Sectioned or whole otoliths? A global review of hard structure preparation techniques used in ageing sparid fishes

While otoliths are considered the most reliable structure to accurately age fish, a variety of otolith preparation techniques are available, which have consequences on the otolith’s optical properties and therefore interpretation of growth bands. Recently, numerous studies from a variety of authors have criticised the use of whole otoliths in ageing sparids with sectioned otoliths subsequently acknowledged as the most reliable preparation technique. Despite this criticism; ageing data is still being generated from whole otoliths and other unreliable structures such as scales. In an attempt to understand the severity of this issue we conducted a global literature review of otolith preparation protocols used for sparids. We identified global spatial inconsistencies in otolith preparation techniques with some regions predominately using methods other than sectioned otoliths to age sparids. The review highlights the need for a standardisation of otolith preparation methods and a move towards the use of sectioned otoliths, or at least valid support where alternative structures or preparation techniques are used. Given that large numbers of studies have been conducted on whole otoliths in certain regions, it may be necessary to revaluate the existing growth parameters to ensure that accurate information is incorporated into management structures

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US

This article contains supporting information online at http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2113561119/-/DCSupplemental.Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multi-model ensemble forecast that combined predictions from dozens of different research groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-week horizon 3-5 times larger than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.Integrative Biolog

Foundations of the Crazy Bastard Hypothesis: Nonviolent physical risk-taking enhances conceptualized formidability

Wilson and Daly's Young Male Syndrome thesis seeks to explain why young men are disproportionally involved in both violence and non-violent activities entailing a risk of injury or death. One interpretation of this thesis, which we term the Crazy Bastard Hypothesis, holds that the correlation between violence and other forms of physical risk-taking occurs because the latter behaviors inherently index the general propensity to take risks with one's life. In violent conflicts, individuals who are indifferent to the prospect of injury or death constitute dangerous adversaries, and valuable allies. Voluntary physical risk-taking may thus serve a signaling function such that risk-prone individuals are perceived as more formidable than risk-averse individuals. Prior work has demonstrated that relative formidability is represented using the dimensions of conceptualized size and strength, providing an avenue for testing the Crazy Bastard Hypothesis. In multiple studies conducted in two disparate societies, we demonstrate that physically risk-prone men are envisioned to be larger, stronger, and more violent than risk-averse men. A separate study reveals that such conceptualizations are unlikely to reflect actual correlations between size/strength and physical risk-proneness, and are instead plausibly interpreted as revealing the contribution of observed physical risk-proneness to assessments of relative formidability. © 2014 Elsevier Inc

Circulating microRNAs in sera correlate with soluble biomarkers of immune activation but do not predict mortality in ART treated individuals with HIV-1 infection: A case control study

Introduction: The use of anti-retroviral therapy (ART) has dramatically reduced HIV-1 associated morbidity and mortality. However, HIV-1 infected individuals have increased rates of morbidity and mortality compared to the non-HIV-1 infected population and this appears to be related to end-organ diseases collectively referred to as Serious Non-AIDS Events (SNAEs). Circulating miRNAs are reported as promising biomarkers for a number of human disease conditions including those that constitute SNAEs. Our study sought to investigate the potential of selected miRNAs in predicting mortality in HIV-1 infected ART treated individuals. Materials and Methods: A set of miRNAs was chosen based on published associations with human disease conditions that constitute SNAEs. This case: control study compared 126 cases (individuals who died whilst on therapy), and 247 matched controls (individuals who remained alive). Cases and controls were ART treated participants of two pivotal HIV-1 trials. The relative abundance of each miRNA in serum was measured, by RTqPCR. Associations with mortality (all-cause, cardiovascular and malignancy) were assessed by logistic regression analysis. Correlations between miRNAs and CD4+ T cell count, hs-CRP, IL-6 and D-dimer were also assessed. Results: None of the selected miRNAs was associated with all-cause, cardiovascular or malignancy mortality. The levels of three miRNAs (miRs -21, -122 and -200a) correlated with IL-6 while miR-21 also correlated with D-dimer. Additionally, the abundance of miRs -31, -150 and -223, correlated with baseline CD4+ T cell count while the same three miRNAs plus miR- 145 correlated with nadir CD4+ T cell count. Discussion: No associations with mortality were found with any circulating miRNA studied. These results cast doubt onto the effectiveness of circulating miRNA as early predictors of mortality or the major underlying diseases that contribute to mortality in participants treated for HIV-1 infection

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks

Development and Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

Ristola M. on työryhmien DAD Study Grp ; Royal Free Hosp Clin Cohort ; INSIGHT Study Grp ; SMART Study Grp ; ESPRIT Study Grp jäsen.Background Chronic kidney disease (CKD) is a major health issue for HIV-positive individuals, associated with increased morbidity and mortality. Development and implementation of a risk score model for CKD would allow comparison of the risks and benefits of adding potentially nephrotoxic antiretrovirals to a treatment regimen and would identify those at greatest risk of CKD. The aims of this study were to develop a simple, externally validated, and widely applicable long-term risk score model for CKD in HIV-positive individuals that can guide decision making in clinical practice. Methods and Findings A total of 17,954 HIV-positive individuals from the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) study with >= 3 estimated glomerular filtration rate (eGFR) values after 1 January 2004 were included. Baseline was defined as the first eGFR > 60 ml/min/1.73 m2 after 1 January 2004; individuals with exposure to tenofovir, atazanavir, atazanavir/ritonavir, lopinavir/ritonavir, other boosted protease inhibitors before baseline were excluded. CKD was defined as confirmed (>3 mo apart) eGFR In the D:A:D study, 641 individuals developed CKD during 103,185 person-years of follow-up (PYFU; incidence 6.2/1,000 PYFU, 95% CI 5.7-6.7; median follow-up 6.1 y, range 0.3-9.1 y). Older age, intravenous drug use, hepatitis C coinfection, lower baseline eGFR, female gender, lower CD4 count nadir, hypertension, diabetes, and cardiovascular disease (CVD) predicted CKD. The adjusted incidence rate ratios of these nine categorical variables were scaled and summed to create the risk score. The median risk score at baseline was -2 (interquartile range -4 to 2). There was a 1: 393 chance of developing CKD in the next 5 y in the low risk group (risk score = 5, 505 events), respectively. Number needed to harm (NNTH) at 5 y when starting unboosted atazanavir or lopinavir/ritonavir among those with a low risk score was 1,702 (95% CI 1,166-3,367); NNTH was 202 (95% CI 159-278) and 21 (95% CI 19-23), respectively, for those with a medium and high risk score. NNTH was 739 (95% CI 506-1462), 88 (95% CI 69-121), and 9 (95% CI 8-10) for those with a low, medium, and high risk score, respectively, starting tenofovir, atazanavir/ritonavir, or another boosted protease inhibitor. The Royal Free Hospital Clinic Cohort included 2,548 individuals, of whom 94 individuals developed CKD (3.7%) during 18,376 PYFU (median follow-up 7.4 y, range 0.3-12.7 y). Of 2,013 individuals included from the SMART/ESPRIT control arms, 32 individuals developed CKD (1.6%) during 8,452 PYFU (median follow-up 4.1 y, range 0.6-8.1 y). External validation showed that the risk score predicted well in these cohorts. Limitations of this study included limited data on race and no information on proteinuria. Conclusions Both traditional and HIV-related risk factors were predictive of CKD. These factors were used to develop a risk score for CKD in HIV infection, externally validated, that has direct clinical relevance for patients and clinicians to weigh the benefits of certain antiretrovirals against the risk of CKD and to identify those at greatest risk of CKD.Peer reviewe

Development of a Fully Convolutional Neural Network to Derive Surf-Zone Bathymetry from Close-Range Imagery of Waves in Duck, NC

Timely observations of nearshore water depths are important for a variety of coastal research and management topics, yet this information is expensive to collect using in situ survey methods. Remote methods to estimate bathymetry from imagery include using either ratios of multi-spectral reflectance bands or inversions from wave processes. Multi-spectral methods work best in waters with low turbidity, and wave-speed-based methods work best when wave breaking is minimal. In this work, we build on the wave-based inversion approaches, by exploring the use of a fully convolutional neural network (FCNN) to infer nearshore bathymetry from imagery of the sea surface and local wave statistics. We apply transfer learning to adapt a CNN originally trained on synthetic imagery generated from a Boussinesq numerical wave model to utilize tower-based imagery collected in Duck, North Carolina, at the U.S. Army Engineer Research and Development Center’s Field Research Facility. We train the model on sea-surface imagery, wave conditions, and associated surveyed bathymetry using three years of observations, including times with significant wave breaking in the surf zone. This is the first time, to the authors’ knowledge, an FCNN has been successfully applied to infer bathymetry from surf-zone sea-surface imagery. Model results from a separate one-year test period generally show good agreement with survey-derived bathymetry (0.37 m root-mean-squared error, with a max depth of 6.7 m) under diverse wave conditions with wave heights up to 3.5 m. Bathymetry results quantify nearshore bathymetric evolution including bar migration and transitions between single- and double-barred morphologies. We observe that bathymetry estimates are most accurate when time-averaged input images feature visible wave breaking and/or individual images display wave crests. An investigation of activation maps, which show neuron activity on a layer-by-layer basis, suggests that the model is responsive to visible coherent wave structures in the input images

Development of a Fully Convolutional Neural Network to Derive Surf-Zone Bathymetry from Close-Range Imagery of Waves in Duck, NC

Timely observations of nearshore water depths are important for a variety of coastal research and management topics, yet this information is expensive to collect using in situ survey methods. Remote methods to estimate bathymetry from imagery include using either ratios of multi-spectral reflectance bands or inversions from wave processes. Multi-spectral methods work best in waters with low turbidity, and wave-speed-based methods work best when wave breaking is minimal. In this work, we build on the wave-based inversion approaches, by exploring the use of a fully convolutional neural network (FCNN) to infer nearshore bathymetry from imagery of the sea surface and local wave statistics. We apply transfer learning to adapt a CNN originally trained on synthetic imagery generated from a Boussinesq numerical wave model to utilize tower-based imagery collected in Duck, North Carolina, at the U.S. Army Engineer Research and Development Center’s Field Research Facility. We train the model on sea-surface imagery, wave conditions, and associated surveyed bathymetry using three years of observations, including times with significant wave breaking in the surf zone. This is the first time, to the authors’ knowledge, an FCNN has been successfully applied to infer bathymetry from surf-zone sea-surface imagery. Model results from a separate one-year test period generally show good agreement with survey-derived bathymetry (0.37 m root-mean-squared error, with a max depth of 6.7 m) under diverse wave conditions with wave heights up to 3.5 m. Bathymetry results quantify nearshore bathymetric evolution including bar migration and transitions between single- and double-barred morphologies. We observe that bathymetry estimates are most accurate when time-averaged input images feature visible wave breaking and/or individual images display wave crests. An investigation of activation maps, which show neuron activity on a layer-by-layer basis, suggests that the model is responsive to visible coherent wave structures in the input images