Structural equation models and small sample bias reduction with application to fishery data

An overview of structural equation models is presented along with an application to fishery data involving estimation and significance testing of the density dependent component of recruitment in 6 cod populations. Estimates and standard errors are based on normal theory and large sample properties of maximum likelihood estimates. The data sets analyzed involve small sample sizes so a sensitivity analysis of the effect (in terms of bias) of small sample sizes and other deviations in model assumptions is conducted. The analysis indicates that sample size is the most influential factor considered on the bias of parameter estimates. The reliability of indicator variables is also important. – Two methods of reducing the bias in estimates are considered, they are the jackknife and a method based on a Taylor’s series expansion of the log likelihood function. The bias reduced estimators are investigated by simulating several confirmatory factor models. Neither the Jackknife nor the Taylor’s series biased reduced estimator works sufficiently well to warrant their application in practice. Both estimators consistently reduce bias in the maximum likelihood estimates only when little bias exists. A difficulty realized in the investigation is that the expectations of some estimators are unbounded and this makes bias reduction difficult

Statistical inference about the relative efficiency of a new survey protocol, based on paired-tow survey calibration data

Paired-tow calibration studies provide information on changes in survey catchability that may occur because of some necessary change in protocols (e.g., change in vessel or vessel gear) in a fish stock survey. This information is important to ensure the continuity of annual time-series of survey indices of stock size that provide the basis for fish stock assessments. There are several statistical models used to analyze the paired-catch data from calibration studies. Our main contributions are results from simulation experiments designed to measure the accuracy of statistical inferences derived from some of these models. Our results show that a model commonly used to analyze calibration data can provide unreliable statistical results when there is between-tow spatial variation in the stock densities at each paired-tow site. However, a generalized linear mixed-effects model gave very reliable results over a wide range of spatial variations in densities and we recommend it for the analysis of paired-tow survey calibration data. This conclusion also applies if there is between-tow variation in catchability

A spatiotemporal model for snow crab (Chionoecetes opilio) stock size in the southern Gulf of St. Lawrence

We develop a high resolution spatio-temporal model of stock size and harvest rates for snow crab (Chionoecetes opilio) in the Southern Gulf of St. Lawrence, which supports an economically important fishery off the east coast of Canada. It is a spatial and weekly model during 1997-2014 that utilizes within-season depletion based on catch per unit of effort (CPUE; kg per pot), and also biomass values from a survey designed specifically for this stock. The model is formulated in a state-space framework. The main contribution of the model is to provide a better understanding of fishery-dependent factors that affect CPUE. There is strong evidence of density-dependence in the relationship with CPUE and stock biomass, in addition to a general increase in CPUE catchability over time that may be related to changes in gear soak time, and spatial variation in catchability. We also find that a natural mortality rate of 0.4 provides a better fit to survey results. Model results suggest that there is no evidence of effort saturation in the fishery.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The UN in the lab

We consider two alternatives to inaction for governments combating terrorism, which we term Defense and Prevention. Defense consists of investing in resources that reduce the impact of an attack, and generates a negative externality to other governments, making their countries a more attractive objective for terrorists. In contrast, Prevention, which consists of investing in resources that reduce the ability of the terrorist organization to mount an attack, creates a positive externality by reducing the overall threat of terrorism for all. This interaction is captured using a simple 3×3 “Nested Prisoner’s Dilemma” game, with a single Nash equilibrium where both countries choose Defense. Due to the structure of this interaction, countries can benefit from coordination of policy choices, and international institutions (such as the UN) can be utilized to facilitate coordination by implementing agreements to share the burden of Prevention. We introduce an institution that implements a burden-sharing policy for Prevention, and investigate experimentally whether subjects coordinate on a cooperative strategy more frequently under different levels of cost sharing. In all treatments, burden sharing leaves the Prisoner’s Dilemma structure and Nash equilibrium of the game unchanged. We compare three levels of burden sharing to a baseline in a between-subjects design, and find that burden sharing generates a non-linear effect on the choice of the efficient Prevention strategy and overall performance. Only an institution supporting a high level of mandatory burden sharing generates a significant improvement in the use of the Prevention strategy

Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cadigan, J., Bekkaye, J., Jafari, N., Zhu, L., Booth, A., Chen, Q., Raubenheimer, B., Harris, B., O’Connor, C., Lane, R., Kemp, G., Day, J., Day, J., & Ulloa, H. Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana. Frontiers in Built Environment, 8, (2022): 885215. https://doi.org/10.3389/fbuil.2022.885215.The Rockefeller Wildlife Refuge, located along the Chenier Plain in Southwest Louisiana, was the location of the sequential landfall of two major hurricanes in the 2020 hurricane season. To protect the rapidly retreating coastline along the Refuge, a system of breakwaters was constructed, which was partially completed by the 2020 hurricane season. Multi-institutional, multi-disciplinary rapid response deployments of wave gauges, piezometers, geotechnical measurements, vegetation sampling, and drone surveys were conducted before and after Hurricanes Laura and Delta along two transects in the Refuge; one protected by a breakwater system and one which was the natural, unprotected shoreline. Geomorphological changes were similar on both transects after Hurricane Laura, while after Delta there was higher inland sediment deposition on the natural shoreline. Floodwaters drained from the transect with breakwater protection more slowly than the natural shoreline, though topography profiles are similar, indicating a potential dampening or complex hydrodynamic interactions between the sediment—wetland—breakwater system. In addition, observations of a fluidized mud deposit in Rollover Bayou in the Refuge are presented and discussed in context of the maintenance of wetland elevation and stability in the sediment starved Chenier Plain.Funding for the study has been partially provided by the National Science Foundation through grants NSF 2139882, 2139883, 1829136, 1848650, and 1939275, as well as through the United States Army Corps of Engineers Regional Sediment Management program. Student support provided through the National Science Foundation Graduate Research Fellowship Program and the Louisiana Coastal Science Assistantship Program

Maximal Voluntary Activation of the Elbow Flexors Is under Predicted by Transcranial Magnetic Stimulation Compared to Motor Point Stimulation Prior to and Following Muscle Fatigue

Transcranial magnetic (TMS) and motor point stimulation have been used to determine voluntary activation (VA). However, very few studies have directly compared the two stimulation techniques for assessing VA of the elbow flexors. The purpose of this study was to compare TMS and motor point stimulation for assessing VA in non-fatigued and fatigued elbow flexors. Participants performed a fatigue protocol that included twelve, 15 s isometric elbow flexor contractions. Participants completed a set of isometric elbow flexion contractions at 100, 75, 50, and 25% of maximum voluntary contraction (MVC) prior to and following fatigue contractions 3, 6, 9, and 12 and 5 and 10 min post-fatigue. Force and EMG of the bicep and triceps brachii were measured for each contraction. Force responses to TMS and motor point stimulation and EMG responses to TMS (motor evoked potentials, MEPs) and Erb's point stimulation (maximal M-waves, Mmax) were also recorded. VA was estimated using the equation: VA% = (1−SITforce/PTforce) × 100. The resting twitch was measured directly for motor point stimulation and estimated for both motor point stimulation and TMS by extrapolation of the linear regression between the superimposed twitch force and voluntary force. MVC force, potentiated twitch force and VA significantly (p < 0.05) decreased throughout the elbow flexor fatigue protocol and partially recovered 10 min post fatigue. VA was significantly (p < 0.05) underestimated when using TMS compared to motor point stimulation in non-fatigued and fatigued elbow flexors. Motor point stimulation compared to TMS superimposed twitch forces were significantly (p < 0.05) higher at 50% MVC but similar at 75 and 100% MVC. The linear relationship between TMS superimposed twitch force and voluntary force significantly (p < 0.05) decreased with fatigue. There was no change in triceps/biceps electromyography, biceps/triceps MEP amplitudes, or bicep MEP amplitudes throughout the fatigue protocol at 100% MVC. In conclusion, motor point stimulation as opposed to TMS led to a higher estimation of VA in non-fatigued and fatigued elbow flexors. The decreased linear relationship between TMS superimposed twitch force and voluntary force led to an underestimation of the estimated resting twitch force and thus, a reduced VA

Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks

The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the region in the parameter space in which the system is functional. In this paper, we show that, in addition to volume, the geometry of this region has important consequences for the robustness and the fragility of a network. We develop an approximation within which we could algebraically specify the feasible region. We analyze the segment polarity gene network to illustrate our approach. The study of random walks in the parameter space and how they exit the feasible region provide us with a rich perspective on the different modes of failure of this network model. In particular, we found that, between two alternative ways of activating Wingless, one is more robust than the other. Our method provides a more complete measure of robustness to parameter variation. As a general modeling strategy, our approach is an interesting alternative to Boolean representation of biochemical networks

Wnt5a Increases Cardiac Gene Expressions of Cultured Human Circulating Progenitor Cells via a PKC Delta Activation

Background: Wnt signaling controls the balance between stem cell proliferation and differentiation and body patterning throughout development. Previous data demonstrated that non-canonical Wnts (Wnt5a, Wnt11) increased cardiac gene expression of circulating endothelial progenitor cells (EPC) and bone marrow-derived stem cells cultured in vitro. Since previous studies suggested a contribution of the protein kinase C (PKC) family to the Wnt5a-induced signalling, we investigated which PKC isoforms are activated by non-canonical Wnt5a in human EPC. Methodology/Principal Findings: Immunoblot experiments demonstrated that Wnt5a selectively activated the novel PKC isoform, PKC delta, as evidenced by phosphorylation and translocation. In contrast, the classical Ca2+-dependent PKC isoforms, PKC alpha and beta2, and one of the other novel PKC isoforms, PKC epsilon, were not activated by Wnt5a. The PKC delta inhibitor rottlerin significantly blocked co-culture-induced cardiac differentiation in vitro, whereas inhibitors directed against the classical Ca2+-dependent PKC isoforms or a PKC epsilon-inhibitory peptide did not block cardiac differentiation. In accordance, EPC derived from PKC delta heterozygous mice exhibited a significant reduction of Wnt5a-induced cardiac gene expression compared to wild type mice derived EPC. Conclusions/Significance: These data indicate that Wnt5a enhances cardiac gene expressions of EPC via an activation of PKC delta

γCOP Is Required for Apical Protein Secretion and Epithelial Morphogenesis in Drosophila melanogaster

Background: There is increasing evidence that tissue-specific modifications of basic cellular functions play an important role in development and disease. To identify the functions of COPI coatomer-mediated membrane trafficking in Drosophila development, we were aiming to create loss-of-function mutations in the γCOP gene, which encodes a subunit of the COPI coatomer complex. Principal Findings: We found that γCOP is essential for the viability of the Drosophila embryo. In the absence of zygotic γCOP activity, embryos die late in embryogenesis and display pronounced defects in morphogenesis of the embryonic epidermis and of tracheal tubes. The coordinated cell rearrangements and cell shape changes during tracheal tube morphogenesis critically depend on apical secretion of certain proteins. Investigation of tracheal morphogenesis in γCOP loss-of-function mutants revealed that several key proteins required for tracheal morphogenesis are not properly secreted into the apical lumen. As a consequence, γCOP mutants show defects in cell rearrangements during branch elongation, in tube dilation, as well as in tube fusion. We present genetic evidence that a specific subset of the tracheal defects in γCOP mutants is due to the reduced secretion of the Zona Pellucida protein Piopio. Thus, we identified a critical target protein of COPI-dependent secretion in epithelial tube morphogenesis. Conclusions/Significance: These studies highlight the role of COPI coatomer-mediated vesicle trafficking in both general and tissue-specific secretion in a multicellular organism. Although COPI coatomer is generally required for protein secretion, we show that the phenotypic effect of γCOP mutations is surprisingly specific. Importantly, we attribute a distinct aspect of the γCOP phenotype to the effect on a specific key target protein