compared masked speech reception thresholds for disyllabic words in either an open-set or a four-alternative forced-choice (4AFC) task. Maskers were speech-shaped noise or two-talker speech. Experiment 2 compared masked speech reception thresholds for monosyllabic words in two 4AFC tasks, one in which the target and foils were phonetically similar and one in which they were dissimilar. Maskers were speech-shaped noise, amplitude-modulated noise, or two-talker speech. For both experiments, it was predicted that children would not benefit from the information provided by the 4AFC context to the same degree as adults, particularly when the masker was complex (two-talker) or when audible speech cues were temporally sparse (modulated-noise). Results indicate that young children do benefit from a 4AFC context to the same extent as adults in speech-shaped noise and amplitude-modulated noise, but the benefit of context increases with listener age for the two-talker speech masker.

Cochlear hearing loss and the detection of sinusoidal versus random amplitude modulation.

This study assessed the effect of cochlear hearing loss on detection of random and sinusoidal amplitude modulation. Listeners with hearing loss and normal-hearing listeners (eight per group) generated temporal modulation transfer functions (TMTFs) for envelope fluctuations carried by a 2000-Hz pure tone. TMTFs for the two groups were similar at low modulation rates but diverged at higher rates presumably because of differences in frequency selectivity. For both groups, detection of random modulation was poorer than for sinusoidal modulation at lower rates but the reverse occurred at higher rates. No evidence was found that cochlear hearing loss, per se, affects modulation detection.