scholarly journals Evidence of underestimation of European hake growth in the Bay of Biscay, and its relationship with bias in the agreed method of age estimation

2006 ◽  
Vol 63 (9) ◽  
pp. 1674-1681 ◽  
Author(s):  
Hélène de Pontual ◽  
Anne Laure Groison ◽  
Carmen Piñeiro ◽  
Michel Bertignac
Keyword(s):  
Age Estimation ◽  
Good Condition ◽  
Estimation Method ◽  
Somatic Growth ◽  
Biological Knowledge ◽  
Data Sets ◽  
Bay Of Biscay ◽  
Age Validation ◽  
Management Advice ◽  
European Hake

Abstract In 2002, a pilot experiment on hake tagging was carried out using methodology specifically developed to catch and handle fish in good condition. By the end of 2005, 36 hake and five tags had been returned to the laboratory (a 3.1% return rate) with a maximum time at liberty of 1066 days. The somatic growth of the recoveries proved to be twofold higher than that expected from published von Bertalanffy growth functions for the species in the Bay of Biscay. The growth underestimation was related to age overestimation, as demonstrated by two independent analyses. The first was based on a blind interpretation of marked otoliths conducted independently by two European experts involved in the routine age estimation of hake. The result shows that the age estimates were neither accurate (inconsistent with oxytetracycline mark positions) nor precise. The second approach compared the predicted otolith growth with the observed growth, and the discrepancy between the two data sets was large. Both types of analyses invalidate the internationally agreed age estimation method and demonstrate a need for further research. Although based on limited data, the study highlights the need to improve biological knowledge of the species in order to improve assessment and management advice. It also strengthens the argument for age validation.

scholarly journals Consequences of bias in age estimation on assessment of the northern stock of European hake (Merluccius merluccius) and on management advice

2007 ◽  
Vol 64 (5) ◽  
pp. 981-988 ◽  
Author(s):  
Michel Bertignac ◽  
Hélène de Pontual
Keyword(s):  
Age Estimation ◽  
Growth Parameters ◽  
Reference Points ◽  
Fishing Mortality ◽  
Merluccius Merluccius ◽  
Stock Biomass ◽  
Spawning Stock ◽  
Management Advice ◽  
The Impact ◽  
European Hake

Abstract Bertignac, M., and de Pontual, H. 2007. Consequences of bias in age estimation on assessment of the northern stock of European hake (Merluccius merluccius) and on management advice. – ICES Journal of Marine Science, 64: 981–988. The results of a pilot tagging study on hake (Merluccius merluccius), conducted in the northern part of the Bay of Biscay in 2002, indicate that growth rates for this stock may be currently underestimated because of biased estimates of age. The impact that such a bias may have on the stock dynamics and the trends of the key population parameters, recruitment, spawning-stock biomass (SSB), and mortality are investigated. Assuming new growth parameters, a new age–length key is derived and used to produce and catch-at-age data and abundance indices, which are then used to assess the stock. Bias in estimating age affects the absolute levels of fishing mortality and stock biomass estimates, and also impacts the trend in SSB. However, trends in fishing mortality and recruitment are comparable, and the stock status with respect to precautionary reference points is broadly the same. As expected, the simulation also shows that the stock may be more reactive to changes in fishing levels, which affect medium-term forecasts. Long-term sustainable yields may also be impacted.

scholarly journals Growth and Age Validation of the Thornback Ray (Raja clavata Linnaeus, 1758) in the South Adriatic Sea (Central Mediterranean)

2020 ◽  
Vol 7 ◽  
Author(s):  
Pierluigi Carbonara ◽  
Andrea Bellodi ◽  
Michele Palmisano ◽  
Antonello Mulas ◽  
Cristina Porcu ◽  
...  
Keyword(s):  
Age Estimation ◽  
Adriatic Sea ◽  
Seasonal Pattern ◽  
Estimation Method ◽  
Logistic Models ◽  
Age And Growth ◽  
Age Validation ◽  
The South ◽  
Central Mediterranean ◽  
Raja Clavata

Raja clavata is the most widespread and landed skate species in the Mediterranean Basin. Despite its diffusion and economic importance, several aspects of its life history, such as age and growth, are poorly understood. This study evaluated the species’ growth in the South Adriatic Sea (Central Mediterranean Sea) and for the first time attempted an age validation through a tagging experiment. Thin sectioning of vertebral centra proved to be a more accurate preparation method in terms of age estimation precision and reproducibility than whole vertebral centrum staining (cobalt nitrate and ammonium sulfide technique). Marginal analysis showed a clear seasonal pattern, confirming the hypothesis of a single annulus deposition per year. A total of 291 vertebral centra were sampled and used for age estimation purposes. The oldest female was estimated to be 12 years old [total length (TL) = 89 cm], while the oldest male was aged 8 years (TL = 79.9 cm). Females were also found to be characterized by a slightly wider longevity range (ωL = 11.5, ωU = 16.8 years) than males (ωL = 7.8, ωU = 11.2 years). The von Bertalanffy growth curve fit the age and length data more accurately than the Gompertz and logistic models. Eighty-three thornback rays were tagged and released, of which two were recaptured. In both recaptured specimens, oxytetracycline marks were clearly visible. The band deposition after oxytetracycline injection and growth during the freedom period (about 1 year) were consistent with the age estimation method and criteria used and with the obtained growth results. Thus, the analysis of the vertebral centra extracted from the two recaptured specimens confirmed the hypothesis of the deposition of a single annulus per year and in general the age estimation criteria used in this study.

scholarly journals A Raman algorithm to estimate human age from protein structural variations in autopsy skin samples: a protein biological clock

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daisuke Miyamori ◽  
Takeshi Uemura ◽  
Wenliang Zhu ◽  
Kei Fujikawa ◽  
Takaaki Nakaya ◽  
...  
Keyword(s):  
Protein Folding ◽  
Age Estimation ◽  
Mean Squared Error ◽  
Pearson Correlation ◽  
Biological Clock ◽  
Estimation Method ◽  
Forensic Identification ◽  
Random Coil ◽  
Coefficient Of Determination ◽  
Skin Samples

AbstractThe recent increase of the number of unidentified cadavers has become a serious problem throughout the world. As a simple and objective method for age estimation, we attempted to utilize Raman spectrometry for forensic identification. Raman spectroscopy is an optical-based vibrational spectroscopic technique that provides detailed information regarding a sample’s molecular composition and structures. Building upon our previous proof-of-concept study, we measured the Raman spectra of abdominal skin samples from 132 autopsy cases and the protein-folding intensity ratio, RPF, defined as the ratio between the Raman signals from a random coil an α-helix. There was a strong negative correlation between age and RPF with a Pearson correlation coefficient of r = 0.878. Four models, based on linear (RPF), squared (RPF2), sex, and RPF by sex interaction terms, were examined. The results of cross validation suggested that the second model including linear and squared terms was the best model with the lowest root mean squared error (11.3 years of age) and the highest coefficient of determination (0.743). Our results indicate that the there was a high correlation between the age and RPF and the Raman biological clock of protein folding can be used as a simple and objective forensic age estimation method for unidentified cadavers.

scholarly journals An edge-cloud collaboration architecture for pattern anomaly detection of time series in wireless sensor networks

2021 ◽  
Author(s):  
Cong Gao ◽  
Ping Yang ◽  
Yanping Chen ◽  
Zhongmin Wang ◽  
Yue Wang
Keyword(s):  
Time Series ◽  
Wireless Sensor Networks ◽  
Sensor Networks ◽  
Anomaly Detection ◽  
Estimation Method ◽  
Feature Representation ◽  
Sensor Data ◽  
Wireless Sensor ◽  
Data Sets ◽  
Edge Node

AbstractWith large deployment of wireless sensor networks, anomaly detection for sensor data is becoming increasingly important in various fields. As a vital data form of sensor data, time series has three main types of anomaly: point anomaly, pattern anomaly, and sequence anomaly. In production environments, the analysis of pattern anomaly is the most rewarding one. However, the traditional processing model cloud computing is crippled in front of large amount of widely distributed data. This paper presents an edge-cloud collaboration architecture for pattern anomaly detection of time series. A task migration algorithm is developed to alleviate the problem of backlogged detection tasks at edge node. Besides, the detection tasks related to long-term correlation and short-term correlation in time series are allocated to cloud and edge node, respectively. A multi-dimensional feature representation scheme is devised to conduct efficient dimension reduction. Two key components of the feature representation trend identification and feature point extraction are elaborated. Based on the result of feature representation, pattern anomaly detection is performed with an improved kernel density estimation method. Finally, extensive experiments are conducted with synthetic data sets and real-world data sets.

scholarly journals Framework for Reconstruction of Pseudo Quad Polarimetric Imagery from General Compact Polarimetry

2021 ◽  
Vol 13 (3) ◽  
pp. 530
Author(s):  
Junjun Yin ◽  
Jian Yang
Keyword(s):  
Linear Equations ◽  
Estimation Method ◽  
Data Sets ◽  
Reconstruction Procedure ◽  
Component Decomposition ◽  
Reconstruction Methods ◽  
Sar Imagery ◽  
Key Aspects ◽  
Non Linear Equations ◽  
Reconstruction Model

Pseudo quad polarimetric (quad-pol) image reconstruction from the hybrid dual-pol (or compact polarimetric (CP)) synthetic aperture radar (SAR) imagery is a category of important techniques for radar polarimetric applications. There are three key aspects concerned in the literature for the reconstruction methods, i.e., the scattering symmetric assumption, the reconstruction model, and the solving approach of the unknowns. Since CP measurements depend on the CP mode configurations, different reconstruction procedures were designed when the transmit wave varies, which means the reconstruction procedures were not unified. In this study, we propose a unified reconstruction framework for the general CP mode, which is applicable to the mode with an arbitrary transmitted ellipse wave. The unified reconstruction procedure is based on the formalized CP descriptors. The general CP symmetric scattering model-based three-component decomposition method is also employed to fit the reconstruction model parameter. Finally, a least squares (LS) estimation method, which was proposed for the linear π/4 CP data, is extended for the arbitrary CP mode to estimate the solution of the system of non-linear equations. Validation is carried out based on polarimetric data sets from both RADARSAT-2 (C-band) and ALOS-2/PALSAR (L-band), to compare the performances of reconstruction models, methods, and CP modes.

scholarly journals The Weibull Birnbaum-Saunders Distribution And Its Applications

2020 ◽  
Vol 9 (1) ◽  
pp. 61-81
Author(s):  
Lazhar BENKHELIFA
Keyword(s):  
Maximum Likelihood ◽  
Estimation Method ◽  
Likelihood Estimation ◽  
Real Data ◽  
Reliability Estimation ◽  
Maximum Likelihood Estimates ◽  
Model Parameters ◽  
Data Sets ◽  
Proposed Model ◽  
Modeling Data

A new lifetime model, with four positive parameters, called the Weibull Birnbaum-Saunders distribution is proposed. The proposed model extends the Birnbaum-Saunders distribution and provides great flexibility in modeling data in practice. Some mathematical properties of the new distribution are obtained including expansions for the cumulative and density functions, moments, generating function, mean deviations, order statistics and reliability. Estimation of the model parameters is carried out by the maximum likelihood estimation method. A simulation study is presented to show the performance of the maximum likelihood estimates of the model parameters. The flexibility of the new model is examined by applying it to two real data sets.

scholarly journals Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity

2020 ◽  
Author(s):  
Lei Deng ◽  
Yideng Cai ◽  
Wenhao Zhang ◽  
Wenyi Yang ◽  
Bo Gao ◽  
...  
Keyword(s):  
Neural Network ◽  
Cancer Cells ◽  
Drug Targets ◽  
Deep Neural Network ◽  
Drug Sensitivity ◽  
Predictive Ability ◽  
Biological Knowledge ◽  
Data Sets ◽  
Source Codes ◽  
Sensitivity Data

AbstractMotivationTo efficiently save cost and reduce risk in drug research and development, there is a pressing demand to develop in-silico methods to predict drug sensitivity to cancer cells. With the exponentially increasing number of multi-omics data derived from high-throughput techniques, machine learning-based methods have been applied to the prediction of drug sensitivities. However, these methods have drawbacks either in the interpretability of mechanism of drug action or limited performance in modeling drug sensitivity.ResultsIn this paper, we presented a pathway-guided deep neural network model, referred to as pathDNN, to predict the drug sensitivity to cancer cells. Biological pathways describe a group of molecules in a cell that collaborates to control various biological functions like cell proliferation and death, thereby abnormal function of pathways can result in disease. To make advantage of both the excellent predictive ability of deep neural network and the biological knowledge of pathways, we reshape the canonical DNN structure by incorporating a layer of pathway nodes and their connections to input gene nodes, which makes the DNN model more interpretable and predictive compared to canonical DNN. We have conducted extensive performance evaluations on multiple independent drug sensitivity data sets, and demonstrate that pathDNN significantly outperformed canonical DNN model and seven other classical regression models. Most importantly, we observed remarkable activity decreases of disease-related pathway nodes during forward propagation upon inputs of drug targets, which implicitly corresponds to the inhibition effect of disease-related pathways induced by drug treatment on cancer cells. Our empirical experiments show that pathDNN achieves pharmacological interpretability and predictive ability in modeling drug sensitivity to cancer cells.AvailabilityThe web server, as well as the processed data sets and source codes for reproducing our work, is available at http://pathdnn.denglab.org

scholarly journals Benchmarking Statistical Multiple Sequence Alignment

2018 ◽  
Author(s):  
Michael Nute ◽  
Ehsan Saleh ◽  
Tandy Warnow
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Structural Alignment ◽  
Estimation Method ◽  
Simulated Data ◽  
Protein Sequences ◽  
Data Sets ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Simulated Data Sets

AbstractThe estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the most popular protein alignment methods as well as the statistical co-estimation method BAli-Phy on 1192 protein data sets from established benchmarks as well as on 120 simulated data sets. Our study (which used more than 230 CPU years for the BAli-Phy analyses alone) shows that BAli-Phy is dramatically more accurate than the other alignment methods on the simulated data sets, but is among the least accurate on the biological benchmarks. There are several potential causes for this discordance, including model misspecification, errors in the reference alignments, and conflicts between structural alignment and evolutionary alignments; future research is needed to understand the most likely explanation for our observations. multiple sequence alignment, BAli-Phy, protein sequences, structural alignment, homology

scholarly journals Age estimation, growth and maturity of the European hake (Merluccius merluccius (Linnaeus, 1758)) from Iberian Atlantic waters

2003 ◽  
Vol 60 (5) ◽  
pp. 1086-1102 ◽  
Author(s):  
C Piñeiro ◽  
M Saínza
Keyword(s):  
Life History ◽  
Age Estimation ◽  
Growth Parameters ◽  
Grey Literature ◽  
Von Bertalanffy ◽  
Merluccius Merluccius ◽  
Consistent Manner ◽  
The Mean ◽  
First Maturity ◽  
European Hake

Abstract Difficulties in age estimation for hake (Merluccius merluccius) have hampered the assessment of stocks. Here, we describe new, agreed ageing criteria based on the interpretation of the pattern of otolith growth. Improved estimates of von Bertalanffy growth parameters, and new estimates of maturity ogive parameters and length–weight relationships for European hake from Iberian Atlantic waters are presented. The results came from a study carried out during 1996–1997 and provide the first published account of the main life history traits of Southern stock hake. von Bertalanffy growth parameters of males were L∞ = 70cm, K = 0.18 year−1, and t0=−0.97 year, and those of females were L∞ = 89cm, K = 0.13 year−1, and t0 = −1.15 year. Growth of sexes differed from age 3 onwards, with females being on average larger and heavier than males. The estimated total length (L, cm)–total weight (W, g) relationships were W=0.0132135L2.8134246 for males and W=0.0086471L2.942563 for females. Spawning took place from December to May with a peak in February. The mean length and age at first maturity were 32.8 cm at 2.5 years for males and 45 cm at 4.4 years for females. Application of new ageing criteria showed that otolith sections may be used to determine ages up to 5 years in a consistent manner. These results indicate that hake of the Southern stock grow at higher rates and mature earlier than previously considered. Summaries of hake's life history parameters from other marine regions are also presented in order to make information that belongs largely to the grey literature available.

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