Lessons to be learned by comparing integrated fisheries stock assessment models (SAMs) with integrated population models (IPMs)

AEP was partially funded by the Cooperative Institute for Climate, Ocean, & Ecosystem Studies (CICOES) under NOAA Cooperative Agreement NA15OAR4320063, Contribution No. 2023-1331.Integrated fisheries stock assessment models (SAMs) and integrated population models (IPMs) are used in biological and ecological systems to estimate abundance and demographic rates. The approaches are fundamentally very similar, but historically have been considered as separate endeavors, resulting in a loss of shared vision, practice and progress. We review the two approaches to identify similarities and differences, with a view to identifying key lessons that would benefit more generally the overarching topic of population ecology. We present a case study for each of SAM (snapper from the west coast of New Zealand) and IPM (woodchat shrikes from Germany) to highlight differences and similarities. The key differences between SAMs and IPMs appear to be the objectives and parameter estimates required to meet these objectives, the size and spatial scale of the populations, and the differing availability of various types of data. In addition, up to now, typical SAMs have been applied in aquatic habitats, while most IPMs stem from terrestrial habitats. SAMs generally aim to assess the level of sustainable exploitation of fish populations, so absolute abundance or biomass must be estimated, although some estimate only relative trends. Relative abundance is often sufficient to understand population dynamics and inform conservation actions, which is the main objective of IPMs. IPMs are often applied to small populations of conservation concern, where demographic uncertainty can be important, which is more conveniently implemented using Bayesian approaches. IPMs are typically applied at small to moderate spatial scales (1 to 104 km2), with the possibility of collecting detailed longitudinal individual data, whereas SAMs are typically applied to large, economically valuable fish stocks at very large spatial scales (104 to 106 km2) with limited possibility of collecting detailed individual data. There is a sense in which a SAM is more data- (or information-) hungry than an IPM because of its goal to estimate absolute biomass or abundance, and data at the individual level to inform demographic rates are more difficult to obtain in the (often marine) systems where most SAMs are applied. SAMs therefore require more 'tuning' or assumptions than IPMs, where the 'data speak for themselves', and consequently techniques such as data weighting and model evaluation are more nuanced for SAMs than for IPMs. SAMs would benefit from being fit to more disaggregated data to quantify spatial and individual variation and allow richer inference on demographic processes. IPMs would benefit from more attempts to estimate absolute abundance, for example by using unconditional models for capture-recapture data.Publisher PDFPeer reviewe

Can diagnostic tests help identify model misspecification in integrated stock assessments?

AbstractA variety of data types can be included in contemporary integrated stock assessments to simultaneously provide information on all estimated parameters. Conflicts between data, which are often a symptom of model misspecification and evident as model misfit, can affect the estimates of important parameters and derived quantities. Unfortunately, there are few standard diagnostic tools available for integrated stock assessment models that can provide the analyst with all the information needed to determine if there is substantial model misspecification. In this study, we use simulation methods to evaluate the ability of commonly-used and recently-proposed diagnostic tests to detect model misspecification in the observation model process (i.e., the incorrect form for survey selectivity), systems dynamics (i.e., incorrect assumed values for steepness of the stock-recruitment relationship and natural mortality), and incorrect data weighting. The diagnostic tests evaluated here were: i) residuals analysis (SDNR and runs test); ii) retrospective analysis; iii) the R0 likelihood component profile; iv) the age-structured production model (ASPM); and v) catch-curve analysis (CCA). The efficacy of the diagnostic tests depended on whether the misspecification was in the observation or systems dynamics model. Residual analyses were easily the best detector of misspecification of the observation model while the ASPM test was the only good diagnostic for detecting misspecification of system dynamics model. Retrospective analysis and the R0 likelihood component profile infrequently detected misspecified models, and CCA had a high probability of rejecting correctly-specified models. Finally, applying multiple carefully selected diagnostics can increase the power to detect misspecification without substantially increasing the probability of falsely concluding there is misspecification when the model is correctly specified

UGT1A1*28 genotype and irinotecan dosage in patients with metastatic colorectal cancer: a Dutch Colorectal Cancer Group study

The aim of the study was to investigate the associations between UGT1A1*28 genotype and (1) response rates, (2) febrile neutropenia and (3) dose intensity in patients with metastatic colorectal cancer treated with irinotecan. UGT1A1*28 genotype was determined in 218 patients receiving irinotecan (either first-line therapy with capecitabine or second-line as monotherapy) for metastatic colorectal cancer. TA7 homozygotes receiving irinotecan combination therapy had a higher incidence of febrile neutropenia (18.2%) compared to the other genotypes (TA6/TA6 : 1.5%; TA6/TA7 : 6.5%, P=0.031). TA7 heterozygotes receiving irinotecan monotherapy also suffered more febrile neutropenia (19.4%) compared to TA6/TA6 genotype (2.2%; P=0.015). Response rates among genotypes were not different for both regimens: combination regimen, P=0.537; single-agent, P=0.595. TA7 homozygotes did not receive a lower median irinotecan dose, number of cycles (P-values ⩾0.25) or more frequent dose reductions compared to the other genotypes (P-values for trend; combination therapy: 0.62 and single-agent: 0.45). Reductions were mainly (>80%) owing to grade ⩾3 diarrhoea, not (febrile) neutropenia. TA7/TA7 patients have a higher incidence of febrile neutropenia upon irinotecan treatment, but were able to receive similar dose and number of cycles compared to other genotypes. Response rates were not significantly different

Pharmacokinetics and Target Attainment of Ceftobiprole in Asian and Non-Asian Subjects

Ceftobiprole is a broad-spectrum cephalosporin. The objective of this study was to test the hypothesis that the pharmacokinetics (PK) and exposure of ceftobiprole in Asian subjects are similar to those in non-Asian subjects. Three approaches were followed. The first compared the individual PK estimates between the 2 subgroups derived from a population PK model previously built. Next, it was determined whether “Asian subject” was a significant covariate. Finally, a pharmacodynamic analysis was performed by comparing measures of exposure and target attainment. No significant differences were found between PK parameter estimates for Asian and non-Asian subjects, with median values (range) for clearance of 4.82 L/h (2.12–10.47) and 4.97 L/h (0.493–20.6), respectively (P =.736). “Asian subject” was not a significant covariate in the population PK model. There were no significant differences between the measures of exposure. The geometric mean ratio for the fAUC was 1.022 (90%CI, 0.91–1.15), indicating bioequivalence. Taking a target of 60% coverage of the dose interval, more than 90% of the population in both subgroups was adequately exposed. This analysis demonstrated that there are no PK or pharmacodynamic differences between Asian and non-Asian subjects for a ceftobiprole dose of 500 mg every 8 hours as a 2-hour infusion

Gastrointestinal ulceration as a possible side effect of bevacizumab which may herald perforation

Chemotherapy plus bevacizumab is currently considered as the standard 1st line treatment of advanced colorectal cancer (ACC). Whereas GI perforation is a known side effect of bevacizumab, the development of GI ulcers has not been reported. We identified 18 patients with ACC who participated in a phase III multicentre trial which included chemotherapy and bevacizumab, who developed a GI ulcer (n = 6), perforation (n = 8) or both (n = 4). The risk of developing a symptomatic GI ulcer or perforation was 1.3% and 1.6%, respectively. Central review of the histology specimens showed ulceration and/or granulation tissue with neovascularisation. The majority (89%) of events developed early during treatment. Given these observations, as well as the relationship between VEGF and mucosal injury healing, we suggest that GI ulcers may occur as a side effect of treatment with bevacizumab and may herald perforation

Estimating the abundance of marine mammal populations

Support for this project was provided by the Lenfest Ocean Program.Motivated by the need to estimate the abundance of marine mammal populations to inform conservation assessments, especially relating to fishery bycatch, this paper provides background on abundance estimation and reviews the various methods available for pinnipeds, cetaceans and sirenians. We first give an “entry-level” introduction to abundance estimation, including fundamental concepts and the importance of recognizing sources of bias and obtaining a measure of precision. Each of the primary methods available to estimate abundance of marine mammals is then described, including data collection and analysis, common challenges in implementation, and the assumptions made, violation of which can lead to bias. The main method for estimating pinniped abundance is extrapolation of counts of animals (pups or all-ages) on land or ice to the whole population. Cetacean and sirenian abundance is primarily estimated from transect surveys conducted from ships, small boats or aircraft. If individuals of a species can be recognized from natural markings, mark-recapture analysis of photo-identification data can be used to estimate the number of animals using the study area. Throughout, we cite example studies that illustrate the methods described. To estimate the abundance of a marine mammal population, key issues include: defining the population to be estimated, considering candidate methods based on strengths and weaknesses in relation to a range of logistical and practical issues, being aware of the resources required to collect and analyze the data, and understanding the assumptions made. We conclude with a discussion of some practical issues, given the various challenges that arise during implementation.Publisher PDFPeer reviewe

Experience in implementing harvest strategies in Australia's south-eastern fisheries

The Southern and Eastern Scalefish and Shark Fishery (SESSF) is a complex multi-species fishery, with 34 stock units under quota management, for which a harvest strategy framework was developed in 2005. The framework involves the application of a set of tier-based harvest control rules (HCR) designed to provide a precautionary approach to management. The harvest strategy framework has been applied from 2005 to 2007, resulting in substantial reductions in quotas across the fishery. The experience in implementing the framework, both positive and negative, is described, and general lessons are drawn. Key lessons include the importance of formally testing such strategies using management strategy evaluation, the impact of external management drivers on implementation of the approach, the need to define strategies for setting "bycatch quotas" in multi-species fisheries, and the need for flexibility and pragmatism in the early stages of implementing such an approach

Beyond gait speed: exploring the added value of Inertial Measurement Unit-based measurements of gait in the estimation of the walking ability in daily life

Background: Gait speed is often used to estimate the walking ability in daily life in people after stroke. While measuring gait with inertial measurement units (IMUs) during clinical assessment yields additional information, it remains unclear if this information can improve the estimation of the walking ability in daily life beyond gait speed. Objective: We evaluated the additive value of IMU-based gait features over a simple gait-speed measurement in the estimation of walking ability in people after stroke. Methods: Longitudinal data during clinical stroke rehabilitation were collected. The assessment consisted of two parts and was administered every three weeks. In the first part, participants walked for two minutes (2MWT) on a fourteen-meter path with three IMUs attached to low back and feet, from which multiple gait features, including gait speed, were calculated. The dimensionality of the corresponding gait features was reduced with a principal component analysis. In the second part, gait was measured for two consecutive days using one ankle-mounted IMU. Next, three measures of walking ability in daily life were calculated, including the number of steps per day, and the average and maximal gait speed. A gait-speed-only Linear Mixed Model was used to estimate the association between gait speed and each of the three measures of walking ability. Next, the principal components (PC), derived from the 2MWT, were added to the gait-speed-only model to evaluate if they were confounders or effect modifiers. Results: Eighty-one participants were measured during rehabilitation, resulting in 198 2MWTs and 135 corresponding walking-performance measurements. 106 Gait features were reduced to nine PCs with 85.1% explained variance. The linear mixed models demonstrated that gait speed was weakly associated with the average and maximum gait speed in daily life and moderately associated with the number of steps per day. The PCs did not considerably improve the outcomes in comparison to the gait speed only models. Conclusions: Gait in people after stroke assessed in a clinical setting with IMUs differs from their walking ability in daily life. More research is needed to determine whether these discrepancies also occur in non-laboratory settings, and to identify additional non-gait factors that influence walking ability in daily life

Reconceiving Reproductive Health

While reproduction is fairly often touched upon in theological and Christian ethical discussions, reproductive health is not. However, reproductive health is a matter of theological and ethical concern. Discussion pertaining to reproductive health includes a number of debates about, for instance, abortion and the termination of pregnancy, reproductive loss, childlessness, infertility, stillbirth, miscarriage and adoption. Additionally, new reproductive possibilities made available by the development of reproductive technology have necessitated theological and ethical reflection on, for example, surrogacy, post-menopausal pregnancies, litter births, single mothers or fathers by choice, in vitro fertilisation and the so-called saviour siblings. These new developments compel us to reconceive our notions of what reproductive health is or should be. Many of these topics are receiving increasing attention in a variety of theological publications. The focus of this volume is unique, however, and to the best of our knowledge, this is the first volume dealing not only with reproductive issues, but also reflecting theologically and ethically on reproductive health. It makes a contribution by providing a variety of perspectives from different theological fields on this theme, and in many chapters, focussing especially on the South African context. These discussions are also part of urgent debates within churches, which require developing life-giving theological language and imaginative theological alternatives that may speak to experiences of matters relating to reproductive health. The popular books, TV series and films that touch upon these discussions – including The Handmaid’s Tale and Mother! – strengthen the perception that a more in-depth theological and ethical discussion on the theme may be necessary, particularly towards exploring stories and confessions from our faith tradition that may provide us with a timely opportunity to do the important work of theological ‘reconceiving’

The glyceraldehyde-3-phosphate dehydrogenase gene of Moniliophthoraperniciosa, the causal agent of witches' broom disease of Theobroma cacao

This report describes the cloning, sequence and expression analysis of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene of Moniliophthora perniciosa, the most important pathogen of cocoa in Brazil. Southern blot analysis revealed the presence of a single copy of the GAPDH gene in the M. perniciosa genome (MpGAPDH). The complete MpGAPDH coding sequence contained 1,461 bp with eight introns that were conserved in the GAPDH genes of other basidiomycete species. The cis-elements in the promoter region of the MpGAPDH gene were similar to those of other basidiomycetes. Likewise, the MpGAPDH gene encoded a putative 339 amino acid protein that shared significant sequence similarity with other GAPDH proteins in fungi, plants, and metazoans. Phylogenetic analyses clustered the MPGAPDH protein with other homobasidiomycete fungi of the family Tricholomataceae. Expression analysis of the MpGAPDH gene by real-time PCR showed that this gene was more expressed (~1.3X) in the saprotrophic stage of this hemibiotrophic plant pathogen than in the biotrophic stage when grown in cacao extracts