Bias in common catch-curve methods applied to age frequency data from fish surveys

2019 ◽  
Vol 76 (7) ◽  
pp. 2090-2101
Author(s):  
Gary A Nelson
Keyword(s):  
Linear Regression ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Standard Errors ◽  
Cluster Sampling ◽  
Probability Models ◽  
Generalized Poisson ◽  
Random Intercept ◽  
Multi Stage ◽  
Wide Range

Abstract Catch curve analysis is often used in data-limited fisheries stock assessments to estimate total instantaneous mortality (Z). There are now six catch-curve methods available in the literature: the Chapman–Robson, linear regression, weighted linear regression, Heincke, generalized Poisson linear, and random-intercept Poisson linear mixed model. An assumption shared among the underyling probability models of these estimators is that fish collected for ageing are sampled from the population by simple random sampling. This type of sampling is nearly impossible in fisheries research because populations are sampled in surveys that use gears that capture individuals in clusters and often fish for ageing are selected from multi-stage sampling. In this study, I explored the effects of multi-stage cluster sampling on the bias of the estimates of Z and their associated standard errors. I found that the generalized Poisson linear model and the Chapman–Robson estimators were the least biased, whereas the random-intercept Poisson linear mixed model was the most biased under a wide range of simulation scenarios that included different levels of recruitment variation, intra-cluster correlation, sample sizes, and methods used to generate age frequencies. Standard errors of all estimators were under-estimated in almost all cases and should not be used in statistical comparisons.

P0786CLINICAL SIGNIFICANCE AND RELATED FACTORS OF GFR SLOPE IN A LARGE MULTICENTER OBSERVATIONAL STUDY IN JAPAN

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Yuji Kamijo ◽  
Koji Hashimoto ◽  
Yosuke Yamada ◽  
Makoto Harada ◽  
Masatsugu Aida ◽  
...  
Keyword(s):  
Linear Regression ◽  
Least Squares ◽  
Clinical Significance ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Surrogate Marker ◽  
Hazard Ratio ◽  
Related Factors ◽  
Ckd Stage ◽  
Egfr Decline

Abstract Background and Aims Recently, glomerular filtration rate (GFR) slope has attracted attention as an important surrogate marker for the prognosis of chronic kidney disease (CKD), with a reduction in slope of eGFR decline by 0.75 mL/min/1.73 m2 per year reportedly having clinical significance. As few large clinical studies on Japanese CKD patients exist, this investigation addresses the clinical significance of GFR slope and its related factors. Method To evaluate the clinical impact of GFR slope, we conducted a prognostic investigation of CKD patients in Japan by means of a large, multicenter, retrospective, observational study. Patients with CKD who were seen at among 15 general hospitals between January and March 2014 were surveyed using medical records. The selection criteria were age ≥20 years, estimated GFR (eGFR) <60 mL/min/1.73 m2, and receiving medical treatment for CKD. Baseline patient characteristics, eGFR changes, and hard endpoints (death or end-stage kidney disease requiring renal replacement therapy) during observation were analysed. We calculated GFR slope using GFR data of 2 years following the observation start point by 2 calculation methods, the linear mixed model and least squares linear regression, and examined the relationship of GFR slope with the hazard ratio of the composite hard endpoints. The factors related to GFR slope were also assessed by multiple regression analysis. Results Among a total of 11233 collected patients, we analyzed the data of 7490 CKD G3 and G4 patients whose GFR data during 2 years could be obtained (60% male, mean age: 71 years, CKD G3a: 55%, G3b: 30%, G4: 15%, mean eGFR: 44.1 mL/min/1.73 m2, urine protein positive: 51%, diabetes mellitus: 49%, use of RAS inhibitors: 57%). The mean observation period was 1040 days. Hard endpoints after the GFR slope measurement period occurred in 301 subjects. The GFR slope of the cohort was -0.948 mL/min/1.73 m2 per year (95% confidence interval [CI] -1.016, -0.880) in the linear mixed model and -0.982 mL/min/1.73 m2 per year (95% CI -1.075, -0.889) according to least squares linear regression. Both calculated GFR slopes were significantly related to the hazard ratio of the composite hard endpoints. Hazard ratio decreased by 0.85 (linear mixed model) and 0.9 (least squares linear regression) times in case of a reduction in slope of eGFR decline by 0.75 mL/min/1.73 m2 per year. Multiple regression analysis revealed strongly significant associations for GFR slope with urine protein and CKD stage and undetectable relationships for GFR slope with diabetes and age. Conclusion This study demonstrated the clinical significance of GFR slope as a surrogate marker for renal prognosis in Japanese CKD patients. In order to reduce slope of eGFR decline, active intervention for proteinuria before the progression to an advanced CKD stage appears to be effective.

scholarly journals Estimation of mean movement rates for blue sharks in the northwestern Pacific Ocean

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Mikihiko Kai ◽  
Yuki Fujinami
Keyword(s):  
Pacific Ocean ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Movement Direction ◽  
Northwestern Pacific ◽  
Migratory Species ◽  
Northwestern Pacific Ocean ◽  
Movement Rate ◽  
Movement Rates ◽  
Wide Range

Abstract Background The blue shark Prionace glauca is a highly migratory species with a circumglobal distribution. Mean movement rate, defined by the horizontal tracking distance between two data points over the duration of time, is commonly used to understand the horizontal displacement of highly migratory species across a wide range. However, the estimation of mean movement rates for blue sharks has never been conducted using a statistical model. We therefore investigated the mean movement rates using a generalized linear mixed model with data from satellite tags to estimate the range of mean movement rates for 10 blue sharks in the northwestern Pacific Ocean and to reveal the interaction of mean movement rate with several factors. Results (1) Estimations of mean movement rates for the 10 blue sharks were significantly influenced by behavioral differences among individuals; (2) uncertainty in the estimation (i.e., predictive and confidence intervals) of mean movement rates for these blue sharks was larger over shorter time periods, and (3) the predictive intervals of mean movement rates for the sharks ranged widely from 0.33 to 5.02 km/h. Conclusion Blue sharks are considered to opportunistically change their mean movement rates regardless of differences in sex, movement direction, or season.

Tone, Rhythm, and Timbre Perception in School-Age Children Using Cochlear Implants and Hearing Aids

2013 ◽  
Vol 24 (09) ◽  
pp. 789-806 ◽  
Author(s):  
Hamish Innes-Brown ◽  
Jeremy P. Marozeau ◽  
Christine M. Storey ◽  
Peter J. Blamey
Keyword(s):  
Hearing Loss ◽  
Hearing Aids ◽  
Repeated Measures ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
School Age Children ◽  
Impaired Hearing ◽  
School Year ◽  
Temporal Cues ◽  
Wide Range

Background: Children with hearing impairments, especially those using hearing devices such as the cochlear implant (CI) or hearing aid (HA), are sometimes not encouraged to attend music classes, as they or their parents and teachers may be unsure whether the child can perform basic musical tasks. Purpose: The objective of the current study was to provide a baseline for the performance of children using CIs and HAs on standardized tests of rhythm and pitch perception as well as an instrument timbre identification task. An additional aim was to determine the effect of structured music training on these measures during the course of a school year. Research Design: The Intermediate Measures of Music Audiation (IMMA) Tonal and Rhythmic subtests were administered four times, with 6 wk between tests. All children in the study were also enrolled in “Music Club” teaching sessions. Measures were compared between groups and across the four testing sessions. Study Sample: Twenty children from a single school in Melbourne, Australia, were recruited. Eleven (four girls) had impaired hearing, including six with a unilateral CI or CI and HA together (two girls) and five with bilateral HAs (two girls). Nine were normally hearing, selected to match the age and gender of the hearing-impaired children. Ages ranged from 9–13 yr. Intervention: All children participated in a weekly Music Club – a 45 min session of musical activities based around vocal play and the integration of aural, visual, and kinesthetic modes of learning. Data Collection and Analysis: Audiological data were collected from clinical files. IMMA scores were converted to percentile ranks using published norms. Between-group differences were tested using repeated-measures analysis of variance, and between-session differences were tested using a linear mixed model. Linear regression was used to model the effect of hearing loss on the test scores. Results: In the first session, normally hearing children had a mean percentile rank of ˜50 in both the Tonal and Rhythmic subtests of the IMMA. Children using CIs showed trends toward lower scores in the Tonal, but not the Rhythmic, subtests. No significant improvements were found between sessions. In the timbre test, children generally made fewer errors within the set of percussive compared to nonpercussive instruments. The hearing loss level partially predicted performance in the Tonal, but not the Rhythmic, task, and predictions were more significant for nonpercussive compared to percussive instruments. Conclusions: The findings highlight the importance of temporal cues in the perception of music, and indicate that temporal cues may be used by children with CIs and HAs in the perception of not only rhythm, but also of some aspects of timbre. We were not able to link participation in the Music Club with increased scores on the Tonal, Rhythmic, and Timbre tests. However, anecdotal evidence from the children and their teachers suggested a wide range of benefits from participation in the Music Club that extended from increased engagement and interest in music classes into the children's social situations.

scholarly journals Linear mixed model for weight analysis in mice infected by Trypanosoma cruzi

2020 ◽  
Vol 42 ◽  
pp. e49916
Author(s):  
Roney Peterson Pereira ◽  
Terezinha Aparecida Guedes ◽  
Érika Cristina Ferreira ◽  
Silvana Marques de Araújo ◽  
Larissa Aparecida Ricardini ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Hierarchical Linear Modeling ◽  
Fixed Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Ratio Test ◽  
Linear Modeling ◽  
Components Of Variance ◽  
Treatment Groups ◽  
Random Intercept

The use of linear mixed models for nested structure longitudinal data is called hierarchical linear modeling. This modeling takes into account the dependence of existing data within each level and between hierarchical levels. The process of modeling, estimating and analyzing diagnoses was illustrated through data on the weights of mice experimentally infected by Trypanosoma cruzi, divided into different treatment groups, with the purpose of verifying the evolution of their body weight as a result of using different types of biotherapeutics produced from Gallus gallus domesticus (chicken) serum to treat Trypanosoma cruzi. Through the model selection criteria AIC and BIC and the likelihood ratio test, a model was chosen to describe the data correctly. Model diagnoses were then performed by means of residual analysis for both levels and an analysis of influential observations to verify if any observations were signaled as influencing the fixed effects, the components of variance and the adjusted values. After the analysis, it was possible to notice that the observations that were signaled as influential had little impact on the Model chosen initially, so it was maintained, with no differences being evidenced between the treatments with the biotherapeutics tested; only the Time variable and the Random intercept were necessary to describe the weight of the mice.

Using mobile wearables to establish sleep bioprofiles in newly diagnosed multiple myeloma (MM) patients.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 8040-8040
Author(s):  
Gil Hevroni ◽  
Donna Mastey ◽  
Elizabet Tavitian ◽  
Andriy Derkach ◽  
Meghan Salcedo ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Well Being ◽  
Cycle Period ◽  
Newly Diagnosed ◽  
Sleep Patterns ◽  
Sleep Monitoring ◽  
Random Intercept ◽  
Sleep Measurement ◽  
Insight Into

8040 Background: Passive monitoring using wearables can objectively measure sleep over extended time periods. MM patients (PTs) are susceptible to fluctuating sleep patterns due to pain and dexamethasone (dex) treatment. In this prospective study, we remotely monitored sleep patterns on 40 newly diagnosed MM (NDMM) PTs while administering electronic PT reported outcome (ePRO) surveys. The study aim was to establish sleep bioprofiles during therapy and correlate with ePROs. Methods: Eligible PTs for the study had untreated NDMM and assigned to either Cohort A – PTs < 65 years or Cohort B – PTs ≥ 65 years. PTs were remotely monitored for sleep 1-7 days at baseline [BL] and continuously up to 6 therapy cycles. PTs completed ePRO surveys (EORTC - QLQC30 and MY20) at BL and after each cycle. Sleep data and completed ePRO surveys were synced to Medidata Rave through Sensorlink technology. Associations between sleep measurement trends and QLQC30 scores were estimated using a linear mixed model with a random intercept. Results: Between Feb 2017 - Sep 2019, 40 PTs (21 M and 19 F) were enrolled with 20 in cohort A (mean 54 yrs, 41-64) and 20 in cohort B (mean 71 yrs, 65-82). Regimens included KRd 14(35%), RVd 12(30%), Dara-KRd 8(20%), VCd 5(12.5%), and Rd 1(2.5%). Sleep data was compiled among 23/40 (57.5%) PTs. BL mean sleep was 578.9 min/24 hr for Cohort A vs. 544.9 min/24 hr for Cohort B (p = 0.41, 95% CI -51.5, 119.5). Overall median sleep trends changed for cohort A by -6.3 min/24 hr per cycle (p = 0.09) and for cohort B by +0.8 min/24 hr per cycle (p = 0.88). EPRO data trends include global health +1.5 score/cycle (p = 0.01, 95% CI 0.31, 3.1), physical +2.16 score/cycle (p < 0.001, 95% CI 1.26, 3.07), insomnia -1.6 score/cycle (p = 0.09, 95% CI [-3.47, 0.26]), role functioning +2.8 score/cycle (p = 0.001, 95% CI 1.15, 4.46), emotional +0.3 score/cycle (p = 0.6, 95% CI -0.73, 1.32), cognitive -0.36 score/cycle (p = 0.44, 95% CI -1.29,0.56), and fatigue -0.36 score/cycle (p = 0.4, 95% CI -1.65, 0.93). No association between sleep measurements and ePRO were detected. Difference in sleep on dex days compared to all other days during the sample cycle period for cohort A was 81.4 min/24 hr (p = 0.004, 95% CI 26, 135) and for cohort B was 37.4 min/24 hr (p = 0.35, 95% CI -41, 115). Conclusions: Our study provides insight into wearable sleep monitoring in NDMM. Overall sleep trends in both cohorts do not demonstrate significant gains or losses, and these trends fit with HRQOL ePRO insomnia responses. Upon further examination, we demonstrate objective differences (younger PTs) in intra-cyclic sleep measurements on dex days compared to other cycle days (less sleep by > 1 hr). For older patients, less variation in sleep profiles was detected during dex days, possibly due to higher levels of fatigue or longer sleep duration. Sleep is an integral part of well-being in the cancer patient. Future studies should continue to characterize sleep patterns as it relates to HRQOL.

32 CLONING OF ELITE QUARANTINE SNIFFING DOG BY SOMATIC CELL NUCLEAR TRANSFER

2013 ◽  
Vol 25 (1) ◽  
pp. 164
Author(s):  
H. J. Oh ◽  
M. J. Kim ◽  
G. A. Kim ◽  
J. Choi ◽  
E. J. Park ◽  
...  
Keyword(s):  
Somatic Cell ◽  
Somatic Cell Nuclear Transfer ◽  
Nuclear Transfer ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Assisted Reproductive Technologies ◽  
Reproductive Technologies ◽  
Donor Cells ◽  
Wide Range ◽  
Sound Sensitivity

Somatic cell nuclear transfer (SCNT) in assisted reproductive technologies has been considered for the conservation of valuable or endangered animals. Dogs that were originally bred for hunting, such as beagles, have an exceptional ability to detect a particular smell from many others. For that reason, the beagles have been used to detect quarantine risk items from a wide range of goods in assorted luggage without scaring or disrupting the passengers. Though very useful and highly in need, elite quarantine sniffing beagles with excellent abilities are rare; much time, effort, and money are required in producing them. Here, we have applied SCNT for propagation of elite quarantine sniffing dogs to save time and economic burden. Ear fibroblasts from a 10-year-old adult male elite quarantine sniffing beagle were isolated and cultured in vitro as donor cells. For SCNT, in vivo-matured oocytes, obtained by flushing the uterine tubes of oocyte donors (mixed breed), were used. The oocytes were enucleated, microinjected with donor cells, fused by electrical stimulation, and activated chemically. Reconstructed oocytes were surgically transferred into the uterine tube of naturally synchronous recipient females. A total of 212 activated cloned embryos were transferred into 12 female recipient dogs and 4 recipients became pregnant. The 4 pregnant recipients delivered 4 pups through caesarean section or natural delivery, but 1 died right after birth and did not show an abnormality. Other live puppies exhibited normal phenotypes; their appearance was similar to that of the donor dog. All cloned pups were genetically identical to the donor dog and their mitochondrial DNA was from their oocyte donor dogs. When the cloned pups were 16 weeks old, we conducted a Volhard test, which is commonly used to describe the following puppy aptitudes: social attraction, following, restraint, social dominance, elevation dominance, retrieving, touch sensitivity, sound sensitivity, and sight sensitivity. Dog behavior data on differences in transcript abundance were analyzed by a general linear mixed model. The 3 cloned pups showed similar behavioral tendencies. The present study demonstrates that NT technique using donor cell derived from 1 elite quarantine sniffing dog is useful to produce a large number of quarantine sniffing dogs. This study was supported by RDA (no. PJ0089752012), RNL Bio (no. 550-20120006), IPET (no. 311062-04-1-SB010), Research Institute for Veterinary Science, Nestlé Purina Korea, and TS Corporation.

scholarly journals The effect of improved dietary control on cognitive and psychiatric functioning in adults with phenylketonuria: the ReDAPT study

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Nicholas M. Burgess ◽  
Wendy Kelso ◽  
Charles B. Malpas ◽  
Toby Winton-Brown ◽  
Timothy Fazio ◽  
...  
Keyword(s):  
Cognitive Function ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Psychiatric Morbidity ◽  
Negative Relationship ◽  
Anxiety And Depression ◽  
Dietary Control ◽  
Wide Range ◽  
Psychiatric Sequelae ◽  
Depression Ratings

Abstract Background Phenylketonuria (PKU) is an autosomal recessive inherited disorder characterised by a deficiency in phenylalanine hydroxylase. Untreated, PKU is associated with a wide range of cognitive and psychiatric sequelae. Contemporary management guidelines recommend lifetime dietary control of phenylalanine (Phe) levels, however many individuals who discontinue dietary control subsequently suffer symptoms of anxiety, depression and disturbances to cognition. We undertook a prospective cohort study of patients with early-treated phenylketonuria who had ceased dietary control to test the hypothesis that resumption of dietary control of PKU is associated with improvements in measures of psychiatric morbidity and cognitive functioning. Methods We re-initiated dietary control for early-treated patients with PKU and monitored cognitive and psychiatric outcomes over a twelve-month period. Assessments included objective cognitive function (measured by cognitive proficiency index (CPI)), anxiety and depression scales. General linear mixed model (GLMM) analyses were performed to assess change in psychometric variables from baseline over twelve months after resumption of dietary control. Results A total of nine patients were recruited. Mean age was 33 years (SD = 8.75), five were female. Mean time off dietary control was 19.1 years (SD = 11.3), and mean baseline phenylalanine (Phe) levels were 1108 µmol/L (SD = 293). GLMM analysis demonstrated a positive relationship between CPI and time on diet (b = 0.56 [95% CI = 0.17, 0.95]). Age, time off diet, Phe levels and depression scores were not associated with cognitive function. There was a negative relationship between time on diet and anxiety (b = − 0.88 95% CI = [− 1.26, − 0.50]) and depression ratings (b = − 0.61, 95% CI = [− 0.95, − 0.26]). Conclusions This study demonstrated improvements in cognitive function, anxiety, and depression ratings associated with resumption of dietary control of PKU. Raw Phe levels were not strongly associated with psychiatric or cognitive scores in this cohort. These findings support the importance of lifelong treatment for PKU in improving the cognitive and psychiatric sequelae of the disease.

A better estimator of mortality rate from age-frequency data

2015 ◽  
Vol 72 (3) ◽  
pp. 364-375 ◽  
Author(s):  
Russell B. Millar
Keyword(s):  
Population Dynamics ◽  
Population Model ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Weighted Regression ◽  
Frequency Data ◽  
Cross Sectional ◽  
Wide Range ◽  
Regression Estimators

The Chapman–Robson and weighted-regression estimators are currently the two preferred methods for estimation of instantaneous mortality, z, from a cross-sectional sample of age-frequency data. They are derived under the assumption of steady-state population dynamics. Here, a new estimator is developed from a population model that explicitly includes annual variability in recruitment. The new estimator is trivial to implement using existing generalized linear mixed model software. It is vastly superior to both the Chapman–Robson and weighted-regression estimators under a wide range of simulation scenarios in which sources of variability include partial recruitment to the fishery, autocorrelated annual recruitment, variability in annual survival, ageing error, and sampling randomness. All estimators produced confidence intervals that had lower actual coverage than their nominal 95% coverage. Nonetheless, the new estimator had the highest actual coverage, and under some scenarios this was achieved with a narrowest confidence interval.

scholarly journals 576Is the method of longitudinal data analysis equally relevant for common versus uncommon endpoints?

2021 ◽  
Vol 50 (Supplement_1) ◽  
Author(s):  
Moleen Dzikiti ◽  
Barbara Laughton ◽  
Steve Innes ◽  
Mark Cotton
Keyword(s):  
Antiretroviral Treatment ◽  
Viral Suppression ◽  
Mixed Model ◽  
Infant Health ◽  
Linear Mixed Model ◽  
Clinical Trial Data ◽  
Correlation Structure ◽  
Random Intercept ◽  
Autoregressive Correlation ◽  
Early Antiretroviral Treatment

Abstract Background We explored the effects of predominant breastfeeding on infection-related hospitalization (uncommon outcome), over the first year of life, using the Mother Infant Health cohort study (MIHS), and the effect of early antiretroviral treatment (ART) on viral suppression (&lt; 400 copies/mL) (common outcome), in children aged 7 to 12 weeks, using a subset of the Children with HIV Early AntiRetroviral Treatment (CHER) clinical trial data. We assessed the sensitivity of findings to different models to account for dependency of uncommon and common binary outcome. Methods We fitted generalized linear mixed model with (1) random intercept and (2) random slope, generalized estimating equations (GEE) with 3) an exchangeable correlation structure; 4) autoregressive correlation structure of order 1 (AR1) and 5) unstructured correlation structure and 6) logistic regression model. Results Eighty four and 119 children from MIHS were non-predominantly and predominantly breastfed, respectively. There were 34 infection-related hospitalizations overall. Most infants were hospitalized once, except for four with two hospitalizations. We analysed 88 HIV-infected children from the CHER trial. On average, a child achieved viral suppression twice, range of one to four. The effect of predominant breastfeeding on infection-related hospitalization was similar across all models, except for the GEE with AR1 that had a high estimate (wider confidence intervals). The effect of early ART exposure on viral suppression varied across models. Conclusions The sensitivity of estimates to the method of analysis was driven by frequency of the outcome.

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