scholarly journals Bathymetric and geographical trends in growth of golden redfish (Sebastes norvegicus)

2019 ◽  
Author(s):  
Natalia Llopis Monferrer ◽  
Benjamin Planque
Keyword(s):  
Age Determination ◽  
Mixed Effects ◽  
Growth Patterns ◽  
Growth Potential ◽  
Small Scale ◽  
Growth Trajectories ◽  
Fundamental Issue ◽  
Linear Mixed Effects ◽  
Size At Age

AbstractGolden redfish (Sebastes norvegicus) are a long-living (>50 years), late maturing (>10 years) species of commercial interest, distributed along the coast, shelves and continental slope of Norway, down to approximately 400 m depth in the water column. In recent years, analyses of size-at-age data have revealed variable growth trajectories for this species. Whilst some individuals appear to grow slowly after sexual maturity (37cm at ~ 15 years), others continue to grow throughout their lifetime up to 100 cm or more. To investigate how depth and latitude affect golden redfish growth patterns, we developed non-linear mixed effects statistical models. Alongside this, small scale experiments were also conducted to assess the quality of age-determination. The results showed that individuals found in deeper, northern waters present a higher growth potential, even when uncertainty in age determination and species identification were considered. The proximal causes for variations in the growth potential of S. norvegicus are still unresolved and the existence of a possible cryptic species remains a fundamental issue that will need to be addressed, in order to understand the causes behind observed growth variations.

scholarly journals Testing heterogeneity in inter-rater reliability

2020 ◽  
Author(s):  
František Bartoš ◽  
Patrícia Martinková ◽  
Marek Brabec
Keyword(s):  
Variance Components ◽  
Generalized Additive Models ◽  
Mixed Effects ◽  
Additive Models ◽  
Mixed Effects Models ◽  
Rater Reliability ◽  
Linear Mixed Effects Models ◽  
Linear Mixed Effects ◽  
Wide Range

Estimating the inter-rater reliability (IRR) is important for assessing and improving the quality of ratings. In some cases, the IRR may differ between groups due to their features. To test heterogeneity in IRR, the second-order generalized estimating equations (GEE2) and linear mixed-effects models (LME) were already used. Another method capable of estimating the components for IRR is generalized additive models (GAM). This paper presents a simulation study evaluating the performance of these methods in estimating variance components and in testing heterogeneity in IRR. We consider a wide range of sample sizes and various scenarios leading to heterogenous IRR. The results show, that while the LME and GAM models perform similarly and yield reliable estimates, the GEE2 models may lead to incorrect results.

scholarly journals Accessible Analysis of Longitudinal Data with Linear Mixed Effects Models

2020 ◽  
Author(s):  
Jessica I. Murphy ◽  
Nicholas E. Weaver ◽  
Audrey E. Hendricks
Keyword(s):  
Longitudinal Data ◽  
Mixed Effects ◽  
Correlated Data ◽  
Growth Trajectories ◽  
False Negatives ◽  
Linear Mixed Effects ◽  
Factors Associated ◽  
Malnourished Children ◽  
Shiny App ◽  
Health And Disease

ABSTRACTLongitudinal mouse models are commonly used to study possible causal factors associated with human health and disease. However, the statistical models, such as two-way ANOVA, often applied in these studies do not appropriately model the experimental design, resulting in biased and imprecise results. Here, we describe the linear mixed effects (LME) model and how to use it for longitudinal mice studies. We re-analyze a dataset published by Blanton et al (Science 2016) that modeled mice growth trajectories after microbiome implantation from nourished or malnourished children. We compare the fit and stability of different parameterizations of ANOVA and LME models; most models found the nourished vs. malnourished growth trajectories differed significantly. We show through simulation that the results from the two-way ANOVA and LME models are not always consistent. Incorrectly modeling correlated data can result in increased rates of false positives or false negatives, supporting the need to model correlated data correctly. We provide an interactive Shiny App to enable accessible and appropriate analysis of longitudinal data using LME models.

scholarly journals Spatial variability in floodplain sedimentation: the use of generalized linear mixed-effects models

2010 ◽  
Vol 7 (1) ◽  
pp. 1589-1619 ◽  
Author(s):  
A. Cabezas ◽  
M. Angulo-Martínez ◽  
M. Gonzalez-Sanchís ◽  
J. J. Jimenez ◽  
F. A. Comín
Keyword(s):  
Spatial Scales ◽  
Size Composition ◽  
Mixed Effects ◽  
Mixed Effects Models ◽  
Small Scale ◽  
Mixed Effect ◽  
Linear Mixed Effects Models ◽  
Linear Mixed Effects ◽  
Generalized Linear Mixed Effects ◽  
Artificial Grass

Abstract. Sediment, Total Organic Carbon (TOC) and total nitrogen (TN) accumulation during one overbank flood (1.15 y) were examined at one reach of the Middle Ebro River (NE Spain) for elucidating spatial patterns. To achieve this goal, four areas with different geomorphological features and located within the study reach were examined by using artificial grass mats. Within each area, 1 m2 study plots consisting on three pseudo-replicates were placed in a semi-regular grid oriented perpendicular to the main channel. TOC, TN and Particle-Size composition of deposited sediments were examined and accumulation rates estimated. Generalized linear mixed-effects models were used to analyze sedimentation patterns in order to handle clustered sampling units, specific-site effects and spatial self-correlation between observations. Our results confirm the importance of channel-floodplain morphology and site micro-topography in explaining sediment, TOC and TN deposition patterns, although the importance of another factors as vegetation morphology should be included in further studies to explain small scale variability. Generalized linear mixed-effect models provide a good framework to deal with the high spatial heterogeneity of this phenomenon at different spatial scales, and should be further investigated in order to explore its validity when examining the importance of factors such as flood magnitude or suspended sediment solid concentration.

scholarly journals Association between Non-Restorative Sleep and Quality of Life in Chinese Adolescents

2020 ◽  
Vol 17 (19) ◽  
pp. 7249 ◽  
Author(s):  
Ningjing Chen ◽  
Daniel Yee Tak Fong ◽  
Sha Li ◽  
Janet Yuen Ha Wong
Keyword(s):  
Quality Of Life ◽  
Hong Kong ◽  
Mixed Effects ◽  
Chinese Adolescents ◽  
World Health ◽  
World Health Organization Quality ◽  
Present Sample ◽  
Linear Mixed Effects ◽  
Restorative Sleep

To examine non-restorative sleep and its impact on quality of life (QOL) in Chinese adolescents, this cross-sectional study included 2827 students aged 12–20 who were selected from 15 secondary schools in Hong Kong, China. Non-restorative sleep was assessed by a single item, rated on a 0–10 scale: “To what extent did you feel refreshed upon awakening over the past month?”. QOL was evaluated by the World Health Organization Quality of Life Measure—Abbreviated Version Hong Kong Chinese Version. Univariable and multivariable linear mixed-effects regressions were conducted to examine the influence of non-restorative sleep (NRS) on QOL. In the present sample, the mean overall QOL was 13.83, and the extent of feeling refreshed upon awakening was 4.75 on average. In multivariable linear mixed-effects regression, one unit feeling less refreshed upon awakening was associated with 0.37 units of poorer overall QOL after adjusting for age, gender, medical conditions, parental education and occupation, weekly hours of aerobic exercises, smoking and drinking habits. Additionally, adolescents with a significantly poorer overall QOL were more likely to be older, have medical problems, have parents with an educational level of primary school or below, have an unemployed father, engage in less weekly aerobic exercise, and be current smokers or former drinkers. Adolescents who experienced non-restorative sleep had a poorer QOL. Future studies are needed to alleviate non-restorative sleep to improve health outcomes in adolescents.

scholarly journals Using linear and natural cubic splines, SITAR, and latent trajectory models to characterise nonlinear longitudinal growth trajectories in cohort studies

2021 ◽  
Author(s):  
Ahmed Elhakeem ◽  
Rachael Hughes ◽  
Kate Tilling ◽  
Diana Cousminer ◽  
Stefan Jackowski ◽  
...  
Keyword(s):  
Cohort Studies ◽  
Mixed Effects ◽  
Cubic Splines ◽  
Growth Patterns ◽  
Longitudinal Growth ◽  
Growth Trajectories ◽  
Advantages And Disadvantages ◽  
Latent Trajectory ◽  
Natural Cubic Splines ◽  
Trajectory Models

Longitudinal data analysis can improve our understanding of the influences on health trajectories across the life-course. There are a variety of statistical models which can be used, and their fitting and interpretation can be complex, particularly where there is a nonlinear trajectory. This paper provides a guide to describing nonlinear growth trajectories for repeatedly measured continuous outcomes using linear mixed-effects (LME) models with linear splines and natural cubic splines, nonlinear mixed effects Super Imposition by Translation and Rotation (SITAR) models, and latent trajectory models. The underlying model for each of the four approaches, the similarities and differences between models, and their advantages and disadvantages are described. Their applications and correct interpretation are illustrated by analysing repeated bone mass measures across three cohort studies with 8,500 individuals and 37,000 measurements covering ages 5-40 years. Linear and natural cubic spline LME models and SITAR provided similar descriptions of the mean bone growth trajectory and growth velocity, and the sex differences in growth patterns. Latent trajectory models identified up to four subgroups of individuals with distinct trajectories during adolescence and similar trajectories in childhood and adulthood. Recommendations for choosing a modelling approach are provided along with a discussion and signposting on further modelling extensions for analysing trajectory exposures and outcomes, and multiple cohorts. In summary, we present a resource for characterising nonlinear longitudinal growth trajectories, that could be adapted for other complex traits. Scripts and synthetic datasets are provided so readers can replicate trajectory modelling and visualisation using the open-source R software.

scholarly journals Growth patterns of infants with in- utero HIV and ARV exposure in Cape Town, South Africa and Lusaka, Zambia

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Dorothy C. Nyemba ◽  
Emma Kalk ◽  
Michael J. Vinikoor ◽  
Hlengiwe P. Madlala ◽  
Mwangelwa Mubiana-Mbewe ◽  
...  
Keyword(s):  
South Africa ◽  
Cape Town ◽  
Mixed Effects ◽  
Growth Patterns ◽  
Mixed Effects Models ◽  
World Health ◽  
Linear Mixed Effects Models ◽  
Linear Mixed Effects ◽  
Increased Risk ◽  
In Pregnancy

Abstract Background Infants born HIV-exposed yet remain uninfected (HEU) are at increased risk of poorer growth and health compared to infants born HIV-unexposed (HU). Whether maternal antiretroviral treatment (ART) in pregnancy ameliorates this risk of poorer growth is not well understood. Furthermore, whether risks are similar across high burden HIV settings has not been extensively explored. Methods We harmonized data from two prospective observational studies conducted in Cape Town, South Africa, and Lusaka, Zambia, to compare weight-for-age (WAZ), length-for-age (LAZ) and weight-for-length (WLZ) Z-scores between infants who were HEU and HU, converting infant anthropometric measures using World Health Organisation Growth Standards adjusted for age and sex. Linear mixed effects models were fit to identify risk factors for differences in anthropometrics at 6–10 weeks and 6 months by infant HIV exposures status and by timing of exposure to maternal ART, either from conception or later in gestation. Results Overall 773 mother-infant pairs were included across two countries: women living with HIV (WLHIV), 51% (n = 395) with 65% on ART at conception and 35% initiating treatment in pregnancy. In linear mixed effects models, WAZ and WLZ at 6–10 weeks were lower among infants who were HEU vs HU [β = − 0.29 (95% CI: − 0.46, − 0.12) and [β = − 0.42 (95% CI: − 0.68, − 0.16)] respectively after adjusting for maternal characteristics and infant feeding with a random intercept for country. At 6 months, LAZ was lower [β = − 0.28 CI: − 0.50, − 0.06)] among infants who were HEU, adjusting for the same variables, with no differences in WAZ and WLZ. Within cohort evaluations identified different results with higher LAZ among infants who were HEU from Zambia at 6–10 weeks, [β = + 0.34 CI: + 0.01, + 0.68)] and lower LAZ among infants who were HEU from South Africa [β = − 0.30 CI: − 0.59, − 0.01)] at 6 months, without other anthropometric differences at either site. Conclusion Infant growth trajectories differed by country, highlighting the importance of studying contextual influences on outcomes of infants who were HEU.

scholarly journals Spatial variability in floodplain sedimentation: the use of generalized linear mixed-effects models

2010 ◽  
Vol 14 (8) ◽  
pp. 1655-1668 ◽  
Author(s):  
A. Cabezas ◽  
M. Angulo-Martínez ◽  
M. Gonzalez-Sanchís ◽  
J. J. Jimenez ◽  
F. A. Comín
Keyword(s):  
Spatial Scales ◽  
Size Composition ◽  
Vegetation Pattern ◽  
Mixed Effects ◽  
Mixed Effects Models ◽  
Small Scale ◽  
Mixed Effect ◽  
Linear Mixed Effects Models ◽  
Linear Mixed Effects ◽  
Generalized Linear Mixed Effects

Abstract. Sediment, Total Organic Carbon (TOC) and total nitrogen (TN) accumulation during one overbank flood (1.15 y return interval) were examined at one reach of the Middle Ebro River (NE Spain) for elucidating spatial patterns. To achieve this goal, four areas with different geomorphological features and located within the study reach were examined by using artificial grass mats. Within each area, 1 m2 study plots consisting of three pseudo-replicates were placed in a semi-regular grid oriented perpendicular to the main channel. TOC, TN and Particle-Size composition of deposited sediments were examined and accumulation rates estimated. Generalized linear mixed-effects models were used to analyze sedimentation patterns in order to handle clustered sampling units, specific-site effects and spatial self-correlation between observations. Our results confirm the importance of channel-floodplain morphology and site micro-topography in explaining sediment, TOC and TN deposition patterns, although the importance of other factors as vegetation pattern should be included in further studies to explain small-scale variability. Generalized linear mixed-effect models provide a good framework to deal with the high spatial heterogeneity of this phenomenon at different spatial scales, and should be further investigated in order to explore its validity when examining the importance of factors such as flood magnitude or suspended sediment concentration.

Subjective cognitive decline is longitudinally associated with lower health-related quality of life

2017 ◽  
Vol 29 (12) ◽  
pp. 1939-1950 ◽  
Author(s):  
Susanne Roehr ◽  
Tobias Luck ◽  
Alexander Pabst ◽  
Horst Bickel ◽  
Hans-Helmut König ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Mixed Effects ◽  
Mixed Effects Models ◽  
Subjective Cognitive Decline ◽  
Linear Mixed Effects Models ◽  
Linear Mixed Effects ◽  
Related Quality ◽  
Health Related ◽  
Eq Vas

ABSTRACTBackground:Subjective cognitive decline (SCD), the potentially earliest notable manifestation of preclinical Alzheimer's disease and other dementias, was consistently associated with lower quality of life in cross-sectional studies. The aim of this study was to investigate whether such an association persists longitudinally – particularly with health-related quality of life (HRQoL) in older individuals without cognitive impairment.Methods:Data were derived from follow-up 2–6 of the prospective Germany Study on Ageing, Cognition and Dementia in Primary Care (AgeCoDe) covering a total six-year observation period. We used linear mixed effects models to estimate the effect of SCD on HRQoL measured by the EQ-5D visual analogue scale (EQ VAS).Results:Of 1,387 cognitively unimpaired individuals aged 82.2 years (SD = 3.2) on average, 702 (50.6%) reported SCD and 230 (16.6%) with SCD-related concerns. Effect estimates of the linear mixed effects models revealed lower HRQoL in individuals with SCD (unadjusted: –3.7 points on the EQ VAS, 95%CI = –5.3 to –2.1; SE = 0.8; p < 0.001; adjusted: –2.9 points, 95%CI = –3.9 to –1.9; SE = 0.5; p < 0.001) than in individuals without SCD. The effect was most pronounced in SCD with related concerns (unadjusted: –5.4, 95%CI = –7.6 to –3.2; SE = 1.1; p < 0.001; adjusted: –4.3, 95%CI = –5.8 to –2.9, SE = 0.7; p < 0.001).Conclusion:SCD constitutes a serious issue to older cognitively unimpaired individuals that is depicted in persisting lower levels of HRQoL beyond depressive symptoms and functional impairment. Therefore, SCD should be taken seriously in clinical practice.

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