Feasible Estimation of Linear Models with N-Fixed Effects

Abstract Temperament impacts skeletal muscle mitochondria in Brahman heifers, but this has not been investigated in steers or between cattle breeds. We hypothesized mitochondrial measures would be greater in Angus than Brahman, temperamental than calm steers, and the trapezius (TRAP) than the longissimus thoracis (LT) muscle. Samples from calm (n = 13 per breed), intermediate (n = 12 per breed), and temperamental (n=13 per breed) Angus and Brahman steers (mean±SD 10.0±0.8 mo) were evaluated for mitochondrial enzyme activities via colorimetry. Calm and temperamental LT samples were evaluated for oxidative phosphorylation (P) and electron transfer (E) capacities by high-resolution respirometry. Data were analyzed using linear models with fixed effects of breed, muscle, temperament, and all interactions. Brahman tended to have greater mitochondrial volume density (citrate synthase activity; CS) than Angus (P = 0.08), while intrinsic (relative to CS) mitochondrial function (cytochrome c oxidase activity) was greater in Angus than Brahman (P = 0.001) and greater in TRAP than LT (P = 0.008). Angus exhibited greater integrative (per mg tissue) and intrinsic P with complex I (PCI), P with complexes I+II (PCI+II), maximum noncoupled E, and E with complex II (ECII; P ≤ 0.04) and tended to have greater intrinsic leak (P = 0.1) than Brahman. Contribution of PCI to total E was greater in Angus than Brahman (P = 0.01), while contribution of ECII to total E was greater in Brahman than Angus (P = 0.05). A trend for the interaction of breed and temperament (P = 0.07) indicated calm Angus had the greatest intrinsic ECII (P ≤ 0.03) while intrinsic ECII was similar between temperamental Angus and calm and temperamental Brahman. Integrative PCI+II and ECII, and the contribution of PCI and PCI+II to overall E tended to be greater in temperamental than calm steers (P ≤ 0.09), while intrinsic ECII tended to be greater in calm than temperamental steers (P = 0.07). The impact of these mitochondrial differences on meat quality measures remains to be determined.

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150PREGNANCY AND PARTURITION FOLLOWING TRANSFER OF BOVINE EMBRYOS CULTURED IN TWO MEDIA UNDER TWO OXYGEN CONCENTRATIONS

Reproduction Fertility and Development ◽

10.1071/rdv16n1ab150 ◽

2004 ◽

Vol 16 (2) ◽

pp. 197 ◽

Cited By ~ 2

Author(s):

A. Fischer-Brown ◽

R. Monson ◽

D. Northey ◽

T. Kuhlka ◽

J. Rutledge

Keyword(s):

Birth Weight ◽

Pregnancy Rate ◽

Repeated Measures ◽

Fixed Effects ◽

Linear Models ◽

Statistical Significance ◽

Bovine Embryos ◽

Crown Rump Length ◽

Oxygen Treatment

Developmental aberrations following transfer of in vitro-produced bovine embryos can result in early gestational losses and offspring abnormalities. An ongoing study tests the hypothesis that such aberrations occur with equal frequency among commonly employed culture systems. In year 1, embryos were produced using oocytes from abattoir-derived ovaries (breed unspecified) and a proven Angus bull selected for low birth weight. IVC treatments were 2×2 factorial for medium (KSOMaa or SOFaa) and oxygen concentration (5% or 20%). Angus recipients (n=61; 32 cows, 29 heifers) were randomly allotted to treatments for Day 7 transfers. Pregnancy was diagnosed with ultrasound several times during gestation (Table 1). At parturition calf weight, shoulder height, chest circumference, crown-rump length, and humeral and femoral length data were collected. Statistical analyses (Statistical Analysis System, Cary, NC) were logistic regression with a binomial distribution for pregnancy rate, and the general linear models procedure for calf measurements; included were fixed effects of medium, oxygen, and their interaction, with additional fixed effects of dam parity and calf sex where appropriate. No significant effects of medium or oxygen were found for pregnancy rate or calf measurements other than birth weight. Mean birth weight was higher in the KSOM, 20% oxygen treatment (Table 1), and medium-oxygen interaction for calf weight was also significant (P<0.01). In year 2 embryos were produced using the same Angus bull and Angus oocytes. Angus recipients (n=38; 32 cows, 6 heifers) were randomly allotted to treatments. Fetal crown-rump lengths were measured by ultrasound weekly from Days 33 to 54 and were analyzed as repeated measures using the mixed procedure. Pregnancy outcome and LS means for crown-rump lengths are included in Table 1. Though insufficient recipient numbers preclude determination of statistical significance, of interest is the relatively small fetal size in early gestation and large birth weights in the KSOM, 20% oxygen treatment. This treatment also contained a Day 33 pregnancy, subsequently lost by Day 40, in which the fetus was too small to obtain an accurate measurement. Fetal growth will continue to be monitored throughout gestation. Data will be collected at parturition as in year 1, and pooled analyses will be done. Table 1

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The Analysis of Reproduction in Population of the Slovak Spotted Dairy Cows

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201967061419 ◽

2019 ◽

Vol 67 (6) ◽

pp. 1419-1426

Author(s):

Jozef Bujko ◽

Juraj Candrák ◽

Peter Strapák ◽

Július Žitný ◽

Cyril Hrnčár ◽

...

Keyword(s):

Dairy Cows ◽

Fixed Effects ◽

Linear Models ◽

Correlation Coefficients ◽

Calving Interval ◽

Factors Affecting ◽

Actual Computation ◽

Reproduction Traits ◽

Days Open ◽

Basic Statistical Analysis

The aim of study was to analyse the reproduction and factors affecting on reproduction traits of dairy cows in population of Slovak Spotted cattle from 2007 to 2016 the results for 37,274 dairy cows: days to first service (DFS), days open (DO), number of inseminations per conception (NIC), age of first calving (AFC) and calving interval (CI). The basic statistical analysis were analysed using the SAS version 9.3. For the actual computation a linear models with fixed effects was used: For the actual computation a linear models with fixed effects was used: yijklm = μ + HYSi + BTj+ Fk+ Bl +eijklm. The linear model represents coefficients determination R2 = 0.452117% (P < 0.001) for DFS, R2 = 0.377715% (P < 0.001) for DO, R2 = 0.348442% (P < 0.001) for NIC and R2 = 0.317128% (P < 0.001) for CI with all fixed effects. Correlation coefficients among DFS with DO, NIC, AFC and CI were r = 0.37275, r = -0.06881, r = 0.06493 and r = 0.08348. These coefficients were highly statistically significant (P < 0.001).

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CALENDAR YEAR EFFECT MODELING FOR CLAIMS RESERVING IN HGLM

Astin Bulletin ◽

10.1017/asb.2019.22 ◽

2019 ◽

Vol 49 (03) ◽

pp. 763-786 ◽

Cited By ~ 1

Author(s):

Patrizia Gigante ◽

Liviana Picech ◽

Luciano Sigalotti

Keyword(s):

Fixed Effects ◽

Linear Models ◽

Parametric Bootstrap ◽

Predictive Distribution ◽

Linear Predictor ◽

Calendar Effects ◽

Year Effect ◽

Run Off ◽

Likelihood Approach ◽

Risk Parameters

AbstractClaims reserving models are usually based on data recorded in run-off tables, according to the origin and the development years of the payments. The amounts on the same diagonal are paid in the same calendar year and are influenced by some common effects, for example, claims inflation, that can induce dependence among payments. We introduce hierarchical generalized linear models (HGLM) with risk parameters related to the origin and the calendar years, in order to model the dependence among payments of both the same origin year and the same calendar year. Besides the random effects, the linear predictor also includes fixed effects. All the parameters are estimated within the model by the h-likelihood approach. The prediction for the outstanding claims and an approximate formula to evaluate the mean square error of prediction are obtained. Moreover, a parametric bootstrap procedure is delineated to get an estimate of the predictive distribution of the outstanding claims. A Poisson-gamma HGLM with origin and calendar year effects is studied extensively and a numerical example is provided. We find that the estimates of the correlations can be significant for payments in the same calendar year and that the inclusion of calendar effects can determine a remarkable impact on the prediction uncertainty.

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Association of casein micelle size and enzymatic curd strength and dry matter curd yield

Ciência Rural ◽

10.1590/0103-8478cr20180409 ◽

2019 ◽

Vol 49 (3) ◽

Author(s):

Denise Ribeiro de Freitas ◽

Fernando Nogueira de Souza ◽

Jamil Silvano de Oliveira ◽

Diêgo dos Santos Ferreira ◽

Cristiane Viana Guimarães Ladeira ◽

...

Keyword(s):

Fixed Effects ◽

Dry Matter ◽

Linear Models ◽

Favorable Effect ◽

Casein Micelle ◽

Casein Micelles ◽

Micelle Size ◽

Milk Protein Content ◽

Bulk Tank ◽

Cheese Production

ABSTRACT: The aim of the present study was to explore the association between milk protein content and casein micelle size and to examine the effects of casein micelle size on enzymatic curd strength and dry matter curd yield using reduced laboratory-scale cheese production. In this research, 140 bulk tank milk samples were collected at dairy farms. The traits were analyzed using two linear models, including only fixed effects. Smaller micelles were associated with higher κ-casein and lower αs-casein contents. The casein micellar size (in the absence of the αs-casein and κ-casein effects) did not affect the enzymatic curd strength; however, smaller casein micelles combined with higher fat, lactose, casein and κ-casein contents exhibited a favorable effect on the dry matter curd yield. Overall, results of the present study provide new insights into the importance of casein micelle size for optimizing cheese production.

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The Analysis of Two-Factor Interactions in Fixed Effects Linear Models

Journal of Educational Statistics ◽

10.3102/10769986018001001 ◽

1993 ◽

Vol 18 (1) ◽

pp. 1-40 ◽

Cited By ~ 9

Author(s):

Robert J. Boik

Keyword(s):

Fixed Effects ◽

Linear Models ◽

Null Distribution ◽

P Value ◽

Omnibus Test ◽

F Test ◽

Data Set ◽

Moment Functions ◽

Product Interaction

This article considers two related issues concerning the analysis of interactions in complex linear models. The first issue concerns the omnibus test for interaction. Apparently, it is not well known that the usual F test for interaction can be replaced, in many applications, by a test that is more powerful against a certain class of alternatives. The competing test is based on the maximal product interaction contrast F statistic and achieves its power advantage by focusing solely on product contrasts. The maximal product interaction F test is reviewed and three new results are reported: (a) An extended table of exact critical values is computed, (b) a table of moment functions useful for approximating the p-value corresponding to an observed maximal F statistic is computed, and (c) a simulation study concerning the null distribution of the maximal F statistic when data are unbalanced or covariates are present is reported. It is conjectured that lack of balance or presence of covariates has no effect on the null distribution. The simulation results support the conjecture. The second issue concerns follow-up tests when the omnibus test is significant. It appears that researchers, in general, do not perform coherent follow-up tests on interactions. To make it easier for researchers to do so, an exposition on the use of product interaction contrasts and partial interactions in complex fixed-effects models is provided. The recommended omnibus and follow-up tests are illustrated on an educational data set analyzed using SAS ( SAS Institute, 1988 ) and SPSS (1990) .

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Health-related quality of life (HRQoL) evaluation in the REGOMA trial: A randomized, phase II clinical trial analyzing regorafenib activity in relapsed glioblastoma patients.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.2045 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 2045-2045

Author(s):

Giuseppe Lombardi ◽

Paola Del Bianco ◽

Alba Ariela Brandes ◽

Marica Eoli ◽

Roberta Ruda ◽

...

Keyword(s):

Clinical Trial ◽

Fixed Effects ◽

Linear Models ◽

Covariance Structure ◽

Type I ◽

Appetite Loss ◽

Specific Domain ◽

Mixed Effect ◽

European Organization ◽

Significant Difference

2045 Background: REGOMA trial showed that regorafenib (REG) significantly improved OS and PFS in relapsed glioblastoma (GBM) patients (pts) with respect to lomustine (LOM). REG showed a different toxicity profile compared to LOM. Here, we report final results of the HRQoL assessment, a secondary end point. Methods: HRQoL was measured using the European Organization for Research and Treatment of Cancer (EORTC) core questionnaire (QLQ-C30) and brain module (QLQ-BN20) administered before any MRI assessments, every 8 weeks (+/- 2 weeks) until disease progression. To evaluate treatment impact on HRQoL, questionnaires at progression were excluded. Mixed-effect linear models were fitted for each of the HRQOL domain to examine the change over progression-free time within and between arms. The models included the time of questionnaire assessment, the treatment group and their interaction, as fixed effects, and a compound symmetry covariance structure for the random effects. Differences of at least 10 points were classified as a clinically meaningful change. To correct for multiple comparisons and to avoid type I error, the level of significance was set at P = 0.01 (2-sided). Results: Of 119 randomized pts, 117 participated in the HRQoL evaluation, and 114 had a baseline assessment (n = 56 REG; n = 58 LOM). No statistically significant differences were observed in any generic or cancer specific domain during treatment in the REG and LOM arms, or between the two arms, except for the appetite loss scale which was significantly worse in PTS treated with REG (Global mean 14.7 (SD = 28.6) vs 7.6 (SD = 16.0); p = 0.0081). The proportion of pts with a clinically meaningful worsening for appetite loss was not statistically different between the two arms (9 out of 24 and 0 out of 13 in the REG and LOM arm, respectively; p = 0.0146). Conclusions: In the REGOMA trial, HRQoL did not change during REG treatment. Pts treated with REG and LOM reported no significant difference in HRQoL. Clinical trial information: NCT02926222. [Table: see text]

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The use of optimal evidence-based chemotherapy (chemo) regimens in physician offices versus hospital outpatient facilities.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.6514 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 6514-6514

Author(s):

Michael Jordan Fisch ◽

Ying Liu ◽

ANN NGUYEN ◽

John Barron ◽

Ezra Fishman ◽

...

Keyword(s):

Quality Of Care ◽

Fixed Effects ◽

Linear Models ◽

Hospital Setting ◽

Administrative Claims ◽

Cancer Type ◽

Strong Basis ◽

Hospital Outpatient ◽

Colorectal Cancer Patients

6514 Background: The proportion of infused chemo administered in hospital outpatient facilities (HOF) increased from 6% in 2004 to 43% in 2014. The average annual cost for patients receiving chemo was significantly higher in HOFs than in physician offices (POs). One option to explore differences in the quality of care between these two settings is to examine the use of chemo regimens, which, based on their efficacy, toxicity, and costs, have been designated as “on-pathway.” This study compared on-pathway rates among patients receiving infused chemo administered in POs vs. those in HOFs. Methods: Using administrative claims data, we identified 61,496 breast, lung, or colorectal cancer patients receiving chemo from 2013 to 2018. Chemo regimens were considered “on-pathway” when they were on payer's program list of optimal regimens when administered. Generalized linear models examined the association between site of service and on-pathway prescribing rates, and costs of care. Models adjusted for age, sex, year, rural status, cancer type and setting, and comorbidities, with fixed effects for providers. Results: Percentage of infused chemo administered in HOFs increased from 44.2% in 2013 to 54.7% in 2018. After adjustment, on-pathway prescribing rate did not differ significantly between HOFs and POs (50.1%, 95% CI: 48.6%-51.5% vs. 49.8%, 95%CI: 48.3%-51.3%, p = 0.65). 6-month chemo cost ($56,885, 95% CI: $54,364-$59,524 vs $32,240, 95% CI: $30,929-$33,605, p < 0.001) and 6-month medical cost ($114,280, 95% CI: $110,716-$117,960 vs $79,455, 95% CI: $77,089-$81,893, p < 0.001) were significantly higher in HOFs vs. POs. Conclusions: Quality of care as measured by use of optimal chemo regimens was similar in hospital and office setting. Cost continues to be significantly higher in hospital setting. These findings provide a strong basis for site-neutral reimbursement policies.

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The Impact of Different Competitive Environments on Pacing and Performance

International Journal of Sports Physiology and Performance ◽

10.1123/ijspp.2017-0407 ◽

2018 ◽

Vol 13 (6) ◽

pp. 701-708 ◽

Cited By ~ 8

Author(s):

Marco J. Konings ◽

Florentina J. Hettinga

Keyword(s):

Fixed Effects ◽

Linear Models ◽

Real Life ◽

Energy Resources ◽

Mixed Linear Models ◽

Start Position ◽

Available Energy ◽

Competitive Environments ◽

And Performance ◽

The Impact

Purpose: In real-life competitive situations, athletes are required to continuously make decisions about how and when to invest their available energy resources. This study attempted to identify how different competitive environments invite elite short-track speed skaters to modify their pacing behavior during head-to-head competition. Methods: Lap times of elite 500-, 1000- and 1500-m short-track speed skating competitions between 2011 and 2016 (N = 34,095 races) were collected. Log-transformed lap and finishing times were analyzed with mixed linear models. The fixed effects in the model were sex, season, stage of competition, start position, competition importance, event number per tournament, number of competitors per race, altitude, and time qualification. The random effects of the model were athlete identity and the residual (within-athlete race-to-race variation). Separate analyses were performed for each event. Results: Several competitive environments, such as the number of competitors in a race (a higher number of competitors evoked most likely a faster initial pace; coefficient of variation [CV] = 1.9–9.3%), the stage of competition (likely to most likely, a slower initial pace was demonstrated in finals; CV = −1.4% to 2.0%), the possibility of time qualification (most likely a faster initial pace; CV = 2.6–5.0%), and competition importance (most likely faster races at the Olympics; CV = 1.3–3.5%), altered the pacing decisions of elite skaters in 1000- and 1500-m events. Stage of competition and start position affected 500-m pacing behavior. Conclusions: As demonstrated in this study, different competitive environments evoked modifications in pacing behavior, in particular in the initial phase of the race, emphasizing the importance of athlete–environment interactions, especially during head-to-head competitions.

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Designing Toxicogenomics Studies that use DNA Array Technology

Bioinformatics and Biology Insights ◽

10.1177/117793220800200003 ◽

2008 ◽

Vol 2 ◽

pp. 117793220800200 ◽

Cited By ~ 1

Author(s):

Robert R. Delongchamp ◽

Cruz Velasco ◽

Varsha G. Desai ◽

Taewon Lee ◽

James C. Fuscoe

Keyword(s):

Fixed Effects ◽

Linear Models ◽

Analysis Of Covariance ◽

Mrna Levels ◽

Dna Arrays ◽

Dna Array ◽

Multiple Endpoints ◽

Tissue Samples ◽

Array Measurements ◽

Sources Of Variation

Background Bioassays are routinely used to evaluate the toxicity of test agents. Experimental designs for bioassays are largely encompassed by fixed effects linear models. In toxicogenomics studies where DNA arrays measure mRNA levels, the tissue samples are typically generated in a bioassay. These measurements introduce additional sources of variation, which must be properly managed to obtain valid tests of treatment effects. Results An analysis of covariance model is developed which combines a fixed-effects linear model for the bioassay with important variance components associated with DNA array measurements. These models can accommodate the dominant characteristics of measurements from DNA arrays, and they account for technical variation associated with normalization, spots, dyes, and batches as well as the biological variation associated with the bioassay. An example illustrates how the model is used to identify valid designs and to compare competing designs. Conclusions Many toxicogenomics studies are bioassays which measure gene expression using DNA arrays. These studies can be designed and analyzed using standard methods with a few modifications to account for characteristics of array measurements, such as multiple endpoints and normalization. As much as possible, technical variation associated with probes, dyes, and batches are managed by blocking treatments within these sources of variation. An example shows how some practical constraints can be accommodated by this modelling and how it allows one to objectively compare competing designs.

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