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Innovative strategies to increase clinical trial accessibility and equity are needed. We conducted a retrospective review of a phase II investigator-initiated trial to determine whether the modification of clinical trial design to decentralize study treatment can improve trial accessibility among underrepresented groups. Sociodemographic characteristics, including area deprivation indices, as well as study site travel distance, time, and costs were compared between enrolled participants who received chemotherapy locally and participants who did not. Participants who received chemotherapy locally lived substantially farther from the study site (median = 95.90 vs 25.20 miles, P = .004), faced a greater time burden traveling to the study site (median = 115.00 vs 34.00 minutes, P = .002), and had higher travel-related costs for a single trip to the study site (median = $62.81 vs $16.51, P = .004). This study highlights opportunities for alleviating financial and time burdens associated with clinical trial participation, promoting equity in clinical research. Trial Registration: ClinicalTrials.gov identifier: NCT04380337.
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Telemedicina , Humanos , Estudos Retrospectivos , Feminino , Masculino , Telemedicina/economia , Telemedicina/estatística & dados numéricos , Pessoa de Meia-Idade , Viagem , Ensaios Clínicos Fase II como Assunto , Acessibilidade aos Serviços de Saúde , Fatores de Tempo , Adulto , Neoplasias/terapia , Neoplasias/tratamento farmacológico , Antineoplásicos/economia , Antineoplásicos/uso terapêutico , Antineoplásicos/administração & dosagem , IdosoRESUMO
Falls among older adults are a costly public health concern. Such falls can be precipitated by balance disturbances, after which a recovery strategy requiring rapid, high force outputs is necessary. Sarcopenia among older adults likely diminishes their ability to produce the forces necessary to arrest gait instability. Age-related changes to tendon stiffness may also delay muscle stretch and afferent feedback and decrease force transmission, worsening fall outcomes. However, the association between muscle strength, tendon stiffness, and gait instability is not well established. Given the ankle's proximity to the onset of many walking balance disturbances, we examined the relation between both plantarflexor strength and Achilles tendon stiffness with walking-related instability during perturbed gait in older and younger adults-the latter quantified herein using margins of stability and whole-body angular momentum including the application of treadmill-induced slip perturbations. Older and younger adults did not differ in plantarflexor strength, but Achilles tendon stiffness was lower in older adults. Among older adults, plantarflexor weakness associated with greater whole-body angular momentum following treadmill-induced slip perturbations. Weaker older adults also appeared to walk and recover from treadmill-induced slip perturbations with more caution. This study highlights the role of plantarflexor strength and Achilles tendon stiffness in regulating lateral gait stability in older adults, which may be targets for training protocols seeking to minimize fall risk and injury severity.
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Tendão do Calcâneo , Transtornos Neurológicos da Marcha , Humanos , Idoso , Marcha/fisiologia , Caminhada/fisiologia , Envelhecimento/fisiologia , Fenômenos Mecânicos , Tendão do Calcâneo/fisiologia , Equilíbrio Postural , Fenômenos BiomecânicosRESUMO
To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density (~10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron's electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to ~3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.
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Balance perturbations are used to study locomotor instability. However, these perturbations are designed to provoke a specific context of instability that may or may not generalize to a broader understanding of falls risk. The purpose of this study was to determine if the effect of balance perturbations on instability generalizes across contexts. 29 younger adults and 28 older adults completed four experimental trials, including unperturbed walking and walking while responding to three perturbation contexts: mediolateral optical flow, treadmill-induced slips, and lateral waist-pulls. We quantified the effect of perturbations as an absolute change in margin of stability from unperturbed walking. We found significant changes in mediolateral and anteroposterior margin of stability for all perturbations compared to unperturbed walking in both cohorts (p-values ≤ 0.042). In older adults, the mediolateral effects of lateral waist-pulls significantly correlated with those of optical flow perturbations and treadmill-induced slips (r ≥ 0.398, p-values ≤ 0.036). In younger adults but not in older adults, we found positive and significant correlations between the anteroposterior effect of waist-pull perturbations and optical flow perturbations, and the anteroposterior and mediolateral effect of treadmill-induced slips (r ≥ 0.428, p-values ≤ 0.021). We found no "goldilocks" perturbation paradigm to endorse that would support universal interpretations about locomotor instability. Building the most accurate patient profiles of instability likely requires a series of perturbation paradigms designed to emulate the variety of environmental contexts in which falls may occur.
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Fluxo Óptico , Equilíbrio Postural , Humanos , Idoso , Caminhada , Acidentes por Quedas/prevenção & controle , Teste de Esforço , Marcha , Fenômenos BiomecânicosRESUMO
Background: Considerable resources are spent to track fish movement in marine environments, often with the intent of estimating behavior, distribution, and abundance. Resulting data from these monitoring efforts, including tagging studies and genetic sampling, often can be siloed. For Pacific salmon in the Northeast Pacific Ocean, predominant data sources for fish monitoring are coded wire tags (CWTs) and genetic stock identification (GSI). Despite their complementary strengths and weaknesses in coverage and information content, the two data streams rarely have been integrated to inform Pacific salmon biology and management. Joint, or integrated, models can combine and contextualize multiple data sources in a single statistical framework to produce more robust estimates of fish populations. Methods: We introduce and fit a comprehensive joint model that integrates data from CWT recoveries and GSI sampling to inform the marine life history of Chinook salmon stocks at spatial and temporal scales relevant to ongoing fisheries management efforts. In a departure from similar models based primarily on CWT recoveries, modeled stocks in the new framework encompass both hatchery- and natural-origin fish. We specifically model the spatial distribution and marine abundance of four distinct stocks with spawning locations in California and southern Oregon, one of which is listed under the U.S. Endangered Species Act. Results: Using the joint model, we generated the most comprehensive estimates of marine distribution to date for all modeled Chinook salmon stocks, including historically data poor and low abundance stocks. Estimated marine distributions from the joint model were broadly similar to estimates from a simpler, CWT-only model but did suggest some differences in distribution in select seasons. Model output also included novel stock-, year-, and season-specific estimates of marine abundance. We observed and partially addressed several challenges in model convergence with the use of supplemental data sources and model constraints; similar difficulties are not unexpected with integrated modeling. We identify several options for improved data collection that could address issues in convergence and increase confidence in model estimates of abundance. We expect these model advances and results provide management-relevant biological insights, with the potential to inform future mixed-stock fisheries management efforts, as well as a foundation for more expansive and comprehensive analyses to follow.
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Oncorhynchus , Salmão , Animais , Salmão/genética , Pesqueiros , Oceano Pacífico , Espécies em Perigo de ExtinçãoRESUMO
BACKGROUND: Understanding the mechanistic effects of novel immunotherapy agents is critical to improving their successful clinical translation. These effects need to be studied in preclinical models that maintain the heterogenous tumor microenvironment (TME) and dysfunctional cell states found in a patient's tumor. We investigated immunotherapy perturbations targeting co-stimulatory molecule GITR and co-inhibitory immune checkpoint TIGIT in a patient-derived ex vivo system that maintains the TME in its near-native state. Leveraging single-cell genomics, we identified cell type-specific transcriptional reprogramming in response to immunotherapy perturbations. METHODS: We generated ex vivo tumor slice cultures from fresh surgical resections of gastric and colon cancer and treated them with GITR agonist or TIGIT antagonist antibodies. We applied paired single-cell RNA and TCR sequencing to the original surgical resections, control, and treated ex vivo tumor slice cultures. We additionally confirmed target expression using multiplex immunofluorescence and validated our findings with RNA in situ hybridization. RESULTS: We confirmed that tumor slice cultures maintained the cell types, transcriptional cell states and proportions of the original surgical resection. The GITR agonist was limited to increasing effector gene expression only in cytotoxic CD8 T cells. Dysfunctional exhausted CD8 T cells did not respond to GITR agonist. In contrast, the TIGIT antagonist increased TCR signaling and activated both cytotoxic and dysfunctional CD8 T cells. This included cells corresponding to TCR clonotypes with features indicative of potential tumor antigen reactivity. The TIGIT antagonist also activated T follicular helper-like cells and dendritic cells, and reduced markers of immunosuppression in regulatory T cells. CONCLUSIONS: We identified novel cellular mechanisms of action of GITR and TIGIT immunotherapy in the patients' TME. Unlike the GITR agonist that generated a limited transcriptional response, TIGIT antagonist orchestrated a multicellular response involving CD8 T cells, T follicular helper-like cells, dendritic cells, and regulatory T cells. Our experimental strategy combining single-cell genomics with preclinical models can successfully identify mechanisms of action of novel immunotherapy agents. Understanding the cellular and transcriptional mechanisms of response or resistance will aid in prioritization of targets and their clinical translation.
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Neoplasias Gastrointestinais , Microambiente Tumoral , Humanos , Imunoterapia , Receptores de Antígenos de Linfócitos T/genética , Receptores Imunológicos/genética , RNARESUMO
BACKGROUND: Adherence to prehabilitation is crucial for optimal benefit, but reasons for low adherence to home-based programs remain unexplored. Our aim was to identify and explore barriers and facilitators to prehabilitation adherence among patients undergoing abdominal surgery. METHODS: Nested in a single-center randomized controlled trial on prehabilitation (Perioperative Optimization With Enhanced Recovery (POWER)), this study had an explanatory sequential design with a connect integration. Patients randomized to the intervention arm were included in the quantitative analysis, and a subset of them was invited for a semi-structured interview. The exposure was the frequency of barriers to physical activity and healthy eating, and the outcome was adherence to those components of prehabilitation. Logistic or linear regression was used as appropriate. RESULTS: Among 133 participants in the intervention arm, 116 (87.2%) completed the initial survey ((56.9% women, median age 61 years old (IQR 49.0; 69.4)). The most frequent barriers to exercise and healthy eating were medical issues (59%) and lack of motivation (31%), respectively. There was no significant association between the barriers to physical activity score and adherence to this component of the program (OR 0.89, 95% CI 0.78-1.02, p=0.09). Higher barriers to healthy eating scores were associated with lower Mediterranean diet scores pre- and post-intervention (coef.: -0.32, 95% CI: -0.49; -0.15, p<0.001; and coef.: -0.27, 95% CI: -0.47; -0.07, p=0.01, respectively). Interviews with 15 participants revealed that participating in prehabilitation was a motivator for healthy eating and exercising through goal setting, time-efficient workouts, and promoting self-efficacy. CONCLUSIONS: We identified key barriers to be addressed and facilitators to be leveraged in future prehabilitation programs. TRIAL REGISTRATION: NCT04504266.
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Cuidados Pré-Operatórios , Exercício Pré-Operatório , Humanos , Feminino , Pessoa de Meia-Idade , Masculino , Cuidados Pré-Operatórios/métodos , Exercício Físico , Terapia por Exercício/métodosRESUMO
Accurate anatomical characterizations are necessary to investigate neural circuitry on a fine scale, but for the rodent claustrum complex (CLCX), this has yet to be fully accomplished. The CLCX is generally considered to comprise two major subdivisions, the claustrum (CL) and the dorsal endopiriform nucleus (DEn), but regional boundaries to these areas are debated. To address this, we conducted a multifaceted analysis of fiber- and cytoarchitecture, genetic marker expression, and connectivity using mice of both sexes, to create a comprehensive guide for identifying and delineating borders to CLCX, including an online reference atlas. Our data indicated four distinct subregions within CLCX, subdividing both CL and DEn into two. Additionally, we conducted brain-wide tracing of inputs to CLCX using a transgenic mouse line. Immunohistochemical staining against myelin basic protein (MBP), parvalbumin (PV), and calbindin (CB) revealed intricate fiber-architectural patterns enabling precise delineations of CLCX and its subregions. Myelinated fibers were abundant dorsally in CL but absent ventrally, whereas PV expressing fibers occupied the entire CL. CB staining revealed a central gap within CL, also visible anterior to the striatum. The Nr2f2, Npsr1, and Cplx3 genes expressed specifically within different subregions of the CLCX, and Rprm helped delineate the CL-insular border. Furthermore, cells in CL projecting to the retrosplenial cortex were located within the myelin sparse area. By combining own experimental data with digitally available datasets of gene expression and input connectivity, we could demonstrate that the proposed delineation scheme allows anchoring of datasets from different origins to a common reference framework.
Mice are a highly tractable model for studying the claustrum complex (CLCX). However, without a consensus on how to delineate the CLCX in rodents, comparing results between studies is challenging. It is therefore important to expand our anatomical knowledge of the CLCX, to match the level of detail needed to study its functional properties. To improve and expand upon preexisting delineation schemes, we used the combinatorial expression of several markers to create a comprehensive guide to delineate the CLCX and its subregions, including an online reference atlas. This anatomical framework will allow researchers to anchor future experimental data into a common reference space. We demonstrated the power of this new structural framework by combining our own experimental data with digitally available data on gene expression and input connectivity of the CLCX.
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Claustrum , Masculino , Feminino , Camundongos , Animais , Claustrum/metabolismo , Calbindinas/metabolismo , Encéfalo/metabolismo , Parvalbuminas/metabolismo , Roedores/metabolismo , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/metabolismo , Proteínas Adaptadoras de Transdução de SinalRESUMO
Climate change drives species distribution shifts, affecting the availability of resources people rely upon for food and livelihoods. These impacts are complex, manifest at local scales, and have diverse effects across multiple species. However, for wild capture fisheries, current understanding is dominated by predictions for individual species at coarse spatial scales. We show that species-specific responses to localized environmental changes will alter the collection of co-occurring species within established fishing footprints along the U.S. West Coast. We demonstrate that availability of the most economically valuable, primary target species is highly likely to decline coastwide in response to warming and reduced oxygen concentrations, while availability of the most abundant, secondary target species will potentially increase. A spatial reshuffling of primary and secondary target species suggests regionally heterogeneous opportunities for fishers to adapt by changing where or what they fish. Developing foresight into the collective responses of species at local scales will enable more effective and tangible adaptation pathways for fishing communities.
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Mudança Climática , Pesqueiros , Animais , Aclimatação , Alimentos , OxigênioRESUMO
Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing-also called metabarcoding-of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.
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DNA Ambiental , Oncorhynchus kisutch , Oncorhynchus mykiss , Animais , Humanos , Ecossistema , Oncorhynchus mykiss/genética , Rios , SalmãoRESUMO
Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing-both of which we can model-but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.
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Código de Barras de DNA Taxonômico , DNA Ambiental , Código de Barras de DNA Taxonômico/métodos , DNA/genética , Reação em Cadeia da Polimerase/métodos , Incerteza , BiodiversidadeRESUMO
Understanding the cellular mechanisms of novel immunotherapy agents in the human tumor microenvironment (TME) is critical to their clinical success. We examined GITR and TIGIT immunotherapy in gastric and colon cancer patients using ex vivo slice tumor slice cultures derived from cancer surgical resections. This primary culture system maintains the original TME in a near-native state. We applied paired single-cell RNA and TCR sequencing to identify cell type specific transcriptional reprogramming. The GITR agonist was limited to increasing effector gene expression only in cytotoxic CD8 T cells. The TIGIT antagonist increased TCR signaling and activated both cytotoxic and dysfunctional CD8 T cells, including clonotypes indicative of potential tumor antigen reactivity. The TIGIT antagonist also activated T follicular helper-like cells and dendritic cells, and reduced markers of immunosuppression in regulatory T cells. Overall, we identified cellular mechanisms of action of these two immunotherapy targets in the patients' TME.
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Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture-struggle to link genetic observations to the underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology, it becomes more important to develop ways to make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying polymerase chain reaction mechanism explains the observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arise, rather than transforming the data post hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.
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Código de Barras de DNA Taxonômico , Microbiota , Código de Barras de DNA Taxonômico/métodos , DNA/genética , Ecologia , BiodiversidadeRESUMO
This quality improvement study evaluates the association of an online home-based patient prehabilitation program with colorectal surgery outcomes.
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Neoplasias Colorretais , Cirurgia Colorretal , Procedimentos Cirúrgicos do Sistema Digestório , Humanos , Exercício Pré-Operatório , Terapia por Exercício , Resultado do Tratamento , Cuidados Pré-Operatórios , Neoplasias Colorretais/cirurgia , Complicações Pós-Operatórias/prevenção & controleRESUMO
The claustrum is known for its extensive connectivity with many other forebrain regions, but its elongated shape and deep location have made further study difficult. We have sought to understand when mouse claustrum neurons are born, where they are located in developing brains, and when they develop their widespread connections to the cortex. We established that a well-characterized parvalbumin plexus, which identifies the claustrum in adults, is only present from postnatal day (P) 21. A myeloarchitectonic outline of the claustrum can be derived from a triangular fiber arrangement from P15. A dense patch of Nurr1+ cells is present at its core and is already evident at birth. Bromodeoxyuridine birth dating of forebrain progenitors reveals that the majority of claustrum neurons are born during a narrow time window centered on embryonic day 12.5, which is later than the adjacent subplate and endopiriform nucleus. Retrograde tracing revealed that claustrum projections to anterior cingulate (ACA) and retrosplenial cortex (RSP) follow distinct developmental trajectories. Claustrum-ACA connectivity matures rapidly and reaches adult-like innervation density by P10, whereas claustrum-RSP innervation emerges later over a protracted time window. This work establishes the timeline of claustrum development and provides a framework for understanding how the claustrum is built and develops its unique connectivity.
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Claustrum , Camundongos , Animais , Gânglios da Base/fisiologia , Vias Neurais/fisiologia , Giro do Cíngulo , NeurôniosRESUMO
BACKGROUND: The use of sensory and mechanical perturbations applied during walking has grown in popularity due to their ability to elicit instability relevant to falls. However, the vast majority of perturbation studies on walking balance are performed on a treadmill at a fixed speed. RESEARCH QUESTION: The aim of this study was to quantify the effects of mediolateral optical flow perturbations on walking speed and balance outcomes in young adults walking with fixed-speed and self-paced treadmill controllers. METHODS: Fifteen healthy young adults (8 female, age: 23.1 ± 4.6 yrs) completed four five-minute randomized walking trials in a speed-matched virtual reality hallway. In two of the trials, we added continuous mediolateral optical flow perturbations to the virtual hallway. Trials with and without optical flow perturbations were performed with either a fixed-speed or self-paced treadmill controller. We measured walking speed, balance outcomes (step width, margin of stability, local dynamic instability) and gait variability (step width variability and margin of stability variability). RESULTS: We found significant increases in step width (+20%, p = 0.004) and local dynamic instability (+11%, p = 0.008) of participants while responding to optical flow perturbations at a fixed treadmill speed. We found no significant differences in these outcome measures when perturbations were applied on a self-paced treadmill. Instead, participants walked 5.7% slower between the self-paced treadmill controller conditions when responding to optical flow perturbations (1.48 ± 0.13 m/s vs. 1.57 ± 0.16 m/s, p = 0.005). SIGNIFICANCE: Our findings suggest that during walking, when presented with a balance challenge, an individual will instinctively reduce their walking speed in order to better preserve stability. However, comparisons to prior literature suggest that this response may depend on environmental and/or perturbation context. Cumulatively, our results point to opportunities for leveraging self-paced treadmill controllers as a more ecologically-relevant option in balance research with potential clinical applications in diagnostics and rehabilitation.
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Fluxo Óptico , Adulto , Teste de Esforço , Feminino , Marcha/fisiologia , Humanos , Masculino , Equilíbrio Postural/fisiologia , Caminhada/fisiologia , Adulto JovemRESUMO
Many ecological data sets are proportional, representing mixtures of constituent elements such as species, populations, or strains. Analyses of proportional data are challenged by categories with zero observations (zeros), all observations (ones), and overdispersion. In lieu of ad hoc data adjustments, we describe and evaluate a zero-and-one inflated Dirichlet regression model, with its corresponding R package (zoid), capable of handling observed data x $$ x $$ consisting of three possible categories: zeros, proportions, or ones. Instead of fitting the model to observations of single biological units (e.g., individual organisms) within a sample, we sum proportional contributions across units and estimate mixture proportions using one aggregated observation per sample. Optional estimation of overdispersion and covariate influences expand model applications. We evaluate model performance, as implemented in Stan, using simulations and two ecological case studies. We show that zoid successfully estimates mixture proportions using simulated data with varying sample sizes and is robust to overdispersion and covariate structure. In empirical case studies, we estimate the composition of a mixed-stock Chinook salmon (Oncorhynchus tshawytscha) fishery and analyze the stomach contents of Atlantic cod (Gadus morhua). Our implementation of the model as an R package facilitates its application to varied ecological data sets composed of proportional observations.
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Modelos Estatísticos , Software , Animais , Pesqueiros , Projetos de Pesquisa , SalmãoRESUMO
All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km2 to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.
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DNA Ambiental , Gadiformes , Animais , Ecossistema , Pesqueiros , Humanos , Oceanos e MaresRESUMO
The claustrum is the most densely interconnected region in the human brain. Despite the accumulating data from clinical and experimental studies, the functional role of the claustrum remains unknown. Here, we systematically review claustrum lesion studies and discuss their functional implications. Claustral lesions are associated with an array of signs and symptoms, including changes in cognitive, perceptual and motor abilities; electrical activity; mental state; and sleep. The wide range of symptoms observed following claustral lesions do not provide compelling evidence to support prominent current theories of claustrum function such as multisensory integration or salience computation. Conversely, the lesions studies support the hypothesis that the claustrum regulates cortical excitability. We argue that the claustrum is connected to, or part of, multiple brain networks that perform both fundamental and higher cognitive functions. As a multifunctional node in numerous networks, this may explain the manifold effects of claustrum damage on brain and behaviour.